skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Approach to the application of free energy perturbation methods using molecular dynamics: applications to the transformations of CH/sub 3/OH. -->. CH/sub 3/CH/sub 3/, H/sub 3/O/sup +/. -->. NH/sub 4//sup +/, glycine. -->. alanine, and alanine. -->. phenylalanine in aqueous solution and to H/sub 3/O/sup +/ (H/sub 2/O)/sub 3/. -->. NH/sub 4//sup +/(H/sub 2/O)/sub 3/ in the gas phase

Journal Article · · J. Am. Chem. Soc.; (United States)
DOI:https://doi.org/10.1021/ja00240a001· OSTI ID:6808960
; ; ;

A general method for the application of free energy perturbation methods using molecular dynamics has been developed which implements both a time dependent and a time independent procedure. The free energy difference between two states is determined by slowly perturbing state A into state B via a coupling factor lambda. This method has been applied to the transformation of methanol into ethane, ammonium into oxonium, glycine into alanine, and alanine into phenylalanine. The calculated changes in free energy for all of these transformations are in reasonable agreement with the related experimental data, which suggests the method can be usefully applied to a wide range of chemical and biochemical problems.

Research Organization:
Univ. of California, San Francisco
OSTI ID:
6808960
Journal Information:
J. Am. Chem. Soc.; (United States), Vol. 109:6
Country of Publication:
United States
Language:
English

Similar Records

Catalytic production of hydrogen from a hydrocarbon. [CH/sub 4/ is filtered through charcoal, passed through a bed of reduced Fe, at 250/sup 0/, and a bath of 35N NH/sub 4/OH mixed with steam in a ratio of 2 mole vol. at 300-550/sup 0/; gas is scrubbed with H/sub 2/O, 3-5N NH/sub 4/OH and 3-6N KOH and cooled; conversion to H is approx. 100 percent]
Patent · Tue Mar 21 00:00:00 EST 1972 · OSTI ID:6808960
New layered uranium(VI) molybdates: Synthesis and structure of (NH{sub 3}(CH{sub 2}){sub 3}NH{sub 3})(H{sub 3}O){sub 2}(UO{sub 2}){sub 3}(MoO{sub 4}){sub 5}, C(NH{sub 2}){sub 3}(UO{sub 2})(OH)(MoO{sub 4}), (C{sub 4}H{sub 12}N{sub 2})(UO{sub 2})(MoO{sub 4}){sub 2}, and (C{sub 5}H{sub 14}N{sub 2})(UO{sub 2})(MoO{sub 4}){sub 2}{center_dot}H{sub 2}O
Journal Article · Mon Jan 25 00:00:00 EST 1999 · Inorganic Chemistry · OSTI ID:6808960
+1 more
Hydrothermal synthesis and characterization of two- and three-dimensional solids of the oxovanadium(IV)-phosphite system. The structures of [HN(Me)(CH{sub 2}CH{sub 2}){sub 2}N(Me)H]-[(VO){sub 4}(OH){sub 2}(HPO{sub 3}){sub 4}], [H{sub 2}N(CH{sub 2}CH{sub 2}){sub 2}NH{sub 2}][(VO){sub 3}(HPO{sub 3}){sub 4}(H{sub 2}O){sub 2}], and [VO(HPO{sub 3})(H{sub 2}O)]
Journal Article · Wed Nov 01 00:00:00 EST 1995 · Chemistry of Materials · OSTI ID:6808960

Related Subjects

37 INORGANIC
ORGANIC
PHYSICAL AND ANALYTICAL CHEMISTRY
ALANINES
FREE ENERGY
AMMONIUM COMPOUNDS
ETHANE
GLYCINE
METHANOL
OXONIUM IONS
BOND LENGTHS
CATIONS
DYNAMICS
MOLECULAR MODELS
MOLECULAR STRUCTURE
PERTURBATION THEORY
THEORETICAL DATA
ALCOHOLS
ALKANES
AMINO ACIDS
CARBOXYLIC ACIDS
CHARGED PARTICLES
DATA
DIMENSIONS
ENERGY
HYDROCARBONS
HYDROXY COMPOUNDS
INFORMATION
IONS
LENGTH
MATHEMATICAL MODELS
MECHANICS
MOLECULAR IONS
NUMERICAL DATA
ORGANIC ACIDS
ORGANIC COMPOUNDS
PHYSICAL PROPERTIES
THERMODYNAMIC PROPERTIES
400201* - Chemical & Physicochemical Properties