понедельник, 17 сентября 2018 г.

The importance of the Gallery page of Chemcraft website

  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:



  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.
  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.
  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:



  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.

вторник, 5 июня 2018 г.

Structural properties of nematic Schiff bases and prediction of their thermal stability by polarizability anisotropy computed via DFT



  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.
  Approximately 50 compounds (Schiff bases) were investigated, e.g., those shown below:










  First, we computed NMR spectra of some of these molecules, and built a correlation between these computed NMR chemical shifts and experiment:




  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).
  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).
  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.
  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:





  We also found a relatively high correlation between the computed polarizability anisotropy of the molecules and experimental polarizability anisotropy of substituent for homologues:


  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):



  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).

References:


1. G. 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
2. G. A. Zhurko, V. V. Aleksandriiskii, M. K. Islyaikin, V. A. Burmistrov. Structure and molecular polarizability of mesogenic Shiff bases from quantum chemical calculation data//  Journal of Structural Chemistry (J STRUCT CHEM+) 48(3):440-446 · May 2007 with 19 Reads DOI: 10.1007/s10947-007-0066-0
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.
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.
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
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.