Amine-hydrogen halide complexes: experimental electric dipole moments and a theoretical decomposition of dipole moments and binding energies

The Stark effect has been observed in the rotational spectra of several gas-phase amine-hydrogen halide complexes and the following electric dipole moments have been determined: H(3)(15)N-H(35)Cl (4.05865 +/- 0.00095 D), (CH(3))(3)(15)N-H(35)Cl (7.128 +/- 0.012 D), H(3)(15)N-H(79)Br (4.2577 +/- 0.0022 D), and (CH(3))(3)(15)N-H(79)Br (8.397 +/- 0.014 D). Calculations of the binding energies and electric dipole moments for the full set of complexes R(n)()(CH(3))(3)(-)(n)()N-HX (n = 0-3; X = F, Cl, Br) at the MP2/aug-cc-pVDZ level are also reported. The block localized wave function (BLW) energy decomposition method has been used to partition the binding energies into contributions from electrostatic, exchange, distortion, polarization, and charge-transfer terms. Similarly, the calculated dipole moments have been decomposed into distortion, polarization, and charge-transfer components. The complexes studied range from hydrogen-bonded systems to proton-transferred ion pairs, and the total interaction energies vary from 7 to 17 kcal/mol across the series. The individual energy components show a much wider variation than this, but cancellation of terms accounts for the relatively narrow range of net binding energies. For both the hydrogen-bonded complexes and the proton-transferred ion pairs, the electrostatic and exchange terms have magnitudes that increase with the degree of proton transfer but are of opposite sign, leaving most of the net stabilization to arise from polarization and charge transfer. In all of the systems studied, the polarization terms contribute the most to the induced dipole moment, followed by smaller but still significant contributions from charge transfer. A significant contribution to the induced moment of the ion pairs also arises from distortion of the HX monomer.     

The role of non-bonding electron pairs in intermetallic compounds

The Electron Localisation Function, ELF pictorially visualises chemists' intuitive ideas of single and multiple bonds as well as non-bonding electron pairs in molecules. The power of the representation of chemical bonds via ELF is that on the one hand covalent, polar, and ionic bonds are distinguishable, and that on the other hand ELF can be calculated for molecules and solids. This enables us to transfer the ideas of chemical bonding from molecular to intermetallic compounds. Localised two-electron-two-centre bonds and lone pairs are present in solid-state valence compounds (Zintl phases) as expected by the 8-N rule. In solids, lone pairs are generally more contracted than in molecules due to 'lone-pair repulsion'. In intermetallic compounds localised electrons predominantly occur in the form of lone pairs. Lattice vibrations influence the strength of lone pair interactions and non-bonded interactions lead to an exchange of delocalised and localised electrons. Such a mechanism of local electron pair formation gives rise to ideas of a chemical view of the phenomenon of superconductivity in intermetallic compounds.     

A theoretical study of potential energy surface and some chemo-physical descriptors of Aspirin,Coupling the rotation of the ester and carboxyl groups

In this paper, the effect of the simultaneous rotation of the carboxyl (COOH) and ester (R'COOR) functional groups on the potential energy surface (PES) of aspirin is studied. Relative energies are reported at the HF/aug-cc-pVDZ and B3LYP/aug-cc-pVDZ levels of theory. To understand the activity and selected electrophilic attack sites, electric dipole moments, atomic charges, HOMO-LUMO energy gap, natural bond orbital (NBO), and molecular electrostatic potential (MEP) analyses, as well as the main structural parameters of the identified conformers, are studied at the same theoretical level. Finally, an NBO analysis is used to demonstrate charge transfer between lone pairs and localized bonds.     

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.     

Experimental studies of light-induced charge transfer and charge redistribution in (X(2)-bipyridine)Re(I)(CO)(3)Cl complexes

Stark emission spectroscopy, transient DC photoconductivity (TDCP), and ground-state dipole moment measurements have been used to evaluate charge transfer (CT) within various (X(2)-bipyridine)Re(I)(CO)(3)Cl complexes following (3)MLCT excited-state formation. The Stark technique reports on vector differences between ground-state (mu(g)) and excited-state (mu(e)) dipole moments, while TDCP, when combined with independently obtained mu(g) information, reports on scalar differences. For systems featuring collinear, same-signed ground- and excited-state dipole moments, the scalar and vector differences are equivalent. However, for the low symmetry systems studied here, they are distinctly different. The vector difference yields the effective adiabatic one-electron-transfer distance (R(12)), while the combined vector and scalar data yield information about dipole rotation upon ground-state/excited-state interconversion. For the systems examined, charge transfer distances are substantially smaller than geometric electron-donor/electron-acceptor site separation distances. The measured distances are significantly affected by changes in acceptor ligand substituent composition. Electron-donating substituents decrease CT distances, while electron-withdrawing substituents increase CT distances, as do aromatic substituents that are capable of expanding the bipyridyl ligand (acceptor ligand) pi system. The Stark measurements additionally indicate that the CT vector and the transition dipole moment are significantly orthogonal, a consequence of strong polarization of the Re-Cl bond (orthogonal to the metal/acceptor-ligand plane) in the ground electronic state and relaxation of the polarization in the upper state. The ground-state Re-Cl bond polarization is sufficiently large that the overall ground-state scalar dipole moment exceeds the overall excited-state scalar dipole moment, despite transfer of an electron from the metal center to the diimine ligand. This finding provides an explanation for the otherwise puzzling negative solvatochromism exhibited in this family of compounds. Combining TDCP and Stark results, we find that the dipole moment can be rotated in some instances by more than 90 degrees upon (3)MLCT excited-state formation. The degree of rotation or reorientation can be modulated by changing the identity of the acceptor ligand substituents. Reorientational effects are smallest when the compounds feature aromatic substituents capable of spatially extending the pi system of the acceptor ligand.     

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.     

Unusual bond formation in aspartic protease inhibitors: a theoretical study

The origin of the formation of the weak bond N|C...O involved in an original class of aspartic protease inhibitors was investigated by means of the electron localization function (ELF) and explicitly correlated wave-function (MRCI) analysis. The distance between the electrophilic C and the nucleophilic N centers appears to be controlled directly by the polarity and proticity of the medium. In light of these investigations, an unusual dative N-C bonding picture was characterized. Formation of this bond is driven by the enhancement of the ionic contribution C(+)-O(-) induced mainly by the polarization effect of the near N lone pair, and to a lesser extent by a weak charge delocalization N-->CO. Although the main role of the solvating environment is to stabilize the ionic configuration, the protic solvent can enhance the C(+)-O(-) configuration through a slight but cumulative charge transfer towards water molecules in the short N-C distance regime. Our revisited bond scheme suggests the possible tuning of the N-CO interaction in the design of specific inhibitors.     

利用浮动电荷力场对N-甲基乙酰胺水溶液的分子动力学模拟

利用原子键电负性均衡结合分子力场方法(ABEEM/MM)对N-甲基乙酰胺(NMA)分子的水溶液体系进行了分子动力学模拟. 与经典的力场模型相比, 该方法中的静电势包含了分子内和分子间的静电极化作用, 以及分子内电荷转移影响, 同时加入了化学键等非原子中心电荷位点, 合理体现了分子中的电荷分布. 相对其它极化力场模型, 该模型具有计算量较小的特点. 在该模型下对NMA纯溶液和其水溶液体系进行了分子动力学模拟, 得到的径向分布函数、汽化热和偶极矩等物理量与实验值和其它极化力场方法符合很好, 合理描述了溶质与溶剂之间的静电极化和分子内的电荷转移.     

Mechanism of the electronic stabilization of the 3MR and divalent carbon of bis(diisopropylamino)cyclopropenylidene

Analysis of the topology of the electron density of bis(dimethylamino)cyclopropenylidene as a model of the recently synthesized, stable bis(diisopropylamino)cyclopropenylidene with the quantum theory of atoms in molecules is used to investigate the stabilizing electronic effects at the reactive carbene site by amino substitution. This work demonstrates that the plane perpendicular lone pairs of nitrogen utilize in-plane sigma-aromaticity as a conduit to delocalize charge to the carbene carbon C2, where it is transferred preferentially back into the pi-plane at the site through sigma-pi polarization. C2 is thus stabilized relative to the parent cyclopropenylidene, c-C(3)H(2), by a very different mechanism than that suggested in the orbital view of n(pi)(N) and pi(C=C) conjugation and n(pi)(N) --> p(pi)*(C2) hyperconjugation. Validation of this premise is also found in properties of asymmetric atomic quadrupole tensors, bond path ellipticities, and diamagnetic/paramagnetic components of NMR shielding tensors.     

New insight into the electronic structure of iron(IV)‐oxo porphyrin compound I. A quantum chemical topological analysis

The electronic structure of iron‐oxo porphyrin π‐cation radical complex Por^·+Fe^IV?O (S? H) has been studied for doublet and quartet electronic states by means of two methods of the quantum chemical topology analysis: electron localization function (ELF) η(r) and electron density ρ(r). The formation of this complex leads to essential perturbation of the topological structure of the carbon–carbon bonds in porphyrin moiety. The double C?C bonds in the pyrrole anion subunits, represented by pair of bonding disynaptic basins V_i=1,2(C,C) in isolated porphyrin, are replaced by single attractor V(C,C)_i=1–20 after complexation with the Fe cation. The iron–nitrogen bonds are covalent dative bonds, N→Fe, described by the disynaptic bonding basins V(Fe,N)_i=1–4, where electron density is almost formed by the lone pairs of the N atoms. The nature of the iron–oxygen bond predicted by the ELF topological analysis, shows a main contribution of the electrostatic interaction, Fe^δ+···O^δ?, as long as no attractors between the C(Fe) and C(O) core basins were found, although there are common surfaces between the iron and oxygen basines and coupling between iron and oxygen lone pairs, that could be interpreted as a charge‐shift bond. The Fe? S bond, characterized by the disynaptic bonding basin V(Fe,S), is partially a dative bond with the lone pair donated from sulfur atom. The change of electronic state from the doublet (M = 2) to quartet (M = 4) leads to reorganization of spin polarization, which is observed only for the porphyrin skeleton (?0.43e to 0.50e) and S? H bond (?0.55e to 0.52e). © 2012 Wiley Periodicals, Inc.     

鸟嘌呤与氨基酸残基体系的极化力场

发展了应用于鸟嘌呤G和氨基酸残基体系的浮动电荷力场, 该力场明确定义了孤对电子和键的电荷和位置, 通过电荷随着环境的浮动来体现极化效应; 通过氢键拟合函数k_HB描绘了氢键键能. 应用量子化学方法, 对G与氨基酸残基体系从氢键、 几何结构及电荷分布3个方面展开计算及分析, 并以其为基准, 确定参数发展了适用于G与氨基酸残基氢键体系的ABEEMσπ PFF. 采用3种不同力场模拟目标分子的结构和性质. 模拟结果表明, 发展的ABEEMσπ PFF与量子化学方法具有最好的一致性, 可用于模拟生物大分子体系.     

On the physical origin of blue-shifted hydrogen bonds

For blue-shifted hydrogen-bonded systems, the hydrogen stretching frequency increases rather than decreases on complexation. In computations at various levels of theory, the blue-shift in the archetypical system, F(3)C-H.FH, is reproduced at the Hartree-Fock level, indicating that electron correlation is not the primary cause. Calculations also demonstrate that a blue-shift does not require either a carbon center or the absence of a lone pair on the proton donor, because F(3)Si-H.OH(2), F(2)NH.FH, F(2)PH.NH(3), and F(2)PH.OH(2) have substantial blue-shifts. Orbital interactions are shown to lengthen the X-H bond and lower its vibrational frequency, and thus cannot be the source of the blue-shift. In the F(3)CH.FH system, the charge redistribution in F(3)CH can be reproduced very well by replacing the FH with a simple dipole, which suggests that the interactions are predominantly electrostatic. When modeled with a point charge for the proton acceptor, attractive electrostatic interactions elongate the F(3)C-H, while repulsive interactions shorten it. At the equilibrium geometry of a hydrogen-bonded complex, the electrostatic attraction between the dipole moments of the proton donor and proton acceptor must be balanced by the Pauli repulsion between the two fragments. In the absence of orbital interactions that cause bond elongation, this repulsive interaction leads to compression of the X-H bond and a blue-shift in its vibrational frequency.     

An atomic charge study of highly ionic diatomic molecular systems

Four atomic charge formalisms are compared using highly ionic diatomic molecules, such as LiF, NaF, KF, LiCl, NaCl, KCl, BF, AlF, GaF, BeO, and MgO. All calculations were done at the QCISD/6‐311G(2df) level. The only formalism consistent with the characteristics of all these systems is Quantum theory of atoms in molecules (QTAIM). Absolute Mulliken charge values are small. ChelpG charges are not reliable for systems in which the atoms are largely anisotropic. Generalized atomic polar tensor values are contaminated with charge fluxes and atomic dipole fluxes and fail when these contributions are important and do not cancel each other. Finally, the charge–charge flux–dipole flux model was applied to dipole moment derivatives with QTAIM. This analysis shows that charge flux and atomic dipole flux contributions during bond stretching are almost null, except for oxides. There are also evidences that the lone electron pair at Group 13 elements in fluorides becomes less localized as the bond is stretched. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

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.     

Gaussian induced dipole polarization model

A new induced dipole polarization model based on interacting Gaussian charge densities is presented. In contrast to the original induced point dipole model, the Gaussian polarization model is capable of finite interactions at short distances. Aspects of convergence related to the Gaussian model will be explored. The Gaussian polarization model is compared with the damped Thole-induced dipole model and the point dipole model. It will be shown that the Gaussian polarization model performs slightly better than the Thole model in terms of fitting to molecular polarizability tensors. An advantage of the model based on Gaussian charge distribution is that it can be easily generalized to other multipole moments and provide effective damping for both permanent electrostatic and polarization models. Finally, a method of parameterizing polarizabilities is presented. This method is based on probing a molecule with point charges and fitting polarizabilities to electrostatic potential. In contrast to the generic atom type polarizabilities fit to molecular polarizability tensors, probed polarizabilities are significantly more accurate in terms of reproducing molecular polarizability tensors and electrostatic potential, while retaining conformational transferability.     

Energy of charged states in the RDX crystal: trapping of charge-transfer pairs as a possible mechanism for initiating detonation

Calculations for the crystalline energetic material RDX (1,3,5-trinitro-1,3,5-triazacyclohexane) yield the effective polarizability (17.2 angstroms3), local electric field tensor, effective dipole moment (9.40 D), and dipole-dipole energy (-27.2 kJ/mol). Fourier-transform techniques give the polarization energy P for a single charge in the perfect crystal as -1.14 eV; the charge-dipole energy W(D) is zero if the crystal carries no bulk dipole moment. Polarization energies for charge-transfer (CT) pairs combine with the Coulomb energy E(C) to give the screened Coulomb energy E(scr); screening is nearly isotropic with E(scr) approximately = E(C)2.6. For CT pairs W(D) reduces to a term deltaW(D) arising from the interaction of the charge on each ion with the change in dipole moment on the other ion relative to the neutral molecule. The dipole moments are calculated as 7.40 D for the neutral molecule and 6.84 D and 7.44 D for the anion and cation, giving the lowest two CT pairs at -1.34 eV and -0.94 eV. The changes in P and W(D) near a molecular vacancy yield traps with depths that reach 400 meV for single charges and 185 meV for the nearest-neighbor CT pair. Divacancies yield traps with depths nearly equal to the sum of those produced by the separate vacancies. These results are consistent with a mechanism in which detonation of RDX is initiated by mechanical generation of CT pairs that localize at vacancies, recombine, and release energy sufficient to break bonds; crystals of molecules with lower dipole moments should be less sensitive.     

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.     

The physical nature of the lone pair

Despite the large number of experimental and theoretical studies on the size, shape, and orientation of lone pairs and their resulting stereochemical character, lone pairs still remain poorly defined in terms of quantitative observable properties of a molecule. Using the conformation of saturated molecules and barriers to internal rotation, experimental chemists have arrived at conflicting sizes and orientations for lone pairs. Most theoretical attempts to define lone pair properties have centered on such non-observables as localized molecular orbitals or have been based on studies on isolated molecules.The use of observable properties to construct a consistent set of physical models to analyze the physical nature of lone pairs is discussed. Much as one probes an electric field with a test charge, probes such as H⁺, H^–, He and H could be used to probe regions of molecules such as NH₃ and H₂O where lone pairs are often postulated to exist.Ab initio quantum mechanical studies can be analyzed using electron density (and resulting changes during interaction), total pair density of electrons, the electrostatic potential about the molecule and bond energy analysis to study lone pair properties. A simple study of NH₃ using an H⁺ probe is presented to clarify the approach.