tag:blogger.com,1999:blog-46651512635164897932024-03-05T18:53:48.181-08:00Simple computational chemistryGrigoriy Andrienkohttp://www.blogger.com/profile/10871921625140429891noreply@blogger.comBlogger12125tag:blogger.com,1999:blog-4665151263516489793.post-16163342861637187422022-11-16T10:21:00.002-08:002022-11-16T10:23:56.338-08:00Using Quantum Chemistry for Interpreting the IR Spectra of Chemisorbed Gases<p></p><p class="MsoNormal"><span style="font-size: medium;"><span lang="EN-US" style="mso-ansi-language: EN-US;">Our
paper: Computations of IR spectra of some transition metal carbonyls and model
clusters of nickel oxide with carbon monoxide. </span>Journal of Molecular
Structure1241(11):130439. DOI:10.1016/j.molstruc.2021.130439</span></p><p class="MsoNormal"><span style="font-size: medium;"><o:p></o:p></span></p><p><span style="font-size: medium;">We investigated some carbonyls, compounds like this:</span></p><p><span style="font-size: medium;"><br /></span></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgGFPIugg7Tcm1LxIJwFI8_02puUi8yrruJ8s82ZtndZEZhug69BdgGu-VbUI24qxSG-UFAW-izbnYz-YoPOv2AHp4xCYukam4ninMAA5avEsOAmBwdzTbU0ROYm4gq-vlTaRArmn_iwnUj6ghDJn4fS0cWXXxFHycbs2gSiA2Z9RHGV0zwS0K8CPzg2A/s606/carb.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><span style="font-size: medium;"><img border="0" data-original-height="411" data-original-width="606" height="217" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgGFPIugg7Tcm1LxIJwFI8_02puUi8yrruJ8s82ZtndZEZhug69BdgGu-VbUI24qxSG-UFAW-izbnYz-YoPOv2AHp4xCYukam4ninMAA5avEsOAmBwdzTbU0ROYm4gq-vlTaRArmn_iwnUj6ghDJn4fS0cWXXxFHycbs2gSiA2Z9RHGV0zwS0K8CPzg2A/s320/carb.png" width="320" /></span></a></div><span style="font-size: medium;"><br /></span><p><span style="font-size: medium;"><br /></span></p><span style="font-size: medium;">We computed the IR spectra of several carbonyls and built the correlation between the theoretical and experimental positions of the bands corresponding to CO-stretching mode:</span><p></p><p><span style="font-size: medium;"><br /></span></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhsGhIweDE77PS9aAbbsFCwl33Vn9i3OU2nmzKTtisqo6EGRfFceG4XB4oJ5AC2ZGTngE2C6_1yLw-w8HT9Po1C8M_b7wr7eKV2Oi4kH15OJKo0k2iJ77ZCBrYDRnMdD6L_f-RHhoHLi_hq0djHgr14TvjVuGGP5dUZDvZ-T_Z_ZLBJDLhY9v9C3pvBZw/s723/corrirco.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><span style="font-size: medium;"><img border="0" data-original-height="449" data-original-width="723" height="249" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhsGhIweDE77PS9aAbbsFCwl33Vn9i3OU2nmzKTtisqo6EGRfFceG4XB4oJ5AC2ZGTngE2C6_1yLw-w8HT9Po1C8M_b7wr7eKV2Oi4kH15OJKo0k2iJ77ZCBrYDRnMdD6L_f-RHhoHLi_hq0djHgr14TvjVuGGP5dUZDvZ-T_Z_ZLBJDLhY9v9C3pvBZw/w400-h249/corrirco.png" width="400" /></span></a></div><div><span style="font-size: medium;"><br /></span></div><span style="font-size: medium;">The marked points are not carbonyls but a Ni4O4..CO complex which serves as a model for CO chemisorbed on nicked oxide. These correlations allow us to confirm the assumption that the IR
spectrum bands above 2000 cm–1 correspond to CO bound to the metal atom
linearly, and bands below 2000 cm–1 correspond to CO forming a bridged bond
with two metal atoms.</span><p class="MsoNormal"><span lang="EN-US"><span style="font-size: medium;"><o:p></o:p></span></span></p><p><br /></p>Grigoriy Andrienkohttp://www.blogger.com/profile/10871921625140429891noreply@blogger.com0tag:blogger.com,1999:blog-4665151263516489793.post-35075139991806285532022-07-22T07:52:00.000-07:002016-07-05T07:52:54.102-07:00About this blog<div dir="ltr" style="text-align: left;" trbidi="on">
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<span style="font-size: large;">The aim of
this blog is to promote the development of computation chemistry, at least to a
small extent.</span></div>
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<br /></div>
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<span lang="EN-US"><span style="font-size: large;">Besides
that, let me introduce my programs:<o:p></o:p></span></span></div>
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<br /></div>
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<span lang="EN-US"><span style="font-size: large;"><a href="http://chemcraftprog.com/">Chemcraft –graphical tool for chemists</a>;<o:p></o:p></span></span></div>
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<span lang="EN-US"><span style="font-size: large;"><br /></span></span></div>
<br />
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<span lang="EN-US"><span style="font-size: large;"><a href="http://backupaider.com/">BackupAider – a simple freeware for backing up your files</a>;</span><o:p></o:p></span></div>
</div>
Grigoriy Andrienkohttp://www.blogger.com/profile/10871921625140429891noreply@blogger.com2tag:blogger.com,1999:blog-4665151263516489793.post-38109307114785515362018-09-17T11:21:00.000-07:002018-09-17T11:21:02.988-07:00The importance of the Gallery page of Chemcraft website<div dir="ltr" style="text-align: left;" trbidi="on">
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<span lang="EN-US" style="mso-ansi-language: EN-US;"> Several
times some people wrote to me that they had been using Chemcraft during several
years, and only after that they found some Chemcraft features which were useful
for them, and it is a pity that they were not aware of these features during
these years. To check how widespread such situation is, I created a poll in the
Chemcraft facebook group:</span></div>
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<span lang="EN-US" style="mso-ansi-language: EN-US;"><br /></span></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhrB7f5oQna75hR2aM7I9g2yMjZn3fpQj7cW4CKxGY6T7HomepBysCFQddenh9Rg0az76sqeo7YjDy_Q2_lBUswz4EfpTtOIuX96CkwVok7HvZ5a0pSZ0REOSj3cjxJCeqK1Dx6Ifi_J9kO/s1600/poll_gallery.JPG" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="516" data-original-width="489" height="320" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhrB7f5oQna75hR2aM7I9g2yMjZn3fpQj7cW4CKxGY6T7HomepBysCFQddenh9Rg0az76sqeo7YjDy_Q2_lBUswz4EfpTtOIuX96CkwVok7HvZ5a0pSZ0REOSj3cjxJCeqK1Dx6Ifi_J9kO/s320/poll_gallery.JPG" width="303" /></a></div>
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<span lang="EN-US" style="mso-ansi-language: EN-US;"> As you can
see from this screenshot, 6 of 11 people voted that they looked through the
Gallery and Hints webpage and after that they indeed found some features useful
for them. Among others, 4 people were already aware of almost all features so
they didn’t need to look through the Gallery.</span></div>
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<span lang="EN-US" style="mso-ansi-language: EN-US;"> This poll
illustrates that many Chemcraft users make a common mistake – they don’t look
through our gallery and don’t know about some good features.</span></div>
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<span lang="EN-US" style="mso-ansi-language: EN-US;"> So, if you
have purchased Chemcraft or plan to do that, we highly recommend you to look
through our gallery. Once again, visit the following two webpages:</span></div>
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<a href="https://chemcraftprog.com/gallery.html"><span lang="EN-US" style="mso-ansi-language: EN-US;">https://chemcraftprog.com/gallery.html</span></a></div>
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<span lang="EN-US" style="mso-ansi-language: EN-US;"></span></div>
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<a href="https://chemcraftprog.com/hints.html"><span lang="EN-US" style="mso-ansi-language: EN-US;">https://chemcraftprog.com/hints.html</span></a></div>
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<span lang="EN-US" style="mso-ansi-language: EN-US;"> One more
advice is to simply read the names of all menu items (including submenus) of
the Chemcraft main window. These menu items have long and descriptive names,
e.g. “Insert dummy atom into center of selected atoms”, “Move coordinate center
to selected atom”, “Release all current captions to supplement the captions
with new ones”, “Calculate the energy of e reaction”, “Modify multiply Gaussian
input files”, “Build animated gif from a set of bitmap/jpeg files”, etc.</span></div>
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Grigoriy Andrienkohttp://www.blogger.com/profile/10871921625140429891noreply@blogger.com7tag:blogger.com,1999:blog-4665151263516489793.post-4538248181034792562018-06-05T12:03:00.001-07:002018-06-05T12:17:08.090-07:00Structural properties of nematic Schiff bases and prediction of their thermal stability by polarizability anisotropy computed via DFT<div dir="ltr" style="text-align: left;" trbidi="on">
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<span lang="EN-US" style="mso-ansi-language: EN-US;"><span style="mso-spacerun: yes;"> </span>My PhD dissertation (“candidate”) was devoted
mostly to the prediction of thermal stability of some liquid crystals (nematic
Schiff bases), or, more precisely, the temperature of mesophase destruction
(the temperature at which a liquid crystal becomes a regular liquid). The
results were published in [1-5]. Several other tasks appeared within this work.</span></div>
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<span lang="EN-US" style="mso-ansi-language: EN-US;"><span style="mso-spacerun: yes;"> </span>Approximately 50 compounds (Schiff bases) were
investigated, e.g., those shown below:</span></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiTgHaxIl4vg9IVZP2lLBJ3Kof4cuwKYBHlxnkr_AtAO4g9XapOZrxEzHfAOgKMsRaY5Ej-wB8gAT2Iq2iw1CynqKsxyUUSifoqEZh5yRHpKrBnWFL9wbrRieThiTFuJgflRKKDUs59lR0t/s1600/mols1.JPG" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="346" data-original-width="671" height="330" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiTgHaxIl4vg9IVZP2lLBJ3Kof4cuwKYBHlxnkr_AtAO4g9XapOZrxEzHfAOgKMsRaY5Ej-wB8gAT2Iq2iw1CynqKsxyUUSifoqEZh5yRHpKrBnWFL9wbrRieThiTFuJgflRKKDUs59lR0t/s640/mols1.JPG" width="640" /></a></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjb7t_wDbCwAXHeJOKAC94xGXHJIpCAHZ9ZcwS7xk8IdTr_3YExHpFs9DcjnJArcxypU8TFoipgEP_JetmV7phs7Bh6COt0wmwtDTOJmMeofCdB_R3bfaBur5yPDrVpkcB8XkF-7VT9DYgl/s1600/mol2.JPG" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="508" data-original-width="1023" height="316" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjb7t_wDbCwAXHeJOKAC94xGXHJIpCAHZ9ZcwS7xk8IdTr_3YExHpFs9DcjnJArcxypU8TFoipgEP_JetmV7phs7Bh6COt0wmwtDTOJmMeofCdB_R3bfaBur5yPDrVpkcB8XkF-7VT9DYgl/s640/mol2.JPG" width="640" /></a></div>
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<span lang="EN-US" style="mso-ansi-language: EN-US;"><span style="mso-spacerun: yes;"> </span>First, we computed NMR spectra of some of
these molecules, and built a correlation between these computed NMR chemical
shifts and experiment:</span></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi5pdKxT-2c7lfC4bHuMRsAmqipKpVIgNVzdQV9Y7h72xcdjkAZhfWJMo35Mnw-7Z8mXcQPJ2icnJra0dnKik8Ax0qo9WqxX1bd6RZCHy1VsPCBKuqmSB9FyWnDcSZL7N-OEsZFiK4Ll0QH/s1600/corr1.JPG" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="447" data-original-width="714" height="400" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi5pdKxT-2c7lfC4bHuMRsAmqipKpVIgNVzdQV9Y7h72xcdjkAZhfWJMo35Mnw-7Z8mXcQPJ2icnJra0dnKik8Ax0qo9WqxX1bd6RZCHy1VsPCBKuqmSB9FyWnDcSZL7N-OEsZFiK4Ll0QH/s640/corr1.JPG" width="640" /></a></div>
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<span lang="EN-US" style="mso-ansi-language: EN-US;"><span style="mso-spacerun: yes;"> </span>The computations were performed using the GIAO
B3LYP/6-311G(D,P) method. B3LYP/6-311++G(2DF,PD) yielded somewhat better
agreement with experiment but this level of theory was too expensive for us.
The GIAO and CSGT algorithms yielded almost identical results (the difference
was much smaller than other sources of error).</span></div>
<div class="MsoNormal">
<span lang="EN-US" style="mso-ansi-language: EN-US;"><span style="mso-spacerun: yes;"> </span>For molecule 1 (see above) the
crystallography data is available. We did the following: the NMR chemical
shifts for this molecule were computed not only with the optimized structure,
but also with the structure taken from the crystallographic data (the bond
lengths C..H were taken from the computation, since the crystallography does
not provide the coordinates of H atoms in molecule). The agreement
(correlation) between the computed and experimental chemical shifts appears to
be much better in the first case; it means that the optimized structure (which
corresponds to the gas phase) is closer to the real structure in liquid state
than the crystal structure (in other words, the computational error is much smaller
than the impact of the packing forces in crystal).</span></div>
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<span lang="EN-US" style="mso-ansi-language: EN-US;"><span style="mso-spacerun: yes;"> </span>We found that the NMR spectra can be used for
getting some information about the structure of the investigated molecules. At
the same time, we found that the structural parameters of these molecules are
much less important for our tasks than anticipated by previous researchers.</span></div>
<div class="MsoNormal">
<span lang="EN-US" style="mso-ansi-language: EN-US;"><span style="mso-spacerun: yes;"> </span>The molecular polarizability of a number of Schiff
bases was computed. For some of these molecules the experimental polarizability
data is available, and we found a good correlation between the computed and
experimental components of the polarizability tenzor:</span></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhAo8A50Ump8dnSjnAs4ayOw7aLdrMeTHVipOM210i22aAw5dNkXRodnHGknWwSw5Ucxv5Y3_8N6gYOBi02MXAQhYtdrYEReGsUR_y3QCorAT21LzNc-rroCu-PpaJX9whcBqAOSa83MmJs/s1600/polar.JPG" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="370" data-original-width="588" height="402" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhAo8A50Ump8dnSjnAs4ayOw7aLdrMeTHVipOM210i22aAw5dNkXRodnHGknWwSw5Ucxv5Y3_8N6gYOBi02MXAQhYtdrYEReGsUR_y3QCorAT21LzNc-rroCu-PpaJX9whcBqAOSa83MmJs/s640/polar.JPG" width="640" /></a></div>
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<span lang="EN-US" style="mso-ansi-language: EN-US;"><span style="mso-spacerun: yes;"> </span>We also found a relatively high correlation
between the computed polarizability anisotropy of the molecules and
experimental polarizability anisotropy of substituent for homologues:</span></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgacIrB3rQHRb33JO_0Ova76LRnzkekJdjY8bRPwNfLYk3HrhyphenhyphenHA2Jl17w12dmDsgEWoJiPDzem2qd_X0eMTM-KZl-VcIUihWwrtHvgRBDYdH0Cb7cJXdfo2OmCX9KTa_gNReh7Q3M1aC91/s1600/zam.JPG" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="302" data-original-width="396" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgacIrB3rQHRb33JO_0Ova76LRnzkekJdjY8bRPwNfLYk3HrhyphenhyphenHA2Jl17w12dmDsgEWoJiPDzem2qd_X0eMTM-KZl-VcIUihWwrtHvgRBDYdH0Cb7cJXdfo2OmCX9KTa_gNReh7Q3M1aC91/s1600/zam.JPG" /></a></div>
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<span lang="EN-US" style="mso-ansi-language: EN-US;"><span style="mso-spacerun: yes;"> </span>Then we plotted a correlation between the
anisotropy of molecular polarizability of our Schiff bases (computed with DFT)
and the experimental temperature of liquid crystal phase destruction
(nematic-isotropic phase transition):</span></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEigNKfs0vbHLCL9yD44_iSWYPa3cKIEt8iQjhlvVKVHLpF4-ryKTtgcDVx9Jo0RD1kgfafs8qrjUbyvSgwpEFb62ybpjmaLx-clEcPF19SDKno1zxAnPQ4DDSMkPjtb50ybup155rmz_9sH/s1600/tni.JPG" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="414" data-original-width="580" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEigNKfs0vbHLCL9yD44_iSWYPa3cKIEt8iQjhlvVKVHLpF4-ryKTtgcDVx9Jo0RD1kgfafs8qrjUbyvSgwpEFb62ybpjmaLx-clEcPF19SDKno1zxAnPQ4DDSMkPjtb50ybup155rmz_9sH/s1600/tni.JPG" /></a></div>
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<span lang="EN-US" style="mso-ansi-language: EN-US;"><span style="mso-spacerun: yes;"> </span>This “correlation” is quite low. Anyway, it
can be stated that the anisotropy of molecular polarizability of nematic liquid
crystals can be used for predicting their thermal stability. It seems evident
that the low degree of correlation is not caused by the computational error
(the picture above proves that this error is much smaller).</span></div>
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<span lang="EN-US" style="mso-ansi-language: EN-US;">References:</span></div>
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<span lang="EN-US" style="mso-ansi-language: EN-US;">1. G</span><span lang="EN-US" style="mso-ansi-language: EN-US;">. A. Zhurko, V. V. Aleksandriiskii,
V. A. Burmistrov. Conformational state of benzilidene aniline derivatives from
ab initio calculation and NMR spectroscopy data// Journal of Structural
Chemistry (J STRUCT CHEM+) 47(4):622-628 · July 2006 with 16 Reads DOI:
10.1007/s10947-006-0348-y</span></div>
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<span lang="EN-US" style="mso-ansi-language: EN-US;">2. G</span><span lang="EN-US" style="mso-ansi-language: EN-US;">. A. Zhurko, V. V. Aleksandriiskii,
M. K. Islyaikin, V. A. Burmistrov. Structure and molecular polarizability of
mesogenic Shiff bases from quantum chemical calculation data// <span style="mso-spacerun: yes;"> </span>Journal of Structural Chemistry (J STRUCT
CHEM+) 48(3):440-446 · May 2007 with 19 Reads DOI: 10.1007/s10947-007-0066-0</span></div>
<div class="MsoNormal">
<span lang="EN-US" style="mso-ansi-language: EN-US;">3. Zhurko
G.A., Alexandriyskiy V.V., Burmistrov V.A. Conformational state of benzilidene
derivatives by NMR 13C
data and quantum chemistry computations//IV Russian conference “New
achievements of NMR in structural investigations.” Kazan, 4-4 April 2005, p.64.</span></div>
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<span lang="EN-US" style="mso-ansi-language: EN-US;">4.
Structure and stability of liquid crystals – proton donor H-complexes in
solutions by 13C
NMR spectroscopy and semi-empirical AM1 method data // Alexandriiskii V. V.,
Burmistrov V. A., Isliyakin M. K., Zhurko G. A. // Intern. Symp. and Summer
School “Nuclear Magnetic Resonance in Condensed Matter”, 3rd Meeting “NMR in
Heterogeneous System”. Saint Petersburg, Petrodvorets, Russia, 9-13 July 2006, p.50.</span></div>
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<span lang="EN-US" style="mso-ansi-language: EN-US;">5.. In Russian: Zhurko G. A. Ispolzovanie
kvantovokhimicheskih raschetov dlya izucheniya molecularnoy structuri nekotorikh
nematicheskih osnovaniy Shiffa // Zhurko G.A., Alexandriyskiy V. V., Burmistrov
V. A. // Zhidkie kristally i ih prakticheskoe ispolzovanie. 2005. N1. c 13-22</span></div>
<div class="MsoNormal">
<span lang="EN-US" style="mso-ansi-language: EN-US;">English:
Zhurko G. A. The use of quantum chemistry computations for investigation of the
molecular structure of some nematic Schiff bases // Zhurko G.A., Alexandriyskiy
V. V., Burmistrov V. A. // Liquid crystals and their practical use. 2005, N1,
p.13-22.</span></div>
</div>
Grigoriy Andrienkohttp://www.blogger.com/profile/10871921625140429891noreply@blogger.com0tag:blogger.com,1999:blog-4665151263516489793.post-13011765717458513322017-06-24T04:37:00.002-07:002017-06-24T04:39:45.507-07:00The basics of high-accuracy ab initio computations (Feller–Peterson–Dixon method)<div dir="ltr" style="text-align: left;" trbidi="on">
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For performing high-level ab initio computations (implying the usage of post-HF methods), three cornerstones must be taken into account: the level of theory for describing the electron correlation effects, the basis set size, and the level of theory for describing relativistic effects. <br />
Currently, the coupled cluster-based techniques (CC) are very powerful ab initio methods for describing the electron correlation effects (for inorganic molecules). The hierarchy of these methods includes CCSD (with singles and doubles excitations), CCSDT (also triple excitations), CCSDTQ, etc. Within this series, the energy quickly converges to a hypothetical point of “full correlation” (for a specified basis set). The advantage of the coupled cluster theory, compared to the configuration interaction (CI) technique, is that with CC the energy converges more quickly upon increasing the excitation rank than with CI. <br />
CCSD(T) is called the “golden standard” of quantum chemistry. Unlike the CCSDT method, in CCSD(T) the triples (triple excitations) are treated non-iteratively, in a perturbative fashion, which reduces computation cost quite significantly. CCSD does not give such good describing of electronic correlation, CCSDT is quite costly, while the CCSD(T) method is a good compromise; in addition, the success of the CCSD(T) approach stems from fortuitous error cancellation (however at Ref. [14] it is stated that CCSD(T) is worse than CCSDT for open shell systems, in contrast to closed shell systems).<br />
Note that for all post-HF methods, upon increasing the basis set size the total energy converges relatively slowly; that’s why, it is a kind of naïve to expect “golden quality” results from the CCSD(T) method with the basis sets as small as DZ or even TZ (the DZ and TZ abbreviations stand for double-zeta and triple-zeta quality basis sets, respectively). <br />
As we have written before, the so-called complete basis set (CBS) limit means that you first compute with cc-pVDZ, then cc-pVTZ, then cc-pVQZ, then cc-pV5Z, etc., and the energy should converge to a hypothetical “complete” basis set limit. At the same time, there are more than 10 extrapolation schemes which give nearly the same result after performing only 2-3 computations (however, these extrapolation schemes are empirical to some extent). <br />
In the work of a quantum chemistry guru Kirk Peterson [1] the following is stated: “<i>To directly achieve chemical accuracy with CCSD(T) without extrapolation would require correlation of both the valence and outer-core electrons with a basis set of at least aug-cc-pCV6Z or augcc-pCV7Z quality</i>”. The “chemical accuracy” term is usually interpreted in the thermochemistry literature as the error of 1 kcal/mol ( 4.184 kJ/mol) for atomization energies; Peterson offers the following arbitrary estimates for spectroscopic parameters: +-0.005 Å for bond lengths and +-15 cm-1 for vibrational frequencies. Without the extrapolation schemes, such computations are possible for very small molecules only; besides that, for heavy atoms (starting, e.g., from post-3d elements), the relativistic effects must be properly included to attain even semiquantitative accuracy [2, 3]. An efficient way of reducing the computation cost is the “composite approach”, which is based on the concept that smaller components are additive and that these terms can be most efficiently calculated at different levels of theory (but comparable levels of accuracy). <br />
Previous composite methods like G1, G2, etc., or W1, W2 comprise computing chemical properties with molecular geometries obtained at HF/6-31G* or MP2/6-31G* level, and are much less reliable than fully ab-initio Feller–Peterson–Dixon method (see below) (unlike the FPD approach, these methods are a “black box”). <br />
For very small molecules, the HEAT model (high-accuracy extrapolated ab initio thermochemistry) can be used; it produced a MAD of 0.09 kcal/mol relative to well-established experimental DHf(0 K) values (for a test set of 26 small molecules involving 5 atoms (H, C, N, O and F)) [5]. The maximum observed error was 0.33 kcal/mol (C2H2). The HEAT approach implies optimizing geometries at CCSD(T)(CV)//cc-pVQZ, then estimating the basis set limit by a 1/lmax 3 extrapolation [4] of aug-cc-pCVQZ and aug-cc-pCV5Z energies. <br />
In the Feller–Peterson–Dixon (FPD) approach, the total energy of atomization of the molecule is usually computed as the sum of the following terms: <br />
1) Estimated complete basis set (CBS) limit of the CCSD(T) energy; <br />
2) Energy of correlation of outer-core electrons with themselves and with the valence electrons (core-valence (CV) term). This term is estimated at CBS limit too, if possible; <br />
3) Scalar relativistic effects term (or, when these effects are already accounted for in the first two stages, the elimination of errors due to using the pseudopotential approximation); <br />
Sometimes it is advised to use all-electron DK-contracted basis sets already for the first two stages if available relativistic sets are of the same size as non-relativistic ones. <br />
4) Spin-orbit (SO) interaction term. This is a relativistic term too; more specifically, there are two levels of spin-orbit effects, the effects of second order are not always necessary to include. For closed shell species, only first order effects should be taken into account; <br />
5) Corrections to the total atomization energy beyond the CCSD(T) level; <br />
6) Zero-point energy (the energy of the first vibrational state). Usually this correction is computed in the harmonic approximation. For polyatomic molecules, this term may be reliably obtained from harmonic frequencies computed at lower levels of theory (DFT, MP2). <br />
<br />
The approach provides flexibility in terms of the use of a particular level of theory for computing individual contributions. In some cases, a few of these components may be excluded without severe loss of accuracy. Below we present two sample formulas of computing the total energy in FPD approach, appropriate for a molecule comprising 2-5 atoms (the first formula demands lower hardware level than the latter): <br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg7HQN0cBO9wVSWZ2yLnRgG3b_M9sO68fah_R9RUPYgK-NBfoBRPQMD9dcg0DixugblGBFZWEEYsTnPjf9HjpYtd0IKGI1RA73Q9P95iYU5Tf65b0TiMv9O63MV1ViZN6y73QU2ymhoiFyt/s1600/form1.JPG" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="287" data-original-width="705" height="260" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg7HQN0cBO9wVSWZ2yLnRgG3b_M9sO68fah_R9RUPYgK-NBfoBRPQMD9dcg0DixugblGBFZWEEYsTnPjf9HjpYtd0IKGI1RA73Q9P95iYU5Tf65b0TiMv9O63MV1ViZN6y73QU2ymhoiFyt/s640/form1.JPG" width="640" /></a></div>
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Particularly, for the Q5 extrapolation algorithm:<br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiU43nrnk6d0bEA6aQhifU7dVT_hZdse_POHHo4KX0IjUjRFTxI9wLPZgWeADDNBkwnW3BzfLxSEQFGgSUqtx9irpKwcnb20WvZmkpk7-AUHK7ehdEOsFZjVZFl4gTg3mK9c3POFIWYhUJs/s1600/form2.JPG" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="107" data-original-width="249" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiU43nrnk6d0bEA6aQhifU7dVT_hZdse_POHHo4KX0IjUjRFTxI9wLPZgWeADDNBkwnW3BzfLxSEQFGgSUqtx9irpKwcnb20WvZmkpk7-AUHK7ehdEOsFZjVZFl4gTg3mK9c3POFIWYhUJs/s1600/form2.JPG" /></a></div>
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<br />
N=4 for QZ, 5 for 5Z; here we have got 2 equations with two variables (Ecbs and A). <br />
∆ESO includes atomic corrections taken from experimental data (NIST) and computed corrections for molecules. <br />
The explanation of this formula is presented in Ref. [6]. We know that the ∆ESO can be computed using the Molpro program (via the state-interacting approach within the first-order perturbation theory) or the Dirac program (spin-orbit coupling is already included at the HF level of theory). <br />
In the FPD approach, when high accuracy is necessary, the molecular geometry is usually optimized using CCSD(T) method with a sequence of the correlation-consistent basis sets in an effort to evaluate energy differences at or near the CBS limit geometries. Besides that, reasonable results can be usually obtained with lower level geometries (e.g. computed at DFT level). <br />
The FPD approach currently seems to be the best solution for computing high-accuracy energies and other properties of relatively small molecules (usually inorganic). As an indication of the performance of the FPD procedure for atomization energies, a mean signed deviation of -0.04 kcal/mol, RMS = 0.28 kcal/mol and MAD = 0.17 kcal/mol is found when comparing against 121 molecules (small organic or inorganic molecules containing s and p elements, like CH4, C2N2, C2H2O, C4H6, SO3, HBr, H2SiO, I2, etc) whose experimental uncertainties are ±1 kcal/mol or less [7]. <br />
Now we should make an important statement. There is a persuasive hypothesis that the FPD approach never produces wrong results, if one reaches convergence in each of the computed contributions to the energy. And when the computation is performed by an experienced quantum chemist, he can always tell whether the convergence is reached in a particular component. For reliability of the FPD method it is required that the additivity approach works, and an experienced quantum chemist can test this approach too. <br />
The term “wrong result” needs to be interpreted in more details. Any computation can be characterized by a specific accuracy. In chemistry, the concepts of “spectroscopic accuracy” and “chemical accuracy” are used. The spectroscopic accuracy (1 cm-1) is needed for the spectroscopy, the chemical accuracy (1 kcal/mole) is needed for thermochemistry, and for the majority of tasks probably even smaller accuracy is required. Using the FPD method on personal computers, one can reach chemical accuracy for the overwhelming majority of small stable inorganic molecules (diatomic and symmetrical polyatomic), or for small- to medium-sized organic molecules. It should be noted that for first and second row compounds the said accuracy can be achieved, using only the first and second step of the FPD procedure (elimination of basis set incompleteness and taking into account the core-valence correlation). <br />
It has been shown [12], that for molecules containing d and f elements the experimental error exceeds 1 kcal/mol, and because of that, for these compounds it was proposed [13] to consider the chemical accuracy being 3 kcal/mol for d elements and 5 kcal/mol for f elements. <br />
The most important point here is as follows: an experienced quantum chemist, if he can’t reach the required accuracy in the computation, is usually aware of that, because the convergence of any FPD component (contribution to the energy) can be estimated via its computation on a higher level of theory. The necessity to analyze individual components is both the disadvantage of the FPD approach (because it makes this method relatively laborious, demanding a high qualification of the chemist and the use of appropriate software), and its advantage (because the quantum chemist can decide which contributions should be calculated at a high level of theory, and which of them may be neglected). Because of that, the FPD method is definitely not a “black box”. And besides that, the error of the computation can be often estimated by comparing the results of the computations for similar molecules with the experimental data (mainly high-accuracy, particularly spectroscopic). For example, to estimate the computational errors for the NdI3 molecule, one can calculate the Nd3+ ion and compare the relative energies of its electronic states with the experiment. <br />
At the moment, only a few groups are performing the FPD computations: groups of Peterson K.A., DeYonker N., Hill J. G., Solomonik V.G.<br />
It should be mentioned that the abbreviation "FPD" should not be considered as some prescribed procedure; this term does not imply using any particular approaches when any energy contribution is computed. A researcher who applies this method must decide himself, what level of theory should be used in the computation of a particular energy contribution (depending on the task level and available hardware and software). So, a significant advantage of the FPD method is that it can immediately benefit from any newest developments of methods, basis sets, and hardware. <br />
While modeling spectra, it is desirable to ensure that the Born-Oppenheimer approach is suitable for the molecule studied. By the term “an approach is non-suitable” we mean that the accuracy of the computation within this approach is worse than required. The Born-Oppenheimer approach can yield large errors, if there are low-lying electronic states in the system: in this case, the reciprocal influence of the PESs of different electronic states will be observed, and this will lead to significant discrepancies between the computed and experimental spectra. When the Born-Oppenheimer approach fails, the electronic and vibrational states interact, and the electronic and vibrational (nuclear) solutions cannot be separated [8]. Ab initio methods, in fact, allow one to deal with the electronic part, while the Born-Oppenheimer approach is related to the nuclear one. <br />
For very heavy elements, other relativistic elements can play a role, in particular the effects of quantum electrodynamics (first of all, the Lamb shift). Kirk Peterson writes: <br />
<i>While generally neglected in most composite methodologies, it has been shown previously by Dyall et al. that the contribution of the Lamb shift to the atomization energy can approach 3–5% of the scalar relativistic contribution. In cases where the scalar relativistic correction is large, for example when the valence s orbital occupation strongly changes, the Lamb shift can contribute ~0.1 to 0.2 kcal/mol to the atomization energy for even relatively light systems like AlF3 and GaF3. </i><br />
The FPD method is usually applied for inorganic molecules. It should be mentioned, that for molecules with complicated electronic structure, even small, the convergence of all contributions for achieving the chemical accuracy still can’t be reached. <br />
Nevertheless, at the moment the properties of the majority of molecules with up to 4 atoms can be computed by the FPD method with accuracy, in practice not worse than the experimental one. <br />
The FPD method is based on the assumption of the additivity of the contributions, which are enlisted above. In some cases, when the researcher needs a very high (spectroscopic) accuracy, the standard approach implying separate accounting for various contributions may fail to yield such accuracy. This can occur when individual contributions (for example, spin-orbit) are relatively high. In such situations several contributions should be taken into account simultaneously. <br />
For molecules, which are to big to be computed via the “traditional” FPD, the following approach becomes righteous: the geometry is optimized at DFT level with triple-zeta basis set, and then a single point FPD computation is performed (for example, in the Peterson’s work [9]). <br />
It should be noted that for the majority of small first and second row compounds, as it can be seen, the chemical accuracy can be reached at the DFT level (not systematically however). In Ref. [10] the computations of 211 molecules were performed using the PBE and PBE0 functionals and quintuple zeta-quality basis sets (aug-cc-pV5Z), and the authors obtained MAEs of lower than 1 kcal/mol and MaxAEs of 2-5 kcal/mol. See this blog [11] for more information. <br />
<br />
<br />
Refs: <br />
<br />
[1] Theor Chem Acc (2012) 131:1079 <br />
<br />
[2] Methods in Computational Chemistry; Wilson , S., Ed.Vol. 2; Plenum Press: New York, 1988. <br />
<br />
[3] Hess, B. A.; Dolg, M. Relativistic Quantum Chemistry with Pseudopotentials and transformed Hamiltonians. Wiley Series in Theoretical Chemistry; John Wiley & Sons: Chichester , 2002; Vol. 57. <br />
<br />
[4] Helgaker T, Klopper W, Koch H, Noga J (1997) J Chem Phys. 106:9639 <br />
<br />
[5] Chemical accuracy in ab initio thermochemistry and spectroscopy: current strategies and future challenges. Kirk A. Peterson • David Feller • David A. Dixon. Theor Chem Acc (2012) 131:1079 DOI 10.1007/s00214-011-1079-5 <br />
<br />
[6] David A. Dixon, David Feller, Kirk A. Peterson. Annual Reports in Computational Chemistry. Volume 8, 2012, Pages 1–28 <br />
<br />
[7] D. Feller, K.A. Peterson, and D.A. Dixon, "A survey of factors contributing to accurate theoretical predictions of atomization energies and molecular structures", J. Chem. Phys. 129, 204105 (2008). <br />
<br />
[8] https://en.wikipedia.org/wiki/Born–Oppenheimer_approximation <br />
<br />
[9] R. Craciun, D. Picone, R.T. Long, S. Li, D.A. Dixon, K.A. Peterson, and K.O. Christe, “Third row transition metal hexafluorides, extraordinary oxidizers and Lewis acids: Electron affinities, fluoride affinities, and heats of formation of WF6, ReF6, OsF6, IrF6, PtF6, and AuF6”, Inorg. Chem. 49, 1056 (2010). <br />
<br />
[10] Jensen, Stig Rune; Saha, Santanu; Flores-Livas, José Abdenago; Huhn, William; Blum, Volker; Goedecker, Stefan; Frediani, Luca, 2017, "GGA-PBE and hybrid-PBE0 energies and dipole moments with MRChem, FHI-aims, NWChem and ELK", doi:10.18710/0EM0EL, UiT Open Research Data Dataverse, V3 <br />
<br />
[11] http://www.compchemhighlights.org/2017/03/the-elephant-in-room-of-density.html <br />
<br />
[12] DeYonker et al. J. Phys. Chem. A, Vol. 111, No. 44, 2007 <br />
<br />
[13] Stephanie Grimmel, George Schoendorff, and Angela K Wilson. J. Chem. Theory Comput., 05 Feb 2016, DOI: 10.1021/acs.jctc.5b01193. <br />
<br />
[14] http://www.compchemhighlights.org/2016/01/assessment-of-accuracy-of-coupled.html</div>
Grigoriy Andrienkohttp://www.blogger.com/profile/10871921625140429891noreply@blogger.com1tag:blogger.com,1999:blog-4665151263516489793.post-27131583083595720772016-11-20T05:47:00.001-08:002017-04-15T10:52:26.080-07:00Integration of Chemcraft with programs such as Excel, Origin, etc.<div dir="ltr" style="text-align: left;" trbidi="on">
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<span lang="EN-US" style="mso-ansi-language: EN-US;"><span style="mso-spacerun: yes;"> </span>Sometimes users ask us to implement a feature
like plotting multiple spectra (from different files) in a single graph. We do
not plan to implement such features, because: </span></div>
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<span lang="EN-US" style="mso-ansi-language: EN-US;">1) This
will require a reconstruction of the user interface, and old users will have to
learn how to use Chemcraft again;</span></div>
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<span lang="EN-US" style="mso-ansi-language: EN-US;">2) For building graphs of any type, powerful
software packages already exist – Excel, Origin, etc. We do not want to compete
with them. But Chemcraft allows one to export any graph, spectrum, diagram in
text format, copying its data to Excel via Clipboard. So, multiple spectra in
one picture can be easily obtained as follows: you should open several output
files in a row, copy the data with spectra to Excel and then combine these
spectra in Excel. Note that the broadened spectrum (Doppler, Lorentzian
broadening of bands) can be exported too.</span></div>
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<span lang="EN-US" style="mso-ansi-language: EN-US;"><span style="mso-spacerun: yes;"> </span>See, for example, this graph built in
Chemcraft:</span></div>
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<span lang="EN-US" style="mso-ansi-language: EN-US;"><span style="mso-spacerun: yes;"> </span>This is a Gaussian09 Born-Oppenheimer
Molecular Dynamics (BOMD) computation, and the graph shows the distance between
atoms C1 and H1 versus time in femtoseconds. There seems to be a problem, or a bug,
with visualization of such files – Chemcraft reads the first 3 points with zero
time. We found the format of the output file quite difficult. Maybe this
problem will be fixed in future, but we are not even sure that this is
necessary: if you need to plot a good graph “Distance vs Time”, click on the
“Copy” button, insert the data into Excel and manually delete the invalid
lines. Of course you should check your graph against the output file – if you
work with BOMD computations, you should understand them well enough.</span></div>
<div class="MsoNormal">
<span lang="EN-US" style="mso-ansi-language: EN-US;"><span style="mso-spacerun: yes;"> </span>We always give our users the possibility to
verify the data visualization in Chemcraft – for example, when you visualize
the molecular orbitals, you can click the “Check orbitals” button to check
whether Chemcraft extracted all orbitals correctly. When we implement
visualization of MOS from output files of new software, it is sometimes
difficult to thoroughly verify whether the MOS are visualized correctly
(probably free software is characterized with such problems to a greater
extent). And don’t forget to check the data shown by Chemcraft using the Source
mode.</span></div>
</div>
Grigoriy Andrienkohttp://www.blogger.com/profile/10871921625140429891noreply@blogger.com0tag:blogger.com,1999:blog-4665151263516489793.post-55885106242774391442016-06-21T06:54:00.001-07:002022-04-26T11:20:01.472-07:00DFT advices<div dir="ltr" style="text-align: left;" trbidi="on">
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<span lang="EN-US" style="font-size: large;">We have
gathered some information from computational chemistry forums, which can be
helpful for you. It should be noted that the following text cannot be
considered as a professional guide; such guides will possibly appear in the
future.<o:p></o:p></span></div>
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<span lang="EN-US" style="font-size: large;"><b>1. The
choice of a DFT functional</b><o:p></o:p></span></div>
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<span lang="EN-US" style="font-size: large;">First of
all, you should read this manual:<o:p></o:p></span></div>
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<span lang="EN-US" style="font-size: large;"><a href="http://www.chem.uci.edu/~kieron/dft/pubs/RCFB08.pdf">Which functional should I choose? (2008)</a><o:p></o:p></span></div>
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<span lang="EN-US" style="font-size: large;"> One of the thesises in this book is that the GGA functionals are ususally more universal (let’s say, closer to
“Ab initio”) than the hybrid functionals </span><span style="font-size: large;">(this statement, however, has some weak points)</span><span style="font-size: large;">. This also means that the errors with
these functionals are more systematic: for example, the PBE functional usually
overestimates the bond lengths and underestimates the vibrational frequencies.
In our opinion, if you choose between, e.g., the PBE and B3LYP functionals, you
should note that the latter should be more accurate for most organic molecules,
but it should be less accurate in some problematic cases; so, the PBE
functional is more reliable. Because of that, at one forum we found the
following advice (written in 2010): always use the PBE functional and don’t
worry. It is CGA, so it must be more universal than, e.g., the B3LYP functional.</span></div>
<div style="text-align: justify;">
<span style="font-size: large;"> It is written in this manual that the B3LYP
functional has shown good results for organic molecules, but it is worse for
transition metal compounds and for large molecules. TPSSh probably is a good functional for transition metal compounds (according to this manual).</span></div>
<div style="text-align: justify;">
<span style="font-size: large;"> The B3LYP functional is commonly used in chemistry, while the PBE, PBE0 functionals are commonly used in</span><span style="font-size: large;"> applications to extended systems (materials) [13].</span></div><div style="text-align: justify;"><span style="font-size: large;"><br /></span></div><div style="text-align: justify;"><span style="font-size: large;"><p class="MsoNormal"><span lang="EN-US">We highly
recommend you to read this paper:<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Markus
Bursch, Jan-Michael Mewes, Andreas Hansen, Stefan Grimme. Best Practice DFT
Protocols for Basic Molecular Computational Chemistry.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">D O I:
10.26434/chemrxiv-2022-n304h<o:p></o:p></span></p><p class="MsoNormal"><br /></p><p class="MsoNormal">Here is
another compilation on the subject:</p></span></div></div>
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<span lang="EN-US" style="font-size: large;"><a href="http://www.marcelswart.eu/dft-poll/newsitem.pdf">The annual popularity poll for density functionals: edition 2015</a><o:p></o:p></span></div>
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<span lang="EN-US" style="font-size: large;">Here is a
screenshot from this paper:<o:p></o:p></span></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiDkqCXMPPNQhODoDfmH-4QhuIJw__XmJV62ktOf0mbn7PtxInfC7VG6-6HgEFL5ZSa-3ZmlrxsFsSGE-aCKJbaAH6CoFibCXofP86iNZNhbJ4BlaXxIq3N0lzoOxDaIEXIAZjO_pF9hEt-/s1600/dft1.JPG" style="margin-left: 1em; margin-right: 1em;"><span style="font-size: large;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiDkqCXMPPNQhODoDfmH-4QhuIJw__XmJV62ktOf0mbn7PtxInfC7VG6-6HgEFL5ZSa-3ZmlrxsFsSGE-aCKJbaAH6CoFibCXofP86iNZNhbJ4BlaXxIq3N0lzoOxDaIEXIAZjO_pF9hEt-/s1600/dft1.JPG" /></span></a></div>
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<span lang="EN-US" style="font-size: large;">It is not
clear from this list, whether the dispersion correction should be always used.
However, at other forums we found the advices to use the dispersion correction
always if possible. In Ref. [1] you can see that the ωB97X-D is the best single-component
functional, while PBE0-D3 perform almost as well. Besides that, on the <a href="http://server.ccl.net/chemistry/resources/messages/2015/08/27.005-dir/index.html">CCL list</a> one can read that B3LYP-D3 is usually better than B3LYP.<o:p></o:p></span></div>
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<span lang="EN-US" style="font-size: large;">Dispersion
correction is the interaction of induced dipoles. This correction becomes
important if two parallel benzene rings interact (stacking). So, the dispersion
correction is important for computing such molecules as tetraphenylporphyrin, bilirubin,
etc. <o:p></o:p></span></div>
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<span lang="EN-US" style="font-size: large;">Here is a
list of favorable and non-favorable DFT functionals from the DFT 2015 poll for
computing particular properties:<o:p></o:p></span></div>
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<span lang="EN-US" style="font-size: large;"><br /></span>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhYMfrvlAQkpVmWDlDMNWm1ROS-FBSa5F-fTw9Lu4Ps6JSGJFiEHv3KZg0ey2VVBj2gAGjwgXXdXbMHM4tZX-e6Hd0Az9qvk54IfF1TUQX4dAK1n-4apqOXR-7FKkWJy3AlOXzuBM17lBYK/s1600/dftprops.JPG" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="508" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhYMfrvlAQkpVmWDlDMNWm1ROS-FBSa5F-fTw9Lu4Ps6JSGJFiEHv3KZg0ey2VVBj2gAGjwgXXdXbMHM4tZX-e6Hd0Az9qvk54IfF1TUQX4dAK1n-4apqOXR-7FKkWJy3AlOXzuBM17lBYK/s640/dftprops.JPG" width="640" /></a></div>
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<div style="text-align: justify;">
<span lang="EN-US" style="font-size: large;"> With all due respect to the creators of the
above list (computational chemistry community), we must mention that we tried to compute the properties of
bilirubin molecule (having intermolecular H-bonds) using the PBE, B3LYP and wB97XD
functionals, and we found that the PBE functional is the worst at describing intermolecular
H bonds (the PMR spectra computed using the PBE/6-311G(D,P) method are in
poorer agreement with the experimental ones than the PMR spectra computed using
the B3LYP/6-311G(D,P) or wB97XD/6-311G(D,P) methods). So, we found that the PBE
functional is not good at describing H-bonds, in contrast to the conclusions
drawn above. So, we think that you should not fully trust these tables.<o:p></o:p></span></div>
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<span lang="EN-US" style="font-size: large;">Another
<a href="http://server.ccl.net/chemistry/resources/messages/2015/09/22.012-dir/index.html">post</a> from CCL states the following:<o:p></o:p></span></div>
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<span lang="EN-US" style="font-size: large;"> - Recommended GGA methods: revPBE-D3, B97-D3<o:p></o:p></span></div>
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<span lang="EN-US" style="font-size: large;"> - Recommended meta-GGA methods: oTPSS-D3,
TPSS-D3<o:p></o:p></span></div>
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<span lang="EN-US" style="font-size: large;"> - Hybrid functionals: PW6B95-D3, M062X-D3<o:p></o:p></span></div>
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<span lang="EN-US" style="font-size: large;"> - Double-hybrids are the most accurate DFT
methods on the market: DSD-BLYP-D3, DSD-PBEP86-D3, PWPB95-D3<o:p></o:p></span></div>
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<span lang="EN-US" style="font-size: large;"> In Ref. [2], a thorough energy benchmark
study of various density functionals (DFs) was carried out. The authors write:<o:p></o:p></span></div>
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<span lang="EN-US" style="font-size: large;">“In
summary, we recommend on the GGA level the B97-D3 and revPBE-D3 functionals.
The best meta-GGA is oTPSS-D3 although meta-GGAs represent in general no clear
improvement compared to numerically simpler GGAs. Notably, the widely used
B3LYP functional performs worse than the average of all tested hybrids and is
also very sensitive to the application of dispersion corrections.”<o:p></o:p></span></div>
</div>
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<div style="text-align: justify;">
<span lang="EN-US" style="font-size: large;">“The
ωB97X-D functional seems to be a promising method. The most robust hybrid is
Zhao and Truhlar's PW6B95 functional in combination with DFT-D3”.<o:p></o:p></span></div>
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<div style="text-align: justify;">
<span lang="EN-US" style="font-size: large;">“If higher
accuracy is required, double-hybrids should be applied. The corresponding
DSD-BLYP-D3 and PWPB95-D3 variants are the most accurate and robust functionals
of the entire study.”<o:p></o:p></span></div>
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<span lang="EN-US" style="font-size: large;">The tests
in this paper were performed on GMTKN30 set – this set covers mainly molecules
containing main group elements, mostly organic (<a href="http://cuby4.molecular.cz/protocol_dataset.html">link</a>).<o:p></o:p></span></div>
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<span lang="EN-US" style="font-size: large;"> So, the double-hybrids seem to be the best
DFT methods at the moment. This is illustrated by the following chart from the
aforementioned paper:<o:p></o:p></span></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhmABzA6OaAH0jjwAV9V-R2rnPmL2iG_D8APQ6BbwPPA5M70qu6t-6abLRTxNuvDmefnt5rHpZ2mGE4FBWAb_NJoq7-pyAGNFxRaOIlg9MybUEPIvGRZnxK_Ga8lk4XJygEjvTyDxtJLXy4/s1600/dft2.JPG" style="margin-left: 1em; margin-right: 1em;"><span style="font-size: large;"><img border="0" height="444" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhmABzA6OaAH0jjwAV9V-R2rnPmL2iG_D8APQ6BbwPPA5M70qu6t-6abLRTxNuvDmefnt5rHpZ2mGE4FBWAb_NJoq7-pyAGNFxRaOIlg9MybUEPIvGRZnxK_Ga8lk4XJygEjvTyDxtJLXy4/s640/dft2.JPG" width="640" /></span></a></div>
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<span lang="EN-US" style="font-size: large;">Another
advantage of PBE is that this functional is “cheap”.<o:p></o:p></span></div>
</div>
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<div style="text-align: justify;">
<span lang="EN-US" style="font-size: large;">Note that
the PBE and PBE0 methods are quite different: PBE is a CGA, while PBE0 is a hybrid method. However, if one compares e.g. BP86, BLYP, BPW91 functionals (GGA) with PBE0, he finds that PBE0 is "less semi-empirical".<o:p></o:p></span></div>
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<span style="font-size: large;"><span lang="EN-US"> </span> </span></div>
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<span lang="EN-US" style="font-size: large;"> Here is
another comparison of DFT functionals. In Ref. [3], a few DFT functionals were benchmarked
for 14 compounds (calculation of vertical excitation energies by TDDFT and their
comparison to experiment). Here are two pictures from this
paper:</span></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhDjqItr54cjMFJbkAvlfhHhLvRwJ0FAZZYL-B1LHfdqW1tMfaS2WhOnMqosLvbftG2DZsZHiVESK47k7WidSQz94w6Ouuu4l-AoQdHHixkSMPTPzgTyeoPL_4AabzvcKMr6yboyinba8Ex/s1600/dft3.JPG" style="margin-left: 1em; margin-right: 1em;"><span style="font-size: large;"><img border="0" height="592" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhDjqItr54cjMFJbkAvlfhHhLvRwJ0FAZZYL-B1LHfdqW1tMfaS2WhOnMqosLvbftG2DZsZHiVESK47k7WidSQz94w6Ouuu4l-AoQdHHixkSMPTPzgTyeoPL_4AabzvcKMr6yboyinba8Ex/s640/dft3.JPG" width="640" /></span></a></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhSrR2eEore2sPy2-Nh_5hFoHVo7qJoAgV47KiK_P7n-i0HkYdAjyXaDMU2-ckzq4kmhI3VZ0fAVOxWy12afQr0T_LQG3l1tiJD-bdxgEQUV_x0b75sUNvbUvRBTXW8g-kBIYBJdEX539CM/s1600/dft4.JPG" style="margin-left: 1em; margin-right: 1em;"><span style="font-size: large;"><img border="0" height="598" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhSrR2eEore2sPy2-Nh_5hFoHVo7qJoAgV47KiK_P7n-i0HkYdAjyXaDMU2-ckzq4kmhI3VZ0fAVOxWy12afQr0T_LQG3l1tiJD-bdxgEQUV_x0b75sUNvbUvRBTXW8g-kBIYBJdEX539CM/s640/dft4.JPG" width="640" /></span></a></div>
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<span style="font-size: large;"><span lang="EN-US">Ref. [4]
reports that the CAM-B3LYP and BHandH functionals yield the best </span>agreement
between computed and experimental vertical absorption energies for a set of
some simple organic molecules (involving first and second row atoms).</span><br />
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<span style="font-size: large;"><span lang="EN-US" style="mso-ansi-language: EN-US;"> We have
performed some benchmark NMR computations with different functionals. The 1H
NMR spectra of 26 simple organic molecules (not containing internal hydrogen
bonds) were computed at PCM wB97XD/6-31G(D,P),</span></span><span style="font-size: large;"><span lang="EN-US" style="mso-ansi-language: EN-US;"><span style="font-size: large;"><span lang="EN-US" style="mso-ansi-language: EN-US;"> PCM B3LYP/6-31G(D,P),</span></span> PCM B3LYP-D3/6-31G(D,P), PCM
B3LYP-D3/aug-cc-pVTZ and some other levels, and the following conclusions were
made:</span></span></div>
<span style="font-size: large;">
</span><br />
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<span style="font-size: large;"><span lang="EN-US" style="mso-ansi-language: EN-US;">1) The
methods PCM wB97XD/6-31G(D,P) and PCM B3LYP-D3/6-31G(D,P) yield very similar standard
deviations (SD) from the experiment of 0.1411 ppm and 0.13005 ppm, respectively;
note that the signals of the protons not attached to carbons do not fit into
common correlation). This, however, does not mean that these two functionals
produce similar results (correlation of the values computed by them has an SD
of 0.06849 ppm);</span></span></div>
<span style="font-size: large;">
</span>
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<span style="font-size: large;"><span lang="EN-US" style="mso-ansi-language: EN-US;">2)
Switching from PCM B3LYP-D3/6-31G(D,P) to PCM B3LYP-D3/aug-cc-pVTZ does not
improve the agreement with the experimental data: the SD is 0.13005 for the
former and 0.13539 ppm for the latter. This is even rather strange for us, why
the enlargement of the basis set does not lead to the improvement of the
agreement with experiment; maybe, the main source of disagreement is the
experimental error or some fundamental problems of NMR computation algorithms.</span></span></div>
<span style="font-size: large;">
</span>
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<span style="font-size: large;"><span lang="EN-US" style="mso-ansi-language: EN-US;">Note that
we have performed some benchmark IR spectra computations (mentioned in a
previous post in this blog), and we found that switching from wB97XD/6-31G(D,P)
to wB97XD/aug-cc-pVTZ method improves the agreement with the experiment
approximately by a factor of 1.2;</span></span></div>
<span style="font-size: large;">
<div class="MsoNormal">
<span lang="EN-US" style="mso-ansi-language: EN-US;">3) It is of
no real importance, whether to perform a full geometry optimization at PCM
B3LYP-D3/aug-cc-pVTZ level of theory, or just perform the geometry optimization
at PCM B3LYP-D3/6-31G(D,P) level and then do a single point with aug-cc-pVTZ
basis set. The NMR shift values obtained by these two approaches correlate with
SD=0.01442 ppm;</span></div>
<div class="MsoNormal">
<span lang="EN-US" style="mso-ansi-language: EN-US;">4) Taking
into account the solvation effects with PCM model improves the agreement with
the experiment with an almost negligible increase in computational costs;</span><br />
<div class="MsoNormal">
<span lang="EN-US" style="mso-ansi-language: EN-US;">5)</span><span lang="EN-US" style="mso-ansi-language: EN-US;"> Switching
from PCM B3LYP/6-31G(D,P) to PCM B3LYP-D3/6-31G(D,P) improves the agreement
with the experiment by 0.4% only (SD changes from 0,13056 to 0,13005). This is
because only such molecules as phenol, biphenyl, anthracene, hexane, etc. were
computed. If we had computed such molecule as benzene dimer, the dispersion
correction would become important. Besides that, for our molecules the energies differ rather significantly with the B3LYP and B3LYP-D3 methods.</span></div>
</div>
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<div class="MsoNormal">
<span lang="EN-US" style="mso-ansi-language: EN-US;">6) Two NMR
computation schemes – GIAO and CSGT – produce almost identical results (SD
between them is 0.016 ppm).</span></div>
<span style="font-size: large;"></span></span></div>
</div>
<div class="MsoNormal">
<div style="text-align: justify;">
<span style="font-size: large;"><br /></span></div>
</div>
<div class="MsoNormal">
<div style="text-align: justify;">
<span lang="EN-US" style="font-size: large;"> The
combination of these advices can confuse an inexperienced user. As for us, we
decided that we should use PBE-D3 for inorganic molecules and ωB97X-D or
B3LYP-D3 for organic ones, since we deal with the Gaussian09A package. Such an
advice should be useful only for “amateurs” who are unable to gather more
information.<o:p></o:p></span></div>
</div>
<div class="MsoNormal">
<div style="text-align: justify;">
<span lang="EN-US" style="font-size: large;"> Anyway, it is better to use several
functionals to ensure that they produce similar results. MP2 should
not also be forgotten (SCS-MP2 seems to be better than conventional MP2, as written in the paper
above; as far as we know, SOS-MP2 is better too).<o:p></o:p></span></div>
</div>
<div class="MsoNormal">
<div style="text-align: justify;">
<span lang="EN-US" style="font-size: large;"> Recently, the B3LYP/6-31G(D,P) method has
been quite popular. We think that using this method for computing organic
molecules (not containing d and f elements) is still rather adequate, but the
snobs can interpret the use of this method as the sign of amateurishness (at
least, if you don’t employ different functionals and/or basis sets in the same
study). See, for example, <a href="http://server.ccl.net/cgi-bin/ccl/message-new?2015+09+22+001">this</a> and <a href="http://www.ccl.net/chemistry/resources/messages/2007/12/13.016-dir/">this</a> posts on the CCL list.<o:p></o:p></span></div>
</div>
<div class="MsoNormal">
<div style="text-align: justify;">
<span style="font-size: large;"><br /></span></div>
</div>
<div class="MsoNormal">
<div style="text-align: justify;">
<span style="font-size: large;"> The flaws of this famous B3LYP/6-31G* model
chemistry are discussed in Ref. [5]:</span></div>
</div>
<div class="MsoNormal">
<span lang="EN-US" style="font-size: large;">
</span></div>
<div class="MsoNormal">
<div style="text-align: justify;">
<span lang="EN-US" style="font-size: large;"> The authors write that the relatively good
performance of B3LYP/6-31G*, which made it so popular, is caused by a hidden
error cancellation. The B3LYP-gCP-D3/6-31G* method, according to the authors, is
much better (it removes the two major deficiencies: missing <st1:city w:st="on"><st1:place w:st="on">London</st1:place></st1:city> dispersion effects and basis set
superposition error). The B3LYP-D3/6-31G* method is slightly worse as it does
not provide a BSSE elimination. This picture illustrates the aforesaid:<o:p></o:p></span></div>
</div>
<div class="separator" style="clear: both; text-align: justify;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgp1F8VHSTfODl0xZX778XJkyaT2jWGem1I7YXUmMXSvG6DAqus2i_O-0kErqTnMscO9SySFvtnGe6QFqSLlrFhUUafufZLHE_4N0ndbdkL_o2Ir9iuC6sNS_L-uZoGT1R9j95-aMR3Fv8Z/s1600/dft5.JPG" style="margin-left: 1em; margin-right: 1em;"><span style="font-size: large;"><img border="0" height="170" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgp1F8VHSTfODl0xZX778XJkyaT2jWGem1I7YXUmMXSvG6DAqus2i_O-0kErqTnMscO9SySFvtnGe6QFqSLlrFhUUafufZLHE_4N0ndbdkL_o2Ir9iuC6sNS_L-uZoGT1R9j95-aMR3Fv8Z/s400/dft5.JPG" width="400" /></span></a></div>
<div class="MsoNormal">
<div style="text-align: justify;">
<span lang="EN-US" style="font-size: large;"><br /></span></div>
</div>
<div class="MsoNormal">
<div style="text-align: justify;">
<span lang="EN-US" style="font-size: large;"><br /></span></div>
</div>
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<span lang="EN-US" style="font-size: large;"></span></div>
<div class="MsoNormal">
<div style="text-align: justify;">
<span lang="EN-US" style="font-size: large;"> As far as
we know, the density fitting / RI </span><span style="font-size: large;">(Resolution of the Identity) </span><span lang="EN-US" style="font-size: large;">approximation is usually a good thing,
as it speeds up your calculations without significant loss of accuracy (it least, this is written in Orca manual). <o:p></o:p></span><span style="font-size: large;">However, in
some cases it can lead to bad SCF convergence or give the error of 1-2 kcal/mol
in energies.</span></div>
<div style="text-align: justify;">
<span style="font-size: large;"> Here is a picture from Ref. [13] illustrating the availability of DFT functionals:</span></div>
<div class="separator" style="clear: both; text-align: justify;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhTS3o5Uz8MabSN9LOJnMsh1707spwFx6ShdK1Fvr67hb5my2TubPse394FL-pl8mw3dHO5XcUeXtfSVJGXzJsoHPv05_Sh6wjugHMjtBChYUr6yb4rUO3ZkYsTbAo7wsPnoz0EeGN6TbCg/s1600/rev1.JPG" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="460" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhTS3o5Uz8MabSN9LOJnMsh1707spwFx6ShdK1Fvr67hb5my2TubPse394FL-pl8mw3dHO5XcUeXtfSVJGXzJsoHPv05_Sh6wjugHMjtBChYUr6yb4rUO3ZkYsTbAo7wsPnoz0EeGN6TbCg/s640/rev1.JPG" width="640" /></a></div>
<div style="text-align: justify;">
<span style="font-size: large;"><br /></span>
</div>
<div class="MsoNormal">
<span lang="EN-US"><o:p></o:p></span></div>
</div>
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<div style="text-align: justify;">
<span lang="EN-US" style="font-size: large;"><br /></span></div>
</div>
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<div style="text-align: justify;">
<span lang="EN-US" style="font-size: large;"><b>2. The
choice of basis set</b><o:p></o:p></span></div>
</div>
<div class="MsoNormal">
<div style="text-align: justify;">
<span style="font-size: large;"><br /></span></div>
</div>
<div class="MsoNormal">
<div style="text-align: justify;">
<span lang="EN-US" style="font-size: large;"> As far as we know, </span><span style="font-size: large;">at the moment </span><span style="font-size: large;">the optimal basis sets for high-accuracy computations are Dunning family sets: cc-pVnZ, aug-cc-pVnZ, cc-pCVnZ, cc-pwCVnZ (n=2,3.4,5,
etc). These basis sets are correlation consistent; this means, that they were
optimized using correlated methods, unlike the 6-31G** basis sets. In Ref. [6] the following is stated:</span><br />
<span style="font-size: large;"> "</span><span style="font-size: large;">One of the primary reasons for the cc basis set family’s lasting</span><br />
<span style="font-size: large;">popularity is due to a series of empirical observations that as</span><br />
<span style="font-size: large;">the cardinal number (n in cc-pVnZ) of the basis set is increased,</span><br />
<span style="font-size: large;">energies and various properties converge smoothly toward the</span><br />
<span style="font-size: large;">complete basis set (CBS) limit.</span><span style="font-size: large;">"</span></div>
</div>
<div class="MsoNormal">
<div style="text-align: justify;">
<span lang="EN-US" style="font-size: large;"> The so-called complete basis set </span><span style="font-size: large;">(CBS) limit</span><span style="font-size: large;"> means that you first compute with cc-pVDZ, then cc-pVTZ,
then cc-pVQZ, then cc-pV5Z, etc., and the energy should converge to a
hypothetical “complete” basis set limit. At the same time, there are more than 10 extrapolation schemes which give nearly the same result after performing only 2-3 computations (however, these extrapolation schemes are empirical to some extent).</span></div>
</div>
<div class="MsoNormal">
<div style="text-align: justify;">
<span lang="EN-US" style="font-size: large;"> For heavy elements (Z>29), relativistic effects are
strong and must be taken into account either using the methods like ZORA, DKH, or
using effective core potentials (ECPs, PPs). The main relativistic effects include relativistic contraction and spin-orbit interaction. For many tasks, even such elements as Fe, Co, Ni do not require including relativistic effects in the computation (you will have a lot of problems besides relativism with these atoms).<o:p></o:p></span></div>
</div>
<div class="MsoNormal">
<div style="text-align: justify;">
<span lang="EN-US" style="font-size: large;"> The Ref. [6] provides an overview of the
development of Gaussian basis sets for molecular calculations, with a focus on
four popular families of modern bases ("Gaussian basis set" means any basis set with Gaussian (not Slater) functions, not a specific set for the GAUSSIAN program). The authors write about the cases when
using ECPs is not advisable (in particular, electron paramagnetic resonance),
and it is written that using the DFT-based ZORA or DKH models with segmented
all-electron relativistic contracted (SARC) basis sets produce good agreement
with experiment and higher level ab initio computations.<o:p></o:p></span></div>
</div>
<div class="MsoNormal">
<div style="text-align: justify;">
<span lang="EN-US" style="font-size: large;"> One interesting point is mentioned in Ref.
[7]: the authors report that the computations with 6-311++G** basis set gave
better molecular geometries than the more costly aug-cc-pVDZ (the methods used
were MP2 and CCSD). In addition, the smaller 6-311++G** invariably leads to
lower calculated total energies than aug-cc-pVDZ. So, it seems that the aug-cc-pVDZ
can be worse than the 6-311++G** set (nevertheless, we suppose that if you need an
expensive basis set or CBS (complete basis set) extrapolation, you should use cc-pVTZ,
cc-pVQZ, cc-pV5Z, etc</span><span style="font-size: large;">).</span><br />
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<span style="font-size: large;"><span lang="EN-US" style="mso-ansi-language: EN-US;"> Some people
say that it is not actual to use basis sets larger than cc-pVTZ with DFT. However,
in Ref. [14] the authors performed energy computations of 211 small first and
second row compounds (mostly organic), and they concluded that the 5Z basis set
(aug-cc-pV5Z) is required to get the MAE of atomization energies below 1
kcal/mol. See <a href="http://www.compchemhighlights.org/2017/03/the-elephant-in-room-of-density.html">this blog</a> for more information.</span></span></div>
<span style="font-size: large;">
</span></div>
</div>
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<div style="text-align: justify;">
<span lang="EN-US" style="font-size: large;">
<span lang="EN-US" style="font-size: 12pt;"> </span><span lang="EN-US" style="font-size: 12pt;">The same is
written at this handbook “<a href="http://vergil.chemistry.gatech.edu/courses/chem6485/pdf/quantum-practical.pdf">Practical Advice for Quantum Chemistry Computations</a>”:</span></span></div>
</div>
<div class="separator" style="clear: both; text-align: justify;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgw2RRwFxK3OphBWJo4W_iHkAWfz8weU7xEAY-sNF_x-CQISNEYtrNfcUN2bXOgnvgIaEOuEIRY0jvR-iH2rfBhtAkkfAzTpTdezTIkA3lZkLhM8Hg_V8UYkMPTK_tKDEOkSDg3gWu_7jI4/s1600/dft6.JPG" style="margin-left: 1em; margin-right: 1em;"><span style="font-size: large;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgw2RRwFxK3OphBWJo4W_iHkAWfz8weU7xEAY-sNF_x-CQISNEYtrNfcUN2bXOgnvgIaEOuEIRY0jvR-iH2rfBhtAkkfAzTpTdezTIkA3lZkLhM8Hg_V8UYkMPTK_tKDEOkSDg3gWu_7jI4/s1600/dft6.JPG" /></span></a></div>
<div class="MsoNormal">
<div style="text-align: justify;">
<span lang="EN-US"><span lang="EN-US" style="font-size: large;"><br /></span></span></div>
</div>
<div class="MsoNormal">
<div style="text-align: justify;">
<span lang="EN-US"><span lang="EN-US" style="font-size: large;"><br /></span></span></div>
</div>
<div class="MsoNormal">
<div style="text-align: justify;">
<span lang="EN-US" style="font-size: large;"> For some small organic molecules, we have
found that the basis sets 6-31++G(D,P) and AUG-cc-pVDZ give almost identical results
(protonation energies of 16 amide-containing molecules computed with wB97XD/</span><span style="font-size: large;">6-31++G(D,P) and</span><span style="font-size: large;"> </span><span style="font-size: large;">wB97XD/</span><span style="font-size: large;">AUG-cc-pVDZ methods</span><span style="font-size: large;"> correlate with R= 0,99966; this difference
is almost negligible for our applied tasks). In contrast to the results
reported in the aforementioned paper, the total energies computed with wB97XD/AUG-cc-pVDZ
method are 3-30 kJ/mol lower than the energies computed with wB97XD/6-31++G(D,P).</span></div>
</div>
<div class="MsoNormal">
<div style="text-align: justify;">
<span lang="EN-US" style="font-size: large;"> At the same time, with the basis set AUG-
cc-pVDZ the computation time was 3-6 times higher than with the 6-31++G(D,P)
basis set. So, the 6-31++G** basis set should be still considered good enough. </span></div>
</div>
<div class="MsoNormal">
<div style="text-align: justify;">
<span lang="EN-US" style="font-size: large;"> <o:p></o:p></span></div>
</div>
<div class="MsoNormal">
<div style="text-align: justify;">
<span lang="EN-US" style="font-size: large;"> It is usually considered that the computation
of anions or significantly electronegative atoms (which show big negative Mulliken
charge) requires the use of diffuse functions (“++” for 6-31G or “aug” for cc-pVnZ).
However, in the paper [8] this conclusion is criticized to a significant
extent. The authors write:<o:p></o:p></span></div>
</div>
<div class="MsoNormal">
<div style="text-align: justify;">
<span lang="EN-US" style="font-size: large;">“We
conclude that the use of diffuse functions for calculating geometrical
parameters for PAH anions in general is unnecessary and does not improve the
calculated results significantly. Energy calculations are affected in much the
same way.”.<o:p></o:p></span></div>
</div>
<div class="MsoNormal">
<div style="text-align: justify;">
<span lang="EN-US" style="font-size: large;"> As the authors write, the only case when the
diffuse functions are important are the computations of absolute values of
chemical shifts; however, in most cases, when the experimental data are
available, it is no necessary to obtain their absolute values as the
correlations between the computed and experimental values can be built instead.<o:p></o:p></span></div>
<div style="text-align: justify;">
<span lang="EN-US" style="font-size: large;"> On the other hand, D. Truhlar who investigated the use of diffuse functions writes <a href="http://comporgchem.com/blog/?p=1943">here</a>:</span></div>
<div style="text-align: justify;">
<span lang="EN-US" style="font-size: large;">"How should one add diffuse functions to the basis set? Diffuse functions are known to be critical in describing the electron distribution of anions (as discussed in my book), but they are also quite important in describing weak interactions, like hydrogen bonds, and can be critical in evaluating activation barriers and other properties."</span></div>
<div style="text-align: justify;">
<span lang="EN-US" style="font-size: large;"> The Truhlar group recommends using the "jun-" basis sets (see below).</span></div>
<div style="text-align: justify;">
<span lang="EN-US" style="font-size: large;"> One more source of information is the review "<a href="http://vergil.chemistry.gatech.edu/courses/chem6485/pdf/basis-sets.pdf">Basis sets in quantum chemistry</a>" by C. David. Sherill. The author writes in this review about the diffuse functions:</span></div>
<div class="separator" style="clear: both; text-align: justify;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjAErUYITFcvdFDuuUJm5xWL709G_6_2bCZ-GV11C0gfcbW4Bub7cn6k8xSALS7o_aiQSh-SJ5hDAz2Tfhz0pp4RkNk1-bwhrPsoDEbShS9IIJKcamlYpinbz6q29V0RLkTy7LKwJAfAuFc/s1600/difffuncs.JPG" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="412" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjAErUYITFcvdFDuuUJm5xWL709G_6_2bCZ-GV11C0gfcbW4Bub7cn6k8xSALS7o_aiQSh-SJ5hDAz2Tfhz0pp4RkNk1-bwhrPsoDEbShS9IIJKcamlYpinbz6q29V0RLkTy7LKwJAfAuFc/s640/difffuncs.JPG" width="640" /></a></div>
<div style="text-align: justify;">
<span lang="EN-US" style="font-size: large;"><br /></span></div>
</div>
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<div style="text-align: justify;">
<span lang="EN-US" style="font-size: large;"> Our knowledge of the subject
and our personal experience says that the diffuse functions indeed should be
used when calculating anions. We have computed the energies of deprotonation of
12 carbon acids (with PCM solvation model), both with diffuse functions and
without them (wB97XD/6-31++G(D,P) method and the wB97XD/6-31G(D,P) method), and
the values calculated by the first method correlate much better with
experimental PKa values than the values computed without diffuse function (the
correlation coefficients R are correspondingly 0,99522 for wB97XD/6-31++G(D,P)
and 0,98884 for wB97XD/6-31G(D,P)).<o:p></o:p></span></div>
</div>
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<div style="text-align: justify;">
<span style="font-size: large;"><span lang="EN-US"> </span> </span></div>
</div>
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<div style="text-align: justify;">
<span style="font-size: large;"><span lang="EN-US">Some
recommendations concerning the choice of basis sets can be found on <a href="https://sites.google.com/site/orcainputlibrary/basis-sets">Orca input library</a>:</span>.
These recommendations are:</span></div>
</div>
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<div style="text-align: justify;">
<span style="font-size: large;"><span lang="EN-US"> </span> </span></div>
</div>
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<div style="text-align: justify;">
<span lang="EN-US" style="font-size: large;"> - Rule of thumb: Energies and geometries are
usually fairly converged at the DFT level when using a balanced polarized
triple-zeta basis set (such as def2-TZVP) while MP2 and other post-HF methods
converge slower w.r.t. the basis set. Ab initio methods are much more basis set
sensitive than DFT methods<o:p></o:p></span></div>
</div>
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<div style="text-align: justify;">
<span style="font-size: large;"><br /></span></div>
</div>
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<div style="text-align: justify;">
<span lang="EN-US" style="font-size: large;"> - Stick with one family of basis sets that is
available for all the elements of your system. Mixing and matching basis sets
from different families can lead to problems.<o:p></o:p></span></div>
</div>
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<span style="font-size: large;"><span lang="EN-US"> - Calculations on heavy elements can either be
performed using an all-electron approach or effective core </span>potentials (ECPs).</span></div>
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<span lang="EN-US"><span lang="EN-US" style="font-size: large;">Here is a picture from the Orca input library:</span></span></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj6M3H03xajcx24-yyNJTTlNJ1jjioVTuSpH7lB6BnFMS05noh4jBKcDFSTBXG7oXZ_0FLFqh3tCK6DJ6gGjdiD9OCZM6YAttF7Hv7o21kMbfwv42LinGG39aJhV2bzzOl70P7nofulIqVg/s1600/dft7.JPG" style="margin-left: 1em; margin-right: 1em;"><span style="font-size: large;"><img border="0" height="343" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj6M3H03xajcx24-yyNJTTlNJ1jjioVTuSpH7lB6BnFMS05noh4jBKcDFSTBXG7oXZ_0FLFqh3tCK6DJ6gGjdiD9OCZM6YAttF7Hv7o21kMbfwv42LinGG39aJhV2bzzOl70P7nofulIqVg/s640/dft7.JPG" width="640" /></span></a></div>
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<span lang="EN-US" style="font-size: large;">So, it
seems that diffuse functions are really important for computing electron affinities.<o:p></o:p></span></div>
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<span lang="EN-US" style="font-size: large;"> As far as we know, usually it is not needed
to use a larger basis set than cc-pVTZ with DFT: further increasing basis set size
will not improve the accuracy of the computation. In contrast, this is not true for ab initio
computations, which will benefit from using larger basis sets, such as cc-pVQZ,
cc-pV5Z, etc. <o:p></o:p></span></div>
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<span lang="EN-US" style="font-size: large;"> Some papers,
in which the results of DFT computations are compared to those of ab initio
methods and to the experimental data, conclude that DFT performs not worse (or even slightly better) [10, 11, 12]. This is caused by employing modest
basis sets (not larger than cc-pVTZ) in these papers.<o:p></o:p></span></div>
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<div style="text-align: justify;">
<span lang="EN-US" style="font-size: large;"> So, the choice between DFT or ab initio
methods depends on which properties are calculated and what accuracy is
required.<o:p></o:p></span></div>
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<span lang="EN-US" style="font-size: large;"> The larger the basis set, the more difficult
the SCF convergence is (especially if diffuse-augmented basis sets are used). We recommend to always specify SCF=XQC in GAUSSIAN input files. With this keyword, the scf is firstly converged using the default DIIS algorithm, and if the convergence is not achieved, Gaussian switches to more reliable and costly quadratically convergent SCF procedure.<o:p></o:p></span></div>
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<span lang="EN-US" style="font-size: large;"> Ref. [9] describes the role of diffuse
functions in computations. It is known, that for many tasks using the diffuse
functions will not lead to significant increase of computational accuracy, but
will increase the cost of the calculation; besides that, using the diffuse
functions can lead to SCF convergence problems and can increase the basis set
superposition error (BSSE). The authors write: “We conclude that much current
practice includes more diffuse functions than are needed. Often, better
accuracy could be achieved if the additional cost were invested in higher-ζ
basis set or more polarization functions.”<o:p></o:p></span></div>
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<span lang="EN-US" style="font-size: large;"> The popular basis set family cc-pVnZ (of Dunning
and co-workers) comprises the diffuse functions, if “aug-” prefix is used. The authors notice that
chemists usually utilize “fully augmented” basis sets, and this may not be
optimal for large molecules. For example, the cc-pVTZ basis set for methane has
s, p, d, and f functions on C and s, p, and d functions on H; aug-cc-pVTZ
contains diffuse s, p, d, and f functions on C and diffuse s, p, and d functions
on H atoms.<o:p></o:p></span></div>
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<span lang="EN-US" style="font-size: large;"> In contrast, the earlier “plus” basis sets
originally systematized by Pople and co-workers contained only diffuse s and p functions
on non-hydrogen atoms and no diffuse functions on hydrogen atoms. In Ref. [9]
this is called “minimal augmentation”. The maug-cc-pVTZ basis set retains the
diffuse s and p functions on carbon with the exponential parameters optimized
for the aug case but deletes all other diffuse functions.<o:p></o:p></span></div>
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<div style="text-align: justify;">
<span lang="EN-US" style="font-size: large;"> So, the authors (Truhlar et al.) conclude that using the
minimal augmentation is usually more optimal than using the full augmentation (particularly
with DFT). The authors recommend the so-called “calendar” basis sets, in
particular the “jun” level of augmentation – for example, the jun-cc-pVTZ set
is recommended in comparison to aug-cc-pVDZ or cc-pVTZ. When increasing the
zeta number in Dunning basis sets (i.e. switching from cc-pVDZ to cc-pVTZ, then to cc-pVQZ, etc), augmentation becomes less important, and using the “calendar”
basis sets provides a more efficient sequence of basis sets (than unaugmented, minimally
augmented, or fully augmented sets) for basis set extrapolation to the complete
basis set limit. We know, however, that many researchers have criticized the approach proposed by the authors.<o:p></o:p></span></div>
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<span style="font-size: large;"><span lang="EN-US"> </span> </span></div>
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<b><span lang="EN-US" style="font-size: large;">3. DFT <o:p></o:p></span></b><span style="font-size: large;"><b>quackery</b></span></div>
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<span style="font-size: large;"><br /></span></div>
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<span lang="EN-US" style="font-size: large;"> Anyway,
density functional theory is a “black box”. Look at this picture from Ref. [13]:<o:p></o:p></span></div>
</div>
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<br /></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgKn-ExiCFypZIMDTSxt-zU-7CtcWfnc0iXx_TAlsmkodenvIT8gtSfsUJhWVVB7nnsyG-W76MHoKh-u4BPhWrz9FyUYiL72JlOzPaQYaoXXiCwAMflvuRhCBktZnVLAnlCwvG6DW6Itxpz/s1600/dft8.JPG" style="margin-left: 1em; margin-right: 1em;"><span style="font-size: large;"><img border="0" height="350" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgKn-ExiCFypZIMDTSxt-zU-7CtcWfnc0iXx_TAlsmkodenvIT8gtSfsUJhWVVB7nnsyG-W76MHoKh-u4BPhWrz9FyUYiL72JlOzPaQYaoXXiCwAMflvuRhCBktZnVLAnlCwvG6DW6Itxpz/s640/dft8.JPG" width="640" /></span></a></div>
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<span lang="EN-US" style="font-size: large;"><br /></span></div>
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<span lang="EN-US" style="font-size: large;"> Our comment
on this picture:<o:p></o:p></span></div>
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<div style="text-align: justify;">
<span lang="EN-US" style="font-size: large;"> First and
second points: In contrast to ab initio methods, DFT is not hierarchical. </span><span style="font-size: large;">Ab initio
(non-empirical) methods are hierarchical: this means that if we increase basis
set size, level of taking into account the electronic correlation (excitation
rank), and possibly the level of taking into account the relativistic effects
(for heavy elements), we approach the exact solution (within the Born–Oppenheimer
approximation). More specifically, if we go, e.g., through CCSD/cc-pVDZ -> CCSDT/cc-pVDZ -> CCSDTQ/cc-pVDZ -> CCSDTQ5/cc-pVDZ, etc., the
results of the computation systematically approach some limit; if
we go through CCSD/cc-pVDZ ->
CCSD/cc-pVTZ -> CCSD/cc-pVQZ -> CCSD/cc-pV5Z -> CCSD/cc-pV6Z,
etc., the results systematically approach the complete basis set (CBS) limit. For the first row, the improvement can be non-monotonic,
while for the second case the improvement seems to be always monotonic.</span><br />
<span style="font-size: large;"> So, we can verify the accuracy
of an ab initio method by comparing its results with the results of a higher
level computation. For DFT, this possibility is much less available.</span></div>
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<span lang="EN-US" style="font-size: large;"> The points
mentioned below are mostly our private opinion, maybe not fully right.<o:p></o:p></span></div>
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<div style="text-align: justify;">
<span lang="EN-US" style="font-size: large;"> As far as
we know, DFT is often used to “confirm” an experiment. This means that if the
experiment and a DFT computation lead to similar conclusions, this increases
the reliability of the investigation. On the contrary, if the experiment and
the DFT calculation give different results, this can be either a discovery or a
failure (inaccuracy of the computation, or maybe the experiment).<o:p></o:p></span></div>
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<div style="text-align: justify;">
<span lang="EN-US" style="font-size: large;"> Speaking of “confirming” an experiment, it
should be noted that this approach is only good with an independent experiment.
We know some cases when the experiment was “adjusted” for better agreement with
the computation (both at DFT and ab initio levels).<o:p></o:p></span></div>
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<span lang="EN-US" style="font-size: large;"> As mentioned above, it is a good practice to
perform the computation with several different DFT functionals, to ensure that
they all give the same results. And as far as we know, some researchers, being
not honest enough, meaningly avoid using more than one functional, because if
different functionals give contradictory results in their work, this makes this
whole work less “publishable”. <o:p></o:p></span></div>
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<br /></div>
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<span style="font-size: large;"><span lang="EN-US"> Here </span>you can
read an ironical essay “<a href="http://www.quantum-chemistry-history.com/Hist_Dat/DFT_Dat/DFT_Ob1.htm">Obituary : Density Functional Theory. 1927-1993</a>”:</span></div>
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<span style="font-size: large;"><br /></span></div>
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<div style="text-align: justify;">
<span lang="EN-US" style="font-size: large;"> The author claims that the density functional
theory in current implementation is not a mathematically correct approach:<o:p></o:p></span></div>
<div style="text-align: justify;">
<span lang="EN-US" style="font-size: large;"><br /></span></div>
</div>
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<div style="text-align: justify;">
<span lang="EN-US" style="font-size: large;"> “The Hohenberg-Kohn argument is what
mathematicians call an existence proof, as opposed to a constructive proof.
That is, although we now know that, <i>in
theory</i>, DFT can extract as much information from r(r) as her brother can
from Y
( r 1, r 2, ... , r n) , no-one knew how to dress her so that
she could achieve this <i>in practice</i>.
All quantum mechanical theories are created equal, but some are more equal than
others.”<o:p></o:p></span></div>
<div style="text-align: justify;">
<span lang="EN-US" style="font-size: large;"><br /></span></div>
</div>
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<div style="text-align: justify;">
<span lang="EN-US" style="font-size: large;"> The hybrid functionals, which appeared in
1993, are even more unreliable and not correct from the theoretical point of
view; in other words, using such functionals may be a kind of “shamanism”, or maybe
even “scientific charlatanism”. The author thinks that the density functional
theory finally died (we should add, it died as a well-grounded scientific
theory) in 1993, after the spreading of hybrid functionals.<o:p></o:p></span><br />
<span lang="EN-US" style="font-size: large;"><br /></span></div>
<div style="text-align: justify;">
<span lang="EN-US" style="font-size: large;"> On the other hand, in Ref. [13] the author states the following:</span></div>
<br />
<div style="text-align: justify;">
<span style="font-size: large;"><br /></span></div>
<div style="text-align: justify;">
<span style="font-size: large;">"</span><span style="font-size: large;">I believe that a fundamental principle underlies the success </span></div>
<div style="text-align: justify;">
<span style="font-size: large;">of DFT, which is that local approximations are a peculiar </span><span style="font-size: large;">type of </span><i style="font-size: x-large;">semiclassical</i><span style="font-size: large;"> approximation to the many-electron </span><span style="font-size: large;">problem. For the last 6 years, with both my group and many </span><span style="font-size: large;">collaborators, I have been trying to uncover this connection, </span><span style="font-size: large;">and make use of it. The underlying math is very challenging, </span><span style="font-size: large;">and some must be invented.</span><span style="font-size: large;">"</span></div>
<br />
<div style="text-align: justify;">
<span lang="EN-US" style="font-size: large;"> The "DFT </span><span style="font-size: large;">shamanism</span><span style="font-size: large;">" can exist in the following form: if different functionals are applied to the same object, the user may select any results consistent with experimental data (even the latter are </span><span style="font-size: large;">invalid or erroneous)</span><span style="font-size: large;"> and explain them. We suggest calling such practive "DFT quackery".</span></div>
<br />
<div style="text-align: justify;">
<span style="font-size: large;"> In Ref. [13] the following is proposed: "</span><span style="font-size: large;">Users should stick to the standard functionals (as most </span><span style="font-size: large;">do, according to Fig. 1), or explain very carefully why not.</span><span style="font-size: large;">"</span></div>
<br />
<div style="text-align: justify;">
<span style="font-size: large;"><br /></span></div>
<div style="text-align: justify;">
<b style="font-size: x-large;">4. DFT future</b></div>
<br />
<div style="text-align: justify;">
<span style="font-size: large;"> Here is a picture from Ref. [13]:</span></div>
<div class="separator" style="clear: both; text-align: justify;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgPffM6omwQF4EqVSTLuKF3OQU4Y1vBDTWZK8ac3-zIblBsD2N80C8FT8f6rbRcRf95YICOhy1JT1z1DabK3TJx_SuyfuDWFaCaAtOolmAkAqBE01P_wWm3UnzVZUUz2GTs5C9J3cm4DDB7/s1600/rev2.JPG" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="516" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgPffM6omwQF4EqVSTLuKF3OQU4Y1vBDTWZK8ac3-zIblBsD2N80C8FT8f6rbRcRf95YICOhy1JT1z1DabK3TJx_SuyfuDWFaCaAtOolmAkAqBE01P_wWm3UnzVZUUz2GTs5C9J3cm4DDB7/s640/rev2.JPG" width="640" /></a></div>
<div style="text-align: justify;">
<span style="font-size: large;"> A fragment of the paper [13]:</span></div>
<br />
<div style="text-align: justify;">
<span style="font-size: large;"><br /></span></div>
<div style="text-align: justify;">
<span style="font-size: large;">"XII. THE FUTURE</span></div>
<br />
<div style="text-align: justify;">
<span style="font-size: large;"> So, where does this leave us? It is clearly both the </span><span style="font-size: large;">best and worst of times for DFT. More calculations, both </span><span style="font-size: large;">good and bad, are being performed than ever. One of the </span><span style="font-size: large;">most frequently asked questions of developers of traditional </span><span style="font-size: large;">approaches to electronic structure is: “When will DFT go </span><span style="font-size: large;">away?.” Judging from Fig. 1, the answer is clearly no </span><span style="font-size: large;">time soon. Although based on exact theorems, as shown in </span><span style="font-size: large;">Fig. 2, these theorems give no simple prescription for constructing </span><span style="font-size: large;">approximations. This leads to the many frustrations </span><span style="font-size: large;">of the now manifold users listed in Table I.Without such guidance, </span><span style="font-size: large;">the swarm of available approximations of Fig. 3 will </span><span style="font-size: large;">continue to evolve and reproduce, perhaps ultimately undermining </span><span style="font-size: large;">the entire field. But I expect that some of the many </span><span style="font-size: large;">excellent ideas being developed by the DFT community will </span><span style="font-size: large;">come to fruition, i.e., produce new and more general standard </span><span style="font-size: large;">approximations, well before that happens."</span></div>
<div style="text-align: justify;">
<span style="font-size: large;"><br /></span>
</div>
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<span lang="EN-US" style="font-size: large;"><b>References</b><o:p></o:p></span></div>
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<span lang="EN-US" style="font-size: large;">[1] <a href="http://pubs.rsc.org/en/Content/ArticleLanding/2011/CP/c1cp20834a#!divAbstract">http://pubs.rsc.org/en/Content/ArticleLanding/2011/CP/c1cp20834a#!divAbstract</a><o:p></o:p></span></div>
</div>
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<span style="font-size: large;"><br /></span></div>
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<span lang="EN-US" style="font-size: large;">[2] <a href="http://pubs.rsc.org/en/Content/ArticleLanding/2011/CP/c0cp02984j#!divAbstract">http://pubs.rsc.org/en/Content/ArticleLanding/2011/CP/c0cp02984j#!divAbstract</a><o:p></o:p></span></div>
</div>
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<span lang="EN-US" style="font-size: large;">[3]
S.S.Leang, F.Zahariev, M.S.Gordon, J.Chem.Phys., 136, 104101 (2012)<o:p></o:p></span></div>
</div>
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<span style="font-size: large;"><br /></span></div>
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<div style="text-align: justify;">
<span lang="EN-US" style="font-size: large;">[4]
G.Garcı´a, C.Adamo, I.Ciofini, Phys. Chem. Chem. Phys., 2013, 15, 20210--20219<o:p></o:p></span></div>
</div>
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<span style="font-size: large;"><br /></span></div>
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<div style="text-align: justify;">
<span lang="EN-US" style="font-size: large;">[5] <a href="http://pubs.acs.org/doi/abs/10.1021/jo302156p">http://pubs.acs.org/doi/abs/10.1021/jo302156p</a><o:p></o:p></span></div>
</div>
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<span style="font-size: large;"><br /></span></div>
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<div style="text-align: justify;">
<span lang="EN-US" style="font-size: large;">[6] <a href="https://www.researchgate.net/publication/263680088_Gaussian_basis_sets_for_molecular_applications_Int_J_Quant_Chem">https://www.researchgate.net/publication/263680088_Gaussian_basis_sets_for_molecular_applications_Int_J_Quant_Chem</a><o:p></o:p></span></div>
</div>
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<span style="font-size: large;"><br /></span></div>
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<div style="text-align: justify;">
<span lang="EN-US" style="font-size: large;">[7] <a href="http://onlinelibrary.wiley.com/doi/10.1002/jcc.20058/abstract">http://onlinelibrary.wiley.com/doi/10.1002/jcc.20058/abstract</a><o:p></o:p></span></div>
</div>
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<span style="font-size: large;"><br /></span></div>
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<span lang="EN-US" style="font-size: large;">[8]
Calculations of PAH anions: When are diffuse functions necessary? Noach
Treitel1, Roy Shenhar, Ivan Aprahamian, Tuvia Sheradsky and Mordecai
Rabinovitz. P h y s . C h e m . C h e m . P h y s . , 2 0 0 4 , 6 , 1 1 1 3 – 1
1 2 1<o:p></o:p></span></div>
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<span style="font-size: large;"><br /></span></div>
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<span lang="EN-US" style="font-size: large;">[9] <a href="http://pubs.acs.org/doi/abs/10.1021/ct200106a">http://pubs.acs.org/doi/abs/10.1021/ct200106a</a><o:p></o:p></span></div>
<div style="text-align: justify;">
<br /></div>
<div style="text-align: justify;">
<span style="font-size: large;">[10] Do Practical Standard Coupled Cluster Calculations</span></div>
<div style="text-align: justify;">
<span style="font-size: large;">Agree Better than Kohn–Sham Calculations with</span></div>
<div style="text-align: justify;">
<span style="font-size: large;">Currently Available Functionals When Compared</span></div>
<div style="text-align: justify;">
<span style="font-size: large;">to the Best Available Experimental Da...</span></div>
<div style="text-align: justify;">
<span style="font-size: large;">Article in Journal of Chemical Theory and Computation · May 2015</span></div>
<div style="text-align: justify;">
<span style="font-size: large;">Impact Factor: 5.5 · DOI: 10.1021/acs.jctc.5b00081</span></div>
<br />
<div style="text-align: justify;">
<span style="font-size: large;"><br /></span></div>
<div style="text-align: justify;">
<span style="font-size: large;">[11] On the dissociation energy of Ti(OH,)+.</span></div>
<br />
<div style="text-align: justify;">
<span style="font-size: large;">An MCSCF, CCSD(T), and DFT study</span></div>
<div style="text-align: justify;">
<span style="font-size: large;">A. Irigoras, J.M. Ugalde, X. Lopez, and C. Sarasola</span></div>
<div style="text-align: justify;">
<span style="font-size: large;">Can. J. Chem. 74: 1824-1829 (1996). Printed in Canada / Imprimt au Canada</span></div>
<br />
<div style="text-align: justify;">
<span style="font-size: large;"><br /></span></div>
<div style="text-align: justify;">
<span style="font-size: large;">[12] </span><a href="https://www.researchgate.net/post/What_do_you_think_about_recent_JCTC_paper_of_Truhlar_et_al_about_benchmarking_DFT_against_CC_for_TM_complexes" style="font-size: x-large;">https://www.researchgate.net/post/What_do_you_think_about_recent_JCTC_paper_of_Truhlar_et_al_about_benchmarking_DFT_against_CC_for_TM_complexes</a></div>
<br />
<div style="text-align: justify;">
<br /></div>
<div style="text-align: justify;">
<span style="font-size: large;">[13] J. Chem. Phys. 136, 150901 (2012). Perspective on density functional theory. </span><span style="font-size: large;">Kieron Burke.</span><br />
<br />
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<![endif]--><span lang="EN-US" style="font-family: "times new roman"; font-size: 12pt;">Jensen</span><span style="font-family: "times new roman"; font-size: 12pt;">, </span><span lang="EN-US" style="font-family: "times new roman"; font-size: 12pt;">Stig</span><span lang="EN-US" style="font-family: "times new roman"; font-size: 12pt;"> </span><span lang="EN-US" style="font-family: "times new roman"; font-size: 12pt;">Rune</span><span style="font-family: "times new roman"; font-size: 12pt;">; </span><span lang="EN-US" style="font-family: "times new roman"; font-size: 12pt;">Saha</span><span style="font-family: "times new roman"; font-size: 12pt;">, </span><span lang="EN-US" style="font-family: "times new roman"; font-size: 12pt;">Santanu</span><span style="font-family: "times new roman"; font-size: 12pt;">; </span><span lang="EN-US" style="font-family: "times new roman"; font-size: 12pt;">Flores</span><span style="font-family: "times new roman"; font-size: 12pt;">-</span><span lang="EN-US" style="font-family: "times new roman"; font-size: 12pt;">Livas</span><span style="font-family: "times new roman"; font-size: 12pt;">, </span><span lang="EN-US" style="font-family: "times new roman"; font-size: 12pt;">Jos</span><span style="font-family: "times new roman"; font-size: 12pt;">é </span><span lang="EN-US" style="font-family: "times new roman"; font-size: 12pt;">Abdenago</span><span style="font-family: "times new roman"; font-size: 12pt;">; </span><span lang="EN-US" style="font-family: "times new roman"; font-size: 12pt;">Huhn</span><span style="font-family: "times new roman"; font-size: 12pt;">, </span><span lang="EN-US" style="font-family: "times new roman"; font-size: 12pt;">William</span><span style="font-family: "times new roman"; font-size: 12pt;">; </span><span lang="EN-US" style="font-family: "times new roman"; font-size: 12pt;">Blum</span><span style="font-family: "times new roman"; font-size: 12pt;">, </span><span lang="EN-US" style="font-family: "times new roman"; font-size: 12pt;">Volker</span><span style="font-family: "times new roman"; font-size: 12pt;">; </span><span lang="EN-US" style="font-family: "times new roman"; font-size: 12pt;">Goedecker</span><span style="font-family: "times new roman"; font-size: 12pt;">, </span><span lang="EN-US" style="font-family: "times new roman"; font-size: 12pt;">Stefan</span><span style="font-family: "times new roman"; font-size: 12pt;">; </span><span lang="EN-US" style="font-family: "times new roman"; font-size: 12pt;">Frediani</span><span style="font-family: "times new roman"; font-size: 12pt;">, </span><span lang="EN-US" style="font-family: "times new roman"; font-size: 12pt;">Luca</span><span style="font-family: "times new roman"; font-size: 12pt;">, 2017,
"</span><span lang="EN-US" style="font-family: "times new roman"; font-size: 12pt;">GGA</span><span style="font-family: "times new roman"; font-size: 12pt;">-</span><span lang="EN-US" style="font-family: "times new roman"; font-size: 12pt;">PBE</span><span lang="EN-US" style="font-family: "times new roman"; font-size: 12pt;"> </span><span lang="EN-US" style="font-family: "times new roman"; font-size: 12pt;">and</span><span lang="EN-US" style="font-family: "times new roman"; font-size: 12pt;"> </span><span lang="EN-US" style="font-family: "times new roman"; font-size: 12pt;">hybrid</span><span style="font-family: "times new roman"; font-size: 12pt;">-</span><span lang="EN-US" style="font-family: "times new roman"; font-size: 12pt;">PBE</span><span style="font-family: "times new roman"; font-size: 12pt;">0 </span><span lang="EN-US" style="font-family: "times new roman"; font-size: 12pt;">energies</span><span lang="EN-US" style="font-family: "times new roman"; font-size: 12pt;"> </span><span lang="EN-US" style="font-family: "times new roman"; font-size: 12pt;">and</span><span lang="EN-US" style="font-family: "times new roman"; font-size: 12pt;"> </span><span lang="EN-US" style="font-family: "times new roman"; font-size: 12pt;">dipole</span><span lang="EN-US" style="font-family: "times new roman"; font-size: 12pt;"> </span><span lang="EN-US" style="font-family: "times new roman"; font-size: 12pt;">moments</span><span lang="EN-US" style="font-family: "times new roman"; font-size: 12pt;"> </span><span lang="EN-US" style="font-family: "times new roman"; font-size: 12pt;">with</span><span lang="EN-US" style="font-family: "times new roman"; font-size: 12pt;"> </span><span lang="EN-US" style="font-family: "times new roman"; font-size: 12pt;">MRChem</span><span style="font-family: "times new roman"; font-size: 12pt;">, </span><span lang="EN-US" style="font-family: "times new roman"; font-size: 12pt;">FHI</span><span style="font-family: "times new roman"; font-size: 12pt;">-</span><span lang="EN-US" style="font-family: "times new roman"; font-size: 12pt;">aims</span><span style="font-family: "times new roman"; font-size: 12pt;">, </span><span lang="EN-US" style="font-family: "times new roman"; font-size: 12pt;">NWChem</span><span lang="EN-US" style="font-family: "times new roman"; font-size: 12pt;"> </span><span lang="EN-US" style="font-family: "times new roman"; font-size: 12pt;">and</span><span lang="EN-US" style="font-family: "times new roman"; font-size: 12pt;"> </span><span lang="EN-US" style="font-family: "times new roman"; font-size: 12pt;">ELK</span><span style="font-family: "times new roman"; font-size: 12pt;">", <a href="http://dx.doi.org/10.18710/0EM0EL" target="_blank"><span lang="EN-US" style="mso-ansi-language: EN-US;">doi</span>:10.18710/0<span lang="EN-US" style="mso-ansi-language: EN-US;">EM</span>0<span lang="EN-US" style="mso-ansi-language: EN-US;">EL</span></a>, </span><span lang="EN-US" style="font-family: "times new roman"; font-size: 12pt;">UiT</span><span lang="EN-US" style="font-family: "times new roman"; font-size: 12pt;"> </span><span lang="EN-US" style="font-family: "times new roman"; font-size: 12pt;">Open</span><span lang="EN-US" style="font-family: "times new roman"; font-size: 12pt;"> </span><span lang="EN-US" style="font-family: "times new roman"; font-size: 12pt;">Research</span><span lang="EN-US" style="font-family: "times new roman"; font-size: 12pt;"> </span><span lang="EN-US" style="font-family: "times new roman"; font-size: 12pt;">Data</span><span lang="EN-US" style="font-family: "times new roman"; font-size: 12pt;"> </span><span lang="EN-US" style="font-family: "times new roman"; font-size: 12pt;">Dataverse</span><span style="font-family: "times new roman"; font-size: 12pt;">, </span><span lang="EN-US" style="font-family: "times new roman"; font-size: 12pt;">V</span><span style="font-family: "times new roman"; font-size: 12pt;">3</span> </span></div>
</div>
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<span lang="EN-US" style="font-size: large;">
</span></div>
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<div style="text-align: justify;">
<br /></div>
<div style="text-align: justify;">
<br /></div>
</div>
</div>
Grigoriy Andrienkohttp://www.blogger.com/profile/10871921625140429891noreply@blogger.com5tag:blogger.com,1999:blog-4665151263516489793.post-89285006831416383842016-04-01T00:04:00.002-07:002016-04-01T00:04:50.923-07:00Some useful links for people dealing with quantum chemistry<div dir="ltr" style="text-align: left;" trbidi="on">
<div class="MsoNormal">
<span lang="EN-US">At this
page we are collecting links we find useful in our own research work. <o:p></o:p></span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span lang="EN-US">1) Gaussian
Error Messages<o:p></o:p></span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span lang="EN-US"><a href="https://www.ace-net.ca/wiki/Gaussian_Error_Messages">https://www.ace-net.ca/wiki/Gaussian_Error_Messages</a><o:p></o:p></span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span lang="EN-US">Here 26
types of Gaussian error messages are explained (e.g., memory allocation
problems, change in point group or standard orientation, convergence failure,
etc.).<o:p></o:p></span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span lang="EN-US">2)
Practical Advice for Quantum Chemistry Computations, by C. David Sherrill.<o:p></o:p></span></div>
<div class="MsoNormal">
<span lang="EN-US"><br /></span></div>
<div class="MsoNormal">
<span lang="EN-US"><a href="http://www.chemcraftprog.com/tmp/quantum-practical.pdf">http://www.chemcraftprog.com/tmp/quantum-practical.pdf</a></span></div>
<div class="MsoNormal">
<span lang="EN-US"><br /></span></div>
<div class="MsoNormal">
<span lang="EN-US">Here many
simple hints are provided:<o:p></o:p></span></div>
<div class="MsoNormal">
<span lang="EN-US"> - The choice of basis set;<o:p></o:p></span></div>
<div class="MsoNormal">
<span lang="EN-US"> - The choice of ab initio/DFT methods for
different tasks.<o:p></o:p></span></div>
<div class="MsoNormal">
<span lang="EN-US">The author
writes that standard HF, semiempirical, and DFT techniques are not appropriate
for van der Waals complexes or systems dominated by <st1:city w:st="on"><st1:place w:st="on">London</st1:place></st1:city> dispersion forces. However, <a href="http://pubs.acs.org/doi/abs/10.1021/jo302156p">Ref</a>. reported that for the compounds under investigation the B3LYP-gCP-D3/6-31G*
method could correctly compute <st1:city w:st="on"><st1:place w:st="on">London</st1:place></st1:city>
dispersion effects (and it does not have the basis set superposition error);<o:p></o:p></span></div>
<div class="MsoNormal">
<span lang="EN-US"> - Hints on the problem of SCF convergence;<o:p></o:p></span></div>
<div class="MsoNormal">
<span lang="EN-US"> - Common hints on imaginary frequencies and
saddle points;<o:p></o:p></span></div>
<br />
<div class="MsoNormal">
<span lang="EN-US"> - Hints on optimization with symmetry.<o:p></o:p></span></div>
</div>
Grigoriy Andrienkohttp://www.blogger.com/profile/10871921625140429891noreply@blogger.com3tag:blogger.com,1999:blog-4665151263516489793.post-25283021520436263812016-03-01T11:09:00.001-08:002016-03-01T11:09:29.675-08:00Blogs on quantum chemistry<div dir="ltr" style="text-align: left;" trbidi="on">
<div class="MsoNormal">
<span lang="EN-US">In our
opinion, blogs are usually more interesting source of information for chemists,
than usual papers. Here we have collected some links to such blogs:<o:p></o:p></span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span lang="EN-US"><a href="http://www.ch.ic.ac.uk/rzepa/blog/">http://www.ch.ic.ac.uk/rzepa/blog/</a><o:p></o:p></span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span lang="EN-US"><a href="http://comporgchem.com/blog/">http://comporgchem.com/blog/</a><o:p></o:p></span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span lang="EN-US"><a href="http://www.compchemhighlights.org/">http://www.compchemhighlights.org/</a><o:p></o:p></span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span lang="EN-US"><a href="http://molecularmodelingbasics.blogspot.ru/">http://molecularmodelingbasics.blogspot.ru/</a><o:p></o:p></span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span lang="EN-US"><a href="http://joaquinbarroso.com/">http://joaquinbarroso.com/</a><o:p></o:p></span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span lang="EN-US"><a href="http://verahill.blogspot.ru/">http://verahill.blogspot.ru/</a><o:p></o:p></span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span lang="EN-US">And one
more – in Russian:<o:p></o:p></span></div>
<div class="MsoNormal">
<br /></div>
<br />
<div class="MsoNormal">
<span lang="EN-US"><a href="http://photon190573.livejournal.com/">http://photon190573.livejournal.com/</a><o:p></o:p></span></div>
</div>
Grigoriy Andrienkohttp://www.blogger.com/profile/10871921625140429891noreply@blogger.com0tag:blogger.com,1999:blog-4665151263516489793.post-5738209631337796172016-02-13T08:45:00.001-08:002016-02-14T01:09:07.663-08:00Why we haven’t yet implemented a GUI for creating input files in Chemcraft<div dir="ltr" style="text-align: left;" trbidi="on">
<div class="MsoNormal">
<div class="MsoNormal">
<span lang="EN-US">Sometimes
the Chemcraft users ask me to implement a GUI for creating input files.
GaussView has such a GUI. <o:p></o:p></span></div>
<div class="MsoNormal">
<span lang="EN-US">I don’t
plan to implement such a GUI in Chemcraft, because I never had the need to use
it in my research work. To create input files for new jobs, I use my archive of
computed jobs; when I need to create a new input file, I take an input file
from this archive and modify it.<o:p></o:p></span></div>
<div class="MsoNormal">
<span lang="EN-US">You can
download such an archive here:<o:p></o:p></span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span lang="EN-US"><a href="http://www.chemcraftprog.com/files/jobsbase.zip">http://www.chemcraftprog.com/files/jobsbase.zip</a><o:p></o:p></span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span lang="EN-US">This archive
contains more than 150 jobs (both input and output files) with different types
of computation. Besides these files, the archive contains text files with
comments. It also contains some examples of interesting computations with
comments, which illustrate the use of quantum chemistry.<o:p></o:p></span></div>
<div class="MsoNormal">
<span lang="EN-US">This
archive is protected with password; to get the password, you need to purchase
Chemcraft (the password will be shown in the “Help/License information”
window).<o:p></o:p></span></div>
<div class="MsoNormal">
<span lang="EN-US">I think
that implementing a GUI for creating input files can be even harmful, because
it will give you a false feeling of easy creation of new jobs; but when you
need to create a non-standard job (e.g., a PES scan), this GUI will become useless.
<o:p></o:p></span></div>
<span lang="EN-US">
<span lang="EN-US" style="font-size: 12pt;">I wrote this statement in our Facebook group, and
two persons fully agreed with my conclusion (none disagreed).</span></span><br />
<br /></div>
</div>
Grigoriy Andrienkohttp://www.blogger.com/profile/10871921625140429891noreply@blogger.com0tag:blogger.com,1999:blog-4665151263516489793.post-27189508592190918692015-12-12T19:59:00.002-08:002017-12-03T02:14:49.451-08:00Correlations between computed and experimental properties<div dir="ltr" style="text-align: left;" trbidi="on">
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<span lang="EN-US">When the
results of quantum chemistry computations are directly compared with
experiment, often quite poor agreement is obtained. However, this agreement
often becomes much better, if a series of homologues is taken and a correlation
is built between the computed and experimental values. Here I present some samples
of such correlations:<o:p></o:p></span></div>
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<br /></div>
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<!--[if !supportLists]--><span lang="EN-US">1)<span style="font-size: 7pt; font-stretch: normal;">
</span></span><!--[endif]--><span lang="EN-US">Correlation
between QC (T1(1)) and experimental heat of formation for a set of 1800 diverse
organic molecules from NIST thermochemical database (from Wikipedia):<o:p></o:p></span></div>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgkbueBQm4CFPwfASyyQy2lwAoKRrSWm-QB42A_BIH8CKf6aAqim1k5wmJHqhOpwLBcKAyUt_JXjYqxYRWLhNFdRIAxa_m_dcsX4dZn9jl2jAXpxDzjeq3CoBQYyASyttfnPtq0G2dGiCoR/s1600/corr1.JPG" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="333" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgkbueBQm4CFPwfASyyQy2lwAoKRrSWm-QB42A_BIH8CKf6aAqim1k5wmJHqhOpwLBcKAyUt_JXjYqxYRWLhNFdRIAxa_m_dcsX4dZn9jl2jAXpxDzjeq3CoBQYyASyttfnPtq0G2dGiCoR/s400/corr1.JPG" width="400" /></a></div>
<div class="separator" style="clear: both; text-align: center;">
<br /></div>
<div class="MsoNormal">
<span lang="EN-US">The mean
absolute and RMS errors are 8.5 and 11.5 kJ/mol, respectively.<o:p></o:p></span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span lang="EN-US">2) Correlation
between computed and experimental NMR spectra.<o:p></o:p></span></div>
<div class="MsoNormal">
<span lang="EN-US">We have found
that usually the computed NMR chemical shifts are rather far from the
experimental ones; maybe the physical meaning of the chemical shifts is not
clear enough. At the same time, the computed values correlate well with the
experimental ones<o:p></o:p></span></div>
<div class="separator" style="clear: both; text-align: center;">
</div>
<div class="MsoNormal">
<span lang="EN-US">a) Such
correlation for several Shiff bases:<o:p></o:p></span></div>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEicM2IFuDWvVnqqF0wIpUs57ULnx9OMEMBUEq0B5oZKsQoMqGUhccVKRzVi_DR4wc4OPLNFaotmMB5bWIJOhrvaDdfdFyCwZ-oSGqh_wb4svedrpgNX7z6d2DU4rQuMV1Qq4navWSV6Y31N/s1600/corr2.JPG" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="168" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEicM2IFuDWvVnqqF0wIpUs57ULnx9OMEMBUEq0B5oZKsQoMqGUhccVKRzVi_DR4wc4OPLNFaotmMB5bWIJOhrvaDdfdFyCwZ-oSGqh_wb4svedrpgNX7z6d2DU4rQuMV1Qq4navWSV6Y31N/s640/corr2.JPG" width="640" /></a></div>
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<span lang="EN-US"><br /></span></div>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhfmZpvu4P2ThcrsoahRDrGNgoQV5WdlkW0L3L5p2_wWhw3ijdsPLtZp-dY72fMiZn4HRpBm2a3hGpKQCXuO5dFRUWrR3Yp2QhA1DjwQUPUdGlUOLgpTGVH25ayPYxyyYY4U_rfAIyUx3RR/s1600/corr3.JPG" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="364" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhfmZpvu4P2ThcrsoahRDrGNgoQV5WdlkW0L3L5p2_wWhw3ijdsPLtZp-dY72fMiZn4HRpBm2a3hGpKQCXuO5dFRUWrR3Yp2QhA1DjwQUPUdGlUOLgpTGVH25ayPYxyyYY4U_rfAIyUx3RR/s640/corr3.JPG" width="640" /></a></div>
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<span lang="EN-US"><br /></span></div>
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<span lang="EN-US"></span></div>
<div class="MsoNormal">
<span lang="EN-US">The calculations were performed with B3LYP/6-311G(D,P) method, but the B3LYP functional is considered obsolete at the moment. You should better use PBE, </span>wB97XD or B3LYP-D3 instead. 6-311 G is not a good basis set too, you should better use, e.g., cc-pVDZ.<br />
<span lang="EN-US"><br /></span>
<span lang="EN-US">b) A bodipy
molecule:<o:p></o:p></span></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhJy4BanBroAq5ptVnblOtieTJWfowR1KZppTWYZa38Xmx_AD55aJ9TZpNr_IFwpm1xBRwVWWSGCH6jRJCiA5COQPj0gDd90Dx5FzcmP2kN-EGXYrVoJRr3n2_44Rl7QxXqocSKqeRv4K-y/s1600/corr4.JPG" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="400" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhJy4BanBroAq5ptVnblOtieTJWfowR1KZppTWYZa38Xmx_AD55aJ9TZpNr_IFwpm1xBRwVWWSGCH6jRJCiA5COQPj0gDd90Dx5FzcmP2kN-EGXYrVoJRr3n2_44Rl7QxXqocSKqeRv4K-y/s400/corr4.JPG" width="270" /></a></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjHmGUIb84JoxkeyXbv3R4flodgG8ckxb3vh3Z4GS2H4fhxAP0rvzRvaiUbzpAF0d7sy3Ts9M4QPNWcVd5c8U1_ypy5Vp61r4qXQFuTU0I6szKViNDPvo6Lg9KNomvvuZFtvYLJYdrklyLo/s1600/corr5.JPG" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="353" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjHmGUIb84JoxkeyXbv3R4flodgG8ckxb3vh3Z4GS2H4fhxAP0rvzRvaiUbzpAF0d7sy3Ts9M4QPNWcVd5c8U1_ypy5Vp61r4qXQFuTU0I6szKViNDPvo6Lg9KNomvvuZFtvYLJYdrklyLo/s400/corr5.JPG" width="400" /></a></div>
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<span lang="EN-US">A similar
correlation can be obtained for H1 chemical shifts (several bodipy molecules):<o:p></o:p></span></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi56iJpRVA0XmKrbISO-ioTkyYfhdsj12squsWk2hgRy6AJmTuZ844EueddfmsGP9PGQ6on_XVxXQOISIgKQFAqB69kvPCA2HkgtvKNREaRx5kkW6qmHudBkH0n52s3K8DXGX2cFM_60c9W/s1600/corr6.JPG" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="382" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi56iJpRVA0XmKrbISO-ioTkyYfhdsj12squsWk2hgRy6AJmTuZ844EueddfmsGP9PGQ6on_XVxXQOISIgKQFAqB69kvPCA2HkgtvKNREaRx5kkW6qmHudBkH0n52s3K8DXGX2cFM_60c9W/s400/corr6.JPG" width="400" /></a></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhgye1I71n79ygV9JLvyN7s3EWT6lvZIk_EN9vvDv9H6npHxoPjaFwHdzF_eXAg2vKj9cipPsZNTvaNbDN5b5urz35TC8qFKl6a1B0sragVeOnWXKEaArmMJ2YEs3t4KHK4RDk1b-TVW9dI/s1600/corr7.JPG" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="400" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhgye1I71n79ygV9JLvyN7s3EWT6lvZIk_EN9vvDv9H6npHxoPjaFwHdzF_eXAg2vKj9cipPsZNTvaNbDN5b5urz35TC8qFKl6a1B0sragVeOnWXKEaArmMJ2YEs3t4KHK4RDk1b-TVW9dI/s400/corr7.JPG" width="352" /></a></div>
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<span lang="EN-US">I have
found that a good correlation is usually obtained for C13 chemical shifts; for
H1 chemical shifts the correlation is rather good too, but only for hydrogen
atoms attached to carbons.<o:p></o:p></span><br />
<span lang="EN-US"><br /></span>
<span lang="EN-US">c) One more correlation from this site:</span><br />
<span lang="EN-US"><br /></span>
<span lang="EN-US"><a href="http://cheshirenmr.info/">http://cheshirenmr.info/</a></span><br />
<br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhdKuOCNZe4BhpxD7POhKQ9qJSU1LtnITryTxoze-vO5mlq3SEN2vXb7OUmHIvOEOauvtKU1eVKFijZc6zqwxImwWS_yi4T8j4hV952FTLSXZdq-P3XWSqcuM4Cw8QSc95iSf85fY4qw5v7/s1600/LinRegExample.gif" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhdKuOCNZe4BhpxD7POhKQ9qJSU1LtnITryTxoze-vO5mlq3SEN2vXb7OUmHIvOEOauvtKU1eVKFijZc6zqwxImwWS_yi4T8j4hV952FTLSXZdq-P3XWSqcuM4Cw8QSc95iSf85fY4qw5v7/s1600/LinRegExample.gif" /></a></div>
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<span lang="EN-US">3) An
important correlation can be obtained between computed energies, or maybe Gibbs
energies, and experimental reaction constants.<o:p></o:p></span></div>
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<br /></div>
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<span lang="EN-US">a) Here is
one such correlation for a set of 9 carboxylic acids:<o:p></o:p></span></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjA8u0YoC4CrtaFD2szBS4xp9pzj-XsrRpSdpzmJyUPFyNb7_nndHV8VuYMkrzMktfM2srbzderuP2yqwk85Fjck2gbNPaE_f5B5Y1BsnVGYgdJIqtrRexVDuD37LB_tKE_uQY1q-qwRiM9/s1600/corr8.JPG" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjA8u0YoC4CrtaFD2szBS4xp9pzj-XsrRpSdpzmJyUPFyNb7_nndHV8VuYMkrzMktfM2srbzderuP2yqwk85Fjck2gbNPaE_f5B5Y1BsnVGYgdJIqtrRexVDuD37LB_tKE_uQY1q-qwRiM9/s1600/corr8.JPG" /></a></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi_RPazre8BO4pZQph5uZdP3gklkt6GcWHQjfGlgAYzeXGqTfoj-RkLxHZtkEQIl0cEy6FXzwvMYkK-Yeu8TJF-sGwtOdcuYrbJsdrIv6rrR-6Yftbp-03OYTOEwfzTE4lYZry6a8_XFYDl/s1600/corr9a.JPG" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi_RPazre8BO4pZQph5uZdP3gklkt6GcWHQjfGlgAYzeXGqTfoj-RkLxHZtkEQIl0cEy6FXzwvMYkK-Yeu8TJF-sGwtOdcuYrbJsdrIv6rrR-6Yftbp-03OYTOEwfzTE4lYZry6a8_XFYDl/s1600/corr9a.JPG" /></a></div>
<span lang="EN-US"><br /></span>
<span lang="EN-US">Computed energies of deprotonation vs
experimental pK<sub>a</sub><o:p></o:p></span></div>
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<div class="MsoNormal">
<span lang="EN-US">The
energies were computed at PCM wB97XD/6-311++G(DP) level (the solvent is water),
with two water molecules added to the model for taking into account the
specific solvation.<o:p></o:p></span></div>
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<br /></div>
<div class="MsoNormal">
The
correlation between QC energies and experimental reaction constants is based on
the assumption that the entropy contribution to the Gibbs energy within a row
of compounds is small relative to the energy contribution (if not, one can
compute the Gibbs energies as well).<br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjW1kkI7wlR9DuZ2UxfYls2m-8kL0PAVHq6yevECgQMEklLWoUihTTCrrtQ2kC29TeUkyZ0LpzPSoLgWRFJ0WwnF3DFDrDoyUj-eqzTT_ewRx-I7E2fz30EWVWipQvC-REU4ZQGe083APJu/s1600/p1.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjW1kkI7wlR9DuZ2UxfYls2m-8kL0PAVHq6yevECgQMEklLWoUihTTCrrtQ2kC29TeUkyZ0LpzPSoLgWRFJ0WwnF3DFDrDoyUj-eqzTT_ewRx-I7E2fz30EWVWipQvC-REU4ZQGe083APJu/s1600/p1.png" /></a></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi67l5j21lIto0oMQmPqN-JtvSZU0q8zeFn4rKbtLOubuaZbif3EPOCu23ikx6siCqMtXCYgq3xgZrbGE_yBFWjPrxCGySwHchcOsSnhIUi396l66NKU2Ps4hShcB2TeGc4jZPPlUnyMo7d/s1600/p2.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi67l5j21lIto0oMQmPqN-JtvSZU0q8zeFn4rKbtLOubuaZbif3EPOCu23ikx6siCqMtXCYgq3xgZrbGE_yBFWjPrxCGySwHchcOsSnhIUi396l66NKU2Ps4hShcB2TeGc4jZPPlUnyMo7d/s1600/p2.png" /></a></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh8T3hEBEAv3bYpaGVNODe2imWhhwISgpQh4vRyBHCG7irNscvuMsM5M6TKqPYiNBdw5fPTw6dblcGlM0iMkbAkn58cKniyjpQLbyNGfWBUVd0nXZmujG0hoVeTk8-85na3uhNXGFUMVoSe/s1600/p3.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh8T3hEBEAv3bYpaGVNODe2imWhhwISgpQh4vRyBHCG7irNscvuMsM5M6TKqPYiNBdw5fPTw6dblcGlM0iMkbAkn58cKniyjpQLbyNGfWBUVd0nXZmujG0hoVeTk8-85na3uhNXGFUMVoSe/s1600/p3.png" /></a></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhv969YrvfLR9rniltTs1lznlVFtRfNdD5r4-Z_4HGJ3bn8lcx9q0KAYy09ywDGkpshKo_6bYkpH2IsTT1NOMvNDQt76nqmjzz0XInSR0gj2OBZhm9hKGtRcRpjfOltKFLWHkQ2ujuzz2Bd/s1600/p4.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhv969YrvfLR9rniltTs1lznlVFtRfNdD5r4-Z_4HGJ3bn8lcx9q0KAYy09ywDGkpshKo_6bYkpH2IsTT1NOMvNDQt76nqmjzz0XInSR0gj2OBZhm9hKGtRcRpjfOltKFLWHkQ2ujuzz2Bd/s1600/p4.png" /></a></div>
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<span lang="EN-US" style="font-size: 12pt;">The difference between <a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgapph2pIEn2wHuKmpxk1_G-_xWcPMswjrXgYt_OdDinHLRJBF67lr7QZd0d_kco5V-e191uYG4rNv8CXRLECsVuGbevjzAElfDKvZhrJaX2D125B08OZiyqppxrDmHp6kfk5tL0Ugzh9nn/s1600/p5.png" imageanchor="1" style="font-size: 12pt; margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgapph2pIEn2wHuKmpxk1_G-_xWcPMswjrXgYt_OdDinHLRJBF67lr7QZd0d_kco5V-e191uYG4rNv8CXRLECsVuGbevjzAElfDKvZhrJaX2D125B08OZiyqppxrDmHp6kfk5tL0Ugzh9nn/s1600/p5.png" /></a> and <a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh2WKziGPWPUfJtaCpnmCme_9CZTfnLXa09AaefS4e5aAZh-kbbh94zXMSKKCVqxEDZTNAUHr41VB-tlLjU9X1nrIR7Q6cT4bQ5lV7jsHV75y63Gn-lPCAORj1Md7NTZR9ZMMT6xqyMQBB6/s1600/p6.png" imageanchor="1" style="font-size: 12pt; margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh2WKziGPWPUfJtaCpnmCme_9CZTfnLXa09AaefS4e5aAZh-kbbh94zXMSKKCVqxEDZTNAUHr41VB-tlLjU9X1nrIR7Q6cT4bQ5lV7jsHV75y63Gn-lPCAORj1Md7NTZR9ZMMT6xqyMQBB6/s1600/p6.png" /></a> within a row of homologues is relatively small, so</span></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhZDTlYo3NAuFWTiDMaXHcW4wccb1y1F6UjGADS9VwW1sIUC8PZn6Fspac00KZO5sfF1K5hxPHMXZtAMSMN_w2kACewsp-o5BqxWt0fDztGvUPtuXKg9ubio54IfIoReYiQAS4cOe8qltrD/s1600/p7.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhZDTlYo3NAuFWTiDMaXHcW4wccb1y1F6UjGADS9VwW1sIUC8PZn6Fspac00KZO5sfF1K5hxPHMXZtAMSMN_w2kACewsp-o5BqxWt0fDztGvUPtuXKg9ubio54IfIoReYiQAS4cOe8qltrD/s1600/p7.png" /></a></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhZy3YxX9GoPNTPONUuqDIiren00yIYHeKo8ELM6LPOACEs2_cFPbSVj2O3HWKj2DJ_ouA8p5unIafm-VHAZc7OPDzpLeIm9tCu63wP33xVcY3MfxYxFZbEg6KzrMWiLbmZnX_Ae0qVWa5Z/s1600/p8.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="33" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhZy3YxX9GoPNTPONUuqDIiren00yIYHeKo8ELM6LPOACEs2_cFPbSVj2O3HWKj2DJ_ouA8p5unIafm-VHAZc7OPDzpLeIm9tCu63wP33xVcY3MfxYxFZbEg6KzrMWiLbmZnX_Ae0qVWa5Z/s200/p8.png" width="200" /></a></div>
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<div>
<div class="MsoNormal">
<span lang="EN-US">b) Some
more correlations between the energy and PKa for 5 sets of compounds, taken from
paper [1]:<o:p></o:p></span></div>
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<span lang="EN-US"><br /></span></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjhG9TWaNgN0yK96jvkl7w1Ev9dIOmCqObtQYuMXAkXgLh_YxRMgOUO7UCkeULDIg726OZXHJRgfH-id3osRgRQJ05RucrzNDNcAzs4kOhwISVFAjiAzQBk3vmvrD6UMYXF2L8fCghU1GqN/s1600/corr10.JPG" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="640" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjhG9TWaNgN0yK96jvkl7w1Ev9dIOmCqObtQYuMXAkXgLh_YxRMgOUO7UCkeULDIg726OZXHJRgfH-id3osRgRQJ05RucrzNDNcAzs4kOhwISVFAjiAzQBk3vmvrD6UMYXF2L8fCghU1GqN/s640/corr10.JPG" width="624" /></a></div>
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<span lang="EN-US">The
theoretical constants were calculated from the Gibbs energies of deprotonation
computed at PCM B3LYP/6-311+G(d,p) level (the solvent was DMSO).</span><br />
<span lang="EN-US"></span><br />
<span lang="EN-US"></span><br />
<br />
<span lang="EN-US"><o:p>3) One more correlation between the calculated and experimental pKa valiues [10]:</o:p></span><br />
<br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjNfdtgUuOuQFezxleB9dyLxf-b1MKnfroGqH2eXvCNUb4QHSCB-4p0oO2ojf7Sago69nDaOLDJwv8vY1LfDioycUiyyfj96RlYlJmrMcSFFLev4EIFOyWn7wnpSCj5DyapPluyMMCZaG4n/s1600/pk2017.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="478" data-original-width="535" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjNfdtgUuOuQFezxleB9dyLxf-b1MKnfroGqH2eXvCNUb4QHSCB-4p0oO2ojf7Sago69nDaOLDJwv8vY1LfDioycUiyyfj96RlYlJmrMcSFFLev4EIFOyWn7wnpSCj5DyapPluyMMCZaG4n/s1600/pk2017.jpg" /></a></div>
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<span lang="EN-US">4) A
similar correlation can be obtained between the computed energies and
experimental rate constants. Here are some samples from our work:<o:p></o:p></span></div>
<div class="MsoNormal" style="text-indent: 35.4pt;">
<span lang="EN-US"> <o:p></o:p></span></div>
<div class="MsoNormal">
<span lang="EN-US">a)<o:p></o:p></span></div>
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<span lang="EN-US">We have studied the reaction of C-Cl bond
elimination of some anion radicals:<o:p></o:p></span></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEilRyC1ZgAaKgGiN9SWaK-IEg_CW4SzuOzNhFXrWAmfcBQPBEvsWOHLG6zs-3hFvOVLyrjwu4KqaFixi8eAjdKFKuJclA-Pb2cgP6LOlpEtKNJE2f6bwdyk4fm_-sROBSRRD3EqEPMGw4_0/s1600/corr11a.JPG" imageanchor="1" style="clear: left; display: inline !important; float: left; margin-bottom: 1em; margin-right: 1em; text-align: center; text-indent: 35.4pt;"><img border="0" height="488" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEilRyC1ZgAaKgGiN9SWaK-IEg_CW4SzuOzNhFXrWAmfcBQPBEvsWOHLG6zs-3hFvOVLyrjwu4KqaFixi8eAjdKFKuJclA-Pb2cgP6LOlpEtKNJE2f6bwdyk4fm_-sROBSRRD3EqEPMGw4_0/s640/corr11a.JPG" width="640" /></a><br />
<br /></div>
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<span lang="EN-US"></span></div>
<div class="MsoNormal">
<span lang="EN-US"><br /></span>
<span lang="EN-US">....</span><br />
<span lang="EN-US">The
computed energies of the C-Cl bonds correlate with the experimental rate
constants of the bond elimination reaction:<o:p></o:p></span></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgNdMQkfWMQwjN0nJKJiGbyegEyF-bFC7Nj_r1vIOPATiiPRp7er0HceQMF6NM59qvILu6UVWStObD77D-6Jq5QcdIH3-bNeys2ZKOF7PjXVV038wC7yxCeDYARY1SnYNB2f7y8iQ2OzGcT/s1600/corr12.JPG" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="524" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgNdMQkfWMQwjN0nJKJiGbyegEyF-bFC7Nj_r1vIOPATiiPRp7er0HceQMF6NM59qvILu6UVWStObD77D-6Jq5QcdIH3-bNeys2ZKOF7PjXVV038wC7yxCeDYARY1SnYNB2f7y8iQ2OzGcT/s640/corr12.JPG" width="640" /></a></div>
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<br /></div>
<div class="MsoNormal">
<span lang="EN-US">b)<o:p></o:p></span></div>
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</div>
<div class="MsoNormal" style="text-indent: 35.4pt;">
<span lang="EN-US">We have studied the reaction of substitution of
alcohol ligands by imidazole using QC and experimental methods:<o:p></o:p></span></div>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgubRhiWF_Wa-WUAtyXKHCz0t_w-lpLnGTk74rEYSjym0Uow0XJ3pI6YidJrI3bj6s57nlcNtM5bxLwYoDeE3D9XWwvob7qBtYSCnch4lphnZBwf0Xek0lbqqrIuqttX0M10ecyj43n9bj8/s1600/corr13.JPG" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="614" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgubRhiWF_Wa-WUAtyXKHCz0t_w-lpLnGTk74rEYSjym0Uow0XJ3pI6YidJrI3bj6s57nlcNtM5bxLwYoDeE3D9XWwvob7qBtYSCnch4lphnZBwf0Xek0lbqqrIuqttX0M10ecyj43n9bj8/s640/corr13.JPG" width="640" /></a></div>
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<br /></div>
<div class="separator" style="clear: both; text-align: center;">
<br /></div>
<div class="MsoNormal" style="text-indent: 35.4pt;">
<span lang="EN-US">Apart from methanol, the data for other
alcohols were also obtained:<o:p></o:p></span></div>
<div class="MsoNormal" style="text-indent: 35.4pt;">
<span lang="EN-US"><br /></span></div>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi8mzIUGnFAtdsSYa7nEKoyHsNXFtTXGAvF4Lp7bEwL4G2qJtpgSqDW2XA5waDeCLXcDsv9LPZBxDR8yDb8XbPlF_S8Ba8Fd16BexYBHUf1izi0gn1VH6ddu3Xna_WmMuTTJnp71tJr8ZI3/s1600/corr14.JPG" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="211" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi8mzIUGnFAtdsSYa7nEKoyHsNXFtTXGAvF4Lp7bEwL4G2qJtpgSqDW2XA5waDeCLXcDsv9LPZBxDR8yDb8XbPlF_S8Ba8Fd16BexYBHUf1izi0gn1VH6ddu3Xna_WmMuTTJnp71tJr8ZI3/s640/corr14.JPG" width="640" /></a></div>
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<br /></div>
<div class="separator" style="clear: both; text-align: center;">
<br /></div>
<div class="MsoNormal" style="text-indent: 35.4pt;">
<span lang="EN-US">The alcohol substitution was studied using
electronic spectra. The experiment showed that this reaction has two stages,
each stage having its own rate constant. Then I computed the energies
Cr-Alcohol, and plotted the graph “Computed energies vs. experimental constants
of correlation (first stage)”:<o:p></o:p></span></div>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhQYDeyq6onu1IOZX1q7c9I7zinQmyGdrMLlTjAXlJR3GozPdf2f44A1bAkgtp5QtVFwcIW1ZBBy-gFPqw188GP7eBjRYMdGQqmQP0zJ_WrN3uuex3nst4Shg4NG48cHwpit8eQCDwmDMWi/s1600/corr15.JPG" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="306" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhQYDeyq6onu1IOZX1q7c9I7zinQmyGdrMLlTjAXlJR3GozPdf2f44A1bAkgtp5QtVFwcIW1ZBBy-gFPqw188GP7eBjRYMdGQqmQP0zJ_WrN3uuex3nst4Shg4NG48cHwpit8eQCDwmDMWi/s400/corr15.JPG" width="400" /></a></div>
<div class="separator" style="clear: both; text-align: center;">
<br /></div>
<div class="MsoNormal">
<span lang="EN-US">Note that
in both cases no solvation modeling was used; this means that if we investigate
the tendency within a series of homologues, the accuracy of a simple quantum
chemistry computation (gas phase modeling) is sufficient to make important
conclusions.<o:p></o:p></span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
5) We have found a correlation between the computed and experimental components of polarizability tensor for some Shiff bases:<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiQGjImADcvYEZTlrmILybjtaO-FrLY7piSWXnozWhaOrjTH9be-xZyYu6oaJxWqi6bIyG9iJoPk1_Sgxovr6vwj-NQlUAYtVH4Kx5QPLtisjfAMQflNIeOdmxVj6K4NytVlT0iFchSvJtA/s1600/corr16.JPG" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiQGjImADcvYEZTlrmILybjtaO-FrLY7piSWXnozWhaOrjTH9be-xZyYu6oaJxWqi6bIyG9iJoPk1_Sgxovr6vwj-NQlUAYtVH4Kx5QPLtisjfAMQflNIeOdmxVj6K4NytVlT0iFchSvJtA/s1600/corr16.JPG" /></a></div>
<br /></div>
<div class="MsoNormal">
<br />
6) For computation of electronic spectra using the TDDFT method, the correlation seems to be worse:<br />
a) [2]:<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiW0V_CEmOTrfsMjnKk58RQKJe2pIS9_c-vy20tfYbapzO3FujV3Up2wiZFtv_rAsk9hfXS1W8QhK-jx5ne9ycCvKyPv7AayqYXE00CU1O1_5rP3rcZHB9JP5r88CguLtZcZK7k3N4ZI0pe/s1600/corr17.JPG" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="636" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiW0V_CEmOTrfsMjnKk58RQKJe2pIS9_c-vy20tfYbapzO3FujV3Up2wiZFtv_rAsk9hfXS1W8QhK-jx5ne9ycCvKyPv7AayqYXE00CU1O1_5rP3rcZHB9JP5r88CguLtZcZK7k3N4ZI0pe/s640/corr17.JPG" width="640" /></a></div>
b) [3]:<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhApjQSj4j3sUJaJ-TRau7scAlaG8u-VzOGJH80yaRn6w-_YHCE8fIkb4hW1KmK6mrX6mSlZ2d7laOoAZ7QBDDIn6MD6V5fwndLH19ObCKA6LPOP-M7MYF9NxhyphenhyphenArr_FhDYpnfwn5oQYr3p/s1600/corr18.JPG" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="640" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhApjQSj4j3sUJaJ-TRau7scAlaG8u-VzOGJH80yaRn6w-_YHCE8fIkb4hW1KmK6mrX6mSlZ2d7laOoAZ7QBDDIn6MD6V5fwndLH19ObCKA6LPOP-M7MYF9NxhyphenhyphenArr_FhDYpnfwn5oQYr3p/s640/corr18.JPG" width="616" /></a></div>
<br />
c) [4]:<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg_9T5ekrAxyN_031-8g7vqQRYWZgq0_TWU4lRKPe-EnKqK4ECfkdFx6WV7s7GpPO8fvk36ED7M1K7BIjSiMq6mgZzGHUghzRO23I39a7iSGXSvN52-68lykzNBkhaA7ckvRil3z_i3jerY/s1600/corr19.JPG" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="566" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg_9T5ekrAxyN_031-8g7vqQRYWZgq0_TWU4lRKPe-EnKqK4ECfkdFx6WV7s7GpPO8fvk36ED7M1K7BIjSiMq6mgZzGHUghzRO23I39a7iSGXSvN52-68lykzNBkhaA7ckvRil3z_i3jerY/s640/corr19.JPG" width="640" /></a></div>
<br />
d) [7]<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgBwToqfrtrQJuI4iAZqhl2z5-23_AFDA9vr_90mAtUIHejLqSjRKluM79s9MDsc6J8Nou9pASZwcjQqiclFULTXGdoxjT878Wv8aptuIlatldMxB1yeU__9PTypAGbhRnwWI8hvuHM3IFd/s1600/tdcorr5.JPG" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="640" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgBwToqfrtrQJuI4iAZqhl2z5-23_AFDA9vr_90mAtUIHejLqSjRKluM79s9MDsc6J8Nou9pASZwcjQqiclFULTXGdoxjT878Wv8aptuIlatldMxB1yeU__9PTypAGbhRnwWI8hvuHM3IFd/s640/tdcorr5.JPG" width="452" /></a></div>
<br />
FIG. 7. Accuracy plots for TDDFT calculated excitation energies for metaGGAs: (a) VS98, (b) PKZB, (c) TPSS, (d) M06-L, (e) TPSSm, (f) revTPSS, (g) TPSSh, (h) M05, (j) M06, (k) M06-2X, (l) M06-HF, (m) M08-HX, and (n) M08-SO. Points above the line indicate positive errors while points below the line indicate negative errors.<br />
<br />
e) [8]<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgxPryNZ9zB5ObDSyzU4Y4La1u9fEDQlxY5bjVOr0bSa5VhT4DqN84SVebJWDRH06F6O1Fm88CivLobPq7bY0uwDw9DGSHNxhAm3HHzuPvq1cigfYSPN4H5fUuoMu1rDlam4qGhvpN85J9U/s1600/tdcorr6.JPG" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgxPryNZ9zB5ObDSyzU4Y4La1u9fEDQlxY5bjVOr0bSa5VhT4DqN84SVebJWDRH06F6O1Fm88CivLobPq7bY0uwDw9DGSHNxhAm3HHzuPvq1cigfYSPN4H5fUuoMu1rDlam4qGhvpN85J9U/s1600/tdcorr6.JPG" /></a></div>
<br />
f) For some Bodipy molecules, the correlation seems to be better [9]:<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiSYLvJ1BpoPRTmpc7NSuSy01akEscwAlfRSABfy9vEgiziAqIxxWnnkumhN1qhqpU7DqnARYhDWcUV9gpkFPHV7786nuDX5PYPwpHd9ZxRxcAlfrjxbI6FXl6-0Fclg1OHkXWm1lZZbD6d/s1600/corr21.JPG" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="518" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiSYLvJ1BpoPRTmpc7NSuSy01akEscwAlfRSABfy9vEgiziAqIxxWnnkumhN1qhqpU7DqnARYhDWcUV9gpkFPHV7786nuDX5PYPwpHd9ZxRxcAlfrjxbI6FXl6-0Fclg1OHkXWm1lZZbD6d/s640/corr21.JPG" width="640" /></a></div>
<br />
<br />
<div class="MsoNormal">
<span lang="EN-US">7) Here is
the correlation between computed and experimental collision diameters of some
molecules (mostly organic):</span><br />
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgVYx36PVExThTgRYYe9KmSMxbpREYf1MST23_PDOt3suWVEfuVB850cORCzMLgF0GsgY-8JqeOOzDH43WnqUhX_qHEhoI511TB2FX2FzT6sUJYrMSg91EyUUj1O5XdMV4Q1nad9uV2U8dq/s1600/colldiam5.JPG" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgVYx36PVExThTgRYYe9KmSMxbpREYf1MST23_PDOt3suWVEfuVB850cORCzMLgF0GsgY-8JqeOOzDH43WnqUhX_qHEhoI511TB2FX2FzT6sUJYrMSg91EyUUj1O5XdMV4Q1nad9uV2U8dq/s1600/colldiam5.JPG" /></a></div>
<br />
<span lang="EN-US"></span><br />
<span lang="EN-US"><o:p></o:p></span></div>
<div class="MsoNormal">
<span lang="EN-US"><br /></span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span lang="EN-US">The
experimental collision diameters were taken from [5,6]. The computed ones were
obtained with Chemcraft: firstly the molecular geometries were obtained at
B3LYP/6-31G(D,P) level (again, we don’t recommend using this method, we just don’t
want to repeat the jobs with another level of theory), and then the diameters
were computed by Chemcraft via “Tools/Calculate collision diameters” menu item.<o:p></o:p></span></div>
<div class="MsoNormal">
<br /></div>
<br />
<div class="MsoNormal">
<span lang="EN-US">8) The
following graph should not be called a “correlation”, but it illustrates some
practical use of quantum chemistry. The X values correspond to the anisotropy
of molecular polarizability of some nematic liquid crystals (Shiff bases), the
Y values correspond to the temperatures of phase transitions (nematic-isotrope).
The first ones were computed with DFT, the latter (experimental values) were
taken from literature:<o:p></o:p></span></div>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj3bhdquGrUKHt6JkGV5_PSMof-qHDtoFBv9BCXg0Btb4jEjde8canNQUz9VM1XOC-NbiiLvxpfgp8X-0w0W1mJ__bxNRROzejX5_9Wv2e057LY1K9SIp1aPW27mlMJY0Qgneoy_6aFQ387/s1600/corr20.JPG" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="471" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj3bhdquGrUKHt6JkGV5_PSMof-qHDtoFBv9BCXg0Btb4jEjde8canNQUz9VM1XOC-NbiiLvxpfgp8X-0w0W1mJ__bxNRROzejX5_9Wv2e057LY1K9SIp1aPW27mlMJY0Qgneoy_6aFQ387/s640/corr20.JPG" width="640" /></a></div>
<div class="MsoNormal">
<span lang="EN-US"><br /></span></div>
<div class="MsoNormal">
<span lang="EN-US"> The symbols above the points represent fragments of molecules which vary among series.</span><br />
<span lang="EN-US"><span lang="EN-US" style="font-size: 12pt;"> This correlation is so
poor not because the computation give wrong results; as it can be seen above,
the computed components of molecular polarizability correlate well with
experimental ones. So, the reason of such bad correlation is the imperfection
of this approach (that the thermal stability of liquid crystal depends on their
molecular polarizability).</span></span></div>
</div>
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<div class="MsoNormal">
<span lang="EN-US" style="mso-ansi-language: EN-US;">9)
Vibrational frequencies</span></div>
<div class="MsoNormal">
<span lang="EN-US" style="mso-ansi-language: EN-US;"> We have
computed the vibrational spectra of some simple organic compounds (toluene,
propene, acetone, benzoic acid, etc) using wB97XD/aug-cc-pVTZ method, and
compared the mode frequencies with the experimental values:</span></div>
<div class="MsoNormal">
<br /></div>
<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgzjIHv76Fp8fKWu9RWCFSKWF_4ceYQ-ySJHnHWx_DRIbQyrbLbEswlMQW5sjNyWd-gLz963uEXrRyLDsXHE4lAw6QUasU7OuW_rWN7WubzU-H9Z6QkLe3BNCPGjdlaN5rbrjTiuu5gijJ9/s1600/freqs.JPG" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" height="473" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgzjIHv76Fp8fKWu9RWCFSKWF_4ceYQ-ySJHnHWx_DRIbQyrbLbEswlMQW5sjNyWd-gLz963uEXrRyLDsXHE4lAw6QUasU7OuW_rWN7WubzU-H9Z6QkLe3BNCPGjdlaN5rbrjTiuu5gijJ9/s640/freqs.JPG" width="640" /></a></div>
<br />
<div class="MsoNormal">
<br />
<span lang="EN-US" style="mso-ansi-language: EN-US;"></span></div>
<div class="MsoNormal">
<span lang="EN-US" style="mso-ansi-language: EN-US;"> The blue
line indicates full theory/experiment match. Some improper attribution of the
bands is possible.</span></div>
<div class="MsoNormal">
<span lang="EN-US" style="mso-ansi-language: EN-US;"> We have
also computed the same frequencies at a lower level (wB97XD/6-31G(D,P)). The
standard deviation turned out to be 29 cm-1 for wB97XD/6-31G(D,P) and 24 cm-1
for wB97XD/aug-cc-pVTZ. The job CPU time with the latter method was 50-100
times higher than with the former method.</span><br />
<span lang="EN-US" style="mso-ansi-language: EN-US;"> When we need to interpret the experimental IR spectra, we usually compute the spectra at </span><br />
<span lang="EN-US" style="mso-ansi-language: EN-US;">wB97XD/6-31G(D,P) level of theory, and multiply the computed frequency values (X values) in Chemcraft by the coefficient of 0.958. The errors of frequencies obtained in such a way are usually not bigger than 60 cm-1.</span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<br /></div>
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<span lang="EN-US">[1] Sergey
L. Khursana and Mikhail Yu. Ovchinnikova. The pKa theoretical estimation of
C―H, N―H, O―H and S―H acids in dimethylsulfoxide solution. Journal of physical
organic chemistry, 9/24/2014, DOI 10.1002/poc.3371.<o:p></o:p></span><br />
<span lang="EN-US">[2] Nesrin Tokay, Zeynel Seferoğlu, Cemil Öğretir and Nermin Ertan. Quantum chemical studies on the structures of some heterocyclic azo disperse dyes.ARKIVOC 2008 (xv) 9-20</span><br />
<span lang="EN-US">[3] S. Kawauchi, L. Antonov, Y. Okuno. Prediction of the color of dyes by using time-dependent density functional theory (TD-DFT). Bulgarian Chemical Communications, Volume 46, Special Issue A (pp. 228 – 237) 2014.</span><br />
<span lang="EN-US">[4] </span>Denis Jacquemin, Eric A. Perpe`te, Gustavo E. Scuseria, Ilaria Ciofini, and Carlo Adamo. TD-DFT Performance for the Visible Absorption Spectra of Organic Dyes: Conventional versus Long-Range Hybrids. J. Chem. Theory Comput. 2008, 4, 123-135<br />
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<span lang="EN-US">[5] H.
Wang, M. Frenklach, Combust. Flame 96, 163 (1994) <o:p></o:p></span></div>
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[6] R.J.
Kee et al.Chemkin Collection, Release 3.6, Reaction design, Inc., San Diego, CA
(2000)<br />
[7]Sarom S. Leang, Federico Zahariev, and Mark S. Gordon.THE JOURNAL OF CHEMICAL PHYSICS 136, 104101 (2012).<br />
[8] K. Okuno et al. J.Photochem.Photobiol A: Chemistry 235 (2012) 29– 34<br />
[9] J. Chem. Theory Comput. 2014, 10, 4574−4582<br />
[10] Bishnu Thapa, and H. Bernhard Schlegel. Improved pKa Prediction of Substituted Alcohols, Phenols and Hydroperoxides in Aqueous Medium Using DFT and a Cluster-Continuum Solvation Model. J. Phys. Chem. A, Just Accepted Manuscript • Publication Date (Web): 31 May 2017</div>
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Grigoriy Andrienkohttp://www.blogger.com/profile/10871921625140429891noreply@blogger.com2tag:blogger.com,1999:blog-4665151263516489793.post-52159112813415341712015-12-10T10:35:00.002-08:002016-03-10T13:57:26.374-08:00The practical use of quantum chemistry (my opinion)<div dir="ltr" style="text-align: left;" trbidi="on">
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The
following is my private opinion, maybe not fully right.</div>
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<span lang="EN-US">The science
can be divided into fundamental (or "pure") and applied branch. The applied science is
funded well by business. The fundamental science, as I think, can be funded by
the state only. The business should not fund an applied (or, for example,
humanitarian) research, not because it is not useful, but because when a
fundamental discovery is made, the profit of it is gained by everyone, not by
those only who funded the investigation.<o:p></o:p></span><br />
<span lang="EN-US">This picture illustrates the thesis, that the applied science is funded better than the theoretical:</span><br />
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi1re6_dMX26VTrhSdKTY9vQB8iaM51tqJo1sXyEoKDraIuYl5Mp7zloS2Cm6mp3LY59IPelva1YAUifx_XekRFaa5sx96VlVGHhtKzAWHRp5qK5_27ZsCTspgArNi7KhAM3M0z6zy8GqGC/s1600/6585877_460s_v1.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi1re6_dMX26VTrhSdKTY9vQB8iaM51tqJo1sXyEoKDraIuYl5Mp7zloS2Cm6mp3LY59IPelva1YAUifx_XekRFaa5sx96VlVGHhtKzAWHRp5qK5_27ZsCTspgArNi7KhAM3M0z6zy8GqGC/s1600/6585877_460s_v1.jpg" /></a></div>
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<span lang="EN-US">So, the
quantum chemistry is mostly a fundamental branch of science. Its applied use is
quite limited (mostly, as far as I know, to the computations of the properties
of small molecules in the gas phase). At the same time, quantum chemistry is
relatively suitable for such “fundamental” tasks as, e.g., exploring the
mechanism of a chemical reaction.<o:p></o:p></span></div>
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<span lang="EN-US">Such
explorations usually do not have a significant applied use, but they can
eventually give the opportunity to perform applied investigations – after
decades. For example, if someone investigates a mechanism of a reaction, in a long
time after that his conclusions can be used by experimentalists for applied
investigations. So, the applied chemistry serves as a kind of “locomotive” for
fundamental chemistry investigations. For humanitarian science, as I suppose,
there is no such a “locomotive”, and because of that the humanitarian science
is in a “mire” (as I think).<o:p></o:p></span><br />
<span lang="EN-US">Figuratively speaking, applied chemistry usually answers the question "How much", while quantum chemistry answers the question "Why". This phrase is somewhat an exxageration; more clear explanation can be read <a href="http://www.ck12.org/chemistry/Pure-and-Applied-Chemistry/lesson/user:ck12science/Pure-and-Applied-Chemistry/">here</a>.</span></div>
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<span lang="EN-US">Performing
quantum chemistry investigations for groups of experimentalists, I have found
that quite often the theoretical and experimental methods give “different
realities”, not intersecting each other. This means that if experimental
methods are used, for example, to investigate a mechanism of a chemical
reaction, or the dependence of experimentally obtained data on some structural
properties of the molecules, these methods often lead to wrong conclusions. The
quantum chemistry methods disprove these conclusions, but often do not give an
alternative, because, as mentioned above, the quantum chemistry is of quite
limited applied use. Maybe in the future these “realities” will intersect, and
then the main method of investigations will be the combination of quantum
chemistry with the experimental methods.<o:p></o:p></span></div>
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<span lang="EN-US">I have
heard that the quantum chemistry has very low predictive power, and is mostly
used to confirm experimental data. Again, this “predictive power” is something
applied, while “confirming an experiment”, “understanding an experiment” is
mainly the fundamental science.<o:p></o:p></span></div>
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<span lang="EN-US">The quantum
chemistry is mainly efficient for investigating the gas phase and replaces some
experimental methods like gas electron diffraction. And again, investigating
the gas phase is often needed mostly in fundamental science – astrophysics,
meteorology.<o:p></o:p></span></div>
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Grigoriy Andrienkohttp://www.blogger.com/profile/10871921625140429891noreply@blogger.com3