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Journal of Chemical Theory and Computation

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https://www.readbyqxmd.com/read/30296084/simple-entropy-terms-for-end-point-binding-free-energy-calculations
#1
William M Menzer, Chen Li, Wenji Sun, Bing Xie, David D L Minh
We introduce a number of computationally inexpensive modifications to the MM/PBSA and MM/GBSA estimators for binding free energies, which are based on average receptor-ligand interaction energies in simulations of a noncovalent complex, to improve the treatment of entropy: second- and higher-order terms in a cumulant expansion and a confining potential on ligand external degrees of freedom. We also consider a filter for snapshots where ligands have drifted from the initial binding pose. The variations were tested on six sets of systems for which binding modes and free energies have previously been experimentally determined...
October 19, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/30336669/on-the-applicability-of-force-fields-to-study-the-aggregation-of-amyloidogenic-peptides-using-molecular-dynamics-simulations
#2
Martín Carballo-Pacheco, Ahmed E Ismail, Birgit Strodel
Molecular dynamics simulations play an essential role in understanding biomolecular processes such as protein aggregation at temporal and spatial resolutions which are not attainable by experimental methods. For a correct modeling of protein aggregation, force fields must accurately represent molecular interactions. Here, we study the effect of five different force fields on the oligomer formation of Alzheimer's Aβ16-22 peptide and two of its mutants: Aβ16-22 (F19V,F20V), which does not form fibrils, and Aβ16-22 (F19L) which forms fibrils faster than the wild type...
October 18, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/30336030/openpathsampling-a-python-framework-for-path-sampling-simulations-i-basics
#3
David Swenson, Jan-Hendrik Prinz, Frank Noé, John Damon Chodera, Peter G Bolhuis
Transition path sampling techniques allow molecular dynamics simulations of complex systems to focus on rare dynamical events, providing insight into mechanisms and the ability to calculate rates inaccessible by ordinary dynamics simulations. While path sampling algorithms are conceptually as simple as impor- tance sampling Monte Carlo, the technical complexity of their implementation has kept these techniques out of reach of the broad community. Here, we introduce an easy-to-use Python framework called Open- PathSampling (OPS) that facilitates path sampling for (bio)molecular systems with minimal effort and yet is still extensible...
October 18, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/30336016/a-protocol-for-identifying-accurate-collective-variables-in-enhanced-molecular-dynamics-simulations-for-the-description-of-structural-transformations-in-flexible-metal-organic-frameworks
#4
Ruben Demuynck, Jelle Wieme, Sven M J Rogge, Karen D Dedecker, Louis Vanduyfhuys, Michel Waroquier, Veronique Van Speybroeck
Various kinds of flexibility have been observed in metal-organic frameworks, which may originate from the topology of the material or the presence of flexible ligands. The construction of free energy profiles describing the full dynamical behavior along the phase transition path is challenging since it is not trivial to identify collective variables able to identify all metastable states along the reaction path. In this work, a systematic three-step protocol to uniquely identify the dominant order parameters for structural transformations in flexible metal-organic frameworks and subsequently construct accurate free energy profiles is presented...
October 18, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/30336015/accelerated-computation-of-free-energy-profile-at-ab-initio-qm-mm-accuracy-via-a-semi-empirical-reference-potential-i-weighted-thermodynamics-perturbation
#5
Pengfei Li, Xiangyu Jia, Xiaoliang Pan, Yihan Shao, Ye Mei
Free energy profile (FE Profile) is an essential quantity for the estimation of reaction rate and the validation of reaction mechanism. For chemical reactions in condensed phase or enzymatic reactions, the computation of FE profile at ab initio ( ai) quantum mechanical/molecular mechanics (QM/MM) level is still far too expensive. Although semiempirical (SE) method can be hundreds or thousands of times faster than the ai methods, the accuracy of SE methods is often unsatisfactory, due to the approximations that have been adopted in these methods...
October 18, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/30336013/structure-dynamics-and-hydration-free-energy-of-carbon-dioxide-in-aqueous-solution-a-quantum-mechanical-molecular-mechanics-molecular-dynamics-thermodynamic-integration-qm-mm-md-ti-simulation-study
#6
Niko Prasetyo, Thomas S Hofer
The solvation of carbon dioxide in solution represents a key step for the capture and fixation CO2 in nature, which may be further influenced by the formation of (bi-)carbonate species and/or the formation of CO2 clusters in solution. The latter processes are strongly dependent on the exact environment of the liquid state (e.g. pH value, solvated ions, etc.) and may interfere with the experimental determination of structural, dynamical and thermodynamic properties. In this work a hybrid quantum mechanical/molecular mechanical (QM/MM) simula- tion approach at correlated ab initio level of theory (RI-MP2) has been applied in the framework of thermodynamic integration (TI) to study structure, dynamics and the hy- dration free energy of single carbon dioxide molecule in aqueous solution...
October 18, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/30335374/efficiently-capturing-weak-interactions-in-ab-initio-molecular-dynamics-with-on-the-fly-basis-set-extrapolation
#7
Timothy C Ricard, Srinivasan Sesha Iyengar
Weak interactions have a critical role in accurately portraying conformational change. However the computational study of these often require large basis electronic structure calculations that are generally cost-prohibitive within ab initio molecular dynamics. Here, we present, a new approach to efficiently obtain AIMD trajectories in agreement with large, triple-zeta, polarized valence basis functions, at much reduced computational cost. For example, it follows from our studies that AIMD trajectories can indeed be constructed in agreement with basis sets such as 6-311++G(2df,2pd) with computational effort commensurate with those from much smaller basis sets such as 6-31+G(d), for polypeptides systems with 100+ atoms...
October 18, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/30299950/lessons-from-the-spin-polarization-spin-contamination-dilemma-of-transition-metal-hyperfine-couplings-for-the-construction-of-exchange-correlation-functionals
#8
Caspar J Schattenberg, Toni M Maier, Martin Kaupp
Hyperfine couplings (HFCs) of open-shell transition-metal centers are known to often depend crucially on core-shell spin polarization (CSSP). The latter is typically underestimated by semilocal density functionals, while admixture of exact exchange (EXX) in (global) hybrid functionals enhances CSSP. Unfortunately, a metal-ligand antibonding character of one or more of the singly occupied molecular orbitals of the complex will cause substantial valence-shell spin polarization (VSSP), which for global hybrids with higher EXX admixtures may lead to substantial spin contamination, thereby deteriorating the overall electronic structure and the dipolar couplings...
October 18, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/30299949/electronically-excited-solute-described-by-rism-approach-coupled-with-multireference-perturbation-theory-vertical-excitation-energies-of-bioimaging-probes
#9
Ryosuke Y Shimizu, Takeshi Yanai, Yuki Kurashige, Daisuke Yokogawa
For theoretically studying molecules with fluorescence in the near-infrared region, high-accuracy determination of state energy level is required for meaningful analyses since the spectra of interest are of very narrow energy range. In particular, these molecules are in many cases handled in solution; therefore, consideration of the solvation effect is essential upon calculation together with the electronic structure of the excited state. Earlier studies showed that they cannot be described with conventional methods such as PCM-TD-DFT, yielding results far from experimental data...
October 18, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/30252467/state-averaged-pair-natural-orbitals-for-excited-states-a-route-toward-efficient-equation-of-motion-coupled-cluster
#10
Chong Peng, Marjory C Clement, Edward F Valeev
A reduced-complexity variant of equation-of-motion coupled-cluster singles and doubles (EOM-CCSD) method is formulated in terms of state-averaged excited-state pair natural orbitals (PNO) designed to describe manifolds of excited states. State-averaged excited-state PNOs for the target manifold are determined by averaging CIS(D) pair densities over the model manifold. The performance of the PNO-EOM-CCSD approach has been tested with the help of a distributed-memory parallel canonical EOM-CCSD implementation within the Massively Parallel Quantum Chemistry program that allows treatment of systems with 50+ atoms using realistic basis sets with 1000+ functions...
October 18, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/30299953/the-nonlocal-kernel-in-van-der-waals-density-functionals-as-an-additive-correction-an-extensive-analysis-with-special-emphasis-on-the-b97m-v-and-%C3%AF-b97m-v-approaches
#11
Asim Najibi, Lars Goerigk
The development of van der Waals density functional approximations (vdW-DFAs) has gained considerable interest over the past decade. While in a strictest sense, energy calculations with vdW-DFAs should be carried out fully self-consistently, we demonstrate conclusively for a total of 11 methods that such a strategy only increases the computational time effort without having any significant effect on energetic properties, electron densities, or orbital-energy differences. The strategy to apply a nonlocal vdW-DFA kernel as an additive correction to a fully converged conventional DFA result is therefore justified and more efficient...
October 17, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/30278124/computation-of-dynamic-polarizabilities-and-van-der-waals-coefficients-from-path-integral-monte-carlo
#12
Juha Tiihonen, Ilkka Kylänpää, Tapio T Rantala
We demonstrate computation of total dynamic multipole polarizabilities using path-integral Monte Carlo method (PIMC). The PIMC approach enables accurate thermal and nonadiabatic mixing of electronic, rotational, and vibrational degrees of freedom. Therefore, we can study the thermal effects, or lack thereof, in the full multipole spectra of the chosen one- and two-electron systems: H, Ps, He, Ps2 , H2 , and HD+ . We first compute multipole-multipole correlation functions up to octupole order in imaginary time...
October 17, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/30303377/a-fast-pairwise-approximation-of-solvent-accessible-surface-area-for-implicit-solvent-simulations-of-proteins-on-cpus-and-gpus
#13
He Huang, Carlos Simmerling
We propose a pairwise and readily parallelizable SASA-based nonpolar solvation approach for protein simulations, inspired by our previous pairwise GB polar solvation model development. In this work, we developed a novel function to estimate the atomic and molecular SASAs of proteins, which results in comparable accuracy as the LCPO algorithm in reproducing numerical icosahedral-based SASA values. Implemented in AMBER software and tested on consumer GPUs, our method reasonably reproduces LCPO simulation results, but accelerates MD simulations up to 30 times compared to the LCPO implementation, which is greatly desirable for protein simulations facing sampling challenges...
October 10, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/30300552/phase-transferable-force-field-for-alkali-halides
#14
Marie-Madeleine Walz, Mohammad Mehdi Ghahremnapour, Paul J van Maaren, David van der Spoel
A longstanding goal of computational chemistry is to predict the state of materials in all phases with a single model. This is particularly relevant for materials that are difficult or dangerous to handle or compounds that have not yet been created. Progress towards this goal has been limited as most work has concentrated on just one phase, often determined by particular applications. In the framework of the development of the Alexandria force field we present here new polarisable force fields for alkali halides with Gaussian charge distributions for molecular dynamics simulations...
October 9, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/30300543/accelerating-qm-mm-free-energy-computations-via-intramolecular-force-matching
#15
Phillip S Hudson, Stefan Boresch, David M Rogers, H Lee Woodcock
The calculation of free energy differences between levels of theory has numerous potential pitfalls. Chief amongst them is the lack of overlap, i.e., ensembles generated at one level of theory (e.g., ``low'') not being good approximations of ensembles at the other (e.g., ``high''). Numerous strategies have been devised to mitigate this issue. However, the most straight-forward approach is to ensure that the ``low'' level ensemble more closely resembles that of the ``high''. Ideally, this is done without increasing computational cost...
October 9, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/30299948/accuracy-of-coupled-cluster-excited-state-potential-energy-surfaces
#16
Attila Tajti, John F Stanton, Devin A Matthews, Péter G Szalay
The validation of the quality of the description of excited electronic states is of special importance in quantum chemistry as the general reliability of ab initio methods shows a much larger variation for these states than for the ground state. In this study, we investigate the quality of excited state energy gradients and potential energy surfaces on selected systems, as provided by the single reference coupled cluster variants CC2, CCSD, CCSD(T)(a)* and CC3. Gradients and surface plots that follow the Franck-Condon forces are compared to the respective CCSDT reference values, thereby establishing a useful strategy for judging each variant's accuracy...
October 9, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/30299941/surface-hopping-within-an-exciton-picture-an-electrostatic-embedding-scheme
#17
Maximilian F S J Menger, Felix Plasser, Benedetta Mennucci, Leticia Gonzalez
We report the development and the implementation of an exciton approach that allows the computing of ab initio non-adiabatic dynamics simulations of electronic excitation energy transfer in multichromophoric systems. For the dynamics a trajectory based strategy is used within the surface hopping formulation. The approach features a consistent hybrid formulation that allows the construction of potential energy surfaces and gradients by combining quantum mechanics and molecular mechanics within an electrostatic embedding scheme...
October 9, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/30252473/t-distributed-stochastic-neighbor-embedding-method-with-the-least-information-loss-for-macromolecular-simulations
#18
Hongyu Zhou, Feng Wang, Peng Tao
Dimensionality reduction methods are usually applied on molecular dynamics simulations of macromolecules for analysis and visualization purposes. It is normally desired that suitable dimensionality reduction methods could clearly distinguish functionally important states with different conformations for the systems of interest. However, common dimensionality reduction methods for macromolecules simulations, including predefined order parameters and collective variables (CVs), principal component analysis (PCA), and time-structure based independent component analysis (t-ICA), only have limited success due to significant key structural information loss...
October 9, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/30252470/topscore-using-deep-neural-networks-and-large-diverse-data-sets-for-accurate-protein-model-quality-assessment
#19
Daniel Mulnaes, Holger Gohlke
The value of protein models obtained with automated protein structure prediction depends primarily on their accuracy. Protein model quality assessment is thus critical to select the model that can best answer biologically relevant questions from an ensemble of predictions. However, despite many advances in the field, different methods capture different types of errors, begging the question of which method to use. We introduce TopScore, a meta Model Quality Assessment Program (meta-MQAP) that uses deep neural networks to combine scores from 15 different primary predictors to predict accurate residue-wise and whole-protein error estimates...
October 9, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/30296092/shear-viscosity-computed-from-the-finite-size-effects-of-self-diffusivity-in-equilibrium-molecular-dynamics
#20
Seyed Hossein Jamali, Remco Hartkamp, Christos Bardas, Jakob Söhl, Thijs J H Vlugt, Othonas A Moultos
A method is proposed for calculating the shear viscosity of a liquid from finite-size effects of self-diffusion coefficients in Molecular Dynamics simulations. This method uses the difference in the self-diffusivities, computed from at least two system sizes, and an analytic equation to calculate the shear viscosity. To enable the efficient use of this method, a set of guidelines is developed. The most efficient number of system sizes is two and the large system is at least four times the small system. The number of independent simulations for each system size should be assigned in such a way that 50%-70% of the total available computational resources should be allocated to the large system...
October 8, 2018: Journal of Chemical Theory and Computation
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