Atomic Charges of the Water Molecule and the Water Dimer

A Theoretical Investigation of Novel Sila- and Germa-Spirocyclic Imines and Their Relevance for Electron-Transporting Materials and Drug Discovery

A new class of spirocyclic imines (SCIs) has been theoretically investigated by applying a variety of quantum chemical methods and basis sets. The uniqueness of these compounds is depicted by various peculiarities, e.g., the incidence of planar six-membered rings each with two imine groups (two π bonds) and the incorporation of the isosteres carbon, silicon, or germanium spiro centers. Additional peculiarities of these novel SCIs are mirrored by their three-dimensionality, the simultaneous occurrence of nucleophilic and electrophilic centers, and the cross-hyperconjugative (spiro-conjugation) interactions, which provoke charge mobility along the spirocyclic scaffold. Substitution of SCIs with strong electron-withdrawing substituents, like the cyano group or fluorine, enhances their docking capability and impacts their reactivity and charge mobility. To gain thorough knowledge about the molecular properties of these SCIs, their structures have been optimized and various quantum chemical concepts and models were applied, e.g., full NBO analysis and the frontier molecular orbitals (FMOs) theory (HOMO-LUMO energy gap) and the chemical reactivity descriptors derived from them. For the assessment of the charge density distribution along the SCI framework, additional complementary quantum chemical methods were used, e.g., molecular electrostatic potential (MESP) and Bader's QTAIM. Additionally, using the aromaticity index NICS (nuclear independent chemical shift) and other criteria, it could be shown that the investigated cross-hyperconjugated sila and germa SCIs are spiro-aromatics of the Heilbronner Craig-type Möbius aromaticity.

Theoretical study of water-assisted reaction between methane and nitrosonium cation

The water-assisted reaction between CH4 and NO+ has been studied employing post Hartree–Fock and density functional theory methods. Two reaction pathways were considered: (i) a frontside NO+ attack on the C–H bond of methane with retention of configuration and (ii) a backside attack with inversion of configuration. The first pathway leads to a thermodynamically more favorable hydrate of N-protonated nitrosomethane, and the second one leads to its O-protonated isomer. The catalytic effect of a single water molecule is expressed in decreasing the activation energy for the elementary step by about a factor of two for the frontside mechanism and by a factor of four to five for the backside one when compared with the calculated literature data on water-free methane nitrosation. The combination of the activation strain model of reactivity and the energy decomposition analysis reveals that the activation barriers are largely determined by the relative stability of the termolecular reactant complexes. The crucial factor that stabilizes these complexes comes from the electrostatic attraction. The catalytic effect of the key water molecule is decreased with introduction of additional one or two explicit water molecules, which form a coordinate O→N bonding with NO+. On the contrary, an additional water molecule hydrogen bonded to the key catalytic water molecule enhances the catalytic effect.

Determining Partial Atomic Charges for Liquid Water: Assessing Electronic Structure and Charge Models

Partial atomic charges provide an intuitive and efficient way to describe the charge distribution and the resulting intermolecular electrostatic interactions in liquid water. Many charge models exist and it is unclear which model provides the best assignment of partial atomic charges in response to the local molecular environment. In this work, we systematically scrutinize various electronic structure methods and charge models (Mulliken, natural population analysis, CHelpG, RESP, Hirshfeld, Iterative Hirshfeld, and Bader) by evaluating their performance in predicting the dipole moments of isolated water, water clusters, and liquid water as well as charge transfer in the water dimer and liquid water. Although none of the seven charge models is capable of fully capturing the dipole moment increase from isolated water (1.85 D) to liquid water (about 2.9 D), the Iterative Hirshfeld method performs best for liquid water, reproducing its experimental average molecular dipole moment, yielding a reasonable amount of intermolecular charge transfer, and showing modest sensitivity to the local water environment. The performance of the charge model is dependent on the choice of the density functional and the quantum treatment of the environment. The computed molecular dipole moment of water generally increases with the percentage of the exact Hartree-Fock exchange in the functional, whereas the amount of charge transfer between molecules decreases. For liquid water, including two full solvation shells of surrounding water molecules (within about 5.5 Å of the central water) in the quantum chemical calculation converges the charges of the central water molecule. Our final pragmatic quantum chemical charge-assigning protocol for liquid water is the Iterative Hirshfeld method with M06-HF/aug-cc-pVDZ and a quantum region cutoff radius of 5.5 Å.

Predicting Entropic Effects of Water Mixing with Ionic Liquids Containing Anions of Strong Hydrogen Bonding Ability: Role of the Cation

Ionic liquids (ILs) such as choline dihydrogen phosphate exhibit an extraordinary solubilizing ability for proteins such as cytochrome C when mixed with 20 wt % water. Most widely used imidazolium-based ionic liquids coupled with dihydrogen phosphate do not exhibit the same solubilizing properties, suggesting that a multifunctional cation such as choline might play a key role in enhancing these properties of ionic liquid mixtures with water. In this theoretical work, we compare intermolecular interactions between the water molecule and ionic liquid ions in two ion-paired clusters of choline- and 1-butyl-3-methyl-imidazolium-based ionic liquids coupled with acetate, dihydrogen phosphate, and mesylate. Gibbs free energy (GFE) of solvation of water in these ionic liquids was calculated. Incorporation of a water molecule into ionic liquid clusters was accompanied by negative GFEs of solvation in both types of cations. These results were in good agreement with previously reported experimental GFEs of solvation of water in ILs. Compared to imidazolium-based clusters, strong interionic interactions of choline ionic liquids resulted in more negative GFEs due to their smaller deformation upon the addition of a water molecule, with dihydrogen phosphate and mesylate predicting the lowest GFEs of -30.1 and -43.5 kJ/mol^-1, respectively. Lower GFEs of solvation of water in choline-based clusters were also accompanied with smaller entropic penalties, suggesting that water easily incorporates itself into the existing ionic network. Analysis of the intramolecular bonds within the water molecule showed that the choline hydroxyl group donates electron density to the neighboring water molecule, leading to additional polarization. The predicted infrared spectra of clusters of ionic liquids with water showed a pronounced red shift due to strongly polarized O-H bonds, in excellent agreement with the experimentally measured infrared spectra of ionic liquid mixtures with water. Increased polarization of water in choline-based ionic liquids undoubtedly creates more effective solvents for stabilizing biological molecules such as proteins.

Heterogeneous nucleation of polymorphs on polymer surfaces: polymer-molecule interactions using a heterogeneous dielectric solvation model

We have investigated the mechanism of the nucleation of acetaminophen on poly(methyl-methacrylate) and poly(vinyl-acetate) utilizing a combination of quantum mechanical computations and electrostatic models. We have used a heterogeneous dielectric solvation model to determine the stability of different orientations of acetaminophen on polymer surfaces. We find that for the nucleation of acetaminophen on the polymer surfaces in vacuum, the most stable orientation is a flat orientation. For the nucleation process in solution where acetaminophen and the polymer surface are surrounded by a solvent, we find that the heterogeneous dielectric solvation model predicts that a sideways orientation is the most stable orientation.

Energy Decomposition Analysis Based on Absolutely Localized Molecular Orbitals for Large-Scale Density Functional Theory Calculations in Drug Design

We report the development and implementation of an energy decomposition analysis (EDA) scheme in the ONETEP linear-scaling electronic structure package. Our approach is hybrid as it combines the localized molecular orbital EDA (Su, P.; Li, H. J. Chem. Phys., 2009, 131, 014102) and the absolutely localized molecular orbital EDA (Khaliullin, R. Z.; et al. J. Phys. Chem. A, 2007, 111, 8753-8765) to partition the intermolecular interaction energy into chemically distinct components (electrostatic, exchange, correlation, Pauli repulsion, polarization, and charge transfer). Limitations shared in EDA approaches such as the issue of basis set dependence in polarization and charge transfer are discussed, and a remedy to this problem is proposed that exploits the strictly localized property of the ONETEP orbitals. Our method is validated on a range of complexes with interactions relevant to drug design. We demonstrate the capabilities for large-scale calculations with our approach on complexes of thrombin with an inhibitor comprised of up to 4975 atoms. Given the capability of ONETEP for large-scale calculations, such as on entire proteins, we expect that our EDA scheme can be applied in a large range of biomolecular problems, especially in the context of drug design.

Ambient-Potential Composite Ewald Method for ab Initio Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulation

A new approach for performing Particle Mesh Ewald in ab initio quantum mechanical/molecular mechanical (QM/MM) simulations with extended atomic orbital basis sets is presented. The new approach, the Ambient-Potential Composite Ewald (CEw) method, does not perform the QM/MM interaction with Mulliken charges nor electrostatically fit charges. Instead the nuclei and electron density interact directly with the MM environment, but in a manner that avoids the use of dense Fourier transform grids. By performing the electrostatics with the underlying QM density, the CEw method avoids self-consistent field instabilities that have been encountered with simple charge mapping procedures. Potential of mean force (PMF) profiles of the p-nitrophenyl phosphate dissociation reaction in explicit solvent are computed from PBE0/6-31G* QM/MM molecular dynamics simulations with various electrostatic protocols. The CEw profiles are shown to be stable with respect to real-space Ewald cutoff, whereas the PMFs computed from truncated and switched electrostatics produce artifacts. PBE0/6-311G**, AM1/d-PhoT, and DFTB2 QM/MM simulations are performed to generate two-dimensional PMF profiles of the phosphoryl transesterification reactions with ethoxide and phenoxide leaving groups. The semiempirical models incorrectly produce a concerted ethoxide mechanism, whereas PBE0 correctly produces a stepwise mechanism. The ab initio reaction barriers agree more closely to experiment than the semiempirical models. The failure of Mulliken-charge QM/MM-Ewald is analyzed.

4-hydroxy-2,5-dimethylphenyl-benzophenone: conformational stability, FT-IR and Raman investigation

In this paper we have studied the 4-hydroxyl-2,5 dimethylphenyl-benzophenone. Also, it was analyzed the vibrational assignment (FT-IR and Raman) in conjunction with computational results. The conformational analysis showed three barrier heights where two are due to the dihedral rotation and the other one is attributed to hydroxyl rotation. While the high dihedral rotational barrier (TS1) is 6.06-7.22 kcal mol(-1), the lower one (TS2) is almost three times smaller. The variations with the change of basis set is 5-8% to TS1, and 3-15% in the values predicted to TS2. In the case of OH rotational barrier, the values range from 3.70 to 4.86 kcal mol(-1), and it is also observed that this transition state is less sensitive to the change of basis set and to the method. Two isomers was detected due to the changes in the OH rotation with the gap energy lower than 0.7 kcal mol(-1), and at this point is seen that semi-empirical methods fail into describe the most stable conformation which may be due to the small energy gap. The enthalpy formation at 0 K and 298 K was 111.71 and 102.20 kcal mol(-1), respectively.

Incorporation of charge transfer into the explicit polarization fragment method by grand canonical density functional theory

Molecular fragmentation algorithms provide a powerful approach to extending electronic structure methods to very large systems. Here we present a method for including charge transfer between molecular fragments in the explicit polarization (X-Pol) fragment method for calculating potential energy surfaces. In the conventional X-Pol method, the total charge of each fragment is preserved, and charge transfer between fragments is not allowed. The description of charge transfer is made possible by treating each fragment as an open system with respect to the number of electrons. To achieve this, we applied Mermin's finite temperature method to the X-Pol wave function. In the application of this method to X-Pol, the fragments are open systems that partially equilibrate their number of electrons through a quasithermodynamics electron reservoir. The number of electrons in a given fragment can take a fractional value, and the electrons of each fragment obey the Fermi-Dirac distribution. The equilibrium state for the electrons is determined by electronegativity equalization with conservation of the total number of electrons. The amount of charge transfer is controlled by re-interpreting the temperature parameter in the Fermi-Dirac distribution function as a coupling strength parameter. We determined this coupling parameter so as to reproduce the charge transfer energy obtained by block localized energy decomposition analysis. We apply the new method to ten systems, and we show that it can yield reasonable approximations to potential energy profiles, to charge transfer stabilization energies, and to the direction and amount of charge transferred.

Validation of critical points in the electron density as descriptors by building quantitative structure-property relationships for the atomic polar tensor

A crucial component of research in the field of quantitative structure-activity/property relationships is the identification of molecular descriptors relevant to the activity or property of interest. Descriptors based on the topology of the electron density as formulated in Bader's theory of atoms in molecules are investigated in detail in this work. In a model study, the authors investigate their ability to predict the atomic polar tensor (the gradient of the molecular dipole moment), which contains information on the vibrational intensities in infrared spectroscopy and constitutes a scheme for partitioning the total charge distribution into atomic charges. The atomic polar tensor may therefore be used to investigate whether the descriptors give adequate information on the local electronic structure in the molecule. Both the trace of the atomic polar tensor and for planar molecules its out-of-plane component may be interpreted as definitions of atomic charges suitable for prediction. Hydrogen and carbon atoms in a set of 60 aromatic compounds with various substituents have been studied. Excellent results for prediction of hydrogen and carbon charges have been achieved with cross-validated squared correlation coefficients between predicted and theoretical values varying from 0.92 and 0.977 for the most complex set of substituents when the value, Laplacian, and ellipticity of the electron density in the bond critical points are used as descriptors. The carbon charges defined from the trace of the atomic polar tensor are correlated with its out-of-plane component whereas such relationship is not observed for the hydrogen charges studied in this work.

Can the pH value of water solutions be estimated by quantum chemical calculations of small water clusters?

In the study, various water clusters were explored from the point of view of the proton transfer between H-bonded neighbors. A relatively modest approach--the MP26-31++G(d,p) level--was chosen as acceptable considering the fact that also larger systems have to be included. The tight ion-pair model (with usually three fixed O-O distances) was adopted for the autodissociation process. First, cluster-estimated pH values rapidly decrease as cluster size increases from 2 to 6. For larger clusters in gas phase, the topology of H bonds plays an important role, varying pH from 7 to 13 in hexamers and from 5 to 15 in octamer clusters. The relationship energy/distance was quantified, too. Enhancing our model with the conductorlike screening model (COSMO) approach brought significant improvement in description of the autodissociation reaction with a stable zwitterionic structure. However, when the O-O restrictions were released, the small barrier for backward reaction disappeared, reforming neutral cluster spontaneously. Also Boltzmann weighting procedure was applied, and for the explored clusters in vacuo, the series of pH 25-18-14-13-10 was obtained for cluster sizes n=2, 3, 4, 6, 8. Using the COSMO approach, the analogous series is 15-14-12-10-9. The limit of the series is still about two to three units above the experimentally known pH. In order to reach the size-independent (bulk) value, larger clusters are needed. However, the situation is far from hopeless since (as it was proven in the study) four-coordinated molecules are not involved in the proton transfer process directly; they can only be a part of the surrounding environment.

CORRELATED ELECTRONIC STRUCTURE NONLINEAR RESPONSE METHODS FOR STRUCTURED ENVIRONMENTS

▪ Abstract  This contribution concerns a brief outline of structural environment models where correlated electronic structure response methods are utilized for the determination of nonlinear optical properties of molecules. The presentation provides theory and applications of a heterogeneous dielectric media model and a quantum mechanical–classical mechanical model at the level of correlated electronic structure response methods. The correlated electronic structure response methods include the multiconfigurational self-consistent field method.

Charge distribution in the water molecule--a comparison of methods

The charge distribution in the water molecule has been analyzed using a broad variety of basis sets, four different quantum mechanical methods (Hartree-Fock, Becke3LYP, MP2, and QCISD), and six population analysis methods (Mulliken, NPA, AIM, CHELPG, Merz-Kollman, and Resp). The influence of the molecular structure on the calculated atomic charges has been studied using small perturbations of the experimentally determined structure.

Atomic dipole moments calculated using analytical molecular second-moment gradients

We have implemented analytical second-moment gradients for Hartree-Fock and multiconfigurational self-consistent-field wave functions. The code is used to calculate atomic dipole moments based on the generalized atomic polar tensor (GAPT) formalism [Phys. Rev. Lett. 62, 1469 (1989)], and the proposal of Dinur and Hagler (DH) for the calculation of atomic multipoles [J. Chem. Phys. 91, 2949 (1989)]. Both approaches display smooth basis-set convergence toward a well-defined basis-set limit and give reasonable electron correlation effects on the calculated atomic properties. However, the atomic charges and atomic dipole moments obtained from the GAPT partitioning scheme are unable to provide even qualitatively meaningful molecular quadrupole moments for some molecules, and thus the atomic multipole moments calculated in this scheme cannot be considered well suited for analyzing the electron density in molecules and for calculating intermolecular interaction energies. In contrast, the DH approach gives atomic charges and dipole moments that by definition exactly reproduce the molecular quadrupole moments. The approach of DH is, however, restricted to planar molecules and thus suffers from not being applicable to molecules of arbitrary shape. Both the GAPT and DH approaches give rather poor results for octupole and hexadecapole moments, indicating that at least atomic quadrupole moments are required for an accurate representation of the molecular charge distribution in terms of atomic electric moments.

Voronoi deformation density (VDD) charges: Assessment of the Mulliken, Bader, Hirshfeld, Weinhold, and VDD methods for charge analysis

We present the Voronoi Deformation Density (VDD) method for computing atomic charges. The VDD method does not explicitly use the basis functions but calculates the amount of electronic density that flows to or from a certain atom due to bond formation by spatial integration of the deformation density over the atomic Voronoi cell. We compare our method to the well-known Mulliken, Hirshfeld, Bader, and Weinhold [Natural Population Analysis (NPA)] charges for a variety of biological, organic, and inorganic molecules. The Mulliken charges are (again) shown to be useless due to heavy basis set dependency, and the Bader charges (and often also the NPA charges) are not realistic, yielding too extreme values that suggest much ionic character even in the case of covalent bonds. The Hirshfeld and VDD charges, which prove to be numerically very similar, are to be recommended because they yield chemically meaningful charges. We stress the need to use spatial integration over an atomic domain to get rid of basis set dependency, and the need to integrate the deformation density in order to obtain a realistic picture of the charge rearrangement upon bonding. An asset of the VDD charges is the transparency of the approach owing to the simple geometric partitioning of space. The deformation density based charges prove to conform to chemical experience.

Atom-bond electronegativity equalization method fused into molecular mechanics. I. A seven-site fluctuating charge and flexible body water potential function for water clusters

Recently, experimental and theoretical studies on the water system are very active and noticeable. A transferable intermolecular potential seven points approach including fluctuation charges and flexible body (ABEEM-7P) based on a combination of the atom-bond electronegativity equalization and molecular mechanics (ABEEM/MM), and its application to small water clusters are explored and tested in this paper. The consistent combination of ABEEM and molecular mechanics (MM) is to take the ABEEM charges of atoms, bonds, and lone-pair electrons into the intermolecular electrostatic interaction term in molecular mechanics. To examine the charge transfer we have used two models coming from the charge constraint types: one is a charge neutrality constraint on whole water system and the other is on each water molecule. Compared with previous water force fields, the ABEEM-7P model has two characters: (1) the ABEEM-7P model not only presents the electrostatic interaction of atoms, bonds and lone-pair electrons and their changing in respond to different ambient environment but also introduces "the hydrogen bond interaction region" in which a new parameter k(lp,H)(R(lp,H)) is used to describe the electrostatic interaction of the lone-pair electron and the hydrogen atom which can form the hydrogen bond; (2) nonrigid but flexible water body permitting the vibration of the bond length and angle is allowed due to the combination of ABEEM and molecular mechanics, and for van der Waals interaction the ABEEM-7P model takes an all atom-atom interaction, i.e., oxygen-oxygen, hydrogen-hydrogen, oxygen-hydrogen interaction into account. The ABEEM-7P model based on ABEEM/MM gives quite accurate predictions for gas-phase state properties of the small water clusters (H(2)O)(n) (n=2-6), such as optimized geometries, monomer dipole moments, vibrational frequencies, and cluster interaction energies. Due to its explicit description of charges and the hydrogen bond, the ABEEM-7P model will be applied to discuss properties of liquid water, ice, aqueous solutions, and biological systems.