J. F. Ogilvie

Models, mysteries, and magic of molecules

PREFACE I. METHODS RAMAN SPECTROSCOPY: THE BIOMOLECULAR DETECTION OF LIFE IN EXTREME ENVIRONMENTS Howell G.M. Edwards and Michael D. Hargreaves SINGLE-CRYSTAL X-RAY DIFFRACTION STUDIES OF PHOTO-INDUCED MOLECULAR SPECIES Jacqueline M. Cole MOLECULAR CONFORMATION AND CRYSTAL LATTICE ENERGY FACTORS IN CONFORMATIONAL POLYMORPHS Ashwini Nangia HOW GUESTS SETTLE AND PLAN THEIR ESCAPE ROUTE IN A CRYSTAL --STRUCTURAL METRICS OF SOLVATION AND DESOLVATION FOR INORGANIC DIOLS Alessia Bacchi STRUCTURAL DETERMINATION OF UNSTABLE SPECIES Yuji Ohashi II. MYSTERIES IS POLYMORPHISM CAUSED BY MOLECULAR CONFORMATIONAL CHANGES? Ivan Bernal CRYSTALLINE AMINO ACIDS - A LINK BETWEEN CHEMISTRY, MATERIALS SCIENCE AND BIOLOGY Elena Boldyreva UNRAVELLING THE CHEMICAL BASIS OF THE BATHOCHROMIC SHIFT OF THE LOBSTER CARAPACE CAROTENOPROTEIN CRUSTACYANIN John R. Helliwell and Madeleine Helliwell TINY STRUCTURAL FEATURES AND THEIR GIANT CONSEQUENCES FOR PROPERTIES OF SOLIDS Andrzej Katrusiak POLYMORPHISM IN LONG-CHAIN N-ALKYLAMMONIUM HALIDES Gert Kruger, Dave Billing and Melanie Rademeyer III. MAGIC MYSTERIOUS CRYSTALLOGRAPHY: FROM SNOW AKE TO VIRUS Aloysio Janner CLUSTERS IN F-PHASE ICOSAHEDRAL QUASICRYSTALS Zorka Papadopolos, Oliver Groening and Roland Widmer PROTEIN-PROTEIN INTERACTIONS IN THE CYANOBACTERIAL KaiABC CIRCADIAN CLOCK Martin Egli, Rekha Pattanayek, Sabuj Pattanayek PROTEIN-PROTEIN DOCKING USING THREE-DIMENSIONAL REDUCED REPRESENTATIONS AND BASED ON A GENETIC ALGORITHM A. Becue, N. Meurice, L. Leherte, and D.P. VercauterenTROPOLONE AS NEUTRAL COMPOUND AND LIGAND IN PALLADIUM COMPLEXES G. Steyl and A. RoodtIV. MODELS THEORETICALAND EXPERIMENTAL MODELS OF MOLECULES ILLUSTRATED WITH2 2 QUANTUM-CHEMICAL CALCULATIONS OF ELECTRONIC STRUCTURE OF H CN ISOMERS J. F. Ogilvie and Feng Wang RECURRENT COMPLEX MODULES INSTEAD OF MOLECULES IN NON-MOLECULAR COMPOUNDS - DESCRIBING AND MODELLING MODULAR INORGANIC STRUCTURES Giovanni Ferraris and Marcella CadoniMODELS FOR ISOMERIC BISPIDINE COMPLEXES - ACCURATE PREDICTION VERSUS THOROUGH UNDERSTANDING Peter Comba and Marion KerscherTHE LIGAND-FIELD PARADIGM: INSIGHT INTO ELECTRONIC PROPERTIES OF TRANSITION-METAL COMPLEXES BASED ON CALCULATIONS OF ELECTRONIC STRUCTURE M. Atanasov, P Comba , C A Daul and F NeeseTHE HOLISTIC MOLECULE J C A Boeyens

Evaluation of adiabatic and nonadiabatic effects from vibration-rotational spectra of LiH X 1Σ+

Abstract We combined radial functions for the rotational g -factor and electric dipole moment, from molecular electronic computations but tested with experimental data, with spectral data of 557 pure rotational and vibration—rotational transitions of LiH in four isotopic variants; on this basis we evaluated separate radial functions related to particular terms in the effective Hamiltonian for adiabatic, nonadiabatic rotational an nonadiabatic vibrational effects of the separate nuclei, in addition to the internuclear potential energy that predominantly determines the wavenumbers of these transitions. The contributions of the former (extra-mechanical) effects to term coefficients defining the energies of vibration—rotational states have comparable magnitudes.

Electric and magnetic molecular properties from analysis of vibration-rotational spectral data of samples measured without applied fields - application to GaH X 1Σ+

Abstract In total 1094 lines of vibration-rotational transitions of 69Ga1H, 71Ga1H, 69Ga2H and 71Ga2H were analyzed to yield the coefficients of radial functions to represent the internuclear potential energy and the adiabatic and nonadiabatic rotational and vibrational effects of the nuclei. From the parameters tGa,H0 that reflect purely the nonadiabatic rotational effects, we show how to estimate the molecular rotational g factor and the electric dipole moment from spectra of samples without the applications of electric and magnetic fields; we apply this method to deduce gJ = −3.22 ± 0.1 for 69Ga1H and elicit information about the magnetic susceptibility of GaH. The maximum range of validity of radial functions of GaH X 1Σ+ is 1.31 ⩽R/10−10 m⩽ 2.36.

Spectra in the vacuum ultraviolet region of CO in gaseous and solid phases and dispersed in solid argon at 10 K

With radiation in the region 104–170 nm from a synchrotron and dispersed with a grating monochromator at spectral resolution 0.02–0.03 nm, we measured absorption spectra of 12C16O in the gaseous phase at 303 K and in the solid phase at 10 K, and dispersed in solid argon at molar ratios Ar:CO = 10, 50 and 250 and at 10 K. We assign observed spectral features to transitions to electronic states A 1Π, B 1Σ+, C 1Σ+ and E 1Π from the ground state X 1Σ+. Vibrational progressions are discernible for all these systems of CO in the gaseous phase, but for only the system A—X for CO in the pure solid phase of CO or a dispersion in solid argon; for all condensed phases, multiple series of features are deducible in this vibrational structure.

Absorption spectra in the vacuum ultraviolet region of small molecules in condensed phases

With radiation from a synchrotron we measured the spectra of several small molecular species, in the solid phase at 10K, either pure--O2, NO, CO2, N2O, H2O and NH3--or, for NH3, also dispersed in Ar at molar ratio 1/250, from the onset of absorption in the ultraviolet region until the limits of transmission by crystalline LiF or solid Ar. In a quantitative treatment of spectral data, we fitted the total absorption profile divided by wavenumber to Gaussian curves of minimal number, and made tentative assignments of electronic transitions and vibrational structure by comparison with spectra of gaseous species. These results illuminate the nature of electronic spectra of samples in solid phases in the vacuum ultraviolet region.

Absorption cross section of molecular oxygen in the transition E 3Σu- v = 0 – X 3Σg- v = 0 at 38 K

Aims. This investigation was undertaken to determine the absorption cross sections of oxygen in the VUV region at temperatures <50 K. Methods. The absorption spectra of gaseous samples cooled with a slit jet and near 300 K were measured with the same absorption system coupled to the VUV beam line of a synchrotron. Results. The maximum absorption cross section for the transition from X 3 Σ − v = 0 to state E 3 Σ − v = 0f or 16 O2 at 38 K was determined to be 98.7 Mb (or 9.87 × 10 −18 cm 2 ). The value of this maximum absorption cross section at 38 K is 1.7 times the value at 303.7 K.

FORMATION AND IDENTIFICATION OF INTERSTELLAR MOLECULE LINEAR C5H FROM PHOTOLYSIS OF METHANE DISPERSED IN SOLID NEON

Photolysis of methane dispersed (1/1000) in solid Ne at 3 K with vacuum-ultraviolet light from a synchrotron produced infrared absorption lines of several products, including new lines at 3319.3 and 1955.5 cm–1. Based on experiments with isotopic labeling and results of quantum-chemical calculations, these lines are assigned to the C-H stretching and C=C stretching modes, respectively, of interstellar molecule linear C5H radicals.

The vibrational g-factor of dihydrogen from theoretical calculation and analysis of vibration-rotational spectra

We present the first results from quantum-chemical calculation of a vibrational g-factor; the calculations were performed at the level of full configuration interaction using a basis set of aug-cc-pVQZ quality. The theoretical results are consistent with experimental results from analysis of pure rotational and vibration-rotational spectra of dihydrogen in six isotopic variants, in which calculated results for either the rotational g-factor or adiabatic corrections are employed to constrain fits of coefficients of radial functions from wave numbers of transitions. When fits are constrained with data for the rotational g-factor, we reproduce also the radial dependence of adiabatic corrections relative to their value at equilibrium internuclear separation.

The Nature of the Chemical Bond 1993

Almost two decades ago a fairly senior biochemist consulted me about the interpretation of optical spectra of simple compounds in the ultraviolet region. After being educated in classical biochemistry in Britain he taught in a relatively isolated institution; he had evidently never become acquainted with the fundaments of quantum chemistry, even to the extent of solving by his own hand the most common such problem, the particle in a one-dimensional box. With the best of intentions he sought however to write a textbook on spectroscopy for students of biochemistry on the grounds that no adequate text existed; without hesitation (or comprehension) he was fully prepared to invoke ‘orbitals’ to explain these spectra and—who knows how many—other phenomena. Although I had previously entertained vague doubts about the conventional description of diverse chemical effects in terms of this panacea, that incident convinced me that the general understanding of quantum chemistry and its relation to macroscopic measurements on chemical, physical and biological systems left much to be desired. During the succeeding fifteen years I collected information from the chemical literature that I cumulatively presented in various lectures around the world; an essay appeared [1] eventually in the Journal of Chemical Education with essentially the same title as that above (apart from the date). That article generated much debate both private and public, according to further papers and letters to the editor of that journal and elsewhere. After a further few years without much improvement of the chronically unsatisfactory general understanding of quantum chemistry and its relationship to various phenomena especially as reflected in the teaching of chemistry, it appears worth while to renew the discussion by means of another explicit attack on ignorance and muddled thinking that the present unsatisfactory conditions in chemical education proclaim still to exist.

Quantum-Chemical Calculations of Radial Functions for Rotational and Vibrational g Factors, Electric Dipolar Moment and Adiabatic Corrections to the Potential Energy for Analysis of Spectra of HeH+

Abstract Computational spectrometry, which implies an interaction between quantum chemistry and analysis of molecular spectra to derive accurate information about molecular properties, is needed for the analysis of the pure rotational and vibration–rotational spectra of HeH + in four isotopic variants to obtain precise values of equilibrium internuclear distance and force coefficient. For this purpose, we have calculated the electronic energy, rotational and vibrational g factors, the electric dipolar moment, and adiabatic corrections for both He and H atomic centres for internuclear distances over a large range 10 −10 m [0.3, 10]. Based on these results we have generated radial functions for atomic contributions for g r , g υ , and adiabatic corrections, involving the coefficients s j He , s j H , t j He , t j H , u j He , and u j H of z  j for 4 He 1 H + for further spectral analysis.