Molecular caps for full quantum mechanical computation of peptide-water interaction energy

We present a systematic study of numerical accuracy of various forms of molecular caps that are employed in a recently developed molecular fractionation scheme for full quantum mechanical computation of protein-molecule interaction energy. A previously studied pentapeptide (Gly-Ser-Ala-Asp-Val) or P5 interacting with a water molecule is used as a benchmark system for numerical testing. One-dimensional potential energy curves are generated for a number of peptide-water interaction pathways. Our study shows that various forms of caps all give consistently accurate energies compared to the corresponding full system calculation with only small deviations. We also tested the accuracy of cutting peptide backbone at different positions and comparisons of results are presented.     

First‐order correlation‐kinetic contribution to Kohn–Sham exchange charge density function in atoms,using quantal density functional theory approach

Using the static exchange‐correlation charge density concept, the total integrated exchange‐charge density function is calculated within the nonrelativistic spin‐restricted exchange‐only (i) optimized effective potential model, and (ii) nonvariational local potential derived from the exchange‐only work potential within the quantal density functional theory, for the ground‐state isoelectronic series: Ga⁺, Zn, Cu^?; In⁺, Cd, Ag^?; and Tl⁺, Hg, Au^?. The difference between the exchange charge density function derived from these potentials is employed to evaluate the first‐order correlation‐kinetic contribution to the integrated exchange charge density. This contribution is found to be important for both the intra‐ and inter‐shell regions. Screening effects on the contribution due to the nd¹⁰ (n = 3–5) subshells are discussed through comparisons with similar calculations on Ca, Sr, and Ba, wherein nd¹⁰ electrons are absent. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Own N-layered integrated molecular orbital and molecular mechanics study of the reaction of OH<Superscript>−</Superscript> with polychlorinated hydrocarbons CH<Subscript>(4−n)</Subscript>Cl<Subscript>n</Subscript> (n=2–4)

The reliability of the two-layer own N-layered integrated molecular orbital and molecular mechanics (ONIOM) method was examined for the S_N2 reaction CH_(4–n)Cl_n+OH^–. In the ONIOM calculation, only the methyl chloride and OH^–were treated at a high level and the effect of polychlorination was taken into account only at a low level. The ONIOM results were compared with the target CCSD(T)/aug-cc-pVDZ//MP2/aug-cc-pVDZ results obtained by Borisov etal. [(2001) J. Phys. Chem. A 105:7724]. The ONIOM[MP2/aug-cc-pVDZ:B3LYP/6-31+G(d)] was found to reproduce well the target geometry and energy at the MP2/aug-cc-pVDZ level. The single-point improved energetics at the ONIOM[CCSD(T)/aug-cc-pVDZ:MP2/6-31+G(d)] is found to give results nearly as accurate as the target CCSD(T)/aug-cc-pVDZ//MP2/aug-cc-pVDZ results. The substantially reduced cost, 20% for optimization and 5% for single-point improved energy of the target cost for n=4, as well as small errors suggest that ONIOM is a powerful tool for accurate potential-energy surfaces of the reaction of large polyhalohydrocarbons.     

Flow injection system with in-line Winkler's procedure using 16-way valve and spectrofluorimetric determination of dissolved oxygen in environmental waters

Flow injection spectrofluorimetry with in-line Winklers procedure was developed for the dissolved oxygen (DO) determination. 2-Thionaphthol reacted with iodine produced by Winkler’s method to form fluorescence inactive disulfide compound. To automate the process completely, a 5-channel flow system with a newly designed 16-way valve was assembled. The system consisted of a dispersion coil (DC), a precipitate formation coil (PFC), a precipitate dissolving coil (PDC), and extraction coil (EC). A calibration can be constructed by using a standard iodine solution for dissolved oxygen. The calibration graph was linear over the range 1.2×10⁻⁴∼6.0×10⁻⁴ mol l⁻¹ iodine (1.96∼9.80 mg O l⁻¹)). The relative standard deviation (n=6) was below 0.3% for the 4×10⁻⁴ mol l⁻¹ iodine (6.27 mg O l⁻¹) determination. The sample throughput was 12/h.     

The delocalisation energy of benzene and the non-empirical MO theory

Algebraic expressions for the vertical Delocalisation Energy (DE) of benzene are derived from non-empirical MO theory. For comparison with early work in the π-electron approximation, and ultimately with Hückel theory, the results are formulated in terms of a core resonance integral,β, and π-electronic repulsion integrals. All integral values are inferred from the results ofab initio SCF calculations. Two expressions are derived, which refer to two ways of forming the localised π MOs: one where three pairs of adjacent atomic orbitals are selected from a set of six orthogonalised orbitals; and another where a non-orthogonal set of atomic orbitals is used. The first expression is formally similar to an expression originally derived by Pople from a different point of view and with many approximations. This expression gives too large a magnitude for DE when used with anab initio value ofβ. The second expression gives a result much closer to an empirical value of DE and shows that the main reason for DE being about 50% of 2β rather than 2β is the stabilising effect of overlap in the localised structure, and that the less important factor is the inclusion of electronic repulsion.     

On the calculation of expectation values and transition matrix elements by coupled cluster method

Summary Finite order expressions are derived for expectation values and transition matrix elements within the framework of the coupled cluster method.     

Computer modelling of the conformational equilibrium of 2-and 2,5,5-substituted 1,3,2-dioxaborinanes

Empirical, semiempirical, and nonempirical quantum-chemical methods were used to study the conformational equilibrium of 2,5,5-substituted 1,3,2-dioxaborinanes. The sofa invertomers were found to correspond to the local and global minima on the potential energy surface. The position of the equilibrium between these forms is a function of the substituents at C₍₅₎ of the heterocycle. __________ Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 12, pp. 1860–1865, December, 2007.     

A conformational analysis method for understanding the energy landscapes of clusters.

A newly developed unbiased structural optimization method, named dynamic lattice searching (DLS), is proposed as an approach for conformational analysis of atomic/molecular clusters and used in understanding the energy landscape of large clusters. The structures of clusters are described in terms of the number of basic tetrahedron (BT) units they contain. We found that the hit numbers of different structural motifs in DLS runs is proportional to the number of BTs. A parameter T(max) is defined to limit the maximal number of atoms moved in a structural transition. Results show that T(max) is a key parameter for modulating the efficiency of the DLS method and has a great influence on the hit number of different motifs in DLS runs. Finally, the effect of potential range on the conformational distribution of the (Morse)(98) cluster is also discussed with different potential-range parameters.     

Preparation, characterization and thermolysis of metal nitrate complexes with 4,4’-bipyridine

Two bis(bipyridine) polymeric metal nitrate complexes with 4,4’-bipyridine of simple formula like [M(bipy)₂](NO₃)2⋅xH₂O (where M=Co, Ni and Cu; x=4, 2 and 0, respectively) have been prepared and characterized. Their thermal decomposition has been undertaken using simultaneous TG-DTG-DTA and DSC in nitrogen atmosphere and non-isothermal TG in air atmosphere. Isothermal TG has been performed at decomposition temperature range of the complexes to evaluate the kinetics of decomposition by applying model-fitting as well as isoconversional method. Possible mechanistic pathways have also been proposed for the thermolysis. Ignition delay measurements have been carried out to investigate the response of these complexes under the condition of rapid heating.     

Synthesis and characterization of Mn-, La-Mn- and La-Ca-Mn-citrates as precursors for LaMnO<Subscript>3</Subscript> and La<Subscript>1−x</Subscript>Ca<Subscript>x</Subscript>MnO<Subscript>3</Subscript>

Mn-, LaMn- and LaCaMn-citrates were synthesized at 60–120°C in ethylene glycol medium using chlorides or nitrates as metal sources. Their composition, IR spectra and thermal decomposition were studied. Equimolar La/Mn ratio has been established in the complex, prepared from chloride solution with the same initial composition of the metals. In the isolated three-metallic complex the molar ratio of the metals deviates from the composition in the initial solution. The final products of the heating of Mn- and mixed-metal LaMn-citrates at 1000°C are phase-homogeneous Mn₃O₄ (hausmannite) and LaMnO₃ respectively. Parasitic phase(s) are observed in La_xCa_1−xMn_yO₃, produced from LaCaMn-citrate.