Fast fragments: the development of a parallel effective fragment potential method

The Effective Fragment Potential (EFP) method for solvation decreases the cost of a fully quantum mechanical calculation by dividing a chemical system into an ab initio region that contains the solute plus some number of solvent molecules, if desired, and an "effective fragment" region that contains the remaining solvent molecules. Interactions introduced with this fragment region (for example, Coulomb and polarization interactions) are added as one-electron terms to the total system Hamiltonian. As larger systems and dynamics are just starting to be studied with the EFP method, more needs to be done to decrease the calculation time of the method. This article considers parallelization of both the EFP fragment-fragment and mixed quantum mechanics (QM)-EFP interaction energy and gradient computation within the GAMESS suite of programs. The iteratively self-consistent polarization term is treated with a new algorithm that makes use of nonblocking communication to obtain better scalability. Results show that reasonable speedup is achieved with a variety of sizes of water clusters and number of processors.     

Noncovalent interactions in extended systems described by the effective fragment potential method: theory and application to nucleobase oligomers

The implementation of the effective fragment potential (EFP) method within the Q-CHEM electronic structure package is presented. The EFP method is used to study noncovalent π-π and hydrogen-bonding interactions in DNA strands. Since EFP is a computationally inexpensive alternative to high-level ab initio calculations, it is possible to go beyond the dimers of nucleic acid bases and to investigate the asymptotic behavior of different components of the total interaction energy. The calculations demonstrated that the dispersion energy is a leading component in π-stacked oligomers of all sizes. Exchange-repulsion energy also plays an important role. The contribution of polarization is small in these systems, whereas the magnitude of electrostatics varies. Pairwise fragment interactions (i.e., the sum of dimer binding energies) were found to be a good approximation for the oligomer energy.     

Theoretical study of the solvation of fluorine and chlorine anions by water

The solvation of fluoride and chloride anions (F(-) and Cl(-), respectively) by water has been studied using effective fragment potentials (EFPs) for the water molecules and ab initio quantum mechanics for the anions. In particular, the number of water molecules required to fully surround each anion has been investigated. Monte Carlo calculations have been used in an attempt to find the solvated system X(-)(H(2)O)(n) (X = F, Cl) with the lowest energy for each value of n. It is predicted that 18 water molecules are required to form a complete solvation shell around a Cl(-) anion, where "complete solvation" is interpreted as an ion that is completely surrounded by solvent molecules. Although fewer water molecules may fully solvate the Cl(-) anion, such structures are higher in energy than partially solvated molecules, up to n > or = 18. Calculations on the F(-) anion suggest that 15 water molecules are required for a complete solvation shell. The EFP predictions are in good agreement with the relative energies predicted by ab initio energy calculations at the EFP geometries.     

Implementation of the analytic energy gradient for the combined time-dependent density functional theory/effective fragment potential method: application to excited-state molecular dynamics simulations

Excited-state quantum mechanics/molecular mechanics molecular dynamics simulations are performed, to examine the solvent effects on the fluorescence spectra of aqueous formaldehyde. For that purpose, the analytical energy gradient has been derived and implemented for the linear-response time-dependent density functional theory (TDDFT) combined with the effective fragment potential (EFP) method. The EFP method is an efficient ab initio based polarizable model that describes the explicit solvent effects on electronic excitations, in the present work within a hybrid TDDFT/EFP scheme. The new method is applied to the excited-state MD of aqueous formaldehyde in the n-π* state. The calculated π*→n transition energy and solvatochromic shift are in good agreement with other theoretical results.     

Ab initio energies of nonconducting crystals by systematic fragmentation

A systematic method for approximating the ab initio electronic energy of molecules from the energies of molecular fragments has been adapted to estimate the total electronic energy of crystal lattices. The fragmentation method can be employed with any ab initio electronic structure method and allows optimization of the crystal structure based on ab initio gradients. The method is demonstrated on SiO(2) polymorphs using the Hartree-Fock approximation, second order Moller-Plesset perturbation theory, and the quadratic configuration interaction method with single and double excitations and triple excitations added perturbatively .     

On the perturbation of the H-bonding interaction in ethylene glycol clusters upon hydration

Ab initio and density functional methods have been employed to study the structure, stability, and spectral properties of various ethylene glycol (EG(m)) and ethylene glycol-water (EG(m)W(n)) (m = 1-3, n = 1-4) clusters. The effective fragment potential (EFP) approach was used to explore various possible EG(m)W(n) clusters. Calculated interaction energies of EG(m)W(n) clusters confirm that the hydrogen-bonding interaction between EG molecules is perturbed by the presence of water molecules and vice versa. Further, energy decomposition analysis shows that both electrostatic and polarization interactions predominantly contribute to the stability of these clusters. It was found from the same analysis that ethylene glycol-water interaction is predominant over the ethylene glycol-ethylene glycol and water-water interactions. Overall, the results clearly illustrate that the presence of water disrupts the ethylene glycol-ethylene glycol hydrogen bonds.     

Anion-pi interactions in cyanuric acids: a combined crystallographic and computational study

Several structures of pi complexes of isocyanuric acid and of several thio derivatives with anions have been computed by using high level ab initio calculations. The nature of the complexes has been studied by means of the method of molecular interaction potential with polarization (MIPp) and Bader's theory of atoms-in-molecules. These molecules form favorable complexes with anions and can be used as binding units for building receptors for the molecular recognition of anions. In several cases, the anion-pi interaction has been demonstrated experimentally by means of X-ray crystallography.     

Key role of the polarization anisotropy of water in modeling classical polarizable force fields

We have evaluated the extent to which classical polarizable force fields, based either on the chemical potential equalization principle or on distributed polarizabilities in the framework of the Sum of Interactions Between Fragments Ab initio computed (SIBFA), can reproduce the ab initio polarization energy and the dipole moment of three distinct water oligomers: bifurcated chains, transverse hydrogen-bonded chains, and longitudinal hydrogen-bonded chains of helical shape. To analyze the many-body polarization effect, chains of different size, i.e., from 2 to 12 water monomers, have been considered. Although the dipole moment is a well-defined quantity in both classical polarizable models and quantum mechanical methods, polarization energy can be defined unequivocally only in the former type of approaches. In this study we have used the Kitaura-Morokuma (KM) procedure. Although the KM approach is on the one hand known to overestimate the polarization energy for strongly interacting molecules, on the other hand it can account for the many-body polarization effectively, whereas some other procedures do not. Our data show that, if off-centered lone pair polarizabilities are explicitly represented, classical polarizable force fields can afford a close agreement with the ab initio results, both in terms of polarization energy and in terms of dipole moment.     

Polarization and charge-transfer effects in aqueous solution via ab initio QM/MM simulations

Combined ab initio quantum mechanical and molecular mechanical (QM/MM) simulations coupled with the block-localized wave function energy decomposition (BLW-ED) method have been conducted to study the solvation of two prototypical ionic systems, acetate and methylammonium ions in aqueous solution. Calculations reveal that the electronic polarization between the targeted solutes and water is the primary many-body effect, whereas the charge-transfer term only makes a small fraction of the total solute-solvent interaction energy. In particular, the polarization effect is dominated by the solvent (water) polarization.     

Implementation of dynamical nucleation theory effective fragment potentials method for modeling aerosol chemistry

In this work, the dynamical nucleation theory (DNT) model using the ab initio based effective fragment potential (EFP) is implemented for evaluating the evaporation rate constant and molecular properties of molecular clusters. Predicting the nucleation rates of aerosol particles in different chemical environments is a key step toward understanding the dynamics of complex aerosol chemistry. Therefore, molecular scale models of nanoclusters are required to understand the macroscopic nucleation process. On the basis of variational transition state theory, DNT provides an efficient approach to predict nucleation kinetics. While most DNT Monte Carlo simulations use analytic potentials to model critical sized clusters, or use ab initio potentials to model very small clusters, the DNTEFP Monte Carlo method presented here can treat up to critical sized clusters using the effective fragment potential (EFP), a rigorous nonempirical intermolecular model potential based on ab initio electronic structure theory calculations, improvable in a systematic manner. The DNTEFP method is applied to study the evaporation rates, energetics, and structure factors of multicomponent clusters containing water and isoprene. The most probable topology of the transition state characterizing the evaporation of one water molecule from a water hexamer at 243 K is predicted to be a conformer that contains six hydrogen bonds, with a topology that corresponds to two water molecules stacked on top of a quadrangular (H(2)O)(4) cluster. For the water hexamer in the presence of isoprene, an increase in the cluster size and a 3-fold increase in the evaporation rate are predicted relative to the reaction in which one water molecule evaporates from a water hexamer cluster.     

Application of a semi-empirical dispersion correction for modeling water clusters

The Grimme-D3 semi-empirical dispersion energy correction has been implemented for the original effective fragment potential for water (EFP1), and for systems that contain water molecules described by both correlated ab initio quantum mechanical (QM) molecules and EFP1. Binding energies obtained with these EFP1-D and QM/EFP1-D methods were tested using 27 benchmark species, including neutral, protonated, deprotonated, and auto-ionized water clusters and nine solute–water binary complexes. The EFP1-D and QM/EFP1-D binding energies are compared with those obtained using fully QM methods: second-order perturbation theory, and coupled cluster theory, CCSD(T), at the complete basis set (CBS) limit. The results show that the EFP1-D and QM/EFP1-D binding energies are in good agreement with CCSD(T)/CBS binding energies with a mean absolute error of 5.9 kcal/mol for water clusters and 0.8 kcal/mol for solute–water binary complexes. © 2018 Wiley Periodicals, Inc.     

The constrained space orbital variation analysis for periodic ab initio calculations

The constrained space orbital variation (CSOV) method for the analysis of the interaction energy has been implemented in the periodic ab initio CRYSTAL03 code. The method allows for the partition of the energy of two interacting chemical entities, represented in turn by periodic models, into contributions which account for electrostatic effects, mutual polarization and charge transfer. The implementation permits one to carry out the analysis both at the Hartree-Fock and density functional theory levels, where in the latter the most popular exchange-correlation functionals can be used. As an illustrating example, the analysis of the interaction between CO and the MgO (001) surface has been considered. As expected by the almost fully ionic character of the support, our periodic CSOV results, in general agree with those previously obtained using the embedded cluster approach, showing the reliability of the present implementation.     

Theoretical method for full ab initio calculation of DNA/RNA-ligand interaction energy

In this paper, we further develop the molecular fractionation with conjugate caps (MFCC) scheme for quantum mechanical computation of DNA-ligand interaction energy. We study three oligonuclear acid interaction systems: dinucleotide dCG/water, trinucleotide dCGT/water, and a Watson-Crick paired DNA segment, dCGT/dGCA. Using the basic MFCC approach, the nucleotide chains are cut at each phosphate group and a pair of conjugate caps (concaps) are inserted. Five cap molecules have been tested among which the dimethyl phosphate anion is proposed to be the standard concap for application. For each system, one-dimensional interaction potential curves are computed using the MFCC method and the calculated interaction energies are found to be in excellent agreement with corresponding results obtained from the full system ab initio calculations. The current study extends the application of the MFCC method to ab initio calculations for DNA- or RNA-ligand interaction energies.     

Analytic gradient and molecular dynamics simulations using the fragment molecular orbital method combined with effective potentials

The completely analytic energy gradients are derived and implemented for the two-body fragment molecular orbital (FMO2) method combined with the model core potentials (MCP) and effective fragment potentials (EFP). The many-body terms in EFP require solving coupled-perturbed Hartree-Fock equations, which are derived and implemented. The molecular dynamics (MD) simulations are performed using the FMO2/MCP method for the capped alanine decamer and with the FMO2/EFP method for the zwitterionic conformer of glycine tetramer immersed in the water layer of 6.0 Å (135 water molecules). The results of the MD simulations using the FMO2/EFP and FMO2/MCP gradients show that the total energy is conserved at the time steps less than 1 fs.     

VBEFP: a valence bond approach that incorporates effective fragment potential method

An ab initio explicit solvation valence bond (VB) method, called VBEFP, is presented. The VBEFP method is one type of QM/MM approach in which the QM part of system is treated within the ab initio valence bond scheme and the solvent water molecules are accounted by the effective fragment potential (EFP) method, which is a polarized force field approach developed by Gordon et al. (J. Chem. Phys. 1996, 105, 1968). This hybrid method enables one to take the first-solvation shell and heterogeneous solvation effects into account explicitly with VB wave function. Therefore, the nature of chemical bonding and the mechanism of chemical reactions with explicit solvent environments can be explored at the ab inito VB level. In this paper, the hydrated metal-ligand complexes [M(2+)L](H(2)O)(n) (M(2+): Mg(2+), Zn(2+); L: NH(3), CH(2)O) are studied by the VBEFP method. Resonance energy and bond order are computed, and the influence of the solvent coordination and hydrogen bonding to the metal-ligand bonding are explored in the paper.     

Li2B2的几何结构和垂直激发态光谱的量子化学研究

在ab initio DZP水平下，用能量梯度法对Li2B2的几何构型进行了优化，并用单、双激发组态相互作用（CISD）进行了垂直激发的和振子强度计算．结果表明：Li2B2（C2v）中存在着三个强度较大的跃迁，分别是从基态跃迁到31B2、11B1、41A1态．Li2B2（D2h）中存在着三个强度较大的跃迁，分别是从基态跃迁到11B2u、21B1u、31B2u态．这些强度较大的跃迁均为粒子穴跃迁．在我们能查阅的文献范围内，本工作是首次性的．     

Effective fragment potential study of the interaction of DNA bases

Hydrogen-bonded and stacked structures of adenine-thymine and guanine-cytosine nucleotide base pairs, along with their methylated analogues, are examined with the ab inito based general effective fragment potential (EFP2) method. A comparison of coupled cluster with single, double, and perturbative triple (CCSD(T)) energies is presented, along with an EFP2 energy decomposition to illustrate the components of the interaction energy.     

Low-energy electron scattering with the purine bases of DNA/RNA using the R-matrix method

R-matrix calculations on electron collisions with the purine bases found in DNA and RNA (i.e., adenine and guanine) are presented. Resonant anion states of these systems are identified by employing different approximation levels of ab initio theoretical methods, such as the static exchange, the static exchange plus polarization, and the close-coupling methods. The results are compared with other available calculations and experiments. All of these ab initio approximations, which we refer to as a scattering "model," give four shape resonances of (2)A' (π) symmetry within the energy range of 10 eV for both molecules. For adenine, the most sophisticated method, the close-coupling model, gives two very narrow (2)A' (σ) symmetry Feshbach-type resonances at energies above 5 eV. Quantitative results for the total elastic and electronic excitation cross sections are also presented.     

Molecular tailoring approach for geometry optimization of large molecules: energy evaluation and parallelization strategies

A linear-scaling scheme for estimating the electronic energy, gradients, and Hessian of a large molecule at ab initio level of theory based on fragment set cardinality is presented. With this proposition, a general, cardinality-guided molecular tailoring approach (CG-MTA) for ab initio geometry optimization of large molecules is implemented. The method employs energy gradients extracted from fragment wave functions, enabling computations otherwise impractical on PC hardware. Further, the method is readily amenable to large scale coarse-grain parallelization with minimal communication among nodes, resulting in a near-linear speedup. CG-MTA is applied for density-functional-theory-based geometry optimization of a variety of molecules including alpha-tocopherol, taxol, gamma-cyclodextrin, and two conformations of polyglycine. In the tests performed, energy and gradient estimates obtained from CG-MTA during optimization runs show an excellent agreement with those obtained from actual computation. Accuracy of the Hessian obtained employing CG-MTA provides good hope for the application of Hessian-based geometry optimization to large molecules.