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Journal of Chemical Theory and Computation

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https://www.readbyqxmd.com/read/29466664/fixed-node-importance-sampling-diffusion-monte-carlo-for-vibrational-structure-with-accurate-and-compact-trial-states
#1
Ireneusz Wieslaw Bulik, Michael J Frisch, Patrick Henry Vaccaro
We present a new approach to importance sampling in diffusion Monte--Carlo (DMC) simulations of vibrational excited states whereby the trial wavefunctions for low--energy states are incorporated into the diffusion equations so as to enforce their orthogonality. For the model systems examined here, simple variational wavefunctions based on the vibrational self--consistent field (VSCF) and the simplest vibrational configuration--interaction (VCI) are effective in importance sampling provided that internal coordinates used in the underlying one-particle functions have been variationally optimized...
February 21, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29466663/cis-to-trans-isomerization-of-azobenzene-derivatives-studied-with-transition-path-sampling-and-qm-mm-molecular-dynamics
#2
Anja Muzdalo, Peter Saalfrank, Jocelyne Vreede, Mark Santer
Azobenzene-based molecular photoswitches are becoming increasingly important for the development of photoresponsive, functional soft-matter material systems. Upon illumination with light, fast interconversion between a more stable trans- and a metastable cis configuration can be established resulting in pronounced changes in conformation, dipole moment or hydrophobicity. A rational design of functional photosensitive molecules with embedded azo moieties requires a thorough understanding of isomerization mechanisms and rates, especially the thermally activated relaxation...
February 21, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29461830/correction-to-effect-of-monovalent-ion-parameters-on-molecular-dynamics-simulations-of-g-quadruplexes
#3
Marek Havrila, Petr Stadlbauer, Barira Islam, Michal Otyepka, Jiří Šponer
No abstract text is available yet for this article.
February 20, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29461829/towards-accurate-conformational-energies-of-smaller-peptides-and-medium-sized-macrocycles-mpconf196-benchmark-energy-data-set
#4
Jan Řezáč, Daniel Bím, Ondrej Gutten, Lubomír Rulíšek
Carefully selected set of acyclic and cyclic model peptides and several other macrocycles comprising 13 compounds in total, has been used to calibrate accuracy of DFT(-D3) method for conformational energies, employing BP86, PBE0, PBE, B3LYP, BLYP, TPSS, TPSSh, M06-2X, B97-D, OLYP, revPBE, M06-L, SCAN, revTPSS, BH-LYP, and ωB97X-D3 functionals. Both high- and low-energy conformers, 15‑16 for each compound adding to 196 in total, denoted as MPCONF196 data set, were included and the reference values were obtained by the composite protocol yielding the CCSD(T)/CBS extrapolated energies or their DLPNO-CCSD(T)/CBS equivalents in the case of larger systems...
February 20, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29461828/spin-orbit-coupling-via-four-component-multiference-methods-benchmarking-on-p-block-elements-and-tentative-recommendations
#5
Boyi Zhang, Jonathon E Vandezande, Ryan D Reynolds, Henry F Schaefer
Within current electronic structure theory methods, fully relativistic four-component (4c) methods based on the Dirac Hamiltonian treat spin-orbit coupling with the most rigor. The spin treatment arises naturally from the formulation and does not need to be included ad hoc. Spin-orbit splittings can provide insightful benchmark criteria for the assessment of 4c methods. However, there have not been extensive studies in this respect due to the computationally demanding nature of relativistic methods and the absence of in publicly available codes...
February 20, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29450992/assessment-of-fragmentation-strategies-for-large-proteins-using-the-multilayer-molecules-in-molecules-approach
#6
Bishnu Thapa, Daniel Beckett, K V Jovan Jose, Krishnan Raghavachari
We present a rigorous evaluation of the potential for the multilayer Molecules-in-Molecules (MIM) fragmentation method to be applied to large biomolecules. Density functional total energies of a test set of 8 peptides, sizes ranging from 107 to 721 atoms, were evaluated with MIM and compared to unfragmented energies to help develop a protocol for the treatment of large proteins. Fragmentation schemes involving subsystems of 4 to 5 covalently bonded fragments (tetramer or pentamer schemes) were tested with a single level of theory (MIM1) and produced errors on the order of 100 kcal/mol due to the relatively small size of the subsystems and the neglect of nonbonded interactions...
February 16, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29447447/dl_mg-a-parallel-multigrid-poisson-and-poisson-boltzmann-solver-for-electronic-structure-calculations-in-vacuum-and-solution
#7
James C Womack, Lucian Anton, Jacek Dziedzic, Philip J Hasnip, Matthew Ian James Probert, Chris-Kriton Skylaris
The solution of the Poisson equation is a crucial step in electronic structure calculations, yielding the electrostatic potential-a key component of the quantum mechanical Hamiltonian. In recent decades, theoretical advances and increases in computer performance have made it possible to simulate the electronic structure of extended systems in complex environments. This requires the solution of more complicated variants of the Poisson equation, featuring nonhomogeneous dielectric permittivities, ionic concentrations with non-linear dependencies, and diverse boundary conditions...
February 15, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29447445/electronic-exchange-and-correlation-in-van-der-waals-systems-balancing-semilocal-and-nonlocal-energy-contributions
#8
Jan Hermann, Alexandre Tkatchenko
Short-range correlations in motion of electrons in matter are captured well by semilocal exchange-correlation (XC) functionals in density functional theory (DFT), but long-range correlations are neglected in such models and must be treated by van der Waals (vdW) dispersion methods.Whereas the effective range of distances at which fluctuations are correlated is usually explicit in the vdW models, the complementary range of semilocal functionals can be observed only implicitly, requiring an introduction of empirical damping functions to couple the semilocal and nonlocal contributions to the XC energy...
February 15, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29446946/rapid-convergence-of-energy-and-free-energy-profiles-with-qm-size-in-qm-mm-simulations-of-proton-transfer-in-dna
#9
Susanta Das, Kwangho Nam, Dan T Major
In recent years, a number of quantum mechanical-molecular mechanical (QM/MM) enzyme studies have investigated the dependence of reaction energetics on the size of the QM region using energy and free energy calculations. Here, we revisit the question of QM region size dependence in QM/MM simulations within the context of energy and free energy calculations using a proton transfer in a DNA base pair as a test case. In the simulations, the QM region was treated with a dispersion-corrected AM1/d-PhoT Hamiltonian, which was developed to accurately describe phosphoryl and proton transfer reactions, in conjunction with an electrostatic embedding scheme using the particle-mesh Ewald summation method...
February 15, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29444408/simple-models-for-difficult-electronic-excitations
#10
Giuseppe M J Barca, Andrew T B Gilbert, Peter M W Gill
We present a single-determinant approach to three challenging topics in the chemistry of excited states: double excitations, charge-transfer states and conical intersections. The results are obtained by using the Initial Maximum Overlap Method (IMOM) which is a modified version of the Maximum Overlap Method (MOM). The new algorithm converges better than the original, especially for these difficult problems. By considering several case studies, we show that a single-determinant framework provides a simple and accurate alternative for modelling excited states in cases where other low-cost methods, such as CIS and TD-DFT, either perform poorly or fail completely...
February 14, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29444404/the-polarizable-density-embedding-coupled-cluster-method
#11
Dalibor Hr Scaron Ak, Jógvan Magnus Haugaard Olsen, Jacob Kongsted
We present theory and implementation of the polarizable density embedding (PDE) model in combination with coupled cluster (CC) theory (PDE-CC). This model has been implemented in the Dalton quantum chemistry program by adapting the CC code to the polarizable embedding library (PElib). In the PDE-CC method, the smaller, but chemically important core region is described with a high-level CC method. The environment surrounding the core region can be separated into two levels of description: an inner and an outer region...
February 14, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29444398/the-importance-of-cell-shape-sampling-to-accurately-predict-flexibility-in-metal-organic-frameworks
#12
Sven M J Rogge, Senne Caroes, Ruben Demuynck, Michel Waroquier, Veronique Van Speybroeck, An Ghysels
In this paper, the influence of cell shape sampling on the predicted stability of the different metastable phases in flexible metal-organic frameworks at finite temperatures is investigated. The influence on the free energy by neglecting cell shape sampling is quantified for the prototypical MIL-53(Al) and the topical DUT-49(Cu). This goal is achieved by constructing free energy profiles in ensembles either in which the phase space associated with the cell shape is sampled explicitly, or in which the cell shape is kept fixed...
February 14, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29439575/density-dependent-formulation-of-dispersion-repulsion-interactions-in-hybrid-qm-mm-models
#13
Carles Curutchet, Lorenzo Cupellini, Jacob Kongsted, Stefano Corni, Luca Frediani, Arnfinn Hykkerud Steindal, Ciro Achille Guido, Giovanni Scalmani, Benedetta Mennucci
Mixed QM/MM models are widely used to explore the structure, reactivity and electronic properties of complex chemical systems. Whereas such models typically include electrostatics, and potentially polarization in so-called electrostatic and polarizable embedding approaches, respectively, non-electrostatic dispersion and repulsion interactions are instead commonly described through classical potentials despite their quantum mechanical origin. Here we present an extension of the Tkatchenko-Scheffler semiempirical van der Waals (vdWTS) scheme aimed at describing dispersion and repulsion interactions between quantum and classical regions within a QM/MM polarizable embedding framework...
February 13, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29439560/multiscale-simulation-of-protein-hydration-using-the-swinger-dynamical-clustering-algorithm
#14
Julija Zavadlav, Siewert J Marrink, Matej Praprotnik
To perform computationally efficient concurrent multiscale simulations of biological macromolecules in solution, where the all-atom (AT) models are coupled to supramolecular coarse-grained (SCG) solvent models, previous studies resorted to a modified AT water models, such as the bundled-SPC models, that use semi-harmonic springs to restrict the relative movement of water molecules within a cluster. Those models can have a significant impact on the simulated biomolecules and can lead, for example, to a partial unfolding of a protein...
February 13, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29438622/amoeba-polarizable-atomic-multipole-force-field-for-nucleic-acids
#15
Changsheng Zhang, Chao Lu, Zhifeng Jing, Chuanjie Wu, Jean-Philip Piquemal, Jay William Ponder, Pengyu Ren
The AMOEBA polarizable atomic multipole force field for nucleic acids is presented. Valence and electrostatic parameters were determined from high-level quantum mechanical data, including structures, conformational energy and electrostatic potentials, of nucleotide model compounds. Previously derived parameters for the phosphate group and nucleobases were incorporated. A total of over 35 microseconds of condensed phase molecular dynamics simulations of DNA and RNA molecules in aqueous solution and crystal lattice were performed to validate and refine the force field...
February 13, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29438621/explicit-solvation-matters-performance-of-qm-mm-solvation-models-in-nucleophilic-addition
#16
Jelle M Boereboom, Paul Fleurat-Lessard, Rosa E Bulo
Nucleophilic addition onto a carbonyl moiety is strongly affected by solvent, and correctly simulating this solvent effect is often beyond the capability of single-scale quantum mechanical (QM) models. This work explores multi-scale approaches for the description of the reversible and highly solvent-sensitive nucleophilic N|···C=O bond formation in an Me 2 N-(CH 2 ) 3 -CH=O molecule. In the first stage of this work we rigorously compare and test four recent quantum mechanical / molecular mechanical (QM/MM) explicit solvation models, employing a QM description of water molecules in spherical regions around both the oxygen and the nitrogen atom of the solute...
February 13, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29438614/molecular-dynamics-simulations-with-quantum-mechanics-molecular-mechanics-and-adaptive-neural-networks
#17
Lin Shen, Weitao Yang
Direct molecular dynamics (MD) simulation with ab initio quantum mechanical and molecular mechanical (QM/MM) methods is very powerful for studying the mechanism of chemical reactions in complex environment but very time consuming. The computational cost on QM/MM calculations during MD simulations can be reduced significantly using semiempirical QM/MM methods with lower accuracy. To achieve higher accuracy at the ab initio QM/MM level, a correction on the existing semiempirical QM/MM model is an attractive way...
February 13, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29438613/comparative-charmm-and-amoeba-simulations-of-lanthanide-hydration-energetics-and-experimental-aqueous-solution-structures
#18
Baofu Qiao, S Skanthakumar, Lynda Soderholm
The accurate understanding of metal ion hydration in solutions is a prerequisite for predicting its stability, reactivity, and solubility. Herein additive CHARMM force field parameters were developed to enable molecular dynamics (MD) simulations of lanthanide (Ln) speciation in water. Quantitatively similar to the much more resource intensive polarizable AMOEBA potential, the CHARMM simulations reproduce the experimental hydration free energies and correlations in the first shell (Ln-oxygen distance and hydration number)...
February 13, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29431996/combining-the-transcorrelated-method-with-full-configuration-interaction-quantum-monte-carlo-application-to-the-homogeneous-electron-gas
#19
Hongjun Luo, Ali Alavi
We suggest an efficient method to resolve electronic cusps in electronic structure calculations, throug the use of an effective transcorrelated Hamiltonian. This effective Hamiltonian takes a simple form for plane wave bases, containing up to two-body operators only, and its use incurs almost no additional computational overhead compared to that of the original Hamiltonian. We apply this method in combination with the full configuration interaction quantum Monte Carlo (FCIQMC) method to the homogeneous electron gas...
February 12, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29425032/floquet-study-of-quantum-control-of-the-cis-trans-photoisomerization-of-rhodopsin
#20
Pablo E Videla, Andreas Markmann, Victor S Batista
Understanding how to control reaction dynamics of polyatomic systems by using ultrafast laser technology is a fundamental challenge of great technological interest. Here, we report a Floquet theoretical study of the effect of light-induced potentials on the ultrafast cis-trans photoisomerization dynamics of rhodopsin. The Floquet Hamiltonian involves an empirical 3-state 25-mode model with frequencies and excited-state gradients parameterized to reproduce the rhodopsin electronic vertical excitation energy, the resonance Raman spectrum, and the photoisomerization time and efficiency as probed by ultrafast spectroscopy...
February 9, 2018: Journal of Chemical Theory and Computation
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