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Journal of Chemical Theory and Computation

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https://www.readbyqxmd.com/read/28212010/assessing-generic-collective-variables-for-determining-reaction-rates-in-metadynamics-simulations
#1
Christopher D Fu, Luiz F L Oliveira, Jim Pfaendtner
A persistent challenge in using the metadynamics method is deciding which degrees of freedom, or collective variables, should be biased because these selections are not obvious and require intuition about the system being studied. There are, however, collective variables, which can be constructed with only basic knowledge about the system studied, that provide an opportunity to alleviate this issue. We simulated two different reacting systems where two types of such collective variables (SPRINT coordinates and the collective variable-driven hyperdynamics method) were biased following the infrequent metadynamics method in order to recover the rates of reactions...
February 17, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28177229/adaptively-compressed-exchange-operator-for-large-scale-hybrid-density-functional-calculations-with-applications-to-the-adsorption-of-water-on-silicene
#2
Wei Hu, Lin Lin, Amartya S Banerjee, Eugene Vecharynski, Chao Yang
Density functional theory (DFT) calculations using hybrid exchange-correlation functionals have been shown to provide an accurate description of the electronic structures of nanosystems. However, such calculations are often limited to small system sizes due to the high computational cost associated with the construction and application of the Hartree-Fock (HF) exchange operator. In this paper, we demonstrate that the recently developed adaptively compressed exchange (ACE) operator formulation [J. Chem. Theory Comput...
February 17, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28207264/steering-orbital-optimization-out-of-local-minima-and-saddle-points-toward-lower-energy
#3
Alain C Vaucher, Markus Reiher
The general procedure underlying Hartree-Fock and Kohn-Sham density functional theory calculations consists in optimizing orbitals for a self-consistent solution of the Roothaan-Hall equations in an iterative process. It is often ignored that multiple self-consistent solutions can exist, several of which may correspond to minima of the energy functional. In addition to the difficulty sometimes encountered to converge the calculation to a self-consistent solution, one must ensure that the correct self-consistent solution was found, typically the one with the lowest electronic energy...
February 16, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28112956/the-theory-of-ultra-coarse-graining-3-coarse-grained-sites-with-rapid-local-equilibrium-of-internal-states
#4
James F Dama, Jaehyeok Jin, Gregory A Voth
When viewed through a coarse-grained lens, important molecular and biophysical systems can appear to undergo discrete, switch-like state changes in addition to more continuous configurational motions. One of our recent papers described a theory for bottom-up coarse-graining of the equilibrium statistics of models with such behavior, called ultra-coarse-grained (UCG) models, and a follow up paper described an implementation when the states of the coarse-grained sites or "beads" change rarely. However, not all systems with this discrete behavior fall under that special limit...
February 16, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28199103/using-the-k-d-tree-data-structure-to-accelerate-monte-carlo-simulations
#5
Qile Paul Chen, Bai Xue, J Ilja Siepmann
The k-d tree data structure is implemented in a Monte Carlo (MC) molecular simulation program to accelerate the range search for particles or interaction sites within the cutoff distance when Lennard-Jones and Coulomb interactions are computed. MC simulations are performed for different molecules in various ensembles to assess the efficiency enhancements due to the k-d tree data structure. It is found that the use of k-d trees accelerates significantly simulations for Lennard-Jones particles in the NVT and NVT-Gibbs ensembles and for n-butane and 2,4,6,8,10,12,14,16,18,20,22-undecamethylpentacosane represented by the TraPPE-UA force field in the NpT ensemble...
February 15, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28157327/discrete-molecular-dynamics-approach-to-the-study-of-disordered-and-aggregating-proteins
#6
Agustí Emperador, Modesto Orozco
We present a refinement of the Coarse Grained PACSAB force field for Discrete Molecular Dynamics (DMD) simulations of proteins in aqueous conditions. As the original version, the refined method provides good representation of the structure and dynamics of folded proteins but provides much better representations of a variety of unfolded proteins, including some very large, impossible to analyze by atomistic simulation methods. The PACSAB/DMD method also reproduces accurately aggregation properties, providing good pictures of the structural ensembles of proteins showing a folded core and an intrinsically disordered region...
February 15, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28195719/generalized-temporal-acceleration-scheme-for-kinetic-monte-carlo-simulations-of-surface-catalytic-processes-by-scaling-the-rates-of-fast-reactions
#7
Eric Christopher Dybeck, Craig Patrick Plaisance, Matthew Neurock
A novel algorithm has been developed to achieve temporal acceleration during kinetic Monte Carlo (KMC) simulations of surface catalytic processes. This algorithm allows for the direct simulation of reaction networks containing kinetic processes occurring on vastly disparate timescales which computationally overburden standard KMC methods. Previously developed methods for temporal acceleration in KMC have been designed for specific systems and often require a priori information from the user such as identifying the fast and slow processes...
February 14, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28195713/ward-clustering-improves-cross-validated-markov-state-models-of-protein-folding
#8
Brooke E Husic, Vijay S Pande
Markov state models (MSMs) are a powerful framework for analyzing protein dynamics. MSMs require the decomposition of conformation space into states via clustering, which can be cross-validated when a prediction method is available for the clustering method. We present an algorithm for predicting cluster assignments of new data points with Ward's minimum variance method. We then show that clustering with Ward's method produces better or equivalent cross-validated MSMs for protein folding than other clustering algorithms...
February 14, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28195707/influence-of-coupling-and-embedding-schemes-on-qm-size-convergence-in-qm-mm-approaches-for-the-example-of-a-proton-transfer-in-dna
#9
Sven Roßbach, Christian Ochsenfeld
The influence of embedding and coupling schemes on the convergence of the QM size in the QM/MM approach is investigated for the transfer of a proton in a DNA base pair. We find that the embedding scheme (mechanical or electrostatic) has a much greater impact on the convergence behavior than the coupling scheme (additive QM/MM or subtractive ONIOM). To achieve size convergence, QM regions with up to 6000 atoms are necessary for pure QM or mechanical embedding. In contrast, electrostatic embedding converges faster: for the example of the transfer of a proton between DNA base pairs, we recommend including at least five base pairs and 5 Å of solvent (including counterions) into the QM region, i...
February 14, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28195473/a-local-order-parameter-based-method-for-simulation-of-free-energy-barriers-in-crystal-nucleation
#10
Neda Khanjari, Hossein Eslami, Florian Müller-Plathe
While global order parameters have widely been used, as reaction coordinates, in nucleation and crystallization studies, their use in nucleation studies is claimed to have a serious drawback. In this work, a local order parameter is introduced, as a local reaction coordinate, to drive the simulation from the liquid to solid phase and vice versa. This local order parameter holds information regarding the order in the first and the second shell neighbors of a particle and has different well-defined values for local crystallites and disordered neighborhoods, but is insensitive to the type of the crystal structure...
February 14, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28195468/structural-distortions-accompanying-noncovalent-interactions-methane-water-the-simplest-c-h-hydrogen-bond
#11
Herzain I Rivera-Arrieta, Justin M Turney, Henry F Schaefer
Neglect of fragment structural distortions resulting from noncovalent interactions is a common practice when examining a potential energy surface (PES). Herein, we make quantitative predictions concerning the magnitude of such distortions in the methane-water system. Coupled cluster methods up to perturbative quadruples [CCSDT(Q)] were used in the structural optimizations to the complete basis set limit (using up to cc-pV6Z basis sets). Our results show that the interaction energy differences between the fully optimized and nonoptimized structures are on the order of 0...
February 14, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28195464/combining-the-martini-and-structure-based-coarse-grained-approaches-for-the-molecular-dynamics-studies-of-conformational-transitions-in-proteins
#12
Adolfo B Poma, Marek Cieplak, Panagiotis E Theodorakis
The application of coarse-grain (CG) models in biology is essential to access large length and time scales required for the description of many biological processes. The ELNEDIN protein model is based on the well-known MARTINI CG force-field and incorporates additionally harmonic bonds of a certain spring constant within a defined cutoff distance between pairs of residues, in order to preserve the native structure of the protein. In this case, the use of unbreakable harmonic bonds hinders the study of unfolded protein structures and unfolding processes...
February 14, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28194972/fragment-based-approach-for-the-evaluation-of-nmr-chemical-shifts-for-large-biomolecules-incorporating-the-effects-of-the-solvent-environment
#13
K V Jovan Jose, Krishnan Raghavachari
We present an efficient implementation of the molecules-in-molecules (MIM) fragment-based quantum chemical method for the evaluation of NMR chemical shifts of large biomolecules. Density functional techniques have been employed in conjunction with large basis sets and including the effects of the solvent environment in these calculations. The MIM-NMR method is initially benchmarked on a set of (alanine)10 conformers containing strong intramolecular interactions. The incorporation of a second low level of theory to recover the missing long-range interactions in the primary fragmentation scheme is critical to yield reliable chemical shifts, with a mean absolute deviation (MAD) from direct unfragmented calculations of 0...
February 14, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28157312/improved-complete-active-space-configuration-interaction-energies-with-a-simple-correction-from-density-functional-theory
#14
Shiela Pijeau, Edward G Hohenstein
Recent algorithmic advances have extended the applicability of complete active space configuration interaction (CASCI) methods to molecular systems with hundreds of atoms. While this enables simulation of photochemical dynamics in the condensed phase, the underlying CASCI method has some well-known problems resulting from a severe neglect of dynamic electron correlation. Vertical excitation energies, vibrational frequencies, and reaction barriers are systematically overestimated; these errors limit the applicability of CASCI...
February 14, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28192669/benchmarking-qm-mm-methods-on-the-thymidylate-synthase-catalyzed-hydride-transfer
#15
Katarzyna Świderek, Kemel Arafet, Amnon Kohen, Vicent Moliner
Given the ubiquity of hydride-transfer reactions in enzyme-catalyzed processes, identifying the appropriate computational method for evaluating such biological reactions is crucial to perform theoretical studies of these processes. In this paper, the hydride-transfer step catalyzed by thymidylate synthase (TSase) is studied by examining hybrid QM/MM potentials via multiple semiempirical methods and the M06-2X hybrid density functional. Calculations of protium and tritium transfer in these reactions across a range of temperatures allowed calculation of the temperature dependence of kinetic isotope effects (KIE)...
February 13, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28192666/cluster-free-energies-from-simple-simulations-of-small-num-bers-of-aggregants-nucleation-of-liquid-mtbe-from-vapor-and-aqueous-phases
#16
Lara A Patel, James T Kindt
We introduce a global fitting analysis method to obtain free energies of association of non-covalent molecular clusters using equilibrated cluster size distributions from unbiased constant-temperature molecular dynamics (MD) simulations. Because the systems simulated are small enough that the law of mass action does not describe the aggregation statistics, the method relies on iteratively determining a set of cluster free energies that, using appropriately weighted sums over all possible partitions of N monomers into clusters, produces the best-fit size distribution...
February 13, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28191949/ultrafast-excited-state-decays-in-re-co-3-n-n-l-n-non-adiabatic-quantum-dynamics
#17
Maria Fumanal, Etienne Gindensperger, Chantal Daniel
The ultrafast luminescent decay of [Re(CO)3(phen)(im)]+, representative of Re(I) carbonyl α-diimine photosensitizers, is investigated by means of wavepacket propagations based on the multiconfiguration time-dependent Hartree (MCTDH) method. On the basis of electronic structure data obtained at the time-dependent density functional theory (TD-DFT) level, the luminescence decay is simulated by solving a fourteen electronic states multimode problem including both vibronic and spin-orbit coupling (SOC) up to fifteen vibrational modes...
February 13, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28135420/diabatic-at-construction-method-for-diabatic-and-adiabatic-ground-and-excited-states-based-on-multistate-density-functional-theory
#18
Adam Grofe, Zexing Qu, Donald G Truhlar, Hui Li, Jiali Gao
We describe a diabatic-at-construction (DAC) strategy for defining diabatic states to determine the adiabatic ground and excited electronic states and their potential energy surfaces using the multistate density functional theory (MSDFT). The DAC approach differs in two fundamental ways from the adiabatic-to-diabatic (ATD) procedures that transform a set of preselected adiabatic electronic states to a new representation. (1) The DAC states are defined in the first computation step to form an active space, whose configuration interaction produces the adiabatic ground and excited states in the second step of MSDFT...
February 13, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28125228/potential-functional-embedding-theory-at-the-correlated-wave-function-level-1-mixed-basis-set-embedding
#19
Jin Cheng, Florian Libisch, Kuang Yu, Mohan Chen, Johannes M Dieterich, Emily A Carter
Embedding theories offer an elegant solution to overcome intrinsic algorithmic scaling and accuracy limitations of simulation methods. These theories also promise to achieve the accuracy of high-level electronic structure techniques at near the computational cost of much less accurate levels of theory by exploiting positive traits of multiple methods. Of crucial importance to fulfilling this promise is the ability to combine diverse theories in an embedding simulation. However, these methods may utilize different basis set and electron-ion potential representations...
February 13, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28125226/potential-functional-embedding-theory-at-the-correlated-wave-function-level-2-error-sources-and-performance-tests
#20
Jin Cheng, Kuang Yu, Florian Libisch, Johannes M Dieterich, Emily A Carter
Quantum mechanical embedding theories partition a complex system into multiple spatial regions that can use different electronic structure methods within each, to optimize trade-offs between accuracy and cost. The present work incorporates accurate but expensive correlated wave function (CW) methods for a subsystem containing the phenomenon or feature of greatest interest, while self-consistently capturing quantum effects of the surroundings using fast but less accurate density functional theory (DFT) approximations...
February 13, 2017: Journal of Chemical Theory and Computation
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