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PubMed Journal Database | Journal of chemical theory and computation RSS

03:19 EDT 25th May 2019 | BioPortfolio

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Showing PubMed Articles 1–25 of 1,300+ from Journal of chemical theory and computation

SS-SR and MS-MR Zeroth-Order Hamiltonians in MS-CASPT2 and Conical Intersections.

Multistate complete active space second-order perturbation theory (MS-CASPT2) is one of the most successful quantum chemical methods for both static and dynamical correlations in photochemistry. In the literature, there are two definitions of the zeroth-order Hamiltonian depending on the form of the one-electron operator: Multistate multireference MS-CASPT2 (MS-MR-MS-CASPT2) and single-state single-reference MS-CASPT2 (SS-SR-MS-CASPT2). Here, we implement an analytical gradient and derivative coupling for S...

Quantitative analysis of QM/MM boundary artifacts and correction in adaptive QM/MM simulations.

A quantum chemical treatment of solvation effects using the standard quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulations is challenging due to QM and MM solvent exchange near the QM solute. To this end, various adaptive QM/MM methods have been proposed, free solvent exchanges are allowed via flexible switching of their identities between QM and MM systems depending on their distances from the QM solute. However, temporal and spatial discontinuities remain in the standard implement...

From Molecular Fragments to the Bulk: Development of a Neural Network Potential for MOF-5.

The development of first-principles-quality reactive atomistic potentials for organic-inorganic hybrid materials is still a substantial challenge because of the very different physics of the atomic interactions - from covalent via ionic bonding to dispersion - that have to be described in an accurate and balanced way. In this work we use a prototypical metal-organic-framework - MOF-5 - as a benchmark case to investigate the applicability of high-dimensional neural network potentials (HDNNP) to this type of ...

Real-Time Propagation TDDFT and Density Analysis for Exciton Coupling Calculations in Large Systems.

Photo-active systems are characterized by their capacity of absorbing the energy of light and transforming it. Usually, more than one chromophore is involved in the light absorption and excitation transport processes in complex systems. Linear-Response Time-Dependent Density Functional (LR-TDDFT) is commonly used to identify excitation energies and transition properties by solving well-known Casida's equation for single molecules. However, in practice LR-TDDFT presents some disadvantages when dealing with m...

Analytical Energy Gradients for the Cluster-in-Molecule MP2 Method and its Application to Geometry Optimizations of Large Systems.

An efficient analytical energy gradient algorithm for the cluster-in-molecule (CIM) second order Møller-Plesset perturbation theory (MP2) method is presented. In our algorithm, the gradient contributions from the non-separable term of the two-body density matrix on a given atom is extracted from calculations on a cluster constructed for this atom. The other terms in the CIM-MP2 energy gradient expression are evaluated by constructing the density matrices of the whole system with the contributions from all ...

Efficient ab initio auxiliary-field quantum Monte Carlo calculations in Gaussian bases via low-rank tensor decomposition.

We describe an algorithm to reduce the cost of auxiliary-field quantum Monte Carlo (AFQMC) calculations for the electronic structure problem. The technique uses a nested low-rank factorization of the electron repulsion integral (ERI). While the cost of conventional AFQMC calculations in Gaussian bases scales as O(N) where N is the size of the basis, we show that ground-state energies can be computed through tensor decomposition with reduced memory requirements and sub-quartic scaling. The algorithm is appli...

Structure and Dynamics of Water at the Water-Air Interface Using First Principles Molecular Dynamics Simulations II: Non-Local vs Empirical van der Waals Corrections.

Van der Waals (vdW) correction schemes have been recognized to be essential for accurate description of liquid water in first-principles molecular dynamics simulation. The description of the structure and dynamics of water is governed by the type of the vdW corrections. So far, two vdW correction schemes have been often used: empirical vdW corrections and non-local vdW corrections. In this paper, we assess the influence of the empirical vs. non-local vdW correction schemes on the structure and dynamics of w...

Exploring the Folding Mechanism of Small Proteins GB1 and LB1.

The computational atomistic description of the folding reactions of the B1 domains, GB1 and LB1, of protein G and protein L, respectively, is an important challenge in current protein folding studies. Although the two proteins have overall very similar backbone structures (β-hairpin-α-helix-β-hairpin), their apparent folding behaviors observed experimentally were remarkably different. LB1 folds in a two-state manner with the single-exponential kinetics, whereas GB1 folds in a more complex manner with an ...

Large-scale quantum-dynamics with matrix product states.

Dynamical electronic- and vibrational-structure theories have received a growing interest in the last years due to their ability to simulate spectra recorded with ultrafast experimental techniques. The exact time evolution of a molecular system can, in principle, be obtained from the time-dependent version of full configuration interaction. Such an approach is, however, limited to few-atom systems due to the exponential increase of its cost with the system dimension. In the present work, we overcome this un...

Kohn-Sham theory with paramagnetic currents: compatibility and functional differentiability.

Recent work has established Moreau-Yosida regularization as a mathematical tool to achieve rigorous functional differentiability in density-functional theory. In this article, we extend this tool to paramagnetic current-density-functional theory, the most common density-functional framework for magnetic field effects. The extension includes a well-defined Kohn-Sham iteration scheme with a partial convergence result. To this end, we rely on a formulation of Moreau-Yosida regularization for reflexive and stri...

Massively parallel implementation of Steered Molecular Dynamics in Tinker-HP: comparisons of polarizable and non-polarizable simulations of realistic systems.

Steered Molecular Dynamic (SMD) is a powerful technique able to accelerate rare events sampling in Molecular Dynamics (MD) simulations by applying an external force to a set of chosen atoms. Despite generating non-equilibrium simulations, SMD remains capable of reconstructing equilibrium properties such as the Potential of Mean Force (PMF). Of course, one would like to use all types of force fields (FF) ranging from classical ones to more advanced polarizable models using point induced dipoles and dis- trib...

OPEP6: A new constant-pH Molecular Dynamics simulation scheme with OPEP coarse-grained force field.

The great importance of pH for molecular processes has motivated the continuous development of numerical methods to improve the physical description of molecular mechanisms in computer simulations. Although rigid titration models are able to provide several useful information, the coupling between the molecular conformational changes and the acid-base equilibrium is necessary to more completely model the pH effects in biomolecules. Previous reported convergence issues with atomistic simulations indicated th...

Active Space Selection Based on Natural Orbital Occupation Numbers From N-Electron Valence Perturbation Theory.

Efficient and robust approximations to the full configuration interaction (Full-CI) method such as the density matrix renormalization group (DMRG) and the Full-CI quantum Monte-Carlo (FCIQMC) algorithm allow for multi-configurational self-consistent field (MC-SCF) calculations of molecules with many strongly correlated electrons. This opens up the possibility to treat large and complex systems that were previously untractable but at the same time it calls for an efficient and reliable active space selection...

Configurational entropy components and their contribution to biomolecular complex formation.

Configurational entropy change is a central constituent of the free energy change in non-covalent interactions between biomolecules. Due to both experimental and computational limitations, however, the impact of individual contributions to configurational entropy change remains underexplored. Here, we develop a novel, fully analytical framework to dissect the configurational entropy change of binding into contributions coming from molecular-internal and external degrees of freedom. Importantly, this framewo...

Anharmonic Vibrational States of Solids from DFT Calculations. Part I: Description of the Potential Energy Surface.

A computational approach is presented to compute anharmonic vibrational states of solids from quantum-mechanical DFT calculations by taking into explicit account phonon-phonon couplings via the vibrational configuration interaction (VCI) method. The Born-Oppenheimer potential energy surface (PES) is expanded in a Taylor's series in terms of harmonic normal coordinates, centered at the equilibrium nuclear configuration, is truncated to quartic order and contains one-mode, two-mode and three-mode interatomic ...

Thermodynamic Stability of polar and non-polar Amyloid Fibrils.

Thermodynamic stabilities of amyloid fibrils remain mostly unknown due to experimental challenges. Here, we use enhanced sampling simulations of all-atom models in explicit water to study the stability of non-polar (Aβ) and polar (IAPP) fibrils. We find that the non-polar fibril becomes more stable with increasing temperature and its stability is dominated by entropy. In contrast, the polar fibril becomes less stable with increasing temperature while it is stabilized by enthalpy. Our results show that the ...

Highly efficient algorithms for CIS type excited state wave function overlaps.

Two algorithms for calculating overlaps between CIS (or TDDFT) type excited state wave functions are presented, one based on an expansion of overlap determinants into level 2 minors (OL2M) and the other based on an expansion of the wave functions into natural transition orbitals (ONTO). Both algorithms are significantly faster than previously available algorithms, with the ONTO algorithm reducing the cost of a single overlap element calculation by a factor of the square of the number of occupied orbitals in...

Anharmonic Vibrational States of Solids from DFT Calculations. Part II: Implementation of the VSCF and VCI Methods.

Two methods are implemented in the CRYSTAL program for the calculation of anharmonic vibrational states of solids: the vibrational self-consistent field (VSCF) and the vibrational configuration-interaction (VCI). While the former is a mean-field approach, where each vibrational mode interacts with the average potential of the others, the latter allows for an explicit and complete account of mode-mode correlation. Both schemes are based on the representation of the adiabatic potential energy surface (PES) di...

The Curious Case of 2-Selenouracil: Efficient Population of Triplet States and Yet Photostable.

Excited-state MS-CASPT2 and ADC(2) quantum chemical calculations and nonadiabatic dynamics simulations show that 2-selenouracil is able to both efficiently populate and depopulate reactive triplet states in an ultrashort time scale. Thus, the heavier homologue of 2-thiouracil unites the ultrafast, high-yield intersystem crossing of 2-thiouracil with the short excited-state lifetime and photostability of the parent nucleobase uracil-two properties that have been traditionally though to be diametrically oppos...

Toward accurate hydrogen bonds by scalable quantum Monte Carlo.

Single-determinant (SD) fixed-node diffusion Monte Carlo (FNDMC) gains popularity as a benchmark method scalable to large noncovalent systems although its accuracy limits are not yet fully mapped out. We report on an interesting example of significant SD FNDMC accuracy variations in middle-sized hydrogen-bonded dimer complexes, formic acid (FA) vs methanediol (MD), distinct by the maximum bond order (2 vs 1). While the traditional SD FNDMC schemes based on bias cancellation are capable of achieving benchmar...

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

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...

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

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 signal...

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

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....

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

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....

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

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. In one case the well-known matrix product state ap- proximation is used whereas in another case ...


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