Molecular simulation of alkyl boronic acids: Molecular mechanics and solvation free energy calculations

Abstract

The alkyl boronic acid moiety is incorporated into many biologically interesting structures. To provide parameters for molecular mechanics and dynamics studies of compounds containing this group, we performed ab initio calculations at the 6-31G* level to obtain bond stretching, bending, and torsion constants. The hydrodynamic formulation of the time-dependent density functional theory was used to calculate the attractive part of van der Waals (VDW) 6-12 potential. The geometry of boronic acid moiety of the 6-31G* optimized methyl boronic acid was similar to that of the X-ray crystal structure of phenyl boronic acid. To test the reliability of nonbonded parameters, Monte Carlo free energy perturbation simulations and the thermodynamic cycle approach were used to estimate the differences in solvation free energy between alkyl alcohol and alkyl boronic acid, both in water and in chloroform. These free energy differences were also obtained experimentally by measuring the vapor-water and water-chloroform partition coefficients. The close agreement between experimental values and the results of our simulations suggests the reliability of new molecular mechanics forcefield parameters for alkyl boronic acids. 0 1994 by John Wiley & Sons, Inc.tease,3 and dihydro~rotase~ and of cell replicat i~n .~ Several side-chain derivatives of natural aamino acids such as leucine and phenylalanine, containing boronic acid moiety, were shown to be inhibitors of amino peptidases.6 ne c5 and c6 rofic acid derivatives of fie pyrimidine &splayed

Molecular Dynamics Simulations of Graphene Oxide Frameworks

“…Force field parameters essential to the description of phenylboronic acid (PBA) related linkers are missing in the literature, which precludes the dynamical studies of GOF-L materials in realistic environments. This is specifically the case for trigonal planar boron atoms (B 3 ) and oxygen atoms bonded to boron atoms (OB 3 , Table ), even though boron-related parameters were introduced in some of the most popular force fields such as AMBER, CHARMM, or OPLS . It is generally assumed that MM parameters may be transferred to larger systems, composed of the same atoms or bonds.…”

“…It is generally assumed that MM parameters may be transferred to larger systems, composed of the same atoms or bonds. Unfortunately, the above parameters − are molecule dependent and are not directly transferable to 44BPDBA linkers. Therefore, new parameters for these two types of atoms need to be determined before an accurate study of the dynamical properties of GOFs can be performed.…”

Ab initio and molecular mechanics (MM3) calculations on alkyl- and arylboronic acids

“…MM3 can accurately handle many different functional groups, including alcohols and ethers, 11 amines, 12 aldehydes and ketones, 13 carboxylic acids and esters, 14 sulfides 15 and sulfones 16 phosphines. 17 Force field parameters for alkylboronic acids have been developed for a generic force field 18 in which reproducing the geometry was the main goal. In this work, however, highly accurate force field parameters for both alkyl-and arylboronic acids were derived by fitting the geometries, vibrational frequencies, and torsional profiles of five model molecules calculated using the RHF/6-31G* basis set.…”

Analysis on Solvated Molecules with a New Energy Partitioning Scheme for Intra- and Intermolecular Interactions

“…Figure illustrates the components of the molecular interactions of the NH 3 −H 2 O system ( R = 3.0 Å) computed by the three different methods, in comparison with the classical model computed by OPLS and TIP3P (Δ E classical ). The label “gas” denotes the interaction energy computed by the standard ab initio molecular orbital (MO) method, and “RISM-SCF” indicates the interaction energy evaluated in an aqueous environment (298.15 K, 1.0 g/cm 3 ) by using the RISM-SCF method. , The parameters for the solute molecule were taken from the literature, ,, as summarized in Table . The sum of all these components for the classical model (Δ E classical ) represents the total interaction energy between water and ammonia (−5.5 kcal/mol).…”