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Journal of Chemical Theory and Computation

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https://www.readbyqxmd.com/read/29906395/universal-implementation-of-a-residue-specific-force-field-based-on-cmap-potentials-and-free-energy-decomposition
#1
Wei Kang, Fan Jiang, Yun-Dong Wu
The coupling between neighboring backbone ϕ and ψ dihedral-angles (torsions) has been well appreciated in protein force field development, as in the correction-map (CMAP) potentials. However, although preferences of backbone torsions are significantly affected by side-chain conformation, there has been no easy way to optimize this coupling. Herein, we prove that the three-dimensional (3D) free energy hyper-surface of joint (ϕ, ψ, χ1) torsions can be decomposed into three separated 2D surfaces. Thus, each of the 2D torsional surfaces can be efficiently and automatically optimized using a CMAP potential...
June 15, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29906111/benchmark-of-excitation-energy-shifts-from-frozen-density-embedding-theory-introduction-of-a-density-overlap-based-applicability-threshold
#2
Alexander Zech, Niccolo Ricardi, Stefan Prager, Andreas Dreuw, Tomasz A Wesolowski
We present a thorough investigation of the errors in results obtained with the combination of Frozen-Density Embedding Theory and the Algebraic Diagrammatic Construction Scheme for the polarization propagator of second order (FDE-ADC(2)). The study was carried out on a set of 52 intermolecular complexes with varying interaction strength, each consisting of a chromophore of fundamental interest and a few small molecules in its environment. The errors emerging in Frozen-Density Embedding Theory based methods originate from: (a) the solver of the quantum many body problem used to obtain the embedded wavefunction (Ψemb), (b) the approximation for the explicit density functional for the embedding potential, and (c) the choice of the density representing the environment (ρB(r))...
June 15, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29906110/effect-of-dna-environment-on-electronically-excited-states-of-methylene-blue-evaluated-by-a-three-layered-qm-qm-mm-oniom-scheme
#3
Juan José Nogueira, Sven Rossbach, Christian Ochsenfeld, Leticia Gonzalez
Interactions between chromophores and biological environments may alter the electronic properties of the chromophores. A three-layered QM/QM/MM ONIOM scheme with electrostatic embedding is implemented to investigate the influence of an additional QM layer on excited-state calculations with respect to a standard QM/MM description. The implemented ONIOM scheme is employed to compute the electronic excitations of the photosensitizer methylene blue interacting with a solvated DNA double strand. It is shown that the additional quantum mechanical description of several nucleobases in the vertical energy calculations induces energy shifts in the excited states of methylene blue, compared to the energies of a traditional QM/MM scheme, where the solvated double strand is described fully classically...
June 15, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29906108/simulations-of-interfacial-tension-of-liquid-liquid-ternary-mixtures-using-optimized-parameterization-for-coarse-grained-models
#4
David Steinmetz, Benoit Creton, Veronique Lachet, Bernard Rousseau, Carlos Nieto-Draghi
In this work, liquid-liquid systems are studied by means of coarse-grained Monte Carlo simulations (CG-MC) and Dissipative Particle Dynamics (DPD). A methodology is proposed to reproduce liquid-liquid equilibrium (LLE) and to provide variation of interfacial tension (IFT) as a function of the solute concentration. A key step is the parameterization method based on the use of Flory-Huggins parameter between DPD beads to calculate solute/solvent interactions. Parameters are determined using a set of experimental compositional data of LLE following four different approaches...
June 15, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29906106/response-potential-in-the-strong-interaction-limit-of-dft-analysis-and-comparison-with-the-coupling-constant-average
#5
Sara Giarrusso, Stefan Vuckovic, Paola Gori-Giorgi
Using the formalism of the conditional amplitude, we study the response part of the exchange-correlation potential in the strong-coupling limit of density functional theory, analysing its peculiar features and comparing it with the response potential averaged over the coupling constant for small atoms and for the hydrogen molecule. We also use a simple one-dimensional model of a stretched heteronuclear molecule to derive exact properties of the response potential in the strong-coupling limit. The simplicity of the model allows us to unveil relevant features also of the exact Kohn-Sham potential and its different components, namely the appearance of a second peak in the correlation kinetic potential on the side of the most electronegative atom...
June 15, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29906105/crystal-field-splittings-in-lanthanide-complexes-inclusion-of-correlation-effects-beyond-second-order-perturbation-theory
#6
Philipp Paul Hallmen, Guntram Rauhut, Hermann Stoll, Alexander O Mitrushchenkov, Joris van Slageren
State-averaged complete active space self-consistent field (CASSCF) calculations and a subsequent spin-orbit calculation mixing the CASSCF wave functions (CASSCF/state-interaction with spin-orbit coupling) is the conventional approach used for ab initio calculations of crystal-field splittings and magnetic properties of lanthanide complexes. However, this approach neglects dynamical correlation. Complete active space second-order perturbation theory (CASPT2) can be used to account for dynamical correlation, but suffers from the well-known problems of multireference perturbation theory, e...
June 15, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29906104/benchmarking-the-variational-reduced-density-matrix-theory-in-the-doubly-occupied-configuration-interaction-space-with-integrable-pairing-models
#7
Alvaro Rubio-Garc Iacute A, Diego Ricardo Alcoba, Pablo Capuzzi, Jorge Dukelsky
The variational reduced density matrix theory has been recently applied with great success to models within the truncated doubly-occupied configuration interaction space, which corresponds to the seniority zero subspace. Conservation of the seniority quantum number restricts the Hamiltonians to be based on the SU(2) algebra. Among them there is a whole family of exactly solvable Richardson-Gaudin pairing Hamiltonians. We benchmark the variational theory against two different exactly solvable models, the Richardson-Gaudin-Kitaev and the reduced BCS Hamiltonians...
June 15, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29905484/efficient-and-linear-scaling-seminumerical-method-for-local-hybrid-density-functionals
#8
Henryk Laqua, Jörg Kussmann, Christian Ochsenfeld
Local hybrid functionals, that is, functionals with local dependence on the exact exchange energy density, generalize the popular class of global hybrid functionals and extend the applicability of density functional theory to electronic structures that require an accurate description of static correlation. However, the higher computational cost compared to conventional Kohn-Sham density functional theory restrained their widespread application. Here, we present a low-prefactor, linear-scaling method to evaluate the local hybrid exchange-correlation potential as well as the corresponding nuclear forces by employing a seminumerical integration scheme...
June 15, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29897750/individual-component-map-of-rotatory-strength-icm-rs-and-rotatory-strength-density-rsd-plots-as-analysis-tools-of-circular-dicroism-spectra-of-complex-systems
#9
Le Chang, Oscar Baseggio, Luca Sementa, Daojian Cheng, Giovanna Fronzoni, Daniele Toffoli, Edoardo Aprà, Mauro Stener, Alessandro Fortunelli
We introduce Individual Component Maps of Rotatory Strength (ICM-RS) and Rotatory Strength Density (RSD) plots as analysis tools of chiro-optical linear response spectra deriving from time-dependent density functional theory (TDDFT) simulations. ICM-RS and RSD allow one to visualize the origin of chiro-optical response in momentum or real space, including signed contributions and therefore highlighting cancellation terms that are ubiquitous in chirality phenomena, and should be especially useful in analyzing the spectra of complex systems...
June 13, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29897748/phaseless-auxiliary-field-quantum-monte-carlo-on-graphical-processing-units
#10
James Shee, Evan J Arthur, Shiwei Zhang, David R Reichman, Richard A Friesner
We present an implementation of phaseless Auxiliary-Field Quantum Monte Carlo (ph-AFQMC) utilizing graphical processing units (GPUs). The AFQMC method is recast in terms of matrix operations which are spread across thousands of processing cores and are executed in batches using custom Compute Unified Device Architecture kernels and the GPU-optimized cuBLAS matrix library. Algorithmic advances include a batched Sherman-Morrison-Woodbury algorithm to quickly update matrix determinants and inverses, density-fitting of the two-electron integrals, an energy algorithm involving a high-dimensional precomputed tensor, and the use of single-precision floating point arithmetic...
June 13, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29897746/response-formalism-within-full-configuration-interaction-quantum-monte-carlo-static-properties-and-electrical-response
#11
Pradipta Kumar Samanta, Nick S Blunt, George Henry Booth
We formulate a general, arbitrary-order stochastic response formalism within the Full Configuration Interaction Quantum Monte Carlo framework. This modified stochastic dynamic allows for the exact response properties of correlated multireference electronic systems to be systematically converged upon for systems far out of reach of traditional exact treatments. This requires a simultaneous coupled evolution of a response state alongside the zeroth-order state, which is shown to be stable, non-transient and unbiased...
June 13, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29894626/membrane-permeability-characteristic-times-and-lengths-for-oxygen-and-a-simulation-based-test-of-the-inhomogeneous-solubility-diffusion-model
#12
Oriana De Vos, Richard M Venable, Tanja Van Hecke, Gerhard Hummer, Richard Walter Pastor, An Ghysels
The balance of normal and radial (lateral) diffusion of oxygen in phospholipid mem-branes is critical for biological function. Based on the Smoluchowski equation for the inhomogeneous solubility-diffusion model, Bayesian analysis (BA) can be applied to molecular dynamics trajectories of oxygen to extract the free energy, and the normal and radial diffusion profiles. This paper derives a theoretical formalism to convert these profiles into characteristic times and lengths associated with entering, escaping, or completely crossing the membrane...
June 12, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29894622/polarizable-molecular-simulations-reveal-how-silicon-containing-functional-groups-govern-the-desalination-mechanism-in-nanoporous-graphene
#13
Yudong Qiu, Benedict R Schwegler, Lee-Ping Wang
We report a molecular dynamics (MD) simulation study of reverse osmosis desalination using nanoporous monolayer graphene passivated by SiH2 and Si(OH)2 functional groups. A highly accurate and detailed polarizable molecular mechanics force field model was developed for simulating graphene nanopores of various sizes and geometries. The simulated water fluxes and ion rejection percentages are explained using detailed atomistic mechanisms derived from analysis of the simulation trajectories. Our main findings are: (1) The Si(OH)2 pores possess superior ion rejection rates due to selective electrostatic repulsion of Cl- ions, but Na+ ions are attracted to the pore and block water transfer...
June 12, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29894196/ab-initio-wavefunction-based-determination-of-element-specific-shifts-for-the-efficient-calculation-of-x-ray-absorption-spectra-of-main-group-elements-and-first-row-transition-metals
#14
Agisilaos Chantzis, Joanna K Kowalska, Dimitrios Maganas, Serena DeBeer, Frank Neese
In this study, a detailed calibration of the performance of modern ab initio wavefunction methods in the domain of X-ray absorption spectroscopy (XAS) is presented. It has been known for some time, that for a given level of approximation, e.g. using time-dependent density functional theory (TD-DFT) in conjunction with a given basis set, there are systematic deviations of the calculated transition energies from their experimental values that depend on the functional, the basis set, and the chosen treatment of scalar relativistic effects...
June 12, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29894183/charge-transfer-excitations-with-range-separated-functionals-using-improved-virtual-orbitals
#15
Rolf W Uuml Rdemann, Michael Walter
We present an implementation of range separated functionals utilizing the Slater-function on grids in real space in the projector augmented waves method. The screened Poisson equation is solved to evaluate the necessary screened exchange integrals on Cartesian grids. The implementation is verified against existing literature and applied to the description of charge transfer excitations. We find very slow convergence for calculations within linear response time-dependent density functional theory and unoccupied orbitals of the canonical Fock operator...
June 12, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29889519/large-scale-electron-correlation-calculations-rank-reduced-full-configuration-interaction
#16
B Scott Fales, Stefan Seritan, Nick F Settje, Benjamin G Levine, Henrik Koch, Todd J Martínez
We present the rank-reduced full configuration interaction (RR-FCI) method, a variational approach for the calculation of extremely large full configuration interaction (FCI) wavefunctions. In this report we show that RR-FCI can provide ground state singlet and triplet energies within kcal/mol accuracy of full CI (FCI) with computational effort scaling as the square root of the number of determinants in the CI space (compared to conventional FCI methods which scale linearly with the number of determinants)...
June 11, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29889514/a-first-order-interacting-space-approach-to-excited-state-molecular-interaction-solvatochromic-shift-of-p-coumaric-acid-and-retinal-schiff-base
#17
Kazuma Yanai, Kazuya Ishimura, Akira Nakayama, Jun-Ya Hasegawa
A triple-layer QM/sQM/MM method was developed for accurately describing the excited-state molecular interactions between chromophore and the molecular environment (J. Hasegawa, K. Yanai, and K. Ishimura, ChemPhysChem 2015, 16, 305). A first-order-interaction space (FOIS) was defined for the interactions between QM and secondary QM (sQM) regions. Moreover, configuration interaction singles (CIS) and its second-order perturbation theory (PT2) calculations were performed within this space. In this study, numerical implementation of this FOISPT2 method significantly reduced the computing time, which realized application to solvatochromic systems, para-coumaric acid in neutral ( p-CA) and anionic forms in aqueous solution, retinal Schiff base in methanol (MeOH) solution, and bacteriorhodopsin (bR)...
June 11, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29883546/accuracy-of-td-dft-geometries-a-fresh-look
#18
Eric Bremond, Marika Savarese, Carlo Adamo, Denis Jacquemin
We benchmark a panel of 48 DFT exchange-correlation functionals in the framework of TD-DFT optimizations of the geometry of electronic excited states. To this end, we use a set of 41 small and medium-sized organic molecules for which reference geometries were obtained at high level of theory, typically, CC3 or CCSDR(3), with the aug-cc-pVTZ atomic basis set. For the ground-state parameters, the tested functionals provide average deviations that are small (0.010 Ang. and 0.5° for bond lengths and valence angles) and not very sensitive to selected (hybrid) functional, but the errors are larger for the most polarized bonds (CO, CN, etc...
June 8, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29883541/structure-optimization-of-temporary-anions
#19
Zsuzsanna Benda, Kerstin Rickmeyer, Thomas-C Jagau
We determine equilibrium structures, adiabatic electron affinities, and resonance widths of various temporary anions to benchmark the complex absorbing potential equation-of-motion coupled-cluster cluster (CAP-EOM-CC) method. The second-order approximation to CAP-EOM-CC with singles and doubles (SD) excitations is found to yield slightly lower resonance positions and widths than full CAP-EOM-CCSD. The basis set dependence of adiabatic resonance positions and widths is similar to that of the vertical quantities...
June 8, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29883539/globally-optimal-catalytic-fields-inverse-design-of-abstract-embeddings-for-maximum-reaction-rate-acceleration
#20
Mark Dittner, Bernd Hartke
The search for, and understanding of, good catalysts for chemical reactions is a central issue for chemists. Here, we present first steps towards developing a general computational framework to better support this task. This framework combines efficient, unbiased global optimization techniques with an abstract representation of the catalytic environment, to shrink the search space. To analyze the resulting catalytic embeddings, we employ dimensionality reduction and clustering techniques. This not only provides an inverse design approach to new catalytic embeddings but also illuminates the actual interactions behind catalytic effects...
June 8, 2018: Journal of Chemical Theory and Computation
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