Dissociative recombination of HeH+. I. Rovibrational spectrum of HeH Rydberg states

The repulsive ground electronic state X²Σ⁺ of HeH is strongly coupled to the Rydberg states at small interatomic distances. Such large couplings also occur between some of the Rydberg states. HeH⁺ ions that capture an electron in a Rydberg state end up in separated He and H atoms by indirect predissociation. This paper presents a study of potential functions and pertinent matrix elements involving the lowest electronic states: the ²Σ⁺ states, X, A, C, and D, and the ²Π states B and E. Individual transition rates as well as total radiative and non-radiative lifetimes have been computed for the lowest vibrational and rotational levels. Received: 22 June 1998 / Accepted: 21 August 1998 / Published online: 12 October 1998     

Anharmonic force field and spectroscopic constants of silene: an ab initio study

High-level ab initio calculations with large basis sets are reported for silene, H₂C=SiH₂. Correlated harmonic force fields are obtained from coupled cluster CCSD(T) calculations with the cc-pVQZ basis (cc-pVTZ for H) while the anharmonic force fields are computed at the MP2/TZ2Pf level. There is excellent agreement with the available experimental data, in particular the equilibrium geometry and the fundamental vibrational frequencies. Many other spectroscopic constants are predicted for the C _{2 v} isotopomers of silene. Received: 27 May 1998 / Accepted: 23 July 1998 / Published online: 9 October 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     

A theoretical study on the first ionic states of vinyl fluoride, vinyl chloride, trifluoroethylene, and trichloroethylene with an analysis of the vibrational structures of the photoelectron spectra

Ab initio calculations have been performed to study the molecular structures and the vibrational levels of the first ionic states of vinyl fluoride, vinyl chloride, trifluoroethylene, and trichloroethylene. The equilibrium molecular structures and vibrational modes of these states are presented. The theoretical ionization intensity curves including the vibrational structures are also presented and compared with the photoelectron spectra. Received: 11 September 1998 / Accepted: 13 October 1998 / Published online: 1 February 1999     

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     

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     

Transition state structure invariance to model system size and calculation levels: a QM/MM study of the carboxylation step catalyzed by Rubisco

The present study elucidates structural features related to the molecular mechanism in the carboxylation step of the reaction catalyzed by Rubisco. Starting from the initial X-ray Protein Data Bank structure of a Rubisco monomer, the reactive subsystem in vacuo is subjected to quantum chemical semiempirical and ab initio studies, while the effects of the protein environments are included by means of a hybrid quantum mechanical/molecular mechanical (QM/MM) approach. The QM/MM is used to characterize the transition structure for carboxylation inside the protein. The calculations were made with the AM1/CHARMM/GRACE scheme. Comparisons between the in vacuo and in situ transition structures show remarkable invariance with respect to geometric parameters, index and transition vector amplitudes. The transition state couples the carbon dioxide attack to the C2 center of the substrate in its dienol form with a simultaneous intramolecular hydrogen transfer from the C2 atom to the hydroxyl group linked to the C3 center. This study suggests that carboxylation may be simultaneously coupled to the activation of the C3 center in the enzyme. Received: 24 March 1998 / Accepted: 3 September 1998 / Published online: 10 December 1998     

Transition-state structures for describing the enzyme-catalyzed mechanisms of rubisco

The carboxylation and oxygenation processes of a model substrate, 3,4-dihydroxy-2-pentanone, have been theoreticaly characterized as a set of steps, mimicking the corresponding reactions of D-ribulose-1,5-bisphosphate catalyzed by rubisco. A theoretical characterization is carried out of transition-state structures and possible molecular intermediates represented as saddle points of index 1 and minimum energy structures, respectively. The quantum chemical characterization, at the HF/3-21G calculation level, of these stationary points is used to rationalize and to discuss both catalyzed sequences. The reported set of these stationary points maps out most experimental aspects of the reaction pathways for the real system. Received: 24 March 1998 / Accepted: 3 September 1998 / Published online: 10 December 1998     

Analytic UHF-CCSD(T) second derivatives: implementation and application to the calculation of the vibration-rotation interaction constants of NCO and NCS

An implementation of analytic open-shell UHF-CCSD(T) second derivatives is presented. To demonstrate applicability and test the accuracy of the UHF-CCSD(T) approach for the determination of spectroscopical parameters, vibration-rotation interaction constants were calculated for the ground (1²Π) and first electronically excited (1²Σ) states of the NCO and NCS radicals. In addition, harmonic vibrational frequencies for both states, the Renner-Teller parameter for the ground state, as well as the 1²Π→1²Σ excitation energy are reported. While the computed values are in good agreement with reliable experimental information for NCO, most of the data presented for NCS are predictions of quantities not well known from experiment. Received: 4 May 1998 / Accepted: 27 July 1998 / Published online: 12 October 1998     

Vibrational and correlation effects on properties of water

Large basis set, ab initio potential energy and property surfaces of water have been used with quantum Monte Carlo vibrational analysis in the evaluation of the molecule's rotational constants, zero-point energy, and dipole moment. While there are clearly differences in vibrational state parameters due to including correlation effects, the vibrational averaging effect on rotational constants is very nearly additive with the correlation effect. This has implications for evaluation and estimation of properties of molecules in specific vibrational states. Received: 9 February 1999 / Accepted: 11 February 1999 / Published online: 5 May 1999     

Transition state for intramolecular C–H bond cleavage in [(LCu)2(μ-O)2]2+ (L = 1,4,7-tribenzyl-1,4,7-triazacyclononane)

Hybrid quantum mechanical/molecular mechanical electronic structure calculations reveal the transition state for C–H bond cleavage in [(LCu)₂ (μ-O)₂]²⁺ (L=1,4,7-tribenzyl-1,4,7-triazacyclononane) to be consistent with a hydrogen-atom-transfer mechanism from carbon to oxygen. At the MPW1K/double-zeta effective core potential(+)|univeral force field level, 0 K activation enthalpies for the parent, p-CF3, and p-OH substituted benzyl systems are predicted to be 8.8, 9.5, and 7.8 kcal/mol. Using a one-dimensional Eckart potential to estimate quantum effects on the reaction coordinate, reaction in the unsubstituted system is predicted to proceed with a primary kinetic isotope effect of 22 at 233 K. Structural parameters associated with the hydrogen-atom transfer are consistent with the Hammond postulate. Received: 10 October 2000 / Accepted: 3 November 2000 / Published online: 3 April 2001     

Frontier-orbital analyses of ketene [2+2] cycloadditions

Twelve kinds of ketene [2+2] cycloadditions have been investigated by ab initio calculations. They are composed of four ketenes (Y–HC=C=O, Y=H, NH₂, Cl, and CN) and three isoelectronic ketenophiles (ethylene, methylenimine, and formaldehyde). All the transition state geometries obtained here are not different significantly, but the extent of formation of two covalent bonds differs appreciably. The difference is attributable to the degree of the charge transfer interactions. One is the interaction from the π orbital and/or the lone pair orbital of a ketenophile to the LUMO of a ketene (dominant charge transfer, CT1). The other is that from the HOMO of the ketene to the π* orbital of the ketenophile (second dominant charge transfer, ct1). CT1 contributes to the formation of only one covalent bond, and ct1 does to the formation of the other. This independent function is characteristic of ketene [2+2] cycloadditions. They are not concerned with the orbital phase. We also have examined Fukui's postulate that the deformation of particular frontier orbitals causes the reaction progress. The role has been verified both by configuration analyses along the intrinsic reaction coordinate of the ketene-ethylene reaction and by the examination of distortions of frontier-orbital shapes along the low-frequency vibrational modes. Received: 25 June 1998 / Accepted: 28 August 1998 / Published online: 11 November 1998     

Chemical potential inequality principle

Regional density functional theory has been extended to treat irreversible thermodynamic electronic processes for application to adiabatic electron-transfer processes of chemical reactions. Onsager's local equilibrium hypothesis is slightly modified to take into account the quantum mechanical nature of the electron. The quantum mechanical interference effect has been demonstrated to be included in the entropy production rate formula associated with electron transfer through an interface. A new formula for the determination of the transition state of a chemical reaction has been postulated that corresponds to the maximum of the regional electron transferability. A quantum mechanical law of mass action has been established and applied to prove the regional electrochemical potential inequality principle. Received: 1 July 1998 / Accepted: 2 September 1998 / Published online: 8 February 1999     

Ab initio quantum chemical study of the formation, decomposition and isomerization of the formaldiminoxy radical (CH2NO): comparison of the Gaussian-2 and CASPT2 techniques in the calculation of potential energy surfaces

The reaction between triplet methylene and nitric oxide, producing the formaldiminoxy (CH₂NO) radical, and the subsequent decomposition and isomerization reactions of CH₂NO have been studied using ab␣initio quantum chemical techniques that include the Gaussian-2 (G2), CASSCF and CASPT2 methods. Stationary points on the potential energy surfaces were located at MP2/6-31G(d) and CASSCF/cc-pVDZ levels of theory, while the electronic energies were determined using G2, G2(MP2), QCISD(T)/cc-pVTZ, RCCSD(T)/cc-pVTZ and CASPT2/cc-pVTZ approaches. G2 is believed to be reliable at equilibrium geometries, but the determination of certain transition state geometries and energies requires a MCSCF-based approach. The calculations suggest that CH₂NO (²A^′) forms in a barrierless reaction and could readily decompose to H+HCNO. A subsequent abstraction reaction then results in H₂+CNO. No molecular elimination channel was found. An alternative pathway is the formation of CH₂ON, which readily isomerizes to CH₂NO. Received: 8 May 1998 / Accepted: 11 August / Published online: 9 October 1998     

Molecular dynamics simulations of the isolated domain 1 of annexin I

Annexin molecules consist of a symmetrical arrangement of four domains of identical folds but very different sequences. Nuclear magnetic resonance (NMR) experiments on the isolated domains of annexin I in aqueous solution have indicated that domain 1 retains its native structure whereas domain 2 unfolds. Therefore these two domains constitute interesting models for comparative simulations of structural stability using molecular dynamics. Here we present the preliminary results of molecular dynamics simulations of the isolated domain 1 in explicit water at 300 K, using two different simulation protocols. For the first, domain 1 was embedded in a 46 ? cubic box of water. A group-based non-bonded cut-off of 9 ? with a 5–9 ? non-bonded switching function was used and a 2 fs integration step. Bonds containing hydrogens were constrained with the SHAKE algorithm. These conditions led to unfolding of the domain within 400 ps at 300 K. In the second protocol, the domain was embedded in a 62 ? cubic box of water. An atom-based non-bonded cut-off of 8–12 ? using a force switching function for electrostatics and a shifting function for van der Waals interactions were used with a 1 fs integration step. This second protocol led to a native-like conformation of the domain in accord with the NMR data which was stable over the whole trajectory (∼2 ns). A small, but well-defined relaxation of the structure, from that observed for the same domain in the entire protein, was observed. This structural relaxation is described and methodological aspects are discussed. Received: 10 May 1998 / Accepted: 4 August 1998 / Published online: 2 November 1998     

A theoretical study on the ionization of OCS with an analysis of vibrational structures of the photoelectron spectrum

 Ab initio calculations have been performed to study the molecular structures and vibrational levels of the four low-lying ionic states (1, 2²Π, and 1, 2²Σ⁺) of carbonyl sulfide. The global regions of the potential-energy surfaces have been obtained by multireference single and double excitation configuration interaction calculations. Vibrational calculations using explicit vibrational Hamiltonians have been used for vibrational analysis. The equilibrium molecular structures and a vibrational analysis of the four ionic states are presented. The theoretical ionization intensity curves including the vibrational structures of the ionic states are also presented and are compared with the photoelectron spectrum. Received: 20 January 2001 / Accepted: 22 August 2001 / Published online: 30 October 2001     

Bifurcation of reaction pathways: the set of valley ridge inflection points of a simple three-dimensional potential energy surface

This paper serves for the better understanding of the branching phenomenon of reaction paths of potential energy hypersurfaces in more than two dimensions. We apply the recently proposed reduced gradient following (RGF) method for the analysis of potential energy hypersurfaces having valley-ridge inflection (VRI) points. VRI points indicate the region of possible reaction path bifurcation. The relation between RGF and the so-called global Newton search for stationary points (Branin method) is shown. Using a 3D polynomial test surface, a whole 1D manifold of VRI points is obtained. Its relation to RGF curves, steepest descent and gradient extremals is discussed as well as the relation of the VRI manifold to bifurcation points of these curves. Received: 8 July 1998 / Accepted: 24 August 1998 / Published online: 23 November 1998     

Structure effects on isomerization pathways and vibrational spectra of epoxysaccharides: a numerical study

Results of a comparative analysis of conformational possibilities of the hexopyranose ring of six epoxysaccharides differing from each other by the position of the oxirane ring within the limits of the hexapyranose ring and having different orientations of substituents and different positions of the oxirane ring with respect to the skeleton plane of the molecules are presented. Numerical simulations based on the Wiberg and Boyd method made it possible to determine all the stationary forms in which anhydropyranose rings can exist. The effect of various structural factors on the character of conformational transformations, heights of transition barriers, and the energy of stationary forms has been investigated. Normal vibrational modes of the stationary forms of the compounds were calculated using molecular mechanics. Based on results of our simulations, we predict a strong effect of steric factors on the vibrational spectra of sugar epoxides. Received: 24 March 1998 / Accepted: 3 September 1998 / Published online: 17 December 1998     

Global geometry optimization of small silicon clusters at the level of density functional theory

By an application to small silicon clusters Si _N (with N = 4,5,7,10) it is shown that truly global geometry optimization on an ab initio or density functional theory level can be achieved, at a computational cost of approximately 1–5 traditional local optimization runs (depending on cluster size). This extends global optimization from the limited area of empirical potentials into the realm of ab initio quantum chemistry. Received: 24 February 1998 / Accepted: 6 March 1998 / Published online: 17 June 1998