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Journal of Chemical Theory and Computation

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https://www.readbyqxmd.com/read/28085284/quantitative-assessment-of-molecular-dynamics-sampling-for-flexible-systems
#1
Mike Nemec, Daniel Hoffmann
Molecular dynamics (MD) simulation is a natural method for the study of flexible molecules, but at the same time limited by the large size of the conformational space of these molecules. We ask by how much the MD sampling quality for flexible molecules can be improved by two means, the use of diverse sets of trajectories starting from different initial conformations to detect deviations between samples, and sampling with enhanced methods such as accelerated MD (aMD) or scaled MD (sMD) that distort the energy landscape in controlled ways...
January 13, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28030769/polarizable-multipole-based-force-field-for-aromatic-molecules-and-nucleobases
#2
Changsheng Zhang, David Bell, Matthew Harger, Pengyu Ren
Aromatic molecules with π electrons are commonly involved in chemical and biological recognitions. For example, nucleobases play central roles in DNA/RNA structure and their interactions with proteins. The delocalization of the π electrons is responsible for the high polarizability of aromatic molecules. In this work, the AMOEBA force field has been developed and applied to 5 regular nucleobases and 12 aromatic molecules. The permanent electrostatic energy is expressed as atomic multipole interactions between atom pairs, and many-body polarization is accounted for by mutually induced atomic dipoles...
January 13, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28081366/an-estimation-of-hybrid-quantum-mechanical-molecular-mechanical-qm-mm-polarization-energies-for-small-molecules-using-polarizable-force-field-approaches
#3
Jing Huang, Ye Mei, Gerhard Koenig, Andrew C Simmonett, Frank C Pickard, Qin Wu, Lee-Ping Wang, Alexander D MacKerell, Bernard R Brooks, Yihan Shao
In this work, we report two polarizable molecular mechanics (polMM) force field models for estimating the polarization energy in hybrid quantum mechanical molecular mechanical (QM/MM) calculations. These two models, named the potential of atomic charges (PAC) and potential of atomic dipoles (PAD), are formulated from the ab initio quantum mechanical (QM) response kernels for the prediction of the QM density response to an external molecular mechanical (MM) environment (as described by external point charges)...
January 12, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28080059/a-computational-approach-for-modeling-neutron-scattering-data-from-lipid-bilayers
#4
Jan-Michael Y Carrillo, John Katsaras, Bobby G Sumpter, Rana Ashkar
Biological cell membranes are responsible for a range of structural and dynamical phenomena crucial to a cell's well-being and its associated functions. Due to the complexity of cell membranes, lipid bilayer systems are often used as biomimetic models. These systems have led to significant insights into vital membrane phenomena such as domain formation, passive permeation and protein insertion. Experimental observations of membrane structure and dynamics are, however, limited in resolution, both spatially and temporally...
January 12, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28080054/bond-dissociation-energies-for-diatomic-molecules-containing-3d-transition-metals-benchmark-scalar-relativistic-coupled-cluster-calculations-for-twenty-molecules
#5
Lan Cheng, Jürgen Gauss, Branko Ruscic, Peter B Armentrout, John F Stanton
Benchmark scalar-relativistic coupled-cluster calculations for dissociation energies of the twenty diatomic molecules containing 3d transition metals in the 3dMLBE20 database (Xu et al., J. Chem. Theory Comput. 2015, 11, 2036) ) are reported. Electron correlation and basis set effects are systematically studied. The agreement between theory and experiment is in general satisfactory. For a subset of sixteen molecules, the standard deviation between computational and experimental values is 9 kJ/mol with the maximum deviation being 15 kJ/mol...
January 12, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28080052/mechanochemical-tuning-of-pyrene-absorption-spectrum-using-force-probes
#6
Miguel Angel Fernández-González, Daniel Rivero, Cristina García-Iriepa, Diego Sampedro, Luis Manuel Frutos
Control of absorption spectra in chromophores is a fundamental aspect of many photochemical and photophysical processes as it constitutes the first step of the global photoinduced process. Here we explore the use of mechanical forces to modulate the light absorption process. Specifically, we develop a computational formalism for determining the type of mechanical forces permitting a global tuning of the absorption spectrum. This control extends to the excitation wavelength, absorption bands overlap and oscillator strength...
January 12, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28080051/prediction-of-bond-dissociation-energies-heat-of-formation-for-diatomic-transition-metal-compounds-ccsd-t-works
#7
Zongtang Fang, Monica Vasiliu, Kirk A Peterson, David A Dixon
It was recently reported (J. Chem. Theory Comput. 2015, 11, 2036-2052) that the coupled cluster singles and doubles with perturbative triples method, CCSD(T), should not be used as a benchmark tool for the prediction of dissociation energies (heats of formation) for the 1st row transition metal diatomics based on a comparison with the experimental thermodynamic values for a set of 20 diatomics. In the present work the bond dissociation energies as well as the heats of formation for those diatomics have been calculated by the Feller-Peterson-Dixon approach at the CCSD(T)/complete basis set (CBS) level of theory including scalar relativistic corrections and correlation of the outer shell of core electrons in addition to the valence electrons...
January 12, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28080049/modeling-diversity-in-structures-of-bacterial-outer-membrane-lipids
#8
Huilin Ma, Daniel D Cummins, Natalie Brooke Edelstein, Jerry Gomez, Aliza Khan, Masud Dikita Llewellyn, Tara Picudella, Sarah Rose Willsey, Shikha Nangia
Lipopolysaccharides are vital components of the outer membrane of gram-negative bacteria, and they act as extremely strong stimulators of innate immunity in diverse eukaryotic species. The primary immunostimulatory center of the LPS molecule is lipid A-a disaccharide-bound lipophilic domain. Considering the broad diversity in bacterial species, there are variations in the lipid A structure and their immunogenic potency. In this work, we model the lipid A structures of eight commensal or human pathogenic bacterial species: Helicobacter pylori, Porphyromonas gingivalis, Bacteroides fragilis, Bordetella pertussis, Chlamydia trachomatis, Campylobacter jejuni, Neisseria meningitidis, and Salmonella minnesota...
January 12, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28075588/accurate-reference-data-for-the-non-additive-non-interacting-kinetic-energy-in-covalent-bonds
#9
Jonathan Nafziger, Kaili Jiang, Adam Wasserman
The non-additive non-interacting kinetic energy (NAKE) is calculated numerically for fragments of H2, Li2, Be2, C2, N2, F2, and Na2 within partition density-functional theory (PDFT). The resulting fragments are uniquely determined and their sum reproduces the Kohn-Sham molecular density of the corresponding XC functional. We present the NAKE of these unique fragments as a function of inter-nuclear separation and compare the use of fractional orbital occupation to the usual PDFT ensemble method for treating the fragment energies and densities...
January 11, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28072537/a-qm-mm-study-of-substituent-and-solvent-effects-on-the-excited-state-dynamics-of-the-photoactive-yellow-protein-chromophore
#10
Francisco Fernández García-Prieto, Aurora Muñoz-Losa, Ignacio Fdez Galván, M Luz Sánchez, Manuel Ángel Aguilar, M Elena Martín
Substituent and solvent effects on the excited state dynamics of the Photoactive Yellow Protein chromophore are studied using the average solvent electrostatic potential from molecular dynamics (ASEP/MD) method. Four molecular models were considered: the ester and thioester derivatives of the p-coumaric acid anion and their methyla ted derivatives. We found that the solvent produces dramatic modifications on the free energy profile of the S1 state: 1) Two twisted structures that are minima in gas phase could not be located in aqueous solution...
January 10, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28072533/coupled-cluster-valence-bond-singles-and-doubles-for-strongly-correlated-systems-block-tensor-based-implementation-and-application-to-oligoacenes
#11
Joonho Lee, David W Small, Evgeny Epifanovsky, Martin Head-Gordon
We demonstrate a block-tensor based implementation of coupled-cluster valence- bond singles and doubles (CCVB-SD) [J. Chem. Phys. 2012, 137, 114103] which is a simple modification to restricted CCSD (RCCSD) that provides a qualitatively correct description of valence correlations even in strongly correlated systems. We derive the Λ-equation of CCVB-SD and the corresponding unrelaxed density matrices. The resulting production-level implementation is applied to oligoacenes, correlating up to 318 electrons in 318 orbitals...
January 10, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28072522/evaluating-electronic-couplings-for-excited-state-charge-transfer-based-on-maximum-occupation-method-mom-%C3%AE-scf-quasi-adiabatic-states
#12
Junzi Liu, Yong Zhang, Peng Bao, Yuanping Yi
Electronic couplings of charge-transfer states with the ground state and localized excited states at the donor/acceptor interface are crucial parameters for controlling the dynamics of exciton dissociation and charge recombination processes in organic solar cells. Here we propose a quasi-adiabatic state approach to evaluate electronic couplings through combining mom-ΔSCF and state diabatization schemes. Compared with TDDFT using global hybrid functional, mom-ΔSCF is superior to estimate the excitation energies of charge-transfer states; moreover it can also provide good excited state wave functions...
January 10, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28005387/dimer-metadynamics
#13
Marco Nava, Ferruccio Palazzesi, Claudio Perego, Michele Parrinello
Sampling complex potential energies is one of the most pressing challenges of contemporary computational science. Inspired by recent efforts that use quantum effects and discretized Feynman's path integrals to overcome large barriers we propose a replica exchange method that we expect to be effective at least for systems of up to 150 atoms roughly. In each replica two copies of the same system with halved potential strengths interact via inelastic springs. The strength of the spring is varied in the different replicas so as to bridge the gap between the infinitely strong spring, that corresponds to the Boltzmann replica, and the less tight ones...
January 10, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28005364/automatic-generation-of-auxiliary-basis-sets
#14
Georgi L Stoychev, Alexander A Auer, Frank Neese
A procedure was developed to automatically generate auxiliary basis sets (ABSs) for use with the resolution of the identity (RI) approximation, starting from a given orbital basis set (OBS). The goal is to provide an accurate and universal solution for cases where no optimized ABSs are available. In this context, "universal" is understood as the ability of the ABS to be used for Coulomb, exchange, and correlation energy fitting. The generation scheme (denoted AutoAux) works by spanning the product space of the OBS using an even-tempered expansion for each atom in the system...
January 10, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28068092/systematic-quantum-mechanical-region-determination-in-qm-mm-simulation
#15
Maria Karelina, Heather J Kulik
Hybrid quantum mechanical-molecular mechanical (QM/MM) simulations are widely used in enzyme simulation. Over ten convergence studies of QM/MM methods have revealed over the past several years that key energetic and structural properties approach asymptotic limits with only very large (ca. 500-1000 atom) QM regions. This slow convergence has been observed to be due in part to significant charge transfer between the core active site and surrounding protein environment, which cannot be addressed by improvement of MM force fields or the embedding method employed within QM/MM...
January 9, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28030771/harmonically-assisted-methods-for-computing-the-free-energy-of-classical-crystals-by-molecular-simulation-a-comparative-study
#16
Sabry G Moustafa, Andrew J Schultz, David A Kofke
Four methods for calculation of the classical free energy of crystalline systems are compared with respect to their efficiency and accuracy. Two of the methods involve thermodynamic integration along an unphysical path (λ integration, λI), and two involve integration in temperature from the low-temperature harmonic limit (T integration, TI). Specifically, the methods considered are (1) Frenkel-Ladd integration from a noninteracting Einstein crystal reference (ECR-λI); (2) conventional integration in temperature (Conv-TI); (3) integration from an interacting quasi-harmonic reference (QHR-λI); and (4) temperature integration using harmonically mapped averaging to evaluate the integrand (HMA-TI)...
January 9, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28009515/efficient-constrained-density-functional-theory-implementation-for-simulation-of-condensed-phase-electron-transfer-reactions
#17
Nico Holmberg, Kari Laasonen
Constrained density functional theory (CDFT) is a versatile tool for probing the kinetics of electron transfer (ET) reactions. In this work, we present a well-scaling parallel CDFT implementation relying on a mixed basis set of Gaussian functions and plane waves, which has been specifically tailored to investigate condensed phase ET reactions using an explicit, quantum chemical representation of the solvent. The accuracy of our implementation is validated against previous theoretical results for predicting electronic couplings and charge transfer energies...
January 9, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28060507/combining-internally-contracted-states-and-matrix-product-states-to-perform-multireference-perturbation-theory
#18
Sandeep Sharma, Gerald Knizia, Sheng Guo, Ali Alavi
We present two efficient and intruder-free methods for treating dynamic correlation on top of general multi-configuration reference wave functions---including such as obtained by the density matrix renormalization group (DMRG) with large active spaces. The new methods are the second order variant of the recently proposed multi-reference linearized coupled cluster method (MRLCC) [S. Sharma, A. Alavi, J. Chem. Phys. 143, 102815 (2015)], and of N-electron valence perturbation theory (NEVPT2), with expected accuracies similar to MRCI+Q and (at least) CASPT2, respectively...
January 6, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28058835/hybrid-basis-close-coupling-interface-to-quantum-chemistry-packages-for-the-treatment-of-ionization-problems
#19
Carlos Marante, Markus Klinker, Inés Corral, Jesús González-Vázquez, Luca Argenti, Fernando Martín
The theoretical description of observables in attosecond pump-probe experiments requires a good representation of the system's ionization continuum. For polyelectronic molecules, however, this is still a challenge, due to the complicated short-range structure of correlated electronic wave functions. Whereas quantum chemistry packages (QCP) implementing sophisticated methods to compute bound electronic molecular states are well-established, comparable tools for the continuum are not widely available yet. To tackle this problem, we have developed a new approach that, by means of a hybrid Gaussian-B-spline basis, interfaces existing QCPs with close-coupling scattering methods...
January 6, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28005360/relativistic-prolapse-free-gaussian-basis-sets-of-quadruple-%C3%AE-quality-aug-rpf-4z-iii-the-f-block-elements
#20
Tiago Quevedo Teodoro, Lucas Visscher, Albérico Borges Ferreira da Silva, Roberto Luiz Andrade Haiduke
The f-block elements are addressed in this third part of a series of prolapse-free basis sets of quadruple-ζ quality (RPF-4Z). Relativistic adapted Gaussian basis sets (RAGBSs) are used as primitive sets of functions while correlating/polarization (C/P) functions are chosen by analyzing energy lowerings upon basis set increments in Dirac-Coulomb multireference configuration interaction calculations with single and double excitations of the valence spinors. These function exponents are obtained by applying the RAGBS parameters in a polynomial expression...
January 6, 2017: Journal of Chemical Theory and Computation
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