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Konig G.,U.S. National Institutes of Health | Mei Y.,East China Normal University | Mei Y.,Center for Computational Chemistry | Pickard F.C.,U.S. National Institutes of Health | And 6 more authors.
Journal of Chemical Theory and Computation | Year: 2016

A recently developed MESS-E-QM/MM method (multiple-environment single-system quantum mechanical molecular/mechanical calculations with a Roothaan-step extrapolation) is applied to the computation of hydration free energies for the blind SAMPL4 test set and for 12 small molecules. First, free energy simulations are performed with a classical molecular mechanics force field using fixed-geometry solute molecules and explicit TIP3P solvent, and then the non-Boltzmann-Bennett method is employed to compute the QM/MM correction (QM/MM-NBB) to the molecular mechanical hydration free energies. For the SAMPL4 set, MESS-E-QM/MM-NBB corrections to the hydration free energy can be obtained 2 or 3 orders of magnitude faster than fully converged QM/MM-NBB corrections, and, on average, the hydration free energies predicted with MESS-E-QM/MM-NBB fall within 0.10-0.20 kcal/mol of full-converged QM/MM-NBB results. Out of five density functionals (BLYP, B3LYP, PBE0, M06-2X, and ωB97X-D), the BLYP functional is found to be most compatible with the TIP3P solvent model and yields the most accurate hydration free energies against experimental values for solute molecules included in this study. © 2015 American Chemical Society. Source


Zhou Y.,Nanjing University | Xie D.,Nanjing University | Zhang Y.,New York University | Zhang Y.,Center for Computational Chemistry
Journal of Physical Chemistry Letters | Year: 2016

Cystine-knot peptides have remarkable stability against protease degradation and are attractive scaffolds for peptide-based therapeutic and diagnostic agents. In this work, by studying the hydrolysis reaction of a cystine-knot inhibitor MCTI-A and its variants with ab initio QM/MM molecular dynamics simulations, we have elucidated an amide rotation hindrance mechanism for proteolysis resistance: The proteolysis of MCTI-A is retarded due to the higher free energy cost during the rotation of NH group around scissile peptide bond at the tetrahedral intermediate of acylation, and covalent constraint provided by disulfide bonds is the key factor to hinder this rotation. A nearly linear correlation has been revealed between free energy barriers of the peptide hydrolysis reaction and the amide rotation free energy changes at the protease-peptide Michaelis complex state. This suggests that amide rotation hindrance could be one useful feature to estimate peptide proteolysis stability. © 2016 American Chemical Society. Source


Mu H.,New York University | Geacintov N.E.,New York University | Zhang Y.,New York University | Zhang Y.,Center for Computational Chemistry | Broyde S.,New York University
Biochemistry | Year: 2015

Mammalian global genomic nucleotide excision repair requires lesion recognition by XPC, whose detailed binding mechanism remains to be elucidated. Here we have delineated the dynamic molecular pathway and energetics of lesion-specific and productive binding by the Rad4/yeast XPC lesion recognition factor, as it forms the open complex [Min, J. H., and Pavletich, N. P. (2007) Nature 449, 570-575; Chen, X., et al. (2015) Nat. Commun. 6, 5849] that is required for excision. We investigated extensively a cis-syn cyclobutane pyrimidine dimer in mismatched duplex DNA, using high-level computational approaches. Our results delineate a preferred correlated motion mechanism, which provides for the first time an atomistic description of the sequence of events as Rad4 productively binds to the damaged DNA. (Figure Presented). © 2015 American Chemical Society. Source


Brkljaca Z.,Institute for Theoretical Physics | Klimczak M.,Crystallography and Structural Physics | Milicevic Z.,Institute for Theoretical Physics | Weisser M.,Crystallography and Structural Physics | And 7 more authors.
Journal of Physical Chemistry Letters | Year: 2015

Understanding the molecular-level behavior of ionic liquids (ILs) at IL-solid interfaces is of fundamental importance with respect to their application in, for example, electrochemical systems and electronic devices. Using a model system, consisting of an imidazolium-based IL ([C2Mim][NTf2]) in contact with a sapphire substrate, we have approached this problem using a complementary combination of high-resolution X-ray reflectivity measurements and atomistic molecular dynamics (MD) simulations. Our strategy enabled us to compare experimental and theoretically calculated reflectivities in a direct manner, thereby critically assessing the applicability of several force-field variants. On the other hand, using the best-matching MD description, we are able to describe the nature of the model IL-solid interface in appreciable detail. More speci fically, we find that characteristic interactions between the surface hydroxyl groups and donor and acceptor sites on the IL constituents have a dominant role in inducing a multidimensional layering profile of the cations and anions. (Graph Presented). © 2015 American Chemical Society. Source


Xu M.,New York University | Ye S.,New York University | Bacic Z.,New York University | Bacic Z.,Center for Computational Chemistry
Journal of Physical Chemistry Letters | Year: 2015

Knowledge of the relevant selection rules is crucial for the accurate interpretation of experimental spectra in general. There has been a consensus for a long time that the incoherent inelastic neutron scattering (INS) spectroscopy of the vibrations of discrete molecular compunds is free from any selection rules. We contradict this widely held view by presenting an analytical derivation of the general selection rule for the INS spectroscopy of a hydrogen molecule inside a near-spherical nanocavity. It defines all forbidden transitions, originating in a range of initial translation-rotation (TR) states, ground and excited, of the caged para- and ortho-H2, as well as HD, that are unobservable in the INS spectra. These predictions are amenable to experimental verification. In addition, we demonstrate that the general selection rule applies to the INS spectroscopy of any diatomic molecule in a nanocavity with near-spherical symmetry, which exhibits strong TR coupling. Its existence strongly suggests that similar selection rules apply to the INS spectra of other molecular and supramolecular systems, and need to be identified. © 2015 American Chemical Society. Source

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