Molecular Clusters of π-Systems: Theoretical Studies of Structures, Spectra, and Origin of Interaction Energies

Kraitchman has shown that a single isotopic substitution on an atom is sufficient to determine directly the coordinates of that atom with respect to the principal axes of the original molecule. Kraitchman's formulas represent exact solutions of the equations for the equilibrium moments of inertia. However, the effects of the zero‐point vibrations are such that the coordinates obtained by substitution from the ground state moments of inertia I0 are systematically less than r0. These coordinates have here been called r (substitution) or rs, and it is found that rs≃(r0+re)/2, and Is= ∑ imirsi2≃(I0+Ie)/2.In the usual method of solution, the coordinate of one atom is determined from the equation for I0, and therefore the difference I0—Is must be made up by this one coordinate. This introduces a large error in the structures normally determined from ground state constants, and results in variations of 0.01 A in structures determined from different sets of isotopic species. If instead, we obtain the structure on...

A new criterion for the determination of molecular structures from ground state rotational constants

We present the fifth release of the UMIST Database for Astrochemistry (UDfA). The new reaction network contains 6173 gas-phase reactions, involving 467 species, 47 of which are new to this release. We have updated rate coefficients across all reaction types. We have included 1171 new anion reactions and updated and reviewed all photorates. In addition to the usual reaction network, we also now include, for download, state-specific deuterated rate coefficients, deuterium exchange reactions and a list of surface binding energies for many neutral species. Where possible, we have referenced the original source of all new and existing data. We have tested the main reaction network using a dark cloud model and a carbon-rich circumstellar envelope model. We present and briefly discuss the results of these models.

The UMIST database for astrochemistry 2012

Organic chemists tend to consider the conformation of compounds as a consequence of repulsive steric interactions. In other words, “the steric effect” means “repulsive” in many cases. Thus, folded conformations observed in organic molecules have been often regarded as unusual, while the reason remained undecided. However, accurate determinations by modern spectroscopic methods, recent crystallographic data, and high-level ab initio MO calculations have demonstrated that the folded conformation is by no means exceptional. We will show that the gauche or folded conformation prevails in organic compounds bearing at least an electronegative or π-group in the molecule. We consider that the above phenomenon finds its origin, in most cases, in nonconventional hydrogen bonds such as the CH/X (X ) O, halogen, etc.) and the XH/π (X ) O, N, C, etc.) hydrogen bonds. * To whom correspondence should be addressed. E-mail: shu@ hiroshima-u.ac.jp. ‡ Hiroshima University. § Yokohama National University. ⊥ The CHPI Institute. Chem. Rev. 2010, 110, 6049–6076 6049

Relevance of Weak Hydrogen Bonds in the Conformation of Organic Compounds and Bioconjugates: Evidence from Recent Experimental Data and High-Level ab Initio MO Calculations

To understand the intermolecular interactions between chalcogen centers (O, S, Se, Te), quantum chemical calculations on pairs of model systems were carried out. For the oxygen derivatives, one of the components of the supermolecules consists of dimethyl ether, while the second component is either dimethyl ether (1) or ethynyl methyl ether (2) or methyl cyanate (3). The model calculations were also extended to the sulfur (4−6), selenium (7−9), and tellurium congeners (10−12). The MP2/SDB-cc-pVTZ, 6-311G* level of theory was used to derive the geometrical parameters and the global energies of the model systems. A detailed analysis based on symmetry adapted perturbation theory (SAPT) reveals that induction and dispersion forces contribute to the bonding in each case. For 1−3 the electrostatic energy also contributes to the intermolecular bonding, but not for 4−12. The NBO analysis reveals that the interaction in the dimers 1−3 is mainly due to weak hydrogen bonding between methyl groups and chalcogen center...

Theoretical Investigations on Chalcogen−Chalcogen Interactions: What Makes These Nonbonded Interactions Bonding?

Observation of the rotational spectra of van der Waals complexes by free jet absorption millimeter wave spectroscopy: pyridine-argon

The ground-state rotational spectrum of the dimethyl ether dimer, (DME)2, has been studied by molecular beam Fourier transform microwave and free jet millimeter wave absorption spectroscopies. The molecular beam Fourier transform microwave spectra of the (DME-d6)2, (DME-13C)2, (DME-d6)···(DME), (DME-13C)···(DME), and (DME)···(DME-13C) isotopomers have also been assigned. The rotational parameters have been interpreted in terms of a Cs geometry with the two monomers bound by three weak C−H···O hydrogen bonds, each with an average interaction energy of about 1.9 kJ/mol. The experimental data combined with high-level ab initio calculations show this kind of interaction to be improper, blue-shifted hydrogen bonding, with an average shortening of the C−H bonds involved in the hydrogen bonding of 0.0014 A. The length of the C−H···O hydrogen bonds, r(O···H), is in the range 2.52−2.59 A.

Weak, improper, C-O...H-C hydrogen bonds in the dimethyl ether dimer.

Relative strengths of the O-H...Cl and O-H...F hydrogen bonds.

Completely planar is the hydrogen-bonded complex of pyrazine and water (see sketch), which was obtained by supersonic expansion and investigated by rotational spectroscopy. The water molecule lies in the plane of the aromatic ring, and the lone pair of electrons on the nitrogen atom functions as the acceptor in the N⋅⋅⋅H-O hydrogen bond, not-as in the corresponding benzene complex-the π electrons.

Intermolecular Hydrogen Bonding between Water and Pyrazine

Investigation of the Rotational Spectrum of Pyrimidine from 3 to 337 GHz: Molecular Structure, Nuclear Quadrupole Coupling, and Vibrational Satellites.

Assimo Maris

Papers

Observation of the rotational spectra of van der Waals complexes by free jet absorption millimeter wave spectroscopy: pyridine-argon

Weak, improper, C-O...H-C hydrogen bonds in the dimethyl ether dimer.

Relative strengths of the O-H...Cl and O-H...F hydrogen bonds.

Intermolecular Hydrogen Bonding between Water and Pyrazine

Investigation of the Rotational Spectrum of Pyrimidine from 3 to 337 GHz: Molecular Structure, Nuclear Quadrupole Coupling, and Vibrational Satellites.