Abstract: We present a method for estimating partial atomic charges that uses all of the measured ionization energies (first, second, third, etc.) for every atom in the periodic table. We build on the charge equilibration (Qeq) method of Rappe and Goddard (which used only the first ionization energies) but reduce the number of ad hoc parameters from at least one for every type of atom to just two global parameters: a dielectric strength and a modified parameter for hydrogen atoms. Periodic electrostatic interactions are calculated via Ewald sums, and the partial charges are determined by simultaneously solving a system of linear equations; no iteration is required. We compare the predicted partial atomic charges of this extended charge equilibration (EQeq) scheme against plane-wave density-functional theory derived charges determined via the REPEAT method for 12 diverse metal–organic frameworks (MOFs). We also compare EQeq charges against ChelpG charges calculated using nonperiodic MOF fragments, as well as against...

Abstract: Molecular ionic liquids are typically characterized by strong electrostatic interactions resulting in a charge ordering and retardation of their translational and rotational behaviour. Unfortunately, this effect is often overestimated in classical molecular dynamics simulations. This can be circumvented in a twofold way: the easiest way is to reduce the partial charges of the ions to sub-integer values of ±0.7–0.9 e. The more realistic model is to include polarizable forces, e.g. Drude-oscillators, but it comes along with an increasing computational effort. On the other hand, charge-scaled models are claimed to take an average polarizability into account. But do both models have the same impact on structure and dynamics of molecular ionic liquids? In the present study several molecular dynamics simulations of 1-ethyl-3-methylimidazolium trifluoromethanesulfonate are performed with different levels of polarization as well as with varying charge scaling factors of 0.74 to 0.90. The analysis of the structural and dynamical results are performed in different levels: from the atomic point of view over the molecular level to collective properties determined by the complete sample.

Abstract: We report AMBER force field parameters for biological simulations involving phosphorylation of serine, threonine, or tyrosine. The initial parameters used RESP fitting for the atomic partial charges and standard values for all other parameters such as Lennard-Jones coefficients. These were refined with the aid of a thermodynamic cycle consisting of experimentally determined pKa values, solvation energies from molecular dynamics free energy simulations, and gas phase basicities from QM calculations. A polarization energy term was included to account for the charge density change between the gas phase and solution, and solvation free energies were determined using thermodynamic integration. Parameter adjustment is required to obtain consistent thermodynamic results with better balanced electrostatic interactions between water and the phosphate oxygens. To achieve this, we modified the phosphate oxygen radii. A thermodynamically consistent parameter set can be derived for monoanions and requires an increase ...

Abstract: The atomic charges for two ionic liquids (ILs), 1-n-butyl-3-methylimidazolium hexafluorophosphate ([BMIM][PF6]) and 1-ethyl-3-methylimidazolium hexafluorophosphate ([EMIM][PF6]), were derived from periodic crystal phase calculations with density functional theory (DFT) and plane wave basis sets (denoted as “AIMD-c charge”). For both ILs, the total charge was found to be ±0.8 e for the cation and anion, respectively, due to the charge transfer between ions and polarization caused by the environment. These atomic charges were used in a force field developed within the general Amber force field framework. Using this force field, static, dynamic, and thermodynamic properties were computed for the two ILs using molecular dynamics simulation. The results were compared against results obtained using the same Amber force field but four different sets of partial charges, denoted as full charge, scaled charge, AIMD-l charge, and AIMD-b charge, respectively. The full charge was derived from quantum chemistry calcula...

Abstract: Molecular junctions are essentially modified electrodes familiar to electrochemists where the electrolyte is replaced by a conducting “contact.” It is generally hypothesized that changing molecular structure will alter system energy levels leading to a change in the transport barrier. Here, we show the conductance of seven different aromatic molecules covalently bonded to carbon implies a modest range ( 2 eV range). These results are explained by considering the effect of bonding the molecule to the substrate. Upon bonding, electronic inductive effects modulate the energy levels of the system resulting in compression of the tunneling barrier. Modification of the molecule with donating or withdrawing groups modulate the molecular orbital energies and the contact energy level resulting in a leveling effect that compresses the tunneling barrier into a range much smaller than expected. Whereas the value of the tunneling barrier can be varied by using a different class of molecules (alkanes), using only aromatic structures results in a similar equilibrium value for the tunnel barrier for different structures resulting from partial charge transfer between the molecular layer and the substrate. Thus, the system does not obey the Schottky-Mott limit, and the interaction between the molecular layer and the substrate acts to influence the energy level alignment. These results indicate that the entire system must be considered to determine the impact of a variety of electronic factors that act to determine the tunnel barrier.

Abstract: The atomic charges for two ionic liquids (ILs), 1-n-butyl-3-methylimidazolium hexafluorophosphate ([BMIM][PF6]) and 1-ethyl-3-methylimidazolium hexafluorophosphate ([EMIM][PF6]), were derived from periodic crystal phase calculations with density functional theory (DFT) and plane wave basis sets (denoted as “AIMD-c charge”). For both ILs, the total charge was found to be ±0.8 e for the cation and anion, respectively, due to the charge transfer between ions and polarization caused by the environment. These atomic charges were used in a force field developed within the general Amber force field framework. Using this force field, static, dynamic, and thermodynamic properties were computed for the two ILs using molecular dynamics simulation. The results were compared against results obtained using the same Amber force field but four different sets of partial charges, denoted as full charge, scaled charge, AIMD-l charge, and AIMD-b charge, respectively. The full charge was derived from quantum chemistry calculation of isolated ions in a vacuum and resulted in a total charge of unity on each ion. The scaled charge was obtained by uniformly scaling the full charge by 0.8. AIMD-l and AIMD-b charges were derived from liquid phase ab initio molecular dynamics simulations. The scaled charges have the same total charge on the ions as the AIMD-c charge but different distributions. It was found that simulation results not only depend on the total charge of each ion, but they are also sensitive to the charge distribution within an ion, especially for dynamic and thermodynamic properties. Overall, for the two ILs under study, the AIMD-c charge was found to predict experimental results better than the other four sets of charges, indicating that fitting charges from crystal phase DFT calculations, instead of extensive sampling of the liquid phase configurations, is a simple and reliable way to derive atomic charges for condensed phase ionic liquid simulations.

Abstract: Molecular simulation techniques are increasingly being used to study biomolecular systems at an atomic level. Such simulations rely on empirical force fields to represent the intermolecular interactions. There are many different force fields available|each based on a different set of assumptions and thus requiring different parametrization procedures. Recently, efforts have been made to fully automate the assignment of force-field parameters, including atomic partial charges, for novel molecules. In this work, we focus on a problem arising in the automated parametrization of molecules for use in combination with the gromos family of force fields: namely, the assignment of atoms to charge groups such that for every charge group the sum of the partial charges is ideally equal to its formal charge. In addition, charge groups are required to have size at most k. We show NƤ-hardness and give an exact algorithm capable of solving practical problem instances to provable optimality in a fraction of a second.

Abstract: We present molecular dynamics simulations of the air–liquid interface for three room temperature ionic liquids with a common anion: bis(trifluoromethylsulfonyl) imide ([Tf2N]), and imidazolium-based cations that differ in the alkyl tail length: 1-butyl-3-methylimidazolium ([C4mim]), 1-hexyl-3-methylimidazolium ([C6mim]), and 1-octyl-3-methylimidazolium ([C8mim]). The CHARMM type force field is used with the partial charges based on quantum calculations for isolated ion pairs. The total charge on cations and anions is around 0.9e and −0.9e, respectively, which somewhat mimics the anion to cation charge transfer and many-body effects. The surface tension at 300 K is computed using the mechanical route and its value slightly overpredicts experimental values. The air–liquid interface is analyzed using the intrinsic method of Identification of the Truly Interfacial Molecules. Structural and dynamic properties of the interfacial, sub-interfacial and central layers are determined. To describe the structure of the interface, we compute the surface roughness, number density and charge density profiles, and orientation ordering of the ions. We further determine the survival probability, normal and lateral self-diffusion coefficients, and re-orientation correlation functions to characterize the dynamics of the cations and anions in the layers. We found a significant enhancement of the cation density and preferential orientation ordering of both the cations and anions at the interface. Overall, the surface of the interfacial layer is smoother than the surface of the sub-interfacial layer and the roughness of both the interfacial and sub-interfacial layers increases with the increase of the length of the cation alkyl tail. Finally, the ions stay considerably longer in the interfacial layer than in the sub-interfacial layer and dynamics of exchange of the ions between the consecutive layers is related to the distinct diffusion and re-orientation dynamics behavior of the ions within the layers.

Abstract: The molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA) and MM-generalized-Born surface area (MM-GBSA) approaches are commonly used in molecular modeling and drug design. Four critical aspects of these approaches have been investigated for their effect on calculated binding energies: (1) the atomic partial charge method used to parameterize the ligand force field, (2) the method used to calculate the solvation free energy, (3) inclusion of entropy estimates, and (4) the protonation state of the ligand. HIV protease has been used as a test case with six structurally different inhibitors covering a broad range of binding strength to assess the effect of these four parameters. Atomic charge methods are demonstrated to effect both the molecular dynamics (MD) simulation and MM-PB(GB)SA binding energy calculation, with a greater effect on the MD simulation. Coefficients of determination and Spearman rank coefficients were used to quantify the performance of the MM-PB(GB)SA methods relative to the experimental data. In general, better performance was achieved using (i) atomic charge models that produced smaller mean absolute atomic charges (Gasteiger, HF/STO-3G and B3LYP/cc-pVTZ), (ii) the MM-GBSA approach over MM-PBSA, while (iii) inclusion of entropy had a slightly positive effect on correlations with experiment. Accurate representation of the ligand protonation state was found to be important. It is demonstrated that these approaches can distinguish ligands according to binding strength, underlining the usefulness of these approaches in computer-aided drug design. © 2012 Wiley Periodicals, Inc.

Abstract: e-Fe2O3 is known to exhibit a large coercive field of 20 kOe at room temperature. In this work, we examine the electronic structure and magnetic properties of e-Fe2O3 using first-principles calculation and discrete variational (DV)-Xα molecular orbital calculation. The first-principles calculation shows that e-Fe2O3 is a charge-transfer type insulator with a valence band of O2p and a conduction band of Fe3d. The optical transition is an indirect transition from Γ to S point. The density of states (DOS) of the four nonequivalent Fe sites (FeA, FeB, FeC, and FeD) indicates that e-Fe2O3 has ferrimagnetic ordering due to α spins on FeB and FeC and β spins on FeA and FeD. The charge density map of the occupied Fe3d band displays a strong hybridization between Fe3d and O2p. Molecular orbital calculation for each Fe site also supports the existence of a strong Fe3d–O2p hybridization. Such a strong hybridization induces nonzero orbital angular momentum L on Fe3d through the partial charge transfer from O2p to Fe3...

Abstract: We theoretically investigate the interplay between charge ordering and magnetic states in quasi-one-dimensional molecular conductors TMTTF(2)X, motivated by the observation of a complex variation of competing and/or coexisting phases. We show that the ferroelectric-type charge order increases two-dimensional antiferromagnetic spin correlation, whereas in the one-dimensional regime two different spin-Peierls states are stabilized. By using first-principles band calculations for the estimation for the transfer integrals and comparing our results with the experiments, we identify the controlling parameters in the experimental phase diagram to be not only the interchain transfer integrals but also the amplitude of the charge order.

Abstract: A valence force field named LDHFF was systematically developed for the layered double hydroxide (LDH) materials. Its potential function was referred from the polymer consistent force field (PCFF) by introducing a double-well potential to describe the oxygen–metal–oxygen (O–M–O) bending in the octahedral host sheets. The bonded (intramolecular) parameters, including the bond stretching constants, angle bending coefficients, as well as cross terms, were obtained from density function theory (DFT) calculations on the simplified but representative cluster models [MII2MIII(OH2)9(OH)4]3+ and [MIII3(OH2)9(OH)4]5+ (MII2MIII = Mg2Al, Zn2Al, Co2Al, Ni2Al, Cu2Al, Mg2Fe, Zn2Fe, Ni2Fe, Mg2Cr, Zn2Cr, Cu2Cr, Co2Cr; MIII = Al, Fe, Cr). In the case of nonbonded potential, the van der Waals parameters were obtained by fitting them to the cluster models mentioned above. The partial charges used to calculate the Coulombic interactions were assigned as Mulliken charge from density functional theory (DFT) calculation. To valid...

Abstract: We propose a new screened charge method for calculating partial atomic charges in molecules by electrostatic potential (ESP) fitting. The model, called full density screening (FDS), is used to approximate the screening effect of full charge densities of atoms in molecules. The results are compared to the conventional ESP fitting method based on point charges and to our previously proposed outer density screening (ODS) method, in which the parameters are reoptimized for the present purpose. In ODS, the charge density of an atom is represented by the sum of a point charge and a smeared negative charge distributed in a Slater-type orbital (STO). In FDS, the charge density of an atom is taken to be the sum of the charge density of the neutral atom and a partial atomic charge (of either sign) distributed in an STO. The ζ values of the STOs used in these two models are optimized in the present study to best reproduce the electrostatic potentials. The quality of the fit to the electrostatics is improved in the s...

Abstract: Molecular dynamics (MD) simulations were conducted to compare the performance of four force fields in predicting thermophysical properties of tri-n-butyl-phosphate (TBP) in the liquid phase. The intramolecular force parameters used were from the Assisted Model Building with Energy Refinement (AMBER) force field model. The van der Waals parameters were based on either the AMBER or the Optimized Potential for Liquid Simulation (OPLS) force fields. The atomic partial charges were either assigned by performing quantum chemistry calculations or utilized previously published data, and were scaled to approximate the average experimental value of the electric dipole moment. Canonical ensemble computations based on the aforementioned parameters were performed near atmospheric pressure and temperature to obtain the electric dipole moment, mass density, and self-diffusion coefficient. In addition, the microscopic structure of the liquid was characterized via pair correlation functions between selected atoms. It has ...

Abstract: Density functional theory (DFT) has been used to study the hydrolysis reaction of (MO2)n (M = Zr, Hf, n = 1–4) nanoclusters in the ground singlet and first triplet states. The reactions for singlet n = 1 were benchmarked at the CCSD(T) level of theory. The reactions of H2O with the metal site having an M═O bond and/or M–O bonds as well as H transfer to both terminal ═O atoms and bridge −O atoms have been studied. The partial charge on M increases as the M═O bonds are replaced with M–OH bonds. The first H2O adsorption (physisorption) energies for these MO2 nanoclusters are calculated to be −20 to −30 kcal/mol for the singlet state and −15 to −48 kcal/mol for the triplet state. These physisorption energies depend on the cluster size and the adsorption site, consistent with existing experimental and computational studies. The first hydrolysis (dissociative chemisorption) reaction energies of the MO2 nanoclusters are calculated to have a much broader range, −30 to −80 kcal/mol for the singlet states and −30 t...

Abstract: In this work, we have carried out theoretical investigation aiming to clarify heteroatomic effect on the electron-transfer mobility of dianthra[2,3-b:2′,3′-f]thieno[3,2-b]thiophene (DATT) and its three derivatives by quantum chemistry calculations combined with the Marcus–Hush electron transfer theory. Partial charge differences of heteroatoms are indicated to be the largest among all atoms of the molecule, which confirms the significant influence of heteroatoms on the mobility, since partial charge changes are related to reorganization energies during the process of charge transfer. Heteroatoms are demonstrated to influence the mobility by two novel parameters: the longitudinal off of heteroatoms in each packing style and the angle among close heteroatoms. The little longitudinal offset and appropriate position between orbitals of S atoms determined by the suitable angle among close S atoms are responsible for the largest charge carrier mobility of DATT among the four systems we investigated. On the othe...

Abstract: Molecular dynamics (MD) simulations have been performed in order to investigate the properties of [C n mim+][Tf2N−] (n = 4, 8, 12) ionic liquids (ILs) in a wide temperature range (298.15−498.15 K) and at atmospheric pressure (1 bar). A previously developed methodology for the calculation of the charge distribution that incorporates ab initio quantum mechanical calculations based on density functional theory (DFT) was used to calculate the partial charges for the classical molecular simulations. The wide range of time scales that characterize the segmental dynamics of these ILs, especially at low temperatures, required very long MD simulations, on the order of several tens of nanoseconds, to calculate the thermodynamic (density, thermal expansion, isothermal compressibility), structural (radial distribution functions between the centers of mass of ions and between individual sites, radial-angular distribution functions) and dynamic (relaxation times of the reorientation of the bonds and the torsion angles,...

Abstract: Fragment methods have been widely studied for computing energies and forces, but less attention has been paid to nonenergetic properties. Here we extend the electrostatically embedded many-body (EE-MB) method to the calculation of cluster dipole moments, dipole moments of molecules in clusters, partial atomic charges, and charge transfer, and we test and validate the method by comparing to results calculated for the entire system without fragmentation. We also compare to calculations carried out by the conventional many-body (MB) method without electrostatic embedding. Systems considered are NH3(H2O)11, (NH3)2(H2O)14, [Cl(H2O)6]−, (HF)4, (HF)5, (HF)2H2O, (HF)3H2O, and (HF)3(H2O)2. With electrostatic embedding, we find that even at the pairwise additive level a quantitatively accurate description of a system's dipole moment and partial charge distribution and a qualitatively accurate description of the amount of intermolecular charge transfer can often be obtained.

Abstract: It is demonstrated that the near-edge X-ray absorption fine structure (NEXAFS) provides a powerful local probe of functional groups in novel charge transfer (CT) compounds and their electronic properties. Microcrystals of tetra-/hexamethoxypyrene as donors with the strong acceptor tetracyano-p-quinodimethane (TMP/HMP-TCNQ) were grown by vapor diffusion. The oxygen and nitrogen K-edge spectra are spectroscopic fingerprints of the functional groups in the donor and acceptor moieties, respectively. The orbital selectivity of the NEXAFS pre-edge resonances allows us to precisely elucidate the participation of specific orbitals in the charge transfer process. Upon complex formation, the intensities of several resonances change substantially and a new resonance occurs in the oxygen K-edge spectrum. This gives evidence of a corresponding change of hybridization of specific orbitals in the functional groups of the donor (those derived from the frontier orbitals 2e and 6a1 of the isolated methoxy group) and accept...

Abstract: Polar and non-polar solutes (acetone and benzene) dissolved in ambient water and supercritical water are investigated theoretically using a sequential quantum mechanics (QM)/molecular mechanics (MM) method which combines classical molecular dynamics simulations and QM/MM calculations. From the detailed analysis of the dependence of the QM region size and point charge background region size as well as the different functionals, it is found that the inclusion of the solvent molecules within the first solvation shell into the QM region to account for the exchange-correlation between a solute and neighboring solvent molecules is important for the highly accurate spectral shift calculations, especially vital for the non-polar solutes whose interactions with the solvents are dominated by the quantum dispersions. At the same time, sufficiently large surrounding partial charge region (r(cutoff) ≥15 A) as well as the functional corrections to describe the long-range dispersion-corrections are also essential for the study of the electronic excited states in condensed phase. Our calculated solvatochromic shift values and their density dependencies at ambient and high temperature conditions are found to be in good agreements with experimental observations. This indicates that sound theoretical studies of solvatochromic shift can be achieved provided that a reasonable computational scheme with sufficiently large N(water) (QM) and r(cutoff) values is implemented. We also find both of aqueous acetone and aqueous benzene under high temperatures present three distinctive regions: low-density gas-like region, supercritical region, and high-density liquid-like region. The plateau behavior of solvatochromic shift in the supercritical region can be ascribed to the solvent clustering around the solute, which is a fundamental phenomenon of supercritical fluids (SCFs). The density dependence of our calculated coordination number of the first solvation shell nicely reproduces the trend of spectral shift and verifies the solvent clustering phenomenon of SCFs and its relationship with SCF's physicochemical properties.

Abstract: The results of evaluating the individual hydrogen bond (H-bond) strength are expected to be helpful for the rational design of new strategies for molecular recognition or supramolecular assemblies. Unfortunately, there is few obvious and unambiguous means of evaluating the energy of a single H-bond within a multiple H-bonds system. We present a local analytic model, ABEEMσπ H-bond energy (HBE) model based on ab initio calculations (MP2) as benchmark, to directly and rapidly evaluate the individual HBE in situ in inter- and intramolecular multiple H-bonds system. This model describes the HBE as the sum of electrostatic and van der Waals (vdW) interactions which all depend upon the geometry and environment, and the ambient environment of H-bond in the model is accounted fairly. Thus, it can fairly consider the cooperative effect and secondary effect. The application range of ABEEMσπ HBE model is rather wide. This work has discussed the individual H-bond in DNA base pair and protein peptide dimers. The results indicate that the interactions among donor H atom, acceptor atom as well as those atoms connected to them with 1,2 or 1,3 relationships are all important for evaluating the HBE, although the interaction between the donor H atom and the acceptor atom is large. Furthermore, our model quantitatively indicates the polarization ability of N, O, and S in a new style, and gives the percentage of the polarization effect in HBE, which can not be given by fixed partial charge force field. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2012

Abstract: In the field of organic electronics, a central issue is to assess how the frontier electronic levels of two adjacent organic layers align with respect to one another at the interface. This alignment can be driven by the presence of a partial charge transfer and the formation of an interface dipole; it plays a key role for instance in determining the rates of exciton dissociation or exciton formation in organic solar cells or light-emitting diodes, respectively. Reliably modeling the processes taking place at these interfaces remains a challenge for the computational chemistry community. Here, we review our recent theoretical work on the influence of the choice of density functional theory (DFT) methodology on the description of the charge-transfer character in the ground state of TTF/TCNQ model complexes and interfaces. Starting with the electronic properties of the isolated TTF and TCNQ molecules and then considering the charge transfer and resulting interface dipole in TTF/TCNQ donor–acceptor stacks and bilayers, we examine the impact of the choice of DFT functional in describing the interfacial electronic structure. Finally, we employ computations based on periodic boundary conditions to highlight the impact of depolarization effects on the interfacial dipole moment.

Abstract: 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.

Abstract: A protein environment can affect the structure and charge distribution of substrate molecules. Here, the structure and partial charges were studied for different phosphorylated amino acid models in ...

Abstract: A continuum solvent model was tested for simulations of amide I′ IR spectra for a 40-residue subdomain of P22 viral coat protein in aqueous solution. Spectra obtained using DFT (BPW91/6-31G**) parameters for a reduced all-Ala representation of the protein were corrected by an electrostatic potential map obtained from the solvent cavity surface and AMBER99 side-chain atom partial charges. Various cavity sizes derived from van der Waals atomic radii with an added effective solvent radius up to 2.0 A were tested. The interplay of the side-chain and solvent electrostatic effects was investigated by considering the side chains and solvent separately as well as together. The sensitivity to side-chain conformational fluctuations and to the parametrization of Cβ group partial charges was also tested. Simulation results were compared to the experimental amide I′ spectra of P22 subdomain, including two 13C isotopically edited variants, as well as to the previous simulations based on the molecular dynamics trajector...