5,887 results match your criteria Journal of chemical theory and computation[Journal]


OPLS3e: Extending Force Field Coverage for Drug-Like Small Molecules.

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

Building upon the OPLS3 force field we report on an enhanced model, OPLS3e, that further extends its coverage of medicinally relevant chemical space by addressing limitations in chemotype transferability. OPLS3e accomplishes this by incorporating new parameter types that recognize moieties with greater chemical specificity and integrating an on-the-fly parameterization approach to the assignment of partial charges. As a consequence, OPLS3e leads to greater accuracy against performance benchmarks that assess small molecule conformational propensities, solvation and protein-ligand binding. Read More

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http://dx.doi.org/10.1021/acs.jctc.8b01026DOI Listing
February 2019

Free Energy Calculations Based on Coupling Proximal Distribution Functions and Thermodynamic Cycles.

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

Techniques to calculate the free energy changes of a system are very useful studying biophysical and biochemical properties. In practice, free energy changes can be described with thermodynamic cycles and free energy change of individual process can be computed by sufficiently sampling the corresponding configurations. However, this is still time consuming especially for large biomolecular systems. Read More

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http://dx.doi.org/10.1021/acs.jctc.8b01157DOI Listing
February 2019

Relative Principal Components Analysis: Application to Analyzing Biomolecular Conformational Changes.

J Chem Theory Comput 2019 Feb 14. Epub 2019 Feb 14.

A new method termed "Relative Principal Components analysis" (RPCA) is introduced that extracts optimal relevant principal components to describe the change between two data samples representing two macroscopic states. The method is widely applicable in data-driven science. Calculating the components is based on a unified physical framework which introduces the objective function, namely the Kullback-Leibler divergence, appropriate for quantifying the change of the macroscopic state as it is effected by the microscopic features. Read More

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http://dx.doi.org/10.1021/acs.jctc.8b01074DOI Listing
February 2019

Open Boundary-Molecular Mechanics/Coarse-Grained Framework for Simulations of Low-Resolution G-Protein-Coupled Receptor/Ligand Complexes.

J Chem Theory Comput 2019 Feb 14. Epub 2019 Feb 14.

G-protein-coupled receptors (GPCRs) constitute as much as 30% of the overall proteins targeted by FDA-approved drugs. However, paucity of structural experimental information and low sequence identity between members of the family impair the reliability of traditional docking approaches and atomistic molecular dynamics simulations for in silico pharmacological applications. We present here a dual-resolution approach tailored for such low-resolution models. Read More

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http://dx.doi.org/10.1021/acs.jctc.9b00040DOI Listing
February 2019

Deriving Force-Field Parameters from First Principles Using a Polarizable and Higher Order Dispersion Model.

J Chem Theory Comput 2019 Feb 14. Epub 2019 Feb 14.

AIMMS Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, Faculty of Science , Vrije Universiteit Amsterdam , De Boelelaan 1108 , 1081 HZ Amsterdam , the Netherlands.

In this work we propose a strategy based on quantum mechanical (QM) calculations to parametrize a polarizable force field for use in molecular dynamics (MD) simulations. We investigate the use of multiple atoms-in-molecules (AIM) strategies to partition QM determined molecular electron densities into atomic subregions. The partitioned atomic densities are subsequently used to compute atomic dispersion coefficients from effective exchange-hole-dipole moment (XDM) calculations. Read More

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http://dx.doi.org/10.1021/acs.jctc.8b01105DOI Listing
February 2019

NanoModeler: A Webserver for Molecular Simulations and Engineering of Nanoparticles.

J Chem Theory Comput 2019 Feb 13. Epub 2019 Feb 13.

Functionalized nanoparticles (NPs) are at the frontier of nanoscience. They hold the promise of innovative applications for human health and technology. Molecular dynamics (MD) simulations of NPs are increasingly popular because they can help researchers better understand the fundamental structural and dynamical features of NPs. Read More

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http://dx.doi.org/10.1021/acs.jctc.8b01304DOI Listing
February 2019

An Improved Lower Bound to the Ground State Energy.

Authors:
Eli Pollak

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

The Arnoldi iterative method for determining eigenvalues is based on the observation that the effect of operating with the Hamiltonian on a vector may be expressed as a sum of parallel and perpendicular contributions. This identity is used here to improve the previous lower bound estimate of the ground state energy by Temple, derived ninety years ago (Proc. Roy. Read More

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http://dx.doi.org/10.1021/acs.jctc.9b00128DOI Listing
February 2019

An Evolutionary Approach to Constructing a Deep Feedforward Neural Network for Prediction of Electronic Coupling Elements in Molecular Materials.

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

We present a general framework for the construction of a deep feedforward neural network (FFNN) to predict distance and orientation dependent electronic coupling elements in disordered molecular materials. An evolutionary algorithm automatizes the selection of an optimal architecture of the artificial neural network within a predefined search space. Systematic guidance, beyond minimizing the model error with stochastic gradient descent based backpropagation, is provided by simultaneous maximization of a model fitness that takes into account additional physical properties, such as the field-dependent carrier mobility. Read More

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http://dx.doi.org/10.1021/acs.jctc.8b01285DOI Listing
February 2019

Comparison of Different Classical, Semiclassical, and Quantum Treatments of Light-Matter Interactions: Understanding Energy Conservation.

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

Department of Chemistry , University of Pennsylvania , Philadelphia , Pennsylvania 19104 , United States.

The optical response of an electronic two-level system (TLS) coupled to an incident continuous wave (cw) electromagnetic (EM) field is simulated explicitly in one dimension by the following five approaches: (i) the coupled Maxwell-Bloch equations, (ii) the optical Bloch equation (OBE), (iii) Ehrenfest dynamics, (iv) the Ehrenfest+R approach, and (v) classical dielectric theory (CDT). Our findings are as follows: (i) standard Ehrenfest dynamics predict the correct optical signals only in the linear response regime where vacuum fluctuations are not important; (ii) both the coupled Maxwell-Bloch equations and CDT predict incorrect features for the optical signals in the linear response regime due to a double-counting of self-interaction; (iii) by exactly balancing the effects of self-interaction versus the effects of quantum fluctuations (and insisting on energy conservation), the Ehrenfest+R approach generates the correct optical signals in the linear regime and slightly beyond, yielding, e.g. Read More

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http://dx.doi.org/10.1021/acs.jctc.8b01232DOI Listing
February 2019

GFN2-xTB-An Accurate and Broadly Parametrized Self-Consistent Tight-Binding Quantum Chemical Method with Multipole Electrostatics and Density-Dependent Dispersion Contributions.

J Chem Theory Comput 2019 Feb 11. Epub 2019 Feb 11.

Mulliken Center for Theoretical Chemistry , Universität Bonn , Beringstr. 4 , 53115 Bonn , Germany.

An extended semiempirical tight-binding model is presented, which is primarily designed for the fast calculation of structures and noncovalent interaction energies for molecular systems with roughly 1000 atoms. The essential novelty in this so-called GFN2-xTB method is the inclusion of anisotropic second order density fluctuation effects via short-range damped interactions of cumulative atomic multipole moments. Without noticeable increase in the computational demands, this results in a less empirical and overall more physically sound method, which does not require any classical halogen or hydrogen bonding corrections and which relies solely on global and element-specific parameters (available up to radon, Z = 86). Read More

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http://dx.doi.org/10.1021/acs.jctc.8b01176DOI Listing
February 2019
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Semiempirical Quantum-Chemical Methods with Orthogonalization and Dispersion Corrections.

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

We present two new semiempirical quantum-chemical methods with orthogonalization and dispersion corrections: ODM2 and ODM3 (ODMx). They employ the same electronic structure model as the OM2 and OM3 (OMx) methods, respectively. In addition, they include Grimme's dispersion correction D3 with Becke-Johnson damping and three-body corrections E^{ABC} for Axilrod-Teller-Muto dispersion interactions as integral parts. Read More

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http://dx.doi.org/10.1021/acs.jctc.8b01265DOI Listing
February 2019
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Intricacies of DFT+U, not only in a Numeric Atom Centered Orbital Framework.

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

We implemented the popular Hubbard density-functional theory +U (DFT+U) method in its spherically averaged form in the all-electron, full-potential DFT code FHI-aims. There, electronic states are expressed in a basis of highly localized numeric atomic orbitals (NAO) which straightforwardly lend themselves as projector functions for the DFT+U correction, yielding the necessary occupations of the correlated Hubbard subspace at no additional cost. We establish the efficacy of our implementation on the prototypical bulk NiO and obtain the well known band-gap opening effect of DFT+U. Read More

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http://dx.doi.org/10.1021/acs.jctc.8b01211DOI Listing
February 2019

Simulation of inelastic neutron scattering spectra using OCLIMAX.

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

Studying the vibration of atoms is of fundamental importance and can provide critical insight for the understanding of materials behavior, such as structure and phase transition, thermodynamics, and chemical reactions. The atomic vibration can be probed using vibrational spectroscopy with various incident particles such as photons, neutrons, or electrons. A major challenge when applying these techniques is often how to interpret the vibrational spectra, and how to make connections to the theory. Read More

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http://dx.doi.org/10.1021/acs.jctc.8b01250DOI Listing
February 2019

Mechanism of Spin-Exchange Internal Conversion: Practical Proxies for Diabatic and Nonadiabatic Couplings.

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

Spin-exchange internal conversion (SEIC) is a general class of reactions having singlet fission and triplet fusion as particular cases. Based on a charge-transfer (CT)-mediated mechanism and analytical derivation with a model Hamiltonian, we propose proxies for estimating the coupling strength in both diabatic and adiabatic pictures for general SEIC reactions. In the diabatic picture, we demonstrated the existence of a bilinear relationship between the coupling strength and molecular orbital overlap, which provides a practical way to predict diabatic couplings. Read More

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http://dx.doi.org/10.1021/acs.jctc.8b00923DOI Listing
February 2019

Anharmonic Vibrational Analysis of Biomolecules and Solvated Molecules Using Hybrid QM/MM Computations.

J Chem Theory Comput 2019 Feb 7. Epub 2019 Feb 7.

Quantum mechanics / molecular mechanics (QM/MM) calculations are applied for anharmonic vibrational analyses of biomolecules and solvated molecules. The QM/MM method is implemented into a molecular dynamics (MD) program, GENESIS, by interfacing with external electronic structure programs. Following the geometry optimization and the harmonic normal mode analysis based on a partial Hessian, the anharmonic potential energy surface (PES) is generated from QM/MM energies and gradients calculated at grid points. Read More

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http://dx.doi.org/10.1021/acs.jctc.8b01193DOI Listing
February 2019
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Modelling Nucleation and Growth of ZnO Nanoparticles in a Low Temperature Plasma by Reactive Dynamics.

J Chem Theory Comput 2019 Feb 7. Epub 2019 Feb 7.

The very first stages of nucleation and growth of ZnO nanoparticles in a plasma reactor are studied by means of a multi-scale computational paradigm where the DFT-GGA approach is used to evaluate structure and electronic energy of small (ZnO)N clusters (N ≤ 24) that are employed as a training set (TS) for the optimization of a Reactive Force Field (RFF). Reactive Molecular Dynamics (RMD) simulations based on this tuned RFF are carried out to reproduce nucleation and growth in a realistic environment. Inside the reaction chamber the temperature is around 1200 K and the zinc atoms are oxidized in an oxygen-rich atmosphere at high pressure (about 20 atm), whereas in the quenching chamber where the temperature is lower (about 800 K) the ZnO embryo-nanoclusters are grown. Read More

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http://dx.doi.org/10.1021/acs.jctc.8b01222DOI Listing
February 2019

Close Relationships between NMR J-Coupling Alternation (JCA) and Molecular Properties of Carbon Chains.

J Chem Theory Comput 2019 Feb 7. Epub 2019 Feb 7.

We propose a J-coupling alternation (JCA) value that is demonstrated to be a suitable parameter to evaluate the nuclear magnetic resonance (NMR) indirect spin-spin coupling constants (SSCCs) as a function of molecular properties of chains, by increasing their length. As an application, we report a theoretical study of the SSCCs for the interactions between neighbor nuclei in increasingly patterned carbon chains, within density functional theory. First, we examine the J-coupling constants between 1H and 13C nuclei (nJHC) considering the separation distance, as well as between two adjacent 13C nuclei (1JCC) considering their relative positions in polyynes and cumulenes. Read More

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http://dx.doi.org/10.1021/acs.jctc.8b01141DOI Listing
February 2019

Enthalpy-entropy Interplay in π-Stacking Interaction of Benzene Dimer in Water.

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

Aromatic groups can engage in an interesting class of non-covalent interactions termed π-π interactions, which play a pivotal role in stabilizing a variety of molecular architectures, including nucleic acids, proteins and supramolecular assemblies. When the aromatic compounds interact with each other in an aqueous environment, their association is facilitated by the hydrophobic effect - the trend of non-polar solutes to aggregate in a polar solution. To develop an in-depth understanding of hydrophobic association, we investigate in the present work π-π interactions in water, employing as a paradigm the benzene dimer. Read More

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http://dx.doi.org/10.1021/acs.jctc.8b00880DOI Listing
February 2019

Assessment of MC-PDFT excitation energies for a set of QM/MM models of rhodopsins.

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

A methodology for the automatic production of quantum mechanical/molecular mechanical (QM/MM) models of retinal-containing rhodopsin proteins and subsequent prediction of their spectroscopic properties has been proposed recently by some of the authors. The technology employed for the evaluation of the excitation energies is called Automatic Rhodopsin Modeling (ARM), and it involves the use of the complete active space self-consistent field (CASSCF) method followed by a multi-configuration second order perturbation theory (in particular, CASPT2) calculation of external correlation energies. Although it was shown that ARM is capable of successfully reproducing and predicting spectroscopic property trends in chromophore-embedding protein sets, practical applications of such technology are limited by the high computational costs of the multi-configuration perturbation theory calculations. Read More

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http://dx.doi.org/10.1021/acs.jctc.8b01069DOI Listing
February 2019

Predicting Phosphorescence Rates of Light Organic Molecules Using Time-Dependent Density Functional Theory and the Path Integral Approach to Dynamics.

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

Max-Planck-Institut für Kohlenforschung , Mülheim an der Ruhr 45470 , Germany.

In this work, we present a general method for predicting phosphorescence rates and spectra for molecules using time-dependent density functional theory (TD-DFT) and a path integral approach for the dynamics that relies on the harmonic oscillator approximation for the nuclear movement. We first discuss the theory involved in including spin-orbit coupling (SOC) among singlet and triplet excited states and then how to compute the corrected transition dipole moments and phosphorescence rates. We investigate the dependence of these rates on some TD-DFT parameters, such as the nature of the functional, the number of roots, and the Tamm-Dancoff approximation. Read More

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http://pubs.acs.org/doi/10.1021/acs.jctc.8b00841
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http://dx.doi.org/10.1021/acs.jctc.8b00841DOI Listing
February 2019
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A DFT/ZORA Study of Cadmium Magnetic Shielding Tensors: Analysis of Relativistic Effects and Electronic-State Approximations.

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

Theoretical considerations are discussed for the accurate prediction of cadmium magnetic shielding tensors using relativistic density functional theory (DFT). Comparison is made between calculations that model the extended lattice of the cadmium-containing solids using periodic boundary conditions and pseudopotentials with calculations that use clusters of atoms. The all-electron cluster-based calculations afford an opportunity to examine the importance of (i) relativistic effects on cadmium magnetic shielding tensors, as introduced through the ZORA Hamiltonian at either the scalar (SC) or spin-orbit (SO) levels and (ii) variation in the class of the DFT approximation. Read More

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http://dx.doi.org/10.1021/acs.jctc.8b01296DOI Listing
February 2019

Two Conical Intersections Control the Luminol Chemiluminescence.

Authors:
Ling Yue Ya-Jun Liu

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

Luminol, the first discovered and man-made effective chemiluminescence (CL) system, is the best known and one of the most widely used CL materials. The chemiluminescent process of the luminol CL has not yet been fully elucidated, although the decomposition of 1,2-dioxane-3,6-dione dianion (CP2-) is verified to be the key step to produce light emitter. However, the mechanisms of the CP2- decomposition and the effective singlet chemiexcitation are totally unknown, which is the outstanding obstacle to comprehending luminol CL. Read More

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http://dx.doi.org/10.1021/acs.jctc.8b01114DOI Listing
February 2019

Reduced-Scaling Approach for Configuration Interaction Singles and Time-Dependent Density Functional Theory Calculations Using Hybrid Functionals.

J Chem Theory Comput 2019 Feb 14. Epub 2019 Feb 14.

Department of Physical Chemistry and Materials Science , Budapest University of Technology and Economics , P.O. Box 91, H-1521 Budapest , Hungary.

An approximation is presented which can efficiently decrease the computational expenses of configuration interaction singles (CIS) and time-dependent density functional theory (TDDFT) methods employing hybrid functionals. The approach is the adaptation of the local density fitting scheme developed for Hartree-Fock (HF) calculations for excited states and reduces the quartic scaling of the methods to cubic. It can also be applied to related methods, such as the time-dependent HF and Tamm-Dancoff approximation TDDFT approaches. Read More

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http://dx.doi.org/10.1021/acs.jctc.8b01199DOI Listing
February 2019
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Benchmark Calculations of K-Edge Ionization Energies for First-Row Elements Using Scalar-Relativistic Core-Valence-Separated Equation-of-Motion Coupled-Cluster Methods.

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

Department of Chemistry , The Johns Hopkins University , Baltimore , Maryland 21218 , United States.

Benchmark scalar-relativistic core-valence-separated (CVS) equation-of-motion coupled-cluster ionization potential (EOMIP-CC) calculations of 21 K-edge ionization energies of C, O, N, and F in 14 molecules are reported. The CVS-EOMIP-CC methods are shown to be numerically more stable and more accurate than the parent EOMIP-CC methods, even when the calculations using the latter can be tightly converged. The superior performance of the CVS scheme is attributed to the exclusion of spurious couplings between core-ionized states and valence continuum states. Read More

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http://dx.doi.org/10.1021/acs.jctc.8b01160DOI Listing
February 2019

Local Energy Decomposition of Open-Shell Molecular Systems in the Domain-Based Local Pair Natural Orbital Coupled Cluster Framework.

J Chem Theory Comput 2019 Jan 31. Epub 2019 Jan 31.

The local energy decomposition (LED) analysis decomposes the interaction energy between two fragments calculated at the domain-based local pair natural orbital CCSD(T) (DLPNO-CCSD(T)) level of theory into a series of chemically meaningful contributions and has found widespread applications in the study of noncovalent interactions. Herein, an extension of this scheme that allows for the analysis of interaction energies of open-shell molecular systems calculated at the UHF-DLPNO-CCSD(T) level is presented. The new scheme is illustrated through applications to the CH2-X (X = He, Ne, Ar, Kr, and water) and heme-CO interactions in the low-lying singlet and triplet spin states. Read More

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http://dx.doi.org/10.1021/acs.jctc.8b01145DOI Listing
January 2019
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Systematic Coarse-Grained Lipid Force Fields with Semiexplicit Solvation via Virtual Sites.

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

Department of Chemistry , The University of Chicago , Chicago , Illinois 60637 , United States.

Despite the central role of lipids in many biophysical functions, the molecular mechanisms that dictate macroscopic lipid behavior remain elusive to both experimental and computational approaches. As such, there has been much interest in the development of low-resolution, implicit-solvent coarse-grained (CG) models to dynamically simulate biologically relevant spatiotemporal scales with molecular fidelity. However, in the absence of solvent, a key challenge for CG models is to faithfully emulate solvent-mediated forces, which include both hydrophilic and hydrophobic interactions that drive lipid aggregation and self-assembly. Read More

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http://dx.doi.org/10.1021/acs.jctc.8b01033DOI Listing
February 2019

Ab Initio Computation of Rotationally-Averaged Pump-Probe X-Ray and Electron Diffraction Signals.

J Chem Theory Comput 2019 Jan 31. Epub 2019 Jan 31.

We develop a new algorithm for the computation of the rotationally-averaged elastic molecular diffraction signal for the cases of perpendicular or parallel pump-probe geometries. The algorithm first collocates the charge density from an arbitrary ab initio wavefunction onto a Becke quadrature grid [A. Becke, J. Read More

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http://dx.doi.org/10.1021/acs.jctc.8b01051DOI Listing
January 2019
5.498 Impact Factor

A Simple Model for Relative Energies of All Fullerenes Reveals the Interplay between Intrinsic Resonance and Structural Deformation Effects in Medium-Sized Fullerenes.

J Chem Theory Comput 2019 Feb 31;15(2):1255-1264. Epub 2019 Jan 31.

RIKEN Center for Computational Science , 7-1-26 Minatojima-minami-machi , Chuo-ku, Kobe , Hyogo 650-0047 , Japan.

Fullerenes are sheets of sp carbon atoms wrapped around to form spheres. With this simple consideration, we have in the present study devised and (with over 3600 DFT data points) successfully validated a simple model, termed R+D, for estimating the relative energies of fullerenes. This model contains a resonance component to account for the intrinsic differences between the π-energies of different fullerenes, and a deformation component for treating the distortions from planarity. Read More

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http://dx.doi.org/10.1021/acs.jctc.8b00981DOI Listing
February 2019

Accurate prediction of hyperfine coupling tensors for main group elements using a unitary group based rigorously spin-adapted coupled-cluster theory.

J Chem Theory Comput 2019 Jan 30. Epub 2019 Jan 30.

We present the development of a perturbative triples correction scheme for the previously reported unitary group based spin-adapted combinatoric open-shell coupled-cluster (CC) singles and doubles (COS-CCSD) approach and report on the applications of the newly developed method, termed ``COS-CCSD(T)'', to the calculation of hyperfine coupling (HFC) tensors for radicals consisting of hydrogen, second- and third-row elements. The COS-CCSD(T) method involves a single noniterative step with N scaling of the computational cost for the calculation of triples corrections to the energy. The key feature of this development is the use of spatial semicanonical orbitals generated from standard restricted open-shell Hartree-Fock (ROHF) orbitals, which allows to define the unperturbed Hamiltonian operator in terms of a diagonal spin-free Fock operator. Read More

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http://dx.doi.org/10.1021/acs.jctc.8b01048DOI Listing
January 2019
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5.498 Impact Factor

Evaluation of Predicted Protein-Protein Complexes by Binding Free Energy Simulations.

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

Physik-Department T38 , Technische Universität München , James-Franck-Strasse 1 , 85748 Garching , Germany.

The accurate prediction of protein-protein complex geometries is of major importance to ultimately model the complete interactome of interacting proteins in a cell. A major bottleneck is the realistic free energy evaluation of predicted docked structures. Typically, simple scoring functions applied to single-complex structures are employed that neglect conformational entropy and often solvent effects completely. Read More

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http://dx.doi.org/10.1021/acs.jctc.8b01022DOI Listing
February 2019

Assessment of GAFF2 and OPLS-AA general force fields in combination with the water models TIP3P, SPCE and OPC3 for the solvation free energy of drug-like organic molecules.

J Chem Theory Comput 2019 Jan 29. Epub 2019 Jan 29.

Molecular dynamics simulations have been performed to compute the solvation free energy and the octanol/water partition coefficients for a challenging set of selected organic molecules, characterized by the simultaneous presence of functional groups coarsely spanning a large portion of the chemical space in drug-like compounds and, in many cases, by a complex conformational landscape (2-propoxyethanol, acetylsalicylic acid, cyclohexanamine, dialifor, ketoprofen, nitralin, profluralin, terbacil). OPLS-AA and GAFF2 parameterizations of the organic molecules and of 1-octanol have been done via the web-based automatic parameter generators, LigParGen [Dodda et al. Nucl. Read More

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http://dx.doi.org/10.1021/acs.jctc.8b01039DOI Listing
January 2019

Mesoscale Electrostatics Driving Particle Dynamics in Nonhomogeneous Dielectrics.

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

Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences , University of Oslo , PO Box 1033 Blindern , 0315 Oslo , Norway.

We introduce a density functional-based formalism to compute the electrostatic energy and forces for a mesoscopic system in the condensed phase, described with molecular resolution. The dielectric permittivity is variable in space, and it is dependent on the density fields of the individual particles present in the system. The electrostatic potential is obtained from standard numerical solutions of the generalized Poisson equation. Read More

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http://dx.doi.org/10.1021/acs.jctc.8b01201DOI Listing
February 2019

Reference Energies for Double Excitations.

J Chem Theory Comput 2019 Jan 28. Epub 2019 Jan 28.

Excited states exhibiting double excitation character are notoriously difficult to model using conventional single-reference methods, such as adiabatic time-dependent density-functional theory (TD-DFT) or equation-of-motion coupled cluster (EOM-CC). In addition, these states are typical experimentally ``dark'' making their detection in photo-absorption spectra very challenging. Nonetheless, they play a key role in the faithful description of many physical, chemical, and biological processes. Read More

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http://dx.doi.org/10.1021/acs.jctc.8b01205DOI Listing
January 2019
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Zero-Field Splitting Parameters from Four-Component Relativistic Methods.

J Chem Theory Comput 2019 Jan 28. Epub 2019 Jan 28.

We report an approach for determination of zero-field splitting parameters from four-component relativistic calculations. Our approach involves neither perturbative treatment of spin-orbit interaction nor truncation of the spin-orbit coupled states. We make use of a multi-state implementation of relativistic complete active space perturbation theory (CASPT2), partially contracted N-electron valence perturbation theory (NEVPT2), and multi-reference configuration interaction theory (MRCI), all with the fully internally contracted ansatz. Read More

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http://pubs.acs.org/doi/10.1021/acs.jctc.8b00910
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http://dx.doi.org/10.1021/acs.jctc.8b00910DOI Listing
January 2019
7 Reads

Implementation of the Many-Pair Expansion for Systematically Improving Density Functional Calculations of Molecules.

J Chem Theory Comput 2019 Feb 1;15(2):1089-1101. Epub 2019 Feb 1.

Department of Chemistry , Massachusetts Institute of Technology , 77 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States.

Density functional theory (DFT) is the method of choice for predicting structures and reaction energies of molecular systems. However, it remains a daunting task to systematically improve the accuracy of an approximate density functional. The recently proposed many-pair expansion (MPE) [ Phys. Read More

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http://dx.doi.org/10.1021/acs.jctc.8b01127DOI Listing
February 2019

Time-Dependent Complete Active Space Embedded in a Polarizable Force Field.

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

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

Electron correlation and environmental effects play important roles in electron dynamics and spectroscopic observables of chemical systems in condensed phase. In this paper, we present a time-dependent complete active space configuration interaction (TD-CASCI) approach embedded in a polarizable force field, MMPol. The present implementation of TD-CASCI/MMPol utilizes a direct matrix-vector contraction, allowing studies of large systems. Read More

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http://dx.doi.org/10.1021/acs.jctc.8b01152DOI Listing
February 2019

Density-matrix coupled time-dependent exchange-correlation functional approximations.

J Chem Theory Comput 2019 Jan 28. Epub 2019 Jan 28.

We present a new class of non-adiabatic approximations in time-dependent density functional theory derived from an exact expression for the time-dependent exchange-correlation potential. The approximations reproduce dynamical step and peak features in the exact potential that are missing in adiabatic approximations. Central to this approach is an approximation for the one-body reduced density-matrix as a functional of the Kohn-Sham density-matrix, and we demonstrate three such examples. Read More

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http://dx.doi.org/10.1021/acs.jctc.8b01159DOI Listing
January 2019

Constructing Molecular π-Orbital Active Spaces for Multireference Calculations of Conjugated Systems.

J Chem Theory Comput 2019 Jan 28. Epub 2019 Jan 28.

Molecules with conjugated π-systems often feature strong electron correlation and therefore require multireference methods for a reliable computational description. A key prerequisite for the successful application of such methods is the choice of a suitable active space. Herein the automated π-orbital space (PiOS) method for selecting active spaces for multireference calculations of conjugated -systems is presented. Read More

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http://dx.doi.org/10.1021/acs.jctc.8b01196DOI Listing
January 2019

Fast Solver for Large Scale Multistate Bennett Acceptance Ratio Equations.

J Chem Theory Comput 2019 Feb 4;15(2):799-802. Epub 2019 Feb 4.

Department of Computational Medicine & Bioinformatics , University of Michigan , Ann Arbor , Michigan 48109 , United States.

The multistate Bennett acceptance ratio method (MBAR) and unbinned weighted histogram analysis method (UWHAM) are widely employed approaches to calculate relative free energies of multiple thermodynamic states that gain statistical precision by employing free energy contributions from configurations sampled at each of the simulated λ states. With the increasing availability of high throughput computing resources, a large number of configurations can be sampled from hundreds or even thousands of states. Combining sampled configurations from all states to calculate relative free energies requires the iterative solution of large scale MBAR/UWHAM equations. Read More

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http://dx.doi.org/10.1021/acs.jctc.8b01010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6372332PMC
February 2019

Solvent-aware Interfaces in Continuum Solvation.

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

Continuum models to handle solvent and electrolyte effects in an effective way have a long tradition in quantum-chemistry simulations and are nowadays also being introduced in computational condensed-matter and materials simulations. A key ingredient of continuum models is the choice of the solute cavity, i.e. Read More

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http://dx.doi.org/10.1021/acs.jctc.8b01174DOI Listing
January 2019

Role of Valence and Semicore Electron Correlation on Spin Gaps in Fe(II)-Porphyrins.

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

Max-Planck-Institut für Festkörperforschung, Heisenbergstraße 1 , 70569 Stuttgart , Germany.

The role of valence and semicore correlation in differentially stabilizing the intermediate spin state of Fe(II)-porphyrins is analyzed. For CASSCF treatments of valence correlation, a (32,34) active space containing metal 3 d, d' orbitals and the entire π system of the porphyrin is necessary to stabilize the intermediate spin state. Semicore correlation provides a minor (-1. Read More

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http://dx.doi.org/10.1021/acs.jctc.8b01277DOI Listing
February 2019

Vertical Ionization Energies and Electron Affinities of Native and Damaged DNA Bases, Nucleotides, and Pairs from Density Functional Theory Calculations: Model Assessment and Implications for DNA Damage Recognition and Repair.

J Chem Theory Comput 2019 Feb 11. Epub 2019 Feb 11.

Laboratory of Computational Chemistry and Biochemistry , École Polytechnique Fédérale de Lausanne , Swiss Federal Institute of Technology, CH-1015 Lausanne , Switzerland.

To assess the effect of an 8-oxoguanine (8OG) defect base on the vertical ionization energies (VIEs) and electron affinities (VEAs) of DNA, density functional theory calculations were carried out for native and defect DNA bases and nucleotides, as well as for larger fragments containing one or multiple pairs. Absolute values of VIE and VEA under implicit solvation did not converge as a function of model size even up to the largest systems taken into consideration (3 base pairs/2 nucleotide pairs). Nonetheless, a consistent trend was observed for the relative difference in the VIE of native and damaged DNA showing that the defect was lowering the VIE by -0. Read More

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http://dx.doi.org/10.1021/acs.jctc.8b00645DOI Listing
February 2019
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The HANDE-QMC project: open-source stochastic quantum chemistry from the ground state up.

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

Building on the success of Quantum Monte Carlo techniques such as diffusion Monte Carlo, alternative stochastic approaches to solve electronic structure problems have emerged over the last decade. The full configuration interaction quantum Monte Carlo (FCIQMC) method allows one to systematically approach the exact solution of such problems, for cases where very high accuracy is desired. The introduction of FCIQMC has subsequently led to the development of coupled cluster Monte Carlo (CCMC) and density matrix quantum Monte Carlo (DMQMC), allowing stochastic sampling of the coupled cluster wave function and the exact thermal density matrix, respectively. Read More

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http://dx.doi.org/10.1021/acs.jctc.8b01217DOI Listing
January 2019

A Top-Down Multiscale Approach to Simulate Peptide Self-Assembly from Monomers.

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

Modeling peptide assembly from monomers on large time and length scales is often intractable at the atomistic resolution. To address this challenge, we present a new approach which integrates coarse-grained (CG), mixed-resolution, and all atom (AA) modeling in a single simulation. We simulate the initial encounter stage with the CG model, while the further assembly and reorganization stages are simulated with the mixed-resolution and AA models. Read More

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http://dx.doi.org/10.1021/acs.jctc.8b01025DOI Listing
January 2019

Library-Based LAMMPS Implementation of High-Dimensional Neural Network Potentials.

J Chem Theory Comput 2019 Feb 7. Epub 2019 Feb 7.

Faculty of Physics , University of Vienna , Boltzmanngasse 5 , 1090 Vienna , Austria.

Neural networks and other machine learning approaches have been successfully used to accurately represent atomic interaction potentials derived from computationally demanding electronic structure calculations. Due to their low computational cost, such representations open the possibility for large scale reactive molecular dynamics simulations of processes with bonding situations that cannot be described accurately with traditional empirical force fields. Here, we present a library of functions developed for the implementation of neural network potentials. Read More

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http://dx.doi.org/10.1021/acs.jctc.8b00770DOI Listing
February 2019
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Addressing Polarization Phenomena in Molecular Machines Containing Transition Metal Ions with an Additive Force Field.

J Chem Theory Comput 2019 Feb 7. Epub 2019 Feb 7.

Research Center for Analytical Sciences, College of Chemistry , Nankai University , Tianjin 300071 , China.

Modeling transition metals in supramolecular assemblies, in general, is extremely challenging due to polarization and charge transfer. In this work, we demonstrate that the inherent shortcomings of additive force fields in modeling Cu-ether-O and Cu-olefin-C interactions are rooted in the Lorentz-Berthelot rules. A general method for investigating transition-metal-containing molecular assays using classical force fields is, therefore, proposed. Read More

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http://pubs.acs.org/doi/10.1021/acs.jctc.8b00972
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http://dx.doi.org/10.1021/acs.jctc.8b00972DOI Listing
February 2019
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Enhancing Side Chain Rotamer Sampling Using Nonequilibrium Candidate Monte Carlo.

J Chem Theory Comput 2019 Feb 11. Epub 2019 Feb 11.

Department of Pharmaceutical Sciences , University of California, Irvine , Irvine , California 92697 , United States.

Molecular simulations are a valuable tool for studying biomolecular motions and thermodynamics. However, such motions can be slow compared to simulation time scales, yet critical. Specifically, adequate sampling of side chain motions in protein binding pockets is crucial for obtaining accurate estimates of ligand binding free energies from molecular simulations. Read More

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http://dx.doi.org/10.1021/acs.jctc.8b01018DOI Listing
February 2019
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Development of Large-Scale Excited-State Calculations Based on the Divide-and-Conquer Time-Dependent Density Functional Tight-Binding Method.

J Chem Theory Comput 2019 Feb 7. Epub 2019 Feb 7.

Department of Chemistry and Biochemistry, School of Advanced Science and Engineering , Waseda University , 3-4-1 Okubo , Shinjuku-ku, Tokyo 169-8555 , Japan.

In this study, the divide-and-conquer (DC) method was extended to time-dependent density functional tight-binding (TDDFTB) theory to enable excited-state calculations of large systems and is denoted by DC-TDDFTB. The efficient diagonalization algorithms of TDDFTB and DC-TDDFTB methods were implemented into our in-house program. Test calculations of polyethylene aldehyde and p-coumaric acid, a pigment in photoactive yellow protein, in water demonstrate the high accuracy and efficiency of the developed DC-TDDFTB method. Read More

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http://pubs.acs.org/doi/10.1021/acs.jctc.8b01214
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http://dx.doi.org/10.1021/acs.jctc.8b01214DOI Listing
February 2019
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Influence of the treatment of non-bonded interactions on thermodynamic and transport properties of pure liquids calculated using the 2016H66 force field.

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

The effect of different treatments of the non-bonded interactions in simulations employing the recently introduced GROMOS-compatible 2016H66 force field is evaluated based on simulations carried out with the GROMACS software. This is done considering four thermodynamic and transport properties (pure liquid density, vaporization enthalpy, surface-tension coefficient and self-diffusion constant) of 57 organic liquids representative of the chemical groups alcohol, ether, aldehyde, ketone, carboxylic acid, ester, amine, amide, thiol, sulfide, disulfide and aromatic compounds, along with water (SPC model). A dipalmitoylphosphatidylcholine bilayer system is considered as well. Read More

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http://dx.doi.org/10.1021/acs.jctc.8b00425DOI Listing
January 2019

Assessment of Initial Guesses for Self-Consistent Field Calculations. Superposition of Atomic Potentials: Simple yet Efficient.

Authors:
Susi Lehtola

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

Department of Chemistry , University of Helsinki , P.O. Box 55, A. I. Virtasen aukio 1 , FI-00014 Helsinki , Finland.

Electronic structure calculations, such as in the Hartree-Fock or Kohn-Sham density functional approach, require an initial guess for the molecular orbitals. The quality of the initial guess has a significant impact on the speed of convergence of the self-consistent field (SCF) procedure. Popular choices for the initial guess include the one-electron guess from the core Hamiltonian, the extended Hückel method, and the superposition of atomic densities (SAD). Read More

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http://dx.doi.org/10.1021/acs.jctc.8b01089DOI Listing
February 2019