5,999 results match your criteria Journal of chemical theory and computation[Journal]


A Variational Relativistic Two-Component Complete Active Space Self-Consistent Field Method.

J Chem Theory Comput 2019 Apr 24. Epub 2019 Apr 24.

The accurate description of the electronic structure of transition metals and their compounds can be complicated by both the large number of close-lying states that often have multi-configurational nature in addition to significant relativistic effects. In order to address these challenges we present a two-component complete-active-space self-consistent field method that includes scalar relativistic effects and one-electron spin-orbit coupling during the self-consistent wave function optimization procedure. These relativistic effects are included via an "exact two-component" transformation of the solution of the one-electron modified Dirac equation. Read More

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http://dx.doi.org/10.1021/acs.jctc.9b00011DOI Listing

Atomistic modeling of the ABL kinase regulation by allosteric modulators using structural perturbation analysis and community-based network reconstruction of allosteric communications.

J Chem Theory Comput 2019 Apr 24. Epub 2019 Apr 24.

In this work, we have examined the molecular mechanisms of allosteric regulation of the ABL tyrosine kinase at the atomic level. Atomistic modeling of the ABL complexes with a panel of allosteric modulators has been performed using a combination of molecular dynamics simulations, structural residue perturbation scanning and a novel community analysis of the residue interaction networks. Our results have indicated that allosteric inhibitors and activators may exert a differential control on allosteric signaling between the kinase binding sites and functional regions. Read More

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http://dx.doi.org/10.1021/acs.jctc.9b00119DOI Listing

Non-orthogonal configuration interaction with single substitutions for core-excited states: An extension to doublet radicals.

J Chem Theory Comput 2019 Apr 24. Epub 2019 Apr 24.

In this paper we present an open-shell extension of the non-orthogonal configuration interaction singles (NOCIS) method for the calculation of core-excited states, intended for peak assignment in XAS spectra of doublet radicals. This extension requires the consideration of additional configurations due to the singly-occupied open-shell orbital, and the addition of essential orbital relaxation effects is found to provide a significant improvement on standard CIS, while maintaining the desirable properties of spin-purity, variationality, and size-consistency. We apply this method to the calculation of core-excitations for several open-shell molecules and demonstrate that it performs competitively with other available methods, despite lack of dynamic correlation. Read More

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http://dx.doi.org/10.1021/acs.jctc.8b01259DOI Listing

Improving the numerical stability of the NAST force field for RNA simulations.

J Chem Theory Comput 2019 Apr 19. Epub 2019 Apr 19.

The NAST force field is a popular tool for modelling RNA and is typical of low-resolution approaches. Unfortunately, some combinations of bond and dihedral angles can reach cliffs on the energy landscape which lead to numerical disasters. We describe changes to the formulation (NAST improved - NASTI) which smooth the dihedral energy term when neighbouring angles become flat. Read More

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http://pubs.acs.org/doi/10.1021/acs.jctc.9b00089
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http://dx.doi.org/10.1021/acs.jctc.9b00089DOI Listing
April 2019
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Interactions of Water and Alkanes: Modifying Additive Force Fields to Account for Polarization Effects.

J Chem Theory Comput 2019 Apr 19. Epub 2019 Apr 19.

Atomistic biomolecular simulations predominantly utilize additive force fields (FF), where the electrostatic potential is modeled by fixed point charges. Among other consequences, the lack of polarizability in these models undermines the balance of hydrophilic/hydrophobic non-bonded interactions. Simulations of water/alkane systems using the TIP3P water model and CHARMM36 parameters reveal a 1 kcal/mol over-estimate of the experimental transfer free energy of water to hexadecane; more recent optimized water models (SPC/E, TIP4P/2005, TIP4P-Ew, TIP3P-FB, TIP4P-FB, OPC, TIP4P-D) overestimate this transfer free energy by approximately 2 kcal/mol. Read More

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http://dx.doi.org/10.1021/acs.jctc.9b00016DOI Listing

Statistical uncertainty analysis for small-sample, high log-variance data: Cautions for bootstrapping and Bayesian bootstrapping.

J Chem Theory Comput 2019 Apr 19. Epub 2019 Apr 19.

Recent advances in molecular simulations allow the evaluation of previously unattainable observables, such as rate constants for protein folding. However, these calculations are usually computationally expensive and even significant computing resources may result in a small number of independent estimates spread over many orders of magnitude. Such small-sample, high "log-variance" data are not readily amenable to analysis using the standard uncertainty (i. Read More

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http://dx.doi.org/10.1021/acs.jctc.9b00015DOI Listing

Adaptive dimensional decoupling for compression of quantum nuclear wavefunctions and efficient potential energy surface representations through tensor network decomposition.

J Chem Theory Comput 2019 Apr 19. Epub 2019 Apr 19.

We present an approach to reduce the computational complexity and storage pertaining to quantum nuclear wavefunctions and potential energy surfaces. The method utilizes tensor net- works implemented through sequential singular value decompositions. Two specific forms of tensor networks are considered to adaptively compress the data in multi-dimensional quantum nuclear wavefunctions and potential energy surfaces. Read More

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http://pubs.acs.org/doi/10.1021/acs.jctc.8b01113
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http://dx.doi.org/10.1021/acs.jctc.8b01113DOI Listing
April 2019
2 Reads

Modeling the structural and thermal properties of loaded metal-organic frameworks. An interplay of quantum and anharmonic fluctuations.

J Chem Theory Comput 2019 Apr 19. Epub 2019 Apr 19.

Metal-organic frameworks show both fundamental interest and great promise for applications in adsorption-based technologies, such as the separation and storage of gases. The flexibility and complexity of the molecular scaffold poses a considerable challenge to atomistic modeling, especially when also considering the presence of guest molecules. We investigate the role played by quantum and anharmonic fluctuations in the archetypical case of MOF-5, comparing the material at various levels of methane loading. Read More

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http://dx.doi.org/10.1021/acs.jctc.8b01297DOI Listing
April 2019
1 Read

Koopmans meets Bethe-Salpeter: Excitonic optical spectra from GW-free simulations.

J Chem Theory Comput 2019 Apr 18. Epub 2019 Apr 18.

The Bethe-Salpeter Equation (BSE) can be applied to compute from first-principles optical spectra that include the effects of screened electron-hole interactions. As input, BSE calculations require single-particle states, quasiparticle energy levels and the screened Coulomb interaction, which are typically obtained with many-body perturbation theory, whose cost limits the scope of possible applications. This work tries to address this practical limitation, instead deriving spectral energies from Koopmans-compliant functionals and introducing a new methodology for handling the screened Coulomb interaction. Read More

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http://pubs.acs.org/doi/10.1021/acs.jctc.8b01271
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http://dx.doi.org/10.1021/acs.jctc.8b01271DOI Listing
April 2019
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The Fragment Molecular Orbital Method Based on Long-range Corrected Density-Functional Tight-Binding.

J Chem Theory Comput 2019 Apr 18. Epub 2019 Apr 18.

The presently available linear scaling approaches to density-functional tight-binding (DFTB) based on the fragment molecular orbital (FMO) method are severely impacted by the problem of artificial charge transfer due to the self-interaction error (SIE), hampering the simulation of zwitterionic systems such as biopolymers or ionic liquids. We here report an extension of FMO-DFTB where we included a long-range corrected (LC) functional designed to mitigate the DFTB SIE, called the FMO-LC-DFTB method, resulting in a robust method which succeeds in simulating zwitterionic systems. Both energy and analytic gradient are developed for the gas phase and the polarizable continuum model of solvation. Read More

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http://dx.doi.org/10.1021/acs.jctc.9b00108DOI Listing

The Three-Legged Tree Tensor Networks with SU(2)- and molecular point group symmetry.

J Chem Theory Comput 2019 Apr 18. Epub 2019 Apr 18.

We extend the three-legged tree tensor network state (T3NS) [J. Chem. Theory Comput. Read More

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http://pubs.acs.org/doi/10.1021/acs.jctc.9b00071
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http://dx.doi.org/10.1021/acs.jctc.9b00071DOI Listing
April 2019
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MiMiC: A Novel Framework for Multiscale Modeling in Computational Chemistry.

J Chem Theory Comput 2019 Apr 18. Epub 2019 Apr 18.

We present a flexible and efficient framework for multiscale modeling in computational chemistry (MiMiC). It is based on a multiple-program multiple-data (MPMD) model with loosely coupled programs. Fast data exchange between programs is achieved through the use of MPI intercommunicators. Read More

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http://dx.doi.org/10.1021/acs.jctc.9b00093DOI Listing

Affordable membrane permeability calculations: Permeation of short-chain alcohols through pure-lipid bilayers and a mammalian cell membrane.

J Chem Theory Comput 2019 Apr 18. Epub 2019 Apr 18.

Determination of membrane permeability to small molecules from first principles represents a promising approach for screening lead compounds according to their permeation properties upstream in the drug discovery process and prior to their synthesis. Theoretical investigation of permeation events requires, at its core, a molecular model of the membrane, and the choice of this model impacts not only the predicted permeability, but also its relation to the experimental measurements commonly performed in pharmaceutical settings with a variety of cell lines capable of mimicking intestinal passive permeation. Homogeneous single-lipid bilayers have traditionally been utilized in computer simulations of membrane permeability predictions due to the ease of sampling all the relevant configurations, as well as the availability of parameters for a range of components of the biological membrane. Read More

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http://dx.doi.org/10.1021/acs.jctc.9b00022DOI Listing

Cosolvent-enhanced Sampling and Unbiased Identification of Cryptic Pockets Suitable for Structure-based Drug Design.

J Chem Theory Comput 2019 Apr 18. Epub 2019 Apr 18.

Modulating protein activity with small molecules binding to cryptic pockets offers great opportunities to overcome hurdles in drug design. Cryptic sites are atypical binding sites in proteins that are closed in the absence of a stabilizing ligand and are thus inherently difficult to identify. Many studies have proposed methods to predict cryptic sites. Read More

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http://dx.doi.org/10.1021/acs.jctc.8b01295DOI Listing

Half-Projected σ Self-Consistent Field For Electronic Excited States.

J Chem Theory Comput 2019 Apr 25. Epub 2019 Apr 25.

Department of Chemistry , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States.

Fully self-consistent mean-field solutions of electronic excited states have been much less accessible compared to ground state solutions (e.g., Hartree-Fock). Read More

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http://pubs.acs.org/doi/10.1021/acs.jctc.8b01224
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http://dx.doi.org/10.1021/acs.jctc.8b01224DOI Listing
April 2019
4 Reads

metaFALCON: A program package for automatic sampling of conical intersection seams using multistate metadynamics.

J Chem Theory Comput 2019 Apr 17. Epub 2019 Apr 17.

The multistate metadynamics for automatic exploration of conical intersection seams and systematic location of minimum energy crossing points in molecular sys- tems and its implementation into the software package metaFALCON is presented. Based on a locally modified energy gap between two Born-Oppenheimer electronic states as a collective variable, multistate metadynamics trajectories are driven towards an intersection point starting from an arbitrary ground state geometry and are subse- quently forced to explore the conical intersection seam landscape. For this purpose, an additional collective variable capable of distinguishing structures within the seam needs to be defined and an additional bias is introduced into the off-diagonal elements of an extended (multistate) electronic Hamiltonian. Read More

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http://dx.doi.org/10.1021/acs.jctc.9b00029DOI Listing

Low-Lying Electromeric States in Chloro-Ligated Iron(IV)-Oxo Porphyrin as a Model for Compound I, Studied with Second-Order Perturbation Theory Based on Density Matrix Renormalization Group.

J Chem Theory Comput 2019 Apr 17. Epub 2019 Apr 17.

Employing second-order perturbation theory based on density matrix renormalization group (DMRG-CASPT2), this work aims at providing a quantitative description of the spin state energetics of a chloro-ligated iron(IV)-oxo porphyrin as a model for the Cytochromes P450 active species, also known as compound I (Cpd I). We explored DMRG-CASPT2 to its full extent with an extensive active space (up to 31 active orbitals) as well as a large number renormalized states m (up to 10000). Different flavours of DMRG-CASPT2, using either the costly exact 4-particle reduced density matrix (4-RDM) or the cheaper cumulant approximated 4-RDM (cu(4)), were analyzed. Read More

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http://dx.doi.org/10.1021/acs.jctc.9b00166DOI Listing

On Obtaining Boltzmann-Distributed Configurational Ensembles from Expanded Ensemble Simulations with Fast State Mixing.

J Chem Theory Comput 2019 Apr 22. Epub 2019 Apr 22.

Theoretical Chemistry , Ruhr University Bochum , D-44780 Bochum , Germany.

In Expanded Ensemble (EXE) or Simulated Tempering simulations, the system's (effective) temperature is frequently updated to enhance configurational sampling. We investigated how short the EXE state update interval τ can become before too frequent updates impede Boltzmann sampling. Simulating alanine dipeptide in explicit water, we show that a hybrid MC/MD integrator reliably yields Boltzmann-distributed configurations regardless of τ. Read More

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http://dx.doi.org/10.1021/acs.jctc.9b00100DOI Listing

Parallel multi-stream training of high-dimensional neural network potentials.

J Chem Theory Comput 2019 Apr 17. Epub 2019 Apr 17.

Over the past years high-dimensional neural network potentials (HDNNPs), fitted to accurately reproduce ab initio potential energy surfaces, have become a powerful tool in chemistry, physics and materials science. Here, we focus on the training of the neural networks that lies at the heart of the HDNNP method. We present an efficient approach for optimizing the weight parameters of the neural network via multi-stream Kalman filtering, using potential energies and forces as reference data. Read More

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http://pubs.acs.org/doi/10.1021/acs.jctc.8b01092
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http://dx.doi.org/10.1021/acs.jctc.8b01092DOI Listing
April 2019
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Transferability of local density assisted implicit solvation models for homogeneous fluid mixtures.

J Chem Theory Comput 2019 Apr 17. Epub 2019 Apr 17.

The application of bottom-up coarse grained (CG) models to study the equilibrium mixing behavior of liquids is rather challenging, since these models can be significantly influenced by the density or the concentration of the state chosen during parametrization. This dependency leads to low transferability in density/concentration space and has been one of the major limitations in bottom-up coarse graining. Recent approaches proposed to tackle this shortcoming range from the addition of thermodynamic constraints, to an extended ensemble parametrization, to the addition of supplementary terms to the system's Hamiltonian. Read More

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http://pubs.acs.org/doi/10.1021/acs.jctc.8b01170
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http://dx.doi.org/10.1021/acs.jctc.8b01170DOI Listing
April 2019
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Spatially-Decomposed Free Energy of Solvation Based on the Endpoint Density-Functional Method.

J Chem Theory Comput 2019 Apr 16. Epub 2019 Apr 16.

Center for Biophysics and Computational Biology, Department of Chemistry, and Institute for Computational Molecular Science , Temple University , Philadelphia , Pennsylvania 19122 , United States.

A spatially resolved version of the density-functional method for solvation thermodynamics is presented by extending the free-energy functional previously established in the one-dimensional, energy representation and formulating a new expression in a mixed four-dimensional representation (three dimensions for position and one dimension for energy). The space was further divided into a set of discrete regions with respect to the relative position of a solvent molecule from the solute, and the spatially decomposed energetics of solvation were analyzed for small molecules with a methyl, amine, or hydroxyl group and alanine dipeptide in solvent water. It was observed that the density of the solvation free energy is weakly dependent on the solute site in the excluded-volume region and is distinctively favorable in the first shells of the solute atoms that can readily form hydrogen bonds with water. Read More

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http://dx.doi.org/10.1021/acs.jctc.8b01309DOI Listing

Quantifying the plasmonic character of optical excitations in a molecular J-aggregate.

J Chem Theory Comput 2019 Apr 15. Epub 2019 Apr 15.

The definition of plasmon at the microscopic scale is far from being understood. Yet, it is very important to recognize plasmonic features in optical excitations, as they can inspire new applications and trigger new discoveries by analogy with the rich phenomenology of metal nanoparticle plasmons. Recently, the concepts of plasmonicity index and the generalized plasmonicity index (GPI) have been devised as computational tools to quantify the plasmonic nature of optical excitations. Read More

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http://dx.doi.org/10.1021/acs.jctc.9b00220DOI Listing
April 2019
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Formulation and Implementation of the Spin-Restricted Ensemble-Referenced Kohn-Sham Method in the Context of the Density Functional Tight Binding Approach.

J Chem Theory Comput 2019 Apr 24. Epub 2019 Apr 24.

Department of Chemistry, School of Natural Science , Ulsan National Institute of Science and Technology (UNIST) , 50 UNIST-gil , Ulsan 44919 , Republic of Korea.

The spin-restricted ensemble-referenced Kohn-Sham (REKS) method and its state-interaction state-averaged variant (SI-SA-REKS, or SSR) provide computational platform for seamless inclusion of multireference effects into the density functional calculations. The SSR method enables an accurate calculation of the vertical excitation energies for the molecules with multireference ground states and describes conical intersections between the ground and excited states with the accuracy matching the most sophisticated ab initio multireference wave function methods. In this work, the SSR method is formulated and implemented in the context of the long-range corrected density functional tight binding (LC-DFTB) approach. Read More

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http://pubs.acs.org/doi/10.1021/acs.jctc.9b00132
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http://dx.doi.org/10.1021/acs.jctc.9b00132DOI Listing
April 2019
4 Reads

Exciton-Phonon Interaction Model for Singlet Fission in Prototypical Molecular Crystals.

J Chem Theory Comput 2019 Apr 22. Epub 2019 Apr 22.

School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , China.

In singlet fission (SF), a spin-conserving splitting of one singlet exciton into two triplet excitation states, the transition between localized electronic states can be controlled and modulated by delocalized lattice phonons. In this work, we built an exciton-phonon (ex-ph) interaction model accounting local electronic states coupled with both local molecular vibrations and low frequency intermolecular phonon modes for SF in crystalline tetracene and rubrene. On the basis of the calculated electronic couplings at the equilibrium structure of the molecular dimer, a superexchange path for SF was found for tetracene while couplings between the triplet pair (TT) state and other diabatic states are zero for rubrene due to the high symmetry. Read More

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http://pubs.acs.org/doi/10.1021/acs.jctc.9b00122
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http://dx.doi.org/10.1021/acs.jctc.9b00122DOI Listing
April 2019
3 Reads

Improved DFT Adsorption Energies with Semiempirical Dispersion Corrections.

J Chem Theory Comput 2019 Apr 24. Epub 2019 Apr 24.

Institute of Theoretical Chemistry , Ulm University , 89069 Ulm , Germany.

Over the past years, density functional theory (DFT) became a widely approved and successful method for calculating properties of various materials and molecules. Especially suited for systems with delocalized electrons like metals, the efficient treatment of the van der Waals interaction remained a problem for DFT functionals within the generalized gradient approximation (GGA). Combining Grimme's D3 correction with the RPBE functional and using a previously published data set, we show that this yields a functional that is well-suited for an accurate and balanced description of adsorption energies. Read More

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http://dx.doi.org/10.1021/acs.jctc.9b00035DOI Listing

Performance of Semilocal Kinetic Energy Functionals for Orbital-Free Density Functional Theory.

J Chem Theory Comput 2019 Apr 19. Epub 2019 Apr 19.

Center for Biomolecular Nanotechnologies @UNILE , Istituto Italiano di Tecnologia , Via Barsanti , I-73010 Arnesano , Italy.

We assess several generalized gradient approximations (GGAs) and Laplacian-level meta-GGAs (LL-MGGA) kinetic energy (KE) functionals for orbital-free density functional theory calculations of bulk metals and semiconductors, considering equilibrium distances, bulk moduli, total and kinetic energies, and the electron densities. We also considered the effects of the pseudopotentials, the vacancy formation energies, and the bond lengths of molecular dimers. We found that LL-MGGA KE functionals are distinctively superior to GGA functionals, showing the importance of the Laplacian of the density in the functional construction. Read More

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http://dx.doi.org/10.1021/acs.jctc.9b00183DOI Listing

A new and efficient equation-of-motion coupled-cluster framework for core-excited and core-ionized states.

J Chem Theory Comput 2019 Apr 9. Epub 2019 Apr 9.

We present a fully analytical implementation of the core-valence separation (CVS) scheme for the equation-of-motion (EOM) coupled-cluster singles and doubles (CCSD) method for calculations of core-level states. Inspired by the CVS idea as originally formulated by Cederbaum, Domcke and Schirmer, pure valence excitations are excluded from the EOM target space and the frozen-core approximation is imposed on the reference-state amplitudes and multipliers. This yields an efficient, robust, practical, and numerically balanced EOM-CCSD framework for calculations of excitation and ionization energies as well as state and transition properties (e. Read More

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http://dx.doi.org/10.1021/acs.jctc.9b00039DOI Listing
April 2019
3 Reads

Assessment of Multi-Scale Approaches for Computing UV-Vis Spectra in Condensed Phases: Toward an Effective yet Reliable Integration of Variational and Perturbative QM/MM Approaches.

J Chem Theory Comput 2019 Apr 17. Epub 2019 Apr 17.

Scuola Normale Superiore di Pisa , Piazza dei Cavalieri 7 , I-56126 Pisa , Italy.

Computational simulation of UV/vis spectra in condensed phases can be performed starting from converged molecular dynamics (MD) simulations and then performing quantum mechanical/molecular mechanical (QM/MM) computations for a statistically significant number of snapshots. However, the need of variational solutions (e.g. Read More

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http://dx.doi.org/10.1021/acs.jctc.9b00120DOI Listing
April 2019
1 Read

Approximate Green's Function Coupled Cluster Method Employing Effective Dimension Reduction.

J Chem Theory Comput 2019 Apr 16. Epub 2019 Apr 16.

Computational Research Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States.

The Green's function coupled cluster (GFCC) method, originally proposed in the early 1990s, is a powerful many-body tool for computing and analyzing the electronic structure of molecular and periodic systems, especially when electrons of the system are strongly correlated. However, in order for the GFCC to become a method that may be routinely used in the electronic structure calculations, robust numerical techniques and approximations must be employed to reduce its extremely high computational overhead. In our recent studies, it has been demonstrated that the GFCC equations can be solved directly in the frequency domain using iterative linear solvers, which can be easily distributed in a massively parallel environment. Read More

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http://dx.doi.org/10.1021/acs.jctc.9b00172DOI Listing
April 2019
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Utility of Covalent Labeling Mass Spectrometry Data in Protein Structure Prediction with Rosetta.

J Chem Theory Comput 2019 Apr 4. Epub 2019 Apr 4.

Department of Chemistry and Biochemistry , Ohio State University , Columbus , Ohio 43210 , United States.

Covalent labeling mass spectrometry experiments are growing in popularity and provide important information regarding protein structure. Information obtained from these experiments correlates with residue solvent exposure within the protein in solution. However, it is impossible to determine protein structure from covalent labeling data alone. Read More

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http://dx.doi.org/10.1021/acs.jctc.9b00101DOI Listing

Exploration of Chemical Compound, Conformer, and Reaction Space with Meta-Dynamics Simulations Based on Tight-Binding Quantum Chemical Calculations.

Authors:
Stefan Grimme

J Chem Theory Comput 2019 Apr 12. Epub 2019 Apr 12.

Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry , University of Bonn , Beringstrasse 4 , 53115 Bonn , Germany.

The semiempirical tight-binding based quantum chemistry method GFN2-xTB is used in the framework of meta-dynamics (MTD) to globally explore chemical compound, conformer, and reaction space. The biasing potential given as a sum of Gaussian functions is expressed with the root-mean-square-deviation (RMSD) in Cartesian space as a metric for the collective variables. This choice makes the approach robust and generally applicable to three common problems (i. Read More

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http://dx.doi.org/10.1021/acs.jctc.9b00143DOI Listing
April 2019
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Infinite Dilution Activity Coefficients as Constraints for Force Field Parametrization and Method Development.

J Chem Theory Comput 2019 Apr 15. Epub 2019 Apr 15.

Department of Chemistry , University of California , Irvine , California 92697 , United States.

Molecular simulations begin with an underlying energy model or force field and from this can predict diverse physical properties. However, force fields were often developed with relatively limited data sets, yet accuracy for diverse properties across a broad chemical space is desirable; therefore, tests of such accuracy are particularly important. Here, to this end, we calculated 237 infinite dilution activity coefficients (IDACs), comparing with experimental values from NIST's ThermoML database. Read More

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http://pubs.acs.org/doi/10.1021/acs.jctc.8b01029
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http://dx.doi.org/10.1021/acs.jctc.8b01029DOI Listing
April 2019
7 Reads

Efficient Ensemble Refinement by Reweighting.

J Chem Theory Comput 2019 Apr 17. Epub 2019 Apr 17.

Department of Theoretical Biophysics , Max Planck Institute of Biophysics , Max-von-Laue-Straße 3 , 60438 Frankfurt am Main , Germany.

Ensemble refinement produces structural ensembles of flexible and dynamic biomolecules by integrating experimental data and molecular simulations. Here we present two efficient numerical methods to solve the computationally challenging maximum-entropy problem arising from a Bayesian formulation of ensemble refinement. Recasting the resulting constrained weight optimization problem into an unconstrained form enables the use of gradient-based algorithms. Read More

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http://dx.doi.org/10.1021/acs.jctc.8b01231DOI Listing
April 2019
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The Fluctuation-Dissipation Theorem as a Diagnosis and Cure for Zero-Point Energy Leakage in Quantum Thermal Bath Simulations.

J Chem Theory Comput 2019 Apr 17. Epub 2019 Apr 17.

Sorbonne Université, CNRS - UMR 7588 , Institut des NanoSciences de Paris, INSP , 4 Place Jussieu , F-75005 Paris , France.

Quantum thermal bath (QTB) simulations reproduce statistical nuclear quantum effects via a Langevin equation with a colored random force. Although this approach has proven efficient for a variety of chemical and condensed-matter problems, the QTB, as many other semiclassical methods, suffers from zero-point energy leakage (ZPEL). The absence of a reliable criterion to quantify the ZPEL without resorting to demanding comparisons with path integral-based calculations has so far hindered the use of the QTB for the simulation of real systems. Read More

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http://dx.doi.org/10.1021/acs.jctc.8b01164DOI Listing
April 2019
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An ab Initio Linear Response Method for Computing Magnetic Circular Dichroism Spectra with Nonperturbative Treatment of Magnetic Field.

J Chem Theory Comput 2019 Apr 12. Epub 2019 Apr 12.

Department of Chemistry , University of Washington , Seattle , Washington 98195 , United States.

Magnetic circular dichroism (MCD) experiments provide a sensitive tool for exploring geometric, magnetic, and electronic properties of chemical complexes and condensed matter systems. They are also challenging to simulate because of the need to simultaneously treat the perturbations of a finite magnetic field as well as an optical field. In this work, we introduce an ab initio approach that treats the external magnetic field nonperturbatively with London orbitals for simulating the MCD spectra of closed-shell systems. Read More

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http://dx.doi.org/10.1021/acs.jctc.9b00095DOI Listing
April 2019
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Vertex Corrections to the Polarizability Do Not Improve the GW Approximation for the Ionization Potential of Molecules.

J Chem Theory Comput 2019 Apr 16. Epub 2019 Apr 16.

Department of Chemistry , Columbia University , New York , New York 10027 , United States.

The GW approximation is based on the neglect of vertex corrections, which appear in the exact self-energy and the exact polarizability. Here, we investigate the importance of vertex corrections in the polarizability only. We calculate the polarizability with equation-of-motion coupled-cluster theory with single and double excitations (EOM-CCSD), which rigorously includes a large class of diagrammatically defined vertex corrections beyond the random phase approximation (RPA). Read More

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http://dx.doi.org/10.1021/acs.jctc.8b00995DOI Listing

Improving Atom-Type Diversity and Sampling in Cosolvent Simulations Using λ-Dynamics.

J Chem Theory Comput 2019 Apr 15. Epub 2019 Apr 15.

Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy , Purdue University , 575 Stadium Mall Drive , West Lafayette , Indiana 47906 , United States.

Cosolvent molecular dynamics (MD) simulations perform MD simulations of the protein in explicit water mixed with cosolvent molecules that represent functional groups of ligands potentially binding to the protein. The competition between different probes and water molecules allows the identification of the energetic preference of functional groups in different binding site moieties including enthalpic and entropic contributions. Cosolvent MD simulations have recently been applied to a variety of different questions in structure-based drug design but still have significant shortcomings. Read More

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http://pubs.acs.org/doi/10.1021/acs.jctc.8b00940
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http://dx.doi.org/10.1021/acs.jctc.8b00940DOI Listing
April 2019
1 Read

Small Basis Set Allowing the Recovery of Dispersion Interactions with Double-Hybrid Functionals.

J Chem Theory Comput 2019 Apr 12. Epub 2019 Apr 12.

Chimie ParisTech, PSL Research University , CNRS, Institute of Chemistry for Life and Health Sciences , 11, rue Pierre et Marie Curie , F-75005 Paris , France.

Taking advantage of the compensation between Basis Set Superposition Error and Basis Set Incompleteness Error, a new basis is developed to improve the performances of Double Hybrid (DH) functionals in reproducing interaction energies in weak noncovalent systems. Using a self-consistent formula, containing only energy terms computed for dimers and the corresponding monomers at the same level of theory, the exponents of the more external functions of the Def2-SVPD basis were optimized on three systems extracted from the S22 set. The transferability of the obtained basis set, called DH-SVPD, was then tested on five benchmark sets, and it is assessed by considering six DH functionals, eventually corrected with empirical dispersion corrections (for a total of 16 methods). Read More

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http://dx.doi.org/10.1021/acs.jctc.8b01203DOI Listing

Cluster-in-Molecule Local Correlation Approach for Periodic Systems.

J Chem Theory Comput 2019 Apr 5. Epub 2019 Apr 5.

School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of MOE, Institute of Theoretical and Computational Chemistry , Nanjing University , Nanjing 210023 , People's Republic of China.

In this article, the cluster-in-molecule (CIM) local correlation approach for periodic systems with periodic boundary condition has been developed, which allows electron-correlation calculations of various crystals computationally tractable. In this approach, the correlation energy per unit cell of a periodic system can be evaluated as the summation of the correlation contributions from electron-correlation calculations on a series of finite-sized clusters. Each cluster is defined to contain a subset of localized Wannier functions (WFs) (for the occupied space) and projected atomic orbitals (for the virtual space), which can be derived from a periodic Hartree-Fock calculation. Read More

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http://dx.doi.org/10.1021/acs.jctc.8b01200DOI Listing
April 2019
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Describing Molecular Polarizability by a Bond Capacity Model.

J Chem Theory Comput 2019 Apr 10. Epub 2019 Apr 10.

Department of Chemistry , Aarhus University , Langelandsgade 140 , DK-8000 Aarhus , Denmark.

We propose a bond capacity model for describing molecular polarization in force field energy functions at the charge-only level. Atomic charges are calculated by allowing charge to flow between atom pairs according to a bond capacity and a difference in electrostatic potential. The bond capacity is closely related to the bond order and decays to zero as the bond distance is increased. Read More

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http://dx.doi.org/10.1021/acs.jctc.8b01215DOI Listing

A Transferable, Multi-Resolution Coarse-Grained Model for Amorphous Silica Nanoparticles.

J Chem Theory Comput 2019 Apr 18. Epub 2019 Apr 18.

Despite the ubiquity of nanoparticles in modern materials research, computational scientists are often forced to choose between simulations featuring detailed models of only a few nanoparticles or simplified models with many nanoparticles. Herein, we present a coarse-grained model for amorphous silica nanoparticles with parameters derived via potential matching to atomistic nanoparticle data, thus enabling large-scale simulations of realistic models of silica nanoparticles. Interaction parameters are optimized to match a range of nanoparticle diameters in order to increase transferability with nanoparticle size. Read More

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http://dx.doi.org/10.1021/acs.jctc.8b01269DOI Listing

Heterogeneous CPU+GPU-Enabled Simulations for DFTB Molecular Dynamics of Large Chemical and Biological Systems.

J Chem Theory Comput 2019 Mar 27. Epub 2019 Mar 27.

We introduce a new heterogeneous CPU+GPU-enhanced DFTB approach for the routine and efficient simulation of large chemical and biological systems. Compared to homogeneous computing with conventional CPUs, heterogeneous computing approaches exhibit substantial performance with only a modest increase in power consumption, both of which are essential to upcoming exascale computing initiatives. We show that DFTB-based molecular dynamics is a natural candidate for heterogeneous computing, since the computational bottleneck in these simulations is the diagonalization of the Hamiltonian matrix, which is performed several times during a single molecular dynamics trajectory. Read More

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http://dx.doi.org/10.1021/acs.jctc.8b01239DOI Listing

a-ARM: Automatic Rhodopsin Modeling with Chromophore Cavity Generation, Ionization State Selection, and External Counterion Placement.

J Chem Theory Comput 2019 Apr 12. Epub 2019 Apr 12.

Department of Biotechnologies, Chemistry and Pharmacy , Università degli Studi di Siena , via A. Moro 2 , I-53100 Siena , Italy.

The Automatic Rhodopsin Modeling (ARM) protocol has recently been proposed as a tool for the fast and parallel generation of basic hybrid quantum mechanics/molecular mechanics (QM/MM) models of wild type and mutant rhodopsins. However, in its present version, input preparation requires a few hours long user's manipulation of the template protein structure, which also impairs the reproducibility of the generated models. This limitation, which makes model building semiautomatic rather than fully automatic, comprises four tasks: definition of the retinal chromophore cavity, assignment of protonation states of the ionizable residues, neutralization of the protein with external counterions, and finally congruous generation of single or multiple mutations. Read More

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http://dx.doi.org/10.1021/acs.jctc.9b00061DOI Listing

Nature of Halide-Water Interactions: Insights from Many-Body Representations and Density Functional Theory.

J Chem Theory Comput 2019 Apr 4. Epub 2019 Apr 4.

Interaction energies of halide-water dimers, X(HO), and trimers, X(HO), with X = F, Cl, Br, and I, are investigated using various many-body models and exchange correlation functionals selected across the hierarchy of density functional theory (DFT) approximations. Analysis of the results obtained with the many-body models demonstrates the need to capture important close-range interactions in the regime of large intermolecular orbital overlap, such as charge transfer and charge penetration. Failure to reproduce these effects can lead to large deviations relative to reference data calculated at the coupled cluster level of theory. Read More

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http://dx.doi.org/10.1021/acs.jctc.9b00064DOI Listing

Chasing the Full Free Energy Landscape of Neuroreceptor/Ligand Unbinding by Metadynamics Simulations.

J Chem Theory Comput 2019 Apr 4. Epub 2019 Apr 4.

Department of Chemistry and Applied Biosciences , ETH Zürich , c/o USI Campus, Via Giuseppe Buffi 13 , CH-6900 Lugano , Ticino , Switzerland.

Predicting the complete free energy landscape associated with protein-ligand unbinding may greatly help designing drugs with highly optimized pharmacokinetics. Here we investigate the unbinding of the iperoxo agonist to its target human neuroreceptor M, embedded in a neuronal membrane. By feeding out-of-equilibrium molecular simulations data in a classification analysis, we identify the few essential reaction coordinates of the process. Read More

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http://dx.doi.org/10.1021/acs.jctc.9b00118DOI Listing

Solvation Entropy Made Simple.

J Chem Theory Comput 2019 Apr 8. Epub 2019 Apr 8.

The Dow Chemical Company , 1776 Building , Midland , Michigan 48674 , United States.

The entropies of molecules in solution are often calculated using gas phase formulas. It is assumed that, because implicit solvation models are fitted to reproduce free energies, this is sufficient for modeling reactions in solution. However, this procedure exaggerates entropic effects in processes that change molecularity. Read More

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http://dx.doi.org/10.1021/acs.jctc.9b00214DOI Listing

LICHEM 1.1: Recent Improvements and New Capabilities.

J Chem Theory Comput 2019 Apr 2. Epub 2019 Apr 2.

Department of Chemistry , University of North Texas , Denton , Texas 76201 , United States.

The QM/MM method has become a useful tool to investigate various properties of complex systems. We previously introduced the layered interacting chemical models (LICHEM) package to enable QM/MM simulations with advanced potentials by combining various (unmodified) QM and MM codes ( J. Comp. Read More

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http://dx.doi.org/10.1021/acs.jctc.9b00028DOI Listing

A pH Replica Exchange Scheme in the Stochastic Titration Constant-pH MD Method.

J Chem Theory Comput 2019 Apr 3. Epub 2019 Apr 3.

Centro de Química e Bioquímica, Departamento de Química e Bioquímica , Faculdade de Ciências, Universidade de Lisboa , 1749-016 Lisboa , Portugal.

Solution pH is a physicochemical property that has a key role in cellular regulation, and its impact at the molecular level is often difficult to study by experimental methods. In this context, several theoretical methods were developed to study pH effects in macromolecules. The stochastic titration constant-pH molecular dynamics method (CpHMD) was developed by coupling molecular sampling methods, which are appropriate to study the conformational ensemble of biomolecules, with continuum electrostatics approaches, which properly describe pH-dependent protonation states. Read More

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http://dx.doi.org/10.1021/acs.jctc.9b00030DOI Listing

Backmapping from Multiresolution Coarse-Grained Models to Atomic Structures of Large Biomolecules by Restrained Molecular Dynamics Simulations Using Bayesian Inference.

J Chem Theory Comput 2019 Apr 3. Epub 2019 Apr 3.

Hefei National Laboratory for Physical Science at Microscale and School of Life Sciences , University of Science and Technology of China , Hefei , Anhui 230026 , People's Republic of China.

Coarse-grained (CG) simulations have allowed access to larger length scales and longer time scales in the study of the dynamic processes of large biomolecules than all-atom (AA) molecular dynamics (MD) simulations. Backmapping from CG models to AA structures has long been studied because it enables us to gain detailed structure insights from CG simulations. Many methods first construct an AA structure from the CG model by fragments, random placement, or geometrical rules and subsequently optimize the solution via energy minimization, simulated annealing or position-restrained simulations. Read More

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http://dx.doi.org/10.1021/acs.jctc.9b00062DOI Listing

Parallel Implementation of a Sequential Markov Chain in Monte Carlo Simulations of Physical Systems with Pairwise Interactions.

J Chem Theory Comput 2019 Apr 12. Epub 2019 Apr 12.

Interdisciplinary Centre for Mathematical and Computational Modelling , University of Warsaw , Warsaw , Poland.

In molecular simulations performed by Markov Chain Monte Carlo (typically employing the Metropolis criterion), each state of a system is obtained by a small random modification of the previous state. Therefore, the process consists of an immense number of small, quick to calculate steps, which are inherently sequential and hence considered to be very hard to parallelise. Here, we present a novel protocol for efficient calculation of multiple sequential steps in parallel. Read More

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http://dx.doi.org/10.1021/acs.jctc.8b01168DOI Listing