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Journal of Chemical Theory and Computation

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https://www.readbyqxmd.com/read/28453287/effective-inclusion-of-mechanical-and-electrical-anharmonicity-in-excited-electronic-states-the-vpt2-tddft-route
#1
Franco Egidi, David B Williams-Young, Alberto Baiardi, Julien Bloino, Giovanni Scalmani, Michael J Frisch, Xiaosong Li, Vincenzo Barone
We present a reliable and cost-effective procedure for the inclusion of anharmonic effects in excited-state energies and spectroscopic intensities by means of second-order vibrational perturbation theory. This development is made possible thanks to a recent efficient implementation of excited-state analytic Hessians and properties within the time-dependent density functional theory framework. As illustrated in this work, by taking advantage of such algorithmic developments, it is possible to perform calculations of excited-state infrared spectra of medium-large isolated molecular systems, with anharmonicity effects included in both the energy and property surfaces...
April 28, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28426221/charge-transport-in-nanostructured-materials-implementation-and-verification-of-constrained-density-functional-theory
#2
Matthew B Goldey, Nicholas P Brawand, Márton Vörös, Giulia Galli
The in silico design of novel complex materials for energy conversion requires accurate, ab initio simulation of charge transport. In this work, we present an implementation of constrained density functional theory (CDFT) for the calculation of parameters for charge transport in the hopping regime. We verify our implementation against literature results for molecular systems, and we discuss the dependence of results on numerical parameters and the choice of localization potentials. In addition, we compare CDFT results with those of other commonly used methods for simulating charge transport between nanoscale building blocks...
April 28, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28358499/investigation-of-a-quantum-monte-carlo-protocol-to-achieve-high-accuracy-and-high-throughput-materials-formation-energies
#3
Kayahan Saritas, Tim Mueller, Lucas Wagner, Jeffrey C Grossman
High-throughput calculations based on density functional theory (DFT) methods have been widely implemented in the scientific community. However, depending on both the properties of interest as well as particular chemical/structural phase space, accuracy even for correct trends remains a key challenge for DFT. In this work, we evaluate the use of quantum Monte Carlo (QMC) to calculate material formation energies in a high-throughput environment. We test the performance of automated QMC calculations on 21 compounds with high quality reference data from the Committee on Data for Science and Technology (CODATA) thermodynamic database...
April 28, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28448125/efficient-computation-of-exchange-energy-density-with-gaussian-basis-functions
#4
Fenglai Liu, Jing Kong
Density Functional Theory(DFT) is widely applied in chemistry and Physics. Still it fails to predict correctly quantitatively or even qualitatively for systems with significant nondynamic correlations. Several DFT functionals were proposed in recently years to treat nondynamic correlation, most of which added the exact exchange energy density as a new variable, which becomes the computational bottleneck for calculations with these new functionals We present an implementation of an efficient seminumerical algorithm in this paper as a solution for this computational bottleneck...
April 27, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28441484/fully-quantum-description-of-the-zundel-ion-combining-variational-quantum-monte-carlo-with-path-integral-langevin-dynamics
#5
Félix Mouhat, Sandro Sorella, Rodolphe Vuilleumier, Antonino Marco Saitta, Michele Casula
We introduce a novel approach for a fully quantum description of coupled electron-ion systems from first principles. It combines the variational quantum Monte Carlo solution of the electronic part with the path integral formalism for the quantum nuclear dynamics. On the one hand, the path integral molecular dynamics includes nuclear quantum effects by adding a set of fictitious classical particles (beads) aimed at reproducing nuclear quantum fluctuations via a harmonic kinetic term. On the other hand, variational quantum Monte Carlo can provide Born-Oppenheimer potential energy surfaces with a precision comparable to the most advanced post Hartree-Fock approaches, and with a favorable scaling with the system size...
April 25, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28441477/local-electron-correlation-treatment-in-extended-multireference-calculations-effect-of-acceptor-donor-substituents-on-the-biradical-character-of-the-polycyclic-aromatic-hydrocarbon-heptazethrene
#6
Anita Das, Thomas Müller, Felix Plasser, David B Krisiloff, Emily A Carter, Hans Lischka
The implementation of a local correlation (LC) treatment of multireference (MR) configuration interaction approaches within the COLUMBUS program system is reported. The LC treatment is based on the weak pairs approximation of Sæbø and Pulay (Ann. Rev. Phys. Chem.44 (1993) 213) and a geometrical analysis of Walter et al. (Chem. Phys. Lett. 346 (2001) 177). The weak pairs interactions have been eliminated considering just the reference doubly occupied space leading to a straightforward program implementation and a conceptual simplicity in terms of well-defined localized orbitals...
April 25, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28418668/computing-the-diamagnetic-susceptibility-and-diamagnetic-anisotropy-of-membrane-proteins-from-structural-subunits
#7
Mahnoush Babaei, Isaac C Jones, Kaushik Dayal, Meagan S Mauter
The behavior of large, complex molecules in the presence of magnetic fields is experimentally challenging to measure and computationally intensive to predict. This work proposes a novel, mixed-methods approach for efficiently computing the principal magnetic susceptibilities and diamagnetic anisotropy of membrane proteins. The hierarchical primary (amino acid), secondary (α helical and β sheet), and tertiary (α helix and β barrel) structure of transmembrane proteins enables analysis of a complex molecule using discrete subunits of varying size and resolution...
April 25, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28437618/state-of-the-art-calculations-of-sublimation-enthalpies-for-selected-molecular-crystals-and-their-computational-uncertainty
#8
Ctirad Červinka, Michal Fulem
A computational methodology for calculation of sublimation enthalpies of molecular crystals from first principles is developed and validated by comparison to critically evaluated literature experimental data. Temperature dependent sublimation enthalpies for a set of selected 22 molecular crystals in their low-temperature phases are calculated. The computational methodology consists in several building blocks based on high level electronic structure methods of quantum chemistry and statistical thermodynamics...
April 24, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28437616/neural-network-and-nearest-neighbour-algorithms-for-enhancing-sampling-of-molecular-dynamics
#9
Raimondas Galvelis, Yuji Sugita
The free energy calculations of complex chemical and biological systems with molecular dynamics (MD) are inefficient due to multiple local minima separated by high-energy barriers. The minima can be escaped using an enhanced sampling method such as metadynamics, which apply bias (i.e. importance sampling) along a set of collective variables (CV), but the maximum number of CVs (or dimensions) is severely limited. We propose a high-dimensional bias potential method (NN2B) based on two machine learning algorithms: the nearest neighbour density estimator (NNDE) and the artificial neural network (ANN) for the bias potential approximation...
April 24, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28437611/dynamical-insights-in-the-decomposition-of-1-2-dioxetane
#10
Morgane Vacher, Anders M Brakestad, Hans O Karlsson, Ignacio Fdez Galván, Roland Lindh
Chemiluminescence in 1,2-dioxetane occurs via a thermally-activated decomposition reaction into two formaldehyde molecules. Both ground state and non-adiabatic dynamics (including singlet excited states) of the decomposition reaction have been simulated, starting from the first O-O bond breaking transition structure. The ground state dissociation occurs between t=30 fs and t=140 fs. The so-called entropic trap leads to frustrated dissociations, postponing the decomposition reaction. Specific geometrical conditions are necessary for the trajectories to escape from the entropic trap and for dissociation to be possible...
April 24, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28437607/the-real-cost-of-speed-the-effect-of-a-time-saving-multiple-time-stepping-algorithm-on-the-accuracy-of-molecular-dynamics-simulations
#11
Sabine Reisser, David Poger, Martin Stroet, Alan Edward Mark
To enhance efficiency in molecular dynamics simulations, forces that vary slowly are often evaluated less often than those that vary rapidly. We show that the multiple-time-step algorithm implemented in recent versions of GROMACS results in significant differences in the collective properties of a system under conditions where the system was previously stable. The implications of changing the simulation algorithm without assessment of potential artifacts on the parameterisation and transferability of effective force fields are discussed...
April 24, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28437115/development-and-implementation-of-advanced-fitting-methods-for-the-calculation-of-accurate-molecular-structures
#12
Marco Mendolicchio, Emanuele Penocchio, Daniele Licari, Nicola Tasinato, Vincenzo Barone
The determination of accurate equilibrium molecular structures plays a fundamental role for understanding many physical-chemical properties of molecules, ranging from the precise evaluation of the electronic structure to the analysis of dynamical and environmental effects in tuning their overall behavior. For this purpose the so-called semi-experimental approach, based on a non-linear least-squares fit of the moments of inertia associated to a set of available isotopologues, allows one to obtain very accurate results, without the unfavorable computational cost characterizing high-level quantum chemical methods...
April 24, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28437107/multiple-state-nonadiabatic-dynamics-simulation-of-photoisomerization-of-acetylacetone-with-the-direct-ab-initio-qtmf-approach
#13
Binbin Xie, Ganglong Cui, Wei-Hai Fang
In the present work, quantum trajectory mean-field (QTMF) approach is numerically implemented by ab initio calculation at the level of the complete active space self-consistent field, which is used to simulate photoisomerization of acetylacetone at ~265 nm. The simulated results shed light on the possible nonadiabatic pathways from the S2 state and mechanism of the photoisomerization. The in-plane proton transfer and the subsequent S2-S1 transition through the E-S2/S1-1 intersection region are the predominant route to the S1 state...
April 24, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28437102/insights-into-the-complex-photophysics-and-photochemistry-of-the-simplest-nitroaromatic-compound-a-caspt2-casscf-study-on-nitrobenzene
#14
Angelo Giussani, Graham A Worth
Nitrobenzene is the simplest nitroaromatic compound and yet is characterized by a challenging and rich photophysics and photochemistry. In the present contribution the main decay paths undertaken by the system after UV absorption from both the brightest 1(La*) and the lowest 1(nA*) singlet excited states have been characterized by means of CASPT2//CASSCF computations. The obtained results match with the main photophysical properties experimentally reported: the lack of fluorescence and phosphorescence emission is justified by the presence of accessible conical intersections and intersystem crossing regions between respectively the 1(nA*) and 3(nA*) states with the ground state, while the high triplet quantum yield is attributable to the strong coupling between the 1(nA*) and 3(O*) states along the main decay path of the former...
April 24, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28437100/reparameterization-of-solute-solute-interactions-for-amino-acid-sugar-systems-using-isopiestic-osmotic-pressure-molecular-dynamics-simulations
#15
Wesley Kayser Lay, Mark S Miller, Adrian Hamilton Elcock
AMBER/GLYCAM and CHARMM are popular force fields for simulations of amino acids and sugars. Here we report excessively attractive amino acid-sugar interactions in both force fields, and corrections to nonbonded interactions that match experimental osmotic pressures of mixed aqueous solutions of diglycine and sucrose. The modified parameters also improve the ∆Gtrans of diglycine from water to aqueous sucrose and, with AMBERff99SB/GLYCAM06, eliminate a caging effect seen in previous simulations of the protein ubiquitin with glucose...
April 24, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28437096/importance-of-mm-polarization-in-qm-mm-studies-of-enzymatic-reactions-assessment-of-the-qm-mm-drude-oscillator-model
#16
Abir Ganguly, Eliot Boulanger, Walter Thiel
For accurate quantum mechanics/molecular mechanics (QM/MM) studies of enzymatic reactions, it is desirable to include MM polarization, for example by using the Drude oscillator (DO) model. For a long time, such studies were hampered by the lack of well-tested polarizable force fields for proteins. Following up on a recent preliminary QM/MM-DO assessment (J. Chem. THEORY: Comput. 2014, 10, 1795-1809) we now report a comprehensive investigation of the effects of MM polarization on two enzymatic reactions, namely the Claisen rearrangement in chorismate mutase and the hydroxylation reaction in p-hydroxybenzoate hydrolase, using the QM/CHARMM-DO model and two QM methods (B3LYP, OM2)...
April 24, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28437074/many-body-energy-decomposition-with-basis-set-superposition-error-corrections
#17
Istvan Mayer, Imre Bako
The problem of performing many-body decompositions of energy is considered in the case when BSSE corrections are also performed. It is discussed that the two different schemes that have been proposed go back to the two different interpretations of the original Boys-Bernardi counterpoise correction scheme. It is argued that from the physical point of view the ``hierarchical" scheme of Valiron and Mayer should be preferred, and not the scheme recently discussed by Ouyang and Bettens, because it permits the energy of the individual monomers and all the two-body, three-body etc...
April 24, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28418655/accuracy-test-of-the-opls-aa-force-field-for-calculating-free-energies-of-mixing-and-comparison-with-pac-mac
#18
Augustinus J M Sweere, Johannes G E M Fraaije
We have calculated the excess free energy of mixing of 1053 binary mixtures with the OPLS-AA force field using two different methods: thermodynamic integration (TI) of molecular dynamics simulations and the Pair Configuration to Molecular Activity Coefficient (PAC-MAC) method. PAC-MAC is a force field based quasi-chemical method for predicting miscibility properties of various binary mixtures. The TI calculations yield a root mean squared error (RMSE) compared to experimental data of 0.132 kBT (0.37 kJ/mol)...
April 24, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28418654/a-robust-and-accurate-tight-binding-quantum-chemical-method-for-structures-vibrational-frequencies-and-noncovalent-interactions-of-large-molecular-systems-parametrized-for-all-spd-block-elements-z-1-86
#19
Stefan Grimme, Christoph Bannwarth, Philip Shushkov
We propose a novel, special purpose semiempirical tight binding (TB) method for the calculation of structures, vibrational frequencies, and noncovalent interactions of large molecular systems with 1000 or more atoms. The functional form of the method is related to the self-consistent density functional TB scheme and mostly avoids element-pair-specific parameters. The parametrization covers all spd-block elements and the lanthanides up to Z = 86 using reference data at the hybrid density functional theory level...
April 24, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28399373/extended-ensemble-approach-to-transferable-potentials-for-low-resolution-coarse-grained-models-of-ionomers
#20
Joseph F Rudzinski, Keran Lu, Scott T Milner, Janna K Maranas, William G Noid
We develop an extended ensemble method for constructing transferable, low-resolution coarse-grained (CG) models of polyethylene-oxide (PEO)-based ionomer chains with varying composition at multiple temperatures. In particular, we consider ionomer chains consisting of 4 isophthalate groups, which may be neutral or sulfonated, that are linked by 13 PEO repeat units. The CG models represent each isophthalate group with a single CG site and also explicitly represent the diffusing sodium counterions but do not explicitly represent the PEO backbone...
April 24, 2017: Journal of Chemical Theory and Computation
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