Effect of hydrogen bond formation on the elastic molecular scattering: a case study with methanol

Rayleigh optical activities of small hydrogen-bonded methanol clusters containing two to five molecules are reported. For the methanol trimer, tetramer, and pentamer both cyclic and linear structures are considered. After the geometry optimizations, the dipole moments and the dipole polarizabilities (mean, interaction, and anisotropic components) are calculated using HF, MP2 and DFT (B3LYP, B3P86 and BH&HLYP) with aug-cc-pVDZ extended basis set. The polarizabilities are used to analyse the depolarization ratios and the Rayleigh scattering activities. The variations in the activity and in the depolarization for Rayleigh scattered radiation with the increase in the cluster size for both cyclic and linear structures are analysed.

Accurate ab initio potential energy surfaces for the (3)A '' and (3)A ' electronic states of the O(P-3) plus HBr system

In this work, we report the construction of potential energy surfaces for the (3)A '' and (3)A' states of the system O(P-3) + HBr. These surfaces are based on extensive ab initio calculations employing the MRCI+Q/CBS+SO level of theory. The complete basis set energies were estimated from extrapolation of MRCI+Q/aug-cc-VnZ(-PP) (n = Q, 5) results and corrections due to spin-orbit effects obtained at the CASSCF/aug-cc-pVTZ(-PP) level of theory. These energies, calculated over a region of the configuration space relevant to the study of the reaction O(P-3) + HBr -> OH + Br, were used to generate functions based on the many-body expansion. The three-body potentials were interpolated using the reproducing kernel Hilbert space method. The resulting surface for the (3)A '' electronic state contains van der Waals minima on the entrance and exit channels and a transition state 6.55 kcal/mol higher than the reactants. This barrier height was then scaled to reproduce the value of 5.01 kcal/mol, which was estimated from coupled cluster benchmark calculations performed to include high-order and core-valence correlation, as well as scalar relativistic effects. The (3)A' surface was also scaled, based on the fact that in the collinear saddle point geometry these two electronic states are degenerate. The vibrationally adiabatic barrier heights are 3.44 kcal/mol for the (3)A '' and 4.16 kcal/mol for the (3)A' state. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.4705428]

Hydrogen bond and the resonance effect on the formamide-water complexes

The interaction of formamide and the two transition states of its amide group rotation with one, two, or three water molecules was studied in vacuum. Great differences between the electronic structure of formamide in its most stable form and the electronic structure of the transition states were noticed. Intermolecular interactions were intense, especially in the cases where the solvent interacted with the amide and the carbonyl groups simultaneously. In the transition states, the interaction between the lone pair of nitrogen and the water molecule becomes important. With the aid of the natural bond orbitals, natural resonance theory, and electron localization function (ELF) analyses an increase in the resonance of planar formamide with the addition of successive water molecules was observed. Such observation suggests that the hydrogen bonds in the formamidewater complexes may have some covalent character. These results are also supported by the quantitative ELF analyses. (C) 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012

Spectroscopic, Structural, and Conformational Properties of (Z)-4,4, 4-Trifluoro-3-(2-hydroxyethylamino)-1-(2-hydroxypheny1)-2-buten-1-one, C12H12F3NO3: A Trifluoromethyl-Substituted beta-Aminoenone

The ( Z)-4,4,4-trifluoro-3-(2-hydroxyethylamino)-1-(2-hydroxyphenyl)-2-buten-1-one (C12H12F3NO3) compound was thoroughly studied by IR, Raman, UV-visible, and C-13 and F-19 NMR spectroscopies. The solid-state molecular structure was determined by X-ray diffraction methods. It crystallizes in the P2(1)/c space group with a = 12.1420(4) angstrom, b = 7.8210(3) angstrom, c := 13.8970(5) angstrom, beta = 116.162(2)degrees, and Z = 4 molecules per unit cell. The molecule shows a nearly planar molecular skeleton, favored by intramolecular OH center dot center dot center dot 0 and NH center dot center dot center dot 0 bonds, which are arranged in the lattice as an OH center dot center dot center dot 0 bonded polymer coiled around crystallographic 2-fold screw-axes. The three postulated tautomers were evaluated using quantum chemical calculations. The lowest energy tautomer (I) calculated with density functional theory methods agrees with the observed crystal structure. The structural and conformational properties are discussed considering the effect of the intra- and intermolecular hydrogen bond interactions.

Insights into Phosphate Cooperativity and Influence of Substrate Modifications on Binding and Catalysis of Hexameric Purine Nucleoside Phosphorylases

The hexameric purine nucleoside phosphorylase from Bacillus subtilis (BsPNP233) displays great potential to produce nucleoside analogues in industry and can be exploited in the development of new anti-tumor gene therapies. In order to provide structural basis for enzyme and substrates rational optimization, aiming at those applications, the present work shows a thorough and detailed structural description of the binding mode of substrates and nucleoside analogues to the active site of the hexameric BsPNP233. Here we report the crystal structure of BsPNP233 in the apo form and in complex with 11 ligands, including clinically relevant compounds. The crystal structure of six ligands (adenine, 2'deoxyguanosine, aciclovir, ganciclovir, 8-bromoguanosine, 6-chloroguanosine) in complex with a hexameric PNP are presented for the first time. Our data showed that free bases adopt alternative conformations in the BsPNP233 active site and indicated that binding of the co-substrate (2'deoxy) ribose 1-phosphate might contribute for stabilizing the bases in a favorable orientation for catalysis. The BsPNP233-adenosine complex revealed that a hydrogen bond between the 5' hydroxyl group of adenosine and Arg(43*) side chain contributes for the ribosyl radical to adopt an unusual C3'-endo conformation. The structures with 6-chloroguanosine and 8-bromoguanosine pointed out that the Cl-6 and Br-8 substrate modifications seem to be detrimental for catalysis and can be explored in the design of inhibitors for hexameric PNPs from pathogens. Our data also corroborated the competitive inhibition mechanism of hexameric PNPs by tubercidin and suggested that the acyclic nucleoside ganciclovir is a better inhibitor for hexameric PNPs than aciclovir. Furthermore, comparative structural analyses indicated that the replacement of Ser(90) by a threonine in the B. cereus hexameric adenosine phosphorylase (Thr(91)) is responsible for the lack of negative cooperativity of phosphate binding in this enzyme.

High Viscosity of Imidazolium Ionic Liquids with the Hydrogen Sulfate Anion: A Raman Spectroscopy Study

Ionic liquids based on 1-alkyl-3-methylimidazolium cations and the hydrogen sulfate (or bisulfate) anion, HSO4-, are much more viscous than ionic liquids with alkyl sulfates, RSO4-. The structural origin of the high viscosity of HSO4- ionic liquids is unraveled from detailed comparison of the anion Raman bands in 1-ethyl-3-methylimidazolium hydrogen sulfate and 1-butyl-3-methylimidazolium hydrogen sulfate with available data for simple HSO(4)(-) salts in crystalline phase, molten phase, and aqueous solution. Two Raman bands at 1046 and 1010 cm(-1) have been assigned as symmetric stretching modes nu(s)(S = O) of HSO4-, the latter being characteristic of chains of hydrogen-bonded anions. The intensity of this component increases in the supercooled liquid phase. For comparison purposes, Raman spectra of 1-ethyl-3-methylimidazolium ethyl sulfate and 1-butyl-3-methylimidazolium methyl sulfate have been also obtained. There is no indication of difference in the strength of hydrogen bond interactions of imidazolium cations with HSO4- or RSO4- anions. Raman spectra at high pressures, up to 2.6 GPa, are also discussed. Raman spectroscopy provides evidence that hydrogen-bonded anions resulting in anion-anion interaction is the reason for the high viscosity of imidazolium ionic liquids with HSO4-. If the ionic liquid is exposed to moisture, these structures are disrupted upon absorption of water from the atmosphere.

Electron collisions with the HCOOH...(H2O)n (n=1, 2 and 3) complexes in liquid phase: the influence on the π* shape resonance of formic acid

In this conference we report cross sections for elastic collisions of low-energy electrons with the HCOOH…(H2O)n complexes, with n = 1, 2 and 3. The scattering cross sections were computed with the Schwinger multichannel method [K. Takatsuka and V. McKoy, Phys. Rev. A 24 , 2473 (1981); Phys. Rev. A 30 , 1734 (1984)] with pseudopotentials [M. H. F. Bettega, L. G. Ferreira, and M. A. P. Lima, Phys. Rev. A 47, 1111 (1993)] in the static-exchange and static-exchange plus polarization approximations, for energies from 0.5 eV to 6 eV. We considered some diÆerent hydrogen-bonded structures for the complexes that were generated with classical Monte Carlo simulations [K. Coutinho and S. Canuto, J. Chem. Phys. 113, 9132, (2000)]. The aim of this work is to investigate the effect of the surrounding water molecules on the π* shape resonance of the solute. Previous theoretical and experimental studies carried out in the gas phase reported a π* state for HCOOH at around 1.9 eV. For the n = 1 case and for all complexes, the stabilization of the resonance was observed (it appears at lower energy compared to the value obtained in the gas phase), as reported previously for the CH2O…H2O complexes [T. C. Freitas, M. A. P. Lima, S. Canuto, and M. H. F. Bettega, Phys. Rev. A 80, 062710 (2009)]. This result indicates that the presence of the solvent may affect the processes related to the π* state, such as the molecular dissociation by electron impact. For the n = 2 case we have observed both stabilization and destabilization of the π* resonance, that is associated with the hydrogen bond donor or acceptor role of the water molecules in the complexes. For the n = 3 case, preliminary static-exchange results show the stabilization of the π* state. We propose an explanation of the stabilization/destabilization of the π* state in terms of the polarization of the solute due to the surrounding water molecules and the net charge in the solute.

Dissociative electron attachment to chloromethane.

A low energy electron may attach to a molecule, forming a metastable resonance, which may dissociate into a stable anion and a neutral radical. Chloromethane has been a good target for dissociative electron attachment studies, since it is a small molecule with a clear dissociative ‘sigma*’ shape resonance. We present potential energy curves for CH3Cl and its anion, as a function of the C-Cl distance. Due to the resonant nature of the anion, a correct description requires a treatment based on scattering calculations. In order to compute elastic cross sections and phase shifts we employed the Schwinger multichannel method, implemented with pseudopotentials of Bachelet, Hamann and Schlüter, at the static-exchange plus polarization approximation. At the equilibrium geometry, the resonance was found arround 3.3 eV, in accordance to experience. The incoming electron is captured by a ‘sigma*’ orbital located at the C-Cl bond, which will relax in the presence of this extra electron. We took this bond as the reaction coordinate, and performed several scattering calculations for a series of nuclear conformations. The phase shift obtained in each calculation was fitted by a two component function, consisting in the usual Breit-Wigner profile, which captures the resonant character, and a second order polynomial in the wave number, which accounts for the background contribution. That way, we obtained position and width of the resonance, which allowed us to build the potential energy curve. For larger distances, the anion becomes stable and usual electronic structure calculations suffice. Furthermore, the existence of a dipole-bound anion state is revealed when we employed a set of very diffuse functions. The knowledge on the behaviour of the neutral and anionic electronic states helps us in elucidating how the dissociation takes place.