Rui Fausto

Cis→trans conversion of formic acid by dissipative tunneling in solid rare gases: Influence of environment on the tunneling rate

The relaxation of the higher-energy cis conformer of formic acid to the lower-energy trans form by a tunneling mechanism has been investigated in low-temperature rare gas matrices. In the temperature range 8–60 K, the tunneling takes place dominantly from the vibrational ground state of the cis form and the temperature dependence of the tunneling rate constant is influenced by the interactions with the environment. The temperature-dependent tunneling rates for HCOOH and DCOOH in solid Ar, Kr, and Xe are measured including data for molecules in different local environments within each host. It was found that the medium and the local environment has a significant influence on the tunneling rate.

Vibrational spectra of acid and alkaline glycine salts

qy . qy . The infrared and Raman spectra of crystalline acid NH CH COOHP Cl and alkaline Na P NH CH COO 32 2 2 glycine salts were recorded and interpreted. The assignments were confirmed by comparison with the infrared and Raman q y . spectra of crystalline glycine zwitterion, NH CH COO and the infrared spectrum of this molecule isolated in an argon 32 . . matrix at low temperature 10 K neutral form, NH CH COOH . Further insight on the features of the vibrational spectra 22 ) . of these substances was achieved by ab initio HFr6-31G frequency and intensity calculations and potential energy distribution calculations resulting from normal coordinate analysis. q 1998 Elsevier Science B.V. . .

Recent experimental and computational advances in molecular spectroscopy

Preface. Protonation of simple unsaturated organic compounds in their electronic ground and low lying excited states I.G. Czismadia. Application of the CI-singles method in predicting the energy, properties, and reactivity of molecules in their excited states J.B. Foresman, H.B. Schlegel. Molecular structure from rotational and vibrational transitions in electronic spectra J.M. Hollas. From qualitative to quantitative analyses of circular dichroism spectra using the convex constraint algorithm A. Perczel. Potential energy surfaces and vibrational anharmonicity I.M. Mills. Development of an ab initio based database of vibrational force fields for organic molecules P.Pulay, X. Zhou, G. Fogarasi. Computer-aided methods for the resolution enhancement of spectral data with special emphasis on infrared spectra H.H. Mantsch, D.J. Moffatt. Raman spectroscopy: a survey on selected topics J.J.C. Teixeira-Dias. alpha,beta-unsaturated caroxylic esters and their hydrogen bond complexes with substituted phenols: vibrational spectra-structure correlations J.J.C. Teixeira-Dias, R. Fausto. Solvent effect on vibrational frequencies of substituted acetaldehydes T. Varnali, V. Aviyente, B. Terryn, M.F. Ruiz-Lopez. Experimental ab initio quantum mechanical studies of the vibrational spectra of isolated pyrimidine bases W.B. Person, K. Szczepaniak, M. Szczesniak, J.E. Del Bene. Pressure-tuning vibrational spectroscopy: applications from basic molecular spectroscopy to human cancer research P.T.T. Wong. Vibrational spectroscopy of polyconjugated materials with electrical and nonlinear optical properties G. Zerbi. Surface molecular spectroscopy A.M. Bradshaw. Neutron molecular spectroscopy J. Tomkinson. Recent advances in gas electron diffraction and structural studies by joint quantum mechanical and experimental procedures L. Schafer, J.D. Ewbank. Principles of multidimensional high-resolution NMR D.L. Turner. NMR structural techniques in biochemical and bioinorganic systems: paramagnetic shift and relaxation probes C.F.G.C. Geraldes. The physics of an atom in a molecule R.F.W. Bader. Frontier orbital theory and chemical reactivity: the utility of spectroscopy and molecular orbital claculations C. Ogetir, N. Kaniskan. Semiempirical molecular orbital theory: facts, myths and legends T. Clark. The consistent force field: development of potential energy functions for conformational analysis Kj. Rasmussen, S.B. Engelsen, J. Fabricius, B. Rasmussen. Experimental and computational projects on molecular spectroscopy S. Engelsen, J. Fabricius, M. Peterson, P.J.A. Ribeiro-Claro, B.J. Whitaker. Author Index. Subject Index.

Synthesis, characterization and biodistribution of bisphosphonates Sm-153 complexes: correlation with molecular modeling interaction studies

Bisphosphonates (BPs) are characterized by a P-C-P backbone structure and two phosphonic acid groups bonded to the same carbon, and are established as osteoclast-mediated bone resorption inhibitors. The nature of the groups attached to the central carbon atom are responsible in determining the potency of bisphosphonates as anti-resorption drugs. However, it is not yet clear the exact relationship between their molecular structure and pharmacologic activities. In this study, molecular geometries of pamidronate, alendronate and neridronate, differing only in the length of the aliphatic chains, were predicted by molecular mechanics and their interactions with hydroxyapatite, the main bone mineral component, were examined. We report the synthesis and radiochemical characterization of 153Sm complexes with pamidronate, alendronate and neridronate. Hydroxyapatite binding and biodistribution studies of these complexes have shown a good correlation with the theoretical molecular modeling interaction studies. So, it is possible to conclude that computational chemistry techniques are a good approach to evaluate specific interactions and may play a relevant role in determining the relative ability of BPs to mineral bone, and open new perspectives to the design of new BPs with increased pharmacological activity. These techniques could be extended to BPs as ligands to carrier radioactive metals, aiming for new bone therapeutic radiopharmaceuticals.

Vibrational spectroscopy of cis - and trans -formic acid in solid argon

Abstract Absorption spectra of cis and trans conformers of formic acid (HCOOH) isolated in solid argon are analyzed in the mid-infrared (4000– 400 cm −1 ) and near-infrared (7800– 4000 cm −1 ) regions. The HCOOH absorption spectrum reveals matrix-site splitting for the trapped molecule. Narrowband tunable infrared radiation is used to pump a suitable vibrational transition of the trans conformer in order to promote site-selectively the conversion to the cis conformer and separate the spectral features of each site group. Several anharmonic resonances are identified for both conformers. The results of anharmonic vibrational ab initio calculations (CC-VSCF) for the trans and cis conformers of formic acid are reported and compared with the experimental spectra.

Missing conformers. Comparative study of conformational cooling in cyanoacetic acid and methyl cyanoacetate isolated in low temperature inert gas matrixes

Abstract A comparative conformational study of two related systems, methyl cyanoacetate (MCA) and cyanoacetic acid (CAA), is presented. Ab initio calculations predicted that both systems have two nearly isoenergetic conformers separated by similar low energy barriers (about 3 kJ mol −1 ). In xenon matrixes deposited at temperatures above 40 K for MCA and above 20 K for CAA only one conformer was observed for each of the two systems. However, below those temperatures two MCA and two CAA conformers were trapped into the matrixes. Conformational cooling was found responsible for this behavior. Factors contributing to this effect are discussed.

Rotational isomerism of acetic acid isolated in rare-gas matrices: Effect of medium and isotopic substitution on IR-induced isomerization quantum yield and cis→trans tunneling rate

Rotational isomerization of acetic acid (CH3COOH) is studied in Ar, Kr, and Xe matrices. The light-induced trans-->cis reaction is promoted using resonant excitation of a number of modes in the 3500-7000 cm(-1) region, and the quantum yields for this process are measured for various acetic acid isotopologues and matrix materials. For excitation of acetic acid at energies above the predicted isomerization energy barrier (> or =4400 cm(-1)), the measured quantum yields are in average 2%-3%, and this is one order of magnitude smaller than the corresponding values known for formic acid (HCOOH). This difference is interpreted in terms of the presence of the methyl group in acetic acid, which enhances energy relaxation channels competing with the rotational isomerization. This picture is supported by the observed large effect of deuteration of the methyl group on the photoisomerization quantum yield. The trans-->cis reaction quantum yields are found to be similar for Ar, Kr, and Xe matrices, suggesting similar energy relaxation processes for this molecule in the various matrices. The IR-induced cis-->trans process, studied for acetic acid deuterated in the hydroxyl group, shows reliably larger quantum yields as compared with the trans-->cis process. For pumping of acetic acid at energies below the predicted isomerization barrier, the trans-->cis reaction quantum yields decrease strongly when the photon energy decreases, and tunneling is the most probable mechanism for this process. For the cis-->trans dark reaction, the observed temperature and medium effects indicate the participation of the lattice phonons in the tunneling-induced process.

Structure of isolated 1,4-butanediol: combination of MP2 calculations, NBO analysis, and matrix-isolation infrared spectroscopy.

Theoretical calculations at the MP2 level, NBO and AIM analysis, and matrix-isolation infrared spectroscopy have been used to investigate the structure of the isolated molecule of 1,4-butanediol (1,4-BDO). Sixty-five structures were found to be minima on the potential energy surface, and the three most stable forms are characterized by a folded backbone conformation leading to the formation of an intramolecular H-bond. To better characterize the intramolecular interactions and particularly the hydrogen bonds, natural bond orbital analysis (NBO) was performed for the four most stable conformers, and was further complemented with an atoms-in-molecules (AIM) topological analysis. Infrared spectra of 1,4-BDO isolated in low-temperature argon and xenon matrixes show a good agreement with a population-weighted mean theoretical spectrum, and the spectral features of the conformers expected to be trapped in the matrixes were observed experimentally. Annealing the xenon matrix from 20 to 60 K resulted in significant spectral changes, which were interpreted based on the barriers to intramolecular rotation. An estimation of the intramolecular hydrogen bond energy was carried out following three different methodologies.

Formic and acetic acids in a nitrogen matrix: Enhanced stability of the higher-energy conformer

Formic acid (HCOOH, FA) and acetic acid (CH(3)COOH, AA) are studied in a nitrogen matrix. The infrared (IR) spectra of cis and trans conformers of these carboxylic acids (and also of the HCOOD isotopologue of FA) are reported and analyzed. The higher-energy cis conformer of these molecules is produced by narrowband near-IR excitation of the more stable trans conformer, and the cis-to-trans tunneling decay is evaluated spectroscopically. The tunneling process in both molecules is found to be substantially slower in a nitrogen matrix than in rare-gas matrices, the cis-form decay constants being approximately 55 and 600 times smaller in a nitrogen matrix than in an argon matrix, for FA and AA respectively. The stabilization of the higher-energy cis conformer is discussed in terms of specific interactions with nitrogen molecule binding with the OH group of the carboxylic acid. This model is in agreement with the observed differences in the IR spectra in nitrogen and argon matrices, in particular, the relative frequencies of the νOH and τCOH modes and the relative intensities of the νOH and νC=O bands.

Low temperature molecular spectroscopy

Spectroscopy of Matrix Isolated Molecules. 1. Principles, Procedures and Pitfalls A.J. Downs. Spectroscopy of Matrix Isolated Molecules. 2. Applications: Pointing the Way to Synthesis and Mechanisms in Inorganic and Organometallic Chemistry A.J. Downs. Matrix Photochemistry of Transition Metal Complexes: Principles, Applications and Links to Other Methods R.N. Perutz. Conformational Isomerism and Photodecomposition of Carboxylic Compounds Studied by Matrix Isolation Infrared Spectroscopy R. Fausto. Combined Matrix-Isolation FT-IR and ab initio 6-31++G** Studies on the Tautomerism and H- Bonding Properties of Nucleic Acid Bases and Simpler Model Molecules G.H. Maes, et al. Low Temperature Spectroscopy: From Ground to Space. The Case of the Diffuse Interstellar Bands F. Salama. Association Between Electron Donor Molecules and HCl in Argon Matrices W.O. George, D.A. Williams. Matrix Perturbation of Vibrational Isotope Effects R.L. Redington. Heavy Atom Effects in Proton Tunneling Phenomena R.L. Redington. The Cooling of Internal Degrees of Freedom of Polyatomic Molecules in Supersonic Free Jets R. Jost. Pulsed Nozzle Fourier Transform Microwave Spectroscopy of Weakly Bound Molecular Complexes A. Bauder. Structure and Dynamics of Van der Waals Complexes A. Bauder. Large Amplitude Vibrations in Electronic Spectra in Supersonic Jets J.M. Hollas. Conformational Analysis by Laser Spectroscopy D.W. Pratt. Infrared Spectroscopy in Liquefied Noble Gases B.J. Van der Veken. Tunneling Spectroscopy with Neutrons: Quantised Rotational States in Solids J. Tomkinson. The Symmetry of Molecules and Molecular Vibrations B. Schrader. Phonon Modes of Molecular Crystals D.T. Durig, J.R. Durig. Spectra of Plastic and Disordered Crystals J.R. Durig, D.T. Durig. Conformational Studies by Vibrational Spectroscopy Under High Pressure P. Klaeboe. NIR FT Raman Spectroscopy: Finding the Optimal Conditions to Record Spectra of Living Systems B. Schrader. Using Low Temperature Spectroscopy to Understand Protein Structure, Dynamics and Function P.R. Carey. Reflection Absorption Infrared Spectroscopy at Low Temperatures W.A. Brown, P. Gardner.