A method and program for mass quantum chemical calculations of protein—ligand docking complexes

A new fast computational method for mass calculations of docking complexes by the AM1/PM3 semiempirical methods is proposed. The computation time is shortened by at least an order of magnitude compared to alternative schemes of quantum chemical calculations. The root-mean-square deviation of the AM1 calculated energies of formation of complexes from the results obtained by conventional diagonalization procedure is at most 0.4 kcal mol⁻¹. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 2, pp. 418–420, February, 2008.     

A density functional theory computational study of the role of ligand on the stability of CuI and CuII species associated with ATRP and SET‐LRP

Atom transfer radical polymerization (ATRP) and single electron‐transfer living radical polymerization (SET‐LRP) both utilize copper complexes of various oxidation states with N‐ligands to perform their respective activation and deactivation steps. Herein, we utilize DFT (B3YLP) methods to determine the preferred ligand‐binding geometries for Cu/N‐ligand complexes related to ATRP and SET‐LRP. We find that those ligands capable of achieving tetrahedral complexes with Cu^I and trigonal bipyramidal with axial halide complexes with [Cu^IIX]⁺ have higher energies of stabilization. We were able to correlate calculated preferential stabilization of [Cu^IIX]⁺ with those ligands that perform best in SET‐LRP. A crude calculation of energy of disproportionation revealed that the same preferential binding of [Cu^IIX]⁺ results in increased propensity for disproportionation. Finally, by examining the relative energies of the basic steps of ATRP and SET‐LRP, we were able to rationalize the transition from the ATRP mechanism to the SET‐LRP mechanism as we transition from typical nonpolar ATRP solvents to polar SET‐LRP solvents. © 2007 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 45: 4950–4964, 2007     

A partial differential equation which describes an interatomic surface

In this work we present a first-order partial differential equationwhich defines the topology of single ‘atomic entities’in multiatomic systems. Such an equation, obtained by R. F.W. Bader, is here analysed and discussed from a general mathematicalpoint of view; a method is then proposed for defining the initialor boundary condition. With this contribution we would liketo promote and stimulate a more detailed analysis which goesbeyond practical purposes and basic mathematical analysis inorder to have a deeper understanding of the theory behind theequation and its consequences for practical applications.     

On Ramsey numbers of uniform hypergraphs with given maximum degree

For every ?>0 and every positive integers Δ and r, there exists C=C(?,Δ,r) such that the Ramsey number, R(H,H) of any r-uniform hypergraph H with maximum degree at most Δ is at most C|V(H)|^1+?.     

An experiment to test an explanation of a possible violation of quantum theory

An experiment to test a possible explanation of the Schmidt backwards causation results is suggested. The experiment might distinguish between many- and one- world interpretations of quantum theory.     

Curvature and finite domination

Upper bounds obtained by Gromov on the Betti numbers of certain closed Riemannian manifolds are shown to be upper bounds on the minimum number of cells in --spaces dominating such manifolds.

     

Calculation of the proton affinities of polyfluorobenzenes and the activation energies for 1,2-hydrogen shifts in their carbocations

Isolated polyfluorobenzene (PFB) molecules and their protonated forms are investigated by the AM1 method with full geometry optimization. The proton affinities of PFB are estimated for different protonated positions. The proton affinity of PFB averaged over all isomers is shown to decrease monotonically as the number of fluorine atoms in the molecule increases. The relative populations of different isomers of arenonium ions (AI) formed by PFB protonation are determined. From the calculated data, the value of ⁺ for the F atom in theipso-position is estimated as 1.00. The activation energies of the 1,2-hydrogen shifts in AI are calculated. The dependences of the proton affinity and the activation energies of 1,2-hydrogen shifts on the number of halogen atoms are found to have distinct characters for PFB and polychlorobenzenes. The physical reasons for these difference are discussed.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 11, pp. 1878–1882, November, 1993.     

Evaluation of Multicenter Electronic Attraction, Electric Field and Electric Field Gradient Integrals with Screened and Nonscreened Coulomb Potentials over Integer and Noninteger n Slater Orbitals

By the use of complete orthonormal sets of -exponential-type orbitals, where ( = 1, 0, –1, –2,...) the multicenter electronic attraction (EA), electric field (EF) and electric field gradient (EFG) integrals of nonscreened and Yukawa-like screened Coulomb potentials are expressed through the two-center overlap integrals with the same screening constants and the auxiliary functions introduced in our previous paper (I.I. Guseinov, J. Phys. B, 3 (1970) 1399). The recurrence relations for auxiliary functions are useful for the calculation of multicenter EA, EF and EFG integrals for arbitrary integer and noninteger values of principal quantum numbers, screening constants, and location of slater-type orbitals. The convergence of the series is tested by calculating concrete cases.     

Basis Set Orbital Relaxation in Atomic and Molecular Hydrogen Systems

Orbital relaxation (OR) amounts to variation of the orbital exponents in hydrogen molecules and ions relative to the exponents of the isolated atom; it is represented as the sum of the one- and two-center contributions depending on the effective atomic charge and on the presence of other atoms in the molecule. The procedure for isolating the contributions of the exponent includes treatment of the OR of hydrogen in a special set of neutral and charged atoms and molecules with certain multiplicities of their electronic states. Within the framework of the spin-unrestricted Hartree-Fock method, we found and discussed the optimal values of the exponents of the basis orbitals of hydrogen atoms and molecules using the minimal split valence-shell basis set, the basis set that includes the polarization function, and the expanded set of grouped natural orbitals. A simple energy model is suggested for OR. Expressions are derived for evaluating the exponents of the relaxed orbitals in hydrogen-containing systems.Original Russian Text Copyright © 2004 by A. I. Ermakov, A. E. Merkulov, A. A. Svechnikova, and V. V. Belousov__________Translated from Zhurnal Strukturnoi Khimii, Vol. 45, No. 6, pp. 973–978, November–December, 2004.