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Journal of Chemical Theory and Computation

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https://www.readbyqxmd.com/read/28618232/toward-fast-and-accurate-binding-affinity-prediction-with-pmemdgti-an-efficient-implementation-of-gpu-accelerated-thermodynamic-integration
#1
Tai-Sung Lee, Yuan Hu, Brad Sherborne, Zhuyan Guo, Darrin M York
We report the implementation of the thermodynamic integration method on the pmemd module of the AMBER 16 package on GPUs (pmemdGTI). The pmemdGTI code typically delivers over 2 orders of magnitude of speed-up relative to a single CPU core for the calculation of ligand-protein binding affinities with no statistically significant numerical differences and thus provides a powerful new tool for drug discovery applications.
June 23, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28641006/dft-simulation-of-structural-and-optical-properties-of-9-aminoacridine-half-sandwich-ru-ii-rh-iii-and-ir-iii-antitumoural-complexes-and-their-interaction-with-dna
#2
José Pedro Cerón-Carrasco, José Ruiz, Consuelo Vicente, Concepcion de Haro, Delia Bautista, Jose Zuniga, Alberto Requena
In this work, we use DFT-based methods to simulate the chemical structures, optical properties and interaction with DNA of a recently synthesized chelated CˆN 9-aminoacridine arene Ru (II) anticancer agent and two new closely related Rh(III) and Ir(III) complexes using DFT-based methods. Four chemical models and a number of theoretical approaches, which representatively include the PBE0, B97D, ωB97X, ωB97X-D, M06, and M06-L density functionals and the LANL2DZ, def2-SVP, def2- TZVP basis sets, are tested...
June 22, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28641004/performance-of-the-g0w0-method-in-predicting-the-electronic-gap-of-tio2-nanoparticles
#3
Ángel Morales-García, Rosendo Valero, Francesc Illas
Using a relativistic all-electron description and numerical atomic centered orbital basis set the performance of the G0W0 method on the electronic band gap of (TiO(2))n nanoparticles (n=1-20) is investigated. Results are presented for G0W0 on top of hybrid (PBE0 and a modified version with 12.5% of Fock exchange) functionals. The underestimation of the electronic band gap from Kohn-Sham orbital energies is corrected by the quasiparticle energies from G0W0 method which are consistent with the variational ΔSCF approach...
June 22, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28640608/numerical-diculties-computing-electrostatic-potentials-near-interfaces-with-the-poisson-boltzmann-equation
#4
Marcia Oliveira Fenley, Alexander H Boschitsch, Robert C Harris
Many researchers compute surface maps of the electrostatic potential with the Poisson-Boltzmann (PB) equation to relate the structural information obtained from X-ray and NMR experiments to biomolecular functions. Here we demonstrate that the usual method of obtaining these surface maps of electrostatic potential, by interpolating from neighboring grid points on the solution grid generated by a PB solver, generates large errors because of the large discontinuity in the dielectric constant (and thus in the normal derivative of the electrostatic potential) at the surface...
June 22, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28640604/parametrizaton-of-a-reactive-force-field-reaxff-for-molecular-dynamics-simulations-of-si-nanoparticles
#5
Giovanni Barcaro, Susanna Monti, Luca Sementa, Vincenzo Carravetta
A novel computational approach, based on classical reactive molecular dynamics simulations (RMD) and quantum chemistry (QC) global energy optimizations, is proposed for modelling large Si nanoparticles. The force field parameters, which can describe bond breaking and formation, are derived by reproducing energetic and structural properties of a set of Si clusters increasing in size. These reference models are obtained through a new protocol based on a joint high temperature RMD/low temperature Basin Hopping QC search...
June 22, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28636825/a-new-mixed-all-atom-coarse-grained-model-application-to-melittin-aggregation-in-aqueous-solution
#6
Mee Y Shelley, Myvizhi Esai Selvan, Jun Zhao, Volodymyr Babin, Chenyi Liao, Jianing Li, John Clarence Shelley
We introduce a new mixed resolution, all-atom/coarse-grained approach (AACG) for modeling peptides in aqueous solution and apply it to characterizing the aggregation of melittin. All of the atoms in peptidic components are represented while a single site is used for each water molecule. With the full flexibility of the peptide retained, our AACG method achieves speedups by a factor of 3-4 for CPU time reduction and another factor of roughly 7 for diffusion. An Ewald treatment permits the inclusion of long-range electrostatic interactions...
June 21, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28636824/bicanonical-ab-initio-molecular-dynamics-for-open-systems
#7
Johannes Frenzel, Bernd Meyer, Dominik Marx
Performing ab initio molecular dynamics simulations of open systems, where the chemical potential rather than the number of both, nuclei and electrons is fixed, still is a challenge. Here, drawing on bicanonical sampling ideas introduced two decades ago by Swope and Andersen to calculate chemical potentials of liquids and solids, an ab initio simulation technique is devised, which introduces a fictitious dynamics of two superimposed but otherwise independent periodic systems including full electronic structure, such that either the chemical potential or the average fractional particle number of a specific chemical species can be kept constant...
June 21, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28636392/hybrid-cpu-gpu-integral-engine-for-strong-scaling-ab-initio-methods
#8
Jörg Kussmann, Christian Ochsenfeld
We present a parallel integral algorithm for two-electron contributions occurring in Hartree-Fock and hybrid density functional theory that allows for a strong scaling parallelization on inhomogeneous compute clusters. With a particular focus on graphic processing units, we show that our approach allows an efficient use of CPUs and graphics processing units (GPUs) simultaneously, although the different architectures demand conflictive strategies in order to ensure efficient program execution. Furthermore, we present a general strategy to use large basis sets like quadruple-ζ split valence on GPUs and investigate the balance between CPUs and GPUs depending on l-quantum numbers of the corresponding basis functions...
June 21, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28636359/relativistic-approximations-to-paramagnetic-nmr-chemical-shift-and-shielding-anisotropy-in-transition-metal-systems
#9
Syed Awais Rouf, Jiří Mareš, Juha Vaara
We apply approximate relativistic methods to calculate the magnetic property tensors, i.e., the g-tensor, zero-field splitting (ZFS) tensor (D), and hyperfine coupling (HFC) tensors, for the purpose of constructing paramagnetic nuclear magnetic resonance (pNMR) shielding tensors. The chemical shift and shielding anisotropy are calculated by applying a modern implementation of the classic Kurland-McGarvey theory (J. Magn. Reson. 1970, 2, 286), which formulates the shielding tensor in terms of the g- and HFC tensors obtained for the ground multiplet, in the case of higher than doublet multiplicity defined by the ZFS interaction...
June 21, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28636358/transferable-atom-centered-potentials-for-the-correction-of-basis-set-incompleteness-errors-in-density-functional-theory
#10
Alberto Otero-de-la-Roza, Gino A DiLabio
Recent progress in the accurate calculation of non-covalent interactions has enabled density-functional theory (DFT) to model systems relevant in biological and supramolecular chemistry. The application of DFT methods using atom-centered Gaussian basis sets to large systems is limited by the number of basis functions required to accurately model thermochemistry and, in particular, weak intermolecular interactions. Basis-set incompleteness error (BSIE) arising from the use of incomplete basis sets leads to erroneous intermolecular energies, bond dissociation energies, and structures...
June 21, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28636351/heats-of-formation-of-medium-size-organic-compounds-from-contemporary-electronic-structure-methods
#11
Yury Minenkov, Heng Wang, Zhandong Wang, S Mani Sarathy, Luigi Cavallo
Computational electronic structure calculations are routinely undertaken to predict thermodynamic properties of the various species. However, the application of highly accurate wave function theory methods, such as the "gold standard" coupled cluster approach including single, double and partly triple excitations in perturbative fashion, CCSD(T), to large molecules is limited due to high computational cost. In this work, the promising domain based local pair natural orbital coupled cluster approach, DLPNO-CCSD(T), has been tested to reproduce 113 accurate formation enthalpies of medium-size molecules (few dozens heavy atoms) important for bio- and combustion chemistry via the reaction based Feller-Peterson-Dixon approach...
June 21, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28635295/coarse-grained-models-of-aqueous-and-pure-liquid-alkanes
#12
Gaurav Gyawali, Samuel Sternfield, Revati Kumar, Steven W Rick
A model for linear alkanes is presented in which interaction sites are only on the carbon atoms and the range of the potential is reduced using the Stillinger-Weber potential. The model is optimized for aqueous and liquid alkane properties and can match thermodynamic and structural properties, including solvation free energies, liquid densities, and liquid/vapor and liquid/water surface tensions for alkanes over a range of lengths.The results for long alkanes indicates that such models can be useful as accurate, yet efficient, coarse-grained potentials for macromolecules in water and other environments...
June 21, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28635293/probing-the-importance-of-charge-flux-in-force-field-modelling
#13
Elaheh Sedghamiz, Balazs Nagy, Frank Jensen
We analyze the conformational dependence of atomic charges and molecular dipole moments for a selection of ~900 conformations of peptide models of the 20 neutral amino acids. Based on a set of reference density functional theory calculations, we partition the changes into effects due to changes in bond distances, bond angles and torsional angles, and into geometry and charge flux contributions. This allows an assessment of the limitations of fixed charge force fields, and indications for how to design improved force fields...
June 21, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28609618/internally-contracted-multireference-coupled-cluster-calculations-with-a-spin-free-dirac-coulomb-hamiltonian-application-to-the-monoxides-of-titanium-zirconium-and-hafnium
#14
Filippo Lipparini, Till Kirsch, Andreas Köhn, Jürgen Gauss
We combine internally contracted multireference coupled cluster theory with a four-component treatment of scalar-relativistic effects based on the spin-free Dirac-Coulomb Hamiltonian. This strategy allows for a rigorous treatment of static and dynamic correlation as well as scalar-relativistic effects, which makes it viable to describe molecules containing heavy transition elements. The use of a spin-free formalism limits the impact of the four-component treatment on the computational cost to the non-rate-determining steps of the calculations...
June 21, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28590736/ozone-and-other-1-3-dipoles-toward-a-quantitative-measure-of-diradical-character
#15
Benoît Braïda, Sérgio E Galembeck, Philippe C Hiberty
Ozone and its sulfur-substituted isomers are studied by means of the Breathing Orbital Valence Bond ab initio method, with the objective of estimating their controversial diradical characters. The calculated weights of the various VB structures and their individual diabatic energies are found to be consistent with each other. All 1,3-dipoles can be described in terms of three major VB structures, one diradical and two zwitterionic ones, out of the six structures, forming a complete basis. Ozone has a rather large diradical character, estimated to 44%-49%...
June 21, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28582625/quantitative-characterization-of-the-binding-and-unbinding-of-millimolar-drug-fragments-with-molecular-dynamics-simulations
#16
Albert C Pan, Huafeng Xu, Timothy Palpant, David E Shaw
A quantitative characterization of the binding properties of drug fragments to a target protein is an important component of a fragment-based drug discovery program. Fragments typically have a weak binding affinity, however, making it challenging to experimentally characterize key binding properties, including binding sites, poses, and affinities. Direct simulation of the binding equilibrium by molecular dynamics (MD) simulations can provide a computational route to characterize fragment binding, but this approach is so computationally intensive that it has thus far remained relatively unexplored...
June 21, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28628742/acceleration-of-semiempirical-qm-mm-methods-through-mpi-hybrid-mpi-openmp-and-scf-accelerator-implementations
#17
Pedro Ojeda-May, Kwangho Nam
The present manuscript describes the strategy and implementation of scalable and efficient semiempirical (SE) QM/MM methods in CHARMM. The serial version of the code was first profiled to identify routines that require parallelization. Afterwards, the code was parallelized and accelerated with three approaches. The first approach was the parallelization of the entire QM/MM routines, including the Fock matrix diagonalization routines, using the CHARMM MPI machinery. In the second approach, two different self-consistent field (SCF) energy convergence accelerators were implemented using density and Fock matrices as targets for their extrapolations in the SCF procedure...
June 19, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28628316/soft-sphere-continuum-solvation-in-electronic-structure-calculations
#18
Giuseppe Fisicaro, Luigi Genovese, Oliviero Andreussi, Sagarmoy Mandal, Nisanth N Nair, Nicola Marzari, Stefan Goedecker
We present an implicit solvation approach where the interface between the quantum-mechanical solute and the surrounding environment is described by a fully continuous permittivity built up with atomic-centered ``soft'' spheres. This approach combines many of the advantages of the self-consistent continuum solvation model in handling solutes and surfaces in contact with complex dielectric environments or electrolytes in electronic-structure calculations. In addition it is able to describe accurately both neutral and charged systems...
June 19, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28628314/benchmarking-the-fundamental-electronic-properties-of-small-tio2-nanoclusters-by-gw-and-coupled-cluster-theory-calculations
#19
Enrico Berardo, Ferdinand Kaplan, Kiran Bhaskaran-Nair, William A Shelton, Michiel J van Setten, Karol Kowalski, Martijn A Zwijnenburg
We study the vertical and adiabatic ionisation potentials and electron affinities of bare and hydroxylated TiO2 nanoclusters, as well as their fundamental gap and exciton binding energy values, to understand how the clusters' electronic properties change as a function of size and hydroxylation. In addition, we have employed a range of many-body methods; including G0W0, qsGW, EA/IP-EOM-CCSD and DFT (B3LYP, PBE), to compare the performance and predictions of the different classes of methods. We demonstrate that for bare clusters, all many-body methods predict the same trend with cluster size...
June 19, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28622469/free-energy-calculations-of-microcin-j25-variants-binding-to-the-fhua-receptor
#20
Pin-Kuang Lai, Yiannis N Kaznessis
Computer simulations are performed to study the antimicrobial peptide microcin J25 (MJ25), a 21-mer peptide with an unusual lasso structure and high activity against Gram-negative bacteria. MJ25 has intracellular targets. The initial step for MJ25 acquisition in bacterial cells is binding to the outer membrane receptor FhuA. Molecular dynamics simulation is implemented to study the binding mechanism of MJ25 to FhuA and to search for important binding residues. The absolute binding free energy calculated from combined free energy perturbation (FEP) and thermodynamic integration (TI) methods agrees well with experimental data...
June 16, 2017: Journal of Chemical Theory and Computation
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