Biomedical subjects

D G Truhlar

Publications and source records attributed to D G Truhlar.

7 recordsLinked to original sources

PubMed2005

Exchange-correlation functional with broad accuracy for metallic and nonmetallic compounds, kinetics, and noncovalent interactions.

By incorporating kinetic-energy density in a balanced way in the exchange and correlational functionals and removing self-correlation effects, we have designed a density functional that is broadly applicable to organometallic, inorganometallic, and nonmetallic bonding, thermochemistry, thermochemical kinetics, and noncovalent interactions as well as satisfying the uniform electron gas limit. The average error is reduced by a factor of 1.3 compared with the best previously available functionals, but even more significantly, we find a functional that has a high accuracy for all four categories of interaction.

Journal Article↗

PubMed2001

Solvent-dependent transition states for decarboxylations.

The rate constants and kinetic isotope effects for decarboxylation of 4-pyridylacetic acid depend strongly on whether the solvent is water or dioxane, and the present paper interprets this finding. We calculate the solvent dependence of the free energy barrier and of the (13)C and (18)O kinetic isotope effects using a quantum mechanical solvation model based on class IV charges and semiempirical atomic surface tensions. The calculations provide a consistent interpretation of the experimental results, which provides a striking confirmation of the soundness of the solvation modeling. Even more significantly, the agreement of theory and experiment gives us confidence in the physical picture of the reaction provided by the model. This indicates that the location of the transition state, as measured by the length of the breaking C--C bond, is 0.24 A later than the gas phase in dioxane and 0.37 A later than the gas phase in water. Charge development at the transition state also depends strongly on the solvent; in particular the CO(2) moiety is 0.07 electronic charge units more negative at the transition state in dioxane than in water.

Journal Article↗

PubMed2001

Reductive dechlorination of hexachloroethane in the environment: mechanistic studies via computational electrochemistry.

Ab initio and density functional levels of electronic structure theory are applied to characterize alternative mechanisms for the reductive dechlorination of hexachloroethane (HCA) to perchloroethylene (PCE). Aqueous solvation effects are included using the SM5.42R continuum solvation model. After correction for a small systematic error in the electron affinity of the chlorine atom, theoretical predictions are accurate to within 23 mV for four aqueous reduction potentials relevant to HCA. A single pathway that proceeds via two successive single-electron transfer/barrierless chloride elimination steps, is predicted to be the dominant mechanism for reductive dechlorination. An alternative pathway predicted to be accessible involves trichloromethylchlorocarbene as a reactive intermediate. Bimolecular reactions of the carbene with other species at millimolar or higher concentrations are predicted to potentially be competitive with its unimolecular rearrangement to form PCE.

Electrochemistry↗

PubMed1999

Application of a universal solvation model to nucleic acid bases: comparison of semiempirical molecular orbital theory, ab initio Hartree-Fock theory, and density functional theory.

The free energies of solvation of six nucleic acid bases (adenine, cytosine, hypoxanthine, guanine, thymine, and uracil) in water and chloroform are calculated using CM2 class IV charges and SM5.42R atomic surface tensions. Using any of three approximations to the electronic wave function (AM1, Hartree-Fock, or DFT), we obtain good agreement with experiment for five cases where the experimental results are known for the partition coefficients between the two solvents. Decomposition of the solvation effects into bulk electrostatic contributions and first-solvation-shell effects shows that the partitioning is dominated by the former, and this illustrates the importance of using accurate partial atomic charges for modeling these molecules in aqueous solution.

Journal Article↗

PubMed1995

Class IV charge models: a new semiempirical approach in quantum chemistry.

We propose a new criterion for defining partial charges on atoms in molecules, namely that physical observables calculated from those partial charges should be as accurate as possible. We also propose a method to obtain such charges based on a mapping from approximate electronic wave functions. The method is illustrated by parameterizing two new charge models called AM1-CM1A and PM3-CM1P, based on experimental dipole moments and, respectively, on AM1 and PM3 semiempirical electronic wave functions. These charge models yield rms errors of 0.30 and 0.26 D, respectively, in the dipole moments of a set of 195 neutral molecules consisting of 103 molecules containing H, C, N and O, covering variations of multiple common organic functional groups, 68 fluorides, chlorides, bromides and iodides, 15 compounds containing H, C, Si or S, and 9 compounds containing C-S-O or C-N-O linkages. In addition, partial charges computed with this method agree extremely well with high-level ab initio calculations for both neutral compounds and ions. The CM1 charge models provide a more accurate point charge representation of the dipole moment than provided by most previously available partial charges, and they are far less expensive to compute.

Alcohols↗

PubMed1992

AM1-SM2 and PM3-SM3 parameterized SCF solvation models for free energies in aqueous solution.

Two new continuum solvation models have been presented recently, and in this paper they are explained and reviewed in detail with further examples. Solvation Model 2 (AM1-SM2) is based on the Austin Model 1 and Solvation Model 3 (PM3-SM3) on the Parameterized Model 3 semiempirical Hamiltonian. In addition to the incorporation of phosphorus parameters, both of these new models address specific deficiencies in the original Solvation Model 1 (AM1-SM1), viz., (1) more accurate account is taken of the hydrophobic effect of hydrocarbons, (2) assignment of heavy-atom surface tensions is based on the presence or absence of bonded hydrogen atoms, and (3) the treatment of specific hydration-shell water molecules is more consistent. The new models offer considerably improved performance compared to AM1-SM1 for neutral molecules and essentially equivalent performance for ions. The solute charges within the Parameterized Model 3 Hamiltonian limit the utility of PM3-SM3 for compounds containing nitrogen and possibly phosphorus. For other systems both AM1-SM2 and PM3-SM3 give realistic results, but AM1-SM2 in general outperforms PM3-SM3. Key features of the models are discussed with respect to alternative approaches.

Electrochemistry↗

PubMed1979

Reliable ab initio calculation of a chemical reaction rate and a kinetic isotope effect: H + H(2) and H + H(2).

We calculate equilibrium rate constants for ortho-para conversion in hydrogen and deuterium by an atomic mechanism. The calculations are based on an accurate ab initio potential surface, transition state theory, and an adiabatic transmission coefficient. The calculated rate constants are demonstrated to be reliable within 40-50%, and they agree with experiment within this margin.

Journal Article↗