Jacques Liévin

The Vibrational Energy Pattern in Acetylene (IV): Updated Global Vibration Constants for 12C2H2

All 253 vibrational levels in the ground electronic state of 12C2H2 with assigned rotational structure reported in the literature from absorption, stimulated emission pumping, and dispersed laser induced fluorescence spectroscopic investigations are gathered. They cover the range up to 18 915 cm−1. Some 219 of these energies are simultaneously fitted using the same so-called Cluster model based on the emergence of three constants of the motion, as previously used to deal with the vibrational energy levels up to 12 000 cm−1 [Abbouti Temsamani and Herman, J. Chem. Phys. 103, 5931 (1995)]. Thirty-nine vibrational constants are produced. The rms value of the fit is 0.81 cm−1. Principal rotational constants are predicted for all levels, which satisfactorily compare with the experimental results. Problems are demonstrated to concern a fraction of the 34 remaining levels only. Thus, the adequacy of the model is fully confirmed. The remaining problems are discussed and globally attributed to problems of a vibrati...

A comparison of two methods for selecting vibrational configuration interaction spaces on a heptatomic system: ethylene oxide.

Two recently developed methods for solving the molecular vibrational Schrodinger equation, namely, the parallel vibrational multiple window configuration interaction and the vibrational mean field configuration interaction, are presented and compared on the same potential energy surface of ethylene oxide, c-C(2)H(4)O. It is demonstrated on this heptatomic system with strong resonances that both approaches converge towards the same fundamental frequencies. This confirms their ability to tackle the vibrational problem of large molecules for which full configuration interaction calculations are not tractable.

Cation–π/H-bond Stair Motifs at Protein–DNA Interfaces

H-bonds and cation-pi interactions between nucleic acid bases and amino acid side-chains are known to occur often concomitantly at the interface between protein and double-stranded DNA. Here we define and analyze stair-shaped motifs, which simultaneously involve base stacking, H-bond and cation-pi interactions. They consist of two successive bases along the DNA stack, one in cation-pi interaction with an amino acid side-chain that carries a total or partial positive charge, and the other H-bonded with the same side-chain. A survey of 52 high-resolution structures of protein/DNA complexes reveals the occurrence of such motifs in the majority of the complexes, the most frequent of these motifs involving Arg side-chains and G bases. These stair motifs are sometimes part of larger motifs, called multiple stair motifs, which contain several successive stairs; zinc finger proteins for example exhibit up to quadruple stairs. In another kind of stair motif extension, termed cation-pi chain motif, an amino acid side-chain or a nucleic acid base forms simultaneously two cation-pi interactions. Such a motif is observed in several homeodomains, where it involves a DNA base in cation-pi interactions with an Arg in the minor groove and an Asn in the major groove. A different cation-pi chain motif contains an Arg in cation-pi with a G and a Tyr, and is found in ets transcription factors. Still another chain motif is encountered in proteins that expulse a base from the DNA stack and replace it by an amino acid side-chain carrying a net or partial positive charge, which forms cation-pi interactions with the two neighboring bases along the DNA strand. The striking conservation of typical stair and cation-pi chain motifs within families of protein/DNA complexes suggests that they might play a structural and/or functional role and might moreover influence electron migration through the DNA double helix.

The vibrational spectrum of pyrrole (C4H5N) and furan (C4H4O) in the gas phase

Abstract We have recorded the absorption spectrum of pyrrole (C 5 H 5 N) and furan (C 4 H 4 O) on a broad spectral range in the infrared region and under various experimental conditions, using a Fourier transform interferometer. The resolution was good enough to reliably identify band shapes. We have performed the vibrational assignment of the vibration–rotation bands observed between 500 and 12,000 cm −1 for pyrrole, and 500 and 9000 cm −1 for furan. The assignment of the fundamental bands is supported by ab initio calculations at the MP2 level of approximation, considering both band positions and absolute absorption intensities. These calculations also allowed the normal mode coordinates to be drawn for the two species and their geometrical structure to be calculated. Vibrational mode numbering and symmetries are updated to latest conventions in the literature. In the combination and overtone spectral ranges, the band shape information guided the assignment, which could be achieved for most of the numerous observed bands. An extensive set of vibration constants was obtained for each species. The results from the literature available on each species are considered at each step of the investigation.

Histidine-aromatic interactions in proteins and protein-ligand complexes: quantum chemical study of X-ray and model structures

His-aromatic complexes, with the His located above the aromatic plane, are stabilized by π-π, δ(+)-π and/or cation-π interactions according to whether the His is neutral or protonated and the partners are in stacked or T-shape conformations. Here we attempt to probe the relative strength of these interactions as a function of the geometry and protonation state, in gas phase, in water and protein-like environments (acetone, THF and CCl4), by means of quantum chemistry calculations performed up to second order of the Møller-Plesset pertubation theory. Two sets of conformations are considered for that purpose. The first set contains 89 interactions between His and Phe, Tyr, Trp, or Ade, observed in X-ray structures of proteins and protein-ligand complexes. The second set contains model structures obtained by moving an imidazolium/imidazole moiety above a benzene ring or an adenine moiety. We found that the protonated complexes are much more stable than the neutral ones in gas phase. This higher stability is due to the electrostatic contributions, the electron correlation contributions being equally important in the two forms. Thus, π-π and δ(+)-π interactions present essentially favorable electron correlation energy terms, whereas cation-π interactions feature in addition favorable electrostatic energies. The protonated complexes remain more stable than the neutral ones in protein-like environments, but the difference is drastically reduced. Furthermore, the T-shape conformation is undoubtedly more favorable than the stacked one in gas phase. This advantage decreases in the solvents, and the stacked conformation becomes even slightly more favorable in water. The frequent occurrence of His-aromatic interactions in catalytic sites, at protein-DNA or protein-ligand interfaces and in 3D domain swapping proteins emphasize their importance in biological processes.

Overtone spectroscopy and dynamics in monodeuteroacetylene (C2HD)

Abstract Complementary experimental, ab initio and dynamical investigations are reported on monodeuteroacetylene, C 2 HD (X 1 Σ + ). All experimental spectroscopic results previously reported in the literature on C 2 HD, i.e. from 500 to 16000 cm −1 are gathered. New results are included, which are obtained from the analysis of absorption data recorded with a Fourier transform interferometer at high resolution between 4600 and 9000 cm −1 . The presence of numerous weak bands along the whole spectral range is analysed in terms of systematic anharmonic couplings. The entire set of energy data is then used to produce thirty-five vibrational frequencies and anharmonicities from a fit of the vibrational energies to a Dunham-type expansion, and the vibrational level density is extrapolated, up to higher energy. One- and two-dimensional potential energy and dipole moment surfaces refined from new ab initio results are fitted to a selected set among those experimental data, associated to the stretch overtones. The iterative procedure involving an original package of computer programs is described. The evolution of the overtone intensities of the CH and CD stretches, up to η = 4, is interpreted on that basis in terms of electric and mechanical anharmonicity contributions. Eventually, dynamical aspects are studied thanks to the newly introduced vibrograms, which allow to obtain the time recurrences of the vibrational dynamics. Using the Gutzwiller and Berry-Tabor trace formulas, these vibrational recurrences are semiclassically assigned to periodic orbits of the classical Hamiltonian given by the Dunham expansion.

The VMFCI method: A flexible tool for solving the molecular vibration problem

The present article introduces a general variational scheme to find approximate solutions of the spectral problem for the molecular vibration Hamiltonian. It is called the “vibrational mean field configuration interaction” (VMFCI) method, and consists in performing vibrational configuration interactions (VCI) for selected modes in the mean field of the others. The same partition of modes can be iterated until self‐consistency, generalizing the vibrational self‐consistent field (VSCF) method. As in contracted‐mode methods, a hierarchy of partitions can be built to ultimately contract all the modes together. So, the VMFCI method extends the traditional variational approaches and can be included in existing vibrational codes based on the latter approaches. The flexibility and efficiency of this new method are demonstrated on several molecules of atmospheric interest.

Ab initio calculation of the rotational spectrum of methane vibrational ground state

In a previous article we have introduced an alternative perturbation scheme to the traditional one starting from the harmonic oscillator, rigid rotator Hamiltonian, to find approximate solutions of the spectral problem for rotation-vibration molecular Hamiltonians. The convergence of our method for the methane vibrational ground state rotational energy levels was quicker than that of the traditional method, as expected, and our predictions were quantitative. In this second article, we study the convergence of the ab initio calculation of effective dipole moments for methane within the same theoretical frame. The first order of perturbation when applied to the electric dipole moment operator of a spherical top gives the expression used in previous spectroscopic studies. Higher orders of perturbation give corrections corresponding to higher centrifugal distortion contributions and are calculated accurately for the first time. Two potential energy surfaces of the literature have been used for solving the anharmonic vibrational problem by means of the vibrational mean field configuration interaction approach. Two corresponding dipole moment surfaces were calculated in this work at a high level of theory. The predicted intensities agree better with recent experimental values than their empirical fit. This suggests that our ab initio dipole moment surface and effective dipole moment operator are both highly accurate.

The equilibrium OH bond length

Twenty eight CC bonds lengths (from a sample of 23 molecules) whose experimental equilibrium structures are thought to be reliable are calculated ab initio. Two different correlated methods are compared: MP2 and CCSD(T). The convergence of Dunnings correlation consistent polarized valence basis sets, cc-pVnZ is also studied. With the CCSD(T)/cc-pVQZ method, a systematic correction of about 0.0034 Å is necessary when the frozen core approximation is used. With this offset of 0.0034 Å taken into account, the accuracy (standard deviation) is 0.0013 Å. With the cc-pVTZ basis set, the correction increases to 0.0066 Å and the accuracy drops to 0.0018 Å. The MP2 method is significantly less accurate and the offset only remains constant for similar bonds. During this work, new structures are calculated for methyl cyanide, oxirane, cyclopropenylidene, allene, and cyclopropene.

The vibrational energy pattern in acetylene. V. 13C2H2

A total of 134 vibrational levels with assigned rotational structure have been gathered in the ground electronic state of 13C2H2. Most of these measurements are updated or new compared to the previously published data. Altogether, they cover the range up to 23 670 cm−1. 118 out of the 119 levels observed below 13 000 cm−1 have been simultaneously fitted using the so-called cluster model, already used to deal with the vibrational energy levels in other isotopomers of acetylene [El Idrissi et al., J. Chem. Phys. 110, 2074 (1999), and references therein]. Twenty-nine vibrational constants have been determined, including the off-diagonal parameters K3/245, K1/244, K1/255, K11/33, K14/35, and r45, with a rms of the fit equal to 0.52 cm−1. The same three constants of the motion as in 12C2H2 emerged, Ns=v1+v2+v3, Nr=5v1+3v2+5v3+v4+v5 and k=l4+l5. The energies of the levels above 13 000 cm−1 calculated with the obtained parameters compare reasonably well with the experimental values. For all levels the predicted ...