Home About us Contact
|
Home About us Contact | ||
|
|
||
Intramolecular H-bonds (intramolecular + h-bond)
Selected AbstractsBinding of ciprofloxacin by humic substances: A molecular dynamics studyENVIRONMENTAL TOXICOLOGY & CHEMISTRY, Issue 1 2010Ludmilla Aristilde Abstract A comprehensive assessment of the potential impacts of antimicrobials released into the environment requires an understanding of their sequestration by natural particles. Of particular interest are the strong interactions of antimicrobials with natural organic matter (NOM), which are believed to reduce their bioavailability, retard their abiotic and biotic degradation, and facilitate their persistence in soils and aquatic sediments. Molecular dynamics (MD) relaxation studies of a widely used fluoroquinolone antibiotic, ciprofloxacin (Cipro), interacting with a model humic substance (HS) in a hydrated environment, were performed to elucidate the mechanisms of these interactions. Specifically, a zwitterionic Cipro molecule, the predominant species at circumneutral pH, was reacted either with protonated HS or deprotonated HS bearing Ca, Mg, or Fe(II) cations. The HS underwent conformational changes through rearrangements of its hydrophobic and hydrophilic regions and disruption of its intramolecular H-bonds to facilitate favorable intermolecular H-bonding interactions with Cipro. Complexation of the metal cations with HS carboxylates appeared to impede binding of the positively charged amino group of Cipro with these negatively charged HS complexation sites. On the other hand, an outer-sphere complex between Cipro and the HS-bound cation led to ternary Cipro,metal,HS complexes in the case of Mg,HS and Fe(II),HS, but no such bridging interaction occurred with Ca,HS. The results suggested that the ionic potential (valence/ionic radius) of the divalent cation may be a determining factor in the formation of the ternary complex, with high ionic potential favoring the bridging interaction. Environ. Toxicol. Chem. 2010;29:90,98. © 2009 SETAC [source] Oligonucleotide Analogues with Integrated Bases and Backbone.HELVETICA CHIMICA ACTA, Issue 4 2007Part 1 Abstract The self-complementary tetrameric propargyl triols 8, 14, 18, and 21 were synthesized to investigate the duplex formation of self-complementary, ethynylene-linked UUAA, AAUU, UAUA, and AUAU analogues with integrated bases and backbone (ONIBs). The linear synthesis is based on repetitive Sonogashira couplings and C -desilylations (34,72% yield), starting from the monomeric propargyl alcohols 9 and 15 and the iodinated nucleosides 3, 7, 11, and 13. Strongly persistent intramolecular H-bonds from the propargylic OH groups to N(3) of the adenosine units prevent the gg -type orientation of the ethynyl groups at C(5,). As such, an orientation is required for the formation of cyclic duplexes, this H-bond prevents the formation of duplexes connected by all four base pairs. However, the central units of the UAUA and AAUU analogues 18 and 14 associate in CDCl3/(D6)DMSO 10,:,1 to form a cyclic duplex characterized by reverse Hoogsteen base pairing. The UUAA tetramer 8 forms a cyclic UU homoduplex, while the AUAU tetramer 21 forms only linear associates. Duplex formation of the O -silylated UUAA and AAUU tetramers is no longer prevented. The self-complementary UUAA tetramer 22 forms Watson,Crick - and Hoogsteen -type base-paired cyclic duplexes more readily than the sequence-isomeric AAUU tetramer 23, further illustrating the sequence selectivity of duplex formation. [source] Properties of 2,2,2-Trifluoroethanol/Water Mixtures: Acidity, Basicity, and DipolarityHELVETICA CHIMICA ACTA, Issue 2 2005Paz Sevilla, Sierra In this report, we focus our attention on the characterization of 2,2,2-trifluoroethanol(TFE)/H2O mixtures and describe their intrinsic parameters; i.e., solvent acidity (SA), solvent basicity (SB), and solvent dipolarity/polarizability (SPP), by the probe/homomorph-couple method for a range of mixtures from 0,100% (v/v) TFE. Variation of these parameters is not linear and has a singular and unpredictable behavior depending on the precise composition of the mixture. Based on these parameters, we describe the TFE-induced changes in some physical properties; i.e., viscosity (,), partial molar volume (V,), density (,), dielectric constant (,), vapor pressure (pv), and spectroscopic properties; i.e., NMR chemical shifts (,(1H)) of TFE Me group for all molar fractions studied. In addition, by means of CD studies, we report that formation of the secondary structure, as percentage of helical content, ,, of a polypeptide, poly(L -lysine), in several TFE/H2O mixtures is adequately described by these mixture parameters. SA, SB, and SPP of TFE/H2O mixtures provide an excellent tool for the interpretation of formation and stability of intramolecular H-bonds, and, thus, of secondary structures in polypeptides. [source] Synthesis, Spectroscopic Studies, and Crystal Structures of Phenylorganotin Derivatives with [Bis(2,6-dimethylphenyl)amino]benzoic Acid: Novel Antituberculosis AgentsHELVETICA CHIMICA ACTA, Issue 8 2004Vaso Dokorou The novel triphenyl adduct of 2-[(2,6-dimethylphenyl)amino]benzoic acid (HDMPA; 1), i.e., [SnPh3(DMPA)] (2), the dimeric tetraorganostannoxane [Ph2(DMPA)SnOSn(DMPA)Ph2]2 (3), and the monomeric adduct [SnPh2(DMPA)2] (4), where DMPA is monodeprotonated HDMPA, have been prepared and structurally characterized by means of IR, 1H-NMR, and 13C-NMR spectroscopy. The structures of 1 and 2 have been determined by X-ray crystallography. Single-crystal X-ray-diffraction analysis of 1 revealed that there are two molecules in the asymmetric unit, HD1 and HD2, differing in conformation, both forming centrosymmetric dimers linked by H-bonds between the carboxylic O-atoms. X-Ray analysis of 2 revealed a pentacoordinate structure containing Ph3Sn coordinated to the carboxylato group. Significant CH/, interactions and intramolecular H-bonds stabilize the structures of 1 and 2, which self-assembled via CH/, and ,/, -stacking interactions. The Ph3Sn adduct 2 was found to be a promising antimycobacterial lead compound, displaying activity against Mycobacterium tuberculosis H37Rv. The cytotoxiciy in the Vero cell line is also reported. [source] A computational study of the carboxylic acid of phloroglucinol in vacuo and in water solutionINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 3 2010Liliana Mammino Abstract 2,4,6-Trihydroxybenzoic acid (FA) is the carboxylic acid of phloroglucinol and, in turn, the parent compound of many biologically active compounds. The biological activities of FA are "extreme" among trihydroxybenzoic acids (e.g., lowest antioxidant activity, highest toxicity toward crustaceans). A complete MP2/6-31++G(d,p) conformational study in vacuo shows that the lowest energy conformers contain two intramolecular hydrogen bonds between the COOH function and the two ortho phenolic OH, with the Z form of COOH preferred over the E form. Comparisons with conformers in which the H-bonds are removed enable fairly reliable evaluations of their energy, because of an off-plane shift of COOH on H-bond removal, decreasing the effects of lone pair repulsion. Comparisons with the other hydroxybenzoic acids (extensively calculated in vacuo at the same level of theory) suggest that FA has the strongest intramolecular H-bonds. PCM calculations of FA in water solution show the same sequence of relative stabilities as in vacuo, with narrower differences because of the greater solvent stabilization of higher energy conformers. Calculations of adducts with water molecules H-bonded to different donor,acceptor centers of FA show the preferred arrangements of water molecules around the different regions of FA and confirm that the stronger intramolecular H-bonds are not broken on competition with the possibility of formation of intermolecular H-bonds. HF/6-31++G(d,p) calculations of adducts, in which the FA molecule is completely surrounded by water molecules, show that 14,16 water molecules (depending on the FA conformer geometry) realize arrangements corresponding to a presumable first solvation layer, with all the water molecules directly H-bonded to donor,acceptor centers of FA or bridging water molecules directly H-bonded to them. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010 [source] Electronic structure and reactivity of guanylthiourea: A quantum chemical studyJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 6 2010Ahmed Mehdi Abstract Electronic structure analysis of guanylthiourea (GTU) and its isomers has been carried out using quantum chemical methods. Two major tautomeric classes (thione and thiol) have been identified on the potential energy (PE) surface. In both the cases conjugation of pi-electrons and intramolecular H-bonds have been found to play a stabilizing role. Various isomers of GTU on its PE surface have been analyzed in two different groups (thione and thiol). The interconversion from the most stable thione conformer (GTU-1) to the most stable thiol conformer (GTU-t1) was found to take place via bimolecular process which involves protonation at sulfur atom of GTU-1 followed by subsequent CN bond rotation and deprotonation. The detailed analysis of the protonation has been carried out in gas phase and aqueous phase (using CPMC model). Sulfur atom (S1) was found to be the preferred protonation site (over N4) in GTU-1 in gas phase whereas N4 was found to be the preferred site of protonation in aqueous medium. The mechanism of S-alkylation reaction in GTU has also been studied. The formation of alkylated analogs of thiol isomers (alkylated guanylthiourea) is believed to take place via bimolecular process which involves alkyl cation attack at S atom followed by CN bond rotation and deprotonation. The reactive intermediate RS(NH2)CNC(NH2)2+ belongs to the newly identified ,N(,L)2 class of species and provides the necessary dynamism for easy conversion of thione to thiol. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] Hybrid ,/,3 -peptides with proteinogenic side chains. monosubstituted analogues of the chemotactic tripeptide For-Met-Leu-Phe-OMeJOURNAL OF PEPTIDE SCIENCE, Issue 8 2004Cesare Giordano Abstract The ,/,3 -mixed tripeptides R-CO-,3 -HMet-Leu-Phe-OMe (1a,b), R-CO-Met-,3 -HLeu-Phe-OMe (2a,b) and R-CO-Met-Leu-,3 -HPhe-OMe (3a,b) (a, R = tert -butyloxy-; b, R = H,), analogues of the potent chemoattractant For-Met-Leu-Phe-OMe, have been synthesized by classical solution methods and fully characterized. The activities of the new analogues as chemoattractants, superoxide anion producers and lysozyme releasers have been determined on human neutrophils. Whereas all of the three N -formyl derivatives are significantly less active than the parent tripeptide as chemoattractants, compound 1b has been found to be highly active as a superoxide anion producer and 3b as a lysozyme releaser. The results show that the replacement of the native Leu residue at the central position is, in each of the examined cases, the least favourable modification. The three N -Boc derivatives are, as expected, devoid of activity as agonists, but they are all good inhibitors of chemotaxis. Information on the solution conformation has been obtained by examining the involvement of the NH groups in intramolecular H-bonds using 1H NMR. The conformation of the N -Boc analogue 1a has also been determined in the crystal state by x-ray diffraction analysis. The molecule is extended at the ,3 -HMet residue (,1 = ,87°;,1 = 172°;,1 = 126° ) and no intramolecular H-bond is present. Copyright © 2004 European Peptide Society and John Wiley & Sons, Ltd. [source] New Fourier transform infrared based computational method for peptide secondary structure determination.BIOPOLYMERS, Issue 2 2001Abstract Fourier transform infrared (FTIR) experiments in dimethylsulfoxide, a solvent incapable of H donation, demonstrate that H , D isotopic replacement on the amide side of peptide bonds involves modifications of both the position and intensity of the amide I band. The effect of the isotopic substitution is particularly significant in the 1710,1670 and 1670,1650 cm,1 regions, which are generally associated with ,-turns and ,-helices. This behavior, attributed to the existence of intramolecular H-bonds in the polypeptide chain, is directly correlated to the presence of different secondary structures. Utilizing the effects induced by isotopic substitution, a method for the quantitative determination of the percentage of intramolecular H-bonds and the correlated secondary structures is proposed. The method consists of three principal steps: resolution of the fine structure of the amide I band with the determination of the number and position of the different components; reconstruction of the experimentally measured amide I band as a combination of Gaussian and Lorentzian functions, centered on the wave numbers set by band-narrowing methods, through a curve-fitting program; and quantitative determination of the population of the H-bonded carbonyls and the correlated secondary structures by comparison of the integrated intensities pertaining to the components with homologous wave numbers before and after isotopic exchange. The method is tested on a synthetic fragment of proocytocin that was previously analyzed by NMR techniques using the same solvent systems. © 2001 John Wiley & Sons, Inc. Biopolymers (Biospectroscopy) 62: 95,108, 2001 [source] Conformational analysis of endomorphin-1 by molecular dynamics methodsCHEMICAL BIOLOGY & DRUG DESIGN, Issue 4 2003B. Leitgeb Abstract: Endomorphin-1 (EM1, H-Tyr-Pro-Trp-Phe-NH2) is a highly potent and selective agonist for the ,-opioid receptor. A conformational analysis of this tetrapeptide was carried out by simulated annealing and molecular dynamics methods. EM1 was modeled in the neutral (NH2 -) and cationic (NH -) forms of the N-terminal amino group. The results of NMR measurements were utilized to perform simulations with restrained cis and trans Tyr1 -Pro2 peptide bonds. Preferred conformational regions in the ,2,,2, ,3,,3 and ,4,,4 Ramachandran plots were identified. The g(+), g(,) and trans rotamer populations of the side-chains of the Tyr1, Trp3 and Phe4 residues were determined in ,1 space. The distances between the N-terminal N atom and the other backbone N and O atoms, and the distances between the centers of the aromatic side-chain rings and the Pro2 ring were measured. The preferred secondary structures were determined as different types of , -turns and , -turns. In the conformers of trans -EM1, an inverse , -turn can be formed in the N-terminal region, but in the conformers of cis -EM1 the N-terminal inverse , -turn is absent. Regular and inverse , -turns were observed in the C-terminal region in both isomers. These , - and , -turns were stabilized by intramolecular H-bonds and bifurcated H-bonds. [source] Thermal Stability of Dehydrophenylalanine-Containing Model Peptides as Probed by Infrared Spectroscopy: a Case Study of an , -Helical and a 310 -Helical PeptideCHEMISTRY & BIODIVERSITY, Issue 3 2006Alka Gupta Abstract The temperature-dependent secondary-structural changes in the two known helical model peptides Boc-Val-,Phe-Ala-Leu-Gly-OMe (1; , -helical) and Boc-Leu-Phe-Ala-,Phe-Leu-OMe (2; 310 -helical), which both comprise a single dehydrophenylalanine (,Phe) residue, were investigated by means of FT-IR spectroscopy (peptide film on KBr). Both the first-order and the better-resolved second-order derivative IR spectra of 1 and 2 were analyzed. The ,(NH) (3240,3340,cm,1), the Amide-I (1600,1700,cm,1), and the Amide-II (1510,1580,cm,1) regions of 1 and 2 showed significant differences in thermal-denaturation experiments (22°,144°), with the 310 -helical peptide (2) being considerably more stable. This observation was rationalized by different patterns and strengths of intramolecular H-bonds, and was qualitatively related to the different geometries of the peptides. Also, a fair degree of residual secondary-structural elements were found even in the ,denatured' states above 104° (1) or 134° (2). [source] | |||||||||||||