NavMol 3.0: enabling the representation of metabolic reactions by blind users.

Summary: The representation of metabolic reactions strongly relies on visualization, which is a major barrier for blind users. The NavMol software renders the communication and interpretation of molecular structures and reactions accessible by integrating chemoinformatics and assistive technology. NavMol 3.

Prediction of 1H NMR coupling constants with associative neural networks trained for chemical shifts.

Fast accurate predictions of 1H NMR spectra of organic compounds play an important role in structure validation, automatic structure elucidation, or calibration of chemometric methods. The SPINUS program is a feed-forward neural network (FFNN) system developed over the last 8 years for the prediction of 1H NMR properties from the molecular structure. It was trained using a series of empirical proton descriptors.

Spectrochemical, ab initio and density functional studies on the conversion of 2-hydroxybenzonitrile (o-cyanophenol) into the oxyanion.

The spectral and structural changes caused by the conversion of 2-hydroxybenzonitrile (o-cyanophenol) into the corresponding oxyanion have been followed by IR spectra, ab initio and density functional force field calculations. In agreement between theory and experiment, the conversion is accompanied by a 29 cm(-1) frequency decrease of the cyano stretching band, 2.7-fold increase in its integrated intensity, 5.

The impact of available experimental data on the prediction of 1H NMR chemical shifts by neural networks.

Two different ways were explored to incorporate new available experimental data into previously trained ensembles of feed-forward neural networks, for the structure-based prediction of (1)H NMR chemical shifts of organic compounds. One approach used the new data as the memory of an associative neural network (ASNN) system. For an independent prediction set of 952 cases, a mean average error of 0.

Structure-based predictions of 1H NMR chemical shifts using feed-forward neural networks.

Feed-forward neural networks were trained for the general prediction of 1H NMR chemical shifts of CH(n) protons in organic compounds in CDCl3. The training set consisted of 744 1H NMR chemical shifts from 120 molecular structures. The method was optimized in terms of selected proton descriptors (selection of variables), the number of hidden neurons, and integration of different networks in ensembles.

The conversion of phenylpropanedinitrile (phenylmalononitrile) into the carbanion, followed by IR spectra, ab initio and DFT force field calculations.

The spectral and structural changes, caused by the conversion of phenylpropanedinitrile (phenylmalononitrile) into the carbanion, have been followed by IR spectra, ab initio HF, MP2 and DFT BLYP force field calculations. In agreement between theory and experiment, the conversion is accompanied with strong frequency decreases (with 114 cm(-1), mean value) of the cyano stretching bands nu(C triple bond N), dramatic increases in the corresponding integrated intensities (136-fold, total value), strong enhancement of the nu(C triple bond N) vibrational coupling and other essential spectral changes. According to the calculations, the strongest structural changes take place at the carbanionic center: (i) shortenings of the Cz-Ph and Cz-CN bonds with 0.

Experimental and ab initio MO studies on the IR spectra and structure of pyridinium dicyanomethylide and trimethylammonium dicyanomethylide.

The structures of the title ylides have been studied by both quantitative infrared (IR) spectra and ab initio HF and MP2 force field calculations. Good agreement has been found between theoretical and experimental data for their spectral and structural characteristics. According to both IR data and geometry parameters the dicyanomethide groups in the ylides studied have a pronounced carbanionic character.

Ab initio HF, density functional and experimental studies on the IR spectra and structure of 1,2-benzisothiazol-3-(2H)-thione-1,1-dioxide (thiosacchanin) and its nitranion.

The spectral and structural changes taking place in the course of the conversion of 1,2-benzisothiazol-3-(2H)-thione-1,1-dioxide (thiosaccharin) into a nitranion have been studied on the basis of both IR spectra and ab initio HF 6-31G(d) and BLYP 6-31G(d,p) force field calculations. The conversion causes nu(as)SO2 and nu(s)SO2 frequency decreases of 47 and 13 cm(-1), respectively, and other spectral changes. The nuC=S coordinate is strongly delocalized.