SCF and CASSCF studies of geometrical rearrangements in LiBO

The minimum energy path for the rearrangement LiOB OBLi was calculated with the SCF approximation using a double-zeta plus polarization basis set. Stationary points on the potential surface were studied with the help of the CASSCF method using different choices of active space. The results indicate that LiBO may be regarded as a polytopic type molecule. The relative energies of different geometrical configurations changed considerably when the CASSCF method was used, compared to those obtained at the SCF level, demonstrating the importance of correlation effects for this system.     

Conformation dependence of pKa’s of the chromophores from the purple asFP595 and yellow zFP538 fluorescent proteins

Two members of the green fluorescent protein family, the purple asFP595 and yellow zFP538 proteins, are perspective fluorescent markers for use in multicolor imaging and resonance energy-transfer applications. We report the results of quantum based calculations of the solution pK_a values for selected protonation sites of the denatured asFP595 and zFP538 chromophores in the trans- and cis-conformations in order to add in the interpretation of photo-physical properties of these proteins. The pK_a values were determined from the theromodynamic cycle based on B3LYP/6-311++G(2df, 2p) calculations of the gas phase free energies of the molecules and the B3LYP/6-311++G(d, p) calculations of solvation energies. The results show that the pK_a’s of the protonation sites of the chromophore from asFP595 noticeably depend on the isomer conformation (cis- or trans-), while those of zFP538 are much less sensitive to isomerization.     

Quantum chemical modeling of reaction mechanism for 2-oxoglutarate dependent enzymes: effect of substitution of iron by nickel and cobalt

Enzymatic hydroxylation reactions carried out by 2-oxoglutarate (2OG) dependent iron-containing oxygenases were recently implicated in oxygen sensing. In addition to oxygen depletion, two metals, cobalt and nickel, are capable of inducing hypoxic stress in cells by inhibiting oxygenase activity. Two possible scenarios have been proposed for the explanation of the hypoxic effects of cobalt and nickel: oxidation of enzyme-bound iron following cobalt or nickel exposure, and substitution of iron by cobalt or nickel. Here, by using density functional theory calculations, we modeled the reaction route from the reaction components to the high-spin metal-oxide intermediate in the activation of oxygen molecule by 2OG-dependent enzymes for three metal ions Fe(II), Ni(II), and Co(II) in the active site. An initial molecular model was constructed based on the crystal structure of iron-containing asparaginyl hydroxylase (FIH-1). Nickel- and cobalt-containing enzymes were modeled by a consequent replacement of the iron in the active center. The energy profiles connecting stationary points on the potential surfaces were computed by using the intrinsic reaction coordinate (IRC) technique from the located transition states. The results of calculations show that the substitution of iron by nickel or cobalt modifies the reaction energy profile; however, qualitatively, the reaction mechanism remains essentially the same. Thus, we would postulate that if the iron ion in the active site were substitutable by nickel and/or cobalt ions enzyme activity would be considerably altered due to high activation barriers.     

Structure of the enzyme-substrate complex for guanosine triphosphate hydrolysis by elongation factor EF-Tu: Comparison of quantum mechanics/molecular mechanics and molecular dynamics results

The equilibrium geometric configurations of the enzyme-substrate complex for guanosine triphosphate hydrolysis by elongation factor EF-Tu calculated using two theoretical approaches, a combined quantum mechanics/molecular mechanics (QM/MM) method and a molecular dynamics method, are compared. The reaction complex geometry determined by the QM/MM method is consistent with the accepted reaction mechanism, whereas, in the enzyme-substrate structure predicted by the molecular dynamics method with the CHARMM force field, the relative positions of the nucleophilic reagent (water molecules) and the base (a histidine side chain) do not correspond to the optimal reagent arrangement.     

Modeling the spectra of matrix-isolated molecules

Modeling the properties of molecules isolated in low-temperature inert matrices is discussed in terms of cluster approaches. The analysis uses molecular dynamic and quantum chemical methods. Particular attention is paid to spectral features resulting from the matrix environment effects. Translated from Zhurnal Struktumoi Khimii, Vol. 38, No. 2, pp. 256–262, March–April, 1997.     

Low-temperature biligand complexes of europium and samarium with mesogenic alkylcyanobiphenyls

For low-temperature cocondensates of europium and samarium (M) with a mesogenic ligand 4-pentyl-4-cyanobiphenyl (L), IR and UV spectroscopy studies have revealed the formation of two ML complexes (M/L = 1:2 and 1:1). Model calculations have been carried out in terms of density functional theory using the B3LYP exchange correlation potential. Biligand structures with an antiparallel arrangement of two ligand molecules including one and two metal atoms, respectively, are suggested. The values of the spectral shifts and the relative thermal stability of the complexes are discussed.Original Russian Text Copyright © 2004 by A. V. Vlasov, T. I. Shabatina, S. V. Konyukhov, A. Yu. Ermilov, A. V. Nemukhin, and G. B. SergeevTranslated from Zhurnal Strukturnoi Khimii, Vol. 45, No. 3, pp. 406–411, May–June, 2004.