Organisation moléculaire dirigée par le groupe CONH2 en 2D et 3D

Notre étude a pour objet la conception, la synthèse ainsi que l’étude structurale d’architectures supramoléculaires obtenues par auto-assemblage, en se basant sur les concepts de la tectonique moléculaire. Cette branche de la chimie supramoléculaire s’occupe de la conception et la synthèse de molécules organiques appelées tectons, du grec tectos qui signifie constructeur. Le tecton est souvent constitué de sites de reconnaissance branchés sur un squelette bien choisi. Les sites de reconnaissance orientés par la géométrie du squelette peuvent participer dans des interactions intermoléculaires qui sont suffisamment fortes et directionnelles pour guider la topologie du cristal résultant. La stratégie envisagée utilise des processus d'auto-assemblage engageant des interactions réversibles entre les tectons. L’auto-assemblage dirigé par de fortes interactions intermoléculaires directionnelles est largement utilisé pour fabriquer des matériaux dont les composants doivent être positionnés en trois dimensions (3D) d'une manière prévisible. Cette stratégie peut également être utilisée pour contrôler l’association moléculaire en deux dimensions (2D), ce qui permet la construction de monocouches organisées et prédéterminées sur différents types des surfaces, tels que le graphite.Notre travail a mis l’accent sur le comportement de la fonction amide comme fonction de reconnaissance qui est un analogue du groupement carboxyle déjà utilisé dans plusieurs études précédentes. Nous avons étudié le comportement d’une série de composés contenant un noyau plat conçu pour faciliter l'adsorption sur le graphite et modifiés par l'ajout de groupes amide pour favoriser la formation de liaisons hydrogène entre les molécules ainsi adsorbées. La capacité de ces composés à former de monocouches organisées à l’échelle moléculaire en 2D a été examinée par microscopie à effet tunnel, etleur organisation en 3D a également été étudiée par cristallographie aux rayons X. Dans notre étude, nous avons systématiquement modifié la géométrie moléculaire et d'autres paramètres afin d'examiner leurs effets sur l'organisation moléculaire. Nos résultats suggèrent que les analyses structurales combinées en 2D et 3D constituent un important atout dans l'effort pour comprendre les interactions entre les molécules adsorbées et l’effet de l’interaction avec la surface du substrat.

Basis set superposition error-counterpoise corrected potential energy surfaces : application to hydrogen peroxide ... X (X=F-, Cl-, Br-, Li+, Na+) complexes

Møller-Plesset (MP2) and Becke-3-Lee-Yang-Parr (B3LYP) calculations have been used to compare the geometrical parameters, hydrogen-bonding properties, vibrational frequencies and relative energies for several X- and X+ hydrogen peroxide complexes. The geometries and interaction energies were corrected for the basis set superposition error (BSSE) in all the complexes (1-5), using the full counterpoise method, yielding small BSSE values for the 6-311 + G(3df,2p) basis set used. The interaction energies calculated ranged from medium to strong hydrogen-bonding systems (1-3) and strong electrostatic interactions (4 and 5). The molecular interactions have been characterized using the atoms in molecules theory (AIM), and by the analysis of the vibrational frequencies. The minima on the BSSE-counterpoise corrected potential-energy surface (PES) have been determined as described by S. Simón, M. Duran, and J. J. Dannenberg, and the results were compared with the uncorrected PES

Density functional energy decomposition into one- and two-atom contributions

The present work provides a generalization of Mayer's energy decomposition for the density-functional theory (DFT) case. It is shown that one- and two-atom Hartree-Fock energy components in Mayer's approach can be represented as an action of a one-atom potential VA on a one-atom density ρ A or ρ B. To treat the exchange-correlation term in the DFT energy expression in a similar way, the exchange-correlation energy density per electron is expanded into a linear combination of basis functions. Calculations carried out for a number of density functionals demonstrate that the DFT and Hartree-Fock two-atom energies agree to a reasonable extent with each other. The two-atom energies for strong covalent bonds are within the range of typical bond dissociation energies and are therefore a convenient computational tool for assessment of individual bond strength in polyatomic molecules. For nonspecific nonbonding interactions, the two-atom energies are low. They can be either repulsive or slightly attractive, but the DFT results more frequently yield small attractive values compared to the Hartree-Fock case. The hydrogen bond in the water dimer is calculated to be between the strong covalent and nonbonding interactions on the energy scale

Analysing the ability to retain sidechain hydrogen-bonds in mutant proteins

Motivation: Hydrogen bonds are one of the most important inter-atomic interactions in biology. Previous experimental, theoretical and bioinformatics analyses have shown that the hydrogen bonding potential of amino acids is generally satisfied and that buried unsatisfied hydrogen-bond-capable residues are destabilizing. When studying mutant proteins, or introducing mutations to residues involved in hydrogen bonding, one needs to know whether a hydrogen bond can be maintained. Our aim, therefore, was to develop a rapid method to evaluate whether a sidechain can form a hydrogen-bond. Results: A novel knowledge-based approach was developed in which the conformations accessible to the residues involved are taken into account. Residues involved in hydrogen bonds in a set of high resolution crystal structures were analyzed and this analysis is then applied to a given protein. The program was applied to assess mutations in the tumour-suppressor protein, p53. This raised the number of distinct mutations identified as disrupting sidechain-sidechain hydrogen bonding from 181 in our previous analysis to 202 in this analysis.

Infrared study of intercomponent interactions in a switchable hydrogen-bonded rotaxane

The macrocycle in rotaxane 1 is preferentially hydrogen bonded to the succinamide station in the neutral form, but can be moved to the naphthalimide station by one-electron reduction of the latter. The hydrogen bonding between the amide NH groups of the macrocycle and the C=O groups in the binding stations in the thread was studied with IR spectroscopy in different solvents in both states. In addition, the solvent effect on the vibrational frequencies was analyzed; a correlation with the solvent acceptor number (AN) was observed. The conformational switching upon reduction could be detected by monitoring the hydrogen-bond-induced shifts of the v(CO) frequencies of the C=O groups of the succinamide and the reduced naphthalimide stations. The macrocycle was found to shield the encapsulated station from the solvent: wavenumbers of v(CO) bands of the C=O groups residing inside the macrocycle cavity remain unaffected by the solvent polarity.

C-H...O hydrogen bonding in 4-phenyl-benzaldehyde: a comprehensive crystallographic, spectroscopic and computational study

The crystal structure of 4-phenyl-benzaldehyde reveals the presence of a dimer linked by the C=O and C( 9)-H groups of adjacent molecules. In the liquid phase, the presence of C-(HO)-O-... bonded forms is revealed by both vibrational and NMR spectroscopy. A Delta H value of - 8.2 +/- 0.5 kJ mol(-1) for the dimerisation equilibrium is established from the temperature-dependent intensities of the bands assigned to the carbonyl-stretching modes. The NMR data suggest the preferential engagement of the C(2,6)-H and C(10/12)/C(11)-H groups as hydrogen bond donors, instead of the C(9)-H group. While ab initio calculations for the isolated dimers are unable to corroborate these NMR results, the radial distribution functions obtained from molecular dynamics simulations show a preference for C(2,6)-H and C(10/12)/C(11)-(HO)-O-... contacts relative to the C(9)-(HO)-O-... ones.

Spectroscopic and theoretical studies of some N-methoxy-N-methyl-2-[(4 `-substituted) phenylthio]propanamides

The analysis of the IR carbonyl band of the N-methoxy-N-methyl-2-[(4`-substituted)phenylthio]propanamides Y-PhSCH(Me)C(O)N(OMe)Me (Y=OMe 1, Me 2, H 3, Cl 4, NO(2) 5), supported by B3LYP/cc-pVDZ calculations of 3, indicated the existence of two gauche conformers (g(1) and g(2)), the g(1) conformer being the more stable and the less polar one (in gas phase and in solution). Both conformers are present in solution of the polar solvents (CH(2)Cl(2) and CH(3)CN) for 1-5 and in solution of the less polar solvent (CHCl(3)) for 1-4, while only the g(1) conformer is present in solution of non polar solvents (n-C(6)H(14) and CCl(4)) and in solution of CHCl(3) for 5. NBO analysis shows that both the sigma(C-S) -> pi*(C=O) (hyperconjugative) and the pi(C=O) -> sigma*(C-S) orbital interactions contribute almost to the same extent for the stabilization of g(1) and g(2) conformers. The pi*(C=O) -> sigma*(C-S), n(S) -> pi*(C=O) and the n(S) -> pi*(C=O) orbital interactions stabilize more the g(1) conformer than the g(2) one. Moreover, the suitable geometry of the g(1) conformer leads to its stabilization through the LP(O2) -> sigma*(C8-H11) orbital interaction (hydrogen bond) along with the strong O([CO])(delta-) center dot center dot center dot H([O-Ph])(delta+) electrostatic interaction. On the other hand, the appropriate geometry of the g(2) conformer leads to its stabilization by the LP(O22) -> sigma*(C9-H13) orbital interaction (hydrogen bond) along with the weak O([OMe])(delta-) center dot center dot center dot H([o`-Ph])(delta+) electrostatic static interaction. As for the 4`-nitro derivative 5 the ortho-phenyl hydrogen atom becomes more acidic, leading to a stronger O([CO])(delta-) center dot center dot center dot H([o-Ph])(delta+) interaction and, thus, into a larger stabilization of the g(1) conformer in the whole series. This trend is responsible for the unique IR carbonyl band in CHCl(3) solution of 5. The larger occupancy of the pi*(C=O) orbital of the g(1) conformer relative to that of the g(2) conformer, along with the O([CO])(delta-) center dot center dot center dot H([o-Ph])(delta+) electrostatic interaction (hydrogen bond) justifies the lower carbonyl frequency of the g(1) conformer with respect to the g(2) one, in gas phase and in solution. (C) 2008 Elsevier B.V. All rights reserved.

Synthesis, spectral studies and X-ray crystal structure of N,N `-(+/-)-trans-1,2-cyclohexylenebis(3-ethoxysalicylideneamine) H-2(t-3-EtOsalchxn)

The synthesis, spectra and X-ray crystal structure of N,N`-(+/-)-trans-1,2-cyclohexylenebis(3-ethoxysalicylideneamine) H-2(t-3-EtOsalchxn), a salen-type ligand, are reported. The Schiff base was characterized by elemental analysis, m.p., IR, electronic spectra, H-1 and C-13 NMR spectra. The spectra are discussed and compared with those of N,N`-(+/-)-trans-1,2-cyclohexylenebis(salicylideneamine), H-2(t-salchxn). The electronic and IR spectra were also resolved by deconvolution. The influence of the ethoxy group on the IR, electronic spectrum, H-1 and C-13 NMR spectra is discussed. Strong intramolecular forces are present as supported by the IR and H-1 NMR spectra and the X-ray crystal structure. An intermolecular hydrogen bond is observed and appears twice in a pair of molecules in the unit cell. (c) 2007 Elsevier B.V. All rights reserved.

C-H center dot center dot center dot O and N-H center dot center dot center dot O hydrogen bonds in liquid amides investigated by Monte Carlo simulation

Monte Carlo simulations of liquid formamide, N-methylformamide (MF), and N,N-dimethylformamide (DMF) have been performed in the isothermal and isobaric ensemble at 298 K and 1 atm, aiming to investigate the C-H ... O and N-H ... O hydrogen bonds. The interaction energy was calculated using the classical 6-12 Lennard-Jones pairwise potential plus a Coulomb term on a rigid six-site molecular model with the potential parameters being optimized in this work. Theoretical values obtained for heat of vaporization and liquid densities are in good agreement with the experimental data. The radial distribution function [RDF, g(r)] obtained compare well with R-X diffraction data available. The RDF and molecular mechanics (MM2) minimization show that the C-H ... O interaction has a significant role in the structure of the three liquids. These results are supported by ab initio calculations. This Interaction is particularly important in the structure of MF. The intensity of the N-H ... O hydrogen bond is greater in the MF than formamide. This could explain some anomalous properties verified in MF. (C) 1997 John Wiley & Sons, Inc.

Trichloro-bridged diruthenium (III,III) complexes: X-ray isomorphous structures of [Ph3X=O center dot center dot center dot H center dot center dot center dot O=XPh3][Ru2Cl7(XPh3)(2)]center dot 0.5(CH2Cl2)(H2O)(X = As or P)

The triply chloro-bridged binuclear complexes [Ph3X=O...H...O=XPh3][Ru2Cl7(XPh3)(2)].0.5(CH2Cl2) (H2O) (X = As or P) were obtained from [RuCl3(XPh3)(2)DMA].DMA (DMA = dimethylacetamide) CH2Cl2/Et2O solution. The structures were characterized by X-ray diffraction studies. The complexes are formed from two Ru atoms bridged by three chloride anions. The two ruthenium atoms are also coordinated to two non-bridging Cl atoms and an AsPh3 or PPh3 ligand respectively. As an interesting feature, the cations of these complexes are protons, trapped in a very short hydrogen bond between two triphenylarsine or triphenylphosphine oxide molecules.

Active and exo-site inhibition of human factor Xa: Structure of des-Gla factor Xa inhibited by NAP5, a potent nematode anticoagulant protein from Ancylostoma caninum

Hookworms are hematophagous nematodes capable of growth, development and subsistence in living host systems such as humans and other mammals. Approximately one billion, or one in six, people worldwide are infected by hookworms causing gastrointestinal blood loss and iron deficiency anemia. The hematophagous hookworm Ancylostoma caninum produces a family of small, disulfide-linked protein anticoagulants (75-84 amino acid residues). One of these nematode anticoagulant proteins, NAP5, inhibits the amidolytic activity of factor Xa (fXa) with K-i = 43 pM, and is the most potent natural fXa inhibitor identified thus far. The crystal structure of NAP5 bound at the active site of gamma-carboxyglutamic acid domainless factor Xa (des-fXa) has been determined at 3.1 angstrom resolution, which indicates that Asp189 (fXa, S1 subsite) binds to Arg40 (NAP5, P1 site) in a mode similar to that of the BPTI/trypsin interaction. However, the hydroxyl group of Ser39 of NAP5 additionally forms a hydrogen bond (2.5 angstrom) with His57 NE2 of the catalytic triad, replacing the hydrogen bond of Ser195 OG to the latter in the native structure, resulting in an interaction that has not been observed before. Furthermore, the C-terminal extension of NAP5 surprisingly interacts with the fXa exosite of a symmetry-equivalent molecule forming a short intermolecular beta-strand as observed in the structure of the NAPc2/fXa complex. This indicates that NAP5 can bind to fXa at the active site, or the exosite, and to fX at the exosite. However, unlike NAPc2, NAP5 does not inhibit fVIIa of the fVIIa/TF complex. (c) 2007 Elsevier Ltd. All rights reserved.

C - H ⋯ 0 and N - H ⋯ 0 hydrogen bonds in liquid amides investigated by monte carlo simulation

Monte Carlo simulations of liquid formamide, N-methylformamide (MF), and N, N-dimethytformamide (DMF) have been performed in the isothermal and isobaric ensemble at 298 K and 1 atm, aiming to investigate the C-H ⋯ O and N-H ⋯ O hydrogen bonds. The interaction energy was calculated using the classical 6-12 Lennard-Jones pairwise potential plus a Coulomb term on a rigid six-site molecular model with the potential parameters being optimized in this work. Theoretical values obtained for heat of vaporization and liquid densities are in good agreement with the experimental data. The radial distribution function [RDF, g(r)] obtained compare well with R-X diffraction data available. The RDF and molecular mechanics (MM2) minimization show that the C-H ⋯ O interaction has a significant role in the structure of the three liquids. These results are supported by ab initio calculations. This interaction is particularly important in the structure of MF. The intensity of the N - H ⋯ O hydrogen bond is greater in the MF than formamide. This could explain some anomalous properties verified in MF. © 1997 John Wiley & Sons, Inc.

Structure and weak hydrogen bonds in liquid acetaldehyde

Monte Carlo simulations have been performed to investigate the structure and hydrogen bonds formation in liquid acetaldehyde. An all atom model for the acetaldehyde have been optimized in the present work. Theoretical values obtained for heat of vaporisation and density of the liquid are in good agreement with experimental data. Graphics of radial distribution function indicate a well structured liquid compared to other similar dipolar organic liquids. Molecular mechanics minimization in gas phase leads to a trimer of very stable structure. The geometry of this complex is in very good agreement with the rdf. The shortest site-site correlation is between oxygen and the carbonyl hydrogen, suggesting that this correlation play a important role in the liquid structure and properties. The O⋯H average distance and the C-H⋯O angle obtained are characteristic of weak hydrogen bonds.

A hybrid neutron diffraction and computer simulation study on the solvation of N-methylformamide in dimethylsulfoxide

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Nano- and macroscale structural and mechanical properties of in situ synthesized bacterial cellulose/PEO-b-PPO-b-PEO biocomposites

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)