Vladimír Špirko

First local minimum of the formic acid dimer exhibits simultaneously red-shifted O–H⋯O and improper blue-shifted C–H⋯O hydrogen bonds

The first local minimum of the formic acid dimer exhibits simultaneously red-shifted O–H⋯O and blue-shifted C–H⋯O hydrogen bonds. The improper, blue-shifted hydrogen bond was investigated by means of the NBO analysis, rehybridization model and optimization in the electric field. It was shown that the electrostatic model cannot describe the nature of the blue-shifted H-bond. From the NBO analysis it becomes evident that the formation of the O–H⋯O hydrogen bond and C–H⋯O improper hydrogen bond can be explained on the basis of an increase of electron density in the σ* antibonding O–H orbital and a decrease of electron density in the σ* antibonding C–H orbital. While the former effect is easily explained on the basis of hyperconjugation, the latter requires the existence of a new mesomeric structure characterized by delocalization of electron density from the C–H σ* antibonding orbital to the remaining part of the complex. The rehybridization model explains properly the formation of both hydrogen bonds but fails to interpret the changes of the other bonds.

ANTI-HYDROGEN BOND BETWEEN CHLOROFORM AND FLUOROBENZENE

Abstract Accurate theoretical calculations (ab initio MP2/6-31G * counterpoise-corrected gradient optimization, harmonic and anharmonic vibrational analysis) on the fluorobenzene⋯chloroform complex predict a new type of bonding, termed the anti-hydrogen bond. This bond distinguishes itself by the contraction of the C–H bond of chloroform and a blue shift of the corresponding stretching frequency, i.e. features opposite to those characteristic for a hydrogen bond. The predicted blue shift was confirmed experimentally by double-resonance infrared ion-depletion spectroscopy. The calculated blue shift of the chloroform C–H stretching frequency (12 cm −1 ) agrees with the experimental value of 14 cm −1 . The anti-hydrogen bond originates from the dispersive interaction between molecules (contrary to the hydrogen bond which is of electrostatic origin). It plays a significant role in benzene-containing molecular clusters and is expected to be of consequence for the structure of biomolecules.

Structure and vibrational dynamics of the benzene dimer

Point-wise evaluated coupled-cluster single double triple [CCSD(T)] stabilization energies are used to parameterize the nonempirical model (NEMO) empirical intermolecular potential of the benzene dimer in the ground electronic state. The potential is used for theoretical interpretation of the dimer structure and the dynamics of its intermolecular motions. Only one energy minimum, corresponding to the T-shaped structure, is found. A parallel displaced structure is the first-order transition structure separating the molecular symmetrically equivalent T-shaped structures. Due to a relatively high transition barrier (∼170 cm−1), the interconversion tunneling is unimportant in the energy region spanned by the available rotational spectra and is thus neglected (accordingly, the molecular symmetry group which is used for interpretation of the available experimental spectra is related to the T-shaped structure with two feasible internal rotations and nonequivalent monomers). The dimer undergoes a nearly free inte...

Amino groups in nucleic acid bases, aniline, aminopyridines, and aminotriazine are nonplanar: Results of correlated ab initio quantum chemical calculations and anharmonic analysis of the aniline inversion motion

The amino group nonplanarity in nucleic acid bases, aniline, aminopyridines, and aminotriazine was investigated by ab initio methods with and without inclusion of correlation energy utilizing medium and extended basis sets. For all the systems studied, the amino group was found to be nonplanar and the coupled cluster method [CCSD(T)] ‘‘nonplanarities’’ and inversion barriers slightly higher than their second‐order many‐body perturbation‐theory (MP2) counterparts. To assess the reliability of the calculations, inversion splittings for aniline and aniline‐ND2 were evaluated by solving a two‐dimensional vibrational Schrodinger equation for the large‐amplitude inversion and torsion motions, while respecting the role of small‐amplitude C–N stretching and H–N–H bending motions. Because a large number of points is required for the description of the aniline potential energy surface, the Hartree–Fock (HF) method with 6‐31G* basis set was utilized. The vibrational calculations were performed within the framework o...

Coupled-cluster methods with internal and semi-internal triply excited clusters: Vibrational spectrum of the HF molecule

The recently proposed, single-reference, coupled-cluster (CC) methods with singly, doubly, and triply excited clusters, in which triexcited clusters T3 are restricted to internal and semi-internal components defined through active orbitals, designated as the CCSD{t′} and CCSDt approaches [P. Piecuch, S. A. Kucharski, and R. J. Bartlett, J. Chem. Phys. 110, 6103 (1999)] have been used to obtain the potential energy function and the vibrational spectrum of the HF molecule, as described by the large, aug-cc-pvtz, basis set. A comparison has been made with the vibrational term values obtained at the very high, full CCSDT (CC singles, doubles, and triples), level and with the experimental (RKR) data. In spite of using the restricted Hartree–Fock reference, the calculated CCSD{t′} and CCSDt vibrational term values have been found to be in much better agreement with the full CCSDT and RKR data than the results of conventional CCSD (CC singles and doubles) calculations, which produce errors of an order of 2000u200acm...

Molecular quadrupole moment functions of HF and N2. I. Ab initio linear‐response coupled‐cluster results

The orthogonally spin‐adapted linear‐response coupled‐cluster (LRCC) theory with singly and doubly excited clusters (CCSD) was employed to calculate quadrupole moment functions of the HF and N2 molecules in their ground electronic states. We also calculated several potential energy curves for both systems using various CC and non‐CC methods, ranging from the limited and full configuration interaction (CI) and first‐order CI (FOCI) to finite‐order many‐body perturbation theory. FOCI and related complete active space self‐consistent field (CASSCF) methods were used in both energy and quadrupole moment calculations. Most of the calculations were performed using the medium‐size basis set of TZ+2P quality devised by Sadlej [A. Sadlej, Coll. Czech. Chem. Commun. 53, 1995 (1988)] for high‐level ab initio calculations of electrostatic molecular properties. In addition, a number of model CC calculations using small basis sets were performed, for which the exact full CI results, both for the energy and multipole mo...

Ab initio study of the phenol‐water cation radical

The phenol‐water cation radical has been investigated by ab initio theory using the spin‐restricted open‐shell Hartree–Fock and spin‐restricted open‐shell second‐order Mo/ller–Plesset theories with 3‐21G*(O) and 6‐31G* basis sets. The full geometrical optimization was performed for several hydrogen‐bonded structures and one hemibonded structure. Clearly, the most stable structure has been found for Cs symmetry with the linear hydrogen bond between the proton of the OH group of the phenol cation radical and the oxygen of the water, and the water hydrogens pointing away from the phenyl ring. For this structure harmonic (and for some intermolecular modes anharmonic) vibrational frequencies have been computed for various isotopic complexes. The computed shifts of phenol‐localized intramolecular modes on complexation and on deuteration as well as the calculated intermolecular frequencies of the different isotopic complexes allow for an assignment of vibrational frequencies observed in the experimental zero‐kin...

Can ordinary single-reference coupled-cluster methods describe potential energy surfaces with nearly spectroscopic accuracy? The renormalized coupled-cluster study of the vibrational spectrum of HF

The recently proposed renormalized (R) and completely renormalized (CR) CCSD(T) and CCSD(TQ) methods, which remove the failing of the standard CCSD(T) and CCSD(TQf) approaches at large internuclear separations, have been used to obtain the potential energy function and the vibrational spectrum of the HF molecule. The vibrational term values obtained in the renormalized and completely renormalized CCSD(T) and CCSD(TQ) calculations have been found to be in a better agreement with the experimental [Rydberg–Klein–Rees (RKR)] data than than the results of the expensive full CCSDT calculations. The simple R-CCSD(T) method gives <10 cm−1 errors for the vibrational energies up to ∼41u2009000 cm−1. The CR-CCSD(T) and CR-CCSD(TQ) methods reduce the ∼300 cm−1 errors in the full CCSDT results for the high-lying states near dissociation to 100–200 cm−1.

The vibrational and temperature dependence of the indirect nuclear spin–spin coupling constants of the oxonium (H3O+) and hydroxyl (OH−) ions

Abstract The indirect nuclear spin–spin coupling constants of the gas phase oxonium (H 3 O + ) and hydroxyl (OH − ) ions, their temperature dependence and isotope shifts are predicted by ab initio calculations. The coupling constants are calculated as a function of the symmetric stretching and the inversional coordinates of H 3 O + and as a function of the bond length of OH − at the uncorrelated level of the random phase approximation (RPA), at the correlated levels of the second order polarization propagator approximation with coupled cluster singles and doubles amplitudes – SOPPA(CCSD) – and of the multiconfigurational random phase approximation (MCRPA) with a large complete active space wavefunction. Effective ro-vibrational state dependent coupling constants are obtained from these functions and the corresponding ro-vibrational wavefunctions. The effective coupling constants for several states are then used to determine the temperature dependence of the coupling constants. The results are compared with the coupling constants of H 2 O and the nuclear magnetic shielding constants of H 3 O + and OH − .

Anharmonic and harmonic intermolecular vibrational modes of the DNA base pairs

Intermolecular vibrational modes of the H-bonded adenine…thymine Watson–Crick (AT) base pair were studied for the first time using multidimensional nonharmonic treatment. Relying on a Born–Oppenheimer–like separation of the fast and slow vibrational motions, the complete multidimensional vibrational problem is reduced to a six-dimensional subproblem in which all rearrangements between the pair fragments (i.e., adenine and thymine) can be described. Following the Hougen–Bunker–Johns approach and using appropriate vibrational coordinates, a nonrigid reference is defined which covers all motions on the low-lying part of the intermolecular potential surface and which facilitates the derivation of a suitable model Hamiltonian. The potential energy surface is determined at the ab initio Hartree–Fock level with minimal basis set (HF/MINI-1) and an analytic potential energy function is obtained by fitting to the ab initio data. This function is used to calculate vibrational energy levels and effective geometries ...