Water−Benzene Interactions: An Effective Fragment Potential and Correlated Quantum Chemistry Study

Structures and binding in small water−benzene complexes (1−8 water molecules and 1−2 benzene molecules) are studied using the general effective fragment potential (EFP) method. The lowest energy conformers of the clusters were found using a Monte Carlo technique. The binding energies in the smallest clusters (dimers, trimers, and tetramers) were also evaluated with second order perturbation theory (MP2) and coupled cluster theory (CCSD(T)). The EFP method accurately predicts structures and binding energies in the water−benzene complexes. Benzene is polarizable and consequently participates in hydrogen bond networking of water. Since the water−benzene interactions are only slightly weaker than water−water interactions, structures with different numbers of water−water, benzene−water, and benzene−benzene bonds often have very similar binding energies. This is a challenge for computational methods

Deconstructing Cation-pi Interactions: Understanding the Binding Energies Involved with Metal and Aromatic Amino Acid Residues

The Effective Fragment Potential (EFP) method is a computationally efficient technique for describing non-covalent interactions, such as hydrogen bonding and van der Waals forces. Cation-pi interactions are a type of non-covalent interactions and are thought to be important in biological processes, such as permittivity of ion channels. The goal of our work is to establish that the EFP method reliably describes the strength, directionality, and composition of cation-pi interactions. Optimal geometries were found for a series of biologically relevant cations (K+, Li+, Na+, Ca2+, and Mg2+) and aryl moieties appearing as residue groups in natural amino acids (3-methyl-1h-indole, p-cresol, phenylalanine, toluene, and tyrosine) using the MP2 level of theory and the cc-pVTZ basis set. The cation was then displaced along a line normal to the aromatic compound with EFP calculations performed for every 0.2 angstroms between 1 and 7 angstroms along the trajectory. The obtained binding energies and relative energy components were compared against Symmetry-Adapted Pertubation Theory (SAPT) calculations at 0.4 angstrom increments along the same trajectory. SAPT has been previously used to test the accuracy of EFP for a variety of systems. Preliminary results indicate that the EFP method accurately predicts equilibrium geometries in cation-pi complexes. The low computational cost of EFP against SAPT provides promise in expansion on the research of cation-pi interactions to larger systems using EFP

Effective Fragment Potentials for Flexible Molecules: Transferability of Parameters and Amino Acid Database

An accurate but efficient description of noncovalent interactions is a key to predictive modeling of biological and materials systems. The effective fragment potential (EFP) is an ab initio-based force field that provides a physically meaningful decomposition of noncovalent interactions of a molecular system into Coulomb, polarization, dispersion, and exchange-repulsion components. An EFP simulation protocol consists of two steps, preparing parameters for molecular fragments by a series of ab initio calculations on each individual fragment, and calculation of interaction energy and properties of a total molecular system based on the prepared parameters. As the fragment parameters (distributed multipoles, polarizabilities, localized wave function, etc.) depend on a fragment geometry, straightforward application of the EFP method requires recomputing parameters of each fragment if its geometry changes, for example, during thermal fluctuations of a molecular system. Thus, recomputing fragment parameters can easily become both computational and human bottlenecks and lead to a loss of efficiency of a simulation protocol. An alternative approach, in which fragment parameters are adjusted to different fragment geometries, referred to as “flexible EFP”, is explored here. The parameter adjustment is based on translations and rotations of local coordinate frames associated with fragment atoms. The protocol is validated on extensive benchmark of amino acid dimers extracted from molecular dynamics snapshots of a cryptochrome protein. A parameter database for standard amino acids is developed to automate flexible EFP simulations in proteins. To demonstrate applicability of flexible EFP in large-scale protein simulations, binding energies and vertical electron ionization and electron attachment energies of a lumiflavin chromophore of the cryptochrome protein are computed. The results obtained with flexible EFP are in a close agreement with the standard EFP procedure but provide a significant reduction in computational cost

The Dispersion Interaction between Quantum Mechanics and Effective Fragment Potential Molecules

A method for calculating the dispersion energy between molecules modeled with the general effective fragment potential (EFP2) method and those modeled using a full quantum mechanics (QM) method, e.g., Hartree-Fock (HF) or second-order perturbation theory, is presented. C6dispersion coefficients are calculated for pairs of orbitals using dynamic polarizabilities from the EFP2 portion, and dipole integrals and orbital energies from the QM portion of the system. Dividing by the sixth power of the distance between localized molecular orbital centroids yields the first term in the commonly employed London series expansion. A C 8 term is estimated from the C 6 term to achieve closer agreement with symmetry adapted perturbation theory values. Two damping functions for the dispersion energy are evaluated. By using terms that are already computed during an ordinary HF or EFP2 calculation, the new method enables accurate and extremely rapid evaluation of the dispersioninteraction between EFP2 and QM molecules

Software for the frontiers of quantum chemistry:An overview of developments in the Q-Chem 5 package

This article summarizes technical advances contained in the fifth major release of the Q-Chem quantum chemistry program package, covering developments since 2015. A comprehensive library of exchange–correlation functionals, along with a suite of correlated many-body methods, continues to be a hallmark of the Q-Chem software. The many-body methods include novel variants of both coupled-cluster and configuration-interaction approaches along with methods based on the algebraic diagrammatic construction and variational reduced density-matrix methods. Methods highlighted in Q-Chem 5 include a suite of tools for modeling core-level spectroscopy, methods for describing metastable resonances, methods for computing vibronic spectra, the nuclear–electronic orbital method, and several different energy decomposition analysis techniques. High-performance capabilities including multithreaded parallelism and support for calculations on graphics processing units are described. Q-Chem boasts a community of well over 100 active academic developers, and the continuing evolution of the software is supported by an “open teamware” model and an increasingly modular design