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Journal of Chemical Theory and Computation

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https://read.qxmd.com/read/30875213/polarizable-qm-mm-approach-with-fluctuating-charges-and-fluctuating-dipoles-the-qm-fqf%C3%AE-model
#1
Tommaso Giovannini, Alessandra Puglisi, Matteo Ambrosetti, Chiara Cappelli
The novel polarizable FQFμ force field is proposed and coupled to a QM SCF Hamiltonian. The peculiarity of the resulting QM/FQFμ approach stands in the fact the polarization effects are modeled in terms of both fluctuating charges and dipoles, which vary as a response to the external electric field/potential. Remarkably, QM/FQFμ is defined in terms of three parameters: electronegativity and chemical hardness, which are well defined in Density Functional Theory, and polarizability, which is a physical observable...
March 15, 2019: Journal of Chemical Theory and Computation
https://read.qxmd.com/read/30875212/ab-initio-calculation-of-total-x-ray-scattering-from-molecules
#2
Andrés Moreno Carrascosa, Haiwang Yong, Deborah L Crittenden, Peter M Weber, Adam Kirrander
We present a method to calculate total x-ray scattering cross sections directly from ab-initio electronic wavefunctions in atoms and molecules. The approach can be used in conjunction with multiconfigurational wavefunctions and exploits analytical integrals of Gaussian-type functions over the scattering operator, which leads to accurate and efficient calculations. The results are validated by comparison to experimental results and previous theory for the molecules H2 and CO2. Importantly, we find that the inelastic component of the total scattering varies strongly with molecular geometry...
March 15, 2019: Journal of Chemical Theory and Computation
https://read.qxmd.com/read/30865832/a-general-purpose-water-model-can-improve-atomistic-simulations-of-intrinsically-disordered-proteins
#3
Parviz S Shabane, Saeed Izadi, Alexey V Onufriev
Unconstrained atomistic simulations of intrinsically disordered proteins and peptides (IDP) remain a challenge: widely used, "general purpose" water models tend to favor overly compact structures relative to experiment. Here we have performed a total of 93 μs of unrestrained MD simulations to explore, in the context of IDPs, a recently developed "general-purpose" 4-point rigid water model OPC, which describes liquid state of water close to experiment. We demonstrate that OPC, together with a popular AMBER force field ff99SB, offers a noticeable improvement over TIP3P in producing more realistic structural ensembles of three common IDPs benchmarks: 55-residue apo N-terminal zinc-binding domain of HIV-1 integrase ("protein IN"), amyloid β-peptide (Aβ42) (residues 1-42), and 26-reside H4 histone tail...
March 13, 2019: Journal of Chemical Theory and Computation
https://read.qxmd.com/read/30865820/temperature-dependence-of-idps-in-simulations-what-are-we-missing
#4
Stephanie Jephthah, Lasse Staby, Birthe B Kragelund, Marie Skepö
The temperature dependence of the conformational properties in simulations of the intrinsically disordered model protein Histatin 5 has been investigated using different combinations of force fields, water models, atomistic and coarse-grained methods. The results have been compared to experimental data obtained from NMR, SAXS and CD experiments in order to assess the accuracy and validity of the simulations. The results showed that neither simulations completely agreed with the experimental data, nor did they agree with each other...
March 13, 2019: Journal of Chemical Theory and Computation
https://read.qxmd.com/read/30865452/oniom-qm-qm-electrostatic-embedding-schemes-for-photochemistry-in-molecular-crystals
#5
Miguel Rivera, Michael Dommett, Rachel Crespo-Otero
Understanding photoinduced processes in molecular crystals is central to the design of highly emissive materials such as organic lasers and organic light-emitting diodes. The modelling of such processes is, however, hindered by the lack of excited state methodologies tailored for these systems. Embedding approaches based on the Ewald sum can be used in conjunction with excited state electronic structure methods to model the localised excitations which characterise these materials. In this article, we describe the implementation of a two-level ONIOM(QM:QM') point charge embedding approach based on the Ewald method, the Ewald Embedded Cluster (EEC) model...
March 13, 2019: Journal of Chemical Theory and Computation
https://read.qxmd.com/read/30865448/ab-initio-derived-force-fields-for-zeolitic-imidazolate-frameworks-mof-ff-for-zifs
#6
Johannes P Dürholt, Guillaume Fraux, François-Xavier Coudert, Rochus Schmid
In this paper we parameterized in a consistent way a new force field for a range of different zeolitic imidazolate framework systems (ZIF-8, IF-8(H), ZIF-8(Br) and ZIF-8(Cl)), extending the MOF-FF parameterization methodology in two aspects. First, we implemented the possibility to use periodic reference data in order to prevent the difficulty of generating representative finite clusters. Second, a new optimizer based on the covariance matrix adaptation evolutionary strategy (CMA-ES) was employed during the parameterization process...
March 13, 2019: Journal of Chemical Theory and Computation
https://read.qxmd.com/read/30860839/learning-from-failure-predicting-electronic-structure-calculation-outcomes-with-machine-learning-models
#7
Chenru Duan, Jon Paul Janet, Fang Liu, Aditya Nandy, Heather J Kulik
High-throughput computational screening for chemical discovery mandates the automated and unsupervised simulation of thousands of new molecules and materials. In challenging materials spaces, such as open shell transition metal chemistry, characterization requires time-consuming first-principles simulation that often necessitates human intervention. These calculations can frequently lead to a null result, e.g., the calculation does not converge or the molecule does not stay intact during a geometry optimization...
March 12, 2019: Journal of Chemical Theory and Computation
https://read.qxmd.com/read/30860838/first-principle-prediction-of-intramolecular-singlet-fission-and-triplet-triplet-annihilation-rates
#8
Hung-Hsuan Lin, Karl Y Kue, Gil C Claudio, Chao-Ping Hsu
Intramolecular singlet fission and triplet-triplet annihilation (TTA) has been experimentally observed and reported. However, problems remain in theoretically accounting for the corresponding intramolecular electronic couplings and their rates. We used the fragment excitation difference (FED) scheme to calculate the coupling with states from restricted active-space spin-flip configuration interaction. We investigated three covalently-linked pentacene dimers via a phenyl group in an ortho-, meta- and para-arrangement...
March 12, 2019: Journal of Chemical Theory and Computation
https://read.qxmd.com/read/30860835/a-multi-layer-approach-to-ip-eom-dlpno-ccsd-method-theory-implementation-and-application
#9
Soumi Haldar, Christoph Riplinger, Baptiste Demoulin, Frank Neese, Robert Izsak, Achintya Kumar Dutta
We present a multilayer implementation of the EOM-CCSD for the computation of ionization potentials of atoms and molecules in the presence of their environment. The method uses local orbitals to partition the system into a number of hypothetical fragments and treat different fragments of the system at different levels of theory. This approach significantly reduces the computational cost with a systematically controllable accuracy and is equally applicable to describe the environmental effect of both bonded and non-bonded nature...
March 12, 2019: Journal of Chemical Theory and Computation
https://read.qxmd.com/read/30860829/non-equilibrium-solvent-polarization-effects-in-real-time-electronic-dynamics-of-solute-molecules-subject-to-time-dependent-electric-fields-a-new-feature-of-the-polarizable-continuum-model
#10
Gabriel Gil, Silvio Pipolo, Alain Delgado, Carlo Andrea Rozzi, Stefano Corni
We develop an extension of the time-dependent equation-of-motion formulation of the Polarizable Continuum Model (EOM-TDPCM) to introduce non-equilibrium cavity field effects in quantum mechanical calculations of solvated molecules subject to time-dependent electric fields. This method has been implemented in Octopus, a state-of-the-art code for real-space, real-time Time Dependent Density Functional Theory (RT-TDDFT) calculations. To show the potential of our methodology, we perform EOM-TDPCM/RT-TDDFT calculations of trans-azobenzene in water and in other model solvents with shorter relaxation times...
March 12, 2019: Journal of Chemical Theory and Computation
https://read.qxmd.com/read/30860828/on-benchmarking-of-automated-methods-for-performing-exhaustive-reaction-path-search
#11
Satoshi Maeda, Yu Harabuchi
In recent years, the importance of computational chemistry approaches has grown rapidly because of recent advances in computational software and hardware. Automated reaction path search is one of promising techniques which would enable to explore unknown chemistry in computers. Several methods have been developed so far, and comparison of the performance of existing methods would be the subject of interest of many chemists. Here, we present the performance of our single-component artificial force induced reaction (SC-AFIR) method...
March 12, 2019: Journal of Chemical Theory and Computation
https://read.qxmd.com/read/30860827/assessment-of-density-functional-theory-in-predicting-interaction-energies-between-water-and-polycyclic-aromatic-hydrocarbons-from-water-on-benzene-to-water-on-graphene
#12
Adeayo O Ajala, Vamsee K Voora, Narbe Mardirossian, Filipp Furche, Francesco Paesani
The interactions of water with polycyclic aromatic hydrocarbons, from benzene to graphene, are investigated using various exchange-correlation functionals selected across the hierarchy of density functional theory (DFT) approximations. The accuracy of the different functionals is assessed through comparisons with random phase approximation (RPA) and coupled-cluster with single, double, and perturbative triple excitations [CCSD(T)] calculations. Diffusion Monte Carlo (DMC) data reported in the literature are also used for comparison...
March 12, 2019: Journal of Chemical Theory and Computation
https://read.qxmd.com/read/30855964/multimodal-structural-distribution-of-the-p53-c-terminal-domain-upon-binding-to-s100b-via-a-generalised-ensemble-method-from-disorder-to-extra-disorder
#13
Shinji Iida, Takeshi Kawabata, Kota Kasahara, Haruki Nakamura, Junichi Higo
Intrinsically disordered regions (IDRs) of a protein employ a flexible binding manner when recognising a partner molecule. Moreover, it is recognised that binding of IDRs to a partner molecule is accompanied with folding, with a variety of bound conformations often being allowed in formation of the complex. In this study, we investigated a fragment of the disordered p53 C-terminal domain (CTDf) that interacts with one of its partner molecules, S100B, as a representative IDR. Although the 3D structure of CTDf in complex with S100B has been previously reported, the specific interactions remained controversial...
March 11, 2019: Journal of Chemical Theory and Computation
https://read.qxmd.com/read/30855953/spin-valence-and-structural-isomerism-in-the-s-3-state-of-the-oxygen-evolving-complex-of-photosystem-ii-as-a-manifestation-of-multimetallic-cooperativity
#14
Hiroshi Isobe, Mitsuo Shoji, Takayoshi Suzuki, Jian-Ren Shen, Kizashi Yamaguchi
Photosynthetic water oxidation is catalyzed by a Mn4 CaO5 -cluster in photosystem II through an S-state cycle. Understanding the roles of heterogeneity in each S-state, as identified recently by the EPR spectroscopy, is very important to gain a complete description of the catalytic mechanism. We performed herein hybrid DFT calculations within the broken-symmetry formalism and associated analyses of Heisenberg spin models to study the electronic and spin structures of various isomeric structural motifs (hydroxo-oxo, oxyl-oxo, peroxo, and superoxo species) in the S3 state...
March 11, 2019: Journal of Chemical Theory and Computation
https://read.qxmd.com/read/30849227/temperature-induced-dynamical-transition-of-biomolecules-in-polarizable-and-nonpolarizable-tip3p-water
#15
Tusar Bandyopadhyay, Arup Kumar Pathak
Temperature induced dynamic transition (DT), associated with sharp rise in molecular flexibility, is well-known to be exhibited between 270-280 K in glycerol to 200-230 K in hydrated biomolecules and is controlled by diffusivity (viscosity) of the solvation layer. In the molecular dynamics (MD) community, especially for water as a solvent, this has been an intense area of research despite decades of investigations. However, in general, water in these studies are described by empirical nonpolarizable force fields in which electronic polarizability are treated implicitly with effective charges and related parameters...
March 8, 2019: Journal of Chemical Theory and Computation
https://read.qxmd.com/read/30848905/the-outer-membrane-proteins-ompa-fhua-ompf-esta-btub-and-ompx-have-unique-lipopolysaccharide-fingerprints
#16
Jonathan Shearer, Damien Jefferies, Syma Khalid
The outer membrane of Gram-negative bacteria has a highly complex asymmetrical architecture, containing a mixture of phospholipids in the inner leaflet, and almost exclusively lipopolysaccharide (LPS) molecules in the outer leaflet. In E. coli, the outer membrane contains a wide range of proteins with a beta barrel architecture, that vary in size from the smallest having eight strands to larger barrels composed of twenty-two strands. Here we report coarse-grained molecular dynamics simulations of six proteins from the E...
March 8, 2019: Journal of Chemical Theory and Computation
https://read.qxmd.com/read/30844271/photophysics-of-molecular-aggregates-from-excited-state-diabatization
#17
Abel Carreras, Olatz Uranga-Barandiaran, Frédéric Castet, David Casanova
The detailed understanding of photophysical processes in molecular aggregates requires the precise characterization of electronic excited states resulting from the interaction between chromophoric units. Theoretical descriptions of such systems are usually achieved by means of excitonic models, using effective Hamiltonians built on a basis of diabatic states that enable physical interpretations in terms of local excitations, charge transfer or multiexcitonic configurations. In this work, we develop an alternative approach based on a diabatization scheme, which allows the decomposition of the adiabatic excited state energies of molecular aggregates into contributions issued from intermolecular couplings, without requiring any a priori definition of diabatic states...
March 7, 2019: Journal of Chemical Theory and Computation
https://read.qxmd.com/read/30836000/robust-determination-of-protein-allosteric-signaling-pathways
#18
Wesley Botello-Smith, Yun Luo
To understand how protein function changes upon an allosteric perturbation, such as ligand binding and mutation, significant progress in characterizing allosteric network from molecular dynamics (MD) simulations has been made. However, determining which amino acid(s) play an essential role in the propagation of signals may prove challenging, even when the location of the source and sink is known for a protein or protein complex. This challenge is mainly due to the large fluctuations in protein dynamics that cause instability of the network topology within a single trajectory or between multiple replicas...
March 5, 2019: Journal of Chemical Theory and Computation
https://read.qxmd.com/read/30835999/simulating-water-exchange-to-buried-binding-sites
#19
Ido Y Ben-Shalom, Charles Lin, Tom Kurtzman, Ross C Walker, Michael K Gilson
Traditional molecular dynamics (MD) simulations of proteins, which rely on integration of Newton's equations of motion, cannot efficiently equilibrate water occupancy for buried cavities in proteins. This leads to slow convergence of thermodynamic averages for such systems. We have addressed this challenge by efficiently integrating standard Metropolis Monte Carlo (MC) translational water moves with MD in the AMBER simulation package. The translational moves allow water to easily enter or exit buried sites in a thermodynamically correct way during a simulation...
March 5, 2019: Journal of Chemical Theory and Computation
https://read.qxmd.com/read/30830778/ion-hydroxyl-interactions-from-high-level-quantum-benchmarks-to-transferable-polarizable-force-fields
#20
Vered Wineman-Fisher, Yasmine Al-Hamdani, Iqbal Addou, Alexandre Tkatchenko, Sameer Varma
Ion descriptors in molecular mechanics models are calibrated against reference data on ion-water interactions. It is then typically assumed that these descriptors will also satisfactorily describe interactions of ions with other functional groups, such as those present in biomolecules. However, several studies now demonstrate that this transferability assumption produces, in many different cases, large errors. Here we address this issue in a representative polarizable model and focus on transferability of cationic interactions from water to a series of alcohols...
March 4, 2019: Journal of Chemical Theory and Computation
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