Proc Natl Acad Sci U S A
October 2016
Replica exchange molecular dynamics (REMD) is a popular method to accelerate conformational sampling of complex molecular systems. The idea is to run several replicas of the system in parallel at different temperatures that are swapped periodically. These swaps are typically attempted every few MD steps and accepted or rejected according to a Metropolis-Hastings criterion.
View Article and Find Full Text PDFThe flavoenzyme monomeric sarcosine oxidase (MSOX) catalyzes a complex set of reactions currently lacking a consensus mechanism. A key question that arises in weighing competing mechanistic models of MSOX function is to what extent ingress of O2 from the solvent (and its egress after an unsuccessful oxidation attempt) limits the overall catalytic rate. To address this question, we have applied to the MSOX/O2 system the relatively new simulation method of Markovian milestoning molecular dynamics simulations, which, as we recently showed [ Yu et al.
View Article and Find Full Text PDFStructures of the α and β phases of resorcinol, a major commodity chemical in the pharmaceutical, agrichemical, and polymer industries, were the first polymorphic pair of molecular crystals solved by X-ray analysis. It was recently stated that "no additional phases can be found under atmospheric conditions" (Druzbicki, K. et al.
View Article and Find Full Text PDFAn extra-large octahedral coordination cage (CIAC-114) was designed and modeled based on Co4-p-tert-butylsulfonylcalix[4]arene (Co4-(SC4A-SO2)) subunits and 4,4',4''-(benzene-1,3,5-triyl-tris(benzene-4,1-diyl))tribenzoate (BBB) ligands via the isomorphic replacement approach built from an analogous cage structure with a smaller size. X-ray crystallography revealed that the crystals obtained through solvothermal synthesis exhibited the anticipated structure. Each CIAC-114 cage is assembled by six tetranuclear Co4-(SC4A-SO2) units as vertices, which bear a four-fold rotational symmetry, and eight tripodal BBB ligands as linkers, which hold a D3h symmetry.
View Article and Find Full Text PDFCoarse graining of complex systems possessing many degrees of freedom can often be a useful approach for analyzing and understanding key features of these systems in terms of just a few variables. The relevant energy landscape in a coarse-grained description is the free energy surface as a function of the coarse-grained variables, which, despite the dimensional reduction, can still be an object of high dimension. Consequently, navigating and exploring this high-dimensional free energy surface is a nontrivial task.
View Article and Find Full Text PDFWe use Markovian milestoning molecular dynamics (MD) simulations on a tessellation of the collective variable space for CO localization in myoglobin to estimate the kinetics of entry, exit, and internal site-hopping. The tessellation is determined by analysis of the free-energy surface in that space using transition-path theory (TPT), which provides criteria for defining optimal milestones, allowing short, independent, cell-constrained MD simulations to provide properly weighted kinetic data. We coarse grain the resulting kinetic model at two levels: first, using crystallographically relevant internal cavities and their predicted interconnections and solvent portals; and second, as a three-state side-path scheme inspired by similar models developed from geminate recombination experiments.
View Article and Find Full Text PDFThe melting of a solid, like other first-order phase transitions, exhibits an intrinsic time-scale disparity: The time spent by the system in metastable states is orders of magnitude longer than the transition times between the states. Using rare-event sampling techniques, we find that melting of representative solids-here, copper and aluminum-occurs via multiple, competing pathways involving the formation and migration of point defects or dislocations. Each path is characterized by multiple barrier-crossing events arising from multiple metastable states within the solid basin.
View Article and Find Full Text PDFThe problem of predicting polymorphism in atomic and molecular crystals constitutes a significant challenge both experimentally and theoretically. From the theoretical viewpoint, polymorphism prediction falls into the general class of problems characterized by an underlying rough energy landscape, and consequently, free energy based enhanced sampling approaches can be brought to bear on the problem. In this paper, we build on a scheme previously introduced by two of the authors in which the lengths and angles of the supercell are targeted for enhanced sampling via temperature accelerated adiabatic free energy dynamics [T.
View Article and Find Full Text PDFMany problems in biology, chemistry, and materials science require knowledge of saddle points on free energy surfaces. These saddle points act as transition states and are the bottlenecks for transitions of the system between different metastable states. For simple systems in which the free energy depends on a few variables, the free energy surface can be precomputed, and saddle points can then be found using existing techniques.
View Article and Find Full Text PDFThe ability of certain organic molecules to form multiple crystal structures, known as polymorphism, has important ramifications for pharmaceuticals and high energy materials. Here, we introduce an efficient molecular dynamics method for rapidly identifying and thermodynamically ranking polymorphs. The new method employs high temperature and adiabatic decoupling to the simulation cell parameters in order to sample the Gibbs free energy of the polymorphs.
View Article and Find Full Text PDFHexatriene electrocyclization, if not disfavored by its harsh reaction conditions, can be highly useful for the synthesis of complex organic molecules. Herein we developed a two-layer ONIOM method which could predict the activation free energy of hexatriene electrocyclization with an accuracy of about 1.0 kcal/mol.
View Article and Find Full Text PDFA first-principle theoretical protocol was developed that could predict the absolute pK(a) values of over 250 structurally unrelated compounds in DMSO with a precision of 1.4 pK(a) units. On this basis we developed the first theoretical protocol that could predict the standard redox potentials of over 250 structurally unrelated organic anions in DMSO with a precision of 0.
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