Electronic energy structure of MBiS2 (M = Li, Na, K) calculated with allowance for the difference between the M-S and Bi-S bond lengths

The modified augmented plane wave method (WIEN2k program) was used to study the electronic energy structure and calculate the SK-absorption spectra of LiBiS₂, NaBiS₂, and KBiS₂. The crystal structures of the compounds were modeled using symmetric structures, in which each sulfur atom was surrounded by three alkali metal atoms and three bismuth atoms in such a way that the alkali metal-sulfur and bismuth-sulfur bond length differed. This difference between bond lengths was calculated from the sum of the ionic radii of the components of compounds and by the geometry optimization of the crystal lattice. The two variants of calculation allowed us to check the applicability of Pauling’s idea about preservation of the bond lengths of elements in compounds for modeling the crystal structures of LiBiS₂, NaBiS₂, and KBiS₂. The SK absorption spectra and optically forbidden bands were calculated.     

A study on the antipicornavirus activity of flavonoid compounds (flavones) by using quantum chemical and chemometric methods

The AM1 semiempirical method is employed to calculate a set of molecular properties (variables) of 45 flavone compounds with antipicornavirus activity, and 9 new flavone molecules are used for an activity prediction study. Principal Component Analysis (PCA), Hierarchical Cluster Analysis (HCA), Stepwise Discriminant Analysis (SDA), and K-Nearest Neighbor (KNN) are employed in order to reduce dimensionality and investigate which subset of variables should be more effective for classifying the flavone compounds according to their degree of antipicornavirus activity. The PCA, HCA, SDA, and KNN methods showed that the variables MR (molar refractivity), B(9) (bond order between C(9) and C(10) atoms), and B(25) (bond order between C(11) and R(7) atoms) are important properties for the separation between active and inactive flavone compounds, and this fact reveals that electronic and steric effects are relevant when one is trying to understand the interaction between flavone compounds with antipicornavirus activity and the biological receptor. In the activity prediction study, using the PCA, HCA, SDA, and KNN methodologies, three of the 9 new flavone compounds studied were classified as potentially active against picornaviruses.     

Polycyclic aromatic hydrocarbons with five-membered rings: Modeling of experimental X-ray and neutron-diffraction structures

Several of the readily available theoretical programs are evaluated as tools for modeling the structures of polycyclic aromatic hydrocarbons with five-membered rings (CPAHs). The experimentally determined bond lengths and angles are compared to calculated values. Experimental bond lengths are also compared to Pauling and Huckel molecular orbital (HMO) bond orders. Previously published experimental X-ray and neutron-diffraction structures of acenaphthene, acenaphthylene, fluoranthene, cyclopent[o,p,q,r]benz[c]phenanthrene, and corannulene are modeled by the programs MMX, AM1, MNDO, and PM3, and previously reported STO-3G and 6-31G * data are also evaluated. In general, the error differences between the experimental and calculated results for all of the semiempirical programs were small. However, PM3 performed slightly better than AM1 and MMX, while MNDO generated structures which exhibited the largest deviation from experiment. Although the standard deviations for all programs are shown to be of comparable magnitude, a particular bond length or bond angle in any given theoretical calculation can exhibit significant error from the experimental data. The scatter in the bond order data computed from Huckel molecular orbital theory and valence bond theory is contrary to results obtained with alternant systems. It appears that these approaches are less successful at modeling accurately the nonalternant hydrocarbon systems described in this paper.     

Bond length features of linear carbon chains of finite to infinite size: Visual interpretation from Pauling bond orders

Schemes for Kekulé structure counting of linear carbon chains are suggested. Mathematical formulas, which calculate the Pauling bond order P(k, N) of a chemical bond numbered by k, are given for the carbon chain with N carbon atoms. By use of the least‐squares fitting of a linearity, relationships between Pauling bond orders and bond lengths are obtained, and such correlation of the Pauling bond order–bond length can be qualitatively extended to the excited states. The relative magnitudes of Pauling bond orders in unsaturated carbon chains dominate C–C bond lengths a well as the bond length feature with the chain size increasing. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem 94: 144–149, 2003     

Extension of semiempirical methods to simulation of surfaces

Various approaches for surface simulation are described. They are based on free, saturated, and embedded clusters, as well as periodic models. The features of semiempirical methods are reviewed and ideas for their improvement are discussed. Special features of the structure and stability of clusters are presented which are suitable for the transition to the solid state. Linear and nonlinear relationships for binding energies and bond lengths in dependence of the average coordination number are discussed. Finally, a systematic way for the simulation of adsorption at ion crystal surfaces by model clusters is suggested. © 1996 John Wiley & Sons, Inc.     

pi bonding in second and third row molecules: testing the strength of Linus's blanket

The flexibility of valence bond (VB) theory provides a new method of calculating pi-bond energies in the double-bonded species H(m)A=BH(n), where A, B = C, N, O, Si, P, S. This new method circumvents the problems usually associated with obtaining pi-bond strengths by targeting only the pi bond, while all other factors remain constant. In this manner, a clean separation between sigma- and pi effects can be achieved which highlights some expected trends in bond strength upon moving from left to right and up and down the Periodic Table. Intra-row pi bonds conform to the classic statement by Pauling [L. Pauling, The Natiure of the Chemical Bond, Cornell University Press, Ithaca, 1960, 3rd edition] regarding the relationship of heteronuclear bond strengths to their homonuclear constituents whereas inter-row pi bonds do not. This variance with Pauling's statement is shown to be due to the constraining effect of the underlying sigma bonds which prevents optimal p(pi)-p(pi) overlap. While Pauling's statement was based on the assumption that the resonance energy (RE) would be large for heteronuclear and small for homonuclear bonds, we have found large REs for all bonds studied herein; this leads to the conclusion that REs are dependent not only on the electronegativity difference but also the electronegativity sum of the constituent atoms. This situation where the bond is neither covalent nor ionic but originates in the covalent-ionic mixing has been termed charge shift (CS) bonding [S. Shaik, P. Maitre, G. Sini, P. C. Hiberty, J. Am. Chem. Soc. 1992, 114, 7861]. We have shown that CS bonding extends beyond single sigma bonds in first row molecules, thus supporting the idea that CS-bonding is a ubiquitous bonding form.     

Calculations for the vibration frequencies of the OH⋯O bond in KH2PO4 by a semiempirical method

The frequencies of the stretching vibration and the bending vibration of the OH⋯O bond in potassium dihydrogen phosphate have been calculated by means of two semiempirical formulae with three parameters. The calculated results can give satisfactory explanation for the experimental spectra of the potassium dihydrogen phosphate crystal. The parameters used in the calculations may be related to the chemical bonding and the charge distribution about the two oxygen atoms of the OH⋯O bond system.     

Similarity transformation of the ab initio density matrix

Bond orders and hybrid populations have been calculated from the density matrix localized in molecular space using similarity transformation for some fluorobenzene with the minimal basis set using Gaussian series of program. The ab initio bond orders and hybrid populations have been compared with the semiempirical calculations on this set of molecules. Also, these bond orders have been used in Coulson's bond order-bond length relationship to estimate bond lengths. The present calculations suggest that the qualitative predictions of molecular geometries are possible from these bond orders.     

Molecular structure and electronic effects of chlorophosphorane from mndo calculations and35Cl NQR data

The molecular geometries of eleven compounds of pentacoordinated phosphorus are optimized and charges on the central phosphorus atom and on the ligands are calculated by the semiempirical MNDO method. In cases of chlorine atoms as ligands, correlations between the chlorine-35 NQR frequencies and charges on the chlorine atoms of P-Cl bonds, on the one hand, and these bond lengths, on the other, are established. Parameters of the corresponding correlation equations are obtained and discussed. The efficiency of this calculation procedure and NQR method for analyzing the geometrical structure and electron distributions in chlorophosphorane molecules is shown. Translated fromZhurnal Struktumoi Khimii, Vol. 38, No. 6, pp. 1074–1082, November–December, 1997.     

Theoretical calculations of chemical interactions-111: The reaction of halonitrobenzenes with nucleophiles

Potential o-zwitterionic complexes formed between fluorobenzene, p- and o-nitrofluorobenzene with ammonia and amide ion where calculated by CNDU, INDO and MNDO semiempirical methods with a wide geometry optimization. Data for bond lengths, bond angles and charge densities are given. In the case of the complexes with ammonia the reaction coordinate was also calculated by the MNDO procedure. The obtained results show that theoretical calculations can provide useful data on these type of complexes and provide models for systems not amenable to experiment yet.     

Synthesis of 4,7,13,16,21,24-hexaoxa-1,10-diazoniabicyclo[8.8.8]hexacosane Dinitrate Hydrate and Its Disordered Crystal Structure

4,7,13,16,21,24-Hexaoxa-1,10-diazoniabicyclo[8.8.8]hexacosane dinitrate hydrate [H₂(Crypt-222)]²⁺?2NO ₃ ^? ?H₂O is prepared as a crystalline salt and studied by single crystal X-ray diffraction. In its crystal structure the 2,2,2-cryptand dication is disordered and has two different conformations with 55.3 and 44.7% probabilities. Hydrogen atoms of this dication at the two protonated bridgehead nitrogen atoms are directed inside the cavity. One of two NO ₃ ^? anions is also disordered and has two different orientations with 77 and 23% probabilities. Geometric parameters of the molecular ions and water molecule (bond lengths, bond angles, etc.) are determined with a reasonable accuracy, and their packing in the crystal structure is established.     

Pharmacophore identification by molecular modeling and chemometrics: The case of HMG-CoA reductase inhibitors

Summary A methodology based on molecular modeling and chemometrics is applied to identify the geometrical pharmacophore and the stereoelectronic requirements for the activity in a series of inhibitors of 3-hydroxy 3-methylglutaryl coenzyme A (HMG-CoA) reductase, an enzyme involved in cholesterol biosynthesis. These inhibitors present two common structural features—a 3,5-dihydroxy heptanoic acid which mimics the active portion of the natural substrate HMG-CoA and a lipophilic region which carries both polar and bulky groups. A total of 432 minimum energy conformations of 11 homologous compounds showing different levels of biological activity are calculated by the molecular mechanics MM2 method. Five atoms are selected as representatives of the relevant fragments of these compounds and three interatomic distances, selected among 10 by means of a Principal Component Analysis (PCA), are used to describe the three-dimensional disposition of these atoms. A cluster analysis procedure, performed on the whole set of conformations described by these three distances, allows the selection of one cluster whose centroid represents a geometrical model for the HMG-CoA reductase pharmacophore and the conformations included are candidates as binding conformations. To obtain a refinement of the geometrical model and to have a better insight into the requirements for the activity of these inhibitors, the Molecular Electrostatic Potential (MEP) distributions are determined by the MNDO semiempirical method.     

3D comparative structural study of 6-hydroxy-4-methyl-5,7-dinitrocoumarin using experimental and theoretical approaches

The compound 6-hydroxy-4-methyl-5,7-dinitrocoumarin (2) was synthesized with high yield by the nitration of compound 1. Its molecular structure was determined using X-ray diffractometry and compared with the structure obtained from semiempirical, HF, and B3LYP methods. B3LYP calculations offer the best conformity with X-ray diffractometry for bond lengths and bond angles, whereas AM1 results are significantly close to them and provide the best superimposition with the entire 3D crystal structure.