Charge calculations in molecular mechanics. V. Silicon compounds and π bonding

A previously published scheme for the calculation of partial atomic charges has been extended to include silicon, and has been parameterized for a range of Si? X bonds (X?C,H,O,F,Cl,Br). For the silicon–halogen and silicon–oxygen bonds, a comparison is made between charges calculated with and without the inclusion of π-bonding. An extensive data set consisting of experimental geometries and dipole moments for the silicon compounds considered is presented and this leads to the selection of standard Si? X bond lengths. The calculated dipole moments for the above compounds are in good agreement with those obtained experimentally only when the π charges are included. A comparison has also been made between the partial charges from this scheme and those obtained from computational methods using the Mulliken population analysis. There is considerable disagreement between the methods. Finally, the implications of the charges and structural data are considered in terms of application to zeolite systems.     

Charge calculations in molecular mechanics. IX. A general parameterisation of the scheme for saturated halogen,oxygen and nitrogen compounds

Summary The CHARGE2 program for the calculation of partial atomic charges has been amended to include bond parameters for a number of organic functional groups, including halogens, nitrogen and oxygen. These minor amendments to the original scheme produce dipole moments for the fluoro and chloro compounds which are in complete agreement with the observed values.The less complete data sets for the bromo and iodo compounds are also well reproduced, and the dipole moments of a variety of mixed halo compounds are now in better agreement with experiment than previously.The calculated dipole moments of the saturated nitrogen and oxygen compounds are now in much better agreement than in the original scheme, thus the revised parameterisation may be employed with confidence to predict the electrostatic energies of these compounds.Furthermore, the revised scheme now gives a precise proportionality between the charge on the proton in a CH group and the ¹H chemical shift of the corresponding proton, allowing the general prediction, in principle, of ¹H chemical shifts. In addition, attempts to include variable electronegativity in the effect are described for fluoro compounds.For part VIII see Ref. 1.     

Solution-state conformations of 2-fluoro-, 2-chloro- and 2-bromo-acetophenone: a dipole moment and kerr effect study

Experimental dipole moments and infinite-dilution Kerr constants for 2-fluoro-, 2-chloro and 2-bromo-acetophenone (CH₃COC₆H₄X; X = F, Cl, Br) as solutes in CCl₄ at 25°C are analysed, yielding the following effective dihedral angles and percentage abundances of the less stable XO-cis conformers: X = F, 10 ± 10°, 5 ± 5%; X = Cl, 40 ± 5°, 10 ± 5%; and X = Br, 65 ± 10°, 25 ± 10%.     

Electrostatic interactions in molecular mechanics (MM2) calculations via PEOE partial charges I. Haloalkanes

The PEOE (partial equalization of orbital electronegativity) procedure has been modified slightly and reparametrized for haloalkanes to calculate partial atomic charges suitable for evaluation of dipole moments and electrostatic energies in conjunction with molecular mechanics (MM2) calculations. Dipole moments of 66 haloalkanes are calculated with an average absolute deviation of 0.14 D from experimental values. The conformational energies of 40 compounds have been calculated and the agreement with experimental data is generally good and compares well with calculations by the IDME (induced dipole moment and energy) method. In addition, carbon and proton charges correlate well with C-1s core binding energies and ¹H-NMR (nuclear magnetic resonance) shifts for halomethanes. The most striking benefit of treating electrostatics through a set of partial charges compared to the standard MM2 bond dipole approach is demonstrated by calculations on 1,4-disubstituted cyclohexanes, for which standard MM2 fails to predict the most stable conformation.     

三卤化硼Lewis酸性的密度泛函理论研究

用密度泛函理论的DFT-LDA/NL方法研究BX₃(X=F,Cl,Br)分子的Lewis酸性.计算BX₃分子的硬度时,采用一个可供选择的方法.该法是密度泛函理论的Janak定理的推广.结果表明,分子硬度是BX₃Lewis酸性的最好表征.应用Pearson的软硬酸碱(HSAB)原理可以合理地解释BX₃酸性的变化规律     

Stereoelectronic and inductive effects on 1H and 13C NMR chemical shifts of some cis-1,3-disubstituted cyclohexanes

This work presents the substituent effects on the 1H and 13C NMR chemical shifts in the cis-isomer of 3-Y-cyclohexanols (Y = Cl, Br, I, CH3, N(CH3)2 and OCH3) and 3-Y-1-methoxycyclohexanes (Y = F, Cl, Br, I, CH3, N(CH3)2 and OCH3). It was observed that the H-3 chemical shift, due to the substituent alpha-effect, increases with the increase of substituent electronegativity when Y is from the second row of the periodic table of elements, (CH3 *sigma(C3--H3a) interaction energy. This interaction energy, for the halogenated compounds, decreases with an increase in size of the halogen, and this is a possible reason for the largest measured chemical shift for H-3 of the iodo-derivatives. The beta-effect of the analyzed compounds showed that the chemical shift of hydrogens at C-2 and C-4 increases with the decrease of n(Y) --> *sigma(C2-C3) and n(Y) --> *sigma(C3-C4) interaction energies, respectively, showing a behavior similar to H-3. The alpha-effect on 13C chemical shifts correlates well with substituent electronegativity, while the beta-effect is inversely related to electronegativity in halogenated compounds. NBO analysis indicated that the substituent inductive effect is the predominant effect on 13C NMR chemical shift changes for the alpha-carbon. It was also observed that C-2 and C-4 chemical shifts for compounds with N(CH3)2, OCH3 and F are more shielded in comparison to the compounds having a halogen, most probably because of the larger interaction of the lone pair of more electronegative atoms (n(N) > n(O) > n(F)) with *sigma(C2-C3), *sigma(C3-C4) and *sigma(C3-H3a) in comparison with the same type of interaction with the lone pair of the other halogens.     

Parameterization of charge model 3 for AM1, PM3, BLYP,and B3LYP

We have recently developed a new Class IV charge model for calculating partial atomic charges in molecules. The new model, called Charge Model 3 (CM3), was parameterized for calculations on molecules containing H, Li, C, N, O, F, Si, S, P, Cl, and Br by Hartree-Fock theory and by hybrid density functional theory (DFT) based on the modified Perdew-Wang density functional with several basis sets. In the present article we extend CM3 to semiempirical molecular orbital theory, in particular Austin Model 1 (AM1) and Parameterized Model 3 (PM3), and to the popular BLYP and B3LYP DFT and hybrid DFT methods, respectively. For the BLYP extension, we consider the 6-31G(d) basis set, and for the B3LYP extension, we consider three basis sets: 6-31G(d), 6-31+G(d), and MIDI!6D. We begin with the previous CM3 strategy, which involves 34 parameters for 30 pairs of elements. We then refine the model to improve the charges in compounds that contain N and O. This modification, involving two new parameters, leads to improved dipole moments for amides, bifunctional H, C, N, O compounds, aldehydes, ketones, esters, and carboxylic acids; the improvement for compounds not containing N results from obtaining more physical parameters for carbonyl groups when the O=C-N conjugation of amides is addressed in the parameterization. In addition, for the PM3 method, we added an additional parameter to improve dipole moments of compounds that contain bonds between C and N. This additional parameter leads to improved accuracy in the dipole moments of aromatic nitrogen heterocycles with five-membered rings.     

Sur un traitement unifie des deplacements chimiques en spectrometrie photoelectronique de rayons—X (ESCA), des moments dipolaires et des polarisabilites

The simplest and most general model for interpreting ESCA chemical shifts, the physical meaning of which is very clear, also allows the discussion of dipole moments and polarisabilities. Sixty-eight ESCA chemical shifts of C_1s, N_1s, O_1s and F_1s in 41 differently-substituted compounds (?F, ?Cl, ?Br, ?OH, ?NH₂), saturated or unsaturated (aldehydes, ketones, acids), have been calculated with this model from electric charge distribution; the mean quadratic deviations are respectively ±1.1 eV for C, ±1.6 eV for N, ±0.8 eV for 0, ±0.7 eV for F.With this model, electric charge repartitions can be deduced from ESCA data, even for aromatic molecules. The calculated electric dipole moments for 12 fluorinated aromatic molecules agree very well with experimental results. Other data have been calculated for molecules for which experimental data are not yet available, including examples where heavy atoms are present.     

Mössbauer study of the Sn resonance in rare-gas matrix-isolated Sn(IV)-and Sn(II)halide molecules

Mössbauer absorption spectra of rare-gas matrix-isolated SnX₄ and SnX₂ molecules (X = F, Cl, Br, I) have been measured at matrix temperatures of a bout 5 K. The hyperfine interaction (hfi) parameters of ¹¹⁹Sn in argon matrix-isolated SnX₄ (X = Cl, Br, 1) molecules are identical with those of the corresponding crystalline compounds. This fact reveals that the inter-molecular interactions are negligible in the crystalline compounds as far as concerning the electronic structure of Sn⁴⁺. The ¹¹⁹Sn hfi parameters of rare-gas matrix-isolated SnX₂ molecules differ from those measured in the crystallin compounds. This arise from the totally different coordination of tin in the two situations. The analysis of the hfi parameters using a simple bonding model yields information about the ionicity of the Sn-halogen bonds and the bonding angle in these molecules. The observed isomer shifts and quadrupole interactions can only be explained in this model with a bonding angle θ = 95° ± 2° for all SnX₂ molecules and a slight increase of θ from Sn1₂ to SnF₂.     

The rearrangement of polyhaloalkyl radicals in solution with 1,2-chlorine atom migration

Radicals XCCl₂CYCH₂Z (l; X=Cl,H,F,CH₃; Y=H,CH₃,Cl,Br; Z=Br,Cl,CCl₃,SR) were generated by homolytic addition of addition of various addenda to unsaturated compounds XCCl₂CY=CH₂. Radicals (I) were shown to rearrange in solution into radicals XCCl---CYCl---CH₂Z (II), the latter being more stable than the former. It was found that compounds XCCl₂CBr=CH₂ with X=Cl,CH₃,F could isomerize under the action of initiators of radical processes to compounds XCCl=CClCH₂Br. This isomerization was proved to be of a radical chain character and involves the 1,2-chlorine migration in the intermediate radical XCCl₂CBrCH₂Br (III). The dependence between the structure of starting radicals and their ability to undergo rearrangement in solution has been established and the effect of the nature of addendum on the reaction course investigated. The polyhaloalkyl radicals were arranged in a sequence according to their relative stability.     

极性分子键角与键偶极矩的关系

研究了基态极性分子的键角和键偶极矩之间的关系。我们采用原子偶极矩校正的Hirshfeld （ADCH）电荷来计算键偶极矩,利用电子的局域函数和键临界点处的局域函数值来分析键的电子结构。通过对IVA族（IVA = C,Si,Ge）、VA族（VA = N,P,As ）、VIA族（VIA = O,S,Se）和VIIA族（VIIA = F,Cl,Br）元素形成的系列共价型基态分子,以及环状基态分子的键角和键偶极矩数据进行分析,发现在键的电子结构类似的情况下,由于键偶极矩的排斥作用,这些分子的键角随键偶极矩的增加而增大。这一发现有助于加深我们对分子几何结构的认识。     

Peculiarities of atomic interaction in organic molecules of 3- and 4-coordinated phosphorus using ab initio calculations and Cl NQR

The results of ab initio calculations at the MP2/6-31G(d) level of molecules of the series ClPXX′ (X, X′=C₂H₅, N(CH₃)₂, OCH₃) and ClP(M)XX′ (M=O, S; X=CH₃, ?CH₃; X′=C₂H₅, OCH₃) with total optimization of their geometry were presented. They were compared with the obtained earlier results of such calculations at the RHF/6-31G(d) level and with experimental ³⁵Cl nuclear quadrupole resonance (NQR) spectra for these compounds. MP2/6-31G(d) calculations confirm non-inductive influence of heteroatoms on the geminal Cl atom in the non-linear three-atomic Cl–P–M groups. They agree to the conclusion that the abnormal correlation of the ³⁵Cl NQR frequencies for the compounds studied at different X, X′ and M is caused, in general, by the P–Cl bond polarization under the action of the geminal atom partial charges directly through the field. The satisfactory conformity between the experimental ³⁵Cl NQR frequencies and those estimated from 3p-components of the Cl atom valence p-orbitals calculated at the MP2/6-31G(d) level was obtained.     

Hirshfeld partitioning of the electron density: atomic dipoles and their relation with functional group properties

Atomic dipole moments, derived within the Hirshfeld partitioning of the molecular electron density, have been studied for compounds of the type H-X and Cl-X, for a series of functional groups X frequently encountered in organic molecules. In the case of the H-X compounds, the component of the atomic dipole moment on H along the axis connecting H with the central atom in X is found to be linearly correlated with the electronegativity of X, the hardness of X playing no significant role. In the case of the Cl-X compounds, the situation is less clear. However, evidence seems to point to the conclusion that for these compounds, also the group hardness plays an important role.     

Halogen effect on structure and 13C NMR chemical shift of 3,6‐disubstituted‐N‐alkyl carbazoles

Structures of selected 3,6‐dihalogeno‐N‐alkyl carbazole derivatives were calculated at the B3LYP/6‐311++G(3df,2pd) level of theory, and their ¹³C nuclear magnetic resonance (NMR) isotropic shieldings were predicted using density functional theory (DFT). The model compounds contained 9H, N‐methyl and N‐ethyl derivatives. The relativistic effect of Br and I atoms on nuclear shieldings was modeled using the spin–orbit zeroth‐order regular approximation (ZORA) method. Significant heavy atom shielding effects for the carbon atom directly bonded with Br and I were observed (~?10 and ~?30 ppm while the other carbon shifts were practically unaffected). The decreasing electronegativity of the halogen substituent (F, Cl, Br, and I) was reflected in both nonrelativistic and relativistic NMR results as decreased values of chemical shifts of carbon atoms attached to halogen (C3 and C6) leading to a strong sensitivity to halogen atom type at 3 and 6 positions of the carbazole ring. The predicted NMR data correctly reproduce the available experimental data for unsubstituted N‐alkylcarbazoles. Copyright © 2013 John Wiley & Sons, Ltd.     

Prediction of proton magnetic resonance shifts: The dependence on hydrogen charges obtained by iterative partial equalization of orbital electronegativity

Proton chemical shifts correlate linearly with charges on hydrogen obtained by a method for iterative partial equalization of orbital electronegativity. The compounds studied comprise a wide variety of classes of molecules; all points fall on a single correlation line, showing the general importance of electronic effects in proton chemical shifts and the physical significance of the atomic charges. On the other hand, as there is no general correlation between charges on carbon and on hydrogen atoms, proton chemical shifts cannot be used as probes for charge densities on carbon atoms. Deviations from the correlation line can be attributed to anisotropy effects and provide an estimate for their magnitude.     

Heteroatom influence in substituted benzenes and pyridine-like heterocycles in terms of direct and indirect intramolecular interactions

The general expression for the one-electron density matrix obtained previously for saturated organic molecules (V. Gineityte, J. Mol. Struct. (Theochem), 343 (1995) 183) is shown to be applicable also to substituted benzenes and pyridine-like heterocycles. On this basis, a new interpretation of the influence of a heteroatom (substituent) upon the remaining fragment of an aromatic molecule is suggested. To this end, the occupation number of a 2p_z AO of the aromatic ring has been expressed as a sum of five terms, two of them describing the intramolecular charge transfer and the remaining ones representing the secondary (induced) dipole moments arising within the ring under the influence of heteroatom, viz. the so-called ipso–ortho (para–meta), para–ipso and ortho–meta dipole moments. Just the latter two moments proved to play the principal role in the formation of the observed picture of the electron density distribution, viz. of an increase (reduction) of occupation numbers of 2p_z AOs in the ortho and para positions after introducing an electron-donating (accepting) substituent. For pyridine-like heterocycles and substituted benzenes, these dipole moments are determined mostly by the direct and the indirect interactions, respectively, between the highest occupied and the lowest vacant MO of benzene. Orbitals of the heteroatom (substituent) play the role of mediators in the above-mentioned indirect interaction.     

Accurate partial atomic charges for high-energy molecules using class IV charge models with the MIDI! basis set

We have recently developed a new class IV charge model for calculating partial atomic charges in molecules. The new model, called charge model 3 (CM3), was parameterized for calculations on molecules containing H, Li, C, N, O, F, Si, S, P, Cl, and Br by Hartree–Fock theory and by hybrid density functional theory (HDFT) based on the modified Perdew–Wang density functional with several basis sets. In the present article, we extend CM3 for calculating partial atomic charges by Hartree–Fock theory with the economical but well balanced MIDI! basis set. Then, using a test set of accurate dipole moments for molecules containing nitramine functional groups (which include many high-energy materials), we demonstrate the utility of several parameters designed to improve the charges in molecules containing both N and O atoms. We also show that one of our most recently developed CM3 models that is designed for use with wave functions calculated at the mPWXPW91/MIDI! level of theory (where X denotes a variable percentage of Hartree–Fock exchange) gives accurate charge distributions in nitramines without additional parameters for N and O. To demonstrate the reliability of partial atomic charges calculated with CM3, we use these atomic charges to calculate polarization free energies for several nitramines, including the commonly used explosives 1,3,5-trinitro-s-triazine (RDX) and 2,4,6,8,10,12-hexanitrohexaazaisowurtzitane (HNIW), in nitromethane. These polarization energies are large and negative, indicating that electrostatic interactions between the charge distribution of the molecule and the solvent make a large contribution to the free energy of solvation of nitramines. By extension, the same conclusion should apply to solid-state condensation. Also, in contrast to some other charge models, CM3 yields atomic charges that are relatively insensitive to the presence of buried atoms and small conformational changes in the molecule, as well as to the level of treatment of electron correlation. This type of charge model should be useful in the future development of solvation models and force fields designed to estimate intramolecular interactions of nitramines in the condensed phase.     

The H method: hydrogen atoms with a fictitious nuclear charge. A versatile theoretical tool for study of atom and group properties as substituents: electronegativity and partition of σ and π contributions

We present a preliminary work for a general method of computing the partition of σ and π electronic effects of a given atom A or substituent R on a given substrate. In this aim, the nuclear charge Z^* of a fictitious hydrogen atom H^* is fitted in order that the A–H^* (or R–H^*) bond be purely covalent, i.e. the Mulliken electron population be one electron on H^*. We obtain this way entities of the same electronegativity as A or R, thus having a comparable σ effect, without any π effect.

The values of Z^* obtained for A–H^* diatomic molecules (A=H–Br) exhibit a good linear correlation with the Allred–Rochow scale of electronegativity, as it could be expected on theoretical grounds. The method, applied to R–H^* molecules, allows a determination of the electronegativity of a variety of polyatomic R substituents, and provides H^*(R) having the same inductive effect as R. These results are discussed by comparison with some previous theoretical and experimental data.

As an example of application, the partition of σ and π contributions of R on the ¹³C chemical shifts in a series of monosubstituted benzenes RC₆H₅ has been computed.