Drude Polarizable Lipid Force Field with Explicit Treatment of Long-Range Dispersion: Parametrization and Validation for Saturated and Monounsaturated Zwitterionic Lipids.

Accurate empirical force fields of lipid molecules are a critical component of molecular dynamics simulation studies aimed at investigating properties of monolayers, bilayers, micelles, vesicles, and liposomes, as well as heterogeneous systems, such as protein-membrane complexes, bacterial cell walls, and more. While the majority of lipid force field-based simulations have been performed using pairwise-additive nonpolarizable models, advances have been made in the development of the polarizable force field based on the classical Drude oscillator model. In the present study, we undertake further optimization of the Drude lipid force field, termed Drude2023, including improved treatment of the phosphate and glycerol linker region of PC and PE headgroups, additional optimization of the alkene group in monounsaturated lipids, and inclusion of long-range Lennard-Jones interactions using the particle-mesh Ewald method.

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.

Elusive Intermediate State Key in the Conversion of ATP Hydrolysis into Useful Work Driving the Ca Pump SERCA.

A key event in the ATP-driven transport cycle of the calcium pump sarco/endoplasmic reticulum Ca-ATPase (SERCA) occurs when autophosphorylation of the pump with two bound ions Ca triggers a large conformational change that opens a gate on the luminal side of the membrane allowing the release of the ions. It is believed that this conformational transition proceeds through a two-step mechanism, with an initial rearrangement of the three cytoplasmic domains of the pump responsible for ATP binding and hydrolysis followed by the opening of the gate toward the luminal side in the transmembrane region. Here, molecular dynamics computation of the free energy landscapes associated with this transition show how, in response to phosphorylation, the cytoplasmic domains are partially reconfigured into an intermediate state on the path toward the E2 state with a closed luminal gate.

Energy Decomposition Analysis for Interactions of Radicals: Theory and Implementation at the MP2 Level with Application to Hydration of Halogenated Benzene Cations and Complexes between CO· and Pyridine and Imidazole.

To study intermolecular interactions involving radicals at the correlated level, the energy decomposition analysis scheme for second-order Mo̷ller-Plesset perturbation theory based on absolutely localized molecular orbitals (ALMO-MP2-EDA) is generalized to unrestricted and restricted open-shell MP2. The benefit of restricted open-shell MP2 is that it can provide accurate binding energies for radical complexes where density functional theory can be error-prone due to delocalization errors. As a model application, the open-shell ALMO-MP2-EDA is applied to study the first solvation step of halogenated benzene radical cations, where both halogen- and hydrogen-bonded isomers are possible.

Reduced Free Energy Perturbation/Hamiltonian Replica Exchange Molecular Dynamics Method with Unbiased Alchemical Thermodynamic Axis.

Replica-exchange molecular dynamics (REMD) has been proven to efficiently improve the convergence of free-energy perturbation (FEP) calculations involving considerable reorganization of their surrounding. We previously introduced the FEP/(λ,H)-REMD algorithm for ligand binding, in which replicas along the alchemical thermodynamic coupling axis λ were expanded as a series of Hamiltonian boosted replicas along a second axis to form a two-dimensional replica-exchange exchange map [Jiang, W.; Roux, B.

Understanding Non-Covalent Interactions: Correlated Energy Decomposition Analysis and Applications to Halogen Bonding.

Non-covalent interactions play a primordial role in chemistry. Beyond their quantification, the detailed understanding of their physical processes is necessary to rationalize chemical trends and improve designs of chemical systems. Energy decomposition analyses allow detailed insight into non-covalent interactions by extracting electrostatics, Pauli repulsion, polarization, dispersion and charge transfer components from interaction energies.

Characterizing the interplay of Pauli repulsion, electrostatics, dispersion and charge transfer in halogen bonding with energy decomposition analysis.

The halogen bond is a class of non-covalent interaction that has attracted considerable attention recently. A widespread theory for describing them is the σ-hole concept, which predicts that the strength of the interaction is proportional to the size of the σ-hole, a region of positive electrostatic potential opposite a σ bond. Previous work shows that in the case of CXI, with X equal to F, Cl, Br, and I, the σ-hole trend is exactly opposite to the trend in binding energy with common electron pair donors.

Efficient Implementation of Energy Decomposition Analysis for Second-Order Møller-Plesset Perturbation Theory and Application to Anion-π Interactions.

Energy decomposition analysis (EDA) is a widely used tool for extracting physical and chemical insights from electronic structure calculations of intermolecular interactions, as well as for the development of advanced force fields for describing those interactions. Recently, the absolutely localized molecular orbital (ALMO) EDA has been extended from the self-consistent field level to the second-order Møller-Plesset (MP2) theory level. This paper reports an efficient implementation of the MP2 ALMO-EDA that scales optimally, employs the resolution of the identity (RI) approximation for post-SCF matrix elements, and is shared-memory parallel.

An energy decomposition analysis for second-order Møller-Plesset perturbation theory based on absolutely localized molecular orbitals.

An energy decomposition analysis (EDA) of intermolecular interactions is proposed for second-order Møller-Plesset perturbation theory (MP2) based on absolutely localized molecular orbitals (ALMOs), as an extension to a previous ALMO-based EDA for self-consistent field methods. It decomposes the canonical MP2 binding energy by dividing the double excitations that contribute to the MP2 wave function into classes based on how the excitations involve different molecules. The MP2 contribution to the binding energy is decomposed into four components: frozen interaction, polarization, charge transfer, and dispersion.

Electrostatic Domination of the Effect of Electron Correlation in Intermolecular Interactions.

The electron-electron correlation energy is negative, and attractive dispersion interactions are entirely a correlation effect; therefore, the contribution of correlation to intermolecular binding is commonly assumed to be negative, or binding in nature. However, there are many cases where the long-range correlation binding energy is positive, with certain geometries of the water dimer as a prominent example. Geometries with dipoles misaligned can also have an electrostatically dominated, though negative, long-range correlation binding.