Effects of phase-breaking on long-range charge transfer in DNA: Partially-coherent-tunneling model study

The mechanism of hole charge transfer in DNA of various lengths and sequences is investigated based on a partially coherent tunneling theory (Zhang et al., J Chem Phys 117:4578, 2002), where the effects of phase-breaking in adenine-thymine and guanine-cytosine base pairs are treated on equal foot. This work aims at providing a self-consistent microscopic interpretation for rate experiments on various DNA systems. We will also clarify the condition under which the simple superexchange-mediated-hopping picture is valid, and make some comments on the further development of present theory.

Density functional study on the reaction mechanism of palladium-catalyzed addition of cyanoboranes to Alkynes

The B3LYP hybrid density functional method has been carried Out to Study theoretically the mechanisin of Pd(0)-catalyzed alkyne cyanoboration reaction. Both the intermolecular and intramolecular alkyne cyanoboration reactions were studied. For each reaction, three paths were proposed. In path A of each reaction, the first step is B-CN bond oxidative addition to bisphosphine complex Pd(PH3)(2), in path B of each reaction, the first step is alkyne coordination to bisphosphine complex Pd(PH3)2, and in path C of each reaction, the first step is the PH3 dissociation front Pd(PH3)2 to form monophosphine complex Pd(PH3) For both reactions, path B is favored.

Investigation of Chemical Bond Characteristics, Thermal Expansion Coefficients and Bulk Moduli of alpha-R2MoO6 and R2Mo2O7 (R = rare earths) by Using a Dielectric Chemical Bond Method

Theoretical researches are performed on the alpha-R2MoO6 (R = Y, Gd, Tb Dy, Ho, Er, Tm and Yb) and pyrochlore-type R2Mo2O7 (R = Y, Nd, Sm, Gd, Tb and Dy) rare earth molybdates by using chemical bond theory of dielectric description. The chemical bonding characteristics and their relationship with thermal expansion property and compressibility are explored. The calculated values of linear thermal expansion coefficient (LTEC) and bulk modulus agree well with the available experimental values. The calculations reveal that the LTECs and the bulk moduli do have linear relationship with the ionic radii of the lanthanides: the LTEC decreases from 6.80 to 6.62 10(-6)/K and the bulk modulus increases from 141 to 154 GPa when R goes in the order Gd, Tb Dy, Ho, Er, Tm, and Yb in the alpha-R2MoO6 series; while in the R2Mo2O7 series, the LTEC ranges from 6.80 to 6.61 10(-6)/K and the bulk modulus ranges from 147 to 163 GPa when R varies in the order Nd, Sm, Gd, Tb and Dy.

Reaction Mechanism of Palladium-Catalyzed Silastannation of Allenes by Density Functional Theory

The reaction mechanism of Pd(O)-catalyzed allenes silastannation reaction is investigated by the density functional method B3LYP. The overall reaction mechanism is examined. For the allene insertion step, the Pd-Si bond is preferred over the Pd-Sn bond. The electronic mechanism of the allene insertion into Pd-Si bond to form sigma-vinylpalladium (terminal-insertion) and sigma-allylpalladium (internal-insertion) insertion products is discussed ill terms of the electron donation and back-donation. It is found that the electron back-donation is significant for both terminal- and internal-insertion. During allene insertion into Pd-Si bond, internal-insertion is preferred over terminal-insertion. By using methylallene, the regio-selectivity for the monosubstituted allene insertion into Pd-Si and Pd-Sn bond is analyzed.

First Principles Investigation on the Ultra-Incompressible and Hard TaN

The structural, electronic, and mechanical properties of TaN were investigated by use of the density functional theory (DFT). Eight structures were considered, i.e.. hexagonal WC TaN, NiAs, wurtzite, and CoSn structures. cubic NaCl. zinc-blende and CsCl structures. The results indicate that TaN in TaN-type structure is the most stable at ambient conditions among the considered structures. Above 5 GPa, TaN in WC-type structure becomes energetically the most stable phase. They are also stable both thermodynamically and mechanically. TaN in WC-type has the largest shear Modulus 243 GPa and large bulk modulus 337 GPa among the considered structures. The Volume compressibility is slightly larger than diamond, but smaller than c-BN at pressures from 0 to 100 GPa. The compressibility along the c axis is smaller than the linear compressibility of both diamond and c-BN.

SOLVENT AND SUBSTITUENT EFFECTS ON THE INTRAMOLECULAR AMIDE HYDROLYSIS OF N-METHYLMALEAMIC ACID

Intramolecular amide hydrolysis of N-methylmaleamic acid is revisited at the B3LYP/6-311G(2df,p)//B3LYP/6-31G(d,p)+ZVPE level, including solvent effects at the CPCM-B3LYP/6-311G(2df,p)//Onsager-B3LYP/6-31G(d,p)+ZPVE level. The concerted reaction mechanism is energetically favorable over stepwise reaction mechanisms in both the gas phase and solution. The calculated reaction barriers are significantly lower in solution than in the gas phase. In addition, it is concluded that the substituents of the four N-methylmaleamic acid derivatives considered herein have a significant effect on the gas-phase reaction barriers but a smaller, or little, effect on the barriers in solution.

Electronic structures and chemical bonding in diatomic ScX to ZnX (X = S, Se, Te)

Bond distances, vibrational frequencies, electron affinities, ionization potentials, dissociation energies, and dipole moments of the title molecules in neutral, positively, and negatively charged ions were studied using density functional method. Ground electronic state was assigned for each molecule. The bonding patterns were analyzed and compared with both the available data and across the series. It was found that, besides ionic component, covalent bonds are formed between the metal s, d orbitals, and the p orbital of S, Se, and Te. For neutral and cationic molecules, the covalent character increases from ScX to CrX and from FeX to CuX with an exception of decrease at MnX and ZnX, while for anionic molecules, the trend is not obvious. For both neutral and charged molecules, the sulfides have the shortest bond distance and largest vibrational frequency, while tellurides have the largest bond distance and smallest vibrational frequency. For neutral and anionic molecules, the dissociation energy of sulfides is the largest, that of tellurides is the smallest, while this only remains true for cationic molecules from ScX+ to FeX+.

Electronic structures and chemical bonding in 4d transition metal monohalides

Bond distances, vibrational frequencies, dipole moments, dissociation energies, electron affinities, and ionization potentials of NIX (XM = Y-Cd, X = F, Cl, Br, I) molecules in neutral, positively, and negatively charged ions were studied by density functional method, B3LYP. The bonding patterns were analyzed and compared with both the available data and across the series. It was found that besides ionic component, covalent bonds are formed between the 4d transition metal s, d orbitals, and the p orbital of halogen. For both neutral and charged molecules, the fluorides have the shortest bond distance, iodides the longest. Although the opposite situation is observed for vibrational frequency, that is, fluorides have the largest value, iodides the smallest. For neutral and anionic species, the dissociation energy tends to decrease with the increasing atomic number from Y to Cd, suggesting the decreasing or weakening of the bond strength. For cationic species, the trend is observed from Y to Ag.

Electronic structures of 3d-metal mononitrides

Bond distances, vibrational frequencies, electron affinities, ionization potentials, and dissociation energies of the title molecules in neutral, positively, and negatively charged ions were studied by use of density functional methods B3LYP, BLYP, BHLYP, BPW91, and B3PW91. The calculated results are compared with experiments and previous theoretical studies. It was found that the calculated properties are highly dependent on the functionals employed, in particular for the dissociation energy and vibrational frequency. For neutral species, pure density functional methods BLYP and BPW91 have relatively good performance in reproducing the experimental bond distance and vibrational frequency. For cations, hybrid exchange functional methods B3LYP and B3PW91 are good in predicting the dissociation energy. For both neutral and charged species, BHLYP tends to give smaller dissociation energy.

QUANTITATIVE STRUCTURE-ACTIVITY-RELATIONSHIPS FOR TOXICITY OF PHENOLS USING REGRESSION-ANALYSIS AND COMPUTATIONAL NEURAL NETWORKS

Quantitative structure-toxicity models were developed that directly link the molecular structures of a et of 50 alkYlated and/or halogenated phenols with their polar narcosis toxicity, expressed as the negative logarithm of the IGC50 (50% growth inhibitor

Chemical kinetics and self-ignition in a model supersonic hydrogen-air combustor

Self-ignition tests of a model scramjet combustor were conducted by using parallel sonic injection of gaseous hydrogen from the base of a blade-like strut into a supersonic vitiated airstream. The range of stagnation pressure and temperature studied varied from 1.0 to 4.5 MPa and from 1300 to 2200 K, respectively. Experimental results show that the self-ignition limit, in terms of either global or local quantities of pressure and temperature, exhibits a nonmonotonic behavior resembling the classical homogeneous explosion limit of the hydrogen-oxygen system. Specifically, for a given temperature, increasing pressure from a low value can render a nonignitable mixture to first become ignitable, then nonignitable again, This correspondence shows that, despite the globally supersonic nonpremixed configuration studied herein, ignition is strongly influenced by the intricate chemical reaction mechanism and thereby exhibits the homogeneous explosion character. Consequently, self-ignition criteria based on a global reaction rate approximating the complex chemistry are inadequate. An auxiliary computational study on counterflow ignition was also conducted to systematically investigate the contamination effects of vitiated air. Results indicate that the net contamination effects for the present experimental data are expected to be substantially smaller than contributions from the individual contamination species because of the counterbalancing influences of the H2O-inhibition and NO-promotion reactions in effecting ignition.