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Journal of Chemical Theory and Computation

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https://www.readbyqxmd.com/read/30516999/boosting-quantum-machine-learning-models-with-multi-level-combination-technique-pople-diagrams-revisited
#1
Peter Zaspel, Bing Huang, Helmut Harbrecht, O Anatole von Lilienfeld
Inspired by Pople diagrams popular in quantum chemistry, we introduce a hierarchical scheme, based on the multi-level combination (C) technique, to combine various levels of approximations made when calculating molecular energies within quantum chemistry. When combined with quantum machine learning (QML) models, the resulting CQML model is a generalized unified recursive kernel ridge regression which exploits correlations implicitly encoded in training data comprised of multiple levels in multiple dimensions...
December 5, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/30516982/experimentally-derived-and-computationally-optimized-backbone-conformational-statistics-for-blocked-amino-acids
#2
Jeong-Mo Choi, Rohit V Pappu
Experimentally derived, amino acid specific backbone dihedral angle distributions are invaluable for modeling data-driven conformational equilibria of proteins and for enabling quantitative assessments of the accuracies of molecular mechanics forcefields. The protein coil library that is extracted from analysis of high-resolution structures of proteins, has served as a useful proxy for quantifying intrinsic and context-dependent conformational distributions of amino acids. However, data that go into coil libraries will have hidden biases, and ad hoc procedures must be used to remove these biases...
December 5, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/30514085/optimal-coarse-grained-site-selection-in-elastic-network-models-of-biomolecules
#3
Patrick Diggins, Changjiang Liu, Markus Deserno, Raffaello Potestio
Elastic network models, simple structure-based representations of biomolecules where atoms interact via short-range harmonic potentials, provide great insight into a molecule's internal dynamics and mechanical properties at extremely low computational cost. Their efficiency and effectiveness have made them a pivotal instrument in the computer-aided study of proteins and, since a few years, also of nucleic acids. In general, the coarse-grained sites, i.e. those effective force centres onto which the all-atom structure is mapped, are constructed based on intuitive rules: a typical choice for proteins is to retain only the Cα atoms of each amino acid...
December 4, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/30514080/why-computed-protein-folding-landscapes-are-sensitive-to-the-water-model
#4
Ramu Anandakrishnan, Saeed Izadi, Alexey V Onufriev
We investigate the effect of solvent models on the computed thermodynamics of protein folding. Atomistic folding simulations of a fast-folding mini-protein CLN025 were employed to compare two commonly used explicit solvent water models, TIP3P and TIP4P/Ew, and one implicit solvent (AMBER generalized Born) model. Although all three solvent models correctly identify the same native folded state (RMSD = 1.5 ± 0.1 ̊A relative to the experimental structure), the corresponding free energy landscapes vary drastically between water models: almost an order-of-magnitude difference is seen in the predicted fraction of the unfolded state between the two explicit solvent models, with even larger differences between the implicit and the explicit models...
December 4, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/30514078/spica-force-field-for-lipid-membranes-domain-formation-induced-by-cholesterol
#5
Sangjae Seo, Wataru Shinoda
Heterogeneity is essential for multicomponent lipid membranes. Especially, sterol-induced domain formation in membranes has recently attracted attention because of its biological importance. To investigate such membrane domains at molecular level, coarse-grained molecular dynamics (CG-MD) simulations are a promising approach since they allow to consider the temporal and spatial scales involved in domain formation. In this paper, we present a new CG force field, named SPICA, which can accurately predict domain formation within various lipids in membranes...
December 4, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/30513204/fingerprinting-electronic-structure-of-heme-iron-by-ab-initio-modeling-of-metal-l-edge-x-ray-absorption-spectra
#6
Meiyuan Guo, Erik Källman, Rahul Vitthal Pinjari, Rafael Carvalho Couto, Lasse Kragh Sørensen, Roland Lindh, Kristine Pierloot, Marcus Lundberg
The capability of the multiconfigurational restricted active space approach to identify electronic structure from spectral fingerprints is explored by applying it to iron L-edge X-ray absorption spectroscopy (XAS) of three heme systems that represent the limiting descriptions of iron in the Fe-O2 bond, ferrous and ferric [Fe(P)(ImH)2 ] (P = porphine,ImH = imidazole), and FeII (P). The level of agreement between experimental and simulated spectral shapes is calculated using the cosine similarity, which gives a quantitative and unbiased assignment...
December 4, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/30512961/nonequilibrium-environment-dynamics-in-a-frequency-dependent-polarizable-embedding-model
#7
Andrew Wildman, Greta Donati, Filippo Lipparini, Benedetta Mennucci, Xiaosong Li
Hybrid quantum mechanical/molecular mechanical (QM/MM) models are some of the most powerful and computationally feasible approaches to account for solvent effects or more general environmental perturbations on quantum chemical systems. In their more recent formulations (known as polarizable embedding) they can account for electrostatic and mutual polarization effects between the QM and the MM subsystems. In this paper, a polarizable embedding scheme based on induced dipoles that is both able to describe electron evolution of the embedded QM system in an efficient manner as well as to capture the frequency dependent behavior of the solvent is proposed, namely ωMMPol...
December 4, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/30512959/constrained-variational-quantum-eigensolver-quantum-computer-search-engine-in-the-fock-space
#8
Ilya G Ryabinkin, Scott N Genin, Artur F Izmaylov
Variational quantum eigensolver (VQE) is an efficient computational method promising chemical accuracy in electronic structure calculations on a universal-gate quantum computer. However, such a simple task as computing the electronic energy of a hydrogen molecular cation, H+2 , is not possible for a general VQE protocol because the calculation will invariably collapse to a lower energy of the corresponding neutral form, H2. The origin of the problem is that VQE effectively performs an unconstrained energy optimization in the Fock space of the original electronic problem...
December 4, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/30512951/toward-learned-chemical-perception-of-force-field-typing-rules
#9
Camila Zanette, Caitlin Colleen Bannan, Christopher I Bayly, Josh Fass, Michael K Gilson, Michael R Shirts, John Damon Chodera, David L Mobley
Molecular mechanics force fields define how the energy and forces in a molecular system are computed from its atomic positions, thus enabling the study of such systems through computational methods like molecular dynamics and Monte Carlo simulations. Despite progress toward automated force field parameterization, considerable human expertise is required to develop or extend force fields. In particular, human input has long been required to define atom types, which encode chemically unique environments that determine which parameters will be assigned...
December 4, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/30511855/a-multi-step-explicit-solvation-protocol-for-calculation-of-redox-potentials
#10
Cody M Sterling, Ragnar Bjornsson
The calculation of molecular redox potentials in aqueous solution presents a challenge to quantum chemistry due to the need to calculate charged, open-shell species experiencing large solvent effects. Traditionally, redox potentials are calculated via the use of density functional theory and continuum solvation methods but such protocols have been found to often suffer from large errors, particularly in the case of aqueous solution. While explicit solvation models hold promise of higher accuracy to describe solvent effects in general, their complicated use and lack of well-defined, reliable protocols has hindered their adoption...
December 4, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/30511845/an-open-source-python-based-redevelopment-of-the-chemshell-multiscale-qm-mm-environment
#11
You Lu, Matthew R Farrow, Pierre Fayon, Andrew J Logsdail, Alexey A Sokol, C Richard A Catlow, Paul Sherwood, Thomas W Keal
ChemShell is a scriptable computational chemistry environment with an emphasis on multiscale simulation of complex systems using combined quantum mechanical and molecular mechanical (QM/MM) methods. Motivated by a scientific need to efficiently and accurately model chemical reactions on surfaces and within microporous solids on massively parallel computing systems, we present a major redevelopment of the ChemShell code, which provides a modern platform for advanced QM/MM embedding models. The new version of ChemShell has been re-engineered from the ground up with a new QM/MM driver module, an improved parallelization framework, new interfaces to high performance QM and MM programs, and a user interface written in the Python programming language...
December 4, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/30507200/mechanism-deduction-from-noisy-chemical-reaction-networks
#12
Jonny Proppe, Markus Reiher
We introduce KiNetX, a fully automated meta-algorithm for the kinetic analysis of complex chemical reaction networks derived from semi-accurate but efficient electronic structure calculations. It is designed to (i) accelerate the automated exploration of such networks, and (ii) cope with model-inherent errors in electronic structure calculations on elementary reaction steps. We developed and implemented KiNetX to possess three features. First, KiNetX evaluates the kinetic relevance of every species in a (yet incomplete) reaction network to confine the search for new elementary reaction steps only to those species that are considered possibly relevant...
December 3, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/30507180/description-of-potential-energy-surfaces-of-molecules-using-fflux-machine-learning-models
#13
Zak E Hughes, Joseph C R Thacker, Alex L Wilson, Paul L A Popelier
A new type of model, FFLUX, to describe the interaction between atoms has been developed as an alternative to traditional force fields. FFLUX models are constructed by applying the kriging machine learning method to the topological energy partitioning method, interacting quantum atoms (IQA). The effect of varying parameters in the construction of the FFLUX models is analyzed, with the most dominant effects found to be the structure of the molecule and the number of conformations used to build the model. Using these models, the optimization of a variety of small organic molecules is performed, with sub kJ mol-1 accuracy in the energy of the optimized molecules...
December 3, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/30501194/computational-probing-of-watson-crick-hoogsteen-breathing-in-a-dna-duplex-containing-n1-methylated-adenine
#14
Changwon Yang, Eunae Kim, Manho Lim, Youngshang Pak
DNA breathing is a local conformational fluctuation spontaneously occurring in double-stranded DNAs. In particular, the possibility of individual base pairs (bps) in duplex DNA to flip between alternate bp modes, i.e. Watson-Crick (WC) like and Hoogsteen (HG) like, at relevant time scales has impacted DNA research fields for many years. In this study, to computationally probe effects of chemical modification on the DNA breathing, we present a free energy landscape of spontaneous thermal transitions between WC and HG bps in a free DNA duplex containing N1-methylated adenine (m1A)...
December 2, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/30501134/interpretation-of-interfacial-protein-spectra-with-enhanced-molecular-simulation-ensembles
#15
Helmut Lutz, Vance Jaeger, Tobias Weidner, Bert L de Groot
An atomistically detailed picture of protein folding at interfaces can effectively be obtained by comparing interface-sensitive spectroscopic techniques to molecular simulations. Here, we present an extensive evaluation of the capability of contemporary force fields to model protein folding at air-water interfaces with a general scheme for sampling and reweighting theoretical conformational ensembles of interfacial peptides. Force field combinations of CHARMM22* / TIP3P and AMBER99SB*-ILDN / SPC/E were found to reproduce experimental observations best...
November 30, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/30500205/orbital-optimized-distinguishable-cluster-theory-with-explicit-correlation
#16
Daniel Kats, David P Tew
A combination of orbital-optimized methods with explicit correlation is discussed for the example of the orbital-optimized distinguishable cluster approach. It is shown that the perturbative approach is applicable even in strongly correlated situations, and it is important in these cases to use Lagrange multipliers together with the amplitudes. The partial amplitude relaxation can be applied to relax the amplitudes and makes absolute energies closer to complete basis set results.
November 30, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/30500197/a-new-hybrid-method-for-the-calculation-of-the-solvation-free-energy-of-small-molecules-in-aqueous-solutions
#17
Wenkun Wu, John Kieffer
The ability to accurately predict the solvation free energies of ionic species using the appropriate thermodynamic cycle is of great importance in many areas of chemistry and biochemistry. To improve the accuracy of calculating solvation free energies we devised a hybrid cluster-continuum approach, where explicit solvent molecules are added to the traditionally employed continuum model. Our computational workflow consists of the following steps: First, the minimum number of explicit water molecules beyond which additional water molecules no longer improve the accuracy of the cluster-continuum model is carefully established...
November 30, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/30500196/protein-residue-networks-from-energetic-and-geometric-data-are-they-identical
#18
Vladimir Sladek, Hiroaki Tokiwa, Hitoshi Shimano, Yasuteru Shigeta
Protein residue networks (PRN) from energetic and geometric data are probably not identical. PRNs constructed from ab initio pair interaction energies are analyzed for the first time and compared to PRN based on center of mass separation. We use modern, previously unused algorithms such as global and local efficiencies to quantitatively confirm that both types of PRNs do exhibit small-world character. The main novelty finding is that interaction energy-based PRNs preserve small-world character even when clustered...
November 30, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/30431264/protein-p-k-a-s-from-adaptive-landscape-flattening-instead-of-constant-ph-simulations
#19
Francesco Villa, Thomas Simonson
Protein acid/base constants, or p Ka 's are often computed from Monte Carlo or molecular dynamics simulations at a series of constant pH values. Instead, we propose to adaptively flatten the free energy landscape in the space of protonation states. The flattening is achieved by a Wang-Landau Monte Carlo, where a bias potential is constructed adaptively during an initial phase, such that all protonation states achieve comparable probabilities. Biased ensembles of states are then reweighted by subtracting out the bias and adding a pH-dependent free energy term...
November 30, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/30496689/investigations-of-stacked-dna-base-pair-steps-highly-accurate-stacking-interaction-energies-energy-decomposition-and-many-body-stacking-effects
#20
Holger Kruse, Pavel Banáš, Jiri Sponer
The stacking energies of ten unique B-DNA base-pair steps were calculated with highly-accurate quantum chemistry and used as reference values in a thorough benchmark of (dispersion-corrected) DFT, wavefunction methods, tight-binding methods, and different force fields, including charge-variants thereof. The reference values were computed using a focal-point energy function based on extrapolated explicitly-correlated MP2-F12 and conventional CCSD(T) data at the triple-ζ level. A collection of 29 different density functionals, sometimes with multiple dispersion-corrections (D3(BJ), D3M(BJ) and VV10) were evaluated, including recent functionals like B97M-V, ωB97M-V and SCAN-D3(BJ), which perform excellently...
November 29, 2018: Journal of Chemical Theory and Computation
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