Halogen bonding: a theoretical study based on atomic multipoles derived from quantum theory of atoms in molecules

Atomic multipole moments derived from quantum theory of atoms in molecules are used to study halogen bonds in dihalogens (with general formula YX, in which X refers to the halogen directly interacted with the Lewis base) and some molecules containing C–X group. Multipole expansion is used to calculate the electrostatic potential in a vicinity of halogen atom (which is involved in halogen bonding) in terms of atomic monopole, dipole, and quadrupole moments. In all the cases, the zz component of atomic traceless quadrupole moments (where z axis taken along Y–X or C–X bonds) of the halogens plays a stabilizing role in halogen bond formation. The effects of atomic monopole and dipole moments on the formation of a halogen bond in YX molecules depend on Y and X atoms. In Br₂ and Cl₂, the monopole moment of halogens is zero and has no contribution in electrostatic potential and hence in halogen bonding, while in ClBr, FBr, and FCl it is positive and therefore stabilize the halogen bonds. On the other hand, the negative sign of dipole moment of X in all the YX molecules weakens the corresponding halogen bonds. In the C–X-containing molecules, monopole and dipole moments of X atom are negative and consequently destabilize the halogen bonds. So, in these molecules the quadrupole moment of X atom is the only electrostatic term which strengthens the halogen bonds. In addition, we found good linear correlations between halogen bonds strength and electrostatic potentials calculated from multipole expansion.     

CHARMM fluctuating charge force field for proteins: I parameterization and application to bulk organic liquid simulations

A first-generation fluctuating charge (FQ) force field to be ultimately applied for protein simulations is presented. The electrostatic model parameters, the atomic hardnesses, and electronegativities, are parameterized by fitting to DFT-based charge responses of small molecules perturbed by a dipolar probe mimicking a water dipole. The nonbonded parameters for atoms based on the CHARMM atom-typing scheme are determined via simultaneously optimizing vacuum water-solute geometries and energies (for a set of small organic molecules) and condensed phase properties (densities and vaporization enthalpies) for pure bulk liquids. Vacuum solute-water geometries, specifically hydrogen bond distances, are fit to 0.19 A r.m.s. error, while dimerization energies are fit to 0.98 kcal/mol r.m.s. error. Properties of the liquids studied include bulk liquid structure and polarization. The FQ model does indeed show a condensed phase effect in the shifting of molecular dipole moments to higher values relative to the gas phase. The FQ liquids also appear to be more strongly associated, in the case of hydrogen bonding liquids, due to the enhanced dipolar interactions as evidenced by shifts toward lower energies in pair energy distributions. We present results from a short simulation of NMA in bulk TIP4P-FQ water as a step towards simulating solvated peptide/protein systems. As expected, there is a nontrivial dipole moment enhancement of the NMA (although the quantitative accuracy is difficult to assess). Furthermore, the distribution of dipole moments of water molecules in the vicinity of the solutes is shifted towards larger values by 0.1-0.2 Debye in keeping with previously reported work.     

Conformational properties of polar polymers. I. Poly(vinyl chloride)

A recently developed method for including polar bonds in conformational energy calculations is applied to poly(vinyl chloride). Inductive effects on dipole moments and the effects of intervening atoms on electrostatic interaction energies are represented by polarizability centers in conjunction with bond centered dipoles. Solvation energies are estimated by means of a continuum dipole–quadrupole electrostatic model. Calculated energies of a number of conformations of meso and racemic 2,4-dichloropentane and the iso, syndio, and hetero forms of 2,4,6-trichloroheptane give satisfactory representations of isomer and conformer populations. Electrostatic effects are found to be quite important. However they appear to be effectively of sufficiently short range that the calculated conformer energies are found to be fit well by a linear combination of interaction parameters (consisting of gauche, skew chlorine, four-bond CH₂…CH₂, CH₂…Cl, and Cl…Cl interactions) conventional to vinyl polymers and a special four-bond interaction that arises when the bond sequence Cl? CH? CH²? CH? Cl is (nearly) coplanar. These interaction parameters when assembled into statistical weight matrices lead to calculated values of both the characteristic ratio and the dipole moment ratio in satisfactory agreement with experiment. Least energy paths for transitions between the most stable conformations are also calculated.     

Calculation of the inductive interaction of two dipoles

The electrostatic interaction is calculated for the dipoles in 1,1-dichloroethylene, dichloroaryl compounds, and some alicyclic 1,2-dihalo compounds and -haloketones. The induced dipoles, bond moments, and molecular dipole moments are calculated. Most of the results agree well with experiment. The induction is found to be dependent on the separation and mutual orientation of the dipoles rather than on the number of bonds between them. It is concluded that the field effect is decisive in induction and that transmission via chains of atoms is relatively unimportant.     

An alternative interpretation of the C-H bond strengths of alkanes

A new model based on 1,3 repulsive steric interactions (geminal repulsion) is proposed for explaining the variation in the C-H bond strengths of the alkanes. The model builds from the assumption that 1,3 repulsive interactions are the major factor in determining the stability of a C-C or C-H bond in an alkane. From this simple premise, the model successfully reproduces the effect of branching on the stability of alkanes, alkyl radicals, and alkenes. The results suggest that geminal repulsion can provide a simple, unified explanation for these fundamental stability trends. Although previous explanations have been widely accepted, it is shown that the theoretical support for them is relatively shallow and that the current hyperconjugative stabilization model is inconsistent with several experimental and computational results concerning alkyl radicals. In contrast, an explanation based on geminal repulsion provides a general conceptual framework for rationalizing each of these stability trends and is based on a physical effect that is known to play a role in the stability of alkanes and related species.     

Advancing beyond charge analysis using the electronic localization function: Chemically intuitive distribution of electrostatic moments

We propose here an evaluation of chemically intuitive distributed electrostatic moments using the topological analysis of the electron localization function (ELF). As this partition of the total charge density provides an accurate representation of the molecular dipole, the distributed electrostatic moments based on the ELF partition (DEMEP) allows computing of local moments located at non atomic centers such as lone pairs, sigma bonds and pi systems. As the local dipole contribution can be decomposed in polarization and charge transfer components, our results indicate that local dipolar polarization of the lone pairs and chemical reactivity are closely related whereas the charge transfer contribution is the key factor driving the local bond dipole. Results on relevant molecules show that local dipole contributions can be used to rationalize inductive polarization effects in alcohols derivatives and typical hydrogen bond interactions. Moreover, bond quadrupole polarization moments being related to a pi character enable to discuss bond multiplicities, and to sort families of molecules according to their bond order. That way, the nature of the C-O bond has been revisited for several typical systems by means of the DEMEP analysis which appears also helpful to discuss aromaticity. Special attention has been given to the carbon monoxide molecule, to the CuCO complex and to a weak intramolecular N|-CO interaction involved in several biological systems. In this latter case, it is confirmed that the bond formation is mainly linked to the CO bond polarization. Transferability tests show that the approach is suitable for the design of advanced force fields.     

烷烃电离能和生成焓的相关性

根据化合物形成过程中价电子能量变化与生成焓之间的关系, 推导出烷烃的生成焓和电离能之间的关系. 以21个烷烃化合物为模型将实验测定的电离能与标准生成焓进行直接关联, 证实了模型方程的适用性, 所得回归方程的相关系数达到0.9999, 估算值与实验值之间的标准偏差仅为0.03 eV. 同时还利用实验测定的标准生成焓对一系列烷烃的电离能作了预测.     

Correlation between MO eigenvectors and enthalpies of formation for alkanes

A new model for the calculation of enthalpies of formation of alkanes (up to C₈) is presented. An additive bond energy scheme, using the experimental methane and diamond values for the CH and CC bond energies, respectively, is supplemented by correction for the CC π antibonding character of the highest occupied molecular orbitals (HOMOs), effectively adjusting the CC bond energies. The effect is calculated by the summation of products of appropriate eigenvectors from semiempirical PM3 or HF/STO-3G calculations, after orthogonal transformation. The enthalpy of formation can then be expressed in terms of only one adjustable parameter. With HF/STO-3G eigenvectors, the mean discrepancy between experimental and calculated enthalpies of formation, after a one-parameter correction for 1,4 steric interactions, is 2.2 kJ mol⁻¹, comparable with more highly parameterized models. The results using PM3 eigenvectors are less satisfactory, probably on account of the neglect of overlap in the semiempirical scheme.     

Molecular mechanics of organic halides. V. Conformational equilibria in solution

With a view of using data on solutions and liquids for parameter fitting in molecular mechanical force fields, Abraham's theory of solvation is incorporated in the force field procedure. Geometries and bond moments are estimated internally, partial account being taken of bond–bond induction, and used to calculate the intramolecular electrostatic energy, dipole moment, and the dipole and quadrupole terms in the solvation energy. Three dielectric constants are used, one for the solute in the vapor, one for the solution, and one for the intramolecular space through which dipole–dipole interactions take place. Examples are given, including such where computation differs with measurement, to illustrate the performance of the scheme.     

Correlations of the physicochemical parameters of azaindoles with their reactions

Using the AM1 semiempirical quantum method the enthalpies of formation, ionization energies, electron affinities, energy differences between highest occupied and lowest unoccupied orbitals, atomic charges, bond orders, and dipole moments have been calculated for 4-, 5-, 6-, and 7-azaindoles. A correlation has been built up between the calculated physicochemical parameters and the Hammett para-substituent and inductive constants. The 1H to 7H proton transfer in 7-azaindole has been quantitatively described. __________ Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 7, pp. 1062–1072, July, 2006.     

Conformational study of charged cyclohexyldiamines and their gas phase acid–base properties

Quantum chemical calculations employing the MP2/aug-cc-pVDZ model chemistry have been used to investigate the structure of mono- and diprotonated forms of cyclohexyldiamine (CHDA) isomers. The strength of the intramolecular hydrogen bonds and ion–dipole interactions between the amino groups, which play a key role in the conformational behaviour of the monoprotonated forms, is estimated by isodesmic reactions and electrostatic calculations. The energy variations found for the diprotonated forms are explained by the electrostatic repulsions between the amino groups. From the Gibbs energies and enthalpies calculated for the neutral and protonated CHDAs, the gas-phase basicities and proton affinities of the neutral and monoprotonated forms were determined and discussed.     

卤素阴离子和取代苯间Anion-π作用强度的快速计算

A scheme that explicitly contains electrostatic, polarization, and dispersion interactions to rapidly simulate anion-π interactions is proposed and assessed by structural and energetic comparison with those produced via the complete basis set limit of the coupled-cluster singles and doubles plus perturbative triples [CCSD (T)/CBS] method for a set of X-…C₆H_6-nR_n complexes where X^-=F^-, Cl^-, Br^- and R=CN, F. We use the chemical bonds C≡N, C―F, and C―H of the substituted benzenes as bond dipoles. The electrostatic interactions are estimated by calculating the interactions between the charge of the anion and the bond dipole moments of the substituted benzene. The polarization interactions are described according to the variation of the magnitudes of the bond dipole moments with the local environment. The parameters needed are produced by fitting the high-quality CCSD (T)/CBS potential energy curves. Calculation results show that our scheme produces equilibrium intermolecular distances with a root-mean-square deviation of 0.004 nm and interaction energies with a root-mean-square deviation of 2.81 kJ·mol^-1 compared with the CCSD (T)/CBS results. The calculation results also show that our scheme reproduces the CCSD (T)/CBS potential energy curves well. These comparisons indicate the scheme proposed here is accurate and efficient, suggesting it may be a helpful tool to design and simulate relevant molecular materials.     

On the formation of H(n=3)dipole moments in collisions of protons on rare gas atoms

We have investigated proton-rare gas atom charge transfer collisions in the energy range from 20 to 100 keV and have extracted the electrostatic dipole moments (EDMs) of the collisionally produced H(n=3) atoms from the optical data. The results show that the EDM decreases with increasing atomic number of the rare gas atoms. Our data provide experimental evidence that post-collisional electrostatic forces do not influence the formation of the EDMs.     

Dipole and quadrupole moments of molecules in crystals: a novel approach based on integration over Hirshfeld surfaces

Elegant expressions are derived for the computation of dipole and quadrupole moments of molecules using the electrostatic potential and electric field evaluated on an oriented molecular surface. These expressions are implemented for Hirshfeld surfaces, applied to various molecular crystals, and compared with the results from the quantum theory of atoms in molecules. The effect of intermolecular interactions is also explored by examining the differences between electrostatic moments derived from a periodic Hartree-Fock electron density and an electron density resulting from a superposition of noninteracting molecules. The enhancement of the dipole moment for hydrogen bonded molecular crystals is typically 30%-40% and shown to be largely independent of the partitioning scheme. Dipole moments calculated from Hirshfeld surfaces systematically underestimate those from zero-flux surfaces, a result attributed to the translation of the Hirshfeld surface relative to the zero-flux surfaces for these molecules. For acetylene and benzene, the differences between a crystal calculation and the sum of noninteracting molecules are small, and both partitioning schemes yield quadrupole and second moment results in close agreement.     

Geometry-dependent atomic charges: Methodology and application to alkanes,aldehydes, ketones,and amides

A general methodology for deriving geometry-dependent atomic charges is presented. The main ingredient of the method is a model that describes the molecular dipole moment in terms of geometry-dependent point charges. The parameters of the model are determined from ab initio calculations of molecular dipole moments and their Cartesian derivatives at various molecular geometries. Transferability of the parameters is built into the model by fitting ab initio calculations for various molecules simultaneously. The results show that charge flux along the bonds is a major contributing factor to the geometry dependence of the atomic charges, with additional contributions from fluxes along valence angles and adjacent bonds. Torsion flux is found to be smaller in magnitude than the bond and valence angle fluxes but is not always unimportant. A set of electrostatic parameters is presented for alkanes, aldehydes, ketones, and amides. Transferability of these parameters for a host of molecules is established to within 3 ?5% error in the predicted dipole moments. A possible extension of the method to include atomic dipoles is outlined. With the inclusion of such atomic dipoles and with the set of transferable point charges and charge flux parameters, it is demonstrated that molecular electrostatic potentials as well as electrostatic forces on nuclei can be reproduced much better than is possible with other models (such as potential derived charges). © 1995 by John Wiley & Sons, Inc.     

Multi-layer coarse-graining polarization model for treating electrostatic interactions of solvated α-conotoxin peptides

A multi-layer coarse-graining (CG) model is presented for treating the electrostatic interactions of solvated α-conotoxin peptides. According to the sensitivity to the electrostatic environment, a hybrid set of electrostatic parameters, such as secondary-structure- and residue-based dipoles, and atom-centered partial charges, are adopted. For the polarization "inert" secondary-structures and residues, the fragment dipole moments are distributed within narrow ranges with the magnitude close to zero. The coarse-graining fragment dipoles are parameterized from a large training set (10,000 configurations) to reproduce the electrostatic features of molecular fragments. In contrast, the electrostatically "sensitive" atoms exhibit large fluctuations of charges with the varied environments. The environment-dependent variable charges are updated in each energetic calculation. The electrostatic interaction of the whole chemical system is hence partitioned into several sub-terms coming from the fragment dipole-dipole, (fragment) dipole-(atom) charge, and atom charge-charge interactions. A large number of test calculations on the relative energies of cyclo-peptide conformers have demonstrated that the multi-layer CG electrostatic model presents better performance than the non-polarized force fields, in comparison with the density-functional theory and the fully polarized force field model. The selection of CG fragment centers, mass or geometric center, has little influence on the fragment-based dipole-dipole interactions. The multi-layer partition of electrostatic polarization is expected to be applied to many biologically interesting and complicated phenomena.     

Chlorosilanes: Development and application of MM2 force field parameters

The geometries, relative conformational energies, and dipole moments of mono and polychlorosilanes have been calculated using ab initio molecular orbital (MO) theory. Calculations at the HF/3–21G(*) level, with the exception of dipole moments, give reasonable agreement with experimental data. A new MM2 force field for chlorosilanes, which includes terms for bond length shortening and bond angle compression due to the attachment of electronegative Cl atoms, has been developed on the basis of experimental and ab initio results. The new force field is generally successful in predicting structural parameters, but is unable to reproduce the dipole moments of several model systems. While dipole moment predictions are not the authors' main interest, this failure defines a shortcoming in the MM2 method. The new parameters have been applied to problems in the prediction of stereochemistries of cyclic systems, and compared with experimental results where data are available.     

Electrostatics,the Chemical Bond and Molecular Stability

Electrostatic models of the chemical bond are based on the Virial Theorem and hold promise for providing a reliable and accurate method for predicting heats of formation of molecules and free radicals. The Principle of Alternating Polarity which states that those compounds are most stable in which atoms of opposite polarity are bonded is shown to be quantitatively described by electrostatic models. Current fixed partial-charge models account for ΔH of hydrocarbon molecules and radicals. With inclusion of polarization effects, whose energies are small, they also account for the dipole moments in hydrocarbons. A brief account is given of a more general model with significant polarization interaction which is under development and which appears to be able to account for both ΔH and dipole moments of polar molecules.     

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.