A new method for the derivation of exact vibration-rotational kinetic energy operator in internal coordinates

An efficient angular momentum method is presented and used to derive analytic expressions for the vibration-rotational kinetic energy operator of polyatomic molecules.The vibration-rotational kinetic energy operator is expressed in terms of the total angular momentum operator J,the angular momentum operator J and the momentum operator p conjugate to Z in the molecule-fixed frame Not only the method of derivation is simpler than that in the previous work,but also the expressions ot the kinetic energy operators arc more compact.Particularly,the operator is easily applied to different vibrational or rovibrational problems of the polyatomic molecules by variations of matrix elements Gn of a mass-dependent constant symmetric matrix     

Study of intermolecular interactions in aqueous solutions by millimeter spectroscopy

The absorption of millimeter electromagnetic radiation (v=1.4, 1.71, and 5 cm⁻¹) by aqueous solutions of glycine (pH 6.1–6.2) in the concentration range of 0.5–2.5 mol L⁻¹ was measured. It was found that the absorbing ability of the water present in the solutions, is higher than that of pure water. This phenomenon is explained by the presence of a center of negative hydration in the structure of the glycine zwitterion, which results in an increase in the rotational mobility of water molecules immobilized in the hydrate shell of the glycine zwitterion. For Part 5, see Ref. 1. Deceased. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 7, pp. 1305–1307, July, 1997.     

First principle calculations study of AlN surface terminal structure evolution under different conditions

The surface structure and properties of aluminum nitride (AlN) play an important role in many applications. Using the first principle calculations method, we analyzed the surface terminal structure of AlN and its evolution under different conditions by determining the surface energy, adsorption energy, and evaporation energy of the Al and N terminals on the AlN(0001) surface. Our results show that the reason why the N terminal is less stable than the Al terminal is not only because of its high surface energy but also because its adsorption performance is extremely sensitive to the adsorption position. The surface N atoms combine to form N₂ molecules that escape during the evaporation process at high temperature. After surface N atoms escape, the AlN surface structure reconstitutes to form a hexagonal closest packing (HCP)–like structure, and the energy barrier for the reconstructing process is 3.2 eV. This shows that the structure and form of the AlN(0001) terminals depend on the environmental conditions.     

Ab initio Computational Modeling of Glyphosate Analogs: Conformational Perspective

A historical perspective on the application of conformational analysis to structure-based ligand design approach is presented. The application of isodensity molecular electrostatic potential surfaces with the conformational energy surfaces (CES) have allowed us to reach pertinent conclusions for aiding synthetic and biochemical studies. Here we illustrate such an application on the modeling of the potent analogs of an important, environmentally stringent herbicidal compound glyphosate by constructing conformational energy surfaces. The systems were modeled by substituting F, Cl, and NH— OH moiety to the position of pharmacophoric nitrogen center in glyphosate structure. All the calculations were thoroughly performed with ab initio MO theory at Hartree–Fock method using 3-21G(d) basis functions. On the basis of the results, we identified the bioactive conformations for N-fluoro-glyphosate, N-chloro-glyphosate, and N-hydroxyamino-glyphosate as (−38^∘, 77^∘), (−61^∘, 111^∘), and (−167^∘, −169^∘), respectively. Geometry optimization of certain selected conformations of these compounds using hybrid DFT method with 6–31+G(d) basis functions provides nearly equal values of φ and ψ. Moreover, the results indicate that the global minimum structures of N-fluoro and N-chloro analogs of glyphosate show cyclic conformation whereas the N-hydroxyamino-glyphosate global minimum structure shows spyrocyclic and zig-zag conformation. Also, the predicted bioactive conformation of N-hydroxyamino analog optimally overlaps with glyphosate backbone in EPSPS complex with 0.1 Å RMSD value. However, the other two compounds slightly deviate from the backbone of glyphosate with RMSD of 0.92 Å for N-fluoro-glyphosate and 0.83 Å for N-chloro-glyphosate. The linear N-hydroxyamino-glyphosate exhibits relatively more number of intermolecular hydrogen bond interactions as compared to the other two analogs. Further, comparison of CES of previously studied glyphosate analogs such as N-hydroxy-glyphosate (2.2 μM) and N-amino-glyphosate (0.61 μM) with the present systems reveals the order of activity as: N-hydroxyamino-glyphosate > N-fluoro-glyphosate > N-chloro-glyphosate based on CES flexibility. Also, the calculated heats of formation of N-fluoro-glyphosate, N-chloro-glyphosate, and N-hydroxyamino-glyphosate are −288, −209, and −288 kcal/mol, respectively, which clearly indicate that the N-hydroxyamino and N-fluoro analogs of glyphosate are thermodynamically more stable than N-amino-glyphosate (−278 kcal/mol).     

Photoinduced intramolecular electron transfer and triplet energy transfer in a steroid-linked norbornadiene-carbazole dyad

Bichromophoric compound 3 beta-((2-(methoxycarbonyl)bicyclo[2.2.1]hepta-2,5-diene-3-yl)carboxy)androst-5-en-17 beta-yl-[2-(N-carbazolyl)acetate] (NBD-S-CZ) was synthesized and its photochemistry was examined by fluorescence quenching, flash photolysis, and chemically induced dynamic nuclear polarization (CIDNP) methods. Fluorescence quenching measurements show that intramolecular electron transfer from the singlet excited state of the carbazole to the norbornadiene group in NBD-S-CZ occurs with an efficiency (Phi SET) of about 14 % and rate constant (kSET) of about 1.6 x 10(7) s-1. Phosphorescence and flash photolysis studies reveal that intramolecular triplet energy transfer and electron transfer from the triplet carbazole to the norbornadiene group proceed with an efficiency (TET + TT) of about 52 % and rate constant (kTET + kTT) of about 3.3 x 10(5) s-1. Upon selective excitation of the carbazole chromophore, nuclear polarization is detected for protons of the norbornadiene group (emission) and its quadricyclane isomer (enhanced absorption); this suggests that the isomerization of the norbornadiene group to the quadricyclane proceeds by a radical-ion pair recombination mechanism in addition to intramolecular triplet sensitization. The long-distance intramolecular triplet energy transfer and electron transfers starting both from the singlet and triplet excited states are proposed to proceed by a through-bond mechanism.     

Gas-Chromatographic Studies of the Interaction between Water and Methanol Molecules and the Surface of Carbon Materials

The gas-chromatographic method is used to study the interaction of water and methanol molecules with active hydrophilic centres existing at the surface of thermally exfoliated graphite and graphitized thermal carbon black. The concentration of carboxyl and phenol hydroxyl groups at the surface of these sorbents is determined, and heats of adsorption of the studied molecules are shown to be and 28−25 kJ/mol, respectively. It is also shown that adsorption of water at the hydrophilic centres at lowest relative pressure values takes place with formation of clusters consisting of n = 2 water molecules.     

Thermochemistry of the solid complex Gd(Et<Subscript>2</Subscript>dtc)<Subscript>3</Subscript>(phen)

Summary A ternary solid complex Gd(Et₂dtc)₃(phen) has been obtained from reactions of sodium diethyldithiocarbamate (NaEt₂dtc), 1,10-phenanthroline (phen) and hydrated gadolinium chloride in absolute ethanol. The title complex was described by chemical and elemental analyses, TG-DTG and IR spectrum. The enthalpy change of liquid-phase reaction of formation of the complex, Δ_rH^Θ_m(l), was determined as (-11.628±0.0204) kJ mol^-1 at 298.15 K by a RD-496 III heat conduction microcalorimeter. The enthalpy change of the solid-phase reaction of formation of the complex, Δ_rH^Θ_m(s), was calculated as (145.306±0.519) kJ mol^-1 on the basis of a designed thermochemical cycle. The thermodynamics of reaction of formation of the complex was investigated by changing the temperature of liquid-phase reaction. Fundamental parameters, the apparent reaction rate constant (k), the apparent activation energy (E), the pre-exponential constant (A), the reaction order (n), the activation enthalpy (Δ_rH^Θ_≠), the activation entropy (Δ_rS^Θ_≠), the activation free energy (Δ_rG^Θ_≠) and the enthalpy (Δ_rH^Θ_≠), were obtained by combination of the thermodynamic and kinetic equations for the reaction with the data of thermokinetic experiments. The constant-volume combustion energy of the complex, Δ_cU, was determined as (-18673.71±8.15) kJ mol^-1 by a RBC-II rotating-bomb calorimeter at 298.15 K. Its standard enthalpy of combustion, Δ_cH^Θ_m, and standard enthalpy of formation, Δ_fH^Θ_m, were calculated to be (-18692.92±8.15) kJ mol^-1 and (-51.28±9.17) kJ mol^-1, respectively.     

Understanding the conformational dependence of spin-spin coupling constants: through-bond and through-space J(31P,31P) coupling in tetraphosphane-1,4-diides [M(L)x]2[P4R4

The characteristic dependence of J(31P,31P) spin-spin coupling constants of alkali metal tetraphosphane-1,4-diides on structure and composition has been analyzed by density functional methods. The computations confirm that the structure of the contact ion pairs is conserved in solution. Calculations on model systems M2P4H4, on naked P4H4(2-) anions, and on models including point charges, show that the role of the cations is mainly structural and to a smaller extent electrostatic. Three of the four J(P,P) coupling constants depend characteristically on the conformation of the anion, which in turn is determined by the substituents R and by cation-anion interactions. Several couplings exhibit a large through-space component and are thus strongly dependent on the relative orientation of nonbonding electron pairs on the phosphorus atoms involved. This is shown by visualization of coupling pathways using the recently introduced coupling energy density (CED), in combination with the electron localization function (ELF).     

RATE OF INTRA-MOLECULAR CONTACT FORMATION IN SHORT TWO-DIMENSIONAL COMPACT POLYMERS CHAINS

It is important to know the rate of intra-molecular contact formation in proteins in order to understand how proteins fold clearly. Here we investigate the rate of intra-molecular contact formation in short two-dimensional compact polymer chains by calculating the probability distribution p(r) of end-to-end distance r using the enumeration calculation method and HP model on two-dimensional square lattice. The probability distribution of end-to-end distance p(r) of short two-dimensional compact polymers chains may consist of two parts, i.e. p(r) = p1(r) p2(r), where p1(r) and p2(r) are different for small r. The rate of contact formation decreases monotonically with the number of bonds N, and the rate approximately conforms to the scaling relation of k(N) ∝ N-α. Here the value of α increases with the contact radius a and it also depends on the percentage of H (hydrophobic) residues in the sequences of compact chains and the energy parameters of εHH, εHP and εPP . Some comparisons of theoretical predictions with experimental results are also made. This investigation may help us to understand the protein folding.     

The scaled-particle theory and solvent isotope effects on the thermodynamic properties of inert solutes in water and methanol

The scaled-particle theory has been applied to the calculation of the thermodynamic changes associated with the formation of a cavity in several isotopic varieties of liquid water and methanol. From these results, the thermodynamic functions for the transfer of a cavity (or a hard-sphere solute) have been computed for the following solvent pairs: H₂OD₂O, H₂OH₂ ¹⁸O, H₂ ¹⁸OD₂ ¹⁸O, D₂OD₂ ¹⁸O, CH₃OHCH₃OD. For the last two of these solvents, density measurements required for the calculations were carried out as a function of temperature. The calculated deuterium solvent isotope effect on the heats and entropies of hard-sphere solutes in water is much greater than the¹⁸O isotope effect; the former also exhibits a more pronounced temperature dependence. The transfer functions computed for hard-sphere solutes are compared to experimental data on the transfer of various solutes from H₂O to D₂O and from CH₃OH to CH₃OD. In most of the cases examined, the cavity effect accounts for a large part of the transfer quantities measured for rare gases, hydrocarbons, and solutes containing a significant hydrocarbon substituent.