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.

Theoretical studies on the stability of N-methylformamide in both liquid and gas phases

Ab initio (restricted Hartree-Fock and DFT) and molecular mechanics calculations at MM2 level were performed for N-methylformamide (NMF) molecule and for three dimers in order to investigate the relative stability of the cis and trans conformers. The ab initio calculations show that no intramolecular interaction is relevant for the stability of the conformers explored. The trans conformer is the most stable. The MM calculations revealed that a double H-bonded cyclic cis-cis dimer is the most stable among the studied dimers, followed by a 'linear' H-bonded trans-trans dimer. This 'linear' dimer, however, is prevalent in the liquid phase. (c) 2006 Elsevier B.V. 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.

L-Histidine-europium(III) complex: A spectroscopical study

Chemical characterization as well as spectroscopical study of the L-histidine-europium(III) complex were developed both experimental and theoretically. Molecular mechanics (MM) simulation was performed in order to have indication of the compound structure and the Eu 3+ chemical environment. The Simple Overlap Model (SOM) was applied to predict spectroscopic quantities as 5D 0→ 7F 0/ 5D 0→ 7F 2 intensity ratio, 5D 0→ 7F 1 transition splitting and the intensity Ω λ parameters (λ = 2 and 4). Satisfactory results are obtained with 0.1 and 2/3 as the effective charges of the nitrogen (gN) and oxygen (gO) respectively, and their polarizabilities (α) depend on the distance. © 1999 Elsevier Science B.V. All rights reserved.

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.

Toxicidade de fármacos nitrofurânicos

During the structural designing of new drugs, it is possible predict the influence of specific chemical groups on pharmacological activity. Among these, the nitro group has potential antiparasitic activity, being present in many antimicrobial drugs, such as metronidazole, nitrofurazone, furazolidone, oxamniquine and chloramphenicol. Also, the introduction of the nitro group into a molecule can modify the physicochemical and electronic properties of the substance. Besides antimicrobial drugs, this group is also found in other drug classes, such as antiulcer, anti-inflamatory and anxiolytic. However, the use of the nitro group in drug design has encountered restrictions, due to the associated toxicity. This article is a review of the toxicity of nitrofuran compounds, as well the possible mechanisms involved and the strategy of latentiation by molecular modification to decrease their toxicity.

Possible mechanism by which zinc protects the testicular function of rats exposed to cigarette smoke

Background: The aim of this study was to evaluate the changes in testicular function of rats due to cigarette smoke exposure and the possible mechanism by which zinc protects against these alterations. Methods: MaleWistar rats (60 days old) were randomly divided into 3 groups: control (G1, n = 10); exposed to cigarette smoke (G2, n = 10; 20 cigarettes/day/9 weeks) and exposed to cigarette smoke and supplemented with zinc (G3, n = 8; 20 cigarettes/day/9 weeks; 20 mg/kg zinc chloride daily for 9 weeks, by gavage). After the treatment period, the animals were euthanized, and materials were collected for analyses. Results: G2 rats showed a reduction in body mass; impaired sperm concentration, motility, morphology and vitality; and increased malonaldehyde and thiol group levels and superoxide dismutase activity as compared to G1. Zinc prevented the reduction of sperm concentration and the excessive increase of lipid peroxidation and induced an increase in plasma testosterone levels, wet weight of testis and thiol group concentration. Conclusions: Exposure to cigarette smoke led to harmful effects on testicular function at least partially due to the exacerbation of oxidative stress. Supplementary zinc had an important modulator/protector effect on certain parameters. The mechanism of zinc protection can be through an increase of SH concentration. Thus, zinc supplementation may be a promising addition to conventional treatments for male infertility related to smoking. Copyright © 2012 by Institute of Pharmacology Polish Academy of Sciences.

Acute exercise decreases PTP-1B protein level and improves insulin signaling in the liver of old rats

It is now commonly accepted that chronic inflammation associated with obesity during aging induces insulin resistance in the liver. In the present study, we investigated whether the improvement in insulin sensitivity and insulin signaling, mediated by acute exercise, could be associated with modulation of protein-tyrosine phosphatase 1B (PTP-1B) in the liver of old rats. Aging rats were subjected to swimming for two 1.5-h long bouts, separated by a 45 min rest period. Sixteen hours after the exercise, the rats were sacrificed and proteins from the insulin signaling pathway were analyzed by immunoblotting. Our results show that the fat mass was increased in old rats. The reduction in glucose disappearance rate (Kitt) observed in aged rats was restored 16 h after exercise. Aging increased the content of PTP-1B and attenuated insulin signaling in the liver of rats, a phenomenon that was reversed by exercise. Aging rats also increased the IRβ/PTP-1B and IRS-1/PTP-1B association in the liver when compared with young rats. Conversely, in the liver of exercised old rats, IRβ/PTP-1B and IRS-1/PTP-1B association was markedly decreased. Moreover, in the hepatic tissue of old rats, the insulin signalling was decreased and PEPCK and G6Pase levels were increased when compared with young rats. Interestingly, 16 h after acute exercise, the PEPCK and G6Pase protein level were decreased in the old exercised group. These results provide new insights into the mechanisms by which exercise restores insulin signalling in liver during aging. © 2013 Moura et al; licensee BioMed Central Ltd.

Androgen deprivation from pre-puberty to peripuberty interferes in proteins expression in pubertal and adult rat epididymis

Few studies have focused on experimental testosterone deprivation in immature animals. Therefore, this study used sexually immature rats aiming to evaluate the testes and epididymis histology and proteins expression in these organs on PND50 and 75, after premature antiandrogen exposure, from PND21 to 44. Although the androgen deprivation from pre-puberty up to peripuberty did not alter the histological organization of the testes and epididymis either at puberty or at adulthood, the treatment impaired the expression of specific proteins in epididymal tissue at puberty and adulthood (androgen receptor, calmodulin, Rab11A). These changes may be related to impaired epididymal function, sperm quality and fertility capacity as observed in a previous study. Further studies are necessary to better investigate the molecular mechanisms involved in the impairment on reproductive competence of male rats after precocious hormonal injury. © 2013 Elsevier Inc.

Cysteine proteinase inhibitors regulate human and mouse osteoclastogenesis by interfering with RANK signaling

The cysteine proteinase inhibitor cystatin C inhibited RANKL-stimulated osteoclast formation in mouse bone marrow macrophage cultures, an effect associated with decreased mRNA expression of Acp5, Calcr, Ctsk, Mmp9, Itgb3, and Atp6i, without effect on proliferation or apoptosis. The effects were concentration dependent with half-maximal inhibition at 0.3 μM. Cystatin C also inhibited osteoclast formation when RANKL-stimulated osteoclasts were cultured on bone, leading to decreased formation of resorption pits. RANKL-stimulated cells retained characteristics of phagocytotic macrophages when cotreated with cystatin C. Three other cysteine proteinase inhibitors, cystatin D, Z-RLVG-CHN2 (IC50 0.1 μM), and E-64 (IC 50 3 μM), also inhibited osteoclast formation in RANKL-stimulated macrophages. In addition, cystatin C, Z-RLVG-CHN2, and E-64 inhibited osteoclastic differentiation of RANKL-stimulated CD14+ human monocytes. The effect by cystatin C on differentiation of bone marrow macrophages was exerted at an early stage after RANKL stimulation and was associated with early (4 h) inhibition of c-Fos expression and decreased protein and nuclear translocation of c-Fos. Subsequently, p52, p65, IκBα, and Nfatc1 mRNA were decreased. Cystatin C was internalized in osteoclast progenitors, a process requiring RANKL stimulation. These data show that cystatin C inhibits osteoclast differentiation and formation by interfering intracellularly with signaling pathways downstream RANK. © FASEB.

Simulação de transporte eletrônico em dispositivos unimoleculares baseados em indicadores de pH

Nas últimas décadas, diversos pesquisadores têm tentado empregar moléculas em dispositivos eletrônicos de nanoescala. Por este motivo, diferentes parâmetros eletro/ópticos, que regem o transporte eletrônico em moléculas orgânicas, precisam ser analisados. Neste trabalho foi desenvolvido um estudo de transporte de carga para o composto Vermelho de Propila, popularmente utilizado como indicador de pH. A motivação para estudá-lo resulta de sua estrutura constituída por subunidades doadora-aceitadora, acopladas via grupo azo (N=N), uma característica bem conhecida em retificadores moleculares. A metodologia utilizada para tratar o sistema em equilíbrio é baseada em métodos de Mecânica Molecular e Hartree-Fock. Sendo que, para simular o sistema em não-equilíbrio, foi empregado o formalismo de Landauer-Büttiker. Através desses métodos, as curvas características do sistema molecular foram traçadas e comparadas. O resultado da comparação permitiu explicar os fenômenos que regem o transporte eletrônico na nanoestrutura. Além disso, foram analisados os efeitos de contatos metálicos, ligados a molécula na presença de campo elétrico externo.

Espectrometria Raman, UV, DOS e Circular Dicroísmo de alcalóides do cigarro

Esta dissertação aborda a análise espectroscópica de algumas estruturas moleculares presentes no tabaco (Nicotiana glauca), matéria-prima do cigarro, e suas interações com a molécula de DNA. De acordo com sua importância, dentre a grande variedade presentes no cigarro, às moléculas estudadas foram as derivadas do ácido nicotínico: ácido nicotínico (niacina/vitamina B3), nicotinamida, trigonelina, nicotina, nornicotina e anabasina. As otimizações dessas estruturas foram inicialmente obtidas no software computacional Hyperchem 8.0, baseadas na teoria da mecânica molecular. Em seguida, elas foram otimizadas, utilizando-se o método de Teoria do Funcional da Densidade, na base B3LYP/ 6-311++G(d,p), simulado no software Gaussian 03. Uma vez as estruturas otimizadas, obtivemos os espectros de absorção UV, Raman, Infravermelho, Dicroísmo Circular e Densidade de Estados para caracterizar as mesmas utilizando método de Teoria do Funcional da Densidade Dependente do Tempo, também simulados no mesmo software. Ao final desse processo, foi também simulado via mecânica molecular, as interações dessas estruturas com a molécula de DNA com o intuito de verificar a potencialidade cancerígena, ou não, dessas substâncias.

Estrutura eletrônica de derivados de politieno[3,4-b]-tiofeno-co-benzoditiofeno para aplicação em camadas ativas de células solares orgânicas

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

ALDH1A2 (RALDH2) genetic variation in human congenital heart disease

Abstract Background Signaling by the vitamin A-derived morphogen retinoic acid (RA) is required at multiple steps of cardiac development. Since conversion of retinaldehyde to RA by retinaldehyde dehydrogenase type II (ALDH1A2, a.k.a RALDH2) is critical for cardiac development, we screened patients with congenital heart disease (CHDs) for genetic variation at the ALDH1A2 locus. Methods One-hundred and thirty-three CHD patients were screened for genetic variation at the ALDH1A2 locus through bi-directional sequencing. In addition, six SNPs (rs2704188, rs1441815, rs3784259, rs1530293, rs1899430) at the same locus were studied using a TDT-based association approach in 101 CHD trios. Observed mutations were modeled through molecular mechanics (MM) simulations using the AMBER 9 package, Sander and Pmemd programs. Sequence conservation of observed mutations was evaluated through phylogenetic tree construction from ungapped alignments containing ALDH8 s, ALDH1Ls, ALDH1 s and ALDH2 s. Trees were generated by the Neighbor Joining method. Variations potentially affecting splicing mechanisms were cloned and functional assays were designed to test splicing alterations using the pSPL3 splicing assay. Results We describe in Tetralogy of Fallot (TOF) the mutations Ala151Ser and Ile157Thr that change non-polar to polar residues at exon 4. Exon 4 encodes part of the highly-conserved tetramerization domain, a structural motif required for ALDH oligomerization. Molecular mechanics simulation studies of the two mutations indicate that they hinder tetramerization. We determined that the SNP rs16939660, previously associated with spina bifida and observed in patients with TOF, does not affect splicing. Moreover, association studies performed with classical models and with the transmission disequilibrium test (TDT) design using single marker genotype, or haplotype information do not show differences between cases and controls. Conclusion In summary, our screen indicates that ALDH1A2 genetic variation is present in TOF patients, suggesting a possible causal role for this gene in rare cases of human CHD, but does not support the hypothesis that variation at the ALDH1A2 locus is a significant modifier of the risk for CHD in humans.

Atomistic simulations of bulk and free standing film smectics

In questa tesi viene descritto lo studio delle fasi liquido-cristalline del 4-n-ottil-4-cianobifenile eseguito tramite simulazioni al calcolatore molecular dynamics, sia per campioni bulk che per film smectici sottili. Impiegando un campo di forze "molecular mechanics" precedentemente usato con successo per studiare sistemi composti da 250 molecole della serie degli n-cianobifenili (nCB, con n pari a 4-8 atomi di carbonio nella catena alifatica), si è simulato il comportamento di un sistema bulk di 750 molecole e di un film smectico di 1500 molecole. Nel primo caso, sottoponendo il campione a un graduale raffreddamento, si è osservata la formazione spontanea di fasi ordinate quali quella nematica e quella smectica. Nel secondo caso, invece, si è studiata l'influenza dell'interfaccia con il vuoto sull'ordine posizionale e orientazionale di film sottili di diverso spessore e temperatura. Si sono confrontate le proprietà di entrambi i sistemi simulati con i dati sperimentali disponibili in letteratura, confermando la bontà del modello nel riprodurre fedelmente le caratteristiche dei campioni reali.