During this fiscal year we devoted major effort to work aimed at introducing polarizability into molecular force fields. Much of the work involved examining multipole expansions as a way to build accuracy into force field calculations. In one of the published studies it was shown that both static and geometry-dependent multipole models are able to reproduce total molecular forces and torques with repect to ab initio, whereas geometry-dependent multipoles are necessary to reproduce ab initio atomic forces. In another published work, a finite field method for calculating spherical tensor molecular polarizability tensors by numerical derivatives of induced molecular multipole with respect to gradients of the electrostatic potential are developed for arbitrary l and l'. These developments should be useful for the development of newer force fields that can be used to more accurately describe bio-macromolecules. Finally, we have developed code for partitioning the electron density into atomic contributions within the Hirshfeld-Iterated scheme. The codes developed in these studies are freely available.

Project Start
Project End
Budget Start
Budget End
Support Year
26
Fiscal Year
2011
Total Cost
$326,934
Indirect Cost
City
State
Country
Zip Code
Zheng, Xunhai; Mueller, Geoffrey A; Kim, Kyungmin et al. (2017) Identification of drivers for the metamorphic transition of HIV-1 reverse transcriptase. Biochem J 474:3321-3338
Lee, Chang Jun; Wu, Sangwook; Eun, Changsun et al. (2010) A revisit to the one form kinetic model of prothrombinase. Biophys Chem 149:28-33
Elking, Dennis M; Perera, Lalith; Duke, Robert et al. (2010) Atomic forces for geometry-dependent point multipole and gaussian multipole models. J Comput Chem 31:2702-13
de Courcy, B; Pedersen, L G; Parisel, O et al. (2010) Understanding selectivity of hard and soft metal cations within biological systems using the subvalence concept. I. Application to blood coagulation: direct cation-protein electronic effects vs. indirect interactions through water networks. J Chem Theory Comput 6:1048-1063
Elking, Dennis M; Cisneros, G Andres; Piquemal, Jean-Philip et al. (2010) Gaussian Multipole Model (GMM). J Chem Theory Comput 6:190-202
Zurita, Adolfo; Zhang, Yinghao; Pedersen, Lee et al. (2010) Obligatory role in GTP hydrolysis for the amide carbonyl oxygen of the Mg(2+)-coordinating Thr of regulatory GTPases. Proc Natl Acad Sci U S A 107:9596-601
Lee, Chang Jun; Chandrasekaran, Vasu; Wu, Sangwook et al. (2010) Recent estimates of the structure of the factor VIIa (FVIIa)/tissue factor (TF) and factor Xa (FXa) ternary complex. Thromb Res 125 Suppl 1:S7-S10
Liu, Shubin; Hu, Hao; Pedersen, Lee G (2010) Steric, quantum, and electrostatic effects on S(N)2 reaction barriers in gas phase. J Phys Chem A 114:5913-8
Cisneros, G Andrés; Perera, Lalith; Schaaper, Roel M et al. (2009) Reaction mechanism of the epsilon subunit of E. coli DNA polymerase III: insights into active site metal coordination and catalytically significant residues. J Am Chem Soc 131:1550-6
Mutoh, Shingo; Osabe, Makoto; Inoue, Kaoru et al. (2009) Dephosphorylation of threonine 38 is required for nuclear translocation and activation of human xenobiotic receptor CAR (NR1I3). J Biol Chem 284:34785-92

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