Theoretical studies of the potential energy surface and wavepacket dynamics of the Li3 system

The three-dimensional (3D) potential energy surface of the ground state of Li₃ was determined by the multireference configuration interaction method. The vibrational motions and pseudorotation were investigated by a 3D time-dependent wavepacket formalism. The analytical expression of the 3D surface is given and the results of vibrational analyses at several critical points are presented. The low-lying excited states of Li₃ were examined for the C _{2 v} structure and the vertical and adiabatic excitation energies were calculated. The ground and singlet excited states of Li₂ were calculated and their spectroscopic constants compare well with the experimental values. A 3D wavepacket calculation was performed for simulations of the stimulated emission pumping spectrum in which the A state was taken as an intermediate. The recurrences of the autocorrelation functions were characterized by classical trajectory calculations. The autocorrelation functions obtained by wavepacket propagation are reproduced well by the accumulation of the classical trajectories in the short-time region. Received: 2 July 1998 / Accepted: 3 September 1998 / Published online: 8 February 1999     

Solution conformations of structured peptides: continuum electrostatics versus distance-dependent dielectric functions

To compare different implicit solvent potentials, the folding thermodynamics of the helical peptide RN24 and the β-hairpin peptide BH8 are studied by molecular dynamics simulation with adaptive umbrella sampling. As the potential energy functions, the analytical continuum solvent (ACS) potential and three simplified variants, termed EPSR₁, EPSR₄, and EPSR₁₀, are used. The ACS potential is a combination of the standard CHARMM force field for the internal energy (bonds, angles, dihedrals) and the van der Waals energy with the analytical continuum electrostatic (ACE) potential and a non-polar solvation potential. The EPSR potentials differ from the ACS potential by the use of Coulomb's law with a distance-dependent dielectric function to calculate the electrostatic energy. With the ACS potential, quantitative agreement with experiment is obtained for the helix propensity (RN24: 62% calculated vs 50–60% experiment) and the β-hairpin propensity (BH8: 33% calculated vs 19–37% experiment) of the peptides. During the simulations with the EPSR potentials, no significant formation of secondary structure is observed. It is shown that the preference for coil conformations over conformations with secondary structure by the EPSR potentials is due to an overestimation of the energy of salt bridge formation, independent of the magnitude of the Coulomb energy relative to the other energy terms. Possible improvements of the distance-dependent dielectric functions which may permit their application to the simulation of peptide folding, are discussed. Received: 11 July 1998 / Accepted: 22 September 1998 / Published online: 17 December 1998     

RISM-SCF study of the free-energy profile of the Menshutkin-type reaction NH3+CH3Cl→NH3CH3++Cl− in aqueous solution

The free-energy profile for the Menshutkin-type reaction NH₃ + CH₃Cl → NH₃CH₃ ⁺ + Cl⁻ in aqueous solution is studied using the RISM-SCF method. The effect of electron correlation on the free-energy profile is estimated by the RISM-MP2 method at the HF optimized geometries along the reaction coordinate. Solvation was found to have a large influence on the vibrational frequencies at the reactant, transition state and product; these vibrational frequencies are utilized to calculate the zero-point energy correction of the free-energy profile. The computed barrier height and reaction exothermicity are in reasonable agreement with those of experiment and previous calculations. The change of solvation structure along the reaction path is represented by radial distribution functions between solute-solvent atomic sites. The mechanisms of the reaction are discussed from the view points of solute electronic and solvation structures. Received: 26 June 1998/Accepted: 28 August 1998 / Published online: 2 November 1998     

The saddle point of the nucleophilic substitution reaction Cl− + CH3Cl: results of large-scale coupled cluster calculations

On the basis of large-scale coupled cluster calculations including connectedz triple substitutions in a perturbative way, the geometrical parameters of the D _{3 h} saddle point of the Walden inversion reaction Cl⁻ + CH₃Cl′→ ClCH₃ + Cl′⁻ are predicted to be R _s (C—Cl) = 2.301 ? and r _s (C—H) = 1.069 ?. The barrier height with respect to the reactants is recommended to be 11.5 ± 1.0 kJ mol⁻¹. Connected triple substitutions lower the barrier height by almost a factor of 2, but have very little influence on the geometric structure of the saddle point. Received: 26 June 1998 / Accepted: 15 July 1998 / Published online: 28 September 1998     

Density functional study of ethylene oxidation on an Ag(111) surface

The mechanism of ethylene epoxidation on Ag surfaces has been investigated using the density functional method and Ag _n clusters (n = 3 to 10) modeling the Ag(111) surface. The adsorption energy of O₂ to the Ag clusters was strongly dependent on the HOMO level of the cluster, and the clusters with higher HOMO levels afforded larger O₂ adsorption energies. The energetics was investigated for both the molecular and atomic oxygen epoxidation mechanisms. For the atomic oxygen mechanism, epoxidation was found to proceed without an activation energy, whereas a small amount of activation energy (about 5 kcal/mol) was calculated for the molecular oxygen mechanism. Received: 2 July 1998 / Accepted: 9 September 1998 / Published online: 8 February 1999     

Direct ab initio dynamics calculations on the rate constants for the hydrogen-abstraction reaction of C2H5F with O (3P)

The hydrogen-abstraction reaction C₂H₅F+O → C₂H₄F+OH has been studied by a dual-level direct dynamics method. For the reaction, three reaction channels, one for α-abstraction and two for β-abstraction, have been identified. The potential-energy surface information is obtained at the MP2(full)/6-311G(d,p) and PMP2(full)/6-311G(3df,3pd) (single-point) levels. By canonical variational transition-state theory, rate constants for each reaction channel are calculated with a small-curvature tunneling correction. The total rate constant is calculated from the sum of the individual rate constants and the temperature dependence of the branching ratios is obtained over a wide range of temperatures from 300 to 5,000 K. The agreement of the rate constants with experiment is good in the experimental temperature range from 1,000 to 1,250 K. The calculated results indicate that at low temperatures α-abstraction is most likely to be the major reaction channel, while β-abstraction channels will significantly contribute to the whole reaction rate as the temperature increases. Received: 23 January 2002 / Accepted: 23 June 2002 / Published online: 20 September 2002     

A new “hydrophobic template” method detects segments forming transmembrane α-helical bundles in ion channels

We present a “hydrophobic template” method enabling recognition of α-helix bundles in membrane channels from sequence analysis. Inspection of hydrophobic properties of pore-forming helices in proteins with known structure (A-B₅ toxins) permits delineation of a common polarity motif: two hydrophobic surface stretches separated by polar areas. The bundles are stabilized by nonpolar interhelical contacts. A number of transmembrane segments were checked for presence of this motif, and it was detected for pore-forming helices of several ion transporters (segments M2 of acetylcholine and GABA_A receptors, α5 peptide of δ-endotoxin), which reveal five α-helix bundle architecture. Applications of the method to modeling of membrane channels are discussed. Received: 24 April 1998 / Accepted: 3 September 1998 / Published online: 7 December 1998     

Electro-catalysis by immobilised human flavin-containing monooxygenase isoform 3 (hFMO3)

Human flavin-containing monooxygenases are the second most important class of drug-metabolizing enzymes after cytochromes P450. Here we report a simple but functional and stable enzyme-electrode system based on a glassy carbon (GC) electrode with human flavin-containing monooxygenase isoform 3 (hFMO3) entrapped in a gel cross-linked with bovine serum albumin (BSA) by glutaraldehyde. The enzymatic electrochemical responsiveness is characterised by using well-known substrates: trimethylamine (TMA), ammonia (NH₃), triethylamine (TEA), and benzydamine (BZD). The apparent Michaelis–Menten constant (K′_M) and apparent maximum current (I′_max) are calculated by fitting the current signal to the Michaelis–Menten equation for each substrate. The enzyme-electrode has good characteristics: the calculated sensitivity was 40.9 ± 0.5 mA mol⁻¹ L cm⁻² for TMA, 43.3 ± 0.1 mA mol⁻¹ L cm⁻² for NH₃, 45.2 ± 2.2 mA mol⁻¹ L cm⁻² for TEA, and 39.3 ± 0.6 mA mol⁻¹ L cm⁻² for BZD. The stability was constant for 3 days and the inter-electrode reproducibility was 12.5%. This is a novel electrochemical tool that can be used to investigate new potential drugs against the catalytic activity of hFMO3.     

Photocurrent and differential capacity measurements at polybithienyl and poly(3-butylthiophene) films

Photocurrent and differential capacity measurements have been carried out at polybithienyl (PBT) and poly(3-butylthiophene) (PBuT) films on platinum. The photocurrents are cathodic, similar to inorganic p-type semiconductors. The band gap energy was determined from the photocurrent spectra (E _g=1.7 eV for PBT and E _g=1.9 eV for PBuT). The dependence of the differential capacity on the potential could be presented as Mott-Schottky plot, at least in a limited potential region. The flatband potential was determined (E _fb= 0.67 V for PBT and E _fb=0.58 V for PBuT). Received: 9 June 1998 / Accepted: 22 August 1998     

A theoretical study of the acetylide anion, HCC−

The results of various ab initio calculations are reported for the electronic ground state of the acetylide anion. An “Eyring's lake” in the T-shaped configuration is identified with six different methods (SCF, MP2, CCSD, CCSD-T, CCSD(T), and CEPA–1). The equilibrium bond lengths of HCC⁻ are estimated to be r _e (CH)=1.0689(3) ? and R _e (CC)=1.2464(2) ?, and the ground-state rotational constant is predicted to be B ₀=41636(20)MHz. The large permanent dipole moment of μ₀=−3.093D should facilitate detection of the anion by microwave spectroscopy. The band centers are predicted to be 3211.3cm⁻¹(ν₁), 511.1cm⁻¹(ν₂), and 1805.0cm⁻¹(ν₃). A large transition dipole moment of 0.477 D is calculated for the ν₂ band. Rovibrational levels of HCC⁻ up to approximately 20 000 cm⁻¹ above equilibrium are calculated with DVR-DGB and FBR methods on the basis of a previous CEPA–1 potential energy surface. Different energy patterns are found and discussed, for which anharmonic and Coriolis resonances are shown to play an important role. Received: 27 July 1998 Accepted: 12 August 1998 / Published online: 19 October 1998     

Electric and magnetic multipole integrals in STO basis sets: an analytical approach

A new method for the evaluation of one- and two-centre magnetic and electric multipole integrals for Slater-type functions is presented. The method is strictly analytical in that no approximations of any kind are involved. Two simple functions, ℐ₁ ^aug and ℐ₂ ^aug, are introduced, which employ only functions that are well known in electronic structure theory. With the use of augmentation exponents these functions apply to multipole integrals as well as other one-electron integrals, such as nuclear attraction integrals. The proposed method includes the analytic determination of derivatives of the integrals with respect to atomic displacements. Some illustrative test calculations are presented and compared to results from the literature. Received: 20 April 1998 / Accepted: 13 October 1998 / Published online: 1 February 1999     

Ab initio calculations find 2,2-disilylcyclopentane-1,3-diyl is a singlet diradical with a high barrier to ring closure

Ab initio calculations on the lowest singlet and triplet states of 2,2-disilylcyclopentane-1,3-diyl find that the singlet lies well below the triplet. The C ₂ singlet diradical is calculated to be a minimum on the potential energy surface with an enthalpic barrier to ring closure of ΔH ^‡ ₂₉₈ = 13.5 kcal/mol at the CASPT2/6-31G* level of theory. The energy of the 1,3-divinyl-substituted singlet diradical is calculated to be only 0.8 kcal/mol higher than that of 5,5-disilyl-1,3-divinylbicyclo[2.1.0]pentane at this level of theory, but the transition state for their equilibration is computed to be 12.8 kcal/mol above the diradical in energy. Received: 2 July 1998 / Accepted: 4 August 1998 / Published online: 16 November 1998     

The spin-forbidden reaction CH(2∏) + N2→ HCN + N(4S) revisited I. Ab initio study of the potential energy surfaces

High-level ab initio electronic structure theories have been applied to investigate the detailed reaction mechanism of the spin-forbidden reaction CH(²∏) + N₂ → HCN + N(⁴S). The G2M(RCC) calculations provide accurate energies for the intermediates and transition states involved in the reaction, whereas the B3LYP/6-311G(d,p) method overestimates the stability of some intermediates by as much as about 10 kcal/mol. A few new structures have been found for both the doublet and quartet electronic states, which are mainly involved in the dative pathways. However, due to the higher energies of these structures, the dominant mechanism remains the one involving the C ₂ intersystem-crossing step. The C ₂ minima on the seam of crossing (MSX) structures and the spin-orbit coupling between the doublet and quartet electronic states are rather close to those found in previous studies. Vibrational frequencies orthogonal to the normal of the seam which have been applied in a separate publication to calculate the rate of the CH(²∏) + N₂ → HCN + N(⁴S) reaction with a newly proposed nonadiabatic transition-state theory for spin-forbidden reactions have been calculated at the MSX from first principles. Received: 23 June 1998 / Accepted: 21 September 1998 / Published online: 8 February 1999     

Modelling the active site of glyceraldehyde-3 phosphate dehydrogenase with the LSCF formalism

In the framework of a theoretical approach to the relationship between structure and reactivity of the catalytic centers of enzymes, glyceraldehyde-3 phosphate dehydrogenase (GAPDH) has been chosen as a model enzyme. In GAPDH, the proximity of His₁₇₆ increases the reactivity of Cys₁₄₉ at neutral pH; however, its presence alone is not sufficient to explain the reactivity of the catalytic Cys. In order to determine which other interactions play an important role, a study of the geometric and electronic structure of the catalytic site has been made using a hybrid quantum mechanics/molecular mechanics local self-consistent field method. This allows the computation of the electronic properties of amino acid residues in subsystems influenced by other parts of the macromolecule. The quantum subsystem was centered on the Cys₁₄₉ residue of GAPDH. The structures of GAPDH taken from the crystallographic database did not include hydrogen atoms and these had to be added taking into account the fact that, in the active site, His₁₇₆ has three tautomeric forms: δ-His protonated, ε-His protonated and His⁺. The results presented here suggest that the most stable His…Cys system in GAPDH is a strongly hydrogen-bonded Cys₁₄₉ ⁻/His₁₇₆ ⁺ ion pair. Received: 24 March 1998 / Accepted: 3 September 1998 / Published online: 23 November 1998     

The structure and energetics of cryolite melts

A method of solvation energy computation is proposed for ions and molecules in the environment of an ionic melt, based on the approximation of the ionic melt as an ideal conductor. The method is used to compute equilibrium constants of some equilibria in cryolite melt. Theoretically obtained results predict that aluminium is bound in tetrafluorocomplexes AlF₄ ⁻. Received: 16 March 1998 / Accepted: 19 June 1998 / Published online: 7 October 1998     

Nafion-based solid-state gas sensors: Pt / Nafion electrodes prepared by an impregnation-reduction method in sensing oxygen

The influences of the reductant concentration of NaBH₄ and the quantity of Pt loading on the active surface area and the sensitivity of the Pt/Nafion electrodes prepared by an impregnation-reduction method in detecting oxygen were investigated in this study. The Pt/Nafion electrodes with a Pt loading of 4.99 mg/cm², obtained at 0.0107 M Pt(NH₃)₄Cl₂ and 0.06 M NaBH₄, show maximum sensitivities of 0.0528 A/ppm and 0.0538 A/ppm obtained in O₂ concentration regions of 0–5000 and 5000–50 000 ppm, respectively. A sensing model was also proposed to illustrate the sensing phenomenon. Received: 21 January 1998 / Accepted: 10 March 1998     

Research on the electrochemistry of oxygen ion conductors in the former Soviet Union. II. Perovskite-related oxides

The review is devoted to the analysis of experimental results on electrochemical and physicochemical properties of the perovskite-related oxide phases obtained at scientific centers of the former Soviet Union. The main attention is focused on oxides with high electronic conductivity, which are potentially useful as electrodes for high-temperature electrochemical cells with oxygen-ion conducting solid electrolytes and interconnectors of solid oxide fuel cells, and on mixed ionic-electronic conductors for oxygen separation membranes. Along with perovskite-like solid solutions based on LnMO_3−δ (Ln is a rare-earth element, M = Cr, Mn, Fe, Co, Ni) and SrCoO_3−δ, properties of the oxide phases Ln₂MO_4±δ (M = Cu, Ni, Co) with the K₂NiF₄-type structure are briefly reviewed. Received: 5 November 1998 / Accepted: 26 November 1998     

Argon-matrix-isolation Raman spectra and density functional study of 1,3-butadiene conformers

s-trans, s-cis and gauche conformers of 1,3-butadiene have been studied using density functional theory and the coupled-cluster method using double substitutions (CCD). Matrix isolation Raman and IR data for the minor conformer were obtained and are used in combination with the theoretical results to resolve earlier ambiguities in vibrational assignments. Based on high-quality Hessians, new harmonic stretching force constants are reported for the carbon backbone of s-trans-1,3-butadiene. For the minor conformer the best unscaled root mean square error of the calculated frequencies for the s-cis and gauche geometries are 17.5 cm⁻¹ and 7.4 cm⁻¹, respectively, primarily due to a better agreement of the gauche results for the vibrations at 983 cm⁻¹, 596 cm⁻¹ and 470 cm⁻¹ which depend strongly on the torsional angle. Although this points towards the gauche form rather than the s-cis form, the calculated transition dipole moment directions at the CCD/6-311G(d,p) level confirm the earlier conclusion that the minor conformer has C _{2 v} symmetry in the matrix. It is concluded that either the better agreement between the frequencies calculated for the gauche form and the observed values is coincidental, or that the molecule is indeed nonplanar in the matrix and tunnels very rapidly between the two mirror-image forms (or its lowest vibrational level lies above the barrier). Received: 1 July 1998 / Accepted: 26 October 1998 / Published online: 15 February 1999     

The effect of the protein environment on the structure and charge distribution of the retinal Schiff base in bacteriorhodopsin

The effects of the amino acid side chains of the binding pocket of bacteriorhodopsin (bR) and of a water molecule on the structure of the retinal Schiff base have been studied using Becke3LYP/6-31G* level of density functional theory. A model protonated Schiff base structure including six conjugated double bonds and methyl substituents was optimized in the presence of several amino acid side chains and of a water molecule, separately. The Schiff base structure was also calculated in the form of a neutral species. At each optimized complex geometry the atomic charges of the model Schiff base were calculated using Mulliken population analysis. In agreement with previously proposed counterion(s) of the protonated retinal Schiff base in bR, the results show that Asp₈₅ and Asp₂₁₂, which are present in the form of negatively charged groups, have significantly large effects on the structure and electronic configuration of both unprotonated and protonated model Schiff bases. The presence of a water molecule in the vicinity of the Schiff base demonstrates significant effects which are comparable to those of aspartate groups. Other side chains studied did not show any significant effect in this direction. Apart from the aspartate groups and the water molecule, in none of the other complexes studied are the atomic charges and the bond alternation of the model Schiff base significantly influenced by the presence of the neighboring amino acids. Received: 24 March 1998 / Accepted: 3 September 1998 / Published online: 10 December 1998     

Poisson-Boltzmann calculations versus molecular dynamics simulations for calculating the electrostatic potential of a solvated peptide

We performed a very long molecular dynamics simulation of a peptide in explicit water molecules and ions and averaged the electrostatic potential caused by peptide, water and ions at eight points in the vicinity of the peptide. These electrostatic potential values were directly compared to the potential calculated by solving the non-linear Poisson-Boltzmann equation for the system, which describes the solvent using continuum electrostatics. We analyze the contribution of dielectric constant, conformational flexibility and solvation effects on the electrostatic potential at these eight points. Received: 24 April 1998 / Accepted: 4 August 1998 / Published online: 23 November 1998