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.

Potential energy surface and moleculardynamics of MbNO: existence of an unsuspected FeON minimum

Ligands such as CO, O2, or NO are involved in the biological function of myoglobin. Here we investigate the energetics and dynamics of NO interacting with the Fe(II) heme group in native myoglobin using ab initio and molecular dynamics simulations. At the global minimum of the ab initio potential energy surface (PES), the binding energy of 23.4 kcal/mol and the Fe-NO structure compare well with the experimental results. Interestingly, the PES is found to exhibit two minima: There exists a metastable, linear Fe-O-N minimum in addition to the known, bent Fe-N-O global minimum conformation. Moreover, the T-shaped configuration is found to be a saddle point, in contrast to the corresponding minimum for NO interacting with Fe(III). To use the ab initio results for finite temperature molecular dynamics simulations, an analytical function was fitted to represent the Fe-NO interaction. The simulations show that the secondary minimum is dynamically stable up to 250 K and has a lifetime of several hundred picoseconds at 300 K. The difference in the topology of the heme-NO PES from that assumed previously (one deep, single Fe-NO minimum) suggests that it is important to use the full PES for a quantitative understanding of this system. Why the metastable state has not been observed in the many spectroscopic studies of myoglobin interacting with NO is discussed, and possible approaches to finding it are outlined.

Self-assembled molecular complexes and coordination polymers of CdII, hexamine, and monocarboxylates: structural analysis and theoretical studies of supramolecular interactions

Four new cadmium(II) complexes [Cd-2(bz)(4)(H2O)(4)(mu 2-hmt)]center dot Hbz center dot H2O (1), [Cd-3(bz)(6)(H2O)(6)(mu 2-hmt)(2)]center dot 6H(2)O (2), [Cd(pa)(2)(H2O)(mu(2)-hmt)](n) (3), and {[Cd-3(ac)(6)(H2O)(3)(mu(3)-hmt)(2)]center dot 6H(2)O}(n) (4) with hexamine (hmt) and monocarboxylate ions, benzoate (bz), phenylacetate (pa), or acetate (ac) have been synthesized and characterized structurally. Structure determinations reveal that 1 is dinuclear, 2 is trinuclear, 3 is a one-dimensional (1D) infinite chain, and 4 is a two-dimensional (2D) polymer with fused hexagonal rings consisting of Cd-II and hmt. All the Cd-II atoms in the four complexes (except one CdII in 2) possess seven-coordinate pentagonal bipyramidal geometry with the various chelating bidentate carboxylate groups in equatorial sites. One of the CdII ions in 2, a complex that contains two monodentate carboxylates is in a distorted octahedral environment. The bridging mode of hmt is mu 2- in complexes 1-3 but is mu 3- in complex 4. In all complexes, there are significant numbers of H-bonds, C-H/pi, and pi-pi interactions which play crucial roles in forming the supramolecular networks. The importance of the noncovalent interactions in terms of energies and geometries has been analyzed using high level ab initio calculations. The effect of the cadmium coordinated to hmt on the energetic features of the C-H/pi interaction is analyzed. Finally, the interplay between C-H/pi and pi-pi interactions observed in the crystal structure of 3 is also studied.

Repulsion-induced surface-migration, by ballistics and bounce

The motion of adsorbate molecules across surfaces is fundamental to self-assembly, material growth, and heterogeneous catalysis. Recent Scanning Tunneling Microscopy studies have demonstrated the electron-induced long-range surface-migration of ethylene, benzene, and related molecules, moving tens of Angstroms across Si(100). We present a model of the previously unexplained long-range recoil of chemisorbed ethylene across the surface of silicon. The molecular dynamics reveal two key elements for directed long-range migration: first ‘ballistic’ motion that causes the molecule to leave the ab initio slab of the surface traveling 3–8 Å above it out of range of its roughness, and thereafter skipping-stone ‘bounces’ that transport it further to the observed long distances. Using a previously tested Impulsive Two-State model, we predict comparable long-range recoil of atomic chlorine following electron-induced dissociation of chlorophenyl chemisorbed at Cu(110)

Molecular insights of p47phox phosphorylation dynamics in the regulation of NADPH oxidase activation and superoxide production

Phagocyte superoxide production by a multicomponent NADPH oxidase is important in host defense against microbial invasion. However inappropriate NADPH oxidase activation causes inflammation. Endothelial cells express NADPH oxidase and endothelial oxidative stress due to prolonged NADPH oxidase activation predisposes many diseases. Discovering the mechanism of NADPH oxidase activation is essential for developing novel treatment of these diseases. The p47phox is a key regulatory subunit of NADPH oxidase; however, due to the lack of full protein structural information, the mechanistic insight of p47phox phosphorylation in NADPH oxidase activation remains incomplete. Based on crystal structures of three functional domains, we generated a computational structural model of the full p47phox protein. Using a combination of in silico phosphorylation, molecular dynamics simulation and protein/protein docking, we discovered that the C-terminal tail of p47phox is critical for stabilizing its autoinhibited structure. Ser-379 phosphorylation disrupts H-bonds that link the C-terminal tail to the autoinhibitory region (AIR) and the tandem Src homology 3 (SH3) domains, allowing the AIR to undergo phosphorylation to expose the SH3 pocket for p22phox binding. These findings were confirmed by site-directed mutagenesis and gene transfection of p47phox_/_ coronary microvascular cells. Compared with wild-type p47phoxcDNAtransfected cells, the single mutation of S379A completely blocked p47phox membrane translocation, binding to p22phox and endothelial O2 . production in response to acute stimulation of PKC. p47phox C-terminal tail plays a key role in stabilizing intramolecular interactions at rest. Ser-379 phosphorylation is a molecular switch which initiates p47phox conformational changes and NADPH oxidase-dependent superoxide production by cells.

Excited state electronic polarization and reappraisal of the n <- pi* emission of acetone in water

Electronic polarization of the acetone molecule in the excited n -> pi* state is considered and its influence on the solvent shift in the emission spectrum is analyzed. Using an iterative procedure the electronic polarizations of both the ground and the excited states are included and compared with previous results obtained with Car-Parrinello dynamics. Analysis of the emission transition obtained using CIS(D)/aug-cc-pVDZ on statistically uncorrelated solute-solvent structures, composed of acetone and twelve explicit water molecules embedded in the electrostatic field of remaining 263 water molecules, corroborates that the solvent effect is mild, calculated here between 80 and 380 cm (1). (c) 2010 Published by Elsevier B.V.

Dipole polarizability and Rayleigh light scattering by the hydrated electron

Assuming the existence of a confined state of the electron in bulk water the polarizability of the hydrated electron is analyzed. Statistically uncorrelated supermolecular structures composed of seven water molecules (first solvation shell) with an extra electron were extracted from classical Monte Carlo simulation and used in quantum mechanical second-order Moller-Plesset calculations. It is found that the bound excess electron contributes with 274 a.u. to the total dipole polarizability of 345 a.u. for (H(2)O)(7)(-). From the calculated polarizabilities the Rayleigh elastic light scattering properties are inferred and found to considerably enhance activity and light depolarization. (C) 2009 Elsevier B.V. All rights reserved.

Classical simulation of deposition of thiophene oligomers on TiO(2)-anatase: Relevance of long-range electrostatic interactions

We performed classical molecular dynamics simulations of the vapor-deposition of alpha-T4 oligomers on the TiO(2)-anatase (101) surface, comparing different sets of charges associated with the atoms of the model. The potential energy surfaces for alpha-T4 and TiO(2) were described by re-parametrizations of the Universal force field with charges given by the charge equilibration (QEq) scheme, or with fixed charges obtained by an ab initio method using the Hirshfeld partition. The two sets of charges lead to completely different results for the interface formation, and for the characteristics of the organic film, with a clearly defined alpha-T4 contact layer in the QEq case, and a more homogeneous molecular distribution when using Hirshfeld charges. The main reason for the discrepancy was found to be the incorrect charge assignment given by QEq to the sulfur and alpha-carbon atoms in thiophenes, and highlight the relevance of long-range interactions in the organization of molecular films. (C) 2009 Elsevier B.V. All rights reserved.

Theoretical investigation of Hf and Zr defects in c-Ge

The introduction of high-permittivity gate dielectric materials into complementary metal oxide semiconductor technology has reopened the interest in Ge as a channel material mainly due to its high hole mobility. Since HfO(2) and ZrO(2) are two of the most promising dielectric candidates, it is important to investigate if Hf and Zr may diffuse into the Ge channel. Therefore, using ab initio density functional theory calculations, we have studied substitutional and interstitial Hf and Zr impurities in c-Ge, looking for neutral defects. We find that (i) substitutional Zr and Hf defects are energetically more favorable than interstitial defects; (ii) under oxygen-rich conditions, neither Zr nor Hf migration towards the channel is likely to occur; (iii) either under Hf- or Zr-rich conditions it is very likely, particularly for Zr, that defects will be incorporated in the channel.

Adsorption Behavior of 5-Fluorouracil on Au(111): An In Situ STM Study

The biological effects of chemical substitution of DNA bases triggered several investigations of their physicochemical properties This paper studies the adsorption behavior of a halogenated uracil, 5-fluorouracil (5FU). at the electrochemical interface of Au(111) and sulfuric acid solution. Upon modulation of the electric field across the interface, four distinct phases could be inferred by means of cyclic voltammetry (CV) At negative potentials relative to the SCE electrode, limited by the threshold of hydrogen evolution, no molecular species could be detected by scanning tunneling microscopy (STM) at the reconstructed Au(111)-(23 x root 3) surface, indicating that any physisorbed molecules are randomly distributed Incursion into more positive potentials increases the surface population but doer not form any two-dimensional (2D) physisorbed ordered structure Instead, we observed metastable structures that are only detectable. on surfaces with high defect density At sufficiently high positive potentials. limited by gold oxidation, the molecules are chemisorbed in a (3 x 2 root 3) ordered structure. with the aromatic ring perpendicular to the surface We report the densest chemisorbed monolayer for pyrimidine-derivative molecules (area per molecule 0 14 +/- 0 04 nm(2)). A comparison of the adsorption behavior of uracil derivatives has been made based on recent results of chemical substitution and solvent effects. We propose that pi-stacking is enhanced when halogens are incorporated in the uracil structure, in a similar fashion to what is observed in then crystal structure

Experimental and theoretical investigation of molecular structure and conformation of the 4-isopropylthioxanthone

In this study, the molecular structure and conformational analyses of the 4-isopropylthioxanthone (4-ITX) are reported according to experimental and theoretical results. The compound crystallizes in the centrosymmetric P (1) over bar space group with only one molecule in the asymmetric unit, presenting the most stable conformation, in which the three fused-rings adopt a planar geometry, and the isopropyl group assumes a torsional angle with less sterical hindrance. The structural and conformational analyses were performed using theoretical calculations such as Hartree-Fock (HF), DFT method in combination with 6-311G(d,p) and 6-31++G(d,p) and the results were compared with infrared spectroscopy (FT-IR) and X-ray diffraction (XRD). The supramolecular assembly of 4-ITX is kept by non-classical C-H center dot center dot center dot O hydrogen bonds and weak interactions such as pi-pi stacking. 4-ITX was also studied by (1)H and (13)C NMR spectroscopy. UV-Vis absorption spectroscopic properties of the 4-ITX showed the long-wavelength maximum shifts towards high energy when the solvent polarity increases. (C) 2011 Elsevier B.V. All rights reserved.

Interação heparina-antitrombina : reconhecimento molecular caracterizado por ferramentas de modelagem molecular

A heparina foi isolada no início do século XX e permanece, até os dias atuais, como um dos mais importantes e eficientes agentes terapêuticos de ação antitrombótica. Sua atividade anticoagulante deve-se à ativação da antitrombina (AT), uma serpina responsável pela inibição fisiológica de serino-proteinases plasmáticas, tais como fIIa e fXa. Os esforços no sentido da elucidação dos aspectos estruturais e dinâmicos associados ao reconhecimento molecular da heparina pela AT, em nível atômico, vêm encontrando diversas dificuldades, principalmente associadas aos compostos sacarídicos. Em decorrência de sua elevada polaridade e flexibilidade, glicosaminoglicanos como a heparina são difíceis de estudar e modelar. Soma-se a isto o fato de que os resíduos de iduronato presentes na heparina (IdoA) apresentam um incomum equilíbrio conformacional entre estados de cadeira (1C4) e bote-torcido (2SO), sendo esta última estrutura postulada como a possível conformação bioativa. Sendo assim, este trabalho apresenta um estudo de modelagem molecular do perfil conformacional da heparina, tanto em solução quanto complexada à AT, utilizando cálculos ab initio e simulações de dinâmica molecular (DM) Em decorrência da ausência de parâmetros capazes de descrever polissacarídeos nos campos de força atualmente disponíveis, cargas atômicas foram geradas, utilizando-se os esquemas de Mulliken, Löwdin e cargas ajustadas ao Potencial Eletrostático, através de cálculos quantum-mecânicos na base 6-31G** e testadas na simulação de DM da heparina. Diversas condições de simulação, tais como modelos de água, concentrações de sais e as conformações 1C4 e 2SO do IdoA, foram avaliadas de forma a identificar as melhores condições para a descrição conformacional da heparina em solução. O protocolo de DM obtido foi então utilizado no estudo do complexo AT-heparina. Os resultados obtidos estão de acordo com os dados experimentais atualmente disponíveis acerca da conformação da heparina e da contribuição energética de cada resíduo de aminoácido da AT para a formação do complexo com a heparina. A partir dos cálculos ab initio realizados, foi proposto um refinamento na estrutura da heparina determinada por RMN, enquanto que as simulações de DM permitiram reinterpretar aspectos da estrutura tridimensional da AT determinada por cristalografia de raios-X. Adicionalmente, os dados obtidos sugerem que não há requerimento conformacional para a interação do IdoA com a AT Globalmente, os dados indicam que simulações de DM podem ser utilizadas para representar adequadamente a conformação da heparina, assim como para caracterizar e quantificar suas interações com a AT. Assim sendo, propomos o uso de simulações de DM do complexo entre a AT e a heparina, ou entre a AT e compostos derivados da heparina, como uma ferramenta útil no processo de desenvolvimento de novos agentes antitrombóticos e anticoagulantes.

Nonzero Gap Two-Dimensional Carbon Allotrope from Porous Graphene

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Structural and vibrational study of cubic Sb2O3 under high pressure

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

A nonzero gap two-dimensional carbon allotrope from porous graphene

Graphene has been one of the hottest topics in materials science in the last years. Because of its special electronic properties graphene is considered one of the most promising materials for future electronics. However, in its pristine form graphene is a gapless semiconductor, which poses some limitations to its use in some transistor electronics. Many approaches have been tried to create, in a controlled way, a gap in graphene. These approaches have obtained limited successes. Recently, hydrogenated graphene-like structures, the so-called porous graphene, have been synthesized. In this work we show, based on ab initio quantum molecular dynamics calculations, that porous graphene dehydrogenation can lead to a spontaneous formation of a nonzero gap two-dimensional carbon allotrope, called biphenylene carbon (BC). Besides exhibiting an intrinsic nonzero gap value, BC also presents well delocalized frontier orbitals, suggestive of a structure with high electronic mobility. Possible synthetic routes to obtain BC from porous graphene are addressed. © 2012 Materials Research Society.