Literature DB >> 11607654

Progress toward chemical accuracy in the computer simulation of condensed phase reactions.

P A Bash1, L L Ho, A D MacKerell, D Levine, P Hallstrom.   

Abstract

We describe a procedure for the generation of chemically accurate computer-simulation models to study chemical reactions in the condensed phase. The process involves (i) the use of a coupled semiempirical quantum and classical molecular mechanics method to represent solutes and solvent, respectively; (ii) the optimization of semiempirical quantum mechanics (QM) parameters to produce a computationally efficient and chemically accurate QM model; (iii) the calibration of a quantum/classical microsolvation model using ab initio quantum theory; and (iv) the use of statistical mechanical principles and methods to simulate, on massively parallel computers, the thermodynamic properties of chemical reactions in aqueous solution. The utility of this process is demonstrated by the calculation of the enthalpy of reaction in vacuum and free energy change in aqueous solution for a proton transfer involving methanol, methoxide, imidazole, and imidazolium, which are functional groups involved with proton transfers in many biochemical systems. An optimized semiempirical QM model is produced, which results in the calculation of heats of formation of the above chemical species to within 1.0 kcal/mol (1 kcal = 4.18 kJ) of experimental values. The use of the calibrated QM and microsolvation QM/MM (molecular mechanics) models for the simulation of a proton transfer in aqueous solution gives a calculated free energy that is within 1.0 kcal/mol (12.2 calculated vs. 12.8 experimental) of a value estimated from experimental pKa values of the reacting species.

Entities:  

Year:  1996        PMID: 11607654      PMCID: PMC39675          DOI: 10.1073/pnas.93.8.3698

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  4 in total

1.  Active site dynamics in protein molecules: a stochastic boundary molecular-dynamics approach.

Authors:  C L Brooks; A Brünger; M Karplus
Journal:  Biopolymers       Date:  1985-05       Impact factor: 2.505

2.  Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme.

Authors:  A Warshel; M Levitt
Journal:  J Mol Biol       Date:  1976-05-15       Impact factor: 5.469

3.  Solvent effects on protein motion and protein effects on solvent motion. Dynamics of the active site region of lysozyme.

Authors:  C L Brooks; M Karplus
Journal:  J Mol Biol       Date:  1989-07-05       Impact factor: 5.469

4.  Free energy calculations by computer simulation.

Authors:  P A Bash; U C Singh; R Langridge; P A Kollman
Journal:  Science       Date:  1987-05-01       Impact factor: 47.728

  4 in total
  8 in total

1.  Sign Learning Kink-based (SiLK) Quantum Monte Carlo for molecular systems.

Authors:  Xiaoyao Ma; Randall W Hall; Frank Löffler; Karol Kowalski; Kiran Bhaskaran-Nair; Mark Jarrell; Juana Moreno
Journal:  J Chem Phys       Date:  2016-01-07       Impact factor: 3.488

Review 2.  Multidimensional tunneling, recrossing, and the transmission coefficient for enzymatic reactions.

Authors:  Jingzhi Pu; Jiali Gao; Donald G Truhlar
Journal:  Chem Rev       Date:  2006-08       Impact factor: 60.622

Review 3.  CHARMM: the biomolecular simulation program.

Authors:  B R Brooks; C L Brooks; A D Mackerell; L Nilsson; R J Petrella; B Roux; Y Won; G Archontis; C Bartels; S Boresch; A Caflisch; L Caves; Q Cui; A R Dinner; M Feig; S Fischer; J Gao; M Hodoscek; W Im; K Kuczera; T Lazaridis; J Ma; V Ovchinnikov; E Paci; R W Pastor; C B Post; J Z Pu; M Schaefer; B Tidor; R M Venable; H L Woodcock; X Wu; W Yang; D M York; M Karplus
Journal:  J Comput Chem       Date:  2009-07-30       Impact factor: 3.376

4.  The importance of reactant positioning in enzyme catalysis: a hybrid quantum mechanics/molecular mechanics study of a haloalkane dehalogenase.

Authors:  E Y Lau; K Kahn; P A Bash; T C Bruice
Journal:  Proc Natl Acad Sci U S A       Date:  2000-08-29       Impact factor: 11.205

5.  Polarized Molecular Orbital Model Chemistry 3. The PMO Method Extended to Organic Chemistry.

Authors:  Miho Isegawa; Luke Fiedler; Hannah R Leverentz; Yingjie Wang; Santhanamoorthi Nachimuthu; Jiali Gao; Donald G Truhlar
Journal:  J Chem Theory Comput       Date:  2013-01-08       Impact factor: 6.006

6.  Molecular simulations of RNA 2'-O-transesterification reaction models in solution.

Authors:  Brian K Radak; Michael E Harris; Darrin M York
Journal:  J Phys Chem B       Date:  2012-12-24       Impact factor: 2.991

7.  QM/MM through the 1990s: The First Twenty Years of Method Development and Applications.

Authors:  Meiyi Liu; Yingjie Wang; Yakun Chen; Martin J Field; Jiali Gao
Journal:  Isr J Chem       Date:  2014-07-31       Impact factor: 3.333

8.  Hydrophobic alkyl chains substituted to the 8-position of cyclic nucleotides enhance activation of CNG and HCN channels by an intricate enthalpy - entropy compensation.

Authors:  Maik Otte; Andrea Schweinitz; Michele Bonus; Uta Enke; Christina Schumann; Holger Gohlke; Klaus Benndorf
Journal:  Sci Rep       Date:  2018-10-08       Impact factor: 4.379

  8 in total

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