Studies of the tautomeric equilibrium of 1,3-thiazolidine-2-thione: Theoretical and experimental approaches

Energy Technology Data Exchange (ETDEWEB)

Abbehausen, Camilla; Paiva, Raphael E.F. de [Institute of Chemistry, University of Campinas - UNICAMP, P.O. Box 6154, 13083-970 Campinas, SP (Brazil); Formiga, Andre L.B., E-mail: formiga@iqm.unicamp.br [Institute of Chemistry, University of Campinas - UNICAMP, P.O. Box 6154, 13083-970 Campinas, SP (Brazil); Corbi, Pedro P. [Institute of Chemistry, University of Campinas - UNICAMP, P.O. Box 6154, 13083-970 Campinas, SP (Brazil)

2012-10-26

Highlights: Black-Right-Pointing-Pointer Tautomeric equilibrium in solution. Black-Right-Pointing-Pointer Spectroscopic and theoretical studies. Black-Right-Pointing-Pointer UV-Vis theoretical and experimental spectra. Black-Right-Pointing-Pointer {sup 1}H NMR theoretical and experimental spectra. -- Abstract: The tautomeric equilibrium of the thione/thiol forms of 1,3-thiazolidine-2-thione was studied by nuclear magnetic resonance, infrared and ultraviolet-visible spectroscopies. Density functional theory was used to support the experimental data and indicates the predominance of the thione tautomer in the solid state, being in agreement with previously reported crystallographic data. In solution, the tautomeric equilibrium was evaluated using {sup 1}H NMR at different temperatures in four deuterated solvents acetonitrile, dimethylsulfoxide, chloroform and methanol. The equilibrium constants, K = (thiol)/(thione), and free Gibbs energies were obtained by integration of N bonded hydrogen signals at each temperature for each solvent, excluding methanol. The endothermic tautomerization is entropy-driven and the combined effect of solvent and temperature can be used to achieve almost 50% thiol concentrations in solution. The nature of the electronic transitions was investigated theoretically and the assignment of the bands was made using time-dependent DFT as well as the influence of solvent on the energy of the most important bands of the spectra.

Tautomerism of 4-hydrazinoquinazolines: vibrational spectra and computational study

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Tetiana Yu. Sergeieva

2014-03-01

Full Text Available The tautomerism of 4-hydrazinoquinazoline and its derivatives was investigated. Geometry and thermodynamic parameters were computed theoretically using Gaussian 03 software. All calculations were performed at the MP2 level of theory using the standard 6-31G(d basis. Energetics and relative stabilities of tautomers were compared and analyzed in a gas phase. The effect of solvents (1,4-dioxane, acetic acid, ethanol and water on the tautomeric equlibria was evaluated using PCM. It was determined that solvents induced slight changes in the relative stability. In all cases 4-hydrazinoquinazoline exists predominantly as the amino form. The variation of dipole moments was studied. The anharmonic vibrational wavenumbers for unsubstituted 4-hydrazinoquinazoline were calculated at MP2/6-31G(d level and compared with experimental data. The modes of IR spectra were assigned. The calculated herein wavenumbers and intensities of amino form are in good agreement with those observed experimentally.      

Water-mediated tautomerization of cytosine to the rare imino form: An ab initio dynamics study

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Fogarasi, Geza [Institute of Chemistry, Eotvos University, H-1518 Budapest, Pf. 32. (Hungary)], E-mail: fg@chem.elte.hu

2008-06-16

Tautomerism in nucleotide bases is one of the possible mechanisms of mutation of DNA. In spite of numerous studies on the structure and energy of cytosine tautomers, little information is available on the process of proton transfer itself. We present here Born-Oppenheimer dynamics calculations, with the potential surface obtained 'on the fly' from ab initio quantum chemistry (QC) and the atoms moving classically. In search for water-mediated tautomerization the monohydrated complex was studied, running about 300 trajectories each of 3000-5000 points of 1 fs steps. One single trajectory has been found to lead to tautomerization. Although the QC method used in the simulations was inevitably modest (B3LYP/3-21G), higher-level test calculations along the same trajectory suggest that the simulation grasped the basic mechanism of proton transfer: a concerted, synchronous process characterized by strong coupling between the motions of the two participating hydrogen atoms.

Tautomerism of pyrazolinones in the solid state: the case of 1-aryl-3-methyl-3-pyrazolin-5-ones. An X-ray and CPMAS NMR study

Energy Technology Data Exchange (ETDEWEB)

Foces-Foces, C. [Departamento de Cristalografia. Instituto de Quimica Fisica. Rocasolano. Madrid (Spain); Fontenas, Ch.; Elguero, J. [Instituto de Quimica Medica. Madrid (Spain); Sobrados, I. [Instituto de Ciencia de Materiales. CSIC. Madrid (Spain)

1997-10-01

The tautomerism of pyrazolines in solution is one of the best-studied cases of tautomerism. Although there are many X-ray structures of these compounds, no systematic study of their tautomerism in the solid state has been carried out. In this paper we present the results obtained by X-ray crystallography and ``13 C CPMAS NMR on two related compounds, 1-phenyl-and 1-p-bromo phenyl-3-methyl pyrazoline, as well as the result of a search in the CSD. Some general conclusions about the tautomerism of pyrazolines have been drawn. (Author) 22 refs.

Determination of thermodynamic parameters of tautomerization in gas phase by mass spectrometry and DFT calculations: Keto-enol versus nitrile-ketenimine equilibria.

Science.gov (United States)

Giussi, Juan M; Gastaca, Belen; Albesa, Alberto; Cortizo, M Susana; Allegretti, Patricia E

2011-02-01

The study of tautomerics equilibria is really important because the reactivity of each compound with tautomeric capacity can be determined from the proportion of each tautomer. In the present work the tautomeric equilibria in some γ,δ-unsaturated β-hydroxynitriles and γ,δ-unsaturated β-ketonitriles were studied. The first family of compounds presents two possible theoretical tautomers, nitrile and ketenimine, while the second one presents four possible theoretical tautomers, keto-nitrile, enol (E and Z)-nitrile and keto-ketenimine. The equilibrium in gas phase was studied by gas chromatography-mass spectrometry (GC-MS). Tautomerization enthalpies were calculated by this methodology, and results were compared with those obtained by density functional theory (DFT) calculations, observing a good agreement between them. Nitrile tautomers were favored within the first family of compounds, while keto-nitrile tautomers were favored in the second family. Copyright © 2010 Elsevier B.V. All rights reserved.

Direct NMR Evidence that Transient Tautomeric and Anionic States in dG·dT Form Watson-Crick-like Base Pairs.

Science.gov (United States)

Szymanski, Eric S; Kimsey, Isaac J; Al-Hashimi, Hashim M

2017-03-29

The replicative and translational machinery utilizes the unique geometry of canonical G·C and A·T/U Watson-Crick base pairs to discriminate against DNA and RNA mismatches in order to ensure high fidelity replication, transcription, and translation. There is growing evidence that spontaneous errors occur when mismatches adopt a Watson-Crick-like geometry through tautomerization and/or ionization of the bases. Studies employing NMR relaxation dispersion recently showed that wobble dG·dT and rG·rU mismatches in DNA and RNA duplexes transiently form tautomeric and anionic species with probabilities (≈0.01-0.40%) that are in concordance with replicative and translational errors. Although computational studies indicate that these exceptionally short-lived and low-abundance species form Watson-Crick-like base pairs, their conformation could not be directly deduced from the experimental data, and alternative pairing geometries could not be ruled out. Here, we report direct NMR evidence that the transient tautomeric and anionic species form hydrogen-bonded Watson-Crick-like base pairs. A guanine-to-inosine substitution, which selectively knocks out a Watson-Crick-type (G)N2H 2 ···O2(T) hydrogen bond, significantly destabilized the transient tautomeric and anionic species, as assessed by lack of any detectable chemical exchange by imino nitrogen rotating frame spin relaxation (R 1ρ ) experiments. An 15 N R 1ρ NMR experiment targeting the amino nitrogen of guanine (dG-N2) provides direct evidence for Watson-Crick (G)N2H 2 ···O2(T) hydrogen bonding in the transient tautomeric state. The strategy presented in this work can be generally applied to examine hydrogen-bonding patterns in nucleic acid transient states including in other tautomeric and anionic species that are postulated to play roles in replication and translational errors.

Spectrometric Study of the Nitrile-Ketenimines Tautomerism

International Nuclear Information System (INIS)

Cisneros, H.S.; Laurella, S.; Ruiz, D.L.; Ponzinibbio, A.; Allegretti, P.E.; Furlong, J.J.P.

2011-01-01

Mass spectrometry is used to evaluate the occurrence of the nitrile-ketenimines tautomerism. Mass spectra of two differently substituted nitriles, ethyl-4,4-dicyano-3-methyl-3-butenoate and diethyl-2-cyano-3-methyl-2-pentenodiate are examined looking for common mass spectral behaviors. Ion fragmentation assignments for specific tautomers allow to predict the presence of the corresponding structures. Additionally, the mass spectrum and nuclear magnetic resonance spectra of ethyl-4,4-dicyano-2,2-diethyl-3-methyl-3-butenoate and that of the corresponding amination product support the occurrence of the ketenimines tautomer in the equilibrium

Spectrometric Study of the Nitrile-Ketenimine Tautomerism

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Hebe Saraví Cisneros

2009-01-01

Full Text Available Mass spectrometry is used to evaluate the occurrence of the nitrile-ketenimine tautomerism. Mass spectra of two differently substituted nitriles, ethyl-4,4-dicyano-3-methyl-3-butenoate and diethyl-2-cyano-3-methyl-2-pentenodiate are examined looking for common mass spectral behaviors. Ion fragmentation assignments for specific tautomers allow to predict the presence of the corresponding structures. Additionally, the mass spectrum and nuclear magnetic resonance spectra of ethyl-4,4-dicyano-2,2-diethyl-3-methyl-3-butenoate and that of the corresponding amination product support the occurrence of the ketenimine tautomer in the equilibrium.

Direct determination of tautomerism in purine derivatives by low-temperature NMR spectroscopy

Czech Academy of Sciences Publication Activity Database

Sečkářová, P.; Marek, R.; Maliňáková, K.; Kolehmainen, E.; Hocková, Dana; Hocek, Michal; Sklenář, V.

2004-01-01

Roč. 45, č. 33 (2004), s. 6259-6263 ISSN 0040-4039 R&D Projects: GA MŠk LN00A016 Institutional research plan: CEZ:AV0Z4055905 Keywords : purine * NMR * tautomerism Subject RIV: CC - Organic Chemistry Impact factor: 2.484, year: 2004

METHOD FOR THE MEASUREMENT OF SITE-SPECIFIC TAUTOMERIC AND ZWITTERIONIC MICROSPECIES EQUILIBRIUM CONSTANTS

Science.gov (United States)

We describe a method for the individual measurement of simultaneously occurring, unimolecular, site-specific “microequilibrium” constants as in, for example, prototropic tautomerism and zwitterionic equilibria. Our method represents an elaboration of that of Nygren et al. (Anal. ...

Tautomerization and Dimerization of 6,13-Disubstituted Derivatives of Pentacene.

Science.gov (United States)

Garcia-Borràs, Marc; Konishi, Akihito; Waterloo, Andreas; Liang, Yong; Cao, Yang; Hetzer, Constantin; Lehnherr, Dan; Hampel, Frank; Houk, Kendall N; Tykwinski, Rik R

2017-05-02

Two new 6,13-disubstituted pentacene derivatives, 1 c and 1 d, with alkyl and triisopropylsilylethynyl substitution have been synthesized and characterized experimentally and computationally. The alkyl substituted 1 c and 1 d represent the first 6-alkyl-substituted pentacene derivative where the fully aromatic species dominates over the corresponding tautomer. Indeed, no tautomerization product is found for either 1 c or 1 d upon heating or in the presence of catalytic amounts of acid. On the other hand, an unexpected dimer (3 c) is formed from 1 c. A plausible mechanism for this new dimerization process of the 6-methyl-substituted pentacene derivative 1 c is proposed, which involves first a bimolecular hydrogen atom transfer followed by an intramolecular [4+2] Diels-Alder cycloaddition. In the case of 6-butyl substitution, neither tautomerization nor dimerization is observed. Computations support the proposed 1 c dehydrodimerization pathway, explain why 1 d does not dimerize, and show the importance of the nature of the group at C-13 in controlling the relative stability of 6-alkyl-substituted pentacene tautomers. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Tautomeric transformations of piroxicam in solution: a combined experimental and theoretical study

DEFF Research Database (Denmark)

Ivanova, D; Deneva, V; Nedeltcheva, D

2015-01-01

Piroxicam tautomerism was studied in solution by using UV-Vis spectroscopy, NMR measurements and advanced chemometrics. It has been found that in ethanol and DMSO the enol-amide tautomer is present mainly as a sandwich type dimer. The addition of water leads to distortion of the aggregate...

Tautomerism of N-(3,4-dichlorophenyl)-1H-indazole-5-carboxamide - A new selective, highly potent and reversible MAO-B inhibitor

Science.gov (United States)

Tzvetkov, Nikolay T.; Stammler, Hans-Georg; Antonov, Liudmil

2017-12-01

The tautomeric properties of an N-(3,4-dichlorophenyl)-1H-indazole-5-carboxamide (NTZ-1006, 2) derivative, developed as highly potent, reversible and selective MAO-B inhibitor useful for the treatment of Parkinson's disease (PD) and other neurological disorders, have been studied both experimentally and theoretically. The theoretical data (M06-2X, B3LYP and MP2-4 quantum chemical calculations) have shown that due to aromaticity reasons the 1H tautomer strongly dominates over the 2H form. There are no substantial spectral changes by changing the solvent and the concentration, which leads to a conclusion that compound 2 exists in solution as 1H tautomer and its tautomerism is not influenced by the solvents and the concentration. The results are in line with the understanding for the tautomerism of 1H-indazole and shows that substitution at the C5 position in the indazole unit does not influence the tautomeric state. The isolated crystal structure of 2 is in an excellent agreement with the computation in respect of the most stable tautomer. Combined single X-ray/molecular modeling studies including HYdrogen-DEsolvation (HYDE) analysis provided not only insights into the enzyme-inhibitor interaction within the binding site of the human MAO-B isoform, but also a valuable information regarding the most stable 1H-indazole tautomeric form of NTZ-1006 that contributes to its high potency against hMAO-B enzyme (IC50 0.586 nm) and selectivity (>17000-fold) over the hMAO-A isoenzyme.

Can tautomerization of the A·T Watson-Crick base pair via double proton transfer provoke point mutations during DNA replication? A comprehensive QM and QTAIM analysis.

Science.gov (United States)

Brovarets, Ol'ha O; Hovorun, Dmytro M

2014-01-01

Trying to answer the question posed in the title, we have carried out a detailed theoretical investigation of the biologically important mechanism of the tautomerization of the A·T Watson-Crick DNA base pair, information that is hard to establish experimentally. By combining theoretical investigations at the MP2 and density functional theory levels of QM theory with quantum theory of atoms in molecules analysis, the tautomerization of the A·T Watson-Crick base pair by the double proton transfer (DPT) was comprehensively studied in vacuo and in the continuum with a low dielectric constant (ϵ = 4) corresponding to a hydrophobic interfaces of protein-nucleic acid interactions. Based on the sweeps of the electron-topological, geometric, and energetic parameters, which describe the course of the tautomerization along its intrinsic reaction coordinate (IRC), it was proved that the A·T → A(∗)·T(∗) tautomerization through the DPT is a concerted (i.e. the pathway without an intermediate) and asynchronous (i.e. protons move with a time gap) process. The limiting stage of this phenomenon is the final PT along the N6H⋯O4 hydrogen bond (H-bond). The continuum with ϵ = 4 does not affect qualitatively the course of the tautomerization reaction: similar to that observed in vacuo, it proceeds via a concerted asynchronous process with the same structure of the transition state (TS). For the first time, the nine key points along the IRC of the A·T base pair tautomerization, which could be considered as electron-topological "fingerprints" of a concerted asynchronous process of the tautomerization via the DPT, have been identified and fully characterized. These nine key points have been used to define the reactant, TS, and product regions of the DPT in the A·T base pair. Considering the energy dependence of each of the three H-bonds, which stabilize the Watson-Crick and Löwdin's base pairs, along the IRC of the tautomerization, it was found that all these H

Density functional theory and surface enhanced Raman spectroscopy studies of tautomeric hypoxanthine and its adsorption behaviors in electrochemical processes

International Nuclear Information System (INIS)

Huang, Wei; Jiang, Jin-Zhi; Chen, Liang; Zhang, Bi-Qi; Deng, Shu-Fen; Sun, Jian Jun; Chen, Wen-Kai

2015-01-01

ABSTRACT: Hypoxanthine, a purine heterocyclic compound with N and O atoms, has capability to combine metal ions or adsorb on metals. By using density functional theory (DFT) method calculation, the energy, charge distribution, molecular orbital and vibration spectra information of tautomeric hypoxanthine were given. Combined with these DFT results, the influence of pH on the structure of tautomeric hypoxanthine was studied by surface enhanced Raman spectroscopy (SERS). Electrochemical SERS was applied to study the properties of hypoxanthine/gold interface. It is found that the structure of adsorbed hypoxanthine was changed from slightly tilted to upright with negatively moving of potentials

A DFT study of solvation effects and NBO analysis on the tautomerism of 1-substituted hydantoin

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Meisam Shabanian

2016-09-01

Full Text Available 1-Substituted hydantoins (1-SH have been known as a benefit intermediate for producing agricultural and pharmaceuticals. The effect of solvent polarity on the tautomeric equilibria of 1-substituted hydantoin ring is studied by the density functional theory calculation (B3LYP/6–31++G(d,p level for predominant tautomeric forms of hydantoin derivatives (1-NO2, 1-CF3, 1-Br, 1-H, 1-CHCH2, 1-OH, 1-CH3 in the gas phase and selected solvents (benzene (non-polar solvent, tetrahydrofuran (THF (polar aprotic solvent and water (protic solvent. For electron withdrawing and releasing derivatives in the gas phase and solution Hy1 forms is more stable and dominant form. In addition variation of dipole moments and charges on atoms in the solvents are studied.

Computational study of the NH-tautomerism in calix[4]phyrins observed by NMR spectroscopy

Czech Academy of Sciences Publication Activity Database

Horníček, Jan; Dvořáková, H.; Bouř, Petr

2009-01-01

Roč. 16, 1a (2009), b31-b31 ISSN 1211-5894. [Meeting of the Czechoslovak and Slovak Biologists /7./. 12.03.2009-14.03.2009, Nové Hrady] Institutional research plan: CEZ:AV0Z40550506 Keywords : calix[4]phyrin * NH-tautomerism * simulation * potential energy surface Subject RIV: CF - Physical ; Theoretical Chemistry

Tautomerism provides a molecular explanation for the mutagenic properties of the anti-HIV nucleoside 5-aza-5,6-dihydro-2'-deoxycytidine.

Science.gov (United States)

Li, Deyu; Fedeles, Bogdan I; Singh, Vipender; Peng, Chunte Sam; Silvestre, Katherine J; Simi, Allison K; Simpson, Jeffrey H; Tokmakoff, Andrei; Essigmann, John M

2014-08-12

Viral lethal mutagenesis is a strategy whereby the innate immune system or mutagenic pool nucleotides increase the error rate of viral replication above the error catastrophe limit. Lethal mutagenesis has been proposed as a mechanism for several antiviral compounds, including the drug candidate 5-aza-5,6-dihydro-2'-deoxycytidine (KP1212), which causes A-to-G and G-to-A mutations in the HIV genome, both in tissue culture and in HIV positive patients undergoing KP1212 monotherapy. This work explored the molecular mechanism(s) underlying the mutagenicity of KP1212, and specifically whether tautomerism, a previously proposed hypothesis, could explain the biological consequences of this nucleoside analog. Establishing tautomerism of nucleic acid bases under physiological conditions has been challenging because of the lack of sensitive methods. This study investigated tautomerism using an array of spectroscopic, theoretical, and chemical biology approaches. Variable temperature NMR and 2D infrared spectroscopic methods demonstrated that KP1212 existed as a broad ensemble of interconverting tautomers, among which enolic forms dominated. The mutagenic properties of KP1212 were determined empirically by in vitro and in vivo replication of a single-stranded vector containing a single KP1212. It was found that KP1212 paired with both A (10%) and G (90%), which is in accord with clinical observations. Moreover, this mutation frequency is sufficient for pushing a viral population over its error catastrophe limit, as observed before in cell culture studies. Finally, a model is proposed that correlates the mutagenicity of KP1212 with its tautomeric distribution in solution.

Supramolecular Influence on Keto-Enol Tautomerism and Thermochromic Properties of o-Hydroxy Schiff Bases

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Marija Zbačnik

2016-06-01

Full Text Available This work presents a study on thermo-optical properties of three Schiff bases (imines in the solid state. The Schiff bases were obtained by means of mechanochemical synthesis using monosubstituted o-hydroxy aromatic aldehydes and monosubstituted aromatic amines. The keto-enol tautomerism and proton transfer via intramolecular O∙∙∙N hydrogen bond of the reported compounds was found to be influenced more by supramolecular interactions than by a temperature change. All products were characterised by powder X-ray diffraction (PXRD, FT-IR spectroscopy, thermogravimetric (TG analysis and differential scanning calorimetry (DSC. Molecular and crystal structures of compounds 1, 2 and 3 were determined by single crystal X-ray diffraction (SCXRD. The molecules of 1 appear to be present as the enol-imine, the molecules of 2 as the keto-amine tautomer and the molecules of 3 exhibit keto-enol tautomeric equilibrium in the solid state. An analysis of Cambridge structural database (CSD data on similar imines has been used for structural comparison. This work is licensed under a Creative Commons Attribution 4.0 International License.

Computational study on a puzzle in the biosynthetic pathway of anthocyanin: Why is an enzymatic oxidation/ reduction process required for a simple tautomerization?

Science.gov (United States)

Sato, Hajime; Wang, Chao; Yamazaki, Mami; Saito, Kazuki; Uchiyama, Masanobu

2018-01-01

In the late stage of anthocyanin biosynthesis, dihydroflavonol reductase (DFR) and anthocyanidin synthase (ANS) mediate a formal tautomerization. However, such oxidation/reduction process requires high energy and appears to be unnecessary, as the oxidation state does not change during the transformation. Thus, a non-enzymatic pathway of tautomerization has also been proposed. To resolve the long-standing issue of whether this non-enzymatic pathway is the main contributor for the biosynthesis, we carried out density functional theory (DFT) calculations to examine this non-enzymatic pathway from dihydroflavonol to anthocyanidin. We show here that the activation barriers for the proposed non-enzymatic tautomerization are too high to enable the reaction to proceed under normal aqueous conditions in plants. The calculations also explain the experimentally observed requirement for acidic conditions during the final step of conversion of 2-flaven-3,4-diol to anthocyanidin; a thermodynamically and kinetically favorable concerted pathway can operate under these conditions.

Tautomerism of 4-hydroxy-2,5-dimethyl-3(2H)-furanone: evidence for its enantioselective biosynthesis.

Science.gov (United States)

Raab, Thomas; Hauck, Tobias; Knecht, Anja; Schmitt, Ulrich; Holzgrabe, Ulrike; Schwab, Wilfried

2003-08-01

Chiral natural flavor compounds exhibit characteristic enantiomeric excesses due to stereoselective, enzymatically catalyzed reactions during biogenesis. Although the enzymatic formation of the strawberry key flavor compound 4-hydroxy-2,5-dimethyl-3(2H)-furanone (HDMF; Furaneol(R)) is anticipated, the naturally occurring compound is racemic. As racemization due to keto-enol-tautomerism of HDMF could account for this observation, HDMF was investigated by (1)H-NMR spectroscopy tracing the exchange of the proton bound to the furanone-ring at C2 with deuteron from the medium (D(2)O). In addition, the racemization rate of HDMF was directly determined by cyclodextrin-modified capillary electrophoresis of enantiomerically enriched HDMF stored at different pH values. Tautomerism and the racemization rate of HDMF was lowest at pH values between 4 and 5. However, tautomerism and thus racemization was catalyzed under stronger acidic conditions (pH 2) and especially at pH values greater than 7, the value published for plant cell cytosol. Approximately 50% of the protons at C2 were exchanged with deuteron within 1 h at pH 7.2. Therefore, in order to demonstrate the enzymatic formation of HDMF, incubation experiments with Zygosaccharomyces rouxii as well as strawberry protein extract were carried out under slightly acidic conditions (pH 5), the most suitable pH value for studies on the enantiomeric ratio of HDMF. In both experiments the formation of enantiomerically enriched HDMF could be demonstrated for the first time, whereas incubation experiments under neutral conditions resulted in the detection of racemic HDMF. Copyright 2003 Wiley-Liss, Inc.

Chemicals from Biomass: Combining Ring-Opening Tautomerization and Hydrogenation Reactions to Produce 1,5-Pentanediol from Furfural.

Science.gov (United States)

Brentzel, Zachary J; Barnett, Kevin J; Huang, Kefeng; Maravelias, Christos T; Dumesic, James A; Huber, George W

2017-04-10

A process for the synthesis of 1,5-pentanediol (1,5-PD) with 84 % yield from furfural is developed, utilizing dehydration/hydration, ring-opening tautomerization, and hydrogenation reactions. Although this process has more reaction steps than the traditional direct hydrogenolysis of tetrahydrofurfuryl alcohol (THFA), techno-economic analyses demonstrate that this process is the economically preferred route for the synthesis of biorenewable 1,5-PD. 2-Hydroxytetrahydropyran (2-HY-THP) is the key reaction pathway intermediate that allows for a decrease in the minimum selling price of 1,5-PD. The reactivity of 2-HY-THP is 80 times greater than that of THFA over a bimetallic hydrogenolysis catalyst. This enhanced reactivity is a result of the ring-opening tautomerization to 5-hydoxyvaleraldehyde and subsequent hydrogenation to 1,5-PD. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Tautomerism provides a molecular explanation for the mutagenic properties of the anti-HIV nucleoside 5-aza-5,6-dihydro-2′-deoxycytidine

Science.gov (United States)

Li, Deyu; Fedeles, Bogdan I.; Singh, Vipender; Peng, Chunte Sam; Silvestre, Katherine J.; Simi, Allison K.; Simpson, Jeffrey H.; Tokmakoff, Andrei; Essigmann, John M.

2014-01-01

Viral lethal mutagenesis is a strategy whereby the innate immune system or mutagenic pool nucleotides increase the error rate of viral replication above the error catastrophe limit. Lethal mutagenesis has been proposed as a mechanism for several antiviral compounds, including the drug candidate 5-aza-5,6-dihydro-2′-deoxycytidine (KP1212), which causes A-to-G and G-to-A mutations in the HIV genome, both in tissue culture and in HIV positive patients undergoing KP1212 monotherapy. This work explored the molecular mechanism(s) underlying the mutagenicity of KP1212, and specifically whether tautomerism, a previously proposed hypothesis, could explain the biological consequences of this nucleoside analog. Establishing tautomerism of nucleic acid bases under physiological conditions has been challenging because of the lack of sensitive methods. This study investigated tautomerism using an array of spectroscopic, theoretical, and chemical biology approaches. Variable temperature NMR and 2D infrared spectroscopic methods demonstrated that KP1212 existed as a broad ensemble of interconverting tautomers, among which enolic forms dominated. The mutagenic properties of KP1212 were determined empirically by in vitro and in vivo replication of a single-stranded vector containing a single KP1212. It was found that KP1212 paired with both A (10%) and G (90%), which is in accord with clinical observations. Moreover, this mutation frequency is sufficient for pushing a viral population over its error catastrophe limit, as observed before in cell culture studies. Finally, a model is proposed that correlates the mutagenicity of KP1212 with its tautomeric distribution in solution. PMID:25071207

Tautomeric transition between wobble A·C DNA base mispair and Watson-Crick-like A·C* mismatch: microstructural mechanism and biological significance.

Science.gov (United States)

Brovarets', Ol'ha O; Hovorun, Dmytro M

2015-06-21

Here, we use MP2/DFT quantum-chemical methods combined with Quantum Theory of Atoms in Molecules to study the tautomeric transition between wobble A·C(w) mismatch and Watson-Crick-like A·C*(WC) base mispair, proceeding non-dissociatively via sequential proton transfer between bases through the planar, highly stable and zwitterionic TS(A∙C-)(A∙C(W)A∙C&(WC)) transition state joined by the participation of (A)N6(+)H∙∙∙N4(-)(C), (A)N1(+)H∙∙∙N4(-)(C) and (A)C2(+)H∙∙∙N3(-)(C) H-bonds. Notably, the A·C(w) ↔ A·C*(WC) tautomerization reaction is accompanied by 10 unique patterns of the specific intermolecular interactions that consistently replace each other. Our data suggest that biologically significant A·C(w) → A·C*(WC) tautomerization is a kinetically controlled pathway for formation of the enzymatically competent Watson-Crick-like A·C*(WC) DNA base mispair in the essentially hydrophobic recognition pocket of the high-fidelity DNA-polymerase, responsible for the occurrence of spontaneous point AC/CA incorporation errors during DNA biosynthesis.

Direct and solvent-assisted thione–thiol tautomerism in 5-(thiophen-2-yl)-1,3,4-oxadiazole-2(3H)-thione: Experimental and molecular modeling study

Energy Technology Data Exchange (ETDEWEB)

Burcu Arslan, N. [Department of Computer Education and Instructional Technology, Faculty of Education, Giresun University, 28100 Giresun (Turkey); Özdemir, Namık, E-mail: namiko@omu.edu.tr [Department of Physics, Faculty of Arts and Sciences, Ondokuz Mayıs University, 55139 Samsun (Turkey); Dayan, Osman, E-mail: osmandayan@comu.edu.tr [Laboratory of Inorganic Synthesis and Molecular Catalysis, Çanakkale Onsekiz Mart University, 17020 Çanakkale (Turkey); Dege, Necmi [Department of Physics, Faculty of Arts and Sciences, Ondokuz Mayıs University, 55139 Samsun (Turkey); Koparır, Metin [Department of Chemistry, Faculty of Science, Fırat University, 23169 Elazığ (Turkey); Koparır, Pelin [Department of Chemistry, Forensic Medicine Institute, 44000 Malatya (Turkey); Muğlu, Halit [Department of Chemistry, Faculty of Arts and Sciences, Kastamonu University, 37200 Kastamonu (Turkey)

2014-08-17

Graphical abstract: - Highlights: • The molecule exists in the thione form in the solid state. • FT-IR and NMR data support the thione form. • The anti-thione conformer has the lowest energy. • The barrier height increases with increasing polarity of the solvent. • Multiple methanol or water-assisted thione–thiol tautomerism may happen. - Abstract: The compound has been synthesized and characterized by IR, NMR and X-ray diffraction. Quantum chemical calculations at B3LYP/6−311++G(d,p) level were performed to study the molecular and spectroscopic properties, conformational equilibrium, thione ↔ thiol tautomerism and intermolecular double proton transfer reaction of the compound. The obtained structural and spectroscopic results are well in agreement with the experimental data. The solvent effect on the proton transfer reaction was investigated in three solvents using the polarizable continuum model approximation and solvent-assisted mechanism. The anti-thione tautomer is the most stable isomer among the four possible structural forms both in the gas phase and in solution phase. A high tautomeric energy barrier is found for the tautomerism between the anti and syn forms of the compound, indicating a quite disfavored process. Although the presence of one methanol or water solvent molecule significantly lowers the energy barrier, it is not adequate for the reaction to occur.

Theoretical and vibrational spectroscopic approach to keto-enol tautomerism in methyl-2-(4-methoxybenzoyl)-3-(4-methoxyphenyl)-3-oxopropanoylcarbamate

Science.gov (United States)

Arı, Hatice; Özpozan, Talat; Büyükmumcu, Zeki; Kabacalı, Yiğit; Saçmaci, Mustafa

2016-10-01

A carbamate compound having tricarbonyl groups, methyl-2-(4-methoxybenzoyl)-3-(4-methoxyphenyl)-3-oxopropanoylcarbamate (BPOC) was investigated from theoretical and vibrational spectroscopic point of view employing quantum chemical methods. Hybrid Density Functionals (B3LYP, X3LYP and B3PW91) with 6-311 G(d,p) basis set were used for the calculations. Rotational barrier and conformational analyses were performed to find the most stable conformers of keto and enol forms of the molecule. Three transition states for keto-enol tautomerism in gas phase were determined. The results of the calculations show that enol-1 form of BPOC is more stable than keto and enol-2 forms. Hydrogen bonding investigation including Natural bond orbital analysis (NBO) for all the tautomeric structures was employed to compare intra-molecular interactions. The energies of HOMO and LUMO molecular orbitals for all tautomeric forms of BPOC were predicted. Normal Coordinate Analysis (NCA) was carried out for the enol-1 to assign vibrational bands of IR and Raman spectra. The scaling factors were calculated as 0.9721, 0.9697 and 0.9685 for B3LYP, X3LYP and B3PW91 methods, respectively. The correlation graphs of experimental versus calculated vibrational wavenumbers were plotted and X3LYP method gave better frequency agreement than the others.

Conformer-Specific IR Spectroscopy of Laser-Desorbed Sulfonamide Drugs: Tautomeric and Conformational Preferences of Sulfanilamide and its Derivatives

Science.gov (United States)

Uhlemann, Thomas; Seidel, Sebastian; Müller, Christian W.

2017-06-01

Molecules containing the sulfonamide group R^{1}-SO_2-NHR^{2} have a longstanding history as antimicrobial agents. Even though nowadays they are not commonly used in treating humans anymore, they continue to be studied as effective inhibitors of metalloenzyme carbonic anhydrases. These enzymes are important targets for a variety of diseases, such as, for instance, breast cancer, glaucoma, and obesity. Here we present the results of our laser desorption single-conformation UV and IR study of sulfanilamide (NH_2Ph-SO_2-NHR, R=H), a variety of singly substituted derivatives, and their monohydrated complexes. Depending on the substituent, the sulfonamide group can either adopt an amino or an imino tautomeric form. The form prevalent in the crystal is not necessarily also the tautomeric form we identified in the molecular beam after laser desorbing the sample. Furthermore, we explored the effect of complexation with a single water molecule on the tautomeric and conformational preferences of the sulfonamides. Our conformer-specific IR spectra in the NH and OH stretch region (3200-3750 \\wn) suggest that the intra- and intermolecular interactions governing the structures of the monomers and water complexes are surprisingly diverse. We have undertaken both Quantum Theory of Atoms in Molecules (QTAIM) and Interacting Quantum Atoms (IQA) analyses of calculated electron densities to quantitatively characterize the nature and strengths of the intra- and intermolecular interactions prevalent in the monomer and water complex structures.

Electronic structure tautomerism, and mechanism of H-D exchange in imidazole aqueous solutions

International Nuclear Information System (INIS)

Borisov, Yu.A.; Vorob'eva, N.P.; Abronin, I.A.; Kolomiets, A.F.

1988-01-01

The imidazole electronic structure in a gaseous phase is studied taking into account the influence of solvation effects in aqueous solutions. Possible mechanisms of tautomeric transformations and H-D exchange reactions with water molecules are discussed. Using the quantum chemistry methods, it is shown that the intramolecular mechanism of imidazole isomerization in the gaseous phase and the aqueous solution is unprofitable, and the intermolecular mechanism can proceed through the stage of protonated and carbene form formation

Modeling Chemical Reactions by QM/MM Calculations: The Case of the Tautomerization in Fireflies Bioluminescent Systems.

Science.gov (United States)

Berraud-Pache, Romain; Garcia-Iriepa, Cristina; Navizet, Isabelle

2018-01-01

In less than half a century, the hybrid QM/MM method has become one of the most used technique to model molecules embedded in a complex environment. A well-known application of the QM/MM method is for biological systems. Nowadays, one can understand how enzymatic reactions work or compute spectroscopic properties, like the wavelength of emission. Here, we have tackled the issue of modeling chemical reactions inside proteins. We have studied a bioluminescent system, fireflies, and deciphered if a keto-enol tautomerization is possible inside the protein. The two tautomers are candidates to be the emissive molecule of the bioluminescence but no outcome has been reached. One hypothesis is to consider a possible keto-enol tautomerization to treat this issue, as it has been already observed in water. A joint approach combining extensive MD simulations as well as computation of key intermediates like TS using QM/MM calculations is presented in this publication. We also emphasize the procedure and difficulties met during this approach in order to give a guide for this kind of chemical reactions using QM/MM methods.

Modelling chemical reactions by QM/MM calculations: the case of the tautomerization in fireflies bioluminescent systems

Science.gov (United States)

Berraud-Pache, Romain; Garcia-Iriepa, Cristina; Navizet, Isabelle

2018-04-01

In less than half a century, the hybrid QM/MM method has become one of the most used technique to model molecules embedded in a complex environment. A well-known application of the QM/MM method is for biological systems. Nowadays, one can understand how enzymatic reactions work or compute spectroscopic properties, like the wavelength of emission. Here, we have tackled the issue of modelling chemical reactions inside proteins. We have studied a bioluminescent system, fireflies, and deciphered if a keto-enol tautomerization is possible inside the protein. The two tautomers are candidates to be the emissive molecule of the bioluminescence but no outcome has been reached. One hypothesis is to consider a possible keto-enol tautomerization to treat this issue, as it has been already observed in water. A joint approach combining extensive MD simulations as well as computation of key intermediates like TS using QM/MM calculations is presented in this publication. We also emphasize the procedure and difficulties met during this approach in order to give a guide for this kind of chemical reactions using QM/MM methods.

Synthesis, Acidity Constants and Tautomeric Structure of the Diazonium Coupling Products of 2-(Benzylsulfanyl-7H-purin-6-one in Its Ground and Excited States

Directory of Open Access Journals (Sweden)

Hosam A. Saad

2011-10-01

Full Text Available A series of new 8-arylhydrazono-2-(benzylsulfanyl-7H-purin-6-ones 6 were synthesized, their electronic absorption spectra in different organic solvents of varying polarities were investigated and their acid dissociation constants in both the ground and excited states were determined spectrophotometrically. The tautomeric structures of such products were elucidated by spectral analyses and correlation of their acid dissociation constants with the Hammett equation. The results indicated that the studied compounds 6 exist predominantly in the hydrazone tautomeric form 6A in both the ground and excited states.

Investigation of tautomeric transformations of adducts of 7,8-dicarba-nido-undecaborana(11) with derivatives of pyridine by 11B NMR spectroscopy method

International Nuclear Information System (INIS)

Volkov, O.V.; Il'inchik, E.A.; Volkov, V.V.

1999-01-01

Tautomeric transformations are investigated in solutions of o-carborane(12) derivatives 7,8-C 2 B 9 H 11 ·Py(X), where Py(X)=4-picoline (4-CH 3 -C 5 H 4 N), 3-picoline (3-CH 3 -C 5 H 4 N), 4-stilbazol (4-C 6 H 5 -C 2 H 2 -C 5 H 4 N), 3-bromopyridine (3-Br-C 5 H 4 N) and 7,8-C 2 B 9 H 10 I·C 5 H 5 N. Uncovered tautomeric transformations are bound with migration of bridge hydrogen of C 2 B 9 H 11 cluster assisting in structure of these compounds. Signal of boron nuclei in 11 B NMR spectra is observed in the region of high field of spectrum if the nearest two atoms of boron are bounded by bridge hydrogen additionally. That permits to fix happening dynamic structural transformations of adducts investigated. The dependence of tautomeric equilibrium on nature of substituents introduced in heterocyclic ligand and carborane cluster. Increase of electron-acceptor properties of substituent induces displacement of equilibrium in the direction of tautomer bridge hydrogen in which is removed from boron atom bounded with substituent [ru

Theoretical study on the molecular tautomerism of the 3-hydroxy-pyridin-4-one system

Science.gov (United States)

Zborowski, Krzysztof K.; Mohammadpour, Mehrdad; Sadeghi, Amir; Proniewicz, Leonard M.

2013-04-01

3-hydroxy-pyridin-4-one is a parent molecule for the family of hydroxypyridinones that are known in coordination chemistry as efficient metal ions chelators. In this work, relative stabilities of some possible tautomers were investigated using several quantum chemical methods: CBS (complete basis set methods), Gn, DFT (density functional theory), Hartree-Fock and MP2. Performed calculations show that the system under consideration exists as a mixture of two tautomers with comparable energies. Among them, the hydroxypyridinone structure of the studied molecular system seems to be a bit more stable than the o-dihydroxypyridine one, by a few kJ/mol only. Aromaticity and intra-molecular hydrogen bonding are the main effects influencing the stability of the studied tautomeric structures. Consequently, aromatic effects were calculated using several indices of aromaticity: HOMA (harmonic oscillator model of aromaticity), NICS (nucleus independent chemical shift), H, PDI (para delocalisation index), MCI (multi-centre index) and ASE (aromatic stabilisation energy). The strength of possible intra-molecular hydrogen bonds (H-bonds) was determined by means of the AIM (atoms-in-molecules) method and by calculating enthalpies for theoretical reactions that do or do not involve H-bonds. The AIM method was employed to understand how variations in atomic energies influence the stability of different tautomeric structures.

Time-resolved spectroscopic characterization of photo-induced valence tautomerism for a cobalt dioxolene complex

Science.gov (United States)

Gentili, Pier Luigi; Bussotti, Laura; Righini, Roberto; Beni, Alessandra; Bogani, Lapo; Dei, Andrea

2005-07-01

The valence tautomerism of low-spin Co III(Cat-N-BQ)(Cat-N-SQ) (where Cat-N-BQ is 2-(2-hydroxy-3,5-di- tert-butylphenylimino)-4,6-di- tert-butylcyclohexa-3,5-dienone and Cat-N-SQ is the dianionic radical analogue) was investigated by means of UV-vis pump-probe transient absorption spectroscopy and 1H NMR technique in chloroform and dichloromethane. By exciting the CT transition of the complex at 480 nm, an intramolecular electron transfer process is selectively triggered. The photo-induced charge transfer is pursued by a cascade of two main molecular events characterized by the ultrafast transient absorption spectroscopy: the first gives rise to the metastable high-spin Co II(Cat-N-BQ) 2 that, secondly, reaches the chemical equilibrium with the reactant species. The rate constant of back valence tautomerization estimated by measuring the lifetime of high-spin Co II(Cat-N-BQ) 2 species and the equilibrium constant for the Co III(Cat-N-BQ)(Cat-N-SQ) ⇄ Co II(Cat-N-BQ) 2 interconversion, is significantly large (on the order of 10 9 s -1). It is interpreted under the point of view of the theory formulated by Jortner and Buhks et al. for non-adiabatic radiationless processes.

Time-resolved spectroscopic characterization of photo-induced valence tautomerism for a cobalt-dioxolene complex

International Nuclear Information System (INIS)

Gentili, Pier Luigi; Bussotti, Laura; Righini, Roberto; Beni, Alessandra; Bogani, Lapo; Dei, Andrea

2005-01-01

The valence tautomerism of low-spin Co III (Cat-N-BQ)(Cat-N-SQ) (where Cat-N-BQ is 2-(2-hydroxy-3,5-di-tert-butylphenylimino)-4,6-di-tert-butylcyclohexa-3, 5-dien one and Cat-N-SQ is the dianionic radical analogue) was investigated by means of UV-vis pump-probe transient absorption spectroscopy and 1 H NMR technique in chloroform and dichloromethane. By exciting the CT transition of the complex at 480 nm, an intramolecular electron transfer process is selectively triggered. The photo-induced charge transfer is pursued by a cascade of two main molecular events characterized by the ultrafast transient absorption spectroscopy: the first gives rise to the metastable high-spin Co II (Cat-N-BQ) 2 that, secondly, reaches the chemical equilibrium with the reactant species. The rate constant of back valence tautomerization estimated by measuring the lifetime of high-spin Co II (Cat-N-BQ) 2 species and the equilibrium constant for the Co III (Cat-N-BQ)(Cat-N-SQ) Co II (Cat-N-BQ) 2 interconversion, is significantly large (on the order of 10 9 s -1 ). It is interpreted under the point of view of the theory formulated by Jortner and Buhks et al. for non-adiabatic radiationless processes

How many tautomerization pathways connect Watson-Crick-like G*·T DNA base mispair and wobble mismatches?

Science.gov (United States)

Brovarets', Ol'ha O; Hovorun, Dmytro M

2015-01-01

In this study, we have theoretically demonstrated the intrinsic ability of the wobble G·T(w)/G*·T*(w)/G·T(w1)/G·T(w2) and Watson-Crick-like G*·T(WC) DNA base mispairs to interconvert into each other via the DPT tautomerization. We have established that among all these transitions, only one single G·T(w) ↔ G*·T(WC) pathway is eligible from a biological perspective. It involves short-lived intermediate - the G·T*(WC) base mispair - and is governed by the planar, highly stable, and zwitterionic [Formula: see text] transition state stabilized by the participation of the unique pattern of the five intermolecular O6(+)H⋯O4(-), O6(+)H⋯N3(-), N1(+)H⋯N3(-), N1(+)H⋯O2(-), and N2(+)H⋯O2(-) H-bonds. This non-dissociative G·T(w) ↔ G*·T(WC) tautomerization occurs without opening of the pair: Bases within mispair remain connected by 14 different patterns of the specific intermolecular interactions that successively change each other along the IRC. Novel kinetically controlled mechanism of the thermodynamically non-equilibrium spontaneous point GT/TG incorporation errors has been suggested. The mutagenic effect of the analogues of the nucleotide bases, in particular 5-bromouracil, can be attributed to the decreasing of the barrier of the acquisition by the wobble pair containing these compounds of the enzymatically competent Watson-Crick's geometry via the intrapair mutagenic tautomerization directly in the essentially hydrophobic recognition pocket of the replication DNA-polymerase machinery. Proposed approaches are able to explain experimental data, namely growth of the rate of the spontaneous point incorporation errors during DNA biosynthesis with increasing temperature.

Tautomerism, ionization, and bond dissociations of 5-nitro-2,4-dihydro-3H-1,2,4-triazolone.

NARCIS (Netherlands)

Harris, N.J.; Lammertsma, K.

1996-01-01

Tautomerization, ionization, and bond dissociations of the insensitive high-energy explosive 5-nitro-2,4-dihydro-3H-1,2,4-triazolone (NTO) were studied by molecular orbital SCF and MP2 theories and with the Becke3LYP hybrid density functional using the 6-31+G* and 6-311+G** basis sets. Energies

Hydroxylamine and methoxyamine mutagenesis: displacement of the tautomeric equilibrium of the promutagen N6-methoxyadenosine by complementary base pairing.

Science.gov (United States)

Stolarski, R; Kierdaszuk, B; Hagberg, C E; Shugar, D

1984-06-19

The imino-amino tautomeric equilibrium of the promutagenic adenosine analogue N6-methoxy-2',3',5'-tri-O-methyladenosine [OMe6A(Me)3], in solvents of various polarities, has been studied with the aid of 1H and 13C NMR spectroscopy. The high energy barrier (free enthalpy delta G = 80 +/- 5 kJ X mol-1) between the two tautomeric species renders possible direct observation of the independent sets of all 1H and 13C signals from each of them. The equilibrium ranges from 10% imino in CCl4 to 90% in aqueous medium. Thermodynamic parameters, including energy barriers and lifetimes, were calculated from the temperature dependence of the equilibrium. Essentially similar results prevail for the promutagenic N6-hydroxy analogue. The conformations of the sugar moieties, and of the base about the glycosidic bond, for both tautomers are similar to those for adenosine. The conformation of the exocyclic N6-OCH3 group, which determines the ability of each species to form planar associates (hydrogen-bonded base pairs), has also been evaluated. Formation of autoassociates of OMe6A(Me)3 and of heteroassociates with the potentially complementary 2',3',5'-tri-O-methyluridine and -cytidine, in chloroform solution, was also investigated. The amino form base pairs with uridine and the imino form with cytidine. Formation of a complementary base pair by a given tautomeric species was accompanied by an increase of up to 10% in the population of this species and a concomitant decrease in population of the other species.(ABSTRACT TRUNCATED AT 250 WORDS)

1,1´,1´´-(2,4,6-Trihydroxybenzene-1,3,5-triyl)triethanone tautomerism revisited

DEFF Research Database (Denmark)

Hansen, Poul Erik; Kamounah, Fadhil S.; Zhiryakova, Diana

2014-01-01

It has recently been suggested that 1,1′,1′′-(2,4,6-trihydroxybenzene-1,3,5-triyl)triethanone may be tautomeric. Using 13C NMR chemical shifts and deuterium isotope effects on 13C chemical shifts, it is demonstrated that this is not the case. This compound occurs as a strongly hydrogen bonded ben...

Electronic effects of substituents in o-hydroxyazo compounds and azoquinone-hydrazone tautomerism

International Nuclear Information System (INIS)

Raikhshtat, M.M.; Zhogina, V.V.; Savvin, S.B.

1987-01-01

The authors have investigated the electronic structure of p-substituted phenylazonaphthol and some o-hydroxyazo compounds of the general structure X-N=N-Y. The influence of structural changes of the X and Y radicals on the electronic structure of the o-hydroxyazo group was studied. The results are compared with experimental data, obtained by NMR 13 C, by tautomerism of these compounds in solution in CDCl 3 . The electronic structure of o-hydroxyazo compounds was calculated by the PPDP/2 method. This method satisfactorily describes the electronic structure of organic compounds and correctly reproduces electronic effects of the substituents

Time-resolved spectroscopic characterization of photo-induced valence tautomerism for a cobalt-dioxolene complex

Energy Technology Data Exchange (ETDEWEB)

Gentili, Pier Luigi [LENS, Universita di Firenze, Via Nello Carrara 1, 50019 Sesto Fiorentino, Firenze (Italy)], E-mail: gentili@lens.unifi.it; Bussotti, Laura [LENS, Universita di Firenze, Via Nello Carrara 1, 50019 Sesto Fiorentino, Firenze (Italy); Righini, Roberto [LENS, Universita di Firenze, Via Nello Carrara 1, 50019 Sesto Fiorentino, Firenze (Italy); Dipartimento di Chimica, Universita di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino, Firenze (Italy)], E-mail: righini@lens.unifi.it; Beni, Alessandra [Dipartimento di Chimica, Universita di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino, Firenze (Italy); Bogani, Lapo [Dipartimento di Chimica, Universita di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino, Firenze (Italy); Dei, Andrea [Dipartimento di Chimica, Universita di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino, Firenze (Italy)

2005-07-18

The valence tautomerism of low-spin Co{sup III}(Cat-N-BQ)(Cat-N-SQ) (where Cat-N-BQ is 2-(2-hydroxy-3,5-di-tert-butylphenylimino)-4,6-di-tert-butylcyclohexa-3, 5-dien one and Cat-N-SQ is the dianionic radical analogue) was investigated by means of UV-vis pump-probe transient absorption spectroscopy and {sup 1}H NMR technique in chloroform and dichloromethane. By exciting the CT transition of the complex at 480 nm, an intramolecular electron transfer process is selectively triggered. The photo-induced charge transfer is pursued by a cascade of two main molecular events characterized by the ultrafast transient absorption spectroscopy: the first gives rise to the metastable high-spin Co{sup II}(Cat-N-BQ){sub 2} that, secondly, reaches the chemical equilibrium with the reactant species. The rate constant of back valence tautomerization estimated by measuring the lifetime of high-spin Co{sup II}(Cat-N-BQ){sub 2} species and the equilibrium constant for the Co{sup III}(Cat-N-BQ)(Cat-N-SQ) <-> Co{sup II}(Cat-N-BQ){sub 2} interconversion, is significantly large (on the order of 10{sup 9} s{sup -1}). It is interpreted under the point of view of the theory formulated by Jortner and Buhks et al. for non-adiabatic radiationless processes.

Tautomeric transformation of temozolomide, their proton affinities and chemical reactivities: A theoretical approach.

Science.gov (United States)

Sang-Aroon, Wichien; Ruangpornvisuti, Vithaya; Amornkitbamrung, Vittaya

2016-05-01

The gas-phase geometry optimizations of bare, mono- and dihydrated complexes of temozolomide isomers were carried out using density functional calculation at the M06-2X/6-31+G(d,p) level of the theory. The structures and protonation energies of protonated species of temozolomide are reported. Chemical indices of all isomers and protonated species are also reported. Energies, thermodynamic quantities, rate constants and equilibrium constants of tautomeric and rotameric transformations of all isomers I1↔TZM↔HIa↔HIb↔I2↔I3 in bare and hydrated systems were obtained. Copyright © 2016 Elsevier Inc. All rights reserved.

Characterization of photo-induced valence tautomerism in a cobalt-dioxolene complex by ultrafast spectroscopy

International Nuclear Information System (INIS)

Beni, A; Bogani, L; Bussotti, L; Dei, A; Gentili, P L; Righini, R

2005-01-01

The valence tautomerism of low-spin Co III (Cat-N-BQ)(Cat-N-SQ) was investigated by means of UV-vis pump-probe transient absorption spectroscopy in chloroform. By exciting the CT transition of the complex at 480 nm, an intramolecular electron transfer process is selectively triggered. The photo-induced charge transfer is pursued by a cascade of two main molecular events characterized by the ultrafast transient absorption spectroscopy: the first gives rise to the metastable high-spin Co II (Cat-N-BQ) 2 that, secondly, reaches the chemical equilibrium with the reactant species

Characterization of photo-induced valence tautomerism in a cobalt-dioxolene complex by ultrafast spectroscopy

Science.gov (United States)

Beni, A.; Bogani, L.; Bussotti, L.; Dei, A.; Gentili, P. L.; Righini, R.

2005-01-01

The valence tautomerism of low-spin CoIII(Cat-N-BQ)(Cat-N-SQ) was investigated by means of UV-vis pump-probe transient absorption spectroscopy in chloroform. By exciting the CT transition of the complex at 480 nm, an intramolecular electron transfer process is selectively triggered. The photo-induced charge transfer is pursued by a cascade of two main molecular events characterized by the ultrafast transient absorption spectroscopy: the first gives rise to the metastable high-spin CoII(Cat-N-BQ)2 that, secondly, reaches the chemical equilibrium with the reactant species.

Controlled shift in the tautomeric equilibrium of 4-​((phenylimino)​methyl)​naphthalen-​1-​ol

DEFF Research Database (Denmark)

Kamounah, Fadhil S.; Deneva, V; Manolova, y

2013-01-01

-​((Phenylimino)​methyl)​naphthalen-​1-​ol and 4-​((phenylimino)​methyl)​-​2-​(piperidin-​1-​ylmethyl)​naphthalen-​1-​ol have been synthesized and their tautomeric properties were investigated using mol. spectroscopy (UV-​vis absorption​/emission and NMR)​, X-​ray crystallog. anal. and quantum-​c...

4-Carboxyl-2,6-dinitrophenylazohydroxynaphthalenes tautomerism NMR re-explained and other methods verified

DEFF Research Database (Denmark)

Hristova, Silvia; Angelova, Silvia; Hansen, Poul Erik

2017-01-01

In two consecutive studies the tautomerism in 4-((2-hydroxynaphthalen-1-yl)diazenyl)-3,5-dinitrobenzoic acid and the structurally similar 1-((2-nitrophenyl)diazenyl)naphthalen-2-ol has been considered from viewpoint of theoretical chemistry, UV–Vis spectroscopy and NMR. Although the theoretical...... data (at M062X level) show that both compounds exist only as a keto tautomer, the experiment proves existence of the enol form. The difference in the results obtained by UV–Vis spectroscopy and NMR requires a deeper consideration and verification of the NMR approach, which is based on using model...... compounds to provide the NMR signal pattern of individual tautomers....

Creatinine and creatininium cation in water solution. Tautomerism and quantitative interpretation of the solution acidity effect on 1H, 13C and 1:4N NMR chemical shifts

International Nuclear Information System (INIS)

Kotsyubynskyy, D.; Molchanov, S.; Gryff-Keller, A.

2004-01-01

1 H, 13 C and 1 :4N NMR chemical shifts for creatinine in water solution of various acidity have been measured. Analysis of these data enabled determination of the acidity constant of creatininium cation and the chemical shifts of the neutral and protonated forms of creatinine. Molecular energies and carbon and nitrogen magnetic shielding constants for various tautomeric structures of the investigated species have been calculated using the quantum chemistry method GIAO DFT B3LYP/6-311++G(2d,p). Compilation of the available experimental and theoretical results has provided additional information on the problem of tautomerism of this important biological molecule. (author)

Characterization of photo-induced valence tautomerism in a cobalt-dioxolene complex by ultrafast spectroscopy

Energy Technology Data Exchange (ETDEWEB)

Beni, A [Dipartimento di Chimica, Universita di Firenze, via della Lastruccia 3, 50019 Sesto Fiorentino, Florence (Italy); Bogani, L [Dipartimento di Chimica, Universita di Firenze, via della Lastruccia 3, 50019 Sesto Fiorentino, Florence (Italy); Bussotti, L [LENS, Universita di Firenze, Via Nello Carrara 1, 50019 Sesto Fiorentino, Florence (Italy); Dei, A [Dipartimento di Chimica, Universita di Firenze, via della Lastruccia 3, 50019 Sesto Fiorentino, Florence (Italy); Gentili, P L [LENS, Universita di Firenze, Via Nello Carrara 1, 50019 Sesto Fiorentino, Florence (Italy); Righini, R [Dipartimento di Chimica, Universita di Firenze, via della Lastruccia 3, 50019 Sesto Fiorentino, Florence (Italy)

2005-01-01

The valence tautomerism of low-spin Co{sup III}(Cat-N-BQ)(Cat-N-SQ) was investigated by means of UV-vis pump-probe transient absorption spectroscopy in chloroform. By exciting the CT transition of the complex at 480 nm, an intramolecular electron transfer process is selectively triggered. The photo-induced charge transfer is pursued by a cascade of two main molecular events characterized by the ultrafast transient absorption spectroscopy: the first gives rise to the metastable high-spin Co{sup II}(Cat-N-BQ){sub 2} that, secondly, reaches the chemical equilibrium with the reactant species.

Tautomerism and the Protonation/Deprotonation of Isocytosine in Liquid- and Solid-States Studied by NMR Spectroscopy and Theoretical Calculations

Czech Academy of Sciences Publication Activity Database

Dračínský, Martin; Jansa, Petr; Ahonen, K.; Buděšínský, Miloš

-, č. 8 (2011), s. 1544-1551 ISSN 1434-193X R&D Projects: GA AV ČR KJB400550903; GA MŠk 1M0508 Grant - others:AV ČR(CZ) M200380901 Institutional research plan: CEZ:AV0Z40550506 Keywords : NMR spectroscopy * tautomerism * nitrogen heterocycles * density functional calculations Subject RIV: CC - Organic Chemistry Impact factor: 3.329, year: 2011

Intermediate-Valence Tautomerism in Decamethylytterbocene Complexes of Methyl-Substituted Bipyridines

Energy Technology Data Exchange (ETDEWEB)

Booth, Corwin H.; Kazhdan, Daniel; Werkema, Evan L.; Walter, Marc D.; Lukens, Wayne W.; Bauer, Eric D.; Hu, Yung-Jin; Maron, Laurent; Eisenstein, Odile; Head-Gordon, Martin; Andersen, Richard A.

2011-01-25

Multiconfigurational, intermediate valent ground states are established in several methyl-substituted bipyridine complexes of bispentamethylcyclopentadienylytterbium, Cp*{sub 2} Yb(Me{sub x}-bipy). In contrast to Cp*{sub 2} Yb(bipy) and other substituted-bipy complexes, the nature of both the ground state and the first excited state are altered by changing the position of the methyl or dimethyl substitutions on the bipyridine rings. In particular, certain substitutions result in multiconfigurational, intermediate valent open-shell singlet states in both the ground state and the first excited state. These conclusions are reached after consideration of single-crystal x-ray diffraction (XRD), the temperature dependence of x-ray absorption near-edge structure (XANES), extended x-ray absorption fine-structure (EXAFS), and magnetic susceptibility data, and are supported by CASSCF-MP2 calculations. These results place the various Cp*{sub 2}Yb(bipy) complexes in a new tautomeric class, that is, intermediate-valence tautomers.

Prototropic tautomerism of 4-Methyl 1,2,4-Triazole-3-Thione molecule in solvent water medium: DFT and Car–Parrinello molecular dynamics study

International Nuclear Information System (INIS)

Dutta, Bipan; De, Rina; Chowdhury, Joydeep

2015-01-01

Highlights: • The tautomerism of 4-MTTN molecule in solvent water medium has been investigated. • CPMD presage the possibility of PT reactions through the solvent water medium. • Concerted PT processes in 4-MTTN have been estimated from the DFT and NBO analyses. • Percentage evolution and breaking of the concerned bonds are estimated. - Abstract: The ground state prototropic tautomerism of 4-Methyl 1,2,4-Triazole-3-Thione molecule in solvent water medium has been investigated with the aid of DFT and Car–Parrinello molecular dynamics (CPMD) simulation studies. The CPMD simulations envisage the possibility of proton transfer reactions of the molecule through the solvent water medium. Probable proton transfer pathways have been predicted from the DFT calculations which are substantiated by the natural bond orbital analyses. The evolution and breaking of the concerned bonds of the molecule for different proton transfer reaction pathways are also estimated.

Wobble↔Watson-Crick tautomeric transitions in the homo-purine DNA mismatches: a key to the intimate mechanisms of the spontaneous transversions.

Science.gov (United States)

Brovarets', Ol'ha O; Hovorun, Dmytro M

2015-01-01

The intrinsic capability of the homo-purine DNA base mispairs to perform wobble↔Watson-Crick/Topal-Fresco tautomeric transitions via the sequential intrapair double proton transfer was discovered for the first time using QM (MP2/DFT) and QTAIM methodologies that are crucial for understanding the microstructural mechanisms of the spontaneous transversions.

Tautomeric and Microscopic Protonation Equilibria of Anthranilic Acid and Its Derivatives.

Science.gov (United States)

Zapała, Lidia; Woźnicka, Elżbieta; Kalembkiewicz, Jan

2014-01-01

The acid-base chemistry of three zwitterionic compounds, namely anthranilic (2-aminobenzoic acid), N -methylanthranilic and N -phenylanthranilic acid has been characterized in terms of the macroconstants K a1 , K a2 , the isoelectric point p H I , the tautomerization constant K z and microconstants k 11 , k 12 , k 21 , k 22 . The potentiometric titration method was used to determine the macrodissociation constants. Due to the very poor water solubility of N -phenylanthranilic acid the dissociation constants p K a1 and p K a2 were determined in MDM-water mixtures [MDM is a co-solvent mixture, consisting of equal volumes of methanol (MeOH), dioxane and acetonitrile (MeCN)]. The Yasuda-Shedlovsky extrapolation procedure has been used to obtain the values of p K a1 and p K a2 in aqueous solutions. The p K a1 and p K a2 values obtained by this method are 2.86 ± 0.01 and 4.69 ± 0.03, respectively. The tautomerization constant K z describing the equilibrium between unionized form ⇌ zwitterionic form was evaluated by the K z method based on UV-VIS spectrometry. The method uses spectral differences between the zwitterionic form (found at isoelectric pH in aqueous solution) and the unionized form (formed in an organic solvent of low dielectric constant). The highest value of the K z constant has been observed in the case of N -methylantranilic acid (log 10 K z  = 1.31 ± 0.04). The values of log 10 K z for anthranilic and N -phenylanthranilic acids are similar and have values of 0.93 ± 0.03 and 0.90 ± 0.05, respectively. The results indicate that the tested compounds, in aqueous solution around the isoelectric point pH I , occur mainly in the zwitterionic form. Moreover, the influence of the type of substituent and pH of the aqueous phase on the equilibrium were analyzed with regard to the formation and the coexistence of different forms of the acids in the examined systems.

Why the tautomerization of the G·C Watson-Crick base pair via the DPT does not cause point mutations during DNA replication? QM and QTAIM comprehensive analysis.

Science.gov (United States)

Brovarets', Ol'ha O; Hovorun, Dmytro M

2014-01-01

The ground-state tautomerization of the G·C Watson-Crick base pair by the double proton transfer (DPT) was comprehensively studied in vacuo and in the continuum with a low dielectric constant (ϵ = 4), corresponding to a hydrophobic interface of protein-nucleic acid interactions, using DFT and MP2 levels of quantum-mechanical (QM) theory and quantum theory "Atoms in molecules" (QTAIM). Based on the sweeps of the electron-topological, geometric, polar, and energetic parameters, which describe the course of the G·C ↔ G*·C* tautomerization (mutagenic tautomers of the G and C bases are marked with an asterisk) through the DPT along the intrinsic reaction coordinate (IRC), it was proved that it is, strictly speaking, a concerted asynchronous process both at the DFT and MP2 levels of theory, in which protons move with a small time gap in vacuum, while this time delay noticeably increases in the continuum with ϵ = 4. It was demonstrated using the conductor-like polarizable continuum model (CPCM) that the continuum with ϵ = 4 does not qualitatively affect the course of the tautomerization reaction. The DPT in the G·C Watson-Crick base pair occurs without any intermediates both in vacuum and in the continuum with ϵ = 4 at the DFT/MP2 levels of theory. The nine key points along the IRC of the G·C base pair tautomerization, which could be considered as electron-topological "fingerprints" of a concerted asynchronous process of the tautomerization via the DPT, have been identified and fully characterized. These key points have been used to define the reactant, transition state, and product regions of the DPT reaction in the G·C base pair. Analysis of the energetic characteristics of the H-bonds allows us to arrive at a definite conclusion that the middle N1H⋯N3/N3H⋯N1 and the lower N2H⋯O2/N2H⋯O2 parallel H-bonds in the G·C/G*·C* base pairs, respectively, are anticooperative, that is, the strengthening of the middle H-bond is accompanied

Crystal and molecular structures of 3-amino-4-hydroxy benzenesulfonamide and its hydrochloride: Quantum-chemical study of their tautomerism

Energy Technology Data Exchange (ETDEWEB)

Kovalchukova, O. V., E-mail: okovalchukova@mail.ru; Strashnova, S. B.; Romashkina, E. P.; Strashnov, P. V.; Zaitsev, B. E. [Peoples' Friendship University of Russia (Russian Federation); Sergienko, V. S. [Russian Academy of Sciences, Kurnakov Institute of General and Inorganic Chemistry (Russian Federation)

2013-03-15

3-amino-4-hydroxy benzenesulfonamide and its hydrochloride have been isolated in the crystalline state. Their crystal and molecular structures are determined by X-ray diffraction. The equilibrium between neutral tautomeric forms of the 3-amino-4-hydroxy benzenesulfonamide molecule is studied within the approximation of density functional theory (B3LYP/aug-cc-pVDZ). The constants of acid-base equilibrium of 3-amino-4-hydroxy benzenesulfonamide are deter-mined using spectrophotometry.

Theoretical Kinetic Study of the Unimolecular and H-Assisted Keto-Enol Tautomerism Propen-2-ol ↔Acetone. Pressure Effects and Implications in the Pyrolysis and Oxidation of tert- And 2-Butanol

KAUST Repository

Grajales Gonzalez, Edwing Javier

2018-05-01

The need for renewable and cleaner sources of energy has made biofuels an interesting alternative to fossil fuels, especially in the case of butanol isomers, with their favorable blend properties and low hygroscopicity. Although C4 alcohols are prospective fuels, some key reactions governing their pyrolysis and combustion have not been adequately studied, leading to incomplete kinetic models. Butanol reactions kinetics is poorly understood. Specifically, the unimolecular and H-assisted tautomerism of propen-2-ol to acetone, which are included in butanol combustion kinetic models, are assigned rate parameters based on the analogous unimolecular tautomerism vinyl alcohol ↔ acetaldehyde and H addition to the double bound of iso-butene, respectively. In an attempt to update current kinetic models for tert- and 2-butanol, a theoretical kinetic study of the unimolecular and H-assisted tautomerism, i-C3H5OH⟺CH3COCH3 and i-C3H5OH+Ḣ⟺CH3COCH3+Ḣ, was carried out by means of CCSD(T,FULL)/aug-cc-pVTZ//CCSD(T)/6-31+G(d,p) and CCSD(T)/aug-cc-pVTZ//M062X/cc-pVTZ ab initio calculations, respectively. For H-assisted tautomerism, the reaction takes place in two consecutive steps: i-C3H5OH+Ḣ⟺CH3ĊOHCH3 and CH3ĊOHCH3⟺CH3COCH3+Ḣ. Multistructural torsional anharmonicity and variational transition state theory were considered in a wide temperature and pressure range (200 K – 3000 K, 0.1 kPa – 108 kPa). It was observed that decreasing pressure leads to a decrease in rate constants, describing the expected falloff behavior for both isomerizations. Results for unimolecular tautomerism differ from vinyl alcohol ↔ acetaldehyde analogue reactions, which shows lower rate constant values. Tunneling turned out to be important, especially at low temperatures. Accordingly, pyrolysis simulations in a batch reactor for tert- and 2-butanol with computed unimolecular rate constants showed important differences in comparison with previous results, such as larger acetone yield and

Electron density reactivity indexes of the tautomeric/ionization forms of thiamin diphosphate.

Science.gov (United States)

Jaña, Gonzalo A; Delgado, Eduardo J

2013-09-01

The generation of the highly reactive ylide in thiamin diphosphate catalysis is analyzed in terms of the nucleophilicity of key atoms, by means of density functional calculations at X3LYP/6-31++G(d,p) level of theory. The Fukui functions of all tautomeric/ionization forms are calculated in order to assess their reactivity. The results allow to conclude that the highly conserved glutamic residue does not protonate the N1' atom of the pyrimidyl ring, but it participates in a strong hydrogen bonding, stabilizing the eventual negative charge on the nitrogen, in all forms involved in the ylide generation. This condition provides the necessary reactivity on key atoms, N4' and C2, to carry out the formation of the ylide required to initiate the catalytic cycle of ThDP-dependent enzymes. This study represents a new approach for the ylide formation in ThDP catalysis.

Sodium dodecyl benzene sulphonate mediated tautomerism of Eriochrome Black-T: Effect of charge transfer interaction

Science.gov (United States)

Ghosh, Sumit

2010-11-01

Interaction between anionic surfactant, sodium dodecyl benzene sulphonate, (SDBS) and an anionic dye Eriochrome Black-T, (EBT) has been investigated by visible spectroscopy, conductometry, dynamic light scattering and zeta potential measurements. Spectral changes of EBT observed on addition of SDBS indicate formation of quinone-hydrazone tautomer at pH 7.0, whereas in absence of SDBS this change appears at pH ˜ 9.45. However, at pH 7.0 this change in tautomerism is not observed in presence of sodium dodecyl sulphate (SDS). Experimental results indicate presence of charge transfer interaction between less stable quinone-hydrazone tautomer of EBT and SDBS molecules, which is confirmed using Benesi-Hildebrand and Scott equations.

Tungsten(VI) Carbyne/Bis(carbene) Tautomerization Enabled by N-Donor SBA15 Surface Ligands: A Solid-State NMR and DFT Study

KAUST Repository

Bendjeriou-Sedjerari, Anissa

2016-08-11

Designing supported well-defined bis(carbene) complexes remains a key challenge in heterogeneous catalysis. The reaction of W(CtBu)(CH(2)tBu)(3) with amine-modified mesoporous SBA15 silica, which has vicinal silanol/silylamine pairs [(SiOH)(SiNH2)], leads to [(SiNH2-)(SiO-)W(CHtBu)(CH(2)tBu)(2)] and [(SiNH2-)(SiO-)W(=CHtBu)(2)(CH(2)tBu). Variable temperature, H-1-H-1 2D double-quantum, H-1-C-13 HETCOR, and HETCOR with spin diffusion solid-state NMR spectroscopy demonstrate tautomerization between the alkyl alkylidyne and the bis(alkylidene) on the SBA15 surface. Such equilibrium is possible through the coordination of W to the surface [(Si-OH)(Si-NH2)] groups, which act as a [N,O] pincer ligand. DFT calculations provide a rationalization for the surface-complex tautomerization and support the experimental results. This direct observation of such a process shows the strong similarity between molecular mechanisms in homogeneous and heterogeneous catalysis. In propane metathesis (at 150 degrees C), the tungsten bis(carbene) tautomer is favorable, with a turnover number (TON) of 262. It is the highest TON among all the tungsten alkyl-supported catalysts.

Tungsten(VI) Carbyne/Bis(carbene) Tautomerization Enabled by N-Donor SBA15 Surface Ligands: A Solid-State NMR and DFT Study

KAUST Repository

Bendjeriou-Sedjerari, Anissa; Sofack-Kreutzer, Julien; Minenkov, Yury; Abou-Hamad, Edy; Hamzaoui, Bilel; Werghi, Baraa; Anjum, Dalaver H.; Cavallo, Luigi; Huang, Kuo-Wei; Basset, Jean-Marie

2016-01-01

Designing supported well-defined bis(carbene) complexes remains a key challenge in heterogeneous catalysis. The reaction of W(CtBu)(CH(2)tBu)(3) with amine-modified mesoporous SBA15 silica, which has vicinal silanol/silylamine pairs [(SiOH)(SiNH2)], leads to [(SiNH2-)(SiO-)W(CHtBu)(CH(2)tBu)(2)] and [(SiNH2-)(SiO-)W(=CHtBu)(2)(CH(2)tBu). Variable temperature, H-1-H-1 2D double-quantum, H-1-C-13 HETCOR, and HETCOR with spin diffusion solid-state NMR spectroscopy demonstrate tautomerization between the alkyl alkylidyne and the bis(alkylidene) on the SBA15 surface. Such equilibrium is possible through the coordination of W to the surface [(Si-OH)(Si-NH2)] groups, which act as a [N,O] pincer ligand. DFT calculations provide a rationalization for the surface-complex tautomerization and support the experimental results. This direct observation of such a process shows the strong similarity between molecular mechanisms in homogeneous and heterogeneous catalysis. In propane metathesis (at 150 degrees C), the tungsten bis(carbene) tautomer is favorable, with a turnover number (TON) of 262. It is the highest TON among all the tungsten alkyl-supported catalysts.

Tautomeric equilibrium of creatinine and creatininium cation in aqueous solutions explored by Raman spectroscopy and density functional theory calculations

International Nuclear Information System (INIS)

Gao, Jiao; Hu, Yongjun; Li, Shaoxin; Zhang, Yanjiao; Chen, Xue

2013-01-01

Highlights: ► The tautomeric equlibrium and behavior of creatinine in aqueous solutions have been firstly studied by means of Raman spectroscopy and theoretical calculations (DFT). ► As 7 water molecules are gradually aggregated around the creatinine, theoretical results show an excellent accordance with the experimental spectrum. ► Analysis of molecular electrostatic potential (MEP) for creatinine (two tautomers and one protonated form) could explain why typical experimental Raman spectra with different pH values have obvious discrepancies at the electrical level. -- Abstract: The Raman spectral studies of creatinine with pH dependence were performed to explore the effects of pH values on the Raman spectroscopy of creatinine. Firstly, we calculated vibrational spectra by DFT to derive the equilibrium geometries and protonated form of creatinine. Comparing simulated and observed Raman spectra of creatinine in aqueous solution at pH 2, it is found the theoretical predicted spectra agree well with those of the experiment while seven water molecules are aggregated around the creatinine. Additionally, the tautomeric equilibrium of creatinine in aqueous solutions was studied and two tautomers are found to coexist by comparing its experimental and calculated Raman spectra. A water dimer being used to solvate creatinine would make the thermodynamic energy favor convert from the imino tautomer to the amino tautomer. Besides, the molecular electrostatic potential (MEP) analysis of the creatinine further confirms their discrepancies of typical experimental Raman spectra at different pH values.

Supercritical fluid chromatography for separation and preparation of tautomeric 7-epimeric spiro oxindole alkaloids from Uncaria macrophylla.

Science.gov (United States)

Yang, Wenzhi; Zhang, Yibei; Pan, Huiqin; Yao, Changliang; Hou, Jinjun; Yao, Shuai; Cai, Luying; Feng, Ruihong; Wu, Wanying; Guo, Dean

2017-02-05

Increasing challenge arising from configurational interconversion in aqueous solvent renders it rather difficult to isolate high-purity tautomeric reference standards and thus largely hinders the holistic quality control of traditional Chinese medicine (TCM). Spiro oxindole alkaloids (SOAs), as the markers for the medicinal Uncaria herbs, can easily isomerize in polar or aqueous solvent via a retro-Mannich reaction. In the present study, supercritical fluid chromatography (SFC) is utilized to separate and isolate two pairs of 7-epimeric SOAs, including rhynchophylline (R) and isorhynchophylline (IR), corynoxine (C) and corynoxine B (CB), from Uncaria macrophylla. Initially, the solvent that can stabilize SOA epimers was systematically screened, and acetonitrile was used to dissolve and as the modifier in SFC. Then, key parameters of ultra-high performance SFC (ultra-performance convergence chromatography, UPC 2 ), comprising stationary phase, additive in modifier, column temperature, ABPR pressure, and flow rate, were optimized in sequence. Two isocratic UPC 2 methods were developed on the achiral Torus 1-AA and Torus Diol columns, suitable for UV and MS detection, respectively. MCI gel column chromatography fractionated the U. macrophylla extract into two mixtures (R/IR and C/CB). Preparative SFC, using a Viridis Prep Silica 2-EP OBD column and acetonitrile-0.2% diethylamine in CO 2 as the mobile phase, was finally employed for compound purification. As a result, the purity of four SOA compounds was all higher than 95%. Different from reversed-phase HPLC, SFC, by use of water-free mobile phase (inert CO 2 and aprotic modifier), provides a solution to rapid analysis and isolation of tautomeric reference standards for quality control of TCM. Copyright © 2016 Elsevier B.V. All rights reserved.

Crystal structure and tautomerism of Pigment Yellow 138 determined by X-ray powder diffraction and solid-state NMR

DEFF Research Database (Denmark)

Gumbert, Silke D.; Körbitzer, Meike; Alig, Edith

2016-01-01

The crystal structure of C.I. Pigment Yellow 138 was determined from X-ray powder diffraction data using real-space methods with subsequent Rietveld refinements. The tautomeric state was investigated by solid-state 1D and 2D multinuclear NMR experiments. In the crystals, the compound exhibits...... the NH-tautomer with a hydrogen atom situated at the nitrogen of the quinoline moiety. Direct evidence of the presence of the NH-tautomer is provided by 1H–14N HMQC solid-state NMR at very fast MAS. Solid-state dispersion-corrected density functional theory calculations with BLYP-D3 confirm...

Thiazol-4-one derivatives from the reaction of monosubstituted thioureas with maleimides: structures and factors determining the selectivity and tautomeric equilibrium in solution

Directory of Open Access Journals (Sweden)

Alena S. Pankova

2016-11-01

Full Text Available 2-(Alkyl(arylaminothiazol-4(5H-ones can regioselectively be prepared from monoalkyl(arylthioureas and maleimides. In solution, the former heterocycles exist in a tautomeric equilibrium with 2-(alkyl(aryliminothiazolidin-4-ones and the substituent on the exocyclic nitrogen atom governs the ratio of these tautomers. Isomers with the alkyl group in the endocyclic position can be obtained from N-methyl(ethylthioureas. 2D NMR spectroscopy and DFT calculations rationalize experimental results.

Electronic and transport properties of Cobalt-based valence tautomeric molecules and polymers

Science.gov (United States)

Chen, Yifeng; Calzolari, Arrigo; Buongiorno Nardelli, Marco

2011-03-01

The advancement of molecular spintronics requires further understandings of the fundamental electronic structures and transport properties of prototypical spintronics molecules and polymers. Here we present a density functional based theoretical study of the electronic structures of Cobalt-based valence tautomeric molecules Co III (SQ)(Cat)L Co II (SQ)2 L and their polymers, where SQ refers to the semiquinone ligand, and Cat the catecholate ligand, while L is a redox innocent backbone ligand. The conversion from low-spin Co III ground state to high-spin Co II excited state is realized by imposing an on-site potential U on the Co atom and elongating the Co-N bond. Transport properties are subsequently calculated by extracting electronic Wannier functions from these systems and computing the charge transport in the ballistic regime using a Non-Equilibrium Green's Function (NEGF) approach. Our transport results show distinct charge transport properties between low-spin ground state and high-spin excited state, hence suggesting potential spintronics devices from these molecules and polymers such as spin valves.

Synthesis, Acidity Constants and Tautomeric Structure of the Diazonium Coupling Products of 2-(Benzylsulfanyl)-7H-purin-6-one in Its Ground and Excited States

OpenAIRE

Darwish, Elham S.; Mosselhi, Mosselhi A.; Altalbawy, Farag M.; Saad, Hosam A.

2011-01-01

A series of new 8-arylhydrazono-2-(benzylsulfanyl)-7H-purin-6-ones 6 were synthesized, their electronic absorption spectra in different organic solvents of varying polarities were investigated and their acid dissociation constants in both the ground and excited states were determined spectrophotometrically. The tautomeric structures of such products were elucidated by spectral analyses and correlation of their acid dissociation constants with the Hammett equation. The results indicated that t...

Tautomeric preferences of the cis and trans isomers of axitinib

Science.gov (United States)

Mirzaei, M. Saeed; Taherpour, Avat Arman

2018-05-01

The tautomeric preferences of axitinib, a potent anticancer drug, as tyrosine kinase inhibitor have been investigated using quantum chemical calculations and docking methods. The energy differences between the two tautomers of trans-isomer are around 4 and 3 kcal mol-1 in vacuo and water, respectively, and for its cis-isomer (major photochemical isomerization product) this equilibrium reversed completely in favour of the second tautomer (not considered previously), which is about 7-8 kcal mol-1 more stable in both gas and aqueous media. The results indicate a very high activation energy for proton exchange for both [1,2] and [1,5] H-shift (around 50 kcal mol-1) in the gas phase, but inclusion of protic solvents (e.g. water) decrease this barrier to around 14 and 35 kcal mol-1 for the both hydrogen shift processes, respectively. In order to have better insight about the electronic structure of axitinib tautomers, the NBO, HOMO-LUMO, NICS and molecular electrostatic potential surfaces (MESP) calculations have been carried out. Docking investigations on the two more stable tautomers revealed that binding of the trans isomer of tautomer I to the active site of the receptor is the most favourable in the terms of energy and structure. This more stability could be attributed to the more hydrogen bonding of this tautomer with the protein residues in comparison to the second tautomer.

Keto - enol, imine - enamine, and nitro - aci-nitro tautomerism and their interrelationship in substituted nitroethylenes. Keto, imine, nitro, and vinyl substituent effects, and the importance of H-bonding

NARCIS (Netherlands)

Lammertsma, K.; Bharatam, P.V.

2000-01-01

Tautomeric isomers and conformers of 2-nitrovinyl alcohol (1), 2-nitrovinylamine (2), and 1-nitropropene (3) are reported at the MP2 and B3LYP levels of theory, using the 6-31G* basis set, with energy evaluation at B3LYP/6-311+G** and G2MP2. The nitroalkenes are the global minima on their respective

Supramolecular architecture in a co-crystal of the N(7—H tautomeric form of N6-benzoyladenine with adipic acid (1/0.5

Directory of Open Access Journals (Sweden)

Robert Swinton Darious

2016-06-01

Full Text Available The asymmetric unit of the title co-crystal, C12H9N5O·0.5C6H10O4, consists of one molecule of N6-benzoyladenine (BA and one half-molecule of adipic acid (AA, the other half being generated by inversion symmetry. The dihedral angle between the adenine and phenyl ring planes is 26.71 (7°. The N6-benzoyladenine molecule crystallizes in the N(7—H tautomeric form with three non-protonated N atoms. This tautomeric form is stabilized by intramolecular N—H...O hydrogen bonding between the carbonyl (C=O group and the N(7—H hydrogen atom on the Hoogsteen face of the purine ring, forming an S(7 ring motif. The two carboxyl groups of adipic acid interact with the Watson–Crick face of the BA molecules through O—H...N and N—H...O hydrogen bonds, generating an R22(8 ring motif. The latter units are linked by N—H...N hydrogen bonds, forming layers parallel to (10-5. A weak C—H...O hydrogen bond is also present, linking adipic acid molecules in neighbouring layers, enclosing R22(10 ring motifs and forming a three-dimensional structure. C=O...π and C—H...π interactions are also present in the structure.

Benchmarking Continuum Solvent Models for Keto-Enol Tautomerizations.

Science.gov (United States)

McCann, Billy W; McFarland, Stuart; Acevedo, Orlando

2015-08-13

Experimental free energies of tautomerization, ΔGT, were used to benchmark the gas-phase predictions of 17 different quantum mechanical methods and eight basis sets for seven keto-enol tautomer pairs dominated by their enolic form. The G4 method and M06/6-31+G(d,p) yielded the most accurate results, with mean absolute errors (MAE's) of 0.95 and 0.71 kcal/mol, respectively. Using these two theory levels, the solution-phase ΔGT values for 23 unique tautomer pairs composed of aliphatic ketones, β-dicarbonyls, and heterocycles were computed in multiple protic and aprotic solvents. The continuum solvation models, namely, polarizable continuum model (PCM), polarizable conductor calculation model (CPCM), and universal solvation model (SMD), gave relatively similar MAE's of ∼1.6-1.7 kcal/mol for G4 and ∼1.9-2.0 kcal/mol with M06/6-31+G(d,p). Partitioning the tautomer pairs into their respective molecular types, that is, aliphatic ketones, β-dicarbonyls, and heterocycles, and separating out the aqueous versus nonaqueous results finds G4/PCM utilizing the UA0 cavity to be the overall most accurate combination. Free energies of activation, ΔG(‡), for the base-catalyzed keto-enol interconversion of 2-nitrocyclohexanone were also computed using six bases and five solvents. The M06/6-31+G(d,p) reproduced the ΔG(‡) with MAE's of 1.5 and 1.8 kcal/mol using CPCM and SMD, respectively, for all combinations of base and solvent. That specific enolization was previously proposed to proceed via a concerted mechanism in less polar solvents but shift to a stepwise mechanism in more polar solvents. However, the current calculations suggest that the stepwise mechanism operates in all solvents.

Supra-molecular architecture in a co-crystal of the N(7)-H tautomeric form of N (6)-benzoyl-adenine with adipic acid (1/0.5).

Science.gov (United States)

Swinton Darious, Robert; Thomas Muthiah, Packianathan; Perdih, Franc

2016-06-01

The asymmetric unit of the title co-crystal, C12H9N5O·0.5C6H10O4, consists of one mol-ecule of N (6)-benzoyl-adenine (BA) and one half-mol-ecule of adipic acid (AA), the other half being generated by inversion symmetry. The dihedral angle between the adenine and phenyl ring planes is 26.71 (7)°. The N (6)-benzoyl-adenine mol-ecule crystallizes in the N(7)-H tautomeric form with three non-protonated N atoms. This tautomeric form is stabilized by intra-molecular N-H⋯O hydrogen bonding between the carbonyl (C=O) group and the N(7)-H hydrogen atom on the Hoogsteen face of the purine ring, forming an S(7) ring motif. The two carboxyl groups of adipic acid inter-act with the Watson-Crick face of the BA mol-ecules through O-H⋯N and N-H⋯O hydrogen bonds, generating an R 2 (2)(8) ring motif. The latter units are linked by N-H⋯N hydrogen bonds, forming layers parallel to (10-5). A weak C-H⋯O hydrogen bond is also present, linking adipic acid mol-ecules in neighbouring layers, enclosing R (2) 2(10) ring motifs and forming a three-dimensional structure. C=O⋯π and C-H⋯π inter-actions are also present in the structure.

Tautomerism and isomerism in some antitrichinellosis active benzimidazoles: Morphological study in polarized light, quantum chemical computations

Science.gov (United States)

Anichina, Kameliya; Mavrova, Anelia; Yancheva, Denitsa; Tsenov, Jordan; Dimitrov, Rasho

2017-12-01

The morphology of the crystal structure of some antitrichinellosis active benzimidazole derivatives including (1H-benzimidazol-2-ylthio)acetic acids, [1,3]thiazolo[3,2-a]benzimidazol-3(2H)-ones, 1H-benzimidazol-2-ylthioacetylpiperazines and starting 2-mercapto benzimidazoles, was studied by the use of Polarized Light Microscopy (PLM). Characterization of the crystal phase was complimented by Differential scanning calorimetry analysis (DSC) and spectroscopic data. DFT computations were performed in order to investigate the prototropic tautomerism and the geometry of the molecule of the synthesized compounds. One distinct type of crystal structure for each one of 5 or 6-methyl-(1H-benzimidazol-2-ylthio)acetic acid 6 was observed by PLM - dendritic and needle-shaped formations. Compound 14, containing a methyl substituent in the benzimidazole ring crystallized also into two phases; while for the unsubstituted compound 13 a separation of phases does not take place. The influence of the both solvents - chloroform and ethanol on the phase separation and the formation of the crystalline structure of compound 14 was investigated. The morphological study showed that the cyclization of 6 in the presence of acetic anhydride in pyridine medium led to a mixture of 6-methyl-[1,3]tiazolo[3,2-a]benzimidazol-3(2H)-one (10a) and 7-methyl-[1,3]thiazolo[3,2-a]-benzimidazole-3(2H)-one (10b), which crystallized in the form of fibrils and spherulites respectively. It was found that a difference in the crystal structures of substituted and unsubstituted benzimidazol-2-thiones, respectively benzimidazol-2-thiol derivatives exists, which may be due not only to the thiol-thione tautomerism but to the prototropic properties of the hydrogen atom in first position of the ring. The calculation results indicated that the thione form is more stable than the thiol tautomer by 51-55 kJ mol-1. But at the same time ΔG for the two thiol tautomers is below 0.5 kJ mol-1. In solid phase the 5

[Quantum-chemical investigation of tautomerization ways of Watson-Crick DNA base pair guanine-cytosine].

Science.gov (United States)

Brovarets', O O; Hovorun, D M

2010-01-01

A novel physico-chemical mechanism of the Watson-Crick DNA base pair Gua.Cyt tautomerization Gua.Cyt*Gua.CytGua*.Cyt (mutagenic tautomers of bases are marked by asterisks) have been revealed and realized in a pathway of single proton transfer through two mutual isoenergetic transition states with Gibbs free energy of activation 30.4 and 30.6 kcal/mol and they are ion pairs stabilized by three (N2H...N3, N1H...N4- and O6+H...N4-) and five (N2H...O2, N1H...O2, N1H...N3, O6+H...N4- and 06+H...N4-) H-bonds accordingly. Stable base pairs Gua-Cyt* and Gua*.Cyt which dissociate comparably easy into monomers have acceptable relative Gibbs energies--12.9 and 14.3 kcal/mol--for the explanation of the nature of the spontaneous transitions of DNA replication. Results are obtained at the MP2/6-311++G(2df,pd)//B3LYP/6-31 1++G(d,p) level of theory in vacuum approach.

Mechanism of Prototropy. III. Kinetics of the Tautomerization of Benzylidene-Benzylamine. comparison of the influence of hydrogen and alkyl groups on the SE2' reaction rate

International Nuclear Information System (INIS)

Perez Ossorio, R.; Gamboa, J. M.; Martinez Utrilla, R.

1961-01-01

The rate of the proto tropic change of benzylidene-benzylamine has been determined by using azomethine 1 4C-labelled in the methylenic group and measuring the distribution of activity between benzaldehyde and benzylamine obtained by hydrolysis at different reaction times. this rate has been compared with those of tautomerization of benzylidene-α-alkyl benzylamine and α-alkyl benzylidene-benzyl amines in the same experimental conditions in order to establish ethe influence of alkyl group on this reaction. (Author) 14 refs

Investigating tautomeric polymorphism in crystalline anthranilic acid using terahertz spectroscopy and solid-state density functional theory.

Science.gov (United States)

Delaney, Sean P; Witko, Ewelina M; Smith, Tiffany M; Korter, Timothy M

2012-08-02

Terahertz spectroscopy is sensitive to the interactions between molecules in the solid-state and recently has emerged as a new analytical tool for investigating polymorphism. Here, this technique is applied for the first time to the phenomenon of tautomeric polymorphism where the crystal structures of anthranilic acid (2-aminobenzoic acid) have been investigated. Three polymorphs of anthranilic acid (denoted Forms I, II and III) were studied using terahertz spectroscopy and the vibrational modes and relative polymorph stabilities analyzed using solid-state density functional theory calculations augmented with London dispersion force corrections. Form I consists of both neutral and zwitterionic molecules and was found to be the most stable polymorph as compared to Forms II and III (both containing only neutral molecules). The simulations suggest that a balance between steric interactions and electrostatic forces is responsible for the favoring of the mixed neutral/zwitterion solid over the all neutral or all zwitterion crystalline arrangements.

Antibacterial Barbituric Acid Analogues Inspired from Natural 3-Acyltetramic Acids; Synthesis, Tautomerism and Structure and Physicochemical Property-Antibacterial Activity Relationships

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Yong-Chul Jeong

2015-02-01

Full Text Available The synthesis, tautomerism and antibacterial activity of novel barbiturates is reported. In particular, 3-acyl and 3-carboxamidobarbiturates exhibited antibacterial activity, against susceptible and some resistant Gram-positive strains of particular interest is that these systems possess amenable molecular weight, rotatable bonds and number of proton-donors/acceptors for drug design as well as less lipophilic character, with physicochemical properties and ionic states that are similar to current antibiotic agents for oral and injectable use. Unfortunately, the reduction of plasma protein affinity by the barbituric core is not sufficient to achieve activity in vivo. Further optimization to reduce plasma protein affinity and/or elevate antibiotic potency is therefore required, but we believe that these systems offer unusual opportunities for antibiotic drug discovery.

Experimental and theoretical studies on tautomeric structures of a newly synthesized 2,2‧(hydrazine-1,2-diylidenebis(propan-1-yl-1-ylidene))diphenol

Science.gov (United States)

Karakurt, Tuncay; Cukurovali, Alaaddin; Subasi, Nuriye Tuna; Onaran, Abdurrahman; Ece, Abdulilah; Eker, Sıtkı; Kani, Ibrahim

2018-02-01

In the present study, a single crystal of a Schiff base, 2,2‧(hydrazine-1,2-diylidenebis(propan-1-yl-1-ylidene))diphenol, was synthesized. The structure of the synthesized crystal was confirmed by 1H and 13C NMR spectroscopic and X-ray diffraction analysis techniques. Experimental and theoretical studies were carried out on two tautomeric structures. It has been observed that the title compound studied can be in two different tautomeric forms, phenol-imine and keto-amine. Theoretical calculations have been performed to support experimental results. Accordingly, the geometric parameters of the compound were optimized by the density functional theory (DFT) method using the Gaussian 09 and Quantum Espresso (QE) packet program was used for periodic boundary conditions (PBC) studies. Furthermore, the compound was also tested for in vitro antifungal activity against Sclerotinia sclerotiorum, Alternaria solani, Fusarium oxysporum f. sp. lycopersici and Monilinia fructigena plant pathogens. Promising inhibition profiles were observed especially towards A. solani. Finally, molecular docking studies and post-docking procedure based on Molecular Mechanics-Generalized Born Surface Area (MM-GBSA) were also carried out to get insight into the compound's binding interactions with the potential. Although theoretical calculations showed that the phenol-imine form was more stable, keto-amine form was predicted to have better binding affinity which was concluded to result from loss of rotational entropy in phenol-imine upon binding. The results obtained here from both experimental and computational methods might serve as a potential lead in the development of novel anti-fungal agents.

Rare configuration of tautomeric benzimidazolecarboxylate ligands in cadmium(II) and copper(II) coordination polymers

International Nuclear Information System (INIS)

Wu, Jing-Yun; Yang, Ciao-Wei; Chen, Hui-Fang; Jao, Yu-Chen; Huang, Sheng-Ming; Tsai, Chiitang; Tseng, Tien-Wen; Lee, Gene-Hsiang; Peng, Shie-Ming; Lu, Kuang-Lieh

2011-01-01

Two Cd(HBimc)-based isomers, [Cd(HBimc N )(HBimc T )(H 2 O)].3.5H 2 O.EtOH (1a.3.5H 2 O.EtOH, H 2 Bimc=1H-benzimidazole-5-carboxylic acid) and [Cd(HBimc N )(HBimc T )(H 2 O)] (1b), and two Cu(HMBimc)-based coordination polymers, [Cu(HMBimc N ) 2 (H 2 O)].1/2H 2 O (2.1/2H 2 O, H 2 MBimc=2-methyl-1H-benzimidazole-5-carboxylic acid) and [Cu(HMBimc T ) 2 ].2THF.H 2 O (3.2THF.H 2 O), were self-assembled from Cd(ClO 4 ) 2 .6H 2 O/H 2 Bimc and Cu(ClO 4 ) 2 .6H 2 O/H 2 MBimc systems, respectively. Compound 1a adopts a ladder-like chain structure, comprised of a hydrogen-bond-stabilized Cd 2 (HBimc N ) 2 -metallocyclic stair and a 1D straight -(Cd-HBimc T ) n - edge, whereas compound 1b exhibits a 2D (4,4)-rhombus layered structure, intercrossed by 1D -(Cd-HBimc N ) n - chains and -(Cd-HBimc T ) n - chains. Compound 2 shows a 1D double-stranded wave-like chain from two single-stranded wave-like -(Cu-HMBimc N ) n - chains and compound 3 adopts a 2D (4,4)-topological layer structure, intercrossed by subunits of 1D -(Cu-HMBimc T ) n - chains. Interestingly, a pair of tautomeric HBimc building blocks-normal (N or HBimc N ) and tautomer (T or HBimc T )-is simultaneously included in the structures of 1a and 1b, whilst the N- and T-configured HMBimc building blocks are present as separate entities in Cu species, 2 and 3, respectively. The existence of only a tautomer (T) mode of the benzimidazolecarboxylate-based ligand in a Cu(II) network is observed for the first time. - Graphical abstract: A pair of tautomeric HBimc building blocks (normal (N) and tautomer (T)) is found simultaneously in two Cd(II) networks, whereas, the normal and tautomer modes of HMBimc are present as separate entities in two Cu(II) frameworks. The isolation of a Cu(II) network with only a tautomer (T) mode of the benzimidazolecarboxylate-based ligand is achieved for the first time. Highlights: →Benzimidazolecarboxylates could exhibit normal (N) and tautomer (T) configurations. → A pair of N- and T

X-Ray, IR, NMR, UV-visible spectra and DFT analysis of 5-aryloxy-(1H-tetrazoles, structure, conformation and tautomerism

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Nader Noroozi Pesyan

2014-03-01

Full Text Available The predominant tautomeric forms of N1–H, N2–H of 5-(2,6-dimethyl- and 5-(2,6-diisopropylphenoxy-(1H-tetrazoles were analyzed at B3LYP method using 6-311G(d,p basis set in the gas phase. The N1–H form of tetrazoles was found to be more stable than N2–H form in both solid and gas phases. Crystal structures of both tetrazoles show an intermolecular H-bond between N1-H and N4 atom of other tetrazole space. The hydrogen bonds between each tautomer of tetrazoles were evaluated at B3LYP/6-311G(d,p level. The geometrical parameters and spectral data of tetrazoles and their variation were studied in both solid and gas phases.

Gas-Phase Thermal Tautomerization of Imidazole-Acetic Acid: Theoretical and Computational Investigations

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Saadullah G. Aziz

2015-11-01

Full Text Available The gas-phase thermal tautomerization reaction between imidazole-4-acetic (I and imidazole-5-acetic (II acids was monitored using the traditional hybrid functional (B3LYP and the long-range corrected functionals (CAM-B3LYP and ωB97XD with 6-311++G** and aug-cc-pvdz basis sets. The roles of the long-range and dispersion corrections on their geometrical parameters, thermodynamic functions, kinetics, dipole moments, Highest Occupied Molecular Orbital–Lowest Unoccupied Molecular Orbital (HOMO–LUMO energy gaps and total hyperpolarizability were investigated. All tested levels of theory predicted the preference of I over II by 0.750–0.877 kcal/mol. The origin of predilection of I is assigned to the H-bonding interaction (nN8→σ*O14–H15. This interaction stabilized I by 15.07 kcal/mol. The gas-phase interconversion between the two tautomers assumed a 1,2-proton shift mechanism, with two transition states (TS, TS1 and TS2, having energy barriers of 47.67–49.92 and 49.55–52.69 kcal/mol, respectively, and an sp3-type intermediate. A water-assisted 1,3-proton shift route brought the barrier height down to less than 20 kcal/mol in gas-phase and less than 12 kcal/mol in solution. The relatively high values of total hyperpolarizability of I compared to II were interpreted and discussed.

Is the DPT tautomerization of the long A·G Watson-Crick DNA base mispair a source of the adenine and guanine mutagenic tautomers? A QM and QTAIM response to the biologically important question.

Science.gov (United States)

Brovarets', Ol'ha O; Zhurakivsky, Roman O; Hovorun, Dmytro M

2014-03-05

Herein, we first address the question posed in the title by establishing the tautomerization trajectory via the double proton transfer of the adenine·guanine (A·G) DNA base mispair formed by the canonical tautomers of the A and G bases into the A*·G* DNA base mispair, involving mutagenic tautomers, with the use of the quantum-mechanical calculations and quantum theory of atoms in molecules (QTAIM). It was detected that the A·G ↔ A*·G* tautomerization proceeds through the asynchronous concerted mechanism. It was revealed that the A·G base mispair is stabilized by the N6H···O6 (5.68) and N1H···N1 (6.51) hydrogen bonds (H-bonds) and the N2H···HC2 dihydrogen bond (DH-bond) (0.68 kcal·mol(-1) ), whereas the A*·G* base mispair-by the O6H···N6 (10.88), N1H···N1 (7.01) and C2H···N2 H-bonds (0.42 kcal·mol(-1) ). The N2H···HC2 DH-bond smoothly and without bifurcation transforms into the C2H···N2 H-bond at the IRC = -10.07 Bohr in the course of the A·G ↔ A*·G* tautomerization. Using the sweeps of the energies of the intermolecular H-bonds, it was observed that the N6H···O6 H-bond is anticooperative to the two others-N1H···N1 and N2H···HC2 in the A·G base mispair, while the latters are significantly cooperative, mutually strengthening each other. In opposite, all three O6H···N6, N1H···N1, and C2H···N2 H-bonds are cooperative in the A*·G* base mispair. All in all, we established the dynamical instability of the А*·G* base mispair with a short lifetime (4.83·10(-14) s), enabling it not to be deemed feasible source of the A* and G* mutagenic tautomers of the DNA bases. The small lifetime of the А*·G* base mispair is predetermined by the negative value of the Gibbs free energy for the A*·G* → A·G transition. Moreover, all of the six low-frequency intermolecular vibrations cannot develop during this lifetime that additionally confirms the aforementioned results. Thus, the A*·G* base mispair cannot be

Theoretical Kinetic Study of the Unimolecular Keto–Enol Tautomerism Propen-2-ol ↔ Acetone. Pressure Effects and Implications in the Pyrolysis of tert- and 2-Butanol

KAUST Repository

Grajales Gonzalez, Edwing

2018-03-21

The need for renewable and cleaner sources of energy has made biofuels an interesting alternative to fossil fuels, especially in the case of butanol isomers, with its favorable blend properties and low hygroscopicity. Although C4 alcohols are prospective fuels, some key reactions governing their pyrolysis and combustion have not been adequately studied, leading to incomplete kinetic models. Enols are important intermediates in the combustion of C4 alcohols, as well as in atmospheric processes. Butanol reactions kinetics is poorly understood. Specifically, the unimolecular tautomerism of propen-2-ol ↔ acetone, which is included in butanol combustion kinetic models, is assigned rate parameters based on the tautomerism vinyl alcohol ↔ acetaldehyde as an analogy. In an attempt to update current kinetic models for tert- and 2-butanol, a theoretical kinetic study of the titled reaction was carried out by means of CCSD(T,FULL)/aug-cc-pVTZ//CCSD(T)/6-31+G(d,p) ab initio calculations, with multistructural torsional anharmonicity and variational transition state theory considerations in a wide temperature and pressure range (200-3000 K; 0.1-108 kPa). Results differ from vinyl alcohol ↔ acetaldehyde analogue reaction, which shows lower rate constant values. It was observed that decreasing pressure leads to a decrease in rate constants, describing the expected falloff behavior. Tunneling turned out to be important, especially at low temperatures. Accordingly, pyrolysis simulations in a batch reactor for tert- and 2-butanol with computed rate constants showed important differences in comparison with previous results, such as larger acetone yield and quicker propen-2-ol consumption.

Theoretical Kinetic Study of the Unimolecular Keto–Enol Tautomerism Propen-2-ol ↔ Acetone. Pressure Effects and Implications in the Pyrolysis of tert- and 2-Butanol

KAUST Repository

Grajales Gonzalez, Edwing Javier; Monge Palacios, Manuel; Sarathy, Mani

2018-01-01

The need for renewable and cleaner sources of energy has made biofuels an interesting alternative to fossil fuels, especially in the case of butanol isomers, with its favorable blend properties and low hygroscopicity. Although C4 alcohols are prospective fuels, some key reactions governing their pyrolysis and combustion have not been adequately studied, leading to incomplete kinetic models. Enols are important intermediates in the combustion of C4 alcohols, as well as in atmospheric processes. Butanol reactions kinetics is poorly understood. Specifically, the unimolecular tautomerism of propen-2-ol ↔ acetone, which is included in butanol combustion kinetic models, is assigned rate parameters based on the tautomerism vinyl alcohol ↔ acetaldehyde as an analogy. In an attempt to update current kinetic models for tert- and 2-butanol, a theoretical kinetic study of the titled reaction was carried out by means of CCSD(T,FULL)/aug-cc-pVTZ//CCSD(T)/6-31+G(d,p) ab initio calculations, with multistructural torsional anharmonicity and variational transition state theory considerations in a wide temperature and pressure range (200-3000 K; 0.1-108 kPa). Results differ from vinyl alcohol ↔ acetaldehyde analogue reaction, which shows lower rate constant values. It was observed that decreasing pressure leads to a decrease in rate constants, describing the expected falloff behavior. Tunneling turned out to be important, especially at low temperatures. Accordingly, pyrolysis simulations in a batch reactor for tert- and 2-butanol with computed rate constants showed important differences in comparison with previous results, such as larger acetone yield and quicker propen-2-ol consumption.

Crystal and molecular structures of benzo[4,5]imidazo[1,2-c]quinazolin-6-one and 10-carboxybenzo[4,5]imidazo[1,2-c]quinazolin-6-one: A quantum-chemical study of their tautomerism

International Nuclear Information System (INIS)

Koval’chukova, O. V.; Stash, A. I.; Strashnov, P. V.; Neborak, E. V.; Strashnova, S. B.; Zaitsev, B. E.

2011-01-01

Benzo[4,5]imidazo[1,2-c]quinazolin-6-one and 10-carboxybenzo[4,5]imidazo[1,2-c]quinazolin-6-one were isolated in the crystalline state and studied by X-ray diffraction. The crystal and molecular structures of these compounds were determined by X-ray diffraction. The energy characteristics of the tautomeric and ionic forms were calculated by the quantum-chemical PM3 method.

Synthesis of New Unsymmetrical 4,5-Dihydroxy-2-imidazolidinones. Dynamic NMR Spectroscopic Study of the Prototropic Tautomerism in 1-(2-Benzimidazolyl-3-phenyl-4,5-dihydroxy-2-imidazolidinone

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Farshid Salimi

2006-10-01

Full Text Available The acid-catalyzed cyclocondensation in refluxing acetonitrile of aqueousglyoxal with N-heteroaryl-N'-phenylureas 4a-f (heteroaryl = 2-thiazolyl, 2-pyrimidinyl,2-pyrazinyl, 2-pyridinyl, 3-pyridinyl and 2-benzimidazolyl led to the formation of thecorresponding 1-heteroaryl-3-phenyl-4,5-dihydroxy-2-imidazolidinones 5a-f. All theproducts were characterized by elemental and spectroscopic analyses. The free-energybarrier (∆GP≠ for prototropic tautomerism in 1-(2-benzimidazolyl-3-phenyl-4,5-dihydroxy-2-imidazolidinone (5f was determined by dynamic NMR studies to be 81 ± 2KJ molP-1

Constant pH molecular dynamics of proteins in explicit solvent with proton tautomerism.

Science.gov (United States)

Goh, Garrett B; Hulbert, Benjamin S; Zhou, Huiqing; Brooks, Charles L

2014-07-01

pH is a ubiquitous regulator of biological activity, including protein-folding, protein-protein interactions, and enzymatic activity. Existing constant pH molecular dynamics (CPHMD) models that were developed to address questions related to the pH-dependent properties of proteins are largely based on implicit solvent models. However, implicit solvent models are known to underestimate the desolvation energy of buried charged residues, increasing the error associated with predictions that involve internal ionizable residue that are important in processes like hydrogen transport and electron transfer. Furthermore, discrete water and ions cannot be modeled in implicit solvent, which are important in systems like membrane proteins and ion channels. We report on an explicit solvent constant pH molecular dynamics framework based on multi-site λ-dynamics (CPHMD(MSλD)). In the CPHMD(MSλD) framework, we performed seamless alchemical transitions between protonation and tautomeric states using multi-site λ-dynamics, and designed novel biasing potentials to ensure that the physical end-states are predominantly sampled. We show that explicit solvent CPHMD(MSλD) simulations model realistic pH-dependent properties of proteins such as the Hen-Egg White Lysozyme (HEWL), binding domain of 2-oxoglutarate dehydrogenase (BBL) and N-terminal domain of ribosomal protein L9 (NTL9), and the pKa predictions are in excellent agreement with experimental values, with a RMSE ranging from 0.72 to 0.84 pKa units. With the recent development of the explicit solvent CPHMD(MSλD) framework for nucleic acids, accurate modeling of pH-dependent properties of both major class of biomolecules-proteins and nucleic acids is now possible. © 2013 Wiley Periodicals, Inc.

Thiol-thione tautomeric analysis, spectroscopic (FT-IR, Laser-Raman, NMR and UV-vis) properties and DFT computations of 5-(3-pyridyl)-4H-1,2,4-triazole-3-thiol molecule.

Science.gov (United States)

Gökce, Halil; Öztürk, Nuri; Ceylan, Ümit; Alpaslan, Yelda Bingöl; Alpaslan, Gökhan

2016-06-15

In this study, the 5-(3-pyridyl)-4H-1,2,4-triazole-3-thiol molecule (C7H6N4S) molecule has been characterized by using FT-IR, Laser-Raman, NMR and UV-vis spectroscopies. Quantum chemical calculations have been performed to investigate the molecular structure (thione-thiol tautomerism), vibrational wavenumbers, electronic transition absorption wavelengths in DMSO solvent and vacuum, proton and carbon-13 NMR chemical shifts and HOMOs-LUMOs energies at DFT/B3LYP/6-311++G(d,p) level for all five tautomers of the title molecule. The obtained results show that the calculated vibrational wavenumbers, NMR chemical shifts and UV-vis wavelengths are in a good agreement with experimental data. Copyright © 2016 Elsevier B.V. All rights reserved.

Synthesis, structure and study of azo-hydrazone tautomeric equilibrium of 1,3-dimethyl-5-(arylazo)-6-amino-uracil derivatives

Science.gov (United States)

Debnath, Diptanu; Roy, Subhadip; Li, Bing-Han; Lin, Chia-Her; Misra, Tarun Kumar

2015-04-01

Azo dyes, 1,3-dimethyl-5-(arylazo)-6-aminouracil (aryl = -C6H5 (1), -p-CH3C6H4 (2), -p-ClC6H4 (3), -p-NO2C6H4 (4)) were prepared and characterized by UV-vis, FT-IR, 1H NMR, 13C NMR spectroscopic techniques and single crystal X-ray crystallographic analysis. In the light of spectroscopic analysis it evidences that of the tautomeric forms, the azo-enamine-keto (A) form is the predominant form in the solid state whereas in different solvents it is the hydrazone-imine-keto (B) form. The study also reveals that the hydrazone-imine-keto (B) form exists in an equilibrium mixture with its anionic form in various organic solvents. The solvatochromic and photophysical properties of the dyes in various solvents with different hydrogen bonding parameter were investigated. The dyes exhibit positive solvatochromic property on moving from polar protic to polar aprotic solvents. They are fluorescent active molecules and exhibit high intense fluorescent peak in some solvents like DMSO and DMF. It has been demonstrated that the anionic form of the hydrazone-imine form is responsible for the high intense fluorescent peak. In addition, the acid-base equilibrium in between neutral and anionic form of hydrazone-imine form in buffer solution of varying pH was investigated and evaluated the pKa values of the dyes by making the use of UV-vis spectroscopic methods. The determined acid dissociation constant (pKa) values increase according to the sequence of 2 > 1 > 3 > 4.

Mechanism of Prototropy. III. Kinetics of the Tautomerization of Benzylidene-Benzylamine. comparison of the influence of hydrogen and alkyl groups on the S{sub E}2' reaction rate; mecanismo de la Prototropia. III. Cinetica de la tautomerizacion de la benciliden-bencilamina. Comparacion de la influencia del hidrogeno y grupos alcohilos sobre la velocidad de la reaccion S{sub E}2'

Energy Technology Data Exchange (ETDEWEB)

Perez Ossorio, R; Gamboa, J M; Martinez Utrilla, R

1961-07-01

The rate of the proto tropic change of benzylidene-benzylamine has been determined by using azomethine {sup 1}4C-labelled in the methylenic group and measuring the distribution of activity between benzaldehyde and benzylamine obtained by hydrolysis at different reaction times. this rate has been compared with those of tautomerization of benzylidene-{alpha}-alkyl benzylamine and {alpha}-alkyl benzylidene-benzyl amines in the same experimental conditions in order to establish ethe influence of alkyl group on this reaction. (Author) 14 refs.

Mechanism of Prototropy. III. Kinetics of the Tautomerization of Benzylidene-Benzylamine. comparison of the influence of hydrogen and alkyl groups on the S{sub E}2' reaction rate; mecanismo de la Prototropia. III. Cinetica de la tautomerizacion de la benciliden-bencilamina. Comparacion de la influencia del hidrogeno y grupos alcohilos sobre la velocidad de la reaccion S{sub E}2'

Energy Technology Data Exchange (ETDEWEB)

Perez Ossorio, R.; Gamboa, J. M.; Martinez Utrilla, R.

1961-07-01

The rate of the proto tropic change of benzylidene-benzylamine has been determined by using azomethine {sup 1}4C-labelled in the methylenic group and measuring the distribution of activity between benzaldehyde and benzylamine obtained by hydrolysis at different reaction times. this rate has been compared with those of tautomerization of benzylidene-{alpha}-alkyl benzylamine and {alpha}-alkyl benzylidene-benzyl amines in the same experimental conditions in order to establish ethe influence of alkyl group on this reaction. (Author) 14 refs.

Solvent isotope effects on the rates of alkylation of thiolamine models of papain

International Nuclear Information System (INIS)

Wandinger, A.; Creighton, D.J.

1980-01-01

As a test of whether it is chemically reasonable to attribute any or all of the observed kinetic solvent deuterium isotope effects reported on papain to the fundamental properties of the tautomerization equilibrium, the magnitudes of the solvent deuterium isotope effects on the rates of alkylation of the tautomeric forms of cysteine and β-mercaptoethylamine were determined for bromo- and chloroacetate, bromo- and chloroacetamide, as well as for methylbromoacetate. These thiolamines are viewed as elementary chemical models of the sulfhydryl group tautomerization equilibrium envisioned in the active site of papain. (Auth.)

Supra-molecular hydrogen-bonding patterns in the N(9)-H protonated and N(7)-H tautomeric form of an N(6) -benzoyl-adenine salt: N (6)-benzoyl-adeninium nitrate.

Science.gov (United States)

Karthikeyan, Ammasai; Jeeva Jasmine, Nithianantham; Thomas Muthiah, Packianathan; Perdih, Franc

2016-02-01

In the title molecular salt, C12H10N5O(+)·NO3 (-), the adenine unit has an N (9)-protonated N(7)-H tautomeric form with non-protonated N(1) and N(3) atoms. The dihedral angle between the adenine ring system and the phenyl ring is 51.10 (10)°. The typical intra-molecular N(7)-H⋯O hydrogen bond with an S(7) graph-set motif is also present. The benzoyl-adeninium cations also form base pairs through N-H⋯O and C-H⋯N hydrogen bonds involving the Watson-Crick face of the adenine ring and the C and O atoms of the benzoyl ring of an adjacent cation, forming a supra-molecular ribbon with R 2 (2)(9) rings. Benzoyl-adeninum cations are also bridged by one of the oxygen atoms of the nitrate anion, which acts as a double acceptor, forming a pair of N-H⋯O hydrogen bonds to generate a second ribbon motif. These ribbons together with π-π stacking inter-actions between the phenyl ring and the five- and six-membered adenine rings of adjacent mol-ecules generate a three-dimensional supra-molecular architecture.

Determination of the Tautomeric Equilibria of Pyridoyl Benzoyl -Diketones in the Liquid and Solid State through the use of Deuterium Isotope Effects on 1H and 13C NMR Chemical Shifts and Spin Coupling Constants

DEFF Research Database (Denmark)

Hansen, Poul Erik; Borisov, Eugeny V.; Lindon, John C.

2015-01-01

The tautomeric equilibria for 2-pyridoyl-, 3-pyridoyl-, and 4-pyridoyl-benzoyl methane have been investigated using deuterium isotope effects on 1H and 13C chemical shifts both in the liquid and the solid state. Equilibria are established both in the liquid and the solid state. In addition......, in the solution state the 2-bond and 3-bond J(1H–13C) coupling constants have been used to confirm the equilibrium positions. The isotope effects due to deuteriation at the OH position are shown to be superior to chemical shift in determination of equilibrium positions of these almost symmetrical -pyridoyl......-benzoyl methanes. The assignments of the NMR spectra are supported by calculations of the chemical shifts at the DFT level. The equilibrium positions are shown to be different in the liquid and the solid state. In the liquid state the 4-pyridoyl derivative is at the B-form (C-1 is OH), whereas the 2-and 3-pyridoyl...

Assessment of tautomer distribution using the condensed reaction graph approach

Science.gov (United States)

Gimadiev, T. R.; Madzhidov, T. I.; Nugmanov, R. I.; Baskin, I. I.; Antipin, I. S.; Varnek, A.

2018-03-01

We report the first direct QSPR modeling of equilibrium constants of tautomeric transformations (logK T ) in different solvents and at different temperatures, which do not require intermediate assessment of acidity (basicity) constants for all tautomeric forms. The key step of the modeling consisted in the merging of two tautomers in one sole molecular graph ("condensed reaction graph") which enables to compute molecular descriptors characterizing entire equilibrium. The support vector regression method was used to build the models. The training set consisted of 785 transformations belonging to 11 types of tautomeric reactions with equilibrium constants measured in different solvents and at different temperatures. The models obtained perform well both in cross-validation (Q2 = 0.81 RMSE = 0.7 logK T units) and on two external test sets. Benchmarking studies demonstrate that our models outperform results obtained with DFT B3LYP/6-311 ++ G(d,p) and ChemAxon Tautomerizer applicable only in water at room temperature.

Síntesis de 3-ciano-4-hidroxicumarina y análisis de su equilibrio tautomérico utilizando la Teoría del Funcional de la Densidad (DFT y el modelo de solvatación continua (PCM | Synthesis of 3-cyanohydroxycoumarin and analysis of its tautomeric equilibrium using Density Functional Theory (DFT and polarizable continuum model (PCM

Directory of Open Access Journals (Sweden)

Gustavo Cabrera

2017-11-01

Full Text Available The procedure for the synthesis of 3-cyano-4-hydroxycoumarin is presented along with the results from the analysis of its tautomeric equilibrium using Density Functional Theory (DFT and Polarizable Continuum Model (PCM. The geometry of the compounds was optimized with Gaussian 03 and from the resulting structures, a group of thermodynamic and kinetic parameters were determined. It was found that 3-cyano-4-hydroxycoumarin was the most stable tautomer, as was also shown by spectroscopic techniques. Other parameters, such as: transition state energy, equlibrium constant, kinetic constant, bond orders and bond angles, were also calculated.

Determination of the major tautomeric form of the covalently modified adenine in the (+)-CC-1065-DNA adduct by 1H and 15N NMR studies

International Nuclear Information System (INIS)

Lin, Chin Hsiung; Hurley, L.H.

1990-01-01

(+)-CC-1065 is an extremely potent antitumor antibiotic produced by Streptomyces zelensis. The potent cytotoxic effects of the drug are thought to be due to the formation of a covalent adduct with DNA through N3 of adenine. Although the covalent linkage sites between (+)-CC-1065 and DNA have been determined, the tautomeric form of the covalently modified adenine in the (+)-CC-1065-DNA duplex adduct was not defined. The [6- 15 N]deoxyadenosine-labeled 12-mer duplex adduct was then studied by 1 H and 15 N NMR. One-dimensional NOE difference and two-dimensional NOESY 1 H NMR experiments on the nonisotopically labeled 12-mer duplex adduct demonstrate that the 6-amino protons of the covalently modified adenine exhibit two signals at 9.19 and 9.08 ppm. Proton NMR experiments on the [6- 15 N]deoxyadenosine-labeled 12-mer duplex adduct show that the two resonance signals for adenine H6 observed on the nonisotopically labeled duplex adduct were split into doublets by the 15 N nucleus with coupling constants of 91.3 Hz for non-hydrogen-bonded and 86.8 Hz for hydrogen-bonded amino protons. The authors conclude that the covalently modified adenine N6 of the (+)-CC-1065-12-mer duplex adduct is predominantly in the doubly protonated form, in which calculations predict that the C6-N6 bond is shortened and the positive charge is delocalized over the entire adenine molecule

Direct Observation of Double Hydrogen Transfer via Quantum Tunneling in a Single Porphycene Molecule on a Ag(110) Surface.

Science.gov (United States)

Koch, Matthias; Pagan, Mark; Persson, Mats; Gawinkowski, Sylwester; Waluk, Jacek; Kumagai, Takashi

2017-09-13

Quantum tunneling of hydrogen atoms (or protons) plays a crucial role in many chemical and biological reactions. Although tunneling of a single particle has been examined extensively in various one-dimensional potentials, many-particle tunneling in high-dimensional potential energy surfaces remains poorly understood. Here we present a direct observation of a double hydrogen atom transfer (tautomerization) within a single porphycene molecule on a Ag(110) surface using a cryogenic scanning tunneling microscope (STM). The tautomerization rates are temperature independent below ∼10 K, and a large kinetic isotope effect (KIE) is observed upon substituting the transferred hydrogen atoms by deuterium, indicating that the process is governed by tunneling. The observed KIE for three isotopologues and density functional theory calculations reveal that a stepwise transfer mechanism is dominant in the tautomerization. It is also found that the tautomerization rate is increased by vibrational excitation via an inelastic electron tunneling process. Moreover, the STM tip can be used to manipulate the tunneling dynamics through modification of the potential landscape.

FT-IR study and solvent-implicit and explicit effect on stepwise tautomerism of Guanylurea: M06-2X as a case of study

Science.gov (United States)

Karimzadeh, Morteza; Manouchehri, Neda; Saberi, Dariush; Niknam, Khodabakhsh

2018-06-01

All 66 conformers of guanylurea were optimized and frequency calculations were performed at M06-2X/6-311++G(d,p) level of theory. Theses conformers were categorized into five tautomers, and the most stable conformer of each tautomer were found. Geometrical parameters indicated that these tautomers have almost planar structure. Complete stepwise tautomerism were studied through both intramolecular proton transfer routs and internal rotations. Results indicated that the proton transfer routs involving four-membered heterocyclic structures were rate-determining steps. Also, intramolecular proton movement having six-membered transition state structures had very low energy barrier comparable to the transition states of internal rotation routs. Differentiation of studied tautomers could easily be done through their FT-IR spectra in the range of 3200 to 3900 cm-1 by comparing absorption bands and intensity of peaks. Solvent-implicit effects on the stability of tautomers were also studied through re-optimization and frequency calculation in four solvents. Water, DMSO, acetone and toluene had stabilization effect on all considered tautomers, but the order of stabilization effect was as follows: water > DMSO > acetone > toluene. Finally, solvent-explicit, base-explicit and acid-explicit effect were also studied by taking place of studied tautomer nearside of acid, base or solvent and optimization of them. Frequency calculation for proton movement by contribution of explicit effect showed that formic acid had a very strong effect on proton transfer from tautomer A1 to tautomer D8 by lowering the energy barrier from 42.57 to 0.8 kcal/mol. In addition, ammonia-explicit effect was found to lower the barrier from 42.57 to 22.46 kcal/mol, but this effect is lower than that of water and methanol-explicit effect.

FT-IR study and solvent-implicit and explicit effect on stepwise tautomerism of Guanylurea: M06-2X as a case of study.

Science.gov (United States)

Karimzadeh, Morteza; Manouchehri, Neda; Saberi, Dariush; Niknam, Khodabakhsh

2018-06-15

All 66 conformers of guanylurea were optimized and frequency calculations were performed at M06-2X/6-311++G(d,p) level of theory. Theses conformers were categorized into five tautomers, and the most stable conformer of each tautomer were found. Geometrical parameters indicated that these tautomers have almost planar structure. Complete stepwise tautomerism were studied through both intramolecular proton transfer routs and internal rotations. Results indicated that the proton transfer routs involving four-membered heterocyclic structures were rate-determining steps. Also, intramolecular proton movement having six-membered transition state structures had very low energy barrier comparable to the transition states of internal rotation routs. Differentiation of studied tautomers could easily be done through their FT-IR spectra in the range of 3200 to 3900cm -1 by comparing absorption bands and intensity of peaks. Solvent-implicit effects on the stability of tautomers were also studied through re-optimization and frequency calculation in four solvents. Water, DMSO, acetone and toluene had stabilization effect on all considered tautomers, but the order of stabilization effect was as follows: water>DMSO>acetone>toluene. Finally, solvent-explicit, base-explicit and acid-explicit effect were also studied by taking place of studied tautomer nearside of acid, base or solvent and optimization of them. Frequency calculation for proton movement by contribution of explicit effect showed that formic acid had a very strong effect on proton transfer from tautomer A1 to tautomer D8 by lowering the energy barrier from 42.57 to 0.8kcal/mol. In addition, ammonia-explicit effect was found to lower the barrier from 42.57 to 22.46kcal/mol, but this effect is lower than that of water and methanol-explicit effect. Copyright © 2018 Elsevier B.V. All rights reserved.

Non-typical fluorescence studies of excited and ground state proton and hydrogen transfer

KAUST Repository

Gil, Michał; Kijak, Michał; Piwonski, Hubert Marek; Herbich, Jerzy; Waluk, Jacek

2017-01-01

Fluorescence studies of tautomerization have been carried out for various systems that exhibit single and double proton or hydrogen translocation in various environments, such as liquid and solid condensed phases, ultracold supersonic jets, and finally, polymer matrices with single emitters.We focus on less explored areas of application of fluorescence for tautomerization studies, using porphycene, a porphyrin isomer, as an example. Fluorescence anisotropy techniques allow investigations of self-exchange reactions, where the reactant and product are formally identical. Excitation with polarized light makes it possible to monitor tautomerization in single molecules and to detect their three-dimensional orientation. Analysis of fluorescence from single vibronic levels of jet-isolated porphycene not only demonstrates coherent tunneling of two internal protons, but also indicates that the process is vibrational mode-specific. Next, we present bifunctional proton donoracceptor systems, molecules that are able, depending on the environment, to undergo excited state single intramolecular or double intermolecular proton transfer. For molecules that have donor and acceptor groups located in separate moieties linked by a single bond, excited state tautomerization can be coupled to mutual twisting of the two subunits.

Non-typical fluorescence studies of excited and ground state proton and hydrogen transfer

KAUST Repository

Gil, Michał

2017-02-03

Fluorescence studies of tautomerization have been carried out for various systems that exhibit single and double proton or hydrogen translocation in various environments, such as liquid and solid condensed phases, ultracold supersonic jets, and finally, polymer matrices with single emitters.We focus on less explored areas of application of fluorescence for tautomerization studies, using porphycene, a porphyrin isomer, as an example. Fluorescence anisotropy techniques allow investigations of self-exchange reactions, where the reactant and product are formally identical. Excitation with polarized light makes it possible to monitor tautomerization in single molecules and to detect their three-dimensional orientation. Analysis of fluorescence from single vibronic levels of jet-isolated porphycene not only demonstrates coherent tunneling of two internal protons, but also indicates that the process is vibrational mode-specific. Next, we present bifunctional proton donoracceptor systems, molecules that are able, depending on the environment, to undergo excited state single intramolecular or double intermolecular proton transfer. For molecules that have donor and acceptor groups located in separate moieties linked by a single bond, excited state tautomerization can be coupled to mutual twisting of the two subunits.

Mispairs with Watson-Crick base-pair geometry observed in ternary complexes of an RB69 DNA polymerase variant.

Science.gov (United States)

Xia, Shuangluo; Konigsberg, William H

2014-04-01

Recent structures of DNA polymerase complexes with dGMPCPP/dT and dCTP/dA mispairs at the insertion site have shown that they adopt Watson-Crick geometry in the presence of Mn(2+) indicating that the tautomeric or ionization state of the base has changed. To see whether the tautomeric or ionization state of base-pair could be affected by its microenvironment, we determined 10 structures of an RB69 DNA polymerase quadruple mutant with dG/dT or dT/dG mispairs at position n-1 to n-5 of the Primer/Template duplex. Different shapes of the mispairs, including Watson-Crick geometry, have been observed, strongly suggesting that the local environment of base-pairs plays an important role in their tautomeric or ionization states. © 2014 The Protein Society.

Wittig Reaction: Domino Olefination and Stereoselectivity DFT Study. Synthesis of the Miharamycins' Bicyclic Sugar Moiety.

Science.gov (United States)

Cachatra, Vasco; Almeida, Andreia; Sardinha, João; Lucas, Susana D; Gomes, Ana; Vaz, Pedro D; Florêncio, M Helena; Nunes, Rafael; Vila-Viçosa, Diogo; Calhorda, Maria José; Rauter, Amélia P

2015-11-20

2-O-Acyl protected-d-ribo-3-uloses reacted with [(ethoxycarbonyl)methylene]triphenylphosphorane in acetonitrile to afford regio- and stereoselectively 2-(Z)-alkenes in 10-60 min under microwave irradiation. This domino reaction is proposed to proceed via tautomerization of 3-ulose to enol, acyl migration, tautomerization to the 3-O-acyl-2-ulose, and Wittig reaction. Alternatively, in chloroform, regioselective 3-olefination of 2-O-pivaloyl-3-uloses gave (E)-alkenes, key precursors for the miharamycins' bicyclic sugar moiety.

Relaxations of fluorouracil tautomers by decorations of fullerene-like SiCs: DFT studies

Energy Technology Data Exchange (ETDEWEB)

Kouchaki, Alireza [Department of Pharmaceutical Chemistry, Faculty of Pharmaceutical Chemistry, Pharmaceutical Sciences Branch, Islamic Azad University, Tehran (Iran, Islamic Republic of); Gülseren, Oğuz [Department of Physics, Faculty of Science, Bilkent University, Ankara (Turkey); Hadipour, Nasser [Department of Chemistry, Faculty of Science, Tarbiat Modares University, Tehran (Iran, Islamic Republic of); Mirzaei, Mahmoud, E-mail: mdmirzaei@pharm.mui.ac.ir [Bioinformatics Research Center, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan (Iran, Islamic Republic of)

2016-06-03

Decorations of silicon carbide (SiC) fullerene-like nanoparticles by fluorouracil (FU) and its tautomers are investigated through density functional theory (DFT) calculations. Two models of fullerene-like particles including Si{sub 12}C{sub 8} and Si{sub 8}C{sub 12} are constructed to be counterparts of decorated hybrid structures, FU@Si{sub 12}C{sub 8} and FU@Si{sub 8}C{sub 12}, respectively. The initial models including original FU and tautomeric structures and SiC nanoparticles are individually optimized and then combined for further optimizations in the hybrid forms. Covalent bonds are observed for FU@Si{sub 12}C{sub 8} hybrids, whereas non-covalent interactions are seen for FU@Si{sub 8}C{sub 12} ones. The obtained properties indicated that Si{sub 12}C{sub 8} model could be considered as a better counterpart for interactions with FU structures than Si{sub 8}C{sub 12} model. The results also showed significant effects of interactions on the properties of atoms close to the interacting regions in nanoparticles. Finally, the tautomeric structures show different behaviors in interactions with SiC nanoparticles, in which the SiC nanoparticles could be employed to detect the situations of tautomeric processes for FU structures. - Highlights: • Possibilities of interaction between fluorouracil and silicon carbides have been recognized. • Possibilities for covalent and non-covalent interactions have been indicated. • Detections of tautomeric structures have been investigated.

The molecular origin of the thiamine diphosphate-induced spectral bands of ThDP-dependent enzymes.

Science.gov (United States)

Kovina, Marina V; De Kok, Aart; Sevostyanova, Irina A; Khailova, Ludmila S; Belkina, Natalya V; Kochetov, German A

2004-08-01

New and previously published data on a variety of ThDP-dependent enzymes such as baker's yeast transketolase, yeast pyruvate decarboxylase and pyruvate dehydrogenase from pigeon breast muscle, bovine heart, bovine kidney, Neisseria meningitidis and E. coli show their spectral sensitivity to ThDP binding. Although ThDP-induced spectral changes are different for different enzymes, their universal origin is suggested as being caused by the intrinsic absorption of the pyrimidine ring of ThDP, bound in different tautomeric forms with different enzymes. Non-enzymatic models with pyrimidine-like compounds indicate that the specific protein environment of the aminopyrimidine ring of ThDP determines its tautomeric form and therefore the changeable features of the inducible effect. A polar environment causes the prevalence of the aminopyrimidine tautomeric form (short wavelength region is affected). For stabilization of the iminopyrimidine tautomeric form (both short- and long-wavelength regions are affected) two factors appear essential: (i) a nonpolar environment and (ii) a conservative carboxyl group of a specific glutamate residue interacting with the N1' atom of the aminopyrimidine ring. The two types of optical effect depend in a different way upon the pH, in full accordance with the hypothesis tested. From these studies it is concluded that the inducible optical rotation results from interaction of the aminopyrimidine ring with its asymmetric environment and is defined by the protonation state of N1' and the 4'-nitrogen. Copyright 2004 Wiley-Liss, Inc.

A temperature induced ferrocene–ferrocenium interconversion in a ferrocene functionalized μ{sub 3}-O chromium carboxylate

Energy Technology Data Exchange (ETDEWEB)

Mereacre, Valeriu, E-mail: valeriu.mereacre@kit.edu [Institut für Anorganische Chemie, Karlsruher Institut für Technologie, D-76131 Karlsruhe (Germany); Schlageter, Martin [Institut für Nanotechnologie, Karlsruher Institut für Technologie, D-76344 Eggenstein-Leopoldshafen (Germany); Powell, Annie K., E-mail: annie.powell@kit.edu [Institut für Anorganische Chemie, Karlsruher Institut für Technologie, D-76131 Karlsruhe (Germany); Institut für Nanotechnologie, Karlsruher Institut für Technologie, D-76344 Eggenstein-Leopoldshafen (Germany)

2015-05-01

The infrared spectra and {sup 57}Fe Mössbauer measurements of a ferrocenecarboxylate functionalized {Cr_3O} complex in solid state are reported. It was established that conjugation of ferrocene Cp orbitals with the π orbitals of the adjacent carboxylic group stabilizes the trapped mixed-valence state leading to an intriguing coexistence of ferrocene and ferrocenium species giving rise to a new type of compound showing valence tautomerism in the solid state. - Highlights: • A stabilized ferrocene trapped mixed-valence state is reported. • New type of compound showing valence tautomerism in solid state. • A thermally induced electron transfer and a mixed-valence state near room temperature.

A temperature induced ferrocene–ferrocenium interconversion in a ferrocene functionalized μ3-O chromium carboxylate

International Nuclear Information System (INIS)

Mereacre, Valeriu; Schlageter, Martin; Powell, Annie K.

2015-01-01

The infrared spectra and 57 Fe Mössbauer measurements of a ferrocenecarboxylate functionalized {Cr 3 O} complex in solid state are reported. It was established that conjugation of ferrocene Cp orbitals with the π orbitals of the adjacent carboxylic group stabilizes the trapped mixed-valence state leading to an intriguing coexistence of ferrocene and ferrocenium species giving rise to a new type of compound showing valence tautomerism in the solid state. - Highlights: • A stabilized ferrocene trapped mixed-valence state is reported. • New type of compound showing valence tautomerism in solid state. • A thermally induced electron transfer and a mixed-valence state near room temperature

Quantum-chemical studies on the favored and rare tautomers of neutral and redox adenine.

Science.gov (United States)

Raczyńska, Ewa D; Makowski, Mariusz; Zientara-Rytter, Katarzyna; Kolczyńska, Katarzyna; Stępniewski, Tomasz M; Hallmann, Małgorzata

2013-02-21

All possible twenty-three prototropic tautomers of neutral and redox adenine (nine amine and fourteen imine forms, including geometric isomerism of the exo ═NH group) were examined in vacuo {DFT(B3LYP)/6-311+G(d,p)}. The NH → NH conversions as well as those usually omitted, NH → CH and CH → CH, were considered. An interesting change of the tautomeric preference occurs when proceeding from neutral to reduced adenine. One-electron reduction favors the nonaromatic amine C8H-N10H tautomer. This tautomeric preference is similar to that (C2H) for reduced imidazole. Water molecules (PCM model) seem to not change this trend. They influence solely the relative energies. The DFT vertical detachment energy in the gas phase is positive for each tautomer, e.g., 0.03 eV for N9H-N10H and 1.84 eV for C8H-N10H. The DFT adiabatic electron affinity for the favored process, neutral N9H-N10H → reduced C8H-N10H (ground states), is equal to 0.18 eV at 0 K (ZPE included). One-electron oxidation does not change the tautomeric preference in the gas phase. The aromatic amine N9H-N10H tautomer is favored for the oxidized molecule similarly as for the neutral one. The DFT adiabatic ionization potential for the favored process, neutral N9H-N10H → oxidized N9H-N10H (ground states), is equal to 8.12 eV at 0 K (ZPE included). Water molecules (PCM model) seem to influence solely the composition of the tautomeric mixture and the relative energies. They change the energies of the oxidation and reduction processes by ca. 2 eV.

Distinguishing tautomerism in the crystal structure of (Z)-N-(5-ethyl-2,3-di-hydro-1,3,4-thiadiazol-2-ylidene) -4-methylbenzenesulfonamide using DFT-D calculations and {sup 13}C solid-state NMR

Energy Technology Data Exchange (ETDEWEB)

Li, Xiaozhou; Bond, Andrew D.; Johansson, Kristoffer E.; Van de Streek, Jacco, E-mail: jacco.vandestreek@sund.ku.dk [Department of Pharmacy, University of Copenhagen, Universitetsparken 2, Copenhagen DK-2100 (Denmark)

2014-08-01

The crystal structure of (Z)-N-(5-ethyl-2,3-di-hydro-1,3,4-thiadiazol-2-ylidene) -4-methylbenzenesulfonamide contains an imine tautomer, rather than the previously reported amine tautomer. The tautomers can be distinguished using dispersion-corrected density functional theory calculations and by comparison of calculated and measured {sup 13}C solid-state NMR spectra. The crystal structure of the title compound, C{sub 11}H{sub 13}N{sub 3}O{sub 2}S{sub 2}, has been determined previously on the basis of refinement against laboratory powder X-ray diffraction (PXRD) data, supported by comparison of measured and calculated {sup 13}C solid-state NMR spectra [Hangan et al. (2010 ▶). Acta Cryst. B66, 615–621]. The mol@@ecule is tautomeric, and was reported as an amine tautomer [systematic name: N-(5-ethyl-1,3,4-thia@@diazol-2-yl)-p-toluene@@sulfonamide], rather than the correct imine tautomer. The protonation site on the mol@@ecule’s 1,3,4-thia@@diazole ring is indicated by the inter@@molecular contacts in the crystal structure: N—H⋯O hydrogen bonds are established at the correct site, while the alternative protonation site does not establish any notable inter molecular inter@@actions. The two tautomers provide essentially identical Rietveld fits to laboratory PXRD data, and therefore they cannot be directly distinguished in this way. However, the correct tautomer can be distinguished from the incorrect one by previously reported qu@@anti@@tative criteria based on the extent of structural distortion on optimization of the crystal structure using dispersion-corrected density functional theory (DFT-D) calculations. Calculation of the {sup 13}C SS-NMR spectrum based on the correct imine tautomer also provides considerably better agreement with the measured {sup 13}C SS-NMR spectrum.

Near-Field Enhanced Photochemistry of Single Molecules in a Scanning Tunneling Microscope Junction.

Science.gov (United States)

Böckmann, Hannes; Gawinkowski, Sylwester; Waluk, Jacek; Raschke, Markus B; Wolf, Martin; Kumagai, Takashi

2018-01-10

Optical near-field excitation of metallic nanostructures can be used to enhance photochemical reactions. The enhancement under visible light illumination is of particular interest because it can facilitate the use of sunlight to promote photocatalytic chemical and energy conversion. However, few studies have yet addressed optical near-field induced chemistry, in particular at the single-molecule level. In this Letter, we report the near-field enhanced tautomerization of porphycene on a Cu(111) surface in a scanning tunneling microscope (STM) junction. The light-induced tautomerization is mediated by photogenerated carriers in the Cu substrate. It is revealed that the reaction cross section is significantly enhanced in the presence of a Au tip compared to the far-field induced process. The strong enhancement occurs in the red and near-infrared spectral range for Au tips, whereas a W tip shows a much weaker enhancement, suggesting that excitation of the localized plasmon resonance contributes to the process. Additionally, using the precise tip-surface distance control of the STM, the near-field enhanced tautomerization is examined in and out of the tunneling regime. Our results suggest that the enhancement is attributed to the increased carrier generation rate via decay of the excited near-field in the STM junction. Additionally, optically excited tunneling electrons also contribute to the process in the tunneling regime.

The use of a versatile o-vanilloyl hydrazone ligand to prepare SMM-like Dy3 molecular cluster pair.

Science.gov (United States)

Xue, Shufang; Zhao, Lang; Guo, Yun-Nan; Zhang, Peng; Tang, Jinkui

2012-09-14

A novel lanthanide molecular cluster pair (MCP), displaying single molecule magnet behaviour, was assembled using the novel o-vanilloyl hydrazone ligand, versatile in terms of denticity, tautomerism and the rotatable C-C bond.

Electronic structure of some adenosine receptor antagonists. III. Quantitative investigation of the electronic absorption spectra of alkyl xanthines

Science.gov (United States)

Moustafa, H.; Shalaby, Samia H.; El-sawy, K. M.; Hilal, Rifaat

2002-07-01

Quantitative and comparative investigation of the electronic absorption spectra of theophylline, caffeine and their derivatives is reported. The spectra of theophylline, caffeine and theobromine were compared to establish the predominant tautomeric species in solution. This comparison, analysis of solvent effects and assignments of the observed transitions via MO computations indicate the exits of only one tautomeric species in solution that is the N7 form. A low-lying triplet state was identified which corresponds to a HOMO-LUMO transition. This relatively long-lived T 1 state is always less polar than the ground state and may very well underlie the photochemical reactivity of alkyl xanthines. Substituents of different electron donating or withdrawing strengths and solvent effects are investigated and analyzed. The present analysis is facilitated via computer deconvolution of the observed spectra and MO computation.

Specific solvent effect on lumazine photophysics: A combined fluorescence and intrinsic reaction coordinate analysis

Energy Technology Data Exchange (ETDEWEB)

Moyon, N. Shaemningwar; Gashnga, Pynsakhiat Miki; Phukan, Smritakshi; Mitra, Sivaprasad, E-mail: smitra@nehu.ac.in

2013-06-27

Highlights: • Correlation of lumazine photophysics with multiparametric Kamlet–Taft equation. • Solvent basicity (β) contributes maximum towards the hydrogen bonding (HB) effect. • HB interaction occurs at N1 and N3 proton in S{sub 0} and S{sub 1} state, respectively. • IRC calculation for different tautomerization processes both in S{sub 0} and S{sub 1} states. • Process related to riboflavin biosynthesis is thermodynamically feasible. - Abstract: The photophysical properties and tautomerization behavior of neutral lumazine were studied by fluorescence spectroscopy and density functional theory calculation. A quantitative estimation of the contributions from different solvatochromic parameters, like solvent polarizibility (π{sup ∗}), hydrogen bond donation (α) and hydrogen bond accepting (β) ability of the solvent, was made using linear free energy relationships based on the Kamlet–Taft equation. The analysis reveals that the hydrogen bond acceptance ability of the solvent is the most important parameter characterizing the excited state behavior of lumazine. Theoretical calculations result predict an extensive charge redistribution of lumazine upon excitation corresponding to the N3 and N1 proton dissociation sites by solvents in the ground and excited states, respectively. Comparison of S{sub 0} and S{sub 1} state potential energy curves constructed for several water mediated tautomerization processes by intrinsic reaction coordinate analysis of lumazine-H{sub 2}O cluster shows that (3,2) and (1,8) hydrogen migrations are the most favorable processes upon excitation.

Replication infidelity via a mismatch with Watson-Crick geometry.

Science.gov (United States)

Bebenek, Katarzyna; Pedersen, Lars C; Kunkel, Thomas A

2011-02-01

In describing the DNA double helix, Watson and Crick suggested that "spontaneous mutation may be due to a base occasionally occurring in one of its less likely tautomeric forms." Indeed, among many mispairing possibilities, either tautomerization or ionization of bases might allow a DNA polymerase to insert a mismatch with correct Watson-Crick geometry. However, despite substantial progress in understanding the structural basis of error prevention during polymerization, no DNA polymerase has yet been shown to form a natural base-base mismatch with Watson-Crick-like geometry. Here we provide such evidence, in the form of a crystal structure of a human DNA polymerase λ variant poised to misinsert dGTP opposite a template T. All atoms needed for catalysis are present at the active site and in positions that overlay with those for a correct base pair. The mismatch has Watson-Crick geometry consistent with a tautomeric or ionized base pair, with the pH dependence of misinsertion consistent with the latter. The results support the original idea that a base substitution can originate from a mismatch having Watson-Crick geometry, and they suggest a common catalytic mechanism for inserting a correct and an incorrect nucleotide. A second structure indicates that after misinsertion, the now primer-terminal G • T mismatch is also poised for catalysis but in the wobble conformation seen in other studies, indicating the dynamic nature of the pathway required to create a mismatch in fully duplex DNA.

Replication infidelity via a mismatch with Watson–Crick geometry

Science.gov (United States)

Bebenek, Katarzyna; Pedersen, Lars C.; Kunkel, Thomas A.

2011-01-01

In describing the DNA double helix, Watson and Crick suggested that “spontaneous mutation may be due to a base occasionally occurring in one of its less likely tautomeric forms.” Indeed, among many mispairing possibilities, either tautomerization or ionization of bases might allow a DNA polymerase to insert a mismatch with correct Watson–Crick geometry. However, despite substantial progress in understanding the structural basis of error prevention during polymerization, no DNA polymerase has yet been shown to form a natural base–base mismatch with Watson–Crick-like geometry. Here we provide such evidence, in the form of a crystal structure of a human DNA polymerase λ variant poised to misinsert dGTP opposite a template T. All atoms needed for catalysis are present at the active site and in positions that overlay with those for a correct base pair. The mismatch has Watson–Crick geometry consistent with a tautomeric or ionized base pair, with the pH dependence of misinsertion consistent with the latter. The results support the original idea that a base substitution can originate from a mismatch having Watson–Crick geometry, and they suggest a common catalytic mechanism for inserting a correct and an incorrect nucleotide. A second structure indicates that after misinsertion, the now primer-terminal G•T mismatch is also poised for catalysis but in the wobble conformation seen in other studies, indicating the dynamic nature of the pathway required to create a mismatch in fully duplex DNA. PMID:21233421

Visualizing Transient Watson-Crick Like Mispairs in DNA and RNA Duplexes

Science.gov (United States)

Kimsey, Isaac J.; Petzold, Katja; Sathyamoorthy, Bharathwaj; Stein, Zachary W.; Al-Hashimi, Hashim M.

2015-01-01

Rare tautomeric and anionic nucleobases are believed to play fundamental biological roles but their prevalence and functional importance has remained elusive because they exist transiently, in low-abundance, and involve subtle movements of protons that are difficult to visualize. Using NMR relaxation dispersion, we show that wobble dG•dT and rG•rU mispairs in DNA and RNA duplexes exist in dynamic equilibrium with short-lived, low-populated Watson-Crick like mispairs that are stabilized by rare enolic or anionic bases. These mispairs can evade Watson-Crick fidelity checkpoints and form with probabilities (10−3-10−5) that strongly imply a universal role in replication and translation errors. Our results indicate that rare tautomeric and anionic bases are widespread in nucleic acids, expanding their structural and functional complexity beyond that attainable with canonical bases. PMID:25762137

Visualizing transient Watson-Crick-like mispairs in DNA and RNA duplexes.

Science.gov (United States)

Kimsey, Isaac J; Petzold, Katja; Sathyamoorthy, Bharathwaj; Stein, Zachary W; Al-Hashimi, Hashim M

2015-03-19

Rare tautomeric and anionic nucleobases are believed to have fundamental biological roles, but their prevalence and functional importance has remained elusive because they exist transiently, in low abundance, and involve subtle movements of protons that are difficult to visualize. Using NMR relaxation dispersion, we show here that wobble dG•dT and rG•rU mispairs in DNA and RNA duplexes exist in dynamic equilibrium with short-lived, low-populated Watson-Crick-like mispairs that are stabilized by rare enolic or anionic bases. These mispairs can evade Watson-Crick fidelity checkpoints and form with probabilities (10(-3) to 10(-5)) that strongly imply a universal role in replication and translation errors. Our results indicate that rare tautomeric and anionic bases are widespread in nucleic acids, expanding their structural and functional complexity beyond that attainable with canonical bases.

How stable are the mutagenic tautomers of DNA bases?

Directory of Open Access Journals (Sweden)

Brovarets’ O. O.

2010-02-01

Full Text Available Aim. To determine the lifetime of the mutagenic tautomers of DNA base pairs through the investigation of the physicochemical mechanisms of their intramolecular proton transfer. Methods. Non-empirical quantum chemistry, the analysis of the electron density by means of Bader’s atom in molecules (AIM theory and physicochemical kinetics were used. Results. Physicochemical character of the transition state of the intramolecular tautomerisation of DNA bases was investigated, the lifetime of mutagenic tautomers was calculated. Conclusions. The lifetime of the DNA bases mutagenic tautomers by 3–10 orders exceeds typical time of DNA replication in the cell (~103 s. This fact confirms that the postulate, on which the Watson-Crick tautomeric hypothesis of spontaneous transitions grounds, is adequate. The absence of intramolecular H-bonds in the canonical and mutagenic tautomeric forms determine their high stability

Protonation preferentially stabilizes minor tautomers of the halouracils: IRMPD action spectroscopy and theoretical studies

NARCIS (Netherlands)

Crampton, K.T.; Rathur, A.I.; Nei, Y.-w.; Berden, G.; Oomens, J.; Rodgers, M.T.

2012-01-01

Tautomerization induced by protonation of halouracils may increase their efficacy as anti-cancer drugs by altering their reactivity and hydrogen bonding characteristics, potentially inducing errors during DNA and RNA replication. The gas-phase structures of protonated complexes of five halouracils,

Protonation Preferentially Stabilizes Minor Tautomers of the Halouracils: IRMPD Action Spectroscopy and Theoretical Studies

NARCIS (Netherlands)

Crampton, K. T.; Rathur, A. I.; Nei, Y. W.; G. Berden,; Oomens, J.; Rodgers, M. T.

2012-01-01

Tautomerization induced by protonation of halouracils may increase their efficacy as anti-cancer drugs by altering their reactivity and hydrogen bonding characteristics, potentially inducing errors during DNA and RNA replication. The gas-phase structures of protonated complexes of five halouracils,

Untitled

Indian Academy of Sciences (India)

Keywords. Organic solid state; topochemistry; crystal engineering; x-ray crystallography; molecular complexes; photochemistry; atom-atom potentials; solid state tautomerism; intercalation. 1. Introduction. How do organic molecules organise themselves in crystals? Can one predict the crystal structure of an organic solid?

On prediction of OH stretching frequencies in intramolecularly hydrogen bonded systems

DEFF Research Database (Denmark)

Hansen, Poul Erik; Spanget-Larsen, Jens

2012-01-01

OH stretching frequencies are investigated for a series of non-tautomerizing systems with intramolecular hydrogen bonds. Effective OH stretching wavenumbers are predicted by the application of empirical correlation procedures based on the results of B3LYP/6-31G(d) theoretical calculations...

Mohammed Rafiq Hussain Siddiqui

Indian Academy of Sciences (India)

Home; Journals; Journal of Chemical Sciences. Mohammed Rafiq Hussain Siddiqui. Articles written in Journal of Chemical Sciences. Volume 127 Issue 9 September 2015 pp 1547-1556. Molecular structure investigation and tautomerism aspects of ()-3-benzylideneindolin-2-one · Assem Barakat Abdullah Mohammed ...

Synthesis and structural characterization of some trisulfide analoges of thiouracil-based antithyroid drugs

Science.gov (United States)

Bhabak, Krishna P.; Bhowmick, Debasish

2012-08-01

Thiourea-based antithyroid drugs are effectively used for the treatment of hyperthyroidism. In this paper, we describe the synthesis of new trisulfides (11-12) from the commonly used thiourea-based antithyroid drugs such as 6-n-propyl-2-thiouracil (PTU) and 6-methyl-2-thiouracil (MTU) in the reaction with I2/KI system. Structural analysis by single crystal X-ray diffraction studies revealed the stabilization of trisulfides by a lactam-lactim tautomerism facilitating effective intramolecular as well as intermolecular non-covalent interactions. Although the structures of both trisulfides were found to be quite similar, a notable difference in the intermolecular interactions was observed between compounds 11 and 12 leading to different structural patterns. Structural stabilization of these trisulfides by tautomerism followed by intramolecular as well as intermolecular H-bonds makes these molecules as perfect examples in molecular recognition with self-complementary donor and acceptor units within a single molecule.

Does Prop-2-ynylideneamine, HC≡CCH=NH, Exist in Space? A Theoretical and Computational Investigation

Directory of Open Access Journals (Sweden)

Osman I. Osman

2014-06-01

Full Text Available MP2, DFT and CCSD methods with 6-311++G** and aug-cc-pvdz basis sets have been used to probe the structural changes and relative energies of E-prop-2-ynylideneamine (I, Z-prop-2-ynylideneamine (II, prop-1,2-diene-1-imine (III and vinyl cyanide (IV. The energy near-equivalence and provenance of preference of isomers and tautomers were investigated by NBO calculations using HF and B3LYP methods with 6-311++G** and aug-cc-pvdz basis sets. All substrates have Cs symmetry. The optimized geometries were found to be mainly theoretical method dependent. All elected levels of theory have computed I/II total energy of isomerization (ΔE of 1.707 to 3.707 kJ/mol in favour of II at 298.15 K. MP2 and CCSD methods have indicated clearly the preference of II over III; while the B3LYP functional predicted nearly similar total energies. All tested levels of theory yielded a global II/IV tautomerization total energy (ΔE of 137.3–148.4 kJ/mol in support of IV at 298.15 K. The negative values of ΔS indicated that IV is favoured at low temperature. At high temperature, a reverse tautomerization becomes spontaneous and II is preferred. The existence of II in space was debated through the interpretation and analysis of the thermodynamic and kinetic studies of this tautomerization reaction and the presence of similar compounds in the Interstellar Medium (ISM.

Journal of Chemical Sciences | Indian Academy of Sciences

Indian Academy of Sciences (India)

Some tautomeric forms of pyridazinone were analyzedand the localized orbital locator maps, electron density maps, Fuzzy, Laplacian, and Mayer bond order methods showed dominant form. Different substituents, amine, chlorine, phenyl, methyl, hydrogen, substituted-phenyl, etc. on both the rings were chosen to search ...

β-Thioxoketones. Part 9

DEFF Research Database (Denmark)

Berg, Ulf; Sandström, Jan; Carlsen, Lars

1983-01-01

Thioacetylacetone (I), 2-acetylcyclohexanethione (II), and 2-thioacetylcyclohexanone (III) have been studied by dynamic 1H n.m.r. spectroscopy from ambient temperature down to ca. 130 K. The general co-existence of two tautomeric constituents has been established, and the constituents, in the cases...

Structural studies on Mannich bases of 2-Hydroxy-3,4,5,6-tetrachlorobenzene. An UV, IR, NMR and DFT study. A mini-review

DEFF Research Database (Denmark)

Hansen, Poul Erik; Spanget-Larsen, Jens

2016-01-01

Mannich bases of 2-Hydroxy-3,4,5,6-tetrachlorobenzene are chosen as an exemplary case for tautomeric Mannich bases. Molecular structures are calculated. OH stretching frequencies are rationalized based on DFT calculations. Intrinsic deuterium isotope effects on 13C chemical shifts in the M-form a...

Journal of Chemical Sciences | Indian Academy of Sciences

Indian Academy of Sciences (India)

Home; Journals; Journal of Chemical Sciences. Vandana. Articles written in Journal of Chemical Sciences. Volume 113 Issue 4 August 2001 pp 297-306 Physical and Theoretical. Theoretical study of the mechanism of proton transfer in tautomeric systems: Alloxan · Rita Kakkar Bhupendra K Sarma Vandana katoch.

Hydrogen bonding properties and intermediate structure of N-(2-carboxyphenyl)salicylidenimine

NARCIS (Netherlands)

Ligtenbarg, Alette G.J.; Hage, Ronald; Meetsma, Auke; Feringa, Ben L.

1999-01-01

The hydrogen bonding properties, the nature of the tautomeric structure and dimerization of N-(2-carboxyphenyl)salicylidenimine 1 has been studied. The crystal and molecular structure of 1 has been determined by single-crystal X-ray diffraction analysis. This compound forms a dimer in the solid

Mohammad Shahidul Islam

Indian Academy of Sciences (India)

Mohammad Shahidul Islam. Articles written in Journal of Chemical Sciences. Volume 127 Issue 9 September 2015 pp 1547-1556. Molecular structure investigation and tautomerism aspects of ()-3-benzylideneindolin-2-one · Assem Barakat Abdullah Mohammed Al-Majid Mohammad Shahidul Islam M Ali Saied M Soliman ...

Saied M Soliman

Indian Academy of Sciences (India)

Saied M Soliman. Articles written in Journal of Chemical Sciences. Volume 127 Issue 9 September 2015 pp 1547-1556. Molecular structure investigation and tautomerism aspects of ()-3-benzylideneindolin-2-one · Assem Barakat Abdullah Mohammed Al-Majid Mohammad Shahidul Islam M Ali Saied M Soliman ...

O tautomerii. Příběh objevu absolutní tautomerie, ojedinělého jevu v chemii

Czech Academy of Sciences Publication Activity Database

Štíbr, Bohumil

2008-01-01

Roč. 102, č. 10 (2008), s. 902-905 ISSN 0009-2770 R&D Projects: GA ČR GA203/05/2646 Institutional research plan: CEZ:AV0Z40320502 Keywords : borane * tautomerism * structural dualism Subject RIV: CA - Inorganic Chemistry Impact factor: 0.593, year: 2008

Four Thermochromic o-Hydroxy Schiff Bases of α-Aminodiphenylmethane: Solution and Solid State Study

Directory of Open Access Journals (Sweden)

Marija Zbačnik

2017-01-01

Full Text Available More than a hundred years after the first studies of the photo- and thermochromism of o-hydroxy Schiff bases (imines, it is still an intriguing topic that fascinates several research groups around the world. The reasons for such behavior are still under investigation, and this work is a part of it. We report the solution-based and mechanochemical synthesis of four o-hydroxy imines derived from α-aminodiphenylmethane. The thermochromic properties were studied for the single crystal and polycrystalline samples of the imines. The supramolecular impact on the keto-enol tautomerism in the solid state was studied using SCXRD and NMR, while NMR spectroscopy was used for the solution state. All four imines are thermochromic, although the color changes of the single crystals are not as strong as of the polycrystalline samples. One of the imines shows negative thermochromism, and that one is in keto-amine tautomeric form, both in the solid state as in solution.

Effect of chemical substitutions on photo-switching properties of 3-hydroxy-picolinic acid studied by ab initio methods

International Nuclear Information System (INIS)

Rode, Michał F.; Sobolewski, Andrzej L.

2014-01-01

Effect of chemical substitutions to the molecular structure of 3-hydroxy-picolinic acid on photo-switching properties of the system operating on excited-state intramolecular double proton transfer (d-ESIPT) process [M. F. Rode and A. L. Sobolewski, Chem. Phys. 409, 41 (2012)] was studied with the aid of electronic structure theory methods. It was shown that simultaneous application of electron-donating and electron-withdrawing substitutions at certain positions of the molecular frame increases the height of the S 0 -state tautomerization barrier (ensuring thermal stability of isomers) and facilitates a barrierless access to the S 1 /S 0 conical intersection from the Franck-Condon region of the S 1 potential-energy surface. Results of study point to the conclusion that the most challenging issue for practical design of a fast molecular photoswitch based on d-ESIPT phenomenon are to ensure a selectivity of optical excitation of a given tautomeric form of the system

Effect of chemical substitutions on photo-switching properties of 3-hydroxy-picolinic acid studied by ab initio methods

Science.gov (United States)

Rode, Michał F.; Sobolewski, Andrzej L.

2014-02-01

Effect of chemical substitutions to the molecular structure of 3-hydroxy-picolinic acid on photo-switching properties of the system operating on excited-state intramolecular double proton transfer (d-ESIPT) process [M. F. Rode and A. L. Sobolewski, Chem. Phys. 409, 41 (2012)] was studied with the aid of electronic structure theory methods. It was shown that simultaneous application of electron-donating and electron-withdrawing substitutions at certain positions of the molecular frame increases the height of the S0-state tautomerization barrier (ensuring thermal stability of isomers) and facilitates a barrierless access to the S1/S0 conical intersection from the Franck-Condon region of the S1 potential-energy surface. Results of study point to the conclusion that the most challenging issue for practical design of a fast molecular photoswitch based on d-ESIPT phenomenon are to ensure a selectivity of optical excitation of a given tautomeric form of the system.

Prototropic processes in benzaurins. ¹⁹F and ¹H NMR spectra of fluoro- and methylsubstituted 4-hydroxyphenyl-diphenylcarbinols, related fuchsones and benzaurins

DEFF Research Database (Denmark)

Hansen, Poul Erik; Peregudov, Alexander S.; Kravtsov, Dmitii N.

2011-01-01

Tautomerism of benzaurins and hydration are studied. 1H and 19F chemical shifts have been determined for a number of substituted 4-hydroxyphenyl-diphenyl carbinols containing fluorine in a 3-, 3*- or 4*-position, and for similar compounds containing additional methyl groups in a position of 3, 3*...

Spectrophotometric and spectrofluorimetric investigation of different equilibria of a recently synthesized Schiff base with the aid of chemometric methods

Energy Technology Data Exchange (ETDEWEB)

Afkhami, Abbas, E-mail: afkhami@basu.ac.i [Faculty of Chemistry, Bu-Ali Sina University, Hamedan 65174 (Iran, Islamic Republic of); Keypour, Hasan; Khajavi, Farzad [Faculty of Chemistry, Bu-Ali Sina University, Hamedan 65174 (Iran, Islamic Republic of); Rezaeivala, Majid [Department of Chemical Engineering, Hamedan University of Technology, Hamedan 65155 (Iran, Islamic Republic of)

2011-07-15

In this study ground and excited states acidic dissociation constants of a recently synthesized Schiff base was obtained in a DMF:water mixture of 30:70 (v/v) using absorption and fluorescent spectra of the Schiff base in different pH values with the aid of chemometric methods. In addition, the fluorescent of the two kinds of tautomers of this Schiff base was investigated and the rate of tautomerization was obtained using rank annihilation factor analysis (RAFA). The effect of different kinds of surfactants such as sodium dodecyl sulfate (SDS), cetyltrimethylammonium bromide (CTAB) and Triton X-100 on fluorescence spectrum of the Schiff base in a DMF:water mixture of 2:98 (v/v) was investigated. CTAB increased the fluorescence intensity of the Schiff base while SDS and Triton X-100 had no significant effect on it. {beta}-Cyclodextrin increased the fluorescence intensity of the Schiff base. Also the sensing behavior of this Schiff base toward metal ions was studied in DMF and ethanol by fluorescence spectroscopy. The Schiff base showed prominent fluorescent signal in the presence of Zn{sup 2+}, whereas other metal ions failed to induce response and ground-state dissociation constant of the complex was determined by direct fluorimetric titration as a function of Zn{sup 2+} concentration. - Highlights: {yields} Acidity and rate of the tautomerization of a recently synthesized Schiff base were studied. {yields} Ground and excited states acidity constants and tautomerization rate constant were obtained. {yields} These parameters were obtained with the aid of hard model and Rank annihilation factor analysis. {yields} The effect of some factors on the fluorescence intensity of the Schiff base was studied.

Spectrophotometric and spectrofluorimetric investigation of different equilibria of a recently synthesized Schiff base with the aid of chemometric methods

International Nuclear Information System (INIS)

Afkhami, Abbas; Keypour, Hasan; Khajavi, Farzad; Rezaeivala, Majid

2011-01-01

In this study ground and excited states acidic dissociation constants of a recently synthesized Schiff base was obtained in a DMF:water mixture of 30:70 (v/v) using absorption and fluorescent spectra of the Schiff base in different pH values with the aid of chemometric methods. In addition, the fluorescent of the two kinds of tautomers of this Schiff base was investigated and the rate of tautomerization was obtained using rank annihilation factor analysis (RAFA). The effect of different kinds of surfactants such as sodium dodecyl sulfate (SDS), cetyltrimethylammonium bromide (CTAB) and Triton X-100 on fluorescence spectrum of the Schiff base in a DMF:water mixture of 2:98 (v/v) was investigated. CTAB increased the fluorescence intensity of the Schiff base while SDS and Triton X-100 had no significant effect on it. β-Cyclodextrin increased the fluorescence intensity of the Schiff base. Also the sensing behavior of this Schiff base toward metal ions was studied in DMF and ethanol by fluorescence spectroscopy. The Schiff base showed prominent fluorescent signal in the presence of Zn 2+ , whereas other metal ions failed to induce response and ground-state dissociation constant of the complex was determined by direct fluorimetric titration as a function of Zn 2+ concentration. - Highlights: → Acidity and rate of the tautomerization of a recently synthesized Schiff base were studied. → Ground and excited states acidity constants and tautomerization rate constant were obtained. → These parameters were obtained with the aid of hard model and Rank annihilation factor analysis. → The effect of some factors on the fluorescence intensity of the Schiff base was studied.

Dynamics of Excited State Proton Transfer in Nitro Substituted 10-Hydroxybenzo[h]quinolines

DEFF Research Database (Denmark)

Marciak, H; Hristova, S.; Deneva, V

2017-01-01

The ground state tautomerism and excited state intramolecular proton transfer (ESIPT) of 10-hydroxybenzo[h]quinoline (HBQ) and its nitro derivatives, 7-nitrobenzo[h]quinolin-10-ol (2) and 7,9-dinitrobenzo[h]quinolin-10-ol (3), have been studied in acetonitrile using steady state as well as time d...

Journal of Chemical Sciences | Indian Academy of Sciences

Indian Academy of Sciences (India)

In this process, quinolin-8-olato (Q) undergoes five-membered chelation, the iminium-phenolato function tautomerizing to the imine-phenol function. In dichloromethane solution, 3 displays a quasireversible 3+/3 couple near 0×50 V vs SCE (3+ is the ruthenium (III) analogue of 3). Coulometrically generated solutions of 3+ ...

Replacement of Oxygen by Sulfur in Small Organic Molecules. 3. Theoretical Studies on the Tautomeric Equilibria of the 2OH and 4OH-Substituted Oxazole and Thiazole and the 3OH and 4OH-Substituted Isoxazole and Isothiazole in the Isolated State and in Solution

Directory of Open Access Journals (Sweden)

Peter I. Nagy

2016-07-01

Full Text Available This follow-up paper completes the author’s investigations to explore the in-solution structural preferences and relative free energies of all OH-substituted oxazole, thiazole, isoxazole, and isothiazole systems. The polarizable continuum dielectric solvent method calculations in the integral-equation formalism (IEF-PCM were performed at the DFT/B97D/aug-cc-pv(q+(dz level for the stable neutral tautomers with geometries optimized in dichloromethane and aqueous solution. With the exception of the predictions for the predominant tautomers of the 3OH isoxazole and isothiazole, the results of the IEF-PCM calculations for identifying the most stable tautomer of the given species in the two selected solvents agreed with those from experimental investigations. The calculations predict that the hydroxy proton, with the exception for the 4OH isoxazole and 4OH isothiazole, moves preferentially to the ring nitrogen or to a ring carbon atom in parallel with the development of a C=O group. The remaining, low-fraction OH tautomers will not be observable in the equilibrium compositions. Relative solvation free energies obtained by the free energy perturbation method implemented in Monte Carlo simulations are in moderate accord with the IEF-PCM results, but consideration of the ΔGsolv/MC values in calculating ΔGstot maintains the tautomeric preferences. It was revealed from the Monte Carlo solution structure analyses that the S atom is not a hydrogen-bond acceptor in any OH-substituted thiazole or isothiazole, and the OH-substituted isoxazole and oxazole ring oxygens may act as a weak hydrogen-bond acceptor at most. The molecules form 1.0−3.4 solute−water hydrogen bonds in generally unexplored numbers at some specific solute sites. Nonetheless, hydrogen-bond formation is favorable with the NH, C=O and OH groups.

Synthesis and structure of Bis(3,3-dimethyl-3,4-dihydroisoquinolyl-1) ketoxime

International Nuclear Information System (INIS)

Sokol, V.I.; Davydov, V.V.; Shklyaev, Yu.V.; Kartashova, I.V.; Sergienko, V.S.; Zaitsev, B.E.

1997-01-01

The reaction of bis(3,3-dimethyl-3,4-dihydroisoquinolyl-1)methane with NaNO 2 resulted in the formation of bis(3,3-dimethyl-3,4-dihydroisoquinolyl-1) ketoxime (I). The crystal and molecular structure of I was determined (x-ray structure analysis, Enraf-Nonius CAD-4, MoK α -radiation, graphite monochromator, θ/2θ scan, 2θ max =58 deg. , 4800 unique reflections; a=10.327(4), b=9.070(5), and c=21.62(1) A; β=94.02(3) deg.; V=2020(1) A 3 ; Z=4; and sp. gr. Pn). In the crystal, I exists in the oxime tautomeric form. Two symmetry-independent molecules are bound into a dimer through the intermolecular N=OH···N cycl 3 hydrogen bond. Both molecules are nonplanar; the dihedral angles between the mean planes of their 3,4-dihydroisoquinoline moieties are 72 deg. and 74 deg. According to IR and electron absorption spectra, the tautomeric form of compound I is also retained in solutions, and the π-conjugation between the 3,4-dihydroisoquinoline fragments of I is actually absent

Density-functional study on the equilibria in the ThDP activation.

Science.gov (United States)

Delgado, Eduardo J; Alderete, Joel B; Jaña, Gonzalo A

2011-11-01

The equilibria among the various ionization and tautomeric states involved in the activation of ThDP is addressed using high level density functional theory calculations, X3LYP/6-311++G(d,p)//X3LYP(PB)/6-31++G(d,p). This study provides the first theoretically derived thermodynamic data for the internal equilibria in the activation of ThDP. The role of the medium polarity on the geometry and thermodynamics of the diverse equilibria of ThDP is addressed. The media chosen are cyclohexane and water, as paradigms of apolar and polar media. The results suggest that all ionization and tautomeric states are accessible during the catalytic cycle, even in the absence of substrate, being APH(+) the form required to interconvert the AP and IP tautomers; and the generation of the ylide proceeds via the formation of the IP form. Additionally, the calculated ΔG° values allow to calculate all the equilibrium constants, including the pK(C2) for the thiazolium C2 atom whose ionization is believed to initiate the catalytic cycle.

Synthesis, crystal structure, and spectra of 3,3- dimethyl-1-N-(1'-phenyl-2',3'-dimethyl-5'-oxo-3'- pyrazolin-4'-yl)imino-1,2,3,4-tetrahydroisoquinoline

International Nuclear Information System (INIS)

Sokol, V.I.; Ryabov, M.A.; Merkur'eva, N.Yu.; Davydov, V.V.; Zaitsev, B.E.; Shklyaev, Yu.V.; Sergienko, V.S.; Zaitsev, B.E.

1996-01-01

The synthesis and the crystal and molecular structure of 3,3-dimethyl-1-N-(1'-phenyl-2',3'- dimethyl-5'-oxo-3'-pyrazolin-4'-yl)imino-1,2,3,4-tetrahydroisoquinoline are reported. As is evidenced by the 1H NMR, IR, and electron spectra, the tautomeric form of the compounds observed in the crystal is also retained in solutions

DFT study on the attacking mechanisms of H and OH radicals to G-C and A-T base pairs in water

Energy Technology Data Exchange (ETDEWEB)

Okutsu, N.; Shimamura, K.; Shimizu, E.; Kurita, N., E-mail: kurita@cs.tut.ac.jp [Department of Computer Science and Engineering, Toyohashi University of Technology, Toyohashi, Aichi, 441-8580 (Japan); Shulga, S. [Institute for Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Kyiv (Ukraine); Danilov, V. I. [Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv (Ukraine)

2016-02-01

To elucidate the effect of radicals on DNA base pairs, we investigated the attacking mechanism of OH and H radicals to the G-C and A-T base pairs, using the density functional theory (DFT) calculations in water approximated by the continuum solvation model. The DFT calculations revealed that the OH radical abstracts the hydrogen atom of a NH{sub 2} group of G or A base and induces a tautomeric reaction for an A-T base pair more significantly than for a G-C base pair. On the other hand, the H radical prefers to bind to the Cytosine NH{sub 2} group of G-C base pair and induce a tautomeric reaction from G-C to G*-C*, whose activation free energy is considerably small (−0.1 kcal/mol) in comparison with that (42.9 kcal/mol) for the reaction of an A-T base pair. Accordingly, our DFT calculations elucidated that OH and H radicals have a significant effect on A-T and G-C base pairs, respectively. This finding will be useful for predicting the effect of radiation on the genetic information recorded in the base sequences of DNA duplexes.

Synthesis and antiinflammatory activity of some 2-arylamino-2-thiazoline-4-ones.

Science.gov (United States)

Lesyk, Roman; Zimenkovsky, Boris; Subtelna, Ivanna; Nektegayev, Igor; Kazmirchuk, Gennadij

2003-01-01

A mild and efficent method of synthesis of 2-arylamino-2-thiazoline-4-ones was established using 2-carboethoxymethylthio-2-thiazolin-4-one (II) as a key intermediate. Reaction of 2-carboethoxymethylthio-2-thiazolin-4-one with m- or p-aminophenole afforded 2-(3-or4-oxyphenylamino)-2-thiazoline-4-ones (V, XV). Condensation of V, XV with aromatic aldehydes, according to the Knoevenagel, gives respective 5-arylidene derivatives V-XIII, XVI-XXIX, which were obtained alternatively using m- or p-oxyarylthioureas. 5-Carboxymethylderivatives XIV, XXX were synthesized by condensation of arylthioureas and maleic anhydride in acetic acid. Quantum-chemical calculations were made to confirm the possibility of dynamic amino-imino tautomerism of synthesized compounds. Structure and tautomerism of the obtained substances were confirmed by UV, IR, MS and NMR spectra. Biological activity prediction using the computer program PASS C&T has been made. According to these prediction results, some compounds were tested in vivio for their antiinflammatory activity. 5-[2-Chloro-3-(4-nitrophenyl)-2-propenilidene]-2-(3-hydroxyanilino-2-thiazoline-4-one (XII) possess significant antiinflammatory effect in comparison with diclofenac sodium, aspirin, acetaminofen and phenylbutazone.

DFT study on the attacking mechanisms of H and OH radicals to G-C and A-T base pairs in water

International Nuclear Information System (INIS)

Okutsu, N.; Shimamura, K.; Shimizu, E.; Kurita, N.; Shulga, S.; Danilov, V. I.

2016-01-01

To elucidate the effect of radicals on DNA base pairs, we investigated the attacking mechanism of OH and H radicals to the G-C and A-T base pairs, using the density functional theory (DFT) calculations in water approximated by the continuum solvation model. The DFT calculations revealed that the OH radical abstracts the hydrogen atom of a NH 2 group of G or A base and induces a tautomeric reaction for an A-T base pair more significantly than for a G-C base pair. On the other hand, the H radical prefers to bind to the Cytosine NH 2 group of G-C base pair and induce a tautomeric reaction from G-C to G*-C*, whose activation free energy is considerably small (−0.1 kcal/mol) in comparison with that (42.9 kcal/mol) for the reaction of an A-T base pair. Accordingly, our DFT calculations elucidated that OH and H radicals have a significant effect on A-T and G-C base pairs, respectively. This finding will be useful for predicting the effect of radiation on the genetic information recorded in the base sequences of DNA duplexes

Tandem Cu-catalyzed ketenimine formation and intramolecular nucleophile capture: Synthesis of 1,2-dihydro-2-iminoquinolines from 1-(o-acetamidophenyl)propargyl alcohols

Science.gov (United States)

Kant, Ruchir

2014-01-01

Summary The copper-catalyzed ketenimine formation reaction of 1-(o-acetamidophenyl)propargyl alcohols with various sulfonyl azides is found to undergo a concomitant intramolecular nucleophile attack to generate 1,2-dihydro-2-iminoquinolines after aromatization (via elimination of acetyl and hydroxy groups) and tautomerization. The reaction produces 4-substituted and 3,4-unsubstituted title compounds in moderate to good yields under mild reaction conditions. PMID:24991276

Synthesis and evaluation of aromaticity and tautomerization of ...

Indian Academy of Sciences (India)

Nurettin Menges

Pyrazolopyridazin(on)e is a bicyclic nitrogen-containing structure and one of the important core of heterocyclic compounds (Figure 1). Their derivatives are applied as ligand for hedge hog signal cascade,1 used for treatment of neuropathic pain2 and as antinociceptive agents.3 In addition to important biological activities, ...

Luminescence properties of isomeric and tautomeric lanthanide pyridinedicarboxylates

International Nuclear Information System (INIS)

Puntus, L.N.; Zolin, V.F.; Babushkina, T.A.; Kutuza, I.B.

2004-01-01

The luminescence and PMR spectra of europium salts of six isomers of 2,3-, 2,4-, 2,5-, 2,6-, 3,4-, and 3,5-pyridinedicarboxylic acids (PDA) had been studied. The distribution of the effective charge in the nearest surroundings of the Eu 3+ ion in these salts was evaluated from Stark splittings of electronic transitions. The values of relative integral intensities of electronic transitions 5 D 0 - 7 F J (J=0-4) in the luminescence spectra were reported. Compounds investigated were divided into three subgroups taking into account the details of the structure of the ligands and details of the luminescence spectra. The ligand coordination manners as well as the strength of interaction between lanthanide ion and ligands were confirmed by data of the PMR and IR spectroscopy

On the tautomerism, planarity, and vibrations of phospholes

International Nuclear Information System (INIS)

Oziminski, Wojciech P.; Dobrowolski, Jan Cz.

2005-01-01

The PH and CH tautomers of mono-, di-, tri-, tetra-, and pentaphospholes were calculated at the B3LYP/aug-cc-pVTZ level. Except for 1,2,3-triphosphole and pentaphosphole, the most stable phosphole form is one of the CH tautomers. For 1,2-diphosphole, 1,3-diphosphole, and 1,2,4-triphosphole, the energy difference between the tautomers is large and only one tautomer may be observed. For other phospholes, especially tetraphosphole, two tautomers may coexist. Non-planarity of the five membered ring is present only in the σ 3 λ 3 -P atom containing molecules, i.e., PH type of tautomers, while in the CH type of tautomers the ring is planar. As earlier reported by Nyulaszi, the PH tautomers flatten, and the energy difference between PH phosphole and the planar transition state structure decreases, as the number of P atoms in the phosphole molecule is increased. Bond length changes were discussed in terms of configuration of the atoms attached to the bond, and the molecular frequency variations were examined according to the different surroundings of the appropriate vibrators

A General and Simple Diastereoselective Reduction by L-Selectride: Efficient Synthesis of Protected (4S,5S)-Dihydroxy Amides

OpenAIRE

Yin; Ye; Yu; Liu

2010-01-01

A general approach to (4S,5S)-4-benzyloxy-5-hydroxy-N-(4-methoxybenzyl) amides 10 based on a diastereoselective reduction of (5S,6RS)-6-alkyl-5-benzyloxy-6-hydroxy-2-piperidinones 6 and their tautomeric ring-opened keto amides 7 is described. The reduction with L-Selectride at -20 °C to room temperature afforded the products 10 in excellent yields and moderate to high syn-diastereoselectivities.

A general and simple diastereoselective reduction by L-Selectride: efficient synthesis of protected (4S,5S)-dihydroxy amides.

Science.gov (United States)

Yin, Bo; Ye, Dong-Nai; Yu, Kai-Hui; Liu, Liang-Xian

2010-04-16

A general approach to (4S,5S)-4-benzyloxy-5-hydroxy-N-(4-methoxybenzyl) amides 10 based on a diastereoselective reduction of (5S,6RS)-6-alkyl-5-benzyloxy-6-hydroxy-2-piperidinones 6 and their tautomeric ring-opened keto amides 7 is described. The reduction with L-Selectride at -20 degrees C to room temperature afforded the products 10 in excellent yields and moderate to high syn-diastereoselectivities.

New fluorescent azo-Schiff base Cu(II) and Zn(II) metal chelates; spectral, structural, electrochemical, photoluminescence and computational studies

Science.gov (United States)

Purtas, Fatih; Sayin, Koray; Ceyhan, Gokhan; Kose, Muhammet; Kurtoglu, Mukerrem

2017-06-01

A new Schiff base containing azo chromophore group obtained by condensation of 2-hydroxy-4-[(E)-phenyldiazenyl]benzaldehyde with 3,4-dimethylaniline (HL) are used for the syntheses of new copper(II) and zinc(II) chelates, [Cu(L)2], and [Zn(L)2], and characterized by physico-chemical and spectroscopic methods such as 1H and 13C NMR, IR, UV.-Vis. and elemental analyses. The solid state structure of the ligand was characterized by single crystal X-ray diffraction study. X-ray diffraction data was then used to calculate the harmonic oscillator model of aromaticity (HOMA) indexes for the rings so as to investigate of enol-imine and keto-amine tautomeric forms in the solid state. The phenol ring C10-C15 shows a considerable deviation from the aromaticity with HOMA value of 0.837 suggesting the shift towards the keto-amine tautomeric form in the solid state. The analytical data show that the metal to ligand ratio in the chelates was found to be 1:2. Theoretical calculations of the possible isomers of the ligand and two metal complexes are performed by using B3LYP method. Electrochemical and photoluminescence properties of the synthesized azo-Schiff bases were also investigated.

Autophagy mediates cytotoxicity of human colorectal cancer cells treated with garcinielliptone FC.

Science.gov (United States)

Won, Shen-Jeu; Yen, Cheng-Hsin; Lin, Ting-Yu; Jiang-Shieh, Ya-Fen; Lin, Chun-Nan; Chen, Jyun-Ti; Su, Chun-Li

2018-01-01

The tautomeric pair of garcinielliptone FC (GFC) is a novel tautomeric pair of polyprenyl benzophenonoid isolated from the pericarps of Garcinia subelliptica Merr. (G. subelliptica, Clusiaceae), a tree with abundant sources of polyphenols. Our previous report demonstrated that GFC induced apoptosis on various types of human cancer cell lines including chemoresistant human colorectal cancer HT-29 cells. In the present study, we observed that many autophagy-related genes in GFC-treated HT-29 cells were up- and down-regulated using a cDNA microarray containing oncogenes and kinase genes. GFC-induced autophagy of HT-29 cells was confirmed by observing the formation of acidic vesicular organelles, LC3 puncta, and double-membrane autophagic vesicles using flow cytometry, confocal microscopy, and transmission electron microscopy, respectively. Inhibition of AKT/mTOR/P70S6K signaling as well as formation of Atg5-Atg12 and PI3K/Beclin-1 complexes were observed using Western blot. Administration of autophagy inhibitor (3-methyladenine and shRNA Atg5) and apoptosis inhibitor Z-VAD showed that the GFC-induced autophagy was cytotoxic form and GFC-induced apoptosis enhanced GFC-induced autophagy. Our data suggest the involvement of autophagy and apoptosis in GFC-induced anticancer mechanisms of human colorectal cancer. © 2017 Wiley Periodicals, Inc.

Two-dimensional IR spectroscopy of the anti-HIV agent KP1212 reveals protonated and neutral tautomers that influence pH-dependent mutagenicity.

Science.gov (United States)

Peng, Chunte Sam; Fedeles, Bogdan I; Singh, Vipender; Li, Deyu; Amariuta, Tiffany; Essigmann, John M; Tokmakoff, Andrei

2015-03-17

Antiviral drugs designed to accelerate viral mutation rates can drive a viral population to extinction in a process called lethal mutagenesis. One such molecule is 5,6-dihydro-5-aza-2'-deoxycytidine (KP1212), a selective mutagen that induces A-to-G and G-to-A mutations in the genome of replicating HIV. The mutagenic property of KP1212 was hypothesized to originate from its amino-imino tautomerism, which would explain its ability to base pair with either G or A. To test the multiple tautomer hypothesis, we used 2D IR spectroscopy, which offers subpicosecond time resolution and structural sensitivity to distinguish among rapidly interconverting tautomers. We identified several KP1212 tautomers and found that >60% of neutral KP1212 is present in the enol-imino form. The abundant proportion of this traditionally rare tautomer offers a compelling structure-based mechanism for pairing with adenine. Additionally, the pKa of KP1212 was measured to be 7.0, meaning a substantial population of KP1212 is protonated at physiological pH. Furthermore, the mutagenicity of KP1212 was found to increase dramatically at pH KP1212 molecules. Overall, our data reveal that the bimodal mutagenic properties of KP1212 result from its unique shape shifting ability that utilizes both tautomerization and protonation.

A neutron diffraction study of the crystal of benzoic acid from 6 to 293 K and a macroscopic-scale quantum theory of the lattice of hydrogen-bonded dimers

Energy Technology Data Exchange (ETDEWEB)

Fillaux, François, E-mail: francois.fillaux@upmc.fr [Sorbonne Universités, UPMC Univ Paris 06, UMR 8233, MONARIS, F-7505 Paris (France); Cousson, Alain, E-mail: alain-f.cousson@cea.fr [Laboratoire Léon Brillouin (CEA-CNRS), C.E. Saclay, 91191 Gif-sur-Yvette cedex (France)

2016-11-10

Highlights: • Proton transfer and tautomerism are revisited from quantum viewpoint. • Neutron-diffraction gives evidence for long-range correlations for protons. • We introduce a decoherence-free macroscopic-scale crystal-state. • All observations accord with the principle of complementarity. • Computational-chemistry models are inappropriate. - Abstract: Measurements via different techniques of the crystal of benzoic acid have led to conflicting conceptions of tautomerism: statistical disorder for diffraction; semiclassical jumps for relaxometry; quantum states for vibrational spectroscopy. We argue that these conflicts follow from the prejudice that nuclear positions and eigenstates are pre-existing to measurements, what is at variance with the principle of complementarity. We propose a self-contained quantum theory. First of all, new single-crystal neutron-diffraction data accord with long-range correlation for proton-site occupancies. Then we introduce a macroscopic-scale quantum-state emerging from phonon condensation, for which nuclear positions and eigenstates are indefinite. As to quantum-measurements, an incoming wave (neutron or photon) entangled with the condensate realizes a transitory state, either in the space of static nuclear-coordinates (diffraction), or in that of the symmetry coordinates (spectroscopy and relaxometry). We derive temperature-laws for proton-site occupancies and for the relaxation rate, which compare favorably with measurements.

Cyanodeoxy-Glycosyl Derivatives as Substrates for Enzymatic Reactions

Czech Academy of Sciences Publication Activity Database

Carmona, A. T.; Bojarová, Pavla; Křen, Vladimír; Ettrich, Rüdiger; Martínková, Ludmila; Moreno-Vargas, A. J.; González, C.; Robina, I.

2006-01-01

Roč. 8, - (2006), s. 1876-1885 ISSN 1434-193X R&D Projects: GA ČR GA203/05/0172; GA ČR GA203/05/2267; GA MŠk OC D25.002; GA MŠk OC D25.001 Institutional research plan: CEZ:AV0Z50200510; CEZ:AV0Z60870520 Keywords : sugar nitrile s * azido-tetrazole tautomerism * glycosidase Subject RIV: EE - Microbiology, Virology Impact factor: 2.769, year: 2006

Two-dimensional IR spectroscopy of the anti-HIV agent KP1212 reveals protonated and neutral tautomers that influence pH-dependent mutagenicity

OpenAIRE

Peng, Chunte Sam; Fedeles, Bogdan I.; Singh, Vipender; Li, Deyu; Amariuta, Tiffany; Essigmann, John M.; Tokmakoff, Andrei

2015-01-01

The anti-HIV drug KP1212 was designed to intentionally increase the mutation rate of HIV, thereby causing viral population collapse. Its mutagenicity and thus antiviral activity was proposed to be the result of tautomerization. We used 2D IR spectroscopy to identify rapidly interconverting tautomers under physiological conditions. The traditionally rare enol–imino tautomer for nucleobases was found to be the major species for KP1212, providing a structural support for the tautomer hypothesis....

A General and Simple Diastereoselective Reduction by L-Selectride: Efficient Synthesis of Protected (4S,5S-Dihydroxy Amides

Directory of Open Access Journals (Sweden)

Bo Yin

2010-04-01

Full Text Available A general approach to (4S,5S-4-benzyloxy-5-hydroxy-N-(4-methoxybenzyl amides 10 based on a diastereoselective reduction of (5S,6RS-6-alkyl-5-benzyloxy-6-hydroxy-2-piperidinones 6 and their tautomeric ring-opened keto amides 7 is described. The reduction with L-Selectride at -20 °C to room temperature afforded the products 10 in excellent yields and moderate to high syn-diastereoselectivities.

5-Diethylamino-2-[(E-(2,4-dimethoxyphenyliminomethyl]phenol

Directory of Open Access Journals (Sweden)

Esen Nur Kantar

2012-06-01

Full Text Available The title Schiff base, C19H24N2O3, exists in the crystal structure in the phenol–imine tautomeric form with an intramolecular O—H...N hydrogen bond. The planes of the aromatic rings form a dihedral angle of 36.8 (8°. The crystal packing is characterized by C—H...O hydrogen bonds and π–π stacking interactions [centroid–centroid distance = 3.478 (4Å].

Synthesis of Hydroxynaphtharines; Sintesis de naftazarinas hidroxiladas

Energy Technology Data Exchange (ETDEWEB)

Farina, F.; Fernandez, E.; Gimeno, V.; Valderrama, J.A. [Instituto de Quimica Organica General, CSIC, Madrid (Spain)

1995-12-01

A variety of naththazarines type 4 and 8 were prepared through Diels-Alder reactions of substituted 1,4-benzoquinones with 1,3-dienes. Thiele-Winter reaction of 5 afforded 6 which by chromic oxidation yielded naththazarines 7 and/or naphthoquinones 9. Hydroxynaphthazarines of type 8 were synthesized from 5 through 2,3-epoxides of the type 14. The structural study of the products, by H-NMR, showed the typical tautomerism of the naphthazarine system. 23 refs.

3-[(2,4-Dichlorophenyliminomethyl]-2-hydroxy-5-methylbenzaldehyde

Directory of Open Access Journals (Sweden)

Işın Kılıç

2009-06-01

Full Text Available The title compound, C15H11Cl2NO2, is a Schiff base which adopts the phenol–imine tautomeric form in the solid state, being stabilized by a strong intramolecular O—H...N hydrogen bond. The molecule is almost planar (r.m.s. deviation for all non-H atoms = 0.049 Å, displaying a dihedral angle of 3.1 (3° between the planes of the two aromatic rings.

Structural studies on Mannich bases of 2-Hydroxy-3,4,5,6-tetrachlorobenzene. An UV, IR, NMR and DFT study. A mini-review

DEFF Research Database (Denmark)

Hansen, Poul Erik; Spanget-Larsen, Jens

2016-01-01

Mannich bases of 2-Hydroxy-3,4,5,6-tetrachlorobenzene are chosen as an exemplary case for tautomeric Mannich bases. Molecular structures are calculated. OH stretching frequencies are rationalized based on DFT calculations. Intrinsic deuterium isotope effects on 13C chemical shifts in the M-form a......-form are estimated based on OH bond lengths. The observed deuterium isotope effects on 13C chemical shifts are demonstrated to be largely of equilibrium type except at ambient temperatures....

Effect of thione–thiol tautomerism on the inhibition of ...

Indian Academy of Sciences (India)

WINTEC

logues due to their high nucleophilic character. In addition to ... to produce the corresponding diselenide.6 In this paper, we describe ... umn chromatography was performed on glass col- ... tography (HPLC) experiments were carried out on a.

The importance of correct tautomeric structures for biological molecules

DEFF Research Database (Denmark)

Hansen, Poul Erik; Mortensen, John; Kamounah, Fadhil S.

2015-01-01

The structures of usnic acid and tetracycline are determined using deuterium isotope effects on 13C chemical shifts in a water environment. In case of usnic acid this is achieved by synthesizing a more water soluble usnic acid with a PEG linker. In the usnic acid case an enolic b-triketone (C-1, ...

Molecular structure investigation and tautomerism aspects of (E)-3 ...

Indian Academy of Sciences (India)

corrections to energy and Gibbs free energy were calcu- lated at the ... importance. We noted that the energy barrier between .... would be predicted that the carbonyl oxygen atom and ... spin allowed singlet-singlet excitations were calculated.

A comprehensive study of the structure, tautomeric properties, and ...

Indian Academy of Sciences (India)

aDepartment of Chemistry, Graduate University of Advanced Technology, Kerman, Iran ... MS received 28 March 2014; revised 05 December 2014; accepted 27 January 2015. Abstract ... an essential micronutrient whose absence from the diet.

Effect of tautomerism on Au-6-mercaptopurine nanocluster stability

Science.gov (United States)

Rashidpour, Neda; Kashid, Vikas; Shah, Vaishali

2013-02-01

We have investigated the stability of conjugated nanoparticles of Au-6-Mercaptopurine (6-MP) using ab initio density functional theory. We have studied the conjugation of the 6 tautomers of 6-MP via the different atomic sites with the gold nanoparticles. Our results show that the least stable tautomer has the strongest adsorption with the Au nanoparticles whereas the most stable tautomer has the weakest adsorption. We will discuss our results to explain the experimentally observed increased plasma half life time of the conjugated drug in vitro.

Chemical potential and reaction electronic flux in symmetry controlled reactions.

Science.gov (United States)

Vogt-Geisse, Stefan; Toro-Labbé, Alejandro

2016-07-15

In symmetry controlled reactions, orbital degeneracies among orbitals of different symmetries can occur along a reaction coordinate. In such case Koopmans' theorem and the finite difference approximation provide a chemical potential profile with nondifferentiable points. This results in an ill-defined reaction electronic flux (REF) profile, since it is defined as the derivative of the chemical potential with respect to the reaction coordinate. To overcome this deficiency, we propose a new way for the calculation of the chemical potential based on a many orbital approach, suitable for reactions in which symmetry is preserved. This new approach gives rise to a new descriptor: symmetry adapted chemical potential (SA-CP), which is the chemical potential corresponding to a given irreducible representation of a symmetry group. A corresponding symmetry adapted reaction electronic flux (SA-REF) is also obtained. Using this approach smooth chemical potential profiles and well defined REFs are achieved. An application of SA-CP and SA-REF is presented by studying the Cs enol-keto tautomerization of thioformic acid. Two SA-REFs are obtained, JA'(ξ) and JA'' (ξ). It is found that the tautomerization proceeds via an in-plane delocalized 3-center 4-electron O-H-S hypervalent bond which is predicted to exist only in the transition state (TS) region. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Hydrolysis of aspartic acid phosphoramidate nucleotides: a comparative quantum chemical study.

Science.gov (United States)

Michielssens, Servaas; Tien Trung, Nguyen; Froeyen, Matheus; Herdewijn, Piet; Tho Nguyen, Minh; Ceulemans, Arnout

2009-09-07

L-Aspartic acid has recently been found to be a good leaving group during HIV reverse transcriptase catalyzed incorporation of deoxyadenosine monophosphate (dAMP) in DNA. This showed that L-Asp is a good mimic for the pyrophosphate moiety of deoxyadenosine triphosphate. The present work explores the thermochemistry and mechanism for hydrolysis of several models for L-aspartic-dAMP using B3LYP/DGDZVP, MP2/6-311++G** and G3MP2 level of theory. The effect of the new compound is gradually investigated: starting from a simple methyl amine leaving group up to the aspartic acid leaving group. The enzymatic environment was mimicked by involving two Mg(2+) ions and some important active site residues in the reaction. All reactions are compared to the corresponding O-coupled leaving group, which is methanol for methyl amine and malic acid for aspartic acid. With methyl amine as a leaving group a tautomeric associative or tautomeric dissociative mechanism is preferred and the barrier is lower than the comparable mechanism with methanol as a leaving group. The calculations on the aspartic acid in the enzymatic environment show that qualitatively the mechanism is the same as for triphosphate but the barrier for hydrolysis by the associative mechanism is higher for L-aspartic-dAMP than for L-malic-dAMP and pyrophosphate.

Tautomers and Acid Dissociation Constants of 6-Selenoguanine from Density Functional Theoretical Calculations

International Nuclear Information System (INIS)

Kim, Yong Seong; Jang, Yun Hee; Cho, Hyun; Hwang, Sun Gu

2010-01-01

The relative stabilities of the tautomers of SeG were calculated. In the aqueous phase, amino-seleno form was the major tautomer of neutral SeG with a minor contribution from the other amino-seleno form. The presence of the selenolic form was negligible from the calculations. The microscopic and macroscopic pKa values in the aqueous phase were calculated from this scheme. The calculated pKa value was in good agreement with the experimental data. These results demonstrated that this method could predict and explain the acid-base properties of SeG and could be used to understand the behavior of the species. A number of analogues of nucleic acid bases have been the target of extensive studies because of their importance in many biological studies. The oxygen of both purine and pyrimidine bases is substituted with sulfur or selenium to produce an important class of analogues. 6-Selenoguanine (SeG) has a significant activity against L5178Y lymphoma cells. However, the detailed mechanism of the antiplastic action is not known yet. Information on the acid dissociation constants and the tautomerism of the molecules is required to provide a molecular level understanding of biological processes. Proton-transfer in the nucleic acid pairs and the presence of the tautomeric equilibrium play an important role in the mispair formation during the DNA replication

The mechanism of ureido-pyrimidinone:2,7-diamido-naphthyridine complexation and the presence of kinetically controlled pathways in multicomponent hydrogen-bonded systems

OpenAIRE

de Greef, T.F.A.; Ligthart, G.B.W.L.; Lutz, M.; Spek, A.L.; Meijer, E.W.

2008-01-01

The kinetics of association of ureido-pyrimidinone (U) dimers, present either in the 4[1H]-keto form or in the pyrimidin-4-ol form, with 2,7-diamido-1,8-naphthyridine (N) into a complementary heterodimer have been investigated. The formation of heterodimers with 2,7-diamido-1,8-naphthyridine from pyrimidin- 4-ol dimers is much faster than from 4[1H]-pyrimidinone dimers. Using a combination of simple measurements and simulations, evidence for a bimolecular tautomerization step is presented. Fi...

The utility of N-15 nuclear magnetic resonance spectroscopy for the study of natural products

International Nuclear Information System (INIS)

Randall, E.W.

1978-01-01

The utility of 15 N NMR spectroscopy for the study of natural products and the difficulties which must be overcome arte discussed. The widespread use of pulse Fourier techniques, decouplings, larger magnetic fields and large tube sizes allows a large number of 15 N studies of natural products, the more recent and important of these being peptides, nucleosides and nucleotides. Sites of protonation, tautomerism, sites of nitrosation and proton exchange behaviour for some of these natrual products have been studied. (A.G.)

8-{(E-[(4-Chlorophenylimino]methyl}-1,1,7,7-tetramethyl-1,2,3,5,6,7-hexahydropyrido[3,2,1-ij]quinolin-9-ol

Directory of Open Access Journals (Sweden)

Esen Nur Kantar

2013-06-01

Full Text Available The title Schiff base, C23H27ClN2O adopts the phenol–imine tautomeric form, with an intramolecular O—H...N hydrogen bond, which generates an S(6 ring motif. Three C atoms of the heterocyclic moiety of the hexahydropyridoquinoline unit, as well as the two methyl groups bonded to one of these C atoms, are disordered over two set of sites, with anoccupancy ratio of 0.740 (4:0.260 (4.

Tetrazole acetic acid: Tautomers, conformers, and isomerization

Energy Technology Data Exchange (ETDEWEB)

Araujo-Andrade, C. [Unidad Académica de Física de la Universidad Autónoma de Zacatecas, Zacatecas (Mexico); Department of Chemistry, University of Coimbra, 3004-535 Coimbra (Portugal); Reva, I., E-mail: reva@qui.uc.pt; Fausto, R. [Department of Chemistry, University of Coimbra, 3004-535 Coimbra (Portugal)

2014-02-14

Monomers of (tetrazol-5-yl)-acetic acid (TAA) were obtained by sublimation of the crystalline compound and the resulting vapors were isolated in cryogenic nitrogen matrices at 13 K. The conformational and tautomeric composition of TAA in the matrix was characterized by infrared spectroscopy and vibrational calculations carried out at the B3LYP/6-311++G(d,p) level. TAA may adopt two tautomeric modifications, 1H- and 2H-, depending on the position of the annular hydrogen atom. Two-dimensional potential energy surfaces (PESs) of TAA were theoretically calculated at the MP2/6-311++G(d,p) level, for each tautomer. Four and six symmetry-unique minima were located on these PESs, for 1H- and 2H-TAA, respectively. The energetics of the detected minima was subsequently refined by calculations at the QCISD level. Two 1H- and three 2H-conformers fall within the 0–8 kJ mol{sup −1} energy range and should be appreciably populated at the sublimation temperature (∼330 K). Observation of only one conformer for each tautomer (1ccc and 2pcc) is explained in terms of calculated barriers to conformational rearrangements. All conformers with the cis O=COH moiety are separated by low barriers (less than 10 kJ mol{sup −1}) and collapse to the most stable 1ccc (1H-) and 2pcc (2H-) forms during deposition of the matrix. On the trans O=COH surfaces, the relative energies are very high (between 12 and 27 kJ mol{sup −1}). The trans forms are not thermally populated at the sublimation conditions and were not detected in matrices. One high-energy form in each tautomer, 1cct (1H-) and 2pct (2H-), was found to differ from the most stable form only by rotation of the OH group and separated from other forms by high barriers. This opened a perspective for their stabilization in a matrix. 1cct and 2pct were generated in the matrices selectively by means of narrow-band near-infrared (NIR) irradiations of the samples at 6920 and 6937 cm{sup −1}, where the first OH stretching overtone

Synthesis of a Benzodiazepine-derived Rhodium NHC Complex by C-H Bond Activation

Energy Technology Data Exchange (ETDEWEB)

Bergman, Roberg G.; Gribble, Jr., Michael W.; Ellman, Jonathan A.

2008-01-30

The synthesis and characterization of a Rh(I)-NHC complex generated by C-H activation of 1,4-benzodiazepine heterocycle are reported. This complex constitutes a rare example of a carbene tautomer of a 1,4-benzodiazepine aldimine stabilized by transition metal coordination and demonstrates the ability of the catalytically relevant RhCl(PCy{sub 3}){sub 2} fragment to induce NHC-forming tautomerization of heterocycles possessing a single carbene-stabilizing heteroatom. Implications for the synthesis of benzodiazepines and related pharmacophores via C-H functionalization are discussed.

Intramolecular tautomerisation and the conformational variability of some classical mutagens – cytosine derivatives: quantum chemical study

Directory of Open Access Journals (Sweden)

Hovorun D. M.

2011-04-01

Full Text Available Aim. To determine the lifetime of the mutagenic cytosine derivatives through the investigation of the physicochemical mechanisms of their intramolecular proton transfer. Methods. Non-empirical quantum chemistry, the analysis of the electron density by means of Bader’s atoms in molecules (AIM theory and physicochemical kinetics were used. Results. It is shown that the modification of all investigated compounds, except DCyt, prevents their pairing in both mutagenic and canonical tautomeric forms with a base which is an interacting partner. This effect can inhibit their mutagenic potential. It is also established that Watson-Crick tautomeric hypothesis can be formally expanded for the investigated molecules so far as a lifetime of the mutagenic tautomers much more exceeds characteristic time for the incorporation of one nucleotides pair by DNA biosynthesis machinery. It seems that just within the frame of this hypothesis it will be possible to give an adequate explanation of the mechanisms of mutagenic action of N4-aminocytosine, N4-methoxycytosine, N4-hydroxycytosine and N4dehydrocytosine, which have much more energy advantageous imino form in comparison with amino form. Conclusions. For the first time the comprehensive conformational analysis of a number of classical mutagens, namely cytosine derivatives, has been performed using the methods of non-empirical quantum chemistry at the MP2/6-311++G (2df,pd//B3LYP/6-311++G(d,p level of theory

Kaxiras’s Porphyrin: DFT Modeling of Redox-Tuned Optical and Electronic Properties in a Theoretically Designed Catechol-Based Bioinspired Platform

Directory of Open Access Journals (Sweden)

Orlando Crescenzi

2017-11-01

Full Text Available A detailed computational investigation of the 5,6-dihydroxyindole (DHI-based porphyrin-type tetramer first described by Kaxiras as a theoretical structural model for eumelanin biopolymers is reported herein, with a view to predicting the technological potential of this unique bioinspired tetracatechol system. All possible tautomers/conformers, as well as alternative protonation states, were explored for the species at various degrees of oxidation and all structures were geometry optimized at the density functional theory (DFT level. Comparison of energy levels for each oxidized species indicated a marked instability of most oxidation states except the six-electron level, and an unexpected resilience to disproportionation of the one-electron oxidation free radical species. Changes in the highest energy occupied molecular orbital (HOMO–lowest energy unoccupied molecular orbital (LUMO gaps with oxidation state and tautomerism were determined along with the main electronic transitions: more or less intense absorption in the visible region is predicted for most oxidized species. Data indicated that the peculiar symmetry of the oxygenation pattern pertaining to the four catechol/quinone/quinone methide moieties, in concert with the NH centers, fine-tunes the optical and electronic properties of the porphyrin system. For several oxidation levels, conjugated systems extending over two or more indole units play a major role in determining the preferred tautomeric state: thus, the highest stability of the six-electron oxidation state reflects porphyrin-type aromaticity. These results provide new clues for the design of innovative bioinspired optoelectronic materials.

Evaluation of calix[4]arene tethered Schiff bases for anion recognition

International Nuclear Information System (INIS)

Chawla, H.M.; Munjal, Priyanka

2016-01-01

Two calix[4]arene tethered Schiff base derivatives (L1 and L2) have been synthesized and their ion recognition capability has been evaluated through NMR, UV–vis and fluorescence spectroscopy. L1 interacts with cyanide ions very selectively to usher a significant change in color and fluorescence intensity. On the other hand L2 does not show selectivity for anion sensing despite having the same functional groups as those present in L1. The differential observations may be attributed to plausible stereo control of anion recognition and tautomerization in the synthesized Schiff base derivatives.

Enol tautomers of Watson-Crick base pair models are metastable because of nuclear quantum effects.

Science.gov (United States)

Pérez, Alejandro; Tuckerman, Mark E; Hjalmarson, Harold P; von Lilienfeld, O Anatole

2010-08-25

Intermolecular enol tautomers of Watson-Crick base pairs could emerge spontaneously via interbase double proton transfer. It has been hypothesized that their formation could be facilitated by thermal fluctuations and proton tunneling, and possibly be relevant to DNA damage. Theoretical and computational studies, assuming classical nuclei, have confirmed the dynamic stability of these rare tautomers. However, by accounting for nuclear quantum effects explicitly through Car-Parrinello path integral molecular dynamics calculations, we find the tautomeric enol form to be dynamically metastable, with lifetimes too insignificant to be implicated in DNA damage.

Fluorescent analysis of interaction of flavonols with hemoglobin and bovine serum albumin

Science.gov (United States)

Sentchouk, V. V.; Bondaryuk, E. V.

2007-09-01

We have studied the fluorescent properties of flavonols (quercetin, fisetin, morin, rutin) with the aim of studying possible interaction with hemoglobin and bovine serum albumin (BSA). We observed an increase in the intensity of intrinsic fluorescence for all the flavonols except rutin in the presence of BSA. From the changes in the fluorescence spectra, we concluded that tautomeric forms are formed on interaction with hemoglobin. We determined the interconnection between the structure of related flavonols and their fluorescent properties on interaction with proteins, and we determined the binding constants for binding with BSA and hemoglobin.

Evaluation of calix[4]arene tethered Schiff bases for anion recognition

Energy Technology Data Exchange (ETDEWEB)

Chawla, H.M., E-mail: hmchawla@chemistry.iitd.ac.in; Munjal, Priyanka

2016-11-15

Two calix[4]arene tethered Schiff base derivatives (L1 and L2) have been synthesized and their ion recognition capability has been evaluated through NMR, UV–vis and fluorescence spectroscopy. L1 interacts with cyanide ions very selectively to usher a significant change in color and fluorescence intensity. On the other hand L2 does not show selectivity for anion sensing despite having the same functional groups as those present in L1. The differential observations may be attributed to plausible stereo control of anion recognition and tautomerization in the synthesized Schiff base derivatives.

Triprotic acid-base microequilibria and pharmacokinetic sequelae of cetirizine.

Science.gov (United States)

Marosi, Attila; Kovács, Zsuzsanna; Béni, Szabolcs; Kökösi, József; Noszál, Béla

2009-06-28

(1)H NMR-pH titrations of cetirizine, the widely used antihistamine and four related compounds were carried out and the related 11 macroscopic protonation constants were determined. The interactivity parameter between the two piperazine amine groups was obtained from two symmetric piperazine derivatives. Combining these two types of datasets, all the 12 microconstants and derived tautomeric constants of cetirizine were calculated. Upon this basis, the conflicting literature data of cetirizine microspeciation were clarified, and the pharmacokinetic absorption-distribution properties could be interpreted. The pH-dependent distribution of the microspecies is provided.

4-(2,3-Dihydroxybenzylideneamino-3-methyl-1H-1,2,4-triazol-5(4H-one

Directory of Open Access Journals (Sweden)

Şamil Işık

2009-12-01

Full Text Available All the non-H atoms of the title compound, C10H10N4O3, are almost coplanar, the maximum deviation from planarity being 0.065 (3 Å. The dihedral angle between the aromatic rings is 1.66 (6°. The molecule adopts the enol–imine tautomeric form with an intramolecular hydrogen-bonding interaction between the Schiff base N atom and the hydroxy group. In the crystal, intermolecular N—H...O and O—H...O hydrogen bonds link the molecules into a three-dimensional network.

4-Methoxy-2-{(E-[(thiophen-2-ylmethylimino]methyl}phenol

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Esen Nur Kantar

2012-09-01

Full Text Available The title Schiff base, C13H13NO2S, adopts the phenol–imine tautomeric form and reveals an intramolecular O—H...N hydrogen bond involving the hydroxy group and the imino N atom, forming an S(6 ring. The molecule is highly twisted with respect to the central imine group, which is reflected in the dihedral angle of 67.83 (10° formed by the thienyl and phenol rings. The crystal packing is characterized by weak C—H...O and C—H...π interactions.

Theoretical study of the mechanism of proton transfer in tautomeric ...

Indian Academy of Sciences (India)

Unknown

transferred is forced to come close to the positively charged carbon atom at ..... geometry of the transition state, and the charge densities on the atoms involved in the ..... One of the authors (VK) thanks the Council of Scientific and Industrial ...

Conformational and tautomeric eccentricities of 2-acetyl-1,8-dihydroxynaphthalenes

DEFF Research Database (Denmark)

Hansen, Poul Erik; Kamounah, Fadhil S.; Hansen, Bjarke Knud Vilster

2007-01-01

-range hydrogen-hydrogen coupling between the OH-1 and the OH-8 and by the isotope effects on 13C caused by deuteration at the CH3C=O methyl group. Compound 2 participates in a degenerate equilibrium between two equivalent nonsymmetrical rotamers (2A and 2B) , each having two intramolecular O...HO hydrogen bonds...

An investigation of tautomeric equilibria by means of mass spectrometry

DEFF Research Database (Denmark)

Zamir, Lolita; Jensen, Bror Skytte; Larsen, Elfinn

1969-01-01

Lafferty type rearrangement and by the ion [M Me]+ resulting from simple -cleavage. The ion [M 42]+. peak increases with the temperature of the inlet system while the ion [M Me]+ peak decreases. By assuming that the ion [M 42]+. represents the keto form and that the ion [M Me]+ represents the cis-enol form...

NMR study of conformational exchange and double-well proton potential in intramolecular hydrogen bonds in monoanions of succinic acid and derivatives.

Science.gov (United States)

Guo, Jing; Tolstoy, Peter M; Koeppe, B; Denisov, Gleb S; Limbach, Hans-Heinrich

2011-09-08

We present a (1)H, (2)H, and (13)C NMR study of the monoanions of succinic (1), meso- and rac-dimethylsuccinic (2, 3), and methylsuccinic (4) acids (with tetraalkylammonium as the counterion) dissolved in CDF(3)/CDF(2)Cl at 300-120 K. In all four monoanions, the carboxylic groups are linked by a short intramolecular OHO hydrogen bond revealed by the bridging-proton chemical shift of about 20 ppm. We show that the flexibility of the carbon skeleton allows for two gauche isomers in monoanions 1, 2, and 4, interconverting through experimental energy barriers of 10-15 kcal/mol (the process itself and the energy barrier are also reproduced in MP2/6-311++G** calculations). In 3, one of the gauche forms is absent because of the steric repulsion of the methyl groups. In all four monoanions, the bridging proton is located in a double-well potential and subject, at least to some extent, to proton tautomerism, for which we estimate the two proton positions to be separated by ca. 0.2 Å. In 1 and 3, the proton potential is symmetric. In 2, slowing the conformational interconversion introduces an asymmetry to the proton potential, an effect that might be strong enough even to synchronize the proton tautomerism with the interconversion of the two gauche forms. In 4, the asymmetry of the proton potential is due to the asymmetric substitution. The intramolecular H-bond is likely to remain intact during the interconversion of the gauche forms in 1, 3, and 4, whereas the situation in 2 is less clear.

The mechanism of stereospecific C-H oxidation by Fe(Pytacn) complexes: bioinspired non-heme iron catalysts containing cis-labile exchangeable sites.

Science.gov (United States)

Prat, Irene; Company, Anna; Postils, Verònica; Ribas, Xavi; Que, Lawrence; Luis, Josep M; Costas, Miquel

2013-05-17

A detailed mechanistic study of the hydroxylation of alkane C-H bonds using H2O2 by a family of mononuclear non heme iron catalysts with the formula [Fe(II)(CF3SO3)2(L)] is described, in which L is a tetradentate ligand containing a triazacyclononane tripod and a pyridine ring bearing different substituents at the α and γ positions, which tune the electronic or steric properties of the corresponding iron complexes. Two inequivalent cis-labile exchangeable sites, occupied by triflate ions, complete the octahedral iron coordination sphere. The C-H hydroxylation mediated by this family of complexes takes place with retention of configuration. Oxygen atoms from water are incorporated into hydroxylated products and the extent of this incorporation depends in a systematic manner on the nature of the catalyst, and the substrate. Mechanistic probes and isotopic analyses, in combination with detailed density functional theory (DFT) calculations, provide strong evidence that C-H hydroxylation is performed by highly electrophilic [Fe(V)(O)(OH)L] species through a concerted asynchronous mechanism, involving homolytic breakage of the C-H bond, followed by rebound of the hydroxyl ligand. The [Fe(V)(O)(OH)L] species can exist in two tautomeric forms, differing in the position of oxo and hydroxide ligands. Isotopic-labeling analysis shows that the relative reactivities of the two tautomeric forms are sensitively affected by the α substituent of the pyridine, and this reactivity behavior is rationalized by computational methods. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Molecular and crystal structure of 2-((E)-[(4-Methylphenyl)imino]methyl)-4-nitrophenol: A redetermination

International Nuclear Information System (INIS)

Kaynar, Nihal Kan; Tanak, Hasan; Şahin, Songul; Dege, Necmi; Ağar, Erbil; Yavuz, Metin

2016-01-01

The crystal structure of the title compound, C_1_4H_1_2N_2O_3, was recently determined as a mixture of its neutral (OH containing) and zwitterionic (NH containing) forms, in a 0.60 (4): 0.40 (4) ratio using the X-ray determination. In this study, the title compound has been characterized by FT-IR and X-ray diffraction. The redetermination showed that the title compound has only enol (OH) form because of lack of the NH stretching vibration in FT-IR spectrum. In addition, the molecular structure and tautomerism of the title compound have been discussed.

NMR insights on the properties of ZnCl2 molten salt hydrate medium through its interaction with SnCl4 and fructose

DEFF Research Database (Denmark)

Qiao, Yan; Pedersen, Christian Marcus; Wang, Yingxiong

2014-01-01

The solvent properties of ZnCl2 molten salt medium and its synergic effect with the Lewis acid catalyst, Sn4+, for biomass conversion, were investigated by nuclear magnetic resonance. The tautomeric distribution of fructose in the ZnCl2 molten salt medium was examined, and its effect for humins...... formation during the biomass conversion was evaluated. The ion complex composed by Sn4+ and Zn2+ indicated that there is a synergic catalytic effect between these two Lewis acid ions. 13C NMR spectra of fructose in different ZnCl2 molten salt hydrate concentrations revealed that the concentration of β...

Quantum chemical study of penicillin: Reactions after acylation

Science.gov (United States)

Li, Rui; Feng, Dacheng; Zhu, Feng

The density functional theory methods were used on the model molecules of penicillin to determine the possible reactions after their acylation on ?-lactamase, and the results were compared with sulbactam we have studied. The results show that, the acylated-enzyme tetrahedral intermediate can evolves with opening of ?-lactam ring as well as the thiazole ring; the thiazole ring-open products may be formed via ?-lactam ring-open product or from tetrahedral intermediate directly. Those products, in imine or enamine form, can tautomerize via hydrogen migration. In virtue of the water-assisted, their energy barriers are obviously reduced.

1-{(Z-[2-Methoxy-5-(trifluoromethylanilino]methylidene}naphthalen-2(1H-one

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Hakan Kargılı

2013-02-01

Full Text Available The title compound, C19H14F3NO2, crystallizes in the keto–amine tautomeric form, with a strong intramolecular N—H...O hydrogen bond. The molecule is almost planar; the dihedral angle between the naphthalene ring system and the benzene ring is 4.60 (7°. In the crystal, molecules are linked into chains along the c axis by C—H...O hydrogen bonds. The F atoms of the trifluoromethyl group are disordered over two positions with refined site occupancies of 0.668 (9 and 0.332 (9.

Redox chemistry of orange I and orange II: a pulse radiolysis study

International Nuclear Information System (INIS)

Yadav, P.; Sharma, K.K.; Rao, B.S.M.; O'Neill, P.; Oakes, J.; Batchelor, S.N.

2004-01-01

The relative reactivities of different tautomeric forms of model azo dyes (Orange I and Orange II) with oxidising and reducing radicals are investigated using pulse radiolysis technique. The rate of the reaction of N 3 with Orange I is diffusion controlled and the order of the reactivity among the tautomers is common ion > hydrazone > azo, whereas a reverse trend was seen in the reaction of e aq . The reducing alcohol radicals react with Orange II with k values in the range (1-3) x 10 9 dm 3 mol -1 s -1 . The relevant reaction mechanism is discussed. (author)

Molecular and crystal structure of 2-((E)-[(4-Methylphenyl)imino]methyl)-4-nitrophenol: A redetermination

Energy Technology Data Exchange (ETDEWEB)

Kaynar, Nihal Kan, E-mail: nihal-kan84@windowslive.com [Ondokuz Mayıs University, Department of Physics, Faculty of Arts and Sciences (Turkey); Tanak, Hasan [Amasya University, Department of Physics, Faculty of Arts and Sciences (Turkey); Şahin, Songul [Ondokuz Mayıs University, Department of Chemistry, Faculty of Arts and Sciences (Turkey); Dege, Necmi [Ondokuz Mayıs University, Department of Physics, Faculty of Arts and Sciences (Turkey); Ağar, Erbil [Ondokuz Mayıs University, Department of Chemistry, Faculty of Arts and Sciences (Turkey); Yavuz, Metin [Ondokuz Mayıs University, Department of Physics, Faculty of Arts and Sciences (Turkey)

2016-03-15

The crystal structure of the title compound, C{sub 14}H{sub 12}N{sub 2}O{sub 3}, was recently determined as a mixture of its neutral (OH containing) and zwitterionic (NH containing) forms, in a 0.60 (4): 0.40 (4) ratio using the X-ray determination. In this study, the title compound has been characterized by FT-IR and X-ray diffraction. The redetermination showed that the title compound has only enol (OH) form because of lack of the NH stretching vibration in FT-IR spectrum. In addition, the molecular structure and tautomerism of the title compound have been discussed.

Novel colorimetric sensors for cyanide based on azo-hydrazone tautomeric skeletons.

Science.gov (United States)

Adegoke, Olajire A; Adesuji, Temitope E; Thomas, Olusegun E

2014-07-15

The monoazo dyes, 4-carboxyl-2, 6-dinitrophenylazohydroxynaphthalenes dyes (AZ-01, AZ-03 and AZ-04), were evaluated as a highly selective colorimetric chemosensor for cyanide ion. The recognition of cyanide ion gave an obvious colour change from light yellow to brownish red and upon dilution with acetone produced a purple to lilac colour. Optimum conditions for the reaction between the azo dyes and cyanide ion were established at 30°C for 5 min, and different variables affecting the reaction were carefully studied and optimised. Under the optimum conditions, linear relationships between the CN(-) concentrations and light absorption were established. Using these azo-hydrazone molecular switch entities, excellent selectivity towards the detection of CN(-) in aqueous solution over miscellaneous competitive anions was observed. Such selectivity mainly results from the possibility of nucleophilic attack on the azo-hydrazone chemosensors by cyanide anions in aqueous system, which is not afforded by other competing anions. The cyanide chemosensor method described here should have potential application as a new family probes for detecting cyanide in aqueous solution. Copyright © 2014 Elsevier B.V. All rights reserved.

Quinoline-2-thiol Derivatives as Fluorescent Sensors for Metals, pH and HNO

Directory of Open Access Journals (Sweden)

Naphtali A. O’Connor

2014-06-01

Full Text Available A tautomeric equilibrium exists for quinoline-2-thiol and quinoline-2(1H-thione. Quantum mechanical calculations predict the thione is the major tautomer and this is confirmed by the absorption spectra. The utility of quinolone-2-thiol/quinoline-2(1H-thione as a chromophore for developing fluorescent sensors is explored. No fluorescence is observed when excited at absorption maxima, however a fluorescence increase is observed when exposed to HNO, a molecule of import as a cardiovascular therapeutic. Alkylated quinoline-2-thiol derivatives are found to be fluorescent and show a reduction in fluorescence when exposed to metals and changes in pH.

Hexacyclic monoterpenoid indole alkaloids from Rauvolfia verticillata.

Science.gov (United States)

Gao, Yuan; Yu, Ai-Lin; Li, Gen-Tao; Hai, Ping; Li, Yan; Liu, Ji-Kai; Wang, Fei

2015-12-01

Five new hexacyclic monoterpenoid indole alkaloids, rauvovertine A (1), 17-epi-rauvovertine A (2), rauvovertine B (3), 17-epi-rauvovertine B (4), and rauvovertine C (5) together with 17 known analogues were isolated from the stems of Rauvolfia verticillata. Compounds 1/2 and 3/4 were obtained as C-17 epimeric mixtures due to rapid hemiacetal tautomerism in solution. The structures of 1-5 were established by spectroscopic analysis and with the aid of molecular modeling. The new alkaloids were evaluated for their cytotoxicity in vitro against human tumor HL-60, SMMC-7721, A-549, MCF-7, and SW-480 cell lines. Copyright © 2015 Elsevier B.V. All rights reserved.

Palladium-catalyzed heteroannulation approach to 7-azatryptophan with a Schöllkopf chiral auxiliary

Energy Technology Data Exchange (ETDEWEB)

Gee, Moon Bae; Kim, Tae Seung; Yun, Eul Kgun [Dept. of Chemistry, Chungnam National University, Daejeon (Korea, Republic of)

2015-05-15

Our previous results on heteroannulation with unprotected 2-amino-3-iodopyridine and internal alkynes showed very low yields of the annulated product. The synthetic limitation could be due to the low nucleophilicity of the nitrogen that exists in the three tautomeric forms of 2-amino-pyridine (Scheme 1) or to the easy formation of a palladium complex with 2-aminopyridine. First, we examined the synthesis of the azaindole precursor, followed by reaction with a Schöllkopf chiral auxiliary. The heteroannulation provided the desired annulated product 5 in 60% yield, along with an uncyclized Sonogawasihra coupling product. After purifying product 5 by column chromatography, it was converted to 7-aza-tryptophan.

Tunnel effect in excited and ionized states of nucleic acid bases and some aspects of radiation-induced point gene mutations

International Nuclear Information System (INIS)

Pleticha-Lansky, R.

1975-01-01

Radiation induced perturbations of the genetic code are discussed from the standpoint of the frequency and specificity of mutations. According to Lowdin's theory of tautomeric rearrangement of nucleic acid base pairs through the tunnel effect, it is probable, that the proton potential in hydrogen bridges can be also effected by the incorporation of some radiolytic products of purines and pyrimidines into DNA as mistake bases. In this way it is possible, to eliminate any exo-or endogeneous energetic irradiation of the biological material and so to eliminate various undesirable damages of DNA. Thus higher specificity in the controlling of the genetic code changes would result. (F.G.)

Amide-transforming activity of Streptomyces: possible application to the formation of hydroxy amides and aminoalcohols.

Science.gov (United States)

Yamada, Shinya; Miyagawa, Taka-Aki; Yamada, Ren; Shiratori-Takano, Hatsumi; Sayo, Noboru; Saito, Takao; Takano, Hideaki; Beppu, Teruhiko; Ueda, Kenji

2013-07-01

To develop an efficient bioconversion process for amides, we screened our collection of Streptomyces strains, mostly obtained from soil, for effective transformers. Five strains, including the SY007 (NBRC 109343) and SY435 (NBRC 109344) of Streptomyces sp., exhibited marked conversion activities from the approximately 700 strains analyzed. These strains transformed diverse amide compounds such as N-acetyltetrahydroquinoline, N-benzoylpyrrolidine, and N-benzoylpiperidine into alcohols or N,O-acetals with high activity and regioselectivity. N,O-acetal was transformed into alcohol by serial tautomerization and reduction reactions. As such, Streptomyces spp. can potentially be used for the efficient preparation of hydroxy amides and aminoalcohols.

Photochemistry of pyrene with water at low temperature: study of atmospherical and astrochemical interest.

Science.gov (United States)

Guennoun, Zohra; Aupetit, Christian; Mascetti, Joëlle

2011-03-17

Photochemistry of a polyaromatic hydrocarbon, pyrene C(16)H(10), with water has been investigated at cryogenic temperatures. Photoprocessing of this species, performed at λ > 235 nm, in argon matrices, adsorbed onto amorphous water surfaces, and trapped in solid water, led to the formation of ketonic isomers, C(16)H(10)O, and possibly quinones. These species have been identified for the first time by infrared spectroscopy with the support of isotopic substitution experiments and DFT calculations. These oxidized pyrene-like species, of atmospherical and astrochemical interest, most likely arise from a tautomeric rearrangement of their analogous hydroxylated molecules, these latter being formed by reaction of water with pyrene cations.

Metal complexes with 1,5- and 1,8-dihydroxy-9,10-anthraquinones: electronic absorption spectra and structure of ligands

International Nuclear Information System (INIS)

Fajn, V.Ya.; Zajtsev, B.E.; Ryabov, M.A.

2004-01-01

By spectrophotometric, quantum-chemical, and correlation methods it is determined that in complexes of metals (Nd, Pr, Sm, Th, UO 2 2+ , V) with 1,5-dihydroxy-9,10-anthraquinone ligand could be in 7 excited states differing not only by ionization degree but primary contribution of tautomeric 9,10-, 1,10-, and 1,5-anthraquinoid structures. On all known complexes with 1,8-dihydroxy-9,10-anthraquinone containing once ionized ligand the last has 1,10-anthraquinoid structure; for complexes containing twofold ionized ligand 9,10-anthraquinoid structure of ligand is the most characteristic. Known complexes are classified in accordance with structure of ligands [ru

A Reversible Photoacid Functioning in PBS Buffer under Visible Light.

Science.gov (United States)

Abeyrathna, Nawodi; Liao, Yi

2015-09-09

A metastable-state photoacid that can reversibly release a proton in PBS buffer (pH = 7.4) under visible light is reported. The design is based on the dual acid-base property and tautomerization of indazole. The quantum yield was as high as 0.73, and moderate light intensity (10(2) μmol·m(2)·s(-1)) is sufficient for the photoreaction. Reversible pH change of 1.7 units was demonstrated using a 0.1 mM aqueous solution. This type of photoacid is promising for control of proton-transfer processes in physiological conditions and may find applications in biomedical areas.

Synthesis IR spectra and crystal structure of N-(4-bromophenyl)-1,1,1-trifluoroacetyl-acetonimine HN(C6H4Br)xC(Me)xCHxC(CF3)xO(HL) and its molecular complex with tungstene(4) oxotetrachloride WOCl4xHL

International Nuclear Information System (INIS)

Sergienko, V.S.; Ilyukhin, A.B.; Abramenko, V.L.

1997-01-01

Synthesis, IR spectroscopic and X-ray diffraction studies of compound HN(C 6 H 4 Br)xC(Me)xCHxC(CF 3 )xO(HL) (1) and of molecular complex WOCl 4 xHL(2) have been conducted. In 1 and 2 HL molecule exists in ketoamine tautomeric form (acid proton is localized at nitrogen atom). The results of 1 and 2 study are compared with literature data on structures of HL type molecules and Mo(6) molecular complexes with β-enaminevinylketone, as well as with the structure of chelate compound WOCl 3 L 1 , where L 1 - anion of N-phenylacetylacetonimine

Photochemistry and photophysics of the amino and imino tautomers of 1-methylcytosine: tautomerisation as a side product of the radiationless decay.

Science.gov (United States)

Li, Quansong; Blancafort, Lluís

2013-08-01

The photochemistry and photophysics of the amino-oxo (AO) and imino-oxo (IO) tautomers of 1-methylcytosine are investigated with ab initio calculations, using the CASPT2//CASSCF approach. Our aim is to rationalize recent experimental results which show that the AO tautomer has an excited state lifetime of about 1 ps, similar to cytosine (J.-W. Ho, H.-C. Yen, W.-K. Chou, C.-N. Weng, L.-H. Cheng, H.-Q. Shi, S.-H. Lai and P.-Y. Cheng, J. Phys. Chem. A, 2011, 115, 8406-8418), and that irradiation with wavelengths shorter than 308 nm induces the AO→IO tautomerization (I. Reva, M. J. Nowak, L. Lapinski and R. Fausto, J. Phys. Chem. B, 2012, 116, 5703-5710). For the canonical AO tautomer we find two analogous decay mechanisms to those described previously for cytosine, involving a conical intersection of ethylenic type and one where the amino group is bent out of plane. Decay through these intersections provides an unreactive return path to the AO ground state species. More importantly, we have identified new decay paths that lead from the two intersections to the trans-IO tautomer, without a barrier. These paths provide the possibility of forming the IO tautomer, presumably in small yields, as a side product of the radiationless decay. Thus, we have established for the first time computationally the mechanism of the UV-induced tautomerization, which is compatible with the well-established decay mechanism for cytosine. For the IO tautomer, we also find a mechanism for the excited state interconversion of the cis and trans forms and for efficient radiationless decay through a conical intersection where the imino group is perpendicular to the ring and bent out of the plane. These results are likely to be valid also for cytosine.

Getting the chemistry right: protonation, tautomers and the importance of H atoms in biological chemistry.

Science.gov (United States)

Bax, Ben; Chung, Chun Wa; Edge, Colin

2017-02-01

There are more H atoms than any other type of atom in an X-ray crystal structure of a protein-ligand complex, but as H atoms only have one electron they diffract X-rays weakly and are `hard to see'. The positions of many H atoms can be inferred by our chemical knowledge, and such H atoms can be added with confidence in `riding positions'. For some chemical groups, however, there is more ambiguity over the possible hydrogen placements, for example hydroxyls and groups that can exist in multiple protonation states or tautomeric forms. This ambiguity is far from rare, since about 25% of drugs have more than one tautomeric form. This paper focuses on the most common, `prototropic', tautomers, which are isomers that readily interconvert by the exchange of an H atom accompanied by the switch of a single and an adjacent double bond. Hydrogen-exchange rates and different protonation states of compounds (e.g. buffers) are also briefly discussed. The difference in heavy (non-H) atom positions between two tautomers can be small, and careful refinement of all possible tautomers may single out the likely bound ligand tautomer. Experimental methods to determine H-atom positions, such as neutron crystallography, are often technically challenging. Therefore, chemical knowledge and computational approaches are frequently used in conjugation with experimental data to deduce the bound tautomer state. Proton movement is a key feature of many enzymatic reactions, so understanding the orchestration of hydrogen/proton motion is of critical importance to biological chemistry. For example, structural studies have suggested that, just as a chemist may use heat, some enzymes use directional movement to protonate specific O atoms on phosphates to catalyse phosphotransferase reactions. To inhibit `wriggly' enzymes that use movement to effect catalysis, it may be advantageous to have inhibitors that can maintain favourable contacts by adopting different tautomers as the enzyme `wriggles'.

Physico-chemical profiles of the wobble ↔ Watson-Crick G*·2AP(w) ↔ G·2AP(WC) and A·2AP(w) ↔ A*·2AP(WC) tautomerisations: a QM/QTAIM comprehensive survey.

Science.gov (United States)

Brovarets', Ol'ha O; Voiteshenko, Ivan S; Hovorun, Dmytro M

2017-12-20

This study is intended to clarify in detail the tautomeric transformations of the wobble (w) G*·2AP(w) and A·2AP(w) nucleobase mispairs involving 2-aminopurine (2AP) into the Watson-Crick (WC) G·2AP(WC) and A*·2AP(WC) base mispairs (asterisks denote mutagenic tautomers of the DNA bases), respectively, by quantum-mechanical methods and Bader's Quantum Theory of Atoms in Molecules. Our previously reported methodology has been used, which allows the evolution of the physico-chemical parameters to be tracked along the entire internal reaction coordinate (IRC), not exclusively in the stationary states of these reactions. These biologically important G*·2AP(w) ↔ G·2AP(WC) and A·2AP(w) ↔ A*·2AP(WC) w ↔ WC tautomerisations, which are involved in mutagenic tautomerically-conformational pathways, determine the origin of the transitions and transversions induced by 2AP. In addition, it is established that they proceed through planar, highly stable, zwitterionic transition states and they exhibit similar physico-chemical profiles and stages of sequential intrapair proton transfer, followed by spatial rearrangement of the nucleobases relative to each other within the base pairs. These w ↔ WC tautomerisations occur non-dissociatively and are accompanied by a significant alteration in geometry (from wobble to Watson-Crick and vice versa) and redistribution of the specific intermolecular interactions, which can be divided into 10 patterns including AHB H-bonds and loosened A-H-B covalent bridges along the IRC of tautomerisation. Based on the redistribution of the geometrical and electron-topological parameters of the intrapair hydrogen bonds, exactly 9 key points have been allocated to characterize the evolution of these reactions.

Kudi: A free open-source python library for the analysis of properties along reaction paths.

Science.gov (United States)

Vogt-Geisse, Stefan

2016-05-01

With increasing computational capabilities, an ever growing amount of data is generated in computational chemistry that contains a vast amount of chemically relevant information. It is therefore imperative to create new computational tools in order to process and extract this data in a sensible way. Kudi is an open source library that aids in the extraction of chemical properties from reaction paths. The straightforward structure of Kudi makes it easy to use for users and allows for effortless implementation of new capabilities, and extension to any quantum chemistry package. A use case for Kudi is shown for the tautomerization reaction of formic acid. Kudi is available free of charge at www.github.com/stvogt/kudi.

Synthesis, structure and solvatochromic properties of 3-cyano-4,6-diphenyl-5-(3- and 4-substituted phenylazo-2-pyridones

Directory of Open Access Journals (Sweden)

NINA TODOROVIĆ

2010-08-01

Full Text Available A series of some new pyridone arylazo dyes was synthesized from the corresponding diazonium salts and 3-cyano-4,6-diphenyl-2-pyridone using the classical reaction for the synthesis of the azo compounds. The structures of these dyes were confirmed by UV–Vis, FT-IR and 1H-NMR spectroscopic techniques. The solvatochromism of the dyes was evaluated with respect to visible absorption properties in various solvents. The effects of solvent dipolarity/polarizability and solvent/solute hydrogen bonding interactions were analyzed by means of the linear solvation energy relationship concept proposed by Kamlet and Taft. The 2-pyridone/2-hydroxypiridine tautomeric equilibration was found to depend on the substituents as well as on the solvents.

Spectral characterization and crystal structure of 2-amino-N′-[(1Z-1-(4-chlorophenylethylidene]-benzohydrazide

Directory of Open Access Journals (Sweden)

Mohammad Arfan

2016-01-01

Full Text Available The crystal structure of 2-amino-N′-[(1Z-1-(4-chlorophenylethylidene]benzohydrazide (I is determined by X-ray diffraction at room temperature. The structure of I also was characterized by elemental analysis, mass, FT-IR and NMR spectroscopic techniques. The compound crystallizes in triclinic system, and space group is P1¯. Unit-cell dimensions are the following: a = 7.05380(10 Å, b = 7.65490(10 Å, c = 13.7094(4 Å, V = 694.01(2 Å3, Z = 2. The title compound is nearly planar and has intermolecular N–H⋯O hydrogen bonding. According to the spectral data, I exhibits an amide-iminol tautomerism.

Experimental test of a four-level kinetic model for excited-state intramolecular proton transfer dye lasers

Energy Technology Data Exchange (ETDEWEB)

Costela, A; Munnoz, J M; Douhal, A; Figuera, J M; Acuna, A U [Inst. de Quimica Fisica ' ' Rocasolano' ' , C.S.I.C., Madrid (Spain)

1989-11-01

The nanosecond pulses of a dye laser oscillator based on the excited-state intramolecular proton-transfer reaction (IPT) of salicylamide and 2'-hydroxylphenyl benzimidazole dyes have been studied as a function of several experimental parameters. To explain the operation of this laser a numerical four-level kinetic model was developed until the lasing properties of these dyes, in the presence of a variable oxygen concentration and pumped with a double pulse technique, could be reproduced. This was possible only by assuming that the efficiency of the laser is controlled by the absorption cross-section of a transient state with a lifetime in the nanosecond-picosecond range, which was tentatively identified as a ground state tautomeric species. (orig.).

Polar and low polar solvents media effect on dipole moments of some diazo Sudan dyes

Science.gov (United States)

Zakerhamidi, M. S.; Golghasemi Sorkhabi, Sh.; Shamkhali, A. N.

2014-06-01

Absorption and fluorescence spectra of three Sudan dyes (SudanIII, SudanIV and Sudan black B) were recorded in various solvents with different polarity in the range of 300-800 nm, at room temperature. The solvatochromic method was used to investigate dipole moments of these dyes in ground and excited states, in different media. The solvatochromic behavior of these substances and their solvent-solute interactions were analyzed via solvent polarity parameters. Obtained results express the effects of solvation on tautomerism and molecular configuration (geometry) of Sudan dyes in solvent media with different polarity. Furthermore, analyze of solvent-solute interactions and value of ground and excited states dipole moments suggests different forms of resonance structures for Sudan dyes in polar and low-polar solvents.

Synthesis, spectroscopic characterization and pH dependent photometric and electrochemical fate of Schiff bases.

Science.gov (United States)

Rauf, Abdur; Shah, Afzal; Abbas, Saghir; Rana, Usman Ali; Khan, Salah Ud-Din; Ali, Saqib; Zia-Ur-Rehman; Qureshi, Rumana; Kraatz, Heinz-Bernhard; Belanger-Gariepy, Francine

2015-03-05

A new Schiff base, 1-((4-bromophenylimino) methyl) naphthalen-2-ol (BPIMN) was successfully synthesized and characterized by (1)H NMR, (13)C NMR, FTIR and UV-Vis spectroscopy. The results were compared with a structurally related Schiff base, 1-((4-chlorophenylimino) methyl) naphthalen-2-ol (CPIMN). The photometric and electrochemical fate of BPIMN and CPIMN was investigated in a wide pH range. The experimental findings were supported by quantum mechanical approach. The redox mechanistic pathways were proposed on the basis of results obtained electrochemical techniques. Moreover, pH dependent UV-Vis spectroscopy of BPIMN and CPIMN was carried out and the appearance of isosbestic points indicated the existence of these compounds in different tautomeric forms. Copyright © 2014 Elsevier B.V. All rights reserved.

Investigating the nature of palladium chain-walking in the enantioselective redox-relay Heck reaction of alkenyl alcohols.

Science.gov (United States)

Hilton, Margaret J; Xu, Li-Ping; Norrby, Per-Ola; Wu, Yun-Dong; Wiest, Olaf; Sigman, Matthew S

2014-12-19

The mechanism of the redox-relay Heck reaction was investigated using deuterium-labeled substrates. Results support a pathway through a low energy palladium-alkyl intermediate that immediately precedes product formation, ruling out a tautomerization mechanism. DFT calculations of the relevant transition structures at the M06/LAN2DZ+f/6-31+G* level of theory show that the former pathway is favored by 5.8 kcal/mol. Palladium chain-walking toward the alcohol, following successive β-hydride eliminations and migratory insertions, is also supported in this study. The stereochemistry of deuterium labels is determined, lending support that the catalyst remains bound to the substrate during the relay process and that both cis- and trans-alkenes form from β-hydride elimination.

Comparison of sugar molecule decomposition through glucose and fructose: a high-level quantum chemical study.

Energy Technology Data Exchange (ETDEWEB)

Assary, R. S.; Curtiss, L. A. (Center for Nanoscale Materials); ( MSD); (Northwestern Univ.)

2012-02-01

Efficient chemical conversion of biomass is essential to produce sustainable energy and industrial chemicals. Industrial level conversion of glucose to useful chemicals, such as furfural, hydroxymethylfurfural, and levulinic acid, is a major step in the biomass conversion but is difficult because of the formation of undesired products and side reactions. To understand the molecular level reaction mechanisms involved in the decomposition of glucose and fructose, we have carried out high-level quantum chemical calculations [Gaussian-4 (G4) theory]. Selective 1,2-dehydration, keto-enol tautomerization, isomerization, retro-aldol condensation, and hydride shifts of glucose and fructose molecules were investigated. Detailed kinetic and thermodynamic analyses indicate that, for acyclic glucose and fructose molecules, the dehydration and isomerization require larger activation barriers compared to the retro-aldol reaction at 298 K in neutral medium. The retro-aldol reaction results in the formation of C2 and C4 species from glucose and C3 species from fructose. The formation of the most stable C3 species, dihydroxyacetone from fructose, is thermodynamically downhill. The 1,3-hydride shift leads to the cleavage of the C-C bond in the acyclic species; however, the enthalpy of activation is significantly higher (50-55 kcal/mol) than that of the retro-aldol reaction (38 kcal/mol) mainly because of the sterically hindered distorted four-membered transition state compared to the hexa-membered transition state in the retro-aldol reaction. Both tautomerization and dehydration are catalyzed by a water molecule in aqueous medium; however, water has little effect on the retro-aldol reaction. Isomerization of glucose to fructose and glyceraldehyde to dihydroxyacetone proceeds through hydride shifts that require an activation enthalpy of about 40 kcal/mol at 298 K in water medium. This investigation maps out accurate energetics of the decomposition of glucose and fructose molecules

Synthesis, crystal structure determination and antiproliferative activity of novel 2-amino-4-aryl-4,10-dihydro[1,3,5]triazino[1,2- a]benzimidazoles

Science.gov (United States)

Hranjec, Marijana; Pavlović, Gordana; Karminski-Zamola, Grace

2012-01-01

This manuscript describes the synthesis of novel 2-amino-4-aryl-4,10-dihydro-[1,3,5]triazino[1,2- a]benzimidazoles as hydrochloride salts 4a-n and 5b which were prepared in the reaction of cyclocondensation between 2-guanidinobenzimidazole and versatile heteroaromatic aldehydes. Structures of all prepared compounds have been studied by using 1H and 13C NMR, IR and UV/Vis spectroscopy. The crystal and molecular structure of 4f was determined by X-ray diffraction on single crystals. The molecule of 2-amino-4-(4'-methylphenyl)-4,10-dihydro[1,3,5]triazino[1,2- a]benzimidazole hydrochloride 4f (C 16H 16N 5+·Cl -) exists in the solid state in one of the possible tautomeric forms, being protonated at the one of the nitrogen atoms of the 1,4-dihydrotriazine ring. The molecule is highly delocalized within the 4,10-dihydro[1,3,5]triazino[1,2- a]benzimidazole moiety with the highest deviation from the plane for the methine carbon atom and the protonated nitrogen atom of the 1,4-dihydrotriazine ring. The cations are joined via N-H⋯N hydrogen bonds into R22(8) centrosymmetric dimers. Cation dimers are further connected with Cl - ions via N-H⋯Cl and C-H⋯Cl hydrogen bonds into 2D chains spreading along the b axis. The obtained single-crystal X-ray structure determination unequivocally confirms tautomeric form of the compound present in the solid-state and can represent tantative pattern for other prepared compounds. All prepared compounds were tested on their antiproliferative activity in vitro on several human cancer cell lines. Compound 4m was the most active one (IC 50 ≈ 20 μM), while compounds 4d, 4f, 4k, 4l4m showed moderate, but non-selective, antiproliferative activity with IC 50 25-60 μM.

On the hybridization of nitrogen in enamines

International Nuclear Information System (INIS)

Ahlbrecht, H.; Papke, G.

1975-01-01

The so far almost unknown hybridization of nitrogen in enamines was investigated. Analogous to the 1 J( 13 C-H) coupling, a linear dependence between the coupling constant and the per cent s-character of the nitrogen orbital can also be proved for the 1 J( 15 N-H) coupling. A number of 15 N-labelled imine-enamine tautomeric systems was produced, and the dependence of the 15 NH coupling on the electronic properties of the substituents is investigated. The result of measurements with N-phenyl enamines is discussed with regard to molecular theory. Some thought is given to the problem of hybridization of the lone-pair electrons at the nitrogen level in consideration of the hybridization index for the N-phenyl and vinyl coupling. (orig./AK) [de

Anion Photoelectron Spectroscopy of the Homogenous 2-Hydroxypyridine Dimer Electron Induced Proton Transfer System

Science.gov (United States)

Vlk, Alexandra; Stokes, Sarah; Wang, Yi; Hicks, Zachary; Zhang, Xinxing; Blando, Nicolas; Frock, Andrew; Marquez, Sara; Bowen, Kit; Bowen Lab JHU Team

Anion photoelectron spectroscopic (PES) and density functional theory (DFT) studies on the dimer anion of (2-hydroxypyridine)2-are reported. The experimentally measured vertical detachment energy (VDE) of 1.21eV compares well with the theoretically predicted values. The 2-hydroxypyridine anionic dimer system was investigated because of its resemblance to the nitrogenous heterocyclic pyrimidine nucleobases. Experimental and theoretical results show electron induced proton transfer (EIPT) in both the lactim and lactam homogeneous dimers. Upon electron attachment, the anion can serve as the intermediate between the two neutral dimers. A possible double proton transfer process can occur from the neutral (2-hydroxypyridine)2 to (2-pyridone)2 through the dimer anion. This potentially suggests an electron catalyzed double proton transfer mechanism of tautomerization. Research supported by the NSF Grant No. CHE-1360692.

Synthesis, structure and solvatochromic properties of some novel 5-arylazo-6-hydroxy-4-phenyl-3-cyano-2-pyridone dyes

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Alimmari Adel

2012-07-01

Full Text Available Abstract Background A series of some novel arylazo pyridone dyes was synthesized from the corresponding diazonium salt and 6-hydroxy-4-phenyl-3-cyano-2-pyridone using a classical reaction for the synthesis of the azo compounds. Results The structure of the dyes was confirmed by UV-vis, FT-IR, 1H NMR and 13C NMR spectroscopic techniques and elemental analysis. The solvatochromic behavior of the dyes was evaluated with respect to their visible absorption properties in various solvents. Conclusions The azo-hydrazone tautomeric equilibration was found to depend on the substituents as well as on the solvent. The geometry data of the investigated dyes were obtained using DFT quantum-chemical calculations. The obtained calculational results are in very good agreement with the experimental data.

4-Hydroxy-1-naphthaldehydes: proton transfer or deprotonation

DEFF Research Database (Denmark)

Manolova, Y; Kurteva, V; Antonov, L

2015-01-01

A series of naphthaldehydes, including a Mannich base, have been investigated by UV-Vis spectroscopy, NMR and theoretical methods to explore their potential tautomerism. In the case of 4-hydroxy-1-naphthaldehyde concentration dependent deprotonation has been detected in methanol and acetonitrile....... For 4-hydroxy-3-(piperidin-1-ylmethyl)-1-naphthaldehyde (a Mannich base) an intramolecular proton transfer involving the OH group and the piperidine nitrogen occurs. In acetonitrile the equilibrium is predominantly at the OH-form, whereas in methanol the proton transferred tautomer is the preferred form....... In chloroform and toluene, the OH form is completely dominant. Both 4-hydroxy-1-naphthaldehyde and 4-methoxy-1-naphthaldehyde (fixed enol form) show dimerization in the investigated solvents and the crystallographic data, obtained for the latter, confirm the existence of a cyclic dimer...

Synthesis and enzymatic evaluation of 2- and 4-aminothiazole-based inhibitors of neuronal nitric oxide synthase

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Graham R. Lawton

2009-06-01

Full Text Available Highly potent and selective inhibitors of neuronal nitric oxide synthase (nNOS possessing a 2-aminopyridine group were recently designed and synthesized in our laboratory and were shown to have significant in vivo efficacy. In this work, analogs of our lead compound possessing 2- and 4-aminothiazole rings in place of the aminopyridine were synthesized. The less basic aminothiazole rings will be less protonated at physiological pH than the aminopyridine ring, and so the molecule will carry a lower net charge. This could lead to an increased ability to cross the blood-brain barrier thereby increasing the in vivo potency of these compounds. The 2-aminothiazole-based compound was less potent than the 2-aminopyridine-based analogue. 4-Aminothiazoles were unstable in water, undergoing tautomerization and hydrolysis to give inactive thiazolones.

Nicholas reactions in the construction of cyclohepta[de]naphthalenes and cyclohepta[de]naphthalenones. The total synthesis of microstegiol.

Science.gov (United States)

Taj, Rafiq A; Green, James R

2010-12-03

The application of the Nicholas reaction chemistry of 2,7-dioxygenated naphthalenes in the synthesis of cyclohepta[de]napthalenes and in the synthesis of (±)-microstegiol (1) is presented. The substitution profile of Nicholas monosubstitution (predominantly C-1) and disubstitution reactions (predominantly 1,6-) on 2,7-dioxygenated napthalenes is reported. Application of a 1,8-dicondensation product and selected C-1 monocondensation products to the construction of cyclohepta[de]naphthalenes by way of ring closing metathesis and intramolecular Friedel-Crafts reactions, respectively, is described. Deprotection of the C-7 oxygen function to the corresponding naphthol allows tautomerization to cyclohepta[de]naphthalene-1-ones upon seven-membered-ring closure in most cases, and replacement of the C-2 oxygen function in the naphthalene by a methyl group ultimately allows the synthesis of (±)-microstegiol.

Synthesis of Arylthiopyrimidines by Copper-catalyzed Aerobic Oxidative C-S Cross-coupling

Energy Technology Data Exchange (ETDEWEB)

Lee, Ok Suk; Kim, Hyeji; Sohn, Jeong-Hun [Chungnam National University, Daejeon (Korea, Republic of); Lee, Hee-Seung [KAIST, Daejeon (Korea, Republic of); Shin, Hyunik [Yonsung Fine Chemicals R and D Center, Suwon (Korea, Republic of)

2016-02-15

Copper-catalyzed C–S cross-coupling reactions have been considered as powerful tools in synthetic chemistry and utilized for diverse heterocycle syntheses. In the reactions, the aspects of no need of ligands has been particular advantage over other metal catalysis. We have developed a Cu-catalyzed cascade reaction for the synthesis of fully substituted 2-arylthiopyrimidines from 3,4-dihydropyrimidine-2(1H)-thiones (DHPMs) under aerobic conditions. This cascade reaction of DHPM with aryl iodide proceeds presumably via sequential tautomerization, C–S cross-coupling, and oxidative dehydrogenation (oxidation followed by elimination). Considering that DHPM substrates were easily synthesized by Biginelli three component coupling reaction of aryl aldehyde, β-ketoester, and thiourea, the present method provides a direct access toward diverse 2-arylthiopyrimidines which have been used as a prominent substructure of drug molecules.

Amino acids as co-amorphous excipients for simvastatin and glibenclamide

DEFF Research Database (Denmark)

Laitinen, Riikka; Löbmann, Korbinian; Grohganz, Holger

2014-01-01

to a few drugs and amino acids. To facilitate the rational selection of amino acids, the practical importance of the amino acid coming from the biological target site of the drug (and associated intermolecular interactions) needs to be established. In the present study, the formation of co......-amorphous systems using cryomilling and combinations of two poorly water-soluble drugs (simvastatin and glibenclamide) with the amino acids aspartic acid, lysine, serine, and threonine was investigated. Solid-state characterization with X-ray powder diffraction, differential scanning calorimetry, and Fourier...... in the mixtures. Interestingly, a favorable effect by the excipients on the tautomerism of amorphous glibenclamide in the co-amorphous blends was seen, as the formation of the thermodynamically less stable imidic acid tautomer of glibenclamide was suppressed compared to that of the pure amorphous drug...

Strecker degradation of amino acids promoted by a camphor-derived sulfonamide

Directory of Open Access Journals (Sweden)

M. Fernanda N. N. Carvalho

2016-04-01

Full Text Available A camphor-derived sulfonimine with a conjugated carbonyl group, oxoimine 1 (O2SNC10H13O, reacts with amino acids (glycine, L-alanine, L-phenylalanine, L-leucine to form a compound O2SNC10H13NC10H14NSO2 (2 which was characterized by spectroscopic means (MS and NMR and supported by DFT calculations. The product, a single diastereoisomer, contains two oxoimine units connected by a –N= bridge, and thus has a structural analogy to the colored product Ruhemann´s purple obtained by the ninhydrin reaction with amino acids. A plausible reaction mechanism that involves zwitterions, a Strecker degradation of an intermediate imine and water-catalyzed tautomerizations was developed by means of DFT calculations on potential transition states.

Novel Rearrangements in the Reactions Directed Toward Preparation of Spiro-N,N-ketals: Reactions of Naphthalene-1,8-diamine with Ninhydrin and Isatin

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Keiji Kobayashi

2012-11-01

Full Text Available Spiro-N,N-ketal 5, consisting of a phthaloperine heterocyclic ring and a naphtha[1,8-ef][1,4]diazepine ring, was obtained along with spiro-N,N-ketal 2 via 2,2-condensation in the reaction of ninhydrin with naphthalene-1,8-diamine. Their molecular structures were elucidated by X-ray crystal structural analysis. Aside from these spiro compounds, the diazapleiadiene compound 3 formed by 1,2-condensation and the 1,4-isoquinolinedione compound 4 arising from ring expansion were isolated. When isatin was reacted with naphthalene-1,8-diamine, spiro-N,N-ketal 6 and the two 1H-perimidine-based compounds 7 and 8 were isolated. Compound 8 was revealed to undergo a fast dynamic prototropic tautomerization in solution. Plausible mechanisms of the formation of the products are proposed.

Tautomerism in 5-aminotetrazole investigated by core-level photoelectron spectroscopy and {Delta}SCF calculations

Energy Technology Data Exchange (ETDEWEB)

Pinto, R.M., E-mail: ruipinto@fct.unl.pt [CFA, Centro de Fisica Atomica, Departamento de Fisica, Faculdade de Ciencias e Tecnologia, FCT, Universidade Nova de Lisboa, 2829-516 Caparica (Portugal); Dias, A.A. [CFA, Centro de Fisica Atomica, Departamento de Fisica, Faculdade de Ciencias e Tecnologia, FCT, Universidade Nova de Lisboa, 2829-516 Caparica (Portugal); Coreno, M. [CNR-IMIP, Montelibretti, Rome I-00016 (Italy); Simone, M. de [CNR-IOM, Laboratorio TASC, 34149 Trieste (Italy); Giuliano, B.M. [Departamento de Quimica da Universidade de Coimbra, 3004-535 Coimbra (Portugal); Santos, J.P.; Costa, M.L. [CFA, Centro de Fisica Atomica, Departamento de Fisica, Faculdade de Ciencias e Tecnologia, FCT, Universidade Nova de Lisboa, 2829-516 Caparica (Portugal)

2012-03-15

Highlights: Black-Right-Pointing-Pointer High-resolution XPS of 5-aminotetrazole reveals different tautomers. Black-Right-Pointing-Pointer 5ATZ exists mainly in the 2H-form. Black-Right-Pointing-Pointer Results obtained with DSCF are in good agreement with the observed binding energies. - Abstract: The C 1s and N 1s photoelectron spectra of gas-phase 5-aminotetrazole (5ATZ) were recorded using synchrotron radiation, with the aim of evaluating 1H/2H tautomer population ratios. The core-electron binding energies (CEBEs) were estimated from computational results, using the delta self-consistent-field ({Delta}SCF) approach. Simulated spectra were generated using these CEBEs and the results from GAUSSIAN-n (Gn, n = 1, 2 and 3) and Complete Basis Set (CBS-4M and CBS-Q) methods. Results reveal the almost exclusive predominance of the 2H-tautomer, with a 1H/2H ratio of ca. 0.12/0.88, taken from a gross analysis of the XPS C 1s spectrum, recorded at 365 K.

Tricyanomethane and Its Ketenimine Tautomer: Generation from Different Precursors and Analysis in Solution, Argon Matrix, and as a Single Crystal.

Science.gov (United States)

Banert, Klaus; Chityala, Madhu; Hagedorn, Manfred; Beckers, Helmut; Stüker, Tony; Riedel, Sebastian; Rüffer, Tobias; Lang, Heinrich

2017-08-01

Solutions of azidomethylidenemalononitrile were photolyzed at low temperatures to produce the corresponding 2H-azirine and tricyanomethane, which were analyzed by low-temperature NMR spectroscopy. The latter product was also observed after short thermolysis of the azide precursor in solution whereas irradiation of the azide isolated in an argon matrix did not lead to tricyanomethane, but to unequivocal detection of the tautomeric ketenimine by IR spectroscopy for the first time. When the long-known "aquoethereal" greenish phase generated from potassium tricyanomethanide, dilute sulfuric acid, and diethyl ether was rapidly evaporated and sublimed, a mixture of hydronium tricyanomethanide and tricyanomethane was formed instead of the previously claimed ketenimine tautomer. Under special conditions of sublimation, single crystals of tricyanomethane could be isolated, which enabled the analysis of the molecular structure by X-ray diffraction. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Rationalization of the Color Properties of Fluorescein in the Solid State: A Combined Computational and Experimental Study.

Science.gov (United States)

Arhangelskis, Mihails; Eddleston, Mark D; Reid, David G; Day, Graeme M; Bučar, Dejan-Krešimir; Morris, Andrew J; Jones, William

2016-07-11

Fluorescein is known to exist in three tautomeric forms defined as quinoid, zwitterionic, and lactoid. In the solid state, the quinoid and zwitterionic forms give rise to red and yellow materials, respectively. The lactoid form has not been crystallized pure, although its cocrystal and solvate forms exhibit colors ranging from yellow to green. An explanation for the observed colors of the crystals is found using a combination of UV/Vis spectroscopy and plane-wave DFT calculations. The role of cocrystal coformers in modifying crystal color is also established. Several new crystal structures are determined using a combination of X-ray and electron diffraction, solid-state NMR spectroscopy, and crystal structure prediction (CSP). The protocol presented herein may be used to predict color properties of materials prior to their synthesis. © 2016 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

Separation of carbohydrates using hydrophilic interaction liquid chromatography.

Science.gov (United States)

Fu, Qing; Liang, Tu; Li, Zhenyu; Xu, Xiaoyong; Ke, Yanxiong; Jin, Yu; Liang, Xinmiao

2013-09-20

A strategy was developed to rapidly evaluate chromatographic properties of hydrophilic interaction chromatography (HILIC) columns for separating carbohydrates. Seven HILIC columns (Silica, Diol, TSK Amide-80, XAmide, Click Maltose, Click β-CD, and Click TE-Cys columns) were evaluated by using three monosaccharide and seven disaccharides as probes. The influence of column temperature on the peak shape and tautomerization of carbohydrates, as well as column selectivity were investigated. The influence of surface charge property on the retention was also studied by using glucose, glucuronic acid, and glucosamine, which indicated that buffer salt concentration and pH value in mobile phase was necessary to control the ionic interactions between ionic carbohydrates and HILIC columns. According to evaluation results, the XAmide column was selected as an example to establish experimental schemes for separation of complex mixtures of oligosaccharide. Copyright © 2013 Elsevier Ltd. All rights reserved.

Role of sugar in controlling reaction pathways: A study with thymine and thymidine

Energy Technology Data Exchange (ETDEWEB)

Bose, Adity [Chemical Sciences Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700 064 (India); Sarkar, Achintya K. [Department of Chemistry, Presidency College, 86/1 College street, Kolkata 700 073 (India); Basu, Samita, E-mail: samita.basu@saha.ac.i [Chemical Sciences Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700 064 (India)

2009-10-15

Magnetic field effect in conjunction with laser flash photolysis have been used for studying interactions of 9,10-anthraquinone and 2-methyl 1,4-naphthoquinone (menadione) with a DNA base, thymine (Thy) and its nucleoside, thymidine (dThd). Irrespective of medium Thy has been found to support both electron transfer (ET) and hydrogen abstraction with the quinones while dThd has exhibited a complete reluctance towards ET. This unique behavior of dThd has been attributed to a failure in attaining aromaticity by virtue of keto-enol tautomerism upon addition of a sugar moiety. Electron withdrawing effect of sugar unit is also considered responsible for reduction of ET from dThd. Again both Thy and dThd have exhibited hydrogen abstraction in homogeneous medium, which is normally unexpected. The above behaviors of the bases have been explained on the basis of their chemical structures.

Role of sugar in controlling reaction pathways: A study with thymine and thymidine

International Nuclear Information System (INIS)

Bose, Adity; Sarkar, Achintya K.; Basu, Samita

2009-01-01

Magnetic field effect in conjunction with laser flash photolysis have been used for studying interactions of 9,10-anthraquinone and 2-methyl 1,4-naphthoquinone (menadione) with a DNA base, thymine (Thy) and its nucleoside, thymidine (dThd). Irrespective of medium Thy has been found to support both electron transfer (ET) and hydrogen abstraction with the quinones while dThd has exhibited a complete reluctance towards ET. This unique behavior of dThd has been attributed to a failure in attaining aromaticity by virtue of keto-enol tautomerism upon addition of a sugar moiety. Electron withdrawing effect of sugar unit is also considered responsible for reduction of ET from dThd. Again both Thy and dThd have exhibited hydrogen abstraction in homogeneous medium, which is normally unexpected. The above behaviors of the bases have been explained on the basis of their chemical structures.

Electrochemical Reduction of Isatin-monohydrazone on Mercury Electrode

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Ender Biçer

2015-07-01

Full Text Available Electrochemical behaviour of isatin monohydrazone (IM on a hanging mercury drop electrode in the Britton-Robinson (B-R buffer solution of pH = 2.00–9.00 has been investigated using square-wave voltammetry (SWV and cyclic voltammetry (CV techniques. In the pH range of 2.00–5.00, the voltammogram of IM exhibited a single cathodic irreversible peak. When the pH value exceeds 5.00, a new cathodic irreversible peak was also seen. According to the voltammetric data, a plausible electrode reaction mechanism of IM was proposed. The first reduction peak of IM is resulted from the reduction of =N–NH– group with consumption of 2e–/2H+. Also, its second cathodic peak is formed by the participation of 2e–/2H+ for the reduction of –N=N– group on its tautomeric form.

Kinetic studies of 2-(2'-Haloethyl) and 2-ethenyl substituted quinazolinone alkylating agents. Acid-catalyzed dehydrohalogenation and alkylation involving a quinazolinone prototropic tautomer.

Science.gov (United States)

Dempcy, R O; Skibo, E B

1993-07-01

The mechanism of halide elimination from 2-haloethyl-5,8-dihydroxyquinazolin-4(3H)-ones was studied in aqueous buffer by means of a pH-rate profile, buffer dilution studies, isotopic labeling, and kinetic isotope effects. From the results of these studies, it is apparent that a quinazolinone tautomer, arising from a prototropic shift of the C(l') proton to the N(1) position, is formed in the rate determining step of elimination. Monobasic phosphate acts as a bifunctional catalyst for the tautomerism. The halide then eliminates from the tautomer to afford the alkene derivative. Conversely, hydroxyethyl mercaptide adds to the alkene to afford the tautomer. The significance of these studies lies in the discovery of a prototropic tautomer of quinazolinone, which is reversibly formed in aqueous buffer under mild conditions, and in the discovery of alkylation chemistry useful in the design of quinazolinone-based enzyme inhibitors.

Azide derivatized anticancer agents of Vitamin K 3: X-ray structural, DSC, resonance spectral and API studies

Science.gov (United States)

Badave, Kirti; Patil, Yogesh; Gonnade, Rajesh; Srinivas, Darbha; Dasgupta, Rajan; Khan, Ayesha; Rane, Sandhya

2011-12-01

Compound 1 [1-imino (acetyl hydrazino)-Vitamin K 3], displays valence tautomerically related electronic isomers as Form I and Form II. Form I exhibits 2D packing fragment with 1D ribbon chains of N-H⋯O hydrogen bonds and shows EPR silent features. While Form II is EPR active and exhibits biradical nature with double quantum transitions at g = 2.0040. 1H NMR of compound 2, [1-imino (hydrazino carboxylate)-Vitamin K 3] and Form II exhibit π delocalization via resonance assisted H-bonding [RAHB] effect compared to Form I. Molecular interactions in Form I and II are visualized by DSC. The electronic structures of compounds 1 and 2 have been correlated to their API values by measuring anticancer activities, mitochondrial potentials and DNA shearing patterns. Form II and compound 2 indicate mitochondria mediated apoptosis (˜75% cell death) while Form I causes 35% cell death.

N-[3-(2,6-Dimethylanilino-1-methylbut-2-enylidene]-2,6-dimethylanilinium chlorideThis paper is dedicated to Professor Dr Dr mult. h.c. Herbert W. Roesky.

Directory of Open Access Journals (Sweden)

Víctor M. Jiménez-Pérez

2009-07-01

Full Text Available The title salt, C21H27N2+·Cl− resulted from the condensation between 2,6-dimethylaniline and acetylacetone in acidified ethanol. The bulky cation is stabilized in a β-iminoenamine tautomeric form, and presents a W-shaped conformation. The benzene rings are arranged almost parallel, with a dihedral angle of 6.58 (4° between the mean planes. Both N—H groups in the cation form strong hydrogen bonds with two symmetry-related chloride anions. The resulting supramolecular structure is a one dimensional polymer running along [001], alternating cations and anions. The π–π interaction observed in the molecule, characterized by a centroid–centroid separation of 4.298 (4 Å, is thus extended to the chains, with separations of 5.222 (4 Å between benzene rings of neighbouring cations in the crystal.

Highly Stereoselective Synthesis of Cyclopentanes bearing Four Stereocenters by a Rhodium Carbene–Initiated Domino Sequence

Science.gov (United States)

Parr, Brendan T.; Davies, Huw M. L.

2014-01-01

Stereoselective synthesis of a cyclopentane nucleus by convergent annulations constitutes a significant challenge for synthetic chemists. Though a number of biologically relevant cyclopentane natural products are known, more often than not, the cyclopentane core is assembled in a stepwise fashion due to lack of efficient annulation strategies. Herein, we report the rhodium-catalyzed reactions of vinyldiazoacetates with (E)-1,3-disubstituted 2-butenols generate cyclopentanes, containing four new stereogenic centers with very high levels of stereoselectivity (99% ee, >97 : 3 dr). The reaction proceeds by a carbene–initiated domino sequence consisting of five distinct steps: rhodium–bound oxonium ylide formation, [2,3]-sigmatropic rearrangement, oxy-Cope rearrangement, enol–keto tautomerization, and finally an intramolecular carbonyl ene reaction. A systematic study is presented detailing how to control chirality transfer in each of the four stereo-defining steps of the cascade, consummating in the development of a highly stereoselective process. PMID:25082301

Optically Guided Photoactivity: Coordinating Tautomerization, Photoisomerization, Inhomogeneity, and Reactive Intermediates within the RcaE Cyanobacteriochrome.

Science.gov (United States)

Gottlieb, Sean M; Chang, Che-Wei; Martin, Shelley S; Rockwell, Nathan C; Lagarias, J Clark; Larsen, Delmar S

2014-05-01

The RcaE cyanobacteriochrome uses a linear tetrapyrrole chromophore to sense the ratio of green and red light to enable the Fremyella diplosiphon cyanobacterium to control the expression of the photosynthetic infrastructure for efficient utilization of incident light. The femtosecond photodynamics of the embedded phycocyanobilin chromophore within RcaE were characterized with dispersed femtosecond pump-dump-probe spectroscopy, which resolved a complex interplay of excited-state proton transfer, photoisomerization, multilayered inhomogeneity, and reactive intermediates. These reactions were integrated within a central model that incorporated a rapid (200 fs) excited-state Le Châtelier redistribution between parallel evolving populations ascribed to different tautomers. Three photoproducts were resolved and originates from four independent subpopulations, each with different dump-induced behavior: Lumi-Go was depleted, Lumi-Gr was unaffected, and Lumi-Gf was enhanced. This suggests that RcaE may be engineered to act either as an in vivo fluorescent probe (after single-pump excitation) or as an in vivo optogenetic sample (after pump and dump excitation).

A pH-responsive molecular switch with tricolor luminescence.

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Ahn, Hyungmin; Hong, Jaewan; Kim, Sung Yeon; Choi, Ilyoung; Park, Moon Jeong

2015-01-14

We developed a new ratiometric pH sensor based on poly(N-phenylmaleimide) (PPMI)-containing block copolymer that emits three different fluorescent colors depending on the pH. The strong solvatochromism and tautomerism of the PPMI derivatives enabled precise pH sensing for almost the entire range of the pH scale. Theoretical calculations have predicted largely dissimilar band gaps for the keto, enol, and enolate tautomers of PPMI owing to low-dimensional conjugation effects. The tunable emission wavelength and intensity of our sensors, as well as the reversible color switching with high-luminescent contrast, were achieved using rational molecular design of PPMI analogues as an innovative platform for accurate H(+) detection. The self-assembly of block copolymers on the nanometer length scale was particularly highlighted as a novel prospective means of regulating fluorescence properties while avoiding the self-quenching phenomenon, and this system can be used as a fast responsive pH sensor in versatile device forms.

Proton tunneling in the A∙T Watson-Crick DNA base pair: myth or reality?

Science.gov (United States)

Brovarets', Ol'ha O; Hovorun, Dmytro M

2015-01-01

The results and conclusions reached by Godbeer et al. in their recent work, that proton tunneling in the A∙T(WC) Watson-Crick (WC) DNA base pair occurs according to the Löwdin's (L) model, but with a small (~10(-9)) probability were critically analyzed. Here, it was shown that this finding overestimates the possibility of the proton tunneling at the A∙T(WC)↔A*∙T*(L) tautomerization, because this process cannot be implemented as a chemical reaction. Furthermore, it was outlined those biologically important nucleobase mispairs (A∙A*↔A*∙A, G∙G*↔G*∙G, T∙T*↔T*∙T, C∙C*↔C*∙C, H∙H*↔H*∙H (H - hypoxanthine)) - the players in the field of the spontaneous point mutagenesis - where the tunneling of protons is expected and for which the application of the model proposed by Godbeer et al. can be productive.

Preferential solvation of fluorenone and 4-hydroxyfluorenone in binary solvent mixtures

International Nuclear Information System (INIS)

Jozefowicz, Marek; Heldt, Janina R.

2003-01-01

Preferential solvation of fluorenone and 4-hydroxyfluorenone in binary solvent mixtures has been studied using steady-state spectroscopic measurements. This study concerns the solvent-induced shift of the absorption and fluorescence spectra of both molecules in two solvent mixtures, i.e., cyclohexane-tetrahydrofuran and cyclohexane-ethanol. The first system contains polar solute molecules, fluorenone and 4-hydroxyfluorenone, in a mixture of polar aprotic (tetrahydrofuran) and non-polar (cyclohexane) solvents. In the second solvents mixture, hydrogen bonding with solute molecules (ethanol) may occur. The results of spectroscopic measurements are analysed using theoretical models of Bakshiev, Mazurenko and Suppan which describe preferential solvation phenomena. In the case of cyclohexane-tetrahydrofuran mixtures, the deviation from linearity in the absorption and fluorescence solvatochromic shifts vs. the solution polarity is due to non-specific dipolar solvent-solute interactions. For cyclohexane-ethanol binary mixtures, both non-specific and specific (hydrogen bond and proton-relay tautomerization) interactions contribute to the observed solvatochromism

Synthesis and intramolecular cyclizationof thiosemicarbazide morpholilacetic acid

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Moldyr Dyusebaeva

2015-12-01

Full Text Available The paper gives details on the synthesis of four new, potentially biologically active compounds based on amorpholineheterocycle structure. By alkylation of morpholine with ethyl bromoacetate, a morfolilacetic acid ethyl ester was synthesized. Its reaction with hydrazine hydrate led to the hydrazide. We developed the method for synthesis and studied cyclization of thiosemicarbazide morfolilaceticacidin in alkaline medium with formation of bisgeterocyclic system. The possibility of the existence of this compound in two tautomeric forms: thione and thiol, i.e. a 3- (1'-morpholyl-methyl -1,2,4-triazole-5-thione and 3- (1-morpholyl-1'-methyl -5-mercapto-1,2,4-triazole was described. In neutral medium, one product was obtained. According to spectral data, it is attributed to the structure of 3-(1'-morpholil-methyl-1,2,4-triazole-5-thione. Structure of newly synthesized compounds is confirmed by IR and 1H-NMR spectra and data of elemental analysis. These compounds are potentially biologically active substances and are promising for further research.

Structure, vibrations, and hydrogen bond parameters of dibenzotetraaza[14]annulene

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Gawinkowski, S.; Eilmes, J.; Waluk, J.

2010-07-01

Geometry and vibrational structure of dibenzo[ b, i][1,4,8,11]tetraaza[14]annulene (TAA) have been studied using infrared and Raman spectroscopy combined with quantum-chemical calculations. The assignments were proposed for 106 out of the total of 108 TAA vibrations, based on comparison of the theoretical predictions with the experimental data obtained for the parent molecule and its isotopomer in which the NH protons were replaced by deuterons. Reassignments were suggesteded for the NH stretching and out-of-plane vibrations. The values of the parameters of the intramolecular NH⋯N hydrogen bonds were analysed in comparison with the corresponding data for porphyrin and porphycene, molecules with the same structural motif, a cavity composed of four nitrogen atoms and two inner protons. Both experiment and calculations suggest that the molecule of TAA is not planar and is present in a trans tautomeric form, with the protons located on the opposite nitrogen atoms.

Photophysical properties of 1-acetoxy-8-hydroxy-1,4,4a,9a-tetrahydroanthraquinone: Evidence for excited state proton transfer reaction

International Nuclear Information System (INIS)

Singh, Rupashree Balia; Mahanta, Subrata; Guchhait, Nikhil

2007-01-01

The photophysical properties of 1-acetoxy-8-hydroxy-1,4,4a,9a-tetrahydroanthraquinone (HTHQ) have been investigated by steady state and time resolved spectroscopy in combination with quantum chemical calculations. The effects of various parameters such as the nature of solvent and pH of the medium on the spectral properties confirm the existence of different neutral and ionic species in the ground and excited states. In the ground state, HTHQ exists as intramolecularly hydrogen bonded closed conformer in non-polar and polar aprotic solvents. Apart from the closed conformer, the intermolecular hydrogen bonded solvated species and the anion of HTHQ are present in hydroxylic solvents. The closed conformer shows excited state intramolecular proton transfer in all solvents and the solvent polarity independent red shifted emission indicates only keto-enol tautomerism. Evaluation of the potential energy surfaces by quantum chemical calculation using density functional theory point towards the possibility of proton transfer reaction in the first excited state but not in the ground state

Above-room-temperature ferroelectricity and antiferroelectricity in benzimidazoles

Science.gov (United States)

Horiuchi, Sachio; Kagawa, Fumitaka; Hatahara, Kensuke; Kobayashi, Kensuke; Kumai, Reiji; Murakami, Youichi; Tokura, Yoshinori

2012-12-01

The imidazole unit is chemically stable and ubiquitous in biological systems; its proton donor and acceptor moieties easily bind molecules into a dipolar chain. Here we demonstrate that chains of these amphoteric molecules can often be bistable in electric polarity and electrically switchable, even in the crystalline state, through proton tautomerization. Polarization-electric field (P-E) hysteresis experiments reveal a high electric polarization ranging from 5 to 10 μC cm-2 at room temperature. Of these molecules, 2-methylbenzimidazole allows ferroelectric switching in two dimensions due to its pseudo-tetragonal crystal symmetry. The ferroelectricity is also thermally robust up to 400 K, as is that of 5,6-dichloro-2-methylbenzimidazole (up to ~373 K). In contrast, three other benzimidazoles exhibit double P-E hysteresis curves characteristic of antiferroelectricity. The diversity of imidazole substituents is likely to stimulate a systematic exploration of various structure-property relationships and domain engineering in the quest for lead- and rare-metal-free ferroelectric devices.

Tautomerism in o-hydroxyanilino-1,4-naphthoquinone derivatives: Structure, NMR, HPLC and density functional theoretic investigations

Science.gov (United States)

Bhand, Sujit; Patil, Rishikesh; Shinde, Yogesh; Lande, Dipali N.; Rao, Soniya S.; Kathawate, Laxmi; Gejji, Shridhar P.; Weyhermüller, Thomas; Salunke-Gawali, Sunita

2016-11-01

Structure and spectral characteristics of 'Ortho' ((E)-4-hydroxy-2-(2‧-(4‧-R)-hydroxyphenyl)-imino)-naphthalen-1(2H)-one) and 'para' (2-(2‧-(4‧-R)-hydroxyphenyl)-amino)-1,4-naphthoquinone) tautomers of o-hydroxyanilino-1,4-naphthoquinone derivatives (Rdbnd H, 1A; sbnd CH3, 2A; and -Cl, 3A) are investigated using the 1H, 13C, DEPT, gDQCOSY, gHSQCAD NMR, HPLC, cyclic voltammetry techniques combined with the density functional theory. The compound 2A crystallizes in monoclinic space group P21/c. wherein the polymer chain is facilitated via Osbnd H⋯O and Csbnd H⋯O intermolecular hydrogen bonding. Marginal variations in bond distances in quinonoid and aminophenol moieties render structural flexibility to these compounds those in solution exist as exist in 'ortho - para' tautomers. 1H and 13C NMR spectra in DMSO-d6 showed two sets of peaks in all compounds; whereas only the para tautomer of for 1A and 2A, the para tautomer is predominant in CD3CN solution. Further the ortho-para interconversion is accompanied by a large up-field signals for C(3)sbnd H(3) in their 1H and 13C NMR spectra. These inferences are corroborated by the density functional theoretic calculations.

Theoretical investigation of cyromazine tautomerism using density functional theory and Møller–Plesset perturbation theory methods

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A computational chemistry analysis of six unique tautomers of cyromazine, a pesticide used for fly control, was performed with density functional theory (DFT) and canonical second order Møller–Plesset perturbation theory (MP2) methods to gain insight into the contributions of molecular structure to ...

The nature of the transition mismatches with Watson-Crick architecture: the G*·T or G·T* DNA base mispair or both? A QM/QTAIM perspective for the biological problem.

Science.gov (United States)

Brovarets', Ol'ha O; Hovorun, Dmytro M

2015-01-01

This study provides the first accurate investigation of the tautomerization of the biologically important guanine*·thymine (G*·T) DNA base mispair with Watson-Crick geometry, involving the enol mutagenic tautomer of the G and the keto tautomer of the T, into the G·T* mispair (∆G = .99 kcal mol(-1), population = 15.8% obtained at the MP2 level of quantum-mechanical theory in the continuum with ε = 4), formed by the keto tautomer of the G and the enol mutagenic tautomer of the T base, using DFT and MP2 methods in vacuum and in the weakly polar medium (ε = 4), characteristic for the hydrophobic interfaces of specific protein-nucleic acid interactions. We were first able to show that the G*·T↔G·T* tautomerization occurs through the asynchronous concerted double proton transfer along two antiparallel O6H···O4 and N1···HN3 H-bonds and is assisted by the third N2H···O2 H-bond, that exists along the entire reaction pathway. The obtained results indicate that the G·T* base mispair is stable from the thermodynamic point of view complex, while it is dynamically unstable structure in vacuum and dynamically stable structure in the continuum with ε = 4 with lifetime of 6.4·10(-12) s, that, on the one side, makes it possible to develop all six low-frequency intermolecular vibrations, but, on the other side, it is by three orders less than the time (several ns) required for the replication machinery to forcibly dissociate a base pair into the monomers during DNA replication. One of the more significant findings to emerge from this study is that the short-lived G·T* base mispair, which electronic interaction energy between the bases (-23.76 kcal mol(-1)) exceeds the analogical value for the G·C Watson-Crick nucleobase pair (-20.38 kcal mol(-1)), "escapes from the hands" of the DNA replication machinery by fast transforming into the G*·T mismatch playing an indirect role of its supplier during the DNA replication. So

Watching Conformations of Biomolecules: a Microwave Spectroscopy Approach

Science.gov (United States)

Lopez, J. C.

2011-06-01

The combination of laser ablation with Fourier transform microwave spectroscopy in supersonic jets (LA-MB-FTMW) has made possible the gas-phase study of solid biomolecules with high melting points. In the experiment, solids are efficiently vaporized by a high-energy laser pulse, supersonically expanded into a evacuated Fabry-Perot cavity and characterised by their rotational spectra. Recent improvements such as the use of picosecond pulse lasers, new ablation nozzles and the extension of the range of the spectrometers to low frequecy have notably increased the sensitivity of our experimental setup. To date different α-, β- and γ-amino acids have been studied using this technique, making possible the characterization of their preferred conformations and gaining insight in the role of intramolecular interactions. Even in conformationally challenging systems the different rotamers of such biomolecules can be identified by rotational spectroscopy as can be illustrated by the assignment of six low-energy conformers in cysteine and aspartic acid, seven in serine and threonine,^a and nine in γ-amino butyric acid (GABA). In all cases the low-energy conformers have been conclusive identified from their experimental rotational and 14N quadrupole coupling constants. The spectra of neurotransmitters and of the nucleic acid bases uracil, thymine, cytosine and guanine have also been studied and their preferred conformers or tautomeric forms determined. The complexes between amino acids and nucleic acid bases with water have also been investigated to obtain information on the possible changes induced in the conformational or tautomeric preferences by the addition of solvent molecules. J. L. Alonso, C. Pérez, M. E. Sanz, J. C. López, S. Blanco, Phys. Chem. Chem. Phys. 11, 617-627 (2009) and references therein M. E. Sanz, J. C. López, J. L. Alonso, Phys. Chem. Chem. Phys., 12, 3573-3578 (2010) S. Blanco, J. C. López, S. Mata and J. L. Alonso, Angew. Chem. Int. Ed. 49, 9187

VUV photoionization and dissociative photoionization of the prebiotic molecule acetyl cyanide: Theory and experiment

International Nuclear Information System (INIS)

Bellili, A.; Hochlaf, M.; Schwell, M.; Bénilan, Y.; Fray, N.; Gazeau, M.-C.; Mogren Al-Mogren, M.; Guillemin, J.-C.; Poisson, L.

2014-01-01

The present combined theoretical and experimental investigation concerns the single photoionization of gas-phase acetyl cyanide and the fragmentation pathways of the resulting cation. Acetyl cyanide (AC) is inspired from both the chemistry of cyanoacetylene and the Strecker reaction which are thought to be at the origin of medium sized prebiotic molecules in the interstellar medium. AC can be formed by reaction from cyanoacetylene and water but also from acetaldehyde and HCN or the corresponding radicals. In view of the interpretation of vacuum ultraviolet (VUV) experimental data obtained using synchrotron radiation, we explored the ground potential energy surface (PES) of acetyl cyanide and of its cation using standard and recently implemented explicitly correlated methodologies. Our PES covers the regions of tautomerism (between keto and enol forms) and of the lowest fragmentation channels. This allowed us to deduce accurate thermochemical data for this astrobiologically relevant molecule. Unimolecular decomposition of the AC cation turns out to be very complex. The implications for the evolution of prebiotic molecules under VUV irradiation are discussed

Synthesis, spectra, and the crystal structure of α-(3,3-dimethyl-3,4-dihydroisoquinolyl-1)-hydroxyiminoacetamide

International Nuclear Information System (INIS)

Sokol, V.I.; Davydov, V.V.; Kartashova, I.V.; Zaitsev, B.E.; Shklyaev, Yu.V.; Ryabov, M.A.; Sergienko, V.S.

1996-01-01

α-(3,3-Dimethyl-3,4-dihydroisoquinolyl-1)-hydroxyiminoacetamide (I) was synthesized, and its x-ray structure analysis was performed (Enraf-Nonius CAD-4 diffractometer; MoKα radiation; graphite monochromator; θ/2θ scan; 2θmax=56 deg. ; 2496 reflections with I≥2σ(I); and R=0.038). Crystals of I are monoclinic; a=11.67(1), b=8.365(3), and c=15.22(2) A; β=107.7(1) deg.; V=1415.2(2) A 3; ρ(calc)=1.236 g/cm3; Z=4; and sp. gr. P21/n. I crystallizes as a monohydrate, and its formula is C13H15N3O2·H2O. In a crystal, I exists in a azomethineoxime tautomeric form. The planes of amideoxime and dihydroisoquinoline moieties are nearly orthogonal to each other. According to IR and electronic spectra, when passing from crystal to solution the conformation of I changes only slightly. An effect of water molecules on the molecular structure of I is discussed

Synthesis, structure characterization and biological studies on a new aromatic hydrazone, 5-(2-(1,5-dimethyl-3-oxo-2-phenyl-2,3-dihydro-1H-pyrazol-4-yl)hydrazono)-2,2-dimethyl-1,3-dioxane-4,6-dione, and its transition metal complexes

Science.gov (United States)

Kumar, Shubha S.; Biju, S.; Sadasivan, V.

2018-03-01

A new aromatic hydrazone 5-(2-(1,5-dimethyl-3-oxo-2-phenyl-2,3-dihydro-1H-pyrazol-4-yl)hydrazono)-2,2-dimethyl-1,3-dioxane-4,6-dione has been synthesized by Japp-Klingemann reaction from diazotized 4-aminoantipyrine and Meldrum's acid. A few 3d-metal ion complexes of this hydrazone were synthesized. The compound and its complexes were characterized by UV-Visible, 1H NMR, ESR, Mass spectral, molar conductance and magnetic susceptibility measurements. The compound was found to exist in hydrazone form in solid state and solution from SXRD and 1H NMR study. The influence of pH on the molecule was studied and found that it shows azo/enol-hydrazone tautomerism in solution. This molecule act as a univalent tridentate ligand and the complexes were assigned to have a 1:2 stoichiometry (M:L). The antioxidant properties of the compounds were explored by DPPH assay and found that the ligand possesses better free radical scavenging effect than the complexes. Antimicrobial activities of these compounds were investigated and were found to be active.

Proton transfer processes in selenourea: UV-induced selenone → selenol photoreaction and ground state selenol → selenone proton tunneling

International Nuclear Information System (INIS)

Rostkowska, Hanna; Lapinski, Leszek; Khvorostov, Artem; Nowak, Maciej J.

2004-01-01

Infrared spectrum of selenourea isolated in low temperature Ar matrix indicates that monomers of this compound adopt exclusively the selenone tautomeric form. UV irradiation (λ>345 nm) of matrix-isolated selenourea leads to generation of the selenol tautomer (isoselenourea). Two conformers of the selenol tautomer with imino N-H bond oriented anti or syn with respect to the Se-H group were photoproduced. For the matrix kept at 10 K and in darkness, a proton tunneling transforming the photoproduced selenol anti form back into the initial selenone tautomer was observed. The time constant of this process was 16 h. The asymmetric barrier for the selenol → selenone proton tunneling was estimated at MP2/6-311++G(2d,p) level to be as high as 95 kJ mol -1 (7940 cm -1 ). The relation between the height of the barrier and the time constant of proton tunneling was discussed by comparing the current case with that previously studied for thiourea [J. Phys. Chem. A 107 (2003) 6373

Specific cationic emission of cisplatin following ionization by swift protons

International Nuclear Information System (INIS)

Moretto-Capelle, P.; Champeaux, J.P.; Deville, C.; Sence, M.; Cafarelli, P.

2016-01-01

We have investigated collision-induced ionization and fragmentation by 100 keV protons of the radio sensitizing molecule cisplatin, which is used in cancer treatments. A large emission of HCl"+ and NH_2"+ is observed, but surprisingly, no cationic fragments containing platinum are detected, in contrast to ionization-dissociation induced by electronic collision. Theoretical investigations show that the ionization processes take place on platinum and on chlorine atoms. We propose new ionization potentials for cisplatin. Dissociation limits corresponding to the measured fragmentation mass spectrum have been evaluated and the theoretical results show that the non-observed cationic fragments containing platinum are mostly associated with low dissociation energies. We have also investigated the reaction path for the hydrogen transfer from the NH_3 group to the Cl atom, as well as the corresponding dissociation limits from this tautomeric form. Here again the cations containing platinum correspond to lower dissociation limits. Thus, the experimental results suggest that excited states, probably formed via inner-shell ionization of the platinum atom of the molecule, correlated to higher dissociation limits are favored. (authors)

Synthesis, spectroscopy, X-ray crystallography, DFT calculations, DNA binding and molecular docking of a propargyl arms containing Schiff base.

Science.gov (United States)

Balakrishnan, C; Subha, L; Neelakantan, M A; Mariappan, S S

2015-11-05

A propargyl arms containing Schiff base (L) was synthesized by the condensation of 1-[2-hydroxy-4-(prop-2-yn-1-yloxy)phenyl]ethanone with trans-1,2-diaminocyclohexane. The structure of L was characterized by IR, (1)H NMR, (13)C NMR and UV-Vis spectroscopy and by single crystal X-ray diffraction analysis. The UV-Visible spectral behavior of L in different solvents exhibits positive solvatochromism. Density functional calculation of the L in gas phase was performed by using DFT (B3LYP) method with 6-31G basis set. The computed vibrational frequencies and NMR signals of L were compared with the experimental data. Tautomeric stability study inferred that the enolimine is more stable than the ketoamine form. The charge delocalization has been analyzed using natural bond orbital (NBO) analysis. Electronic absorption and emission spectral studies were used to study the binding of L with CT-DNA. The molecular docking was done to identify the interaction of L with A-DNA and B-DNA. Copyright © 2015 Elsevier B.V. All rights reserved.

Molecular structure, vibrational spectra and photochemistry of 5-mercapto-1-methyltetrazole

Science.gov (United States)

Gómez-Zavaglia, A.; Reva, I. D.; Frija, L.; Cristiano, M. L.; Fausto, R.

2006-04-01

In this work, 5-mercapto-1-methyltetrazole was studied by low temperature matrix-isolation and solid-state infrared spectroscopy, DFT(B3LYP)/6-311++G(d,p) calculations and photochemical methods. In the low temperature neat solid phase and isolated in an argon matrix, the compound was found to exist in the 1-methyl-1,4-dihydro-5 H-tetrazole-5-thione tautomeric form. The infrared spectra of the compound were fully assigned and correlated with structural properties. In situ UV-irradiation ( λ>235 nm) of the matrix-isolated monomer is shown to induce different photochemical processes, all of them involving cleavage of the tetrazole ring: e.g. (1) molecular nitrogen expulsion, with production of 1-methyl-1 H-diazirene-3-thiol, which is produced in two different conformers; (2) ring cleavage leading to production of methyl isothiocyanate and azide; (3) simultaneous elimination of nitrogen and sulphur with production of N-methylcarbodiimide. Following these photoprocesses, subsequent reactions occur, leading to production of methyl diazene, carbon monosulphide and nitrogen hydride. Spectroscopic evidence of the production of the above-mentioned chemical species is provided.

Specific cationic emission of cisplatin following ionization by swift protons

Science.gov (United States)

Moretto-Capelle, Patrick; Champeaux, Jean-Philippe; Deville, Charlotte; Sence, Martine; Cafarelli, Pierre

2016-05-01

We have investigated collision-induced ionization and fragmentation by 100 keV protons of the radio sensitizing molecule cisplatin, which is used in cancer treatments. A large emission of HCl+ and NH2+ is observed, but surprisingly, no cationic fragments containing platinum are detected, in contrast to ionization-dissociation induced by electronic collision. Theoretical investigations show that the ionization processes take place on platinum and on chlorine atoms. We propose new ionization potentials for cisplatin. Dissociation limits corresponding to the measured fragmentation mass spectrum have been evaluated and the theoretical results show that the non-observed cationic fragments containing platinum are mostly associated with low dissociation energies. We have also investigated the reaction path for the hydrogen transfer from the NH3 group to the Cl atom, as well as the corresponding dissociation limits from this tautomeric form. Here again the cations containing platinum correspond to lower dissociation limits. Thus, the experimental results suggest that excited states, probably formed via inner-shell ionization of the platinum atom of the molecule, correlated to higher dissociation limits are favored.

VUV photoionization and dissociative photoionization of the prebiotic molecule acetyl cyanide: Theory and experiment

Energy Technology Data Exchange (ETDEWEB)

Bellili, A.; Hochlaf, M., E-mail: hochlaf@univ-mlv.fr, E-mail: martin.schwell@lisa.u-pec.fr [Laboratoire Modélisation et Simulation Multi Echelle, MSME UMR 8208 CNRS, Université Paris-Est, 5 bd Descartes, 77454 Marne-la-Vallée (France); Schwell, M., E-mail: hochlaf@univ-mlv.fr, E-mail: martin.schwell@lisa.u-pec.fr; Bénilan, Y.; Fray, N.; Gazeau, M.-C. [Laboratoire Interuniversitaire des Systèmes Atmosphériques (LISA), UMR 7583 CNRS, Institut Pierre et Simon Laplace, Universités Paris-Est Créteil et Paris Diderot, 61 Avenue du Général de Gaulle, 94010 Créteil (France); Mogren Al-Mogren, M. [Chemistry Department, Faculty of Science, King Saud University, P.O. Box 2455, Riyadh 11451 (Saudi Arabia); Guillemin, J.-C. [Institut des Sciences Chimiques de Rennes, Ecole Nationale Supérieure de Chimie de Rennes, CNRS, UMR 6226, Allée de Beaulieu, CS 50837, 35708 Rennes Cedex 7 (France); Poisson, L. [Laboratoire Francis Perrin, CNRS URA 2453, CEA, IRAMIS, Laboratoire Interactions Dynamique et Lasers, Bât 522, F-91191 Gif/Yvette (France)

2014-10-07

The present combined theoretical and experimental investigation concerns the single photoionization of gas-phase acetyl cyanide and the fragmentation pathways of the resulting cation. Acetyl cyanide (AC) is inspired from both the chemistry of cyanoacetylene and the Strecker reaction which are thought to be at the origin of medium sized prebiotic molecules in the interstellar medium. AC can be formed by reaction from cyanoacetylene and water but also from acetaldehyde and HCN or the corresponding radicals. In view of the interpretation of vacuum ultraviolet (VUV) experimental data obtained using synchrotron radiation, we explored the ground potential energy surface (PES) of acetyl cyanide and of its cation using standard and recently implemented explicitly correlated methodologies. Our PES covers the regions of tautomerism (between keto and enol forms) and of the lowest fragmentation channels. This allowed us to deduce accurate thermochemical data for this astrobiologically relevant molecule. Unimolecular decomposition of the AC cation turns out to be very complex. The implications for the evolution of prebiotic molecules under VUV irradiation are discussed.

2-(2-Chlorobenzoylimino)-1,3-thiazolidine: structure refinement from neutron diffraction data at 113 K and charge density deformation maps

International Nuclear Information System (INIS)

Cohen-Addad, C.; Savariault, J.-M.; Lehmann, M.S.

1981-01-01

The structure of 2-(2-chlorobenzoylimino)-1,3-thiazolidine, C 10 H 9 ClN 2 OS, has been redetermined by neutron diffraction at 113 K. The space group is P2 1 /c with lattice parameters a = 19.950 (4), b = 7.420 (2), c = 11.566 (3) A, β = 109.10 (3) 0 , Z = 4, Msub(r) = 240.7 and dsub(calc) = 1.52 Mg m -3 . The final R(F 2 ) was 0.045 for 1768 reflections. The structural results show unambiguously that the molecule is found in the imino form with an H atom located near the endocyclic N atom of the thiazolidine group. Based on deformation electron density maps and the interatomic distances it is speculated that the difference in geometry between the two tautomeric forms (imino and amino) is small and that the occurrence of one or the other is strongly dependent on the substituents. A short intramolecular S-O contact of 2.68 A is found and is believed to constitute a very weak bond. (Auth.)

First hyperpolarizability in a new benzimidazole derivative

International Nuclear Information System (INIS)

Rodembusch, Fabiano Severo; Buckup, Tiago; Segala, Maximiliano; Tavares, Luciana; Correia, Ricardo Rego Bordalo; Stefani, Valter

2004-01-01

A new benzimidazole, 2-(4'-amino-2'-hydroxyphenyl)-6-nitrobenzimidazole (LEN), with promising applications in nonlinear optics were synthesized, purified and characterized by classical techniques. The UV-Vis and steady-state fluorescence of LEN in solution were applied in order to characterize the photophysical behaviour of this new fluorescent dye. The Hyper-Rayleigh Scattering study indicates a remarkable increase in the β absolute value (1197.3 ± 1.2 x 10 -30 esu) of the LEN in acetone at 1064 nm, when comparing with a previously described benzoxazole (BO6). The ratio between the experimental β and the maximum theoretical value using a two-level model was also improved by a factor 6. Ab initio and semi-empirical calculations of the dipole moments and the first hyperpolarizability are also presented. The enhancement in the experimental hyperpolarizability value in relation to BO6 is explained in terms of the benzimidazolic ring basicity and a prototropic effect (annular tautomerism) present in the LEN, identified as a resonance-assisted hydrogen bond, which leads to a stronger electronic delocalization

A study by nitrogen-15 nuclear magnetic resonance spectroscopy of the state of histidine in the catalytic triad of α-lytic protease

International Nuclear Information System (INIS)

Bachovchin, W.W.; Roberts, J.D.

1978-01-01

The ionization behaviour of the histidine of the catalytic triad of α-lytic protease using N-15 NMR spectroscopy is studied. This technique is especially informative about the protonation, hydrogen-bond formation, and tautomeric equilibrium of imidazole rings. The efficient and specific incorporation of N-15 labelled histidine into α-lytic protease was achieved by inducing and isolating an auxotroph of myxobacter 495 for which histidine is an essential amino acid. The results show that histidine of the catalytic triad of α-lytic protease appears to have a base strength which is essentially normal for an imidazole derivative but, in the pH range where the enzymatic activity is high, the histidine tautomer is favoured with the hydrogen located on N3 (π), as the result of hydrogen bonding to the asparate anion and possible the serine hydroxyl. Thus, the N-15 NMR shifts support the general geometry postulated for the ''charge-relay'' mechanism but not the idea of an unusually weakly basic histidine or an unusually strongly basic asparate carboxylate anion. (A.G.)

N3 and O2 Protonated Tautomeric Conformations of 2 '-Deoxycytidine and Cytidine Coexist in the Gas Phase

NARCIS (Netherlands)

Wu, R.R.; Yang, B.; Frieler, C.E.; Berden, G.; Oomens, J.; Rodgers, M.T.

2015-01-01

Infrared multiple photon dissociation action spectra of the protonated forms of the cytidyl nucleosides, 2'-deoxycytidine, [dCyd+H](+), and cytidine, [Cyd+H](+), are acquired over the IR fingerprint and hydrogen-stretching regions. Electronic structure calculations are performed at the

Mechanism of Prototropy. V. Arrhenius parameters of the tautomerization of Benzylidene Benzylamine and its α-α-alkyl derivatives

International Nuclear Information System (INIS)

Perez Ossorio, R.; Gomez Herrera, F.; Utrilla, R. M.; Hidalgo, A.; Gamboa, J. M.

1961-01-01

The reactions were conducted in ethyl alcohol-dioxan, in the presence of EtONa, as catalyst. Rates were followed by a radioactive tracer method when R=H and by spectroscopic method when R= alkyl as described in previous papers. The results suggest that polar effects alone cannot account for the relative Arrhenius parameters obtained. (Author) 3 refs

Fluorescence ratiometric sensing of polyols by phenylboronic acid complexes with ligands exhibiting excited-state intramolecular proton transfer in aqueous micellar media

Energy Technology Data Exchange (ETDEWEB)

Trejo-Huizar, Karla Elisa; Jiménez-Sánchez, Arturo; Martínez-Aguirre, Mayte A.; Yatsimirsky, Anatoly K., E-mail: anatoli@unam.mx

2016-11-15

2-Phenyl-3-hydroxy-4(1H)-quinolone possessing dual fluorescence due to excited-state intramolecular proton transfer (ESIPT) forms stable complex with phenylboronic acid with blue shifted emission maximum in micellar medium of a cationic surfactant even though the compound lacks required for complexation with boronic acids cis-diol structure. No complexation is observed in the presence of neutral or anionic surfactants. Titrations of this complex with polyols including sugars and nucleotides at pH 8 displace free quinolone showing ratiometric response, which allows determination of polyols with detection limits 0.05–1 mM and unusually wide linear dynamic ranges. Another ESIPT dye 2-(2′-hydroxyphenyl)−1H-benzimidazole also lacking cis-diol structure forms equally stable complex with phenylboronic acid and allows ratiometric determination of polyols with similar characteristics. The results of this study demonstrate that blocking ESIPT of signaling molecule by complexation of the receptor with the proton donor group eliminates the low energy emission from tautomeric form but strongly enhances the high energy emission typical for “normal” form of signaling molecule creating a possibility of ratiometric sensing.

Research on Synthesis of New Azo Calix[4]arene and its Dyeing Properties

Directory of Open Access Journals (Sweden)

Tang Jun

2015-01-01

Full Text Available With the raw materials of calix[4]arene, benzocaine, tricaine and procaine hydrochloride, three new azo calix[4]arene derivatives—6a, 6b and 6c are synthesized by diazotization–coupling reaction of an aromatic amine, with its yield of 83%, 81% and 83% respectively. The structural characterization is in a way of IR, 1H NMR and elemental analysis. This paper investigates the spectral properties of azo calix[4]arene derivatives under different solution pH conditions through the UV–visible spectroscopy, and researches the dyeing properties through the dyeing curve, color yield test and fastness test. The results show that, with the increase of pH value, the azo calix[4]arene derivatives—6a, 6b and 6c form azo–hydrazone tautomeric isomers with the maximum absorption peak redshift; the dyeing effect of the compound is good, of which the dye–uptake rate of the compound 6a is as high as 78%; the surface depth of color yield is 2.798, and the dry and wet rubbing fastness and the soaping fastness are respectively 4, which is a better disperse dye.

Aryliminopropadienone-C-Amidoketenimine- Amidinoketene-2-Aminoquinolone Cascades and the Ynamine-Isocyanate Reaction.

Science.gov (United States)

Wentrup, Curt; Rao, V. V. Ramana; Frank, Wilhelm; Fulloon, Belinda E.; Moloney, Daniel W. J.; Mosandl, Thomas

1999-05-14

Imidoylketenes 11 and oxoketenimines 12 are generated by flash vacuum thermolysis of Meldrum's acid derivatives 9, pyrrolediones 17 and 18, and triazole 19 and are observed by IR spectroscopy. Ketenimine-3-carboxylic acid esters 12a are isolable at room temperature. Ketenes 11 and ketenimines 12 undergo rapid interconversion in the gas phase, and the ketenes cyclize to 4-quinolones 13. When using an amine leaving group in Meldrum's acid derivatives 9c, the major reaction products are aryliminopropadienones, ArN=C=C=C=O (15). The latter react with 1 equiv of nucleophile to produce ketenimines 12 and with 2 equiv to afford malonic acid imide derivatives 16. N-Arylketenimine-C-carboxamides 12c cyclize to quinolones 13c via the transient amidinoketenes 11c at temperatures of 25-40 degrees C. This implies rapid interconversion of ketenes and ketenimines by a 1,3-shift of the dimethylamino group, even at room temperature. This interconversion explains previously poorly understood outcomes of the ynamine-isocyanate reaction. The solvent dependence of the tautomerism of 4-quinolones/4-quinolinols is discussed. Rotational barriers of NMe(2) groups in amidoketenimines 12c and malonioc amides and amidines 16 (24) are reported.

Rotational and vibrational spectra of ethynol from quantum-mechanical calculations

Science.gov (United States)

Defrees, D. J.; Mclean, A. D.

1982-01-01

It is noted that ethynol (HCCOH), despite the theoretical prediction of its stability to tautomerization to ketene, has thus far not been observed. It is shown here that the identification of this unknown molecule, both in space and in the laboratory, can be aided by an ab initio calculation of spectroscopic parameters. At the HF/3-21G level, harmonic vibrational frequencies are computed by way of analytic second differentiation of the Hartee-Fock (HF) energy with respect to the nuclear coordinates. After applying an empirical scale factor, the resultant frequencies are (per cm) 473, 517, 773, 841, 1003, 1217, 2206, 3285, and 3418. The computed dipole moment at the CISD/DZ+P level is 1.79 D. At the CISD+Q/DZ+P level, the molecule's rotational constants are determined. After scaling by empirical correction factors, they are used in deriving the 4(04) - 3(03) frequency of 76.81 + or - 0.3 GHz with a triplet splitting of 0.30 + or - 0.01 GHz. The triplet splitting involves 4(14) - 3(13) and 4(13) - 3(12) relative to the 4(04) - 3(03) transition as the central line.

Characterisation and properties of homo- and heterogenously phosphorylated nanocellulose.

Science.gov (United States)

Kokol, Vanja; Božič, Mojca; Vogrinčič, Robert; Mathew, Aji P

2015-07-10

Nano-sized cellulose ester derivatives having phosphoryl side groups were synthesised by phosphorylation of nanofibrilated cellulose (NFC) and nanocrystaline cellulose (NCC), using different heterogeneous (in water) and homogeneous (in molten urea) processes with phosphoric acid as phosphoryl donor. The phosphorylation mechanism, efficacy, stability, as well as its influence on the NC crystallinity and thermal properties, were evaluated using ATR-FTIR and (13)C NMR spectroscopies, potentiometric titration, capillary electrophoresis, X-ray diffraction, colorimetry, thermogravimmetry and SEM. Phosphorylation under both processes created dibasic phosphate and monobasic tautomeric phosphite groups at C6 and C3 positioned hydroxyls of cellulose, yielded 60-fold (∼1,173 mmol/kg) and 2-fold (∼1.038 mmol/kg) higher surface charge density for p-NFC and p-NCC, respectively, under homogenous conditions. None of the phosphorylations affected neither the NC crystallinity degree nor the structure, and noticeably preventing the derivatives from weight loss during the pyrolysis process. The p-NC showed high hydrolytic stability to water at all pH mediums. Reusing of the treatment bath was examined after the heterogeneous process. Copyright © 2015 Elsevier Ltd. All rights reserved.

Q-mode curve resolution of UV-vis spectra for structural transformation studies of anthocyanins in acidic solutions

International Nuclear Information System (INIS)

Marco, Paulo Henrique; Scarminio, Ieda Spacino

2007-01-01

Chemometric analysis of ultraviolet-visible (UV-vis) spectra for pH values 1.0, 3.3, 5.3, and 6.9 was used to investigate the kinetics and the structural transformations of anthocyanins in extracts of calyces of hibiscus flowers of the Hibiscus acetosella Welw. ex Finicius for the first time. Six different species were detected: the quinoidal base (A), the flavylium cation (AH + ), the pseudobase or carbinol pseudobase (B), cis-chalcone (C C ), trans-chalcone (C t ), and ionized cis-chalcone (C C - ). Four equilibrium constant values were calculated using relative concentrations, hydration, pK h =2.60+/-0.01, tautomeric, K T =0.14+/-0.01, acid-base, pK a =4.24+/-0.04, and ionization of the cis-chalcone, pK C C =8.74+/-1.5x10 -2 . The calculated protonation rate of the tautomers is K H + =0.08+/-7.6x10 -3 . These constants are in excellent agreement with those measured previously in salt form. From a kinetic viewpoint, the situation encountered is interesting since the reported investigation is limited to visible light absorption in acid medium. These models have not been reported in the literature

Extended mechanistic aspects on photoinitiated polymerization of 1,6-hexanediol diacrylate by hexaarylbisimidazoles and heterocyclic mercapto compounds.

Science.gov (United States)

Berdzinski, Stefan; Strehmel, Nadine; Lindauer, Heike; Strehmel, Veronika; Strehmel, Bernd

2014-05-01

Chlorine substituted hexaarylbisimidazole (o-Cl-HABI) efficiently initiates radical polymerization of multifunctional acrylic esters in the presence of a heterocyclic mercapto compound if the latter can form its tautomeric thione. Exposure of o-Cl-HABI results in lophyl radicals, which efficiently add to the thione in the first step while the second step releases a highly reactive thiyl radical from this intermediate. LC-MS and CID-MS measurements support this reaction scheme. Furthermore, photo-DSC experiments applying UV light between 320 and 380 nm showed that mercaptotriazole and phenylmercaptotriazole exhibited the best reactivity in the monomer 1,6-hexanediol diacrylate (HDDA) while alkyl substituted mercaptotriazoles showed less reactivity. Change of the triazole heterocycle by mercaptoimidazole resulted in a significant decrease of photoinitiation efficiency. This heterocycle does not form the corresponding thione in HDDA as shown by NMR measurements. Replacement of mercaptotriazole by an alkylthiol leads to a system showing the lowest photoinitiation efficiency in this series. Formation of thione structure in the case of heterocyclic mercapto compounds may cause higher reactivity of the heterocyclic mercapto compounds with the lophyl radical in the monomer chosen.

Novel acid mono azo dye compound: Synthesis, characterization, vibrational, optical and theoretical investigations of 2-[(E)-(8-hydroxyquinolin-5-yl)-diazenyl]-4,5-dimethoxybenzoic acid

Science.gov (United States)

Saçmacı, Mustafa; Çavuş, Hatice Kanbur; Arı, Hatice; Şahingöz, Recep; Özpozan, Talat

2012-11-01

Novel acid mono azo dye, 2-[(E)-(8-hydroxyquinolin-5yl)-diazenyl]-4,5-dimethoxybenzoic acid (HQD), was synthesized by coupling diazonium salt solution of 2-amino-4,5-dimethoxybenzoic acid (DMA) with 8-hydroxyquinoline (HQ). This dye was characterized by UV-vis, IR & Raman, 1H and 13C NMR spectroscopic techniques and elemental analysis. The normal coordinate analysis of HQD was also performed to assign each band in vibrational spectra. DFT (B3LYP and B3PW91) calculations were employed to optimize the geometry, to interpret NMR spectra, to calculate and to determine the stable tautomeric structure of the compound. Natural Bond Orbital (NBO) analysis was performed to investigate intramolecular interactions. The vibrational spectral data obtained from solid phase IR & Raman spectra were assigned based on the results of the theoretical calculations. UV-vis spectroscopic technique was employed to obtain the optical band gap of HQD. The analysis of the optical absorption data revealed the existence of direct and indirect transitions in the optical band gaps. The optical band gaps of HQD have been found 1.95 and 1.90 eV for direct and indirect transitions, respectively.

Energy transformation in molecular electronic systems

International Nuclear Information System (INIS)

Kasha, M.

1985-01-01

Our new optical pumping spectroscopy (steady state, and double-laser pulse) allows the production and study of the unstable rare tautomer in its ground and excited states, including picosecond dynamic studies. Molecules under study here included 7-azaindole (model for biological purines), 3-hydroxyflavone (model for plant flavones), lumichrome, and other heterocyclics. New detailed molecular mechanisms for proton transfer are derived, especially with catalytic assisting molecules. A new proton-transfer laser of extraordinary efficiency has become a side dividend, possibly worth of industrial development. The excited and highly reactive singlet molecular oxygen species 1 Δ/sub g/) has proven to be ubiquitous in chemical peroxide systems and in physically excited sensitizer-oxygen systems. Hyperbaric oxygen mechanisms in biology probably involve singlet oxygen. We have undertaken a spectroscopic study of tris - dibenzoylmethane chelates of Al, Gd, Eu, and Yb trivalent ions. These chelates offer a variety of electronic behaviors, from Z-effects on π-electron spin-orbital coupling (Al, Gd) to Weissman intramolecular energy transfer to 4f mestable levels (Eu, Gd). Elegant new spectroscopic resolution at 77K permits separation of tautomeric, parasitic self-absorption, dissociation, and cage effects to be resolved. 18 refs., 4 figs

Synthesis, characterization and computational studies of 3-{(E)-[(2-hydroxyphenyl)imino]methyl}benzene-1,2-diol and molecular structure of its zwitterionic form

Science.gov (United States)

Ezeorah, Julius Chigozie; Ossai, Valentine; Obasi, Lawrence Nnamdi; Elzagheid, Mohamed I.; Rhyman, Lydia; Lutter, Michael; Jurkschat, Klaus; Dege, Necmi; Ramasami, Ponnadurai

2018-01-01

The Schiff base 3-{(E)-[(2-hydroxyphenyl)imino]methyl}benzene-1,2-diol was synthesized by the condensation of 2,3-dihydroxybenzaldehyde and 2-aminophenol in water at room temperature. The crystal was grown using two solvents (dry methanol and 60% methanol). The compound was characterized using elemental microanalysis, IR, NMR, UV spectroscopies and single-crystal X-ray diffraction crystallography. The X-ray structure reveals that the Schiff base crystallizes as a methanol solvate in dry methanol with triclinic crystal system, space group P-1 and Z = 2 in the unit cell and as a non-methanol solvate in 60% methanol with triclinic crystal system, space group P-1 and Z = 4 in the unit cell. The compound showed absorption bands at 272, 389, 473 and 602 nm in DMSO. These bands were assigned as π → π ∗, n → π∗ and n-σ∗ transitions. The 473 and 602 nm bands in DMSO reveal that the compound exists in tautomeric forms. The presence of N-H, C-O and Cdbnd N stretching vibrations in the IR spectrum indicates that the compound is zwitterionic in the solid state. This study was supplemented using density functional theory method.

Broadband Two-Photon Absorption Characteristics of Highly Photostable Fluorenyl-Dicyanoethylenylated [60]Fullerene Dyads

Directory of Open Access Journals (Sweden)

Seaho Jeon

2016-05-01

Full Text Available We synthesized four C60-(light-harvesting antenna dyads C60 (>CPAF-Cn (n = 4, 9, 12, or 18 1-Cn for the investigation of their broadband nonlinear absorption effect. Since we have previously demonstrated their high function as two-photon absorption (2PA materials at 1000 nm, a different 2PA wavelength of 780 nm was applied in the study. The combined data taken at two different wavelength ranges substantiated the broadband characteristics of 1-Cn. We proposed that the observed broadband absorptions may be attributed by a partial π-conjugation between the C60 > cage and CPAF-Cn moieties, via endinitrile tautomeric resonance, giving a resonance state with enhanced molecular conjugation. This transient state could increase its 2PA and excited-state absorption at 800 nm. In addition, a trend of concentration-dependent 2PA cross-section (σ2 and excited-state absorption magnitude was detected showing a higher σ value at a lower concentration that was correlated to increasing molecular separation with less aggregation for dyads C60(>CPAF-C18 and C60(>CPAF-C9, as better 2PA and excited-state absorbers.

Antioxidant activity and electrochemical elucidation of the enigmatic redox behavior of curcumin and its structurally modified analogues

International Nuclear Information System (INIS)

Jha, Niki S.; Mishra, Satyendra; Jha, Shailendra K.; Surolia, Avadhesha

2015-01-01

Highlights: • Structural analogues of curcumin have been synthesized. • Confirmation of redox behaviour emanates from H- shift from central methylene group in curcumin. • Mechanism of curcumin oxidation has been proposed. • Correlation between redox behavior and antioxidant activity has been established. - Abstract: Here, we report studies on the antioxidant activity and redox behavior of curcumin and its structurally modified synthetic analogues. We have synthesized a number of analogues of curcumin which abrogate its keto-enol tautomerism or substitute the methylene group at the centre of its heptadione moiety implicated in the hydride transfer and studied their redox property. From cyclic voltammetric studies, it is demonstrated that H- atom transfer from CH 2 group at the center of the heptadione link also plays an important role in the antioxidant properties of curcumin along with that of its phenolic –OH group. In addition, we also show that the conversion of 1, 3- dicarbonyl moiety of curcumin to an isosteric heterocycle as in pyrazole curcumin, which decreases its rotational freedom, leads to an improvement of its redox properties as well as its antioxidant activity

Chemical Equilibrium Models for the S3 State of the Oxygen-Evolving Complex of Photosystem II.

Science.gov (United States)

Isobe, Hiroshi; Shoji, Mitsuo; Shen, Jian-Ren; Yamaguchi, Kizashi

2016-01-19

We have performed hybrid density functional theory (DFT) calculations to investigate how chemical equilibria can be described in the S3 state of the oxygen-evolving complex in photosystem II. For a chosen 340-atom model, 1 stable and 11 metastable intermediates have been identified within the range of 13 kcal mol(-1) that differ in protonation, charge, spin, and conformational states. The results imply that reversible interconversion of these intermediates gives rise to dynamic equilibria that involve processes with relocations of protons and electrons residing in the Mn4CaO5 cluster, as well as bound water ligands, with concomitant large changes in the cluster geometry. Such proton tautomerism and redox isomerism are responsible for reversible activation/deactivation processes of substrate oxygen species, through which Mn-O and O-O bonds are transiently ruptured and formed. These results may allow for a tentative interpretation of kinetic data on substrate water exchange on the order of seconds at room temperature, as measured by time-resolved mass spectrometry. The reliability of the hybrid DFT method for the multielectron redox reaction in such an intricate system is also addressed.

3-Benzyl-4-ethyl-1H-1,2,4-triazole-5(4H)-thione.

Science.gov (United States)

Karczmarzyk, Zbigniew; Pitucha, Monika; Wysocki, Waldemar; Pachuta-Stec, Anna; Stańczuk, Andrzej

2013-02-01

The title compound, C(11)H(13)N(3)S, exists in the 5-thioxo tautomeric form. The benzene ring exhibits disorder with a refined ratio of 0.77 (2):0.23 (2) for components A and B with a common bridgehead C atom. The 1,2,4-triazole ring is essentially planar, with a maximum deviation of 0.002 (3) Å for the benzyl-substituted C atom, and forms dihedral angles of 88.94 (18) and 86.56 (49)° with the benzene rings of components A and B, respectively. The angle between the plane of the ethyl chain and the mean plane of 1,2,4-triazole ring is 88.55 (15)° and this conformation is stabilized by an intra-molecular C-H⋯S contact. In the crystal, pairs of N-H⋯S hydrogen bonds link mol-ecules into inversion dimers. π-π inter-actions are observed between the triazole and benzene rings, with centroid-centroid separations of 3.547 (4) and 3.544 (12) Å for components A and B, and slippages of 0.49 (6) and 0.58 (15) Å, respectively.

Role of keto–enol tautomerization in a chiral phosphoric acid catalyzed asymmetric thiocarboxylysis of meso-epoxide: a DFT study

KAUST Repository

Ajitha, Manjaly John; Huang, Kuo-Wei

2015-01-01

The mechanism of a chiral phosphoric acid catalyzed thiocarboxylysis of meso-epoxide was investigated by density functional theory (DFT) calculations (M06-2X). The nucleophilic ring opening of epoxide by thiobenzoic acid was found to proceed via a concerted termolecular transition state with a simultaneous dual proton transfer to yield the β-hydroxy thioester product. Electrostatic interactions together with the steric environment inside the chiral catalyst play an important role in determining the enantioselectivity of the reaction.

Role of keto–enol tautomerization in a chiral phosphoric acid catalyzed asymmetric thiocarboxylysis of meso-epoxide: a DFT study

KAUST Repository

Ajitha, Manjaly John

2015-09-15

The mechanism of a chiral phosphoric acid catalyzed thiocarboxylysis of meso-epoxide was investigated by density functional theory (DFT) calculations (M06-2X). The nucleophilic ring opening of epoxide by thiobenzoic acid was found to proceed via a concerted termolecular transition state with a simultaneous dual proton transfer to yield the β-hydroxy thioester product. Electrostatic interactions together with the steric environment inside the chiral catalyst play an important role in determining the enantioselectivity of the reaction.

Density functional and ab initio study of the tautomeric forms of 3-acetyl tetronic and 3-acetyl tetramic acids

International Nuclear Information System (INIS)

Skylaris, Chris-Kriton; Igglessi-Markopoulou, Olga; Detsi, Anastasia; Markopoulos, John

2003-01-01

We propose all the accessible paths of interconversion between the tautomers of 3-acetyl tetronic and 3-acetyl tetramic acids by performing calculations with the density functional B3LYP method and the ab initio MP2 method. Our findings clarify at the atomic level the mechanisms of the equilibria between these tautomers, a topic so far only partially understood on the basis of studies by nuclear magnetic resonance (NMR) spectroscopy. We show that thermal effects via relative Gibbs free energies ΔG must be taken into account in order to reach good quantitative agreement with the available experimental information on the ratios of the most stable tautomers. The calculated 1 H and 13 C chemical shifts are in agreement with the experimental values from NMR spectroscopy

Applied Biological and Physicochemical Activity of Isoquinoline Alkaloids: Oxoisoaporphine and Boldine

Directory of Open Access Journals (Sweden)

María Eliana Hidalgo

2012-09-01

Full Text Available The aim of this study was to determine the electronic influence of substituent groups and annelated rings such as oxazole-oxazinone on the physicochemical and photoprotection, antioxidant capacity, toxicity and singlet oxygen photosensitization biological properties of isoquinoline alkaloid frameworks. Thus, oxoisoaporphine derivatives 1–5 and 3-azaoxoisoaporphine (6, some of them with phenolic structures, did not present any antioxidant capacity, possibly either by formation of keto-enol tautomerism species or the formation of unstable free radicals. Due to the singlet oxygen quantum yields (FD near to unity, and greater photostability than phenalenone, oxoisoaporphines 4–6 may be considered as photosensitizers for singlet oxygen production and can be used as new universal study tools. The biological application as antibacterial agents is an important and possible tool in the study of compounds with low cytotoxicity and high reactivity in antineoplastic chemotherapy. On the other hand, when boldine and its annelated derivatives B1–4 are irradiated, a photoprotector effect is observed (SPF = 2.35, even after 30 minutes of irradiation. They also act as photoprotectors in cell fibroblast cultures. No hemolysis was detected for boldine hydrochloride and its salts without irradiation. In solutions irradiated before incubation (at concentrations over 200 ppm photoproducts were toxic to the nauplii of Artemia salina.

Chemical speciation and equilibria of some nucleic acid compounds and their iron(III) complexes

Science.gov (United States)

Masoud, Mamdouh S.; Abd El-Kaway, Marwa Y.; Hindawy, Ahmed M.; Soayed, Amina A.

The pH effect on electronic absorption spectra of some biologically active nucleic acid constituents have been studied at room temperature and the mechanism of ionization was explained. These compounds are of two categories (pyrimidines: [barbital; 5,5'-diethyl-barbituric acid], [SBA; 4,6-dihydroxy-2-mercapto-pyrimidin], [NBA; 5-nitro-2,4,6(1H,3H,5H)-pyrimidine trione] and [TU; 2,3-dihydro-2-thioxo-pyrimidin-4(1H)-one]) and (purines: [adenine; 6-amino purine], its [Schiff bases derived from adenine-acetylacetone; (Z)-4-(7H-purin-6-ylimino)pentan-2-one) and adenine-salicylaldehyde; 2-((7H-purin-6-ylimino) methyl) phenol] and its [Azo derived from adenine-resorcinol; 4-((7H-purin-6-yl)-diazenyl) benzene-1,3-diol]. The phenomena of tautomerization assigned different tautomers. Different spectrophotometric methods are applied to evaluate the pK's values that explained with their molecular structures. The interaction of Fe3+ with some selected pyrimidines (barbital, NBA and SBA) was explained using familiar six spectrophotometric methods. The data typified the existence of different absorbing species with the different stoichiometries 1:1, 1:2, 1:3 and 2:3. The stability constant of the complexes was computed. More approach was deduced to assign the existence of different species applying the distribution diagrams.

Q-mode curve resolution of UV-vis spectra for structural transformation studies of anthocyanins in acidic solutions

Energy Technology Data Exchange (ETDEWEB)

Marco, Paulo Henrique [Laboratorio de Quimiometria em Ciencias Naturais, Departamento de Quimica, Universidade Estadual de Londrina, Caixa Postal 6001, CEP 86051-970 Londrina, Parana (Brazil); Scarminio, Ieda Spacino [Laboratorio de Quimiometria em Ciencias Naturais, Departamento de Quimica, Universidade Estadual de Londrina, Caixa Postal 6001, CEP 86051-970 Londrina, Parana (Brazil)]. E-mail: ieda@qui.uel.br

2007-01-30

Chemometric analysis of ultraviolet-visible (UV-vis) spectra for pH values 1.0, 3.3, 5.3, and 6.9 was used to investigate the kinetics and the structural transformations of anthocyanins in extracts of calyces of hibiscus flowers of the Hibiscus acetosella Welw. ex Finicius for the first time. Six different species were detected: the quinoidal base (A), the flavylium cation (AH{sup +}), the pseudobase or carbinol pseudobase (B), cis-chalcone (C{sub C}), trans-chalcone (C{sub t}), and ionized cis-chalcone (C{sub C}{sup -}). Four equilibrium constant values were calculated using relative concentrations, hydration, pK{sub h}=2.60+/-0.01, tautomeric, K{sub T}=0.14+/-0.01, acid-base, pK{sub a}=4.24+/-0.04, and ionization of the cis-chalcone, pK{sub C{sub C}}=8.74+/-1.5x10{sup -2}. The calculated protonation rate of the tautomers is K{sub H{sup +}}=0.08+/-7.6x10{sup -3}. These constants are in excellent agreement with those measured previously in salt form. From a kinetic viewpoint, the situation encountered is interesting since the reported investigation is limited to visible light absorption in acid medium. These models have not been reported in the literature.

Indexing molecules with chemical graph identifiers.

Science.gov (United States)

Gregori-Puigjané, Elisabet; Garriga-Sust, Rut; Mestres, Jordi

2011-09-01

Fast and robust algorithms for indexing molecules have been historically considered strategic tools for the management and storage of large chemical libraries. This work introduces a modified and further extended version of the molecular equivalence number naming adaptation of the Morgan algorithm (J Chem Inf Comput Sci 2001, 41, 181-185) for the generation of a chemical graph identifier (CGI). This new version corrects for the collisions recognized in the original adaptation and includes the ability to deal with graph canonicalization, ensembles (salts), and isomerism (tautomerism, regioisomerism, optical isomerism, and geometrical isomerism) in a flexible manner. Validation of the current CGI implementation was performed on the open NCI database and the drug-like subset of the ZINC database containing 260,071 and 5,348,089 structures, respectively. The results were compared with those obtained with some of the most widely used indexing codes, such as the CACTVS hash code and the new InChIKey. The analyses emphasize the fact that compound management activities, like duplicate analysis of chemical libraries, are sensitive to the exact definition of compound uniqueness and thus still depend, to a minor extent, on the type and flexibility of the molecular index being used. Copyright © 2011 Wiley Periodicals, Inc.

Mechanisms of the Knoevenagel hetero Diels-Alder sequence in multicomponent reactions to dihydropyrans: experimental and theoretical investigations into the role of water.

Science.gov (United States)

Frapper, Gilles; Bachmann, Christian; Gu, Yanlong; Coval De Sousa, Rodolphe; Jérôme, François

2011-01-14

The role of water in a multicomponent domino reaction (MCR) involving styrene, 2,4-pentanedione, and formaldehyde was studied. Whereas anhydrous conditions produced no reaction, the MCR successfully proceeded in the presence of water, affording the targeted dihydropyran derivatives with good yield. The mechanism of this MCR (Knoevenagel hetero Diels-Alder sequence) was studied with and without explicit water molecules using the SMD continuum solvation model in combination with the B3LYP density functional and the 6-311++G** basis set to compute the water and acetone (aprotic organic solvent) solution Gibbs free energies. In the Knoevenagel step, we found that water acted as a proton relay to favor the formation of more flexible six-membered ring transition state structures both in concerted (direct H(2)O elimination) and stepwise (keto-enol tautomerization and dehydration) pathways. The inclusion of a water molecule in our model resulted in a significant decrease (-8.5 kcal mol(-1)ΔG(water)(‡)) of the direct water elimination activation barrier. Owing to the presence of water, all chemical steps involved in the MCR mechanism had activation free energies barriers lower than 39 kcal mol(-1) at 25 °C in aqueous solvent (ZPE corrected electronic energies barriers). Consequently, the MCR proceeded without the assistance of any catalyst.

Experimental evidence of high pressure decoupling between charge transport and structural dynamics in a protic ionic glass-former.

Science.gov (United States)

Wojnarowska, Z; Rams-Baron, M; Knapik-Kowalczuk, J; Połatyńska, A; Pochylski, M; Gapinski, J; Patkowski, A; Wlodarczyk, P; Paluch, M

2017-08-01

In this paper the relaxation dynamics of ionic glass-former acebutolol hydrochloride (ACB-HCl) is studied as a function of temperature and pressure by using dynamic light scattering and broadband dielectric spectroscopy. These unique experimental data provide the first direct evidence that the decoupling between the charge transport and structural relaxation exists in proton conductors over a wide T-P thermodynamic space, with the time scale of structural relaxation being constant at the liquid-glass transition (τ α  = 1000 s). We demonstrate that the enhanced proton transport, being a combination of intermolecular H + hopping between cation and anion as well as tautomerization process within amide moiety of ACB molecule, results in a breakdown of the Stokes-Einstein relation at ambient and elevated pressure with the fractional exponent k being pressure dependent. The dT g /dP coefficient, stretching exponent β KWW and dynamic modulus E a /ΔV # were found to be the same regardless of the relaxation processes studied. This is in contrast to the apparent activation volume parameter that is different when charge transport and structural dynamics are considered. These experimental results together with theoretical considerations create new ideas to design efficient proton conductors for potential electrochemical applications.

Multispectroscopic and Theoretical Exploration of the Comparative Binding Aspects of Bioflavonoid Fisetin with Triple- and Double-Helical Forms of RNA.

Science.gov (United States)

Bhuiya, Sutanwi; Haque, Lucy; Goswami, Rapti; Das, Suman

2017-12-14

The interactions of RNA triplex (U.A*U) and duplex (A.U) with naturally occurring flavonoid fisetin (FTN) have been examined at pH 7.0 using various spectroscopic, viscometric, and theoretical studies. Experimental observations showed that the ligand binds with both double- and triple-helical forms of RNA, although the binding affinity is greater for the triplex structure (5.94 × 10 6 M -1 ) compared to that for the duplex counterpart (1.0 × 10 5 M -1 ). Thermal melting experiments revealed that the Hoogsteen base-paired third strand of triplex was stabilized to a greater extent (∼14 °C) compared with the Watson-Crick base-paired second strand (∼4 °C) in the presence of FTN. From fluorimetric study, we observed that U.A*U and A.U primarily bind to the photoproduced tautomer of FTN in the excited state. Steady-state and time-resolved anisotropy measurements illustrate considerable modulations of the spectroscopic properties of the tautomeric FTN within the RNA environment. Viscometric, fluorescence quenching, and thermal melting studies all together support the mode of binding to be intercalation. Theoretical study explains the experimental absorption and emission (dual fluorescence) behavior of FTN along with the excited-state intramolecular proton transfer process.

In situ FT-IR spectroelectrochemical study of electrooxidation of pyridoxol on a gold electrode

International Nuclear Information System (INIS)

Wang Meiling; Zhang Youyu; Xie Qingji; Yao Shouzhuo

2005-01-01

The electrochemical oxidation of pyridoxol (PN) on a polycrystalline gold electrode was investigated by cyclic voltammetry and in situ Fourier transform infrared spectroscopy (FTIRS). In 0.1 M aqueous NaOH solution, the gold electrode showed a high catalytic activity for the irreversible oxidation process of PN. The individual ionic species and the major tautomeric equilibria of PN molecules in aqueous solutions were evidenced well from the pH-dependent attenuated total reflectance (ATR) spectra, and the results were in good agreement with the voltammetric observations. In situ single potential alteration infrared reflectance spectroscopy (SPAIRS) demonstrated that a lactone form of PN, rather than pyridoxal aldehyde, was likely formed, which was subsequently diffused into the thin layer solution and underwent hydrolysis slowly to pyridoxic acid (PA) as the final product. In addition, the adsorption of PN at Au electrode was characterized by in situ subtractively normalized interfacial Fourier transform infrared reflectance spectroscopy (SNIFTIRS) method, which revealed that the adsorption of deprotonated PN, via nitrogen atom in vertical configuration on electrode surface, occurred from -0.5 V versus Ag vertical bar AgCl vertical bar KCl(sat), which was much lower than the potential of PN electrooxidation observed from ca. 0 V

Disassembly of Bacterial Biofilms by the Self-Assembled Glycolipids Derived from Renewable Resources.

Science.gov (United States)

Prasad, Yadavali Siva; Miryala, Sandeep; Lalitha, Krishnamoorthy; Ranjitha, K; Barbhaiwala, Shehnaz; Sridharan, Vellaisamy; Maheswari, C Uma; Srinandan, C S; Nagarajan, Subbiah

2017-11-22

More than 80% of chronic infections of bacteria are caused by biofilms. It is also a long-term survival strategy of the pathogens in a nonhost environment. Several amphiphilic molecules have been used in the past to potentially disrupt biofilms; however, the involvement of multistep synthesis, complicated purification and poor yield still remains a major problem. Herein, we report a facile synthesis of glycolipid based surfactant from renewable feedstocks in good yield. The nature of carbohydrate unit present in glycolipid influence the ring chain tautomerism, which resulted in the existence of either cyclic structure or both cyclic and acyclic structures. Interestingly, these glycolipids self-assemble into gel in highly hydrophobic solvents and vegetable oils, and displayed foam formation in water. The potential application of these self-assembled glycolipids to disrupt preformed biofilm was examined against various pathogens. It was observed that glycolipid 6a disrupts Staphylococcus aureus and Listeria monocytogenes biofilm, while the compound 6c was effective in disassembling uropathogenic E. coli and Salmonella enterica Typhimurium biofilms. Altogether, the supramolecular self-assembled materials, either as gel or as surfactant solution could be potentially used for surface cleansing in hospital environments or the food processing industries to effectively reduce pathogenic biofilms.

Mechanistic Effects of Water on the Fe-Catalyzed Hydrodeoxygenation of Phenol. The Role of Brønsted Acid Sites

Energy Technology Data Exchange (ETDEWEB)

Hensley, Alyssa J. R. [The; amp, Linda Voiland School of Chemical Engineering and Bioengineering, ∥Department of Physics; Institute for Integrated Catalysis and §Fundamental and; Wang, Yong [The; amp, Linda Voiland School of Chemical Engineering and Bioengineering, ∥Department of Physics; Institute for Integrated Catalysis and §Fundamental and; Mei, Donghai [The; amp, Linda Voiland School of Chemical Engineering and Bioengineering, ∥Department of Physics; Institute for Integrated Catalysis and §Fundamental and; McEwen, Jean-Sabin [The; amp, Linda Voiland School of Chemical Engineering and Bioengineering, ∥Department of Physics; Institute for Integrated Catalysis and §Fundamental and

2018-01-30

A mechanistic understanding of the roles of water is essential for developing highly active and selective catalysts for hydrodeoxygenation (HDO) reactions since water is ubiquitous in such reaction systems. Here, we present a study for phenol HDO on Fe catalysts using density functional theory which examines the effect of water on three elementary pathways for phenol HDO using an explicit solvation model. The presence of water is found to significantly decrease activation barriers required by hydrogenation reactions via two pathways. First, the proton transfer in the hydrogen bonding network of the liquid water phase is nearly barrierless, which significantly promotes the direct through space tautomerization of phenol. Second, due to the high degree of oxophilicity on Fe, liquid water molecules are found to be easily dissociated into surface hydroxyl groups that can act as Brønsted acid sites. These sites dramatically promote hydrogenation reactions on the Fe surface. As a result, the hydrogen assisted dehydroxylation becomes the dominant phenol HDO pathway. This work provides new fundamental insights into aqueous phase HDO of biomass-derived oxygenates over Fe-based catalysts; e.g., the activity of Fe-based catalysts can be optimized by tuning the surface coverage of Brønsted acid sites via surface doping.

Construction of 6-thioguanine and 6-mercaptopurine carriers based on βcyclodextrins and gold nanoparticles.

Science.gov (United States)

Sierpe, R; Noyong, Michael; Simon, Ulrich; Aguayo, D; Huerta, J; Kogan, Marcelo J; Yutronic, N

2017-12-01

As a novel strategy to overcome some of the therapeutic disadvantages of 6-thioguanine (TG) and 6-mercaptopurine (MP), we propose the inclusion of these drugs in βcyclodextrin (βCD) to form the complexes βCD-TG and βCD-MP, followed by subsequent interaction with gold nanoparticles (AuNPs), generating the ternary systems: βCD-TG-AuNPs and βCD-MP-AuNPs. This modification increased their solubility and improved their stability, betting by a site-specific transport due to their nanometric dimensions, among other advantages. The formation of the complexes was confirmed using powder X-ray diffraction, thermogravimetric analysis and one and two-dimensional NMR. A theoretical study using DFT and molecular modelling was conducted to obtain the more stable tautomeric species of TG and MP in solution and confirm the proposed inclusion geometries. The deposition of AuNPs onto βCD-TG and βCD-MP via sputtering was confirmed by UV-vis spectroscopy. Subsequently, the ternary systems were characterized by TEM, FE-SEM and EDX to directly observe the deposited AuNPs and evaluate their sizes, size dispersion, and composition. Finally, the in vitro permeability of the ternary systems was studied using parallel artificial membrane permeability assay (PAMPA). Copyright © 2017 Elsevier Ltd. All rights reserved.

3-Benzyl-4-ethyl-1H-1,2,4-triazole-5(4H-thione

Directory of Open Access Journals (Sweden)

Zbigniew Karczmarzyk

2013-02-01

Full Text Available The title compound, C11H13N3S, exists in the 5-thioxo tautomeric form. The benzene ring exhibits disorder with a refined ratio of 0.77 (2:0.23 (2 for components A and B with a common bridgehead C atom. The 1,2,4-triazole ring is essentially planar, with a maximum deviation of 0.002 (3 Å for the benzyl-substituted C atom, and forms dihedral angles of 88.94 (18 and 86.56 (49° with the benzene rings of components A and B, respectively. The angle between the plane of the ethyl chain and the mean plane of 1,2,4-triazole ring is 88.55 (15° and this conformation is stabilized by an intramolecular C—H...S contact. In the crystal, pairs of N—H...S hydrogen bonds link molecules into inversion dimers. π–π interactions are observed between the triazole and benzene rings, with centroid–centroid separations of 3.547 (4 and 3.544 (12 Å for components A and B, and slippages of 0.49 (6 and 0.58 (15 Å, respectively.

Synthesis, Characterization, Tautomeric Structure and Solvatochromic Behavior of Novel 4-(5-Arylazo-2-Hydroxystyryl-1-Methylpyridinium Iodide as Potential Molecular Photoprobe

Directory of Open Access Journals (Sweden)

Farag Altalbawy

2016-12-01

Full Text Available A novel series of the title compound 4-(5-arylazo-2-hydroxystyryl-1-methylpyridinium iodide 6 has been synthesized via condensation reactions of the arylazosalicylaldehyde derivatives 4a–i with 1-methyl-picolinium iodide 5. The structures of the new arylazo compounds were characterized by 1H NMR, IR, mass spectroscopy, as well as spectral and elemental analyses. The electronic absorption spectra of arylazomerocyanine compounds 6 were measured in different buffer solutions and solvents. The pK′s and pK*′s in both the ground and excited states, respectively, were determined for the series and their correlations with the Hammett equation were examined. The results indicated that the title arylazomerocyanine dyes 6 exist in the azo form 6A in both ground and excited states. The substituent and solvent effects (solvatochromism of the title compound arylazomerocyanine dyes were determined using the Kamlet-Taft equation and subsequently discussed.

The role of the surrounding polarity on the phototautomerization process in a diazaaromatic compound: An UV–vis and NMR study

Energy Technology Data Exchange (ETDEWEB)

Reyman, Dolores, E-mail: dolores.reyman@uam.es [Departamento de Química Física Aplicada, Universidad Autónoma de Madrid, E-28049 (Spain); Montoro, Teresa [EUIT Forestales, Universidad Politécnica de Madrid, 28040 Madrid (Spain); Viñas, Montserrat H. [Departamento de Sistemas Inteligentes Aplicados, Universidad Politécnica de Madrid, E-28031 Madrid (Spain); Díaz-Oliva, Cristina [Departamento de Química Física Aplicada, Universidad Autónoma de Madrid, E-28049 (Spain); Tardajos, Gloria [Departamento de Química Física I, Universidad Complutense de Madrid, E-28040 Madrid (Spain)

2014-04-15

Fluorescence steady-state and decay measurements of the azaaromatic derivative norharmane were obtained in solvents with different polarities: dichloromethane (DCM) and acetonitrile (ACN), at different temperatures, in the absence and the presence of a donor/acceptor hydrogen bond such as acetic acid. 2D NOESY experiments confirmed that this compound forms a hydrogen-bonding cyclic complex with acetic acid in the ground state. This complex induced a phototautomeric equilibrium, which produced new emission bands at 400 and 500 nm. This tautomeric process was established only in the first excited state via a concerted proton–electron transfer. Indeed, the cyclic complex formed in the ground state evolved to a like-cation upon cooling from room temperature to 225 K, and a new emission band at 450 nm is observed. The fluorescence decay times confirmed these results. -- Highlights: • 2D NOESY experiments confirm that norharmane forms a hydrogen-bonding cyclic complex with acetic acid molecules • This complex induces a phototautomeric equilibrium via a concerted proton–electron transfer. • A monotonous transformation of the type OH···N→ O{sup δ−}···H···N{sup δ+}→ O{sup −}···HN{sup +} occurs when the temperature is lowered. • Resulting from this transformation, the four fluorescence bands observed at room temperature are converted into a single fluorescence band at 225 K.

2-{(E-[(2Z-2-(1,2-Dihydrophthalazin-1-ylidenehydrazinylidene]methyl}phenol

Directory of Open Access Journals (Sweden)

M. K. Prasanna

2013-10-01

Full Text Available The title compound, C15H12N4O, adopts an E conformation with respect to the azomethine bond and crystallizes in its hydrazinylidene tautomeric form. The dihedral angle between the ring systems is 15.98 (7°. The phenol O—H group forms an intramolecular O—H...N hydrogen bond. In the crystal, pairs of N—H...N and C—H...O hydrogen bonds link neighbouring molecules into centrosymmetric dimers. These dimers are interconnected by means of three types of π–π stacking interactions. One, with a centroid–centroid distance of 3.577 (1 Å [interplanar separation = 3.4673 (6 Å], connects adjacent molecules into centrosymmetric dimers. The other two interactions, on the outward facing sides of the dimers, are between phenol rings of neighboring molecules [centroid–centroid separation = 3.7907 (13 Å and interplanar separation = 3.5071 (8 Å], and between phthalazin units [centroid–centroid separation = 3.6001 (12 Å and interplanar separation = 3.4891 (7 Å]. In combination, the π–π interactions lead to the formation of infinite layers with molecules stacked along [0-11]. These layers are, in turn, connected with neighbouring layers through the N—H...N and C—H...O hydrogen bonds, yielding a three-dimensional supramolecular architecture.

Taxon- and Site-Specific Melatonin Catabolism

Directory of Open Access Journals (Sweden)

Rüdiger Hardeland

2017-11-01

Full Text Available Melatonin is catabolized both enzymatically and nonenzymatically. Nonenzymatic processes mediated by free radicals, singlet oxygen, other reactive intermediates such as HOCl and peroxynitrite, or pseudoenzymatic mechanisms are not species- or tissue-specific, but vary considerably in their extent. Higher rates of nonenzymatic melatonin metabolism can be expected upon UV exposure, e.g., in plants and in the human skin. Additionally, melatonin is more strongly nonenzymatically degraded at sites of inflammation. Typical products are several hydroxylated derivatives of melatonin and N1-acetyl-N2-formyl-5-methoxykynuramine (AFMK. Most of these products are also formed by enzymatic catalysis. Considerable taxon- and site-specific differences are observed in the main enzymatic routes of catabolism. Formation of 6-hydroxymelatonin by cytochrome P450 subforms are prevailing in vertebrates, predominantly in the liver, but also in the brain. In pineal gland and non-mammalian retina, deacetylation to 5-methoxytryptamine (5-MT plays a certain role. This pathway is quantitatively prevalent in dinoflagellates, in which 5-MT induces cyst formation and is further converted to 5-methoxyindole-3-acetic acid, an end product released to the water. In plants, the major route is catalyzed by melatonin 2-hydroxylase, whose product is tautomerized to 3-acetamidoethyl-3-hydroxy-5-methoxyindolin-2-one (AMIO, which exceeds the levels of melatonin. Formation and properties of various secondary products are discussed.

Theoretical modeling of the spectroscopic absorption properties of luciferin and oxyluciferin: A critical comparison with recent experimental studies

Energy Technology Data Exchange (ETDEWEB)

Anselmi, Massimiliano, E-mail: m.anselmi@caspur.it [Department of Chemistry, University of Rome ' La Sapienza' , P.le Aldo Moro 5, 00185 Rome (Italy); Marocchi, Simone [Department of Chemistry, University of Rome ' La Sapienza' , P.le Aldo Moro 5, 00185 Rome (Italy); Aschi, Massimiliano [Department of Chemistry, Chemical Engineering and Materials, University of L' Aquila, Via Vetoio (Coppito 1), 67100 Coppito, L' Aquila (Italy); Amadei, Andrea [Department of Chemistry, University of Rome ' Tor Vergata' , Via della Ricerca Scientifica 1, 00133 Rome (Italy)

2012-01-02

Highlights: Black-Right-Pointing-Pointer The calculated absorption spectra were compared with experimental data. Black-Right-Pointing-Pointer Shapes and absorption maxima were reproduced for luciferin and oxyluciferin spectra. Black-Right-Pointing-Pointer The effect of the solvent largely changes the electronic transition probabilities. Black-Right-Pointing-Pointer Higher excitations provide an important contribution to the main absorption peak. - Abstract: Firefly luciferin and its oxidated form, oxyluciferin, are two heterocyclic compounds involved in the enzymatic reaction, catalyzed by redox proteins called luciferases, which provides the bioluminescence in a wide group of arthropods. Whereas the electronic absorption spectra of D-luciferin in water at different pHs are known since 1960s, only recently reliable experimental electronic spectra of oxyluciferin have become available. In addition oxyluciferin is involved in a triple chemical equilibria (deprotonation of the two hydroxyl groups and keto-enol tautomerism of the 4-hydroxythiazole ring), that obligates to select during an experiment a predominant species, tuning pH or solvent polarity besides introducing chemical modifications. In this study we report the absorption spectra of luciferin and oxyluciferin in each principal chemical form, calculated by means of perturbed matrix method (PMM), which allowed us to successfully introduce the effect of the solvent on the spectroscopic absorption properties, and compare the result with available experimental data.

Synthesis and spectral characterization of mono- and binuclear copper(II) complexes derived from 2-benzoylpyridine-N4-methyl-3-thiosemicarbazone: Crystal structure of a novel sulfur bridged copper(II) box-dimer

Science.gov (United States)

Jayakumar, K.; Sithambaresan, M.; Aiswarya, N.; Kurup, M. R. Prathapachandra

2015-03-01

Mononuclear and binuclear copper(II) complexes of 2-benzoylpyridine-N4-methyl thiosemicarbazone (HL) were prepared and characterized by a variety of spectroscopic techniques. Structural evidence for the novel sulfur bridged copper(II) iodo binuclear complex is obtained by single crystal X-ray diffraction analysis. The complex [Cu2L2I2], a non-centrosymmetric box dimer, crystallizes in monoclinic C2/c space group and it was found to have distorted square pyramidal geometry (Addison parameter, τ = 0.238) with the square basal plane occupied by the thiosemicarbazone moiety and iodine atom whereas the sulfur atom from the other coordinated thiosemicarbazone moiety occupies the apical position. This is the first crystallographically studied system having non-centrosymmetrical entities bridged via thiolate S atoms with Cu(II)sbnd I bond. The tridentate thiosemicarbazone coordinates in mono deprotonated thionic tautomeric form in all complexes except in sulfato complex, [Cu(HL)(SO4)]·H2O (1) where it binds to the metal centre in neutral form. The magnetic moment values and the EPR spectral studies reflect the binuclearity of some of the complexes. The spin Hamiltonian and bonding parameters are calculated based on EPR studies. In all the complexes g|| > g⊥ > 2.0023 and the g values in frozen DMF are consistent with the dx2-y2 ground state. The thermal stabilities of some of the complexes were also determined.

Structural and kinetic characterization of two 4-oxalocrotonate tautomerases in Methylibium petroleiphilum strain PM1.

Science.gov (United States)

Terrell, Cassidy R; Burks, Elizabeth A; Whitman, Christian P; Hoffman, David W

2013-09-01

Methylibium petroleiphilum strain PM1 uses various petroleum products including the fuel additive methyl tert-butyl ether and straight chain and aromatic hydrocarbons as sole carbon and energy sources. It has two operons, dmpI and dmpII, that code for the enzymes in a pair of parallel meta-fission pathways. In order to understand the roles of the pathways, the 4-oxalocrotonate tautomerase (4-OT) isozyme from each pathway was characterized. Tautomerase I and tautomerase II have the lowest pairwise sequence identity (35%) among the isozyme pairs in the parallel pathways, and could offer insight into substrate preferences and pathway functions. The kinetic parameters of tautomerase I and tautomerase II were determined using 2-hydroxymuconate and 5-(methyl)-2-hydroxymuconate. Both tautomerase I and tautomerase II process the substrates, but with different efficiencies. Crystal structures were determined for both tautomerase I and tautomerase II, at 1.57 and 1.64Å resolution, respectively. The backbones of tautomerase I and tautomerase II are highly similar, but have distinct active site environments. The results, in combination with those for other structurally and kinetically characterized 4-OT isozymes, suggest that tautomerase I catalyzes the tautomerization of both 2-hydroxymuconate and alkyl derivatives, whereas tautomerase II might specialize in other aromatic hydrocarbon metabolites. Copyright © 2013 Elsevier Inc. All rights reserved.

Photoelectron spectroscopy of the 6-azauracil anion.

Science.gov (United States)

Chen, Jing; Buonaugurio, Angela; Dolgounitcheva, Olga; Zakrzewski, V G; Bowen, Kit H; Ortiz, J V

2013-02-14

We report the photoelectron spectrum of the 6-azauracil anion. The spectrum is dominated by a broad band exhibiting a maximum at an electron binding energy (EBE) of 1.2 eV. This spectral pattern is indicative of a valence anion. Our calculations were carried out using ab initio electron propagator and other many-body methods. Comparison of the anion and corresponding neutral of 6-azauracil with those of uracil shows that substituting a nitrogen atom for C-H at the C6 position of uracil gives rise to significant changes in the electronic structure of 6-azauracil versus that of uracil. The adiabatic electron affinity (AEA) of the canonical 6-azauracil tautomer is substantially larger than that of canonical uracil. Among the five tautomeric, 6-azauracil anions studied computationally, the canonical structure was found to be the most stable. The vertical detachment energies (VDE) of the canonical, valence-bound anion of 6-azauracil and its closest "very-rare" tautomer have been calculated. Electron propagator calculations on the canonical anion yield a VDE value that is in close agreement with the experimentally determined VDE value of 1.2 eV. The AEA value of 6-azauracil, assessed at the CCSD(T) level of theory to be 0.5 eV, corresponds with the EBE value of the onset of the experimental spectrum.

Structural, absorption, and molecular properties of o,o'-dihydroxyazo resorcinol dyes bearing an acryloyloxy group

Science.gov (United States)

Özkınalı, Sevil; Çavuş, M. Serdar; Ceylan, Abdullah; Gür, Mahmut

2017-12-01

To the best of our knowledge, this is the first study reporting the synthesis and characterization of o,o‧-dihydroxyazo dyes bearing an acryloyl group. The o,o‧-dihydroxyazo dyes were synthesized through coupling of resorcinol with the diazonium salts of 2-amino-4-methylphenol, 2-aminophenol, 2-amino-4-chlorophenol, and 2-amino-4-nitrophenol. Their acryloyl derivatives were synthesized using metallic sodium and acryloyl chloride under an inert atmosphere. Characterization of the compounds was conducted using infrared (IR), ultraviolet-visible (UV-vis), proton nuclear magnetic resonance (1H NMR), and carbon nuclear magnetic resonance (13C NMR) spectroscopic methods. The tautomerism of the synthesized compounds' was also evaluated. The results were compared with theoretical results obtained by density functional theory (DFT). The DFT calculations were performed to obtain ground-state optimized geometries and calculate the relevant electronic and chemical reactivity parameters. Furthermore, possible tautomers deduced from the UV-vis spectra were investigated using theoretical calculations. Both the IR and NMR spectral data showed that azo tautomers predominate in the solid state and DMSO solvent. The effects of pH, solvent, and substituent on the predominant tautomers were further investigated through UV-vis spectroscopy. The results indicate that hydrazone tautomers were dominant at pH 12 in dimethylformamide (DMF), whereas azo tautomers were dominant at pH 2 in EtOH or CHCl3.

Tautomerism provides a molecular explanation for the mutagenic properties of the anti-HIV nucleoside 5-aza-5,6-dihydro-2′-deoxycytidine

OpenAIRE

Li, Deyu; Fedeles, Bogdan I.; Singh, Vipender; Peng, Chunte Sam; Silvestre, Katherine J.; Simi, Allison K.; Simpson, Jeffrey H.; Tokmakoff, Andrei; Essigmann, John M.

2014-01-01

Unlike conventional antiviral therapy, lethal mutagenesis is a therapeutic strategy that exploits the high mutation rates of certain viruses. It works by intentionally increasing the viral mutation rate, causing excessive error accumulation and viral population collapse. The mutagenic nucleoside analog 5-aza-5,6-dihydro-2′-deoxycytidine (KP1212) is specifically designed to use lethal mutagenesis against HIV. The mechanism of KP1212 mutagenesis was proposed to involve tautomerism—the repositio...

Fluorescence of tautomeric forms of curcumin in different pH and biosurfactant rhamnolipids systems: Application towards on-off ratiometric fluorescence temperature sensing.

Science.gov (United States)

Moussa, Zeinab; Chebl, Mazhar; Patra, Digambara

2017-08-01

Medicinal properties of curcumin are widely getting realized. For its applicability as a hydrophobic drug molecule and food spice interaction of curcumin with rhamnolipids, a biosurfactant, bears importance. Here we have explored interaction of curcumin with rhamnolipids biosurfactant and its aggregation behavior. The impact of pH on critical micelle concentration (cmc) of rhamnolipids has been studied using fluorescence of curcumin and found that cmc of rhamnolipids increases with increase in pH of the medium. In acidic, neutral and slightly alkaline medium (pH8), at λ ex =355nm (for β-diketone form) curcumin undergoes excited state hydrogen transfer (ESHT) and emits solely from enol form both in the presence and absence of rhamnolipids, but first time we report that in extreme alkaline condition, at pH13, at λ ex =355nm curcumin emits from both β-diketone as well as enolic ESHT forms in absence of rhamnolipids but in the presence of rhamnolipids β-diketone is stabilized and the emission solely comes from β-diketone by completely revoking ESHT process. Fluorescence quenching by hydrophobic cetylpyridinium bromide confirms curcumin penetrates deep inside the hydrophobic pocket of rhamnolipid aggregates/micelle by reducing the distance between N + -atom of pyridinium ion and curcumin. On the other hand hydrophobic molecule like pyrene stays near to the Stern layer of rhamnolipids facilitating electron transfer from pyrene to N + -atom of pyridinium ion. Even in neutral condition, in the presence of rhamnolipids the β-diketone form, though in small proportions, can be stabilized in higher temperature in expense of enolic ESHT form, thus, offering an on off ratiometric fluorescence temperature sensing in solution, which bears significance as ratiometric probe molecules. Interaction of curcumin with rhamnolipids stabilizes curcumin in acidic, neutral and moderate alkaline condition but fails at extreme pH13. Copyright © 2017 Elsevier B.V. All rights reserved.

Calorimetric and computational studies for three nitroimidazole isomers

International Nuclear Information System (INIS)

Carvalho, Tânia M.T.; Amaral, Luísa M.P.F.; Morais, Victor M.F.; Ribeiro da Silva, Maria D.M.C.

2017-01-01

Highlights: • Energy of combustion of 4-nitroimidazole was measured by static bomb calorimetry. • Enthalpy of sublimation of 4-nitroimidazole was determined by Calvet microcalorimetry. • Gas-phase enthalpy of formation of 4-nitroimidazole derived from experimental measurements. • Gas-phase enthalpies of nitroimidazole isomers formation estimated from G3 calculations. - Abstract: In the present work, a combined experimental and computational thermochemical study of nitroimidazole isomers was carried out. The standard (p° = 0.1 MPa) molar enthalpy of combustion, in the crystalline phase, for 4-nitroimidazole was determined, at the temperature of 298.15 K, using a static bomb combustion calorimeter. Calvet microcalorimetry experiments were performed to measure its standard molar enthalpy of sublimation. The standard molar enthalpy of formation of 4-nitroimidazole, in the gaseous phase, at T = 298.15 K, (116.9 ± 2.9) kJ·mol −1 , has been derived from the corresponding standard molar enthalpy of formation in the crystalline phase and the standard molar enthalpy of sublimation. Computational studies for 4-nitroimidazole were performed to complement the experimental work. These were also extended to the 2- and 5-nitroimidazole isomers. The gas-phase enthalpies of formation were estimated from high level ab initio molecular orbital calculations, at the G3 level. Also investigated were the tautomeric equilibrium of 4(5)-nitroimidazole in the gaseous phase and it was concluded that the two tautomers are equally stable.

Synthesis and spectral characterization of mono- and binuclear copper(II) complexes derived from 2-benzoylpyridine-N⁴-methyl-3-thiosemicarbazone: crystal structure of a novel sulfur bridged copper(II) box-dimer.

Science.gov (United States)

Jayakumar, K; Sithambaresan, M; Aiswarya, N; Kurup, M R Prathapachandra

2015-03-15

Mononuclear and binuclear copper(II) complexes of 2-benzoylpyridine-N(4)-methyl thiosemicarbazone (HL) were prepared and characterized by a variety of spectroscopic techniques. Structural evidence for the novel sulfur bridged copper(II) iodo binuclear complex is obtained by single crystal X-ray diffraction analysis. The complex [Cu2L2I2], a non-centrosymmetric box dimer, crystallizes in monoclinic C2/c space group and it was found to have distorted square pyramidal geometry (Addison parameter, τ=0.238) with the square basal plane occupied by the thiosemicarbazone moiety and iodine atom whereas the sulfur atom from the other coordinated thiosemicarbazone moiety occupies the apical position. This is the first crystallographically studied system having non-centrosymmetrical entities bridged via thiolate S atoms with Cu(II)I bond. The tridentate thiosemicarbazone coordinates in mono deprotonated thionic tautomeric form in all complexes except in sulfato complex, [Cu(HL)(SO4)]·H2O (1) where it binds to the metal centre in neutral form. The magnetic moment values and the EPR spectral studies reflect the binuclearity of some of the complexes. The spin Hamiltonian and bonding parameters are calculated based on EPR studies. In all the complexes g||>g⊥>2.0023 and the g values in frozen DMF are consistent with the d(x2-y2) ground state. The thermal stabilities of some of the complexes were also determined. Copyright © 2014 Elsevier B.V. All rights reserved.

Electrochemical behavior of some new pyrimidine derivatives

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MUSTAFA LUTFU BERKEM

2004-09-01

Full Text Available Electrochemical reduction of two recently synthesized pyrimidine compounds, 1-amino-5-benzoyil-4-phenyl-1H-pyrimidine-2-one (I, and 1-amino-5-benzoil-4-phenyl-1H-pyrimidine-2-thione (II were investigated by cyclic volatmmetry at a hanging mercury drop electrode in aqueous methanol (36 % v/v and in non-aqueous methanol. A series of cathodic peaks without the corresponding anodic peaks were observed for I. As the pH of the solution was increased, some of the cathodic peaks overlapped resulting in the loss of the previously observed peaks. For II, three cathodic peaks and one anodic peak were observed in addition to those observed for I. The peak potentials shifted in the negative direction with increasing pH. This shift was measured over a large pH range (1.80 – 12.30 to determine the pKa values of the compounds. The acidity constants related to the amino groups were 4.80 and 9.80 for I and 5.50 and 9.80 for II. A thiol-thione tautomerization was observed for II, which was more pronounced in the non-aqueous methanol medium. The pK values for both protonation and deprotonation of the thiocarbonyl group were also determined. The pK values were 5.80 and 9.80 for protonation and deprotonation in aqueous methanol and 6.80 and 10.80 in non-aqueous methanol.

Physico-chemical state influences in vitro release profile of curcumin from pectin beads.

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Nguyen, An Thi-Binh; Winckler, Pascale; Loison, Pauline; Wache, Yves; Chambin, Odile

2014-09-01

Curcumin is a polyphenolic compound with diverse effects interesting to develop health benefit products but its formulation in functional foods or in food supplement is hampered by its poor water solubility and susceptibility to alkaline conditions, light, oxidation and heat. Encapsulation of curcumin could be a mean to overcome these difficulties. In this paper, curcumin was encapsulated by ionotropic gelation method in low methoxyl pectin beads associated with different surfactants: Solutol(®), Transcutol(®) and sodium caseinate. After encapsulation, physico-chemical properties of encapsulated curcumin such as its solubility, physical state, tautomeric forms and encapsulation efficiency as well as encapsulation yield were characterized. In vitro dissolution of curcumin from beads displayed different kinetic profiles according to bead composition due to different matrix network. As Solutol(®) was a good solvent for curcumin, the drug was present into amorphous form in these beads inducing a rapid release of curcumin in the simulated digestive fluids. In contrast, drug release was slower from sodium caseinate beads since curcumin was not totally dissolved during the manufacturing process. Moreover, the FLIM studies showed that a part of curcumin was encapsulated in caseinate micelles and that 34% of this drug was in keto form which may delay the curcumin release. The Transcutol beads showed also a slow drug release because of the low curcumin solubility and the high density of the matrix. Copyright © 2014 Elsevier B.V. All rights reserved.

Temperature- and moisture-dependent phase changes in crystal forms of barbituric acid

International Nuclear Information System (INIS)

Zencirci, Neslihan; Gstrein, Elisabeth; Langes, Christoph; Griesser, Ulrich J.

2009-01-01

The dihydrate of barbituric acid (BAc) and its dehydration product, form II were investigated by means of moisture sorption analysis, hot-stage microscopy, differential scanning calorimetry, thermogravimetry, solution calorimetry, IR- and Raman-spectroscopy as well as powder X-ray diffraction. The dihydrate desolvates already at and below 50% relative humidity (RH) at 25 deg. C whereas form II is stable up to 80% RH, where it transforms back to the dihydrate. The thermal dehydration of barbituric acid dihydrate (BAc-H2) is a single step, nucleation controlled process. The peritectic reaction of the hydrate was measured at 77 deg. C and a transformation enthalpy of Δ trs H H2-II = 17.3 kJ mol -1 was calculated for the interconversion between the hydrate and form II. An almost identical value of 17.0 kJ mol -1 was obtained from solution calorimetry in water as solvent (Δ sol H H2 = 41.5, Δ sol H II = 24.5 kJ mol -1 ). Additionally a high-temperature form (HT-form) of BAc, which is enantiotropically related to form II and unstable at ambient conditions has been characterized. Furthermore, we observed that grinding of BAc with potassium bromide (KBr) induces a tautomeric change. Therefore, IR-spectra recorded with KBr-discs usually display a mixture of tautomers, whereas the IR-spectra of the pure trioxo-form of BAc are obtained if alternative preparation techniques are used

Temperature- and moisture-dependent phase changes in crystal forms of barbituric acid

Energy Technology Data Exchange (ETDEWEB)

Zencirci, Neslihan; Gstrein, Elisabeth; Langes, Christoph [Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Innsbruck, Innrain 52, 6020 Innsbruck (Austria); Griesser, Ulrich J. [Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Innsbruck, Innrain 52, 6020 Innsbruck (Austria)], E-mail: ulrich.griesser@uibk.ac.at

2009-03-10

The dihydrate of barbituric acid (BAc) and its dehydration product, form II were investigated by means of moisture sorption analysis, hot-stage microscopy, differential scanning calorimetry, thermogravimetry, solution calorimetry, IR- and Raman-spectroscopy as well as powder X-ray diffraction. The dihydrate desolvates already at and below 50% relative humidity (RH) at 25 deg. C whereas form II is stable up to 80% RH, where it transforms back to the dihydrate. The thermal dehydration of barbituric acid dihydrate (BAc-H2) is a single step, nucleation controlled process. The peritectic reaction of the hydrate was measured at 77 deg. C and a transformation enthalpy of {delta}{sub trs}H{sub H2-II} = 17.3 kJ mol{sup -1} was calculated for the interconversion between the hydrate and form II. An almost identical value of 17.0 kJ mol{sup -1} was obtained from solution calorimetry in water as solvent ({delta}{sub sol}H{sub H2} = 41.5, {delta}{sub sol}H{sub II} = 24.5 kJ mol{sup -1}). Additionally a high-temperature form (HT-form) of BAc, which is enantiotropically related to form II and unstable at ambient conditions has been characterized. Furthermore, we observed that grinding of BAc with potassium bromide (KBr) induces a tautomeric change. Therefore, IR-spectra recorded with KBr-discs usually display a mixture of tautomers, whereas the IR-spectra of the pure trioxo-form of BAc are obtained if alternative preparation techniques are used.

Experimental and theoretical dipole moments of purines in their ground and lowest excited singlet states

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Aaron, Jean-Jacques; Diabou Gaye, Mame; Párkányi, Cyril; Cho, Nam Sook; Von Szentpály, László

1987-01-01

The ground-state dipole moments of seven biologically important purines (purine, 6-chloropurine, 6-mercaptopurine, hypoxanthine, theobromine, theophylline and caffeine) were determined at 25°C in acetic acid (all the above compounds with the exception of purine) and in ethyl acetate (purine, theophylline and caffeine). Because of its low solubility, it was not possible to measure the dipole moment of uric acid. The first excited singlet-state dipole moments were obtained on the basis of the Bakhshiev and Chamma—Viallet equations using the variation of the Stokes shift with the solvent dielectric constant-refractive index term. The theoretical dipole moments for all the purines listed above and including uric acid were calculated by combining the use of the PPP (π-LCI-SCF-MO) method for the π-contribution to the overall dipole moment with the σ-contribution obtained as a vector sum of the σbond moments and group moments. The experimental and theoretical values were compared with the data available in the literature for some of the purines under study. For several purines, the calculations were carried out for different tautomeric forms. Excited singlet-state dipole moments are smaller than the ground-state values by 0.8 to 2.2 Debye units for all purines under study with the exception of 6-chloropurine. The effects of the structure upon the ground- and excited-state dipole moments of the purines are discussed.

Electrochemistry of Phosphorous and Hypophosphorous Acid on a Pt electrode

International Nuclear Information System (INIS)

Prokop, M.; Bystron, T.; Bouzek, K.

2015-01-01

Highlights: • H 3 PO 3 and H 3 PO 2 oxidation on Pt electrode proceed at high overpotential. • H 3 PO 2 oxidation proceeds via H 3 PO 3 as intermediate. • H 3 PO 3 and H 3 PO 2 adsorb on Pt electrode, adsorption isotherms determined. • Adsorption is more pronounced at elevated temperature. • Tautomeric equilibria plays an important role in the acids behaviour. - Abstract: H 3 PO 4 is commonly used as a proton-conducting phase in high temperature proton exchange membrane fuel cell membranes. However, its reduction with hydrogen at elevated temperatures yields compounds like H 3 PO 3 and phosphorus. The aim of this work was to describe the basic electrochemical behaviour of H 3 PO 3 and H 3 PO 2 on a Pt electrode in diluted aqueous H 2 SO 4 solutions. The results show that adsorption of both phosphorus acids studied becomes important at an oxoacid bulk concentration around and below 10 mol dm −3 . Adsorption isotherms at 25 and 70 °C were determined for both acids. Unusually, the extent of adsorption increases with rising temperature. H 3 PO 3 is anodically oxidised on a bare Pt as well as on a PtO surface. H 3 PO 2 oxidation proceeds mainly on a PtO surface, with the intermediate product being H 3 PO 3 . High overvoltage around 1 V is characteristic of all anodic oxidation reactions occurring in the temperature range studied

Accurate and computationally efficient prediction of thermochemical properties of biomolecules using the generalized connectivity-based hierarchy.

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Sengupta, Arkajyoti; Ramabhadran, Raghunath O; Raghavachari, Krishnan

2014-08-14

In this study we have used the connectivity-based hierarchy (CBH) method to derive accurate heats of formation of a range of biomolecules, 18 amino acids and 10 barbituric acid/uracil derivatives. The hierarchy is based on the connectivity of the different atoms in a large molecule. It results in error-cancellation reaction schemes that are automated, general, and can be readily used for a broad range of organic molecules and biomolecules. Herein, we first locate stable conformational and tautomeric forms of these biomolecules using an accurate level of theory (viz. CCSD(T)/6-311++G(3df,2p)). Subsequently, the heats of formation of the amino acids are evaluated using the CBH-1 and CBH-2 schemes and routinely employed density functionals or wave function-based methods. The calculated heats of formation obtained herein using modest levels of theory and are in very good agreement with those obtained using more expensive W1-F12 and W2-F12 methods on amino acids and G3 results on barbituric acid derivatives. Overall, the present study (a) highlights the small effect of including multiple conformers in determining the heats of formation of biomolecules and (b) in concurrence with previous CBH studies, proves that use of the more effective error-cancelling isoatomic scheme (CBH-2) results in more accurate heats of formation with modestly sized basis sets along with common density functionals or wave function-based methods.

Saccharomyces cerevisiae Differential Functionalization of Presumed ScALT1 and ScALT2 Alanine Transaminases Has Been Driven by Diversification of Pyridoxal Phosphate Interactions

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Erendira Rojas-Ortega

2018-05-01

Full Text Available Saccharomyces cerevisiae arose from an interspecies hybridization (allopolyploidiza-tion, followed by Whole Genome Duplication. Diversification analysis of ScAlt1/ScAlt2 indicated that while ScAlt1 is an alanine transaminase, ScAlt2 lost this activity, constituting an example in which one of the members of the gene pair lacks the apparent ancestral physiological role. This paper analyzes structural organization and pyridoxal phosphate (PLP binding properties of ScAlt1 and ScAlt2 indicating functional diversification could have determined loss of ScAlt2 alanine transaminase activity and thus its role in alanine metabolism. It was found that ScAlt1 and ScAlt2 are dimeric enzymes harboring 67% identity and intact conservation of the catalytic residues, with very similar structures. However, tertiary structure analysis indicated that ScAlt2 has a more open conformation than that of ScAlt1 so that under physiological conditions, while PLP interaction with ScAlt1 allows the formation of two tautomeric PLP isomers (enolimine and ketoenamine ScAlt2 preferentially forms the ketoenamine PLP tautomer, indicating a modified polarity of the active sites which affect the interaction of PLP with these proteins, that could result in lack of alanine transaminase activity in ScAlt2. The fact that ScAlt2 forms a catalytically active Schiff base with PLP and its position in an independent clade in “sensu strictu” yeasts suggests this protein has a yet undiscovered physiological function.

Studies on activated cytostatic fluorouracil as photosensitizer: to use in eye tumor treatment

Science.gov (United States)

Pascu, Mihail-Lucian; Carstocea, Benone D.; Brezeanu, Mihail; Voicu, Letitia; Staicu, Angela; Gazdaru, Doina M.; Pascu, Ruxandra A.

2004-09-01

Hydroxypyrimidine 5-fluorouracil (5-FU) belongs to the cytostatics group known as antimetabolites. The effect of UV irradiation on 5-FU was investigated by absorption and fluorescence spectroscopy. The study of the photosensitizer properties of 5-FU was made since their effects could be enhanced by exposure to UV radiation at different doses. Solutions 2.5x10-4M in natural saline water (0.8% NaCl), irradiated with optical beams emitted by N2 laser and UV Hg classic lamp, were used. The 5-FU was chosen due to its strong absorption along a large spectral range which makes possible the fluorescence excitation in UV. The absorption spectra exhibit bands between 250 - 450 nm. The emission fluorescence was measured in the 400-550 nm spectral range, with λex=320 and 350 nm for samples irradiated with Hg lamp and with λex=360 nm for samples irradiated with N2 laser. The excitation fluorescence was measured in the spectral range 200-400 nm, with λem=440 nm for samples irradiated with N2 laser. The spectra reveal a fluorescence enhancement with the exposure time, with a maximum at 3 min due to the transformation of 5-FU molecule into a fluorescent tautomeric form. The destruction more rapid than usual of the neovascularisation was observed for conjunctive of rabbit eyes, when they are impregnated with 5-FU solution and exposed to incoherent UV and visible light.

Electronic structure and spectroscopy of nucleic acid bases: Ionization energies, ionization-induced structural changes, and photoelectron spectra

Energy Technology Data Exchange (ETDEWEB)

Bravaya, Ksenia B.; Kostko, Oleg; Dolgikh, Stanislav; Landau, Arie; Ahmed, Musahid; Krylov, Anna I.

2010-08-02

We report high-level ab initio calculations and single-photon ionization mass spectrometry study of ionization of adenine (A), thymine (T), cytosine (C) and guanine (G). For thymine and adenine, only the lowest-energy tautomers were considered, whereas for cytosine and guanine we characterized five lowest-energy tautomeric forms. The first adiabatic and several vertical ionization energies were computed using equation-of-motion coupled-cluster method for ionization potentials with single and double substitutions. Equilibrium structures of the cationic ground states were characterized by DFT with the {omega}B97X-D functional. The ionization-induced geometry changes of the bases are consistent with the shapes of the corresponding molecular orbitals. For the lowest-energy tautomers, the magnitude of the structural relaxation decreases in the following series G > C > A > T, the respective relaxation energies being 0.41, 0.32, 0.25 and 0.20 eV. The computed adiabatic ionization energies (8.13, 8.89, 8.51-8.67 and 7.75-7.87 eV for A,T,C and G, respectively) agree well with the onsets of the photoionization efficiency (PIE) curves (8.20 {+-} 0.05, 8.95 {+-} 0.05, 8.60 {+-} 0.05 and 7.75 {+-} 0.05 eV). Vibrational progressions for the S{sub 0}-D{sub 0} vibronic bands computed within double-harmonic approximation with Duschinsky rotations are compared with previously reported experimental photoelectron spectra.

Proton transfer in a short hydrogen bond caused by solvation shell fluctuations: an ab initio MD and NMR/UV study of an (OHO)(-) bonded system.

Science.gov (United States)

Pylaeva, Svetlana; Allolio, Christoph; Koeppe, Benjamin; Denisov, Gleb S; Limbach, Hans-Heinrich; Sebastiani, Daniel; Tolstoy, Peter M

2015-02-14

We present a joint experimental and quantum chemical study on the influence of solvent dynamics on the protonation equilibrium in a strongly hydrogen bonded phenol-acetate complex in CD2Cl2. Particular attention is given to the correlation of the proton position distribution with the internal conformation of the complex itself and with fluctuations of the aprotic solvent. Specifically, we have focused on a complex formed by 4-nitrophenol and tetraalkylammonium-acetate in CD2Cl2. Experimentally we have used combined low-temperature (1)H and (13)C NMR and UV-vis spectroscopy and showed that a very strong OHO hydrogen bond is formed with proton tautomerism (PhOH···(-)OAc and PhO(-)···HOAc forms, both strongly hydrogen bonded). Computationally, we have employed ab initio molecular dynamics (70 and 71 solvent molecules, with and without the presence of a counter-cation, respectively). We demonstrate that the relative motion of the counter-cation and the "free" carbonyl group of the acid plays the major role in the OHO bond geometry and causes proton "jumps", i.e. interconversion of PhOH···(-)OAc and PhO(-)···HOAc tautomers. Weak H-bonds between CH(CD) groups of the solvent and the oxygen atom of carbonyl stabilize the PhOH···(-)OAc type of structures. Breaking of CH···O bonds shifts the equilibrium towards PhO(-)···HOAc form.

Saccharomyces cerevisiae Differential Functionalization of Presumed ScALT1 and ScALT2 Alanine Transaminases Has Been Driven by Diversification of Pyridoxal Phosphate Interactions

Science.gov (United States)

Rojas-Ortega, Erendira; Aguirre-López, Beatriz; Reyes-Vivas, Horacio; González-Andrade, Martín; Campero-Basaldúa, Jose C.; Pardo, Juan P.; González, Alicia

2018-01-01

Saccharomyces cerevisiae arose from an interspecies hybridization (allopolyploidiza-tion), followed by Whole Genome Duplication. Diversification analysis of ScAlt1/ScAlt2 indicated that while ScAlt1 is an alanine transaminase, ScAlt2 lost this activity, constituting an example in which one of the members of the gene pair lacks the apparent ancestral physiological role. This paper analyzes structural organization and pyridoxal phosphate (PLP) binding properties of ScAlt1 and ScAlt2 indicating functional diversification could have determined loss of ScAlt2 alanine transaminase activity and thus its role in alanine metabolism. It was found that ScAlt1 and ScAlt2 are dimeric enzymes harboring 67% identity and intact conservation of the catalytic residues, with very similar structures. However, tertiary structure analysis indicated that ScAlt2 has a more open conformation than that of ScAlt1 so that under physiological conditions, while PLP interaction with ScAlt1 allows the formation of two tautomeric PLP isomers (enolimine and ketoenamine) ScAlt2 preferentially forms the ketoenamine PLP tautomer, indicating a modified polarity of the active sites which affect the interaction of PLP with these proteins, that could result in lack of alanine transaminase activity in ScAlt2. The fact that ScAlt2 forms a catalytically active Schiff base with PLP and its position in an independent clade in “sensu strictu” yeasts suggests this protein has a yet undiscovered physiological function. PMID:29867852

The Hydractinia echinata Test-System. III: Structure-Toxicity Relationship Study of Some Azo-, Azo-Anilide, and Diazonium Salt Derivatives

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Sergiu Adrian Chicu

2014-07-01

Full Text Available Structure-toxicity relationships for a series of 75 azo and azo-anilide dyes and five diazonium salts were developed using Hydractinia echinata (H. echinata as model species. In addition, based on these relationships, predictions for 58 other azo-dyes were made. The experimental results showed that the measured effectiveness Mlog(1/MRC50 does not depend on the number of azo groups or the ones corresponding to metobolites, but it is influenced by the number of anilide groups, as well as by the substituents’ positions within molecules. The conformational analysis pointed out the intramolecular hydrogen bonds, especially the simple tautomerization of quinoidic (STOH or aminoidic (STNH2 type. The effectiveness is strongly influenced by the “push-pull” electronic effect, specific to two hydroxy or amino groups separated by an azo moiety (double alternate tautomery, (DAT, to the –COOH or –SO3H groups which are located in ortho or para position with respect to the azo group. The levels of the lipophylic/hydrophilic, electronic and steric equilibriums, pointed out by the Mlog(1/MRC50 values, enabled the calculation of their average values Clog(1/MRC50 (“Köln model”, characteristic to one derivative class (class isotoxicity. The azo group reduction and the hydrolysis of the amido/peptidic group are two concurrent enzymatic reactions, which occur with different reaction rates and mechanisms. The products of the partial biodegradation are aromatic amines. No additive or synergic effects are noticed among them.

Subtle trade-off existing between (anti)aromaticity, push-pull interaction, keto-enol tautomerism, and steric hindrance when defining the electronic properties of conjugated structures.

Science.gov (United States)

Kleinpeter, Erich; Bölke, Ute; Koch, Andreas

2010-07-22

The spatial magnetic properties (through space NMR shieldings, TSNMRS) of conjugated structures (benzenoid/quinonoid keto/enol tautomers, 1,3-dihydroxyaryl-2-aldehydes, Don-pi-Acc chromophores with trade-off existing push-pull vs aromatic behavior) have been calculated by the GIAO perturbation method employing the nucleus independent chemical shift (NICS) concept, and visualized as iso-chemical-shielding surfaces (ICSS) of various size and direction. The TSNMRS values, thus obtained, can be successfully employed to quantify and visualize (anti)aromaticity and to identify readily hereby zwitterionic structures due to push-pull behavior of the compounds studied. In addition, the push-pull behavior was quantified by the quotient (pi*/pi) approach of the central partial C=C double bond.

BIO-ORGANIC CHEMISTRY QUARTERLY REPORT. June through August1963

Energy Technology Data Exchange (ETDEWEB)

Various

1963-10-02

This report covers the following titles: (1) The Effects of 8-Methyl Lipoic Acid on the Evolution of Oxygen and Reduction of Carbon Dioxide during Photosynthesis; (2) Further {sup 14}C and {sup 15}N Tracer Studies of Amino Acid Synthesis during Photosynthesis by Chlorella Pyrenoidosa; (3) Two-Dimensional High Voltage, Low-Temperature Paper Electrophoresis of {sup 14}C-Labeled Products of Photosynthesis with {sup 14}CO{sub 2}; (4) A Search for Enzymic and Nonenzymic Reactions Between Thiamine Derivatives and Sugar Phosphates; (5) The Cytochrome Content of Purified Spinach Chloroplast Lamellae; (6) The Osmium Tetroxide Fixation of Chloroplast Lamellae; (7) Kinetics of Exoenzymes and Applications to the Determination of the Sequence of Nucleic Acids; (8) Brain Biochemistry and Behavior in Rats; (9) Experiments on Classical Conditioning and Light Habituation in Planarians; (10) Operant Conditioning in Planarians; (11) Manganese Porphyrin Complexes; (12) EPR Studies of Some Complex Organic Solutions; (13) Transient Response of Light-induced Photosynthetic Electron Paramagnetic Resonance Signals: Rhodospirillum rubrum Chromatophores; (14) Studies of the Tautomerism of Amides; (15) Structure and Mechanism of Hydrolysis of the Product of Reaction of PZ05 and Ethyl Ether; (16) A Study of the Irradiation Products of Several Nitrones; (17) Biosynthesis of the Opium Alkaloids; (18) Synthesis of methyl-{beta}-D-thiogalactoside-{sup 35}S; (19) Effect of Acridine Orange and Visible Light on Thymine Dimer Formation and Disruption; (20) Some Aspects of the Radiation Chemistry of DNA; (21) Nuclear Magnetic Resonance; and (22) Studies on the Inhibition of the Photoreduction of FMN.

Carbonic anhydrase inhibitors. Comparison of chlorthalidone, indapamide, trichloromethiazide, and furosemide X-ray crystal structures in adducts with isozyme II, when several water molecules make the difference.

Science.gov (United States)

Temperini, Claudia; Cecchi, Alessandro; Scozzafava, Andrea; Supuran, Claudiu T

2009-02-01

Thiazide and high ceiling diuretics were recently shown to inhibit all mammalian isoforms of carbonic anhydrase (CA, EC 4.2.1.1) with a very different profile as compared to classical inhibitors, such as acetazolamide, methazolamide, and ethoxzolamide. Some of these structurally related compounds have a very different behavior against the widespread isozyme CA II, with chlorthalidone, trichloromethiazide, and furosemide being efficient inhibitors against CA II (K(I)s of 65-138 nM), whereas indapamide is a much weaker one (K(I) of 2520 nM). Furthermore, some of these diuretics are quite efficient (low nanomolar) inhibitors of other isoforms, for example, chlorthalidone against hCA VB, VII, IX, and XIII; indapamide against CA VII, IX, XII, and XIII, trichloromethiazide against CA VII and IX, and furosemide against CA I and XIV. Examining the four X-ray crystal structures of their CA II adducts, we observed several (2-3) active site water molecules interacting with the chlorthalidone, trichloromethiazide, and furosemide scaffolds which may be responsible for this important difference of activity. Indeed, indapamide bound to CA II has no interactions with active site water molecules. Chlorthalidone bound within the CA II active site is in an enolic (lactimic) tautomeric form, with the enolic OH also participating in two strong hydrogen bonds with Asn67 and a water molecule. The newly evidenced binding modes of these diuretics may be exploited for designing better CA II inhibitors as well as compounds with selectivity/affinity for various isoforms with medicinal chemistry applications.

Anti-Mycobacterial Evaluation of 7-Chloro-4-Aminoquinolines and Hologram Quantitative Structure–Activity Relationship (HQSAR Modeling of Amino–Imino Tautomers

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Marcelle L. F. Bispo

2017-06-01

Full Text Available In an ongoing research program for the development of new anti-tuberculosis drugs, we synthesized three series (A, B, and C of 7-chloro-4-aminoquinolines, which were evaluated in vitro against Mycobacterium tuberculosis (MTB. Now, we report the anti-MTB and cytotoxicity evaluations of a new series, D (D01–D21. Considering the active compounds of series A (A01–A13, B (B01–B13, C (C01–C07, and D (D01–D09, we compose a data set of 42 compounds and carried out hologram quantitative structure–activity relationship (HQSAR analysis. The amino–imino tautomerism of the 4-aminoquinoline moiety was considered using both amino (I and imino (II forms as independent datasets. The best HQSAR model from each dataset was internally validated and both models showed significant statistical indexes. Tautomer I model: leave-one-out (LOO cross-validated correlation coefficient (q2 = 0.80, squared correlation coefficient (r2 = 0.97, standard error (SE = 0.12, cross-validated standard error (SEcv = 0.32. Tautomer II model: q2 = 0.77, r2 = 0.98, SE = 0.10, SEcv = 0.35. Both models were externally validated by predicting the activity values of the corresponding test set, and the tautomer II model, which showed the best external prediction performance, was used to predict the biological activity responses of the compounds that were not evaluated in the anti-MTB trials due to poor solubility, pointing out D21 for further solubility studies to attempt to determine its actual biological activity.

Designing new catalytic C-C and C-N bond formations promoted by organoactinides

International Nuclear Information System (INIS)

Eisen, M.S.; Straub, T.; Haskel, A.

1998-01-01

Organoactinides of the type Cp 2 * AcMe 2 (Cp * =C 5 Me 5 ; Ac=Th; U) are active catalytic precursors for the oligomerization of terminal alkynes HC≡CR (R=alkyl, aryl, SiMe 3 ). The regioselectivity and the extent of oligomerization depend strongly on the alkyne substituent R, whereas the catalytic reactivity is similar for both organoactinides. Reaction with tert-butylacetylene yields regioselectively the E-2,4-disubstituted 1-buten-3-yne dimer whereas trimethylsilylacetylene is regioselective trimerized to the E,E-1,4,6-tris(trimethylsilyl)-1,3-hexa diene-5-yne, with small amounts (3-5%) of the corresponding E-2,4-disubstituted 1-buten-3-yne dimer. Oligomerization with less bulky alkyl and aryl substituted alkynes produces a mixture of higher oligomers with no regioselectivity. Using the Cp 2 * ThMe 2 catalyst, we have recently developed a strategic method to control the extent and in some cases the regioselectivity of the catalyzed oligomerization of nonbulky terminal alkynes to dimers and/or trimers. The metallocene catalytic precursors ensure the selective synthesis of small oligomers by the addition of specific amines. Catalytic ''tailoring'' to dimer and trimers can be achieved by using small or bulky amines, respectively. Kinetic and mechanistic data for the controlling experiments argue that the turnover-limiting step involves the acetylide actinide complex formation with the rapid insertion of the alkyne and protonolysis by the amine. The analog Cp 2 * UMe 2 in the presence of primary amines induce the selective C-N bond formation, producing enamines which are tautomerized to the corresponding imines. (orig.)

Chameleonic reactivity of vicinal diazonium salt of acetylenyl-9,10-anthraquinones: synthetic application toward two heterocyclic targets.

Science.gov (United States)

Stepanov, A A; Gornostaev, L M; Vasilevsky, S F; Arnold, E V; Mamatyuk, V I; Fadeev, D S; Gold, B; Alabugin, I V

2011-11-04

The nature of products in the diazotization of 1-amino-2-acetylenyl-9,10-anthraquinones strongly depends on the nature of substituents at both the alkyne and at the anthraquinone core. Donor substitution (NHAr, OH) at the fourth position stabilizes the diazonium salt at C1, decelerating electrophilic cyclization at the arylethynyl substituent at C2. This effect allows the replacement of the diazonium with azide group and subsequent closure into isoxazole ring with preservation of the alkyne. In contrast, electrophilic 5-exo-dig cyclizations to condensed pyrazoles is observed for the combination of donor substituents at the aryl alkyne moiety and an OAc substituent at C4. The latter process provides a new synthetic route to 3-ethynyl-[1,9-cd]isoxazol-6-ones that are difficult to access otherwise. DFT calculations suggest that donor substituents have only a minor effect on alkyne and diazonium polarization in the reactant but provide specific transition state stabilization by stabilizing the incipient vinyl cation. This analysis provides the first computational data on electrophilic 5-exo-dig cyclization in its parent form and the nucleophile-promoted version. This cyclization is a relatively fast but endothermic process that is rendered thermodynamically feasible by the enol-keto tautomerization with concomitant aromatization in the five-membered heteroaromatic ring. Computations suggest that the importance of nucleophilic assistance in the transition state for a relatively weak nucleophile such as water is minor because the energy gain due to the Lewis base coordination to the carbocationic center is more than compensated for by the unfavorable entropic term for the bimolecular proces.

Electrochemical and Density Functional Theory Study on the Reactivity of Fisetin and Its Radicals: Implications on in Vitro Antioxidant Activity

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Marković, Zoran S.; Mentus, Slavko V.; Dimitrić Marković, Jasmina M.

2009-12-01

Antioxidative properties of naturally occurring flavon-3-ol, fisetin, were examined by both cyclic voltammetry and quantum-chemical based calculations. The three voltametrically detectable consecutive steps, reflected the fisetin molecular structure, catecholic structural unit in the ring B, C3-OH, and C7-OH groups in the rings C and A. Oxidation potential values, used as quantitative parameter in determining its oxidation capability, indicated good antioxidative properties found with this molecule. Oxidation of the C3'C4' dixydroxy moiety at the B ring occurred first at the lowest positive potentials. The first oxidation step induced fast intramolecular transformations in which the C3 hydroxy group disappeared and the product of this transformation participated in the second oxidation step. The highest potential of oxidation was attributed to the oxidation of C7 hydroxy group. The structural and electronic features of fisetin were investigated at the B3LYP/6-311++G** level of theory. Particularly, the interest was focused on the C3' and C4'-OH sites in the B ring and on C3-OH site in the C ring. The calculated bond dissociation enthalpy values for all OH sites of fisetin clearly indicated the importance of the B ring and C3' and C4'-OH group. The importance of keto-enol tautomerism has also been considered. The analysis also included the Mulliken spin density distribution for the radicals formed after H removal on each OH site. The results showed the higher values of the BDE on the C7-OH and C3-OH sites.

Redetermined structure of gossypol (P3 polymorph

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Muhabbat Honkeldieva

2015-07-01

Full Text Available An improved crystal structure of the title compound, C30H30O8 (systematic name: 1,1′,6,6′,7,7′-hexahydroxy-5,5′-diisopropyl-3,3′-dimethyl[2,2′-binaphthalene]-8,8′-dicarbaldehyde, was determined based on modern CCD data. Compared to the previous structure [Talipov et al. (1985. Khim. Prirod. Soedin. (Chem. Nat. Prod., 6, 20–24], geometrical precision has been improved (typical C—C bond-distance s.u. = 0.002 Å in the present structure compared to 0.005 Å in the previous structure and the locations of several H atoms have been corrected. The gossypol molecules are in the aldehyde tautomeric form and the dihedral angle between the naphthyl fragments is 80.42 (4°. Four intramolecular O—H...O hydrogen bonds are formed. In the crystal, inversion dimers with graph-set motif R22(20 are formed by pairs of O—H...O hydrogen bonds; another pair of O—H...O hydrogen bonds with the same graph-set motif links the dimers into [001] chains. The packing of such chains in the crystal leads to the formation of channels (diameter = 5–8 Å propagating in the [101] direction. The channels presumably contain highly disordered solvent molecules; their contribution to the scattering was removed with the SQUEEZE [Spek (2015. Acta Cryst. C71, 9–18] routine in PLATON and the stated molecular mass, density etc., do not take them into account.

Synthesis and structure of 1,3-dimethyl-5-(p-sulfonamide-phenylazo)-6-aminouracil and its Ni(II) complex: Topological insights and investigation for noncovalent interactions

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Debnath, Diptanu; Roy, Subhadip; Purkayastha, Atanu; Bauzá, Antonio; Choudhury, Rupasree; Ganguly, Rakesh; Frontera, Antonio; Misra, Tarun Kumar

2017-08-01

The azo-derivative, 1,3-dimethyl-5-(p-sulfonamide-phenylazo)-6-aminouracil (HL) containing 6-aminouracil (a biomolecule) and sulfonamide functionality (commonly found in sulfa-drugs), and its Ni(II) complex, NiIIL2 were synthesized. Single-crystal X-ray diffraction studies show that the ligand (HL) consists of an E conformation about the azo-linkage with a nearly planar geometry and the complex possesses distorted square planar geometry. The H-bonded underlying networks of HL and NiIIL2 were topologically classified revealing distinct topological types, namely tts and hxl, respectively. Moreover, topology of molecular packings in HL and NiIIL2 has also been discussed. Density functional theory (DFT) calculations, at the M06-2X/def2TZVP level of theory, are employed to characterize a great variety of non-covalent interactions that explicitly show the importance of antiparallel stacking interactions established by π--π+ interactions and H-bonds in the self-assembled dimmers in HL and lp-π/C-H⋯π interactions in NiIIL2. The results of NMR and UV-vis spectroscopies evidence that the ligand exists in hydrazone-imine-keto (B) tautomeric form in solution. The ligand absorption bands consist of the overlapping bands of π→π* and n→π* transitions. The complex experiences electronic transitions that consist of basically ILCT in character with some sort of participation of the atomic d-orbitals of the nickel. The pKa value of the ligand is found to be 4.09.

Highly selective probe based on imine linkage for Zn{sup 2+} and HSO{sub 3}{sup −} in mixed aqueous media

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Kaur, Kamaljot; Chaudhary, Savita; Singh, Sukhjinder; Mehta, S.K., E-mail: skmehta@pu.ac.in

2015-04-15

A simple salicylaldehyde derived Schiff base N, N′- bis (p-chloro salicylidene)-1, 2- ethylenediamine (L) was synthesized and characterized. The receptor demonstrates simultaneous dual channel chromogenic and fluorogenic signaling towards HSO{sub 3}{sup −} and Zn{sup 2+} in mixed aqueous media. Solvatochromism was employed systematically for modulating its optoelectronic properties. The probe was successfully assessed to monitor HSO{sub 3}{sup −} detection via UV–vis spectroscopy. DFT calculations and {sup 1}H NMR spectroscopy further support the results based on shifting of equilibrium. Moreover, the sensor showed large fluorescence enhancement with blue-shift of 48 nm after addition of Zn{sup 2+}. The probe exhibits high selectivity over other competitive ions with high detection limit of 6.54×10{sup −5} M and 3.21×10{sup −6} M for HSO{sub 3}{sup −} and Zn{sup 2+}, respectively. Importantly, this is one of the rare reports in which Schiff base was utilized for the fabrication of chromogenic or fluorogenic sensor using solvent effect for multianalyte detection. - Highlights: • Easy synthesis of highly selective and sensitive Salicylideneaniline moiety. • Solvatochromism induced tautomerism between the enol-imine and keto-amine forms. • Computational studies revealing the effect of solvent on stability of NH form. • Discriminative detection of HSO{sub 3}{sup −} and Zn{sup 2+} by different spectroscopic techniques. • Optical feedbacks as absorption transitions with HSO{sub 3}{sup −} on bisulphite adduct formation. • Fluorescence enhancement for Zn{sup 2+} based on imine binding mechanism.

Structural investigation of nitrogen-linked saccharinate-tetrazole

Science.gov (United States)

Gómez-Zavaglia, A.; Ismael, A.; Cabral, L. I. L.; Kaczor, A.; Paixão, J. A.; Fausto, R.; Cristiano, M. L. S.

2011-09-01

The molecular structure of nitrogen-linked saccharinate-tetrazole, N-(1,1-dioxo-1,2-benzisothiazol-3-yl)-amine-1 H-tetrazole (BAT), was investigated in the crystalline state using X-ray crystallography and infrared and Raman spectroscopies, and isolated in argon matrix by infrared spectroscopy. Interpretation of the experimental results was supported by quantum chemical calculations undertaken at the DFT(B3LYP)/6-311++G(3df,3pd) level of theory. In the neat crystalline solid (space group C2/ c, a = 21.7493(3) Å, b = 8.85940(10) Å, c = 10.76900(10) Å, β = 103.3300(10) deg; Z = 8), BAT units exist in the (1 H)-tetrazole aminosaccharin tautomeric form, with the NH spacer establishing a hydrogen bond to the nitrogen in position-4 of the tetrazole group of a neighbour molecule, and the NH group of the tetrazole fragment forming a bifurcated H-bond to the saccharyl nitrogen of the same molecule and to one of the oxygen atoms of a second neighbour molecule. On the other hand, according to both the matrix isolation infrared studies and the theoretical calculations, the isolated BAT molecule exists preferentially as the (1 H)-tetrazole iminosaccharin tautomer, where the main stabilizing interaction is the intramolecular H-bond established between the NH group of the saccharyl ring and the tetrazole nitrogen atom in position 4. A detailed conformational analysis of the studied molecule and full assignment of the vibrational spectra for both the matrix-isolated compound and crystalline sample were undertaken.

Reaction pathways of proton transfer in hydrogen-bonded phenol-carboxylate complexes explored by combined UV-vis and NMR spectroscopy.

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Koeppe, Benjamin; Tolstoy, Peter M; Limbach, Hans-Heinrich

2011-05-25

Combined low-temperature NMR/UV-vis spectroscopy (UVNMR), where optical and NMR spectra are measured in the NMR spectrometer under the same conditions, has been set up and applied to the study of H-bonded anions A··H··X(-) (AH = 1-(13)C-2-chloro-4-nitrophenol, X(-) = 15 carboxylic acid anions, 5 phenolates, Cl(-), Br(-), I(-), and BF(4)(-)). In this series, H is shifted from A to X, modeling the proton-transfer pathway. The (1)H and (13)C chemical shifts and the H/D isotope effects on the latter provide information about averaged H-bond geometries. At the same time, red shifts of the π-π* UV-vis absorption bands are observed which correlate with the averaged H-bond geometries. However, on the UV-vis time scale, different tautomeric states and solvent configurations are in slow exchange. The combined data sets indicate that the proton transfer starts with a H-bond compression and a displacement of the proton toward the H-bond center, involving single-well configurations A-H···X(-). In the strong H-bond regime, coexisting tautomers A··H···X(-) and A(-)···H··X are observed by UV. Their geometries and statistical weights change continuously when the basicity of X(-) is increased. Finally, again a series of single-well structures of the type A(-)···H-X is observed. Interestingly, the UV-vis absorption bands are broadened inhomogeneously because of a distribution of H-bond geometries arising from different solvent configurations.

IR spectroscopy study of SBA-15 silicas functionalized with the ethylthiocarbamidepropyl groups and their interactions with Ag(I) and Hg(II) ions

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Melnyk, Inna V.; Nazarchuk, Galyna I.; Václavíková, Miroslava; Zub, Yuriy L.

2018-04-01

Mesoporous structure of silica is determined by the type of template, but the introduction of functional groups during the synthesis has additional influence. The structure of SBA-15 may be violated by the introduction of long functions, such as ≡Si(CH2)3NHC(=S)NHC2H5. These ethylthiocarbamidepropyl groups can form complexes with metal ions in thiol or thione tautomeric forms. We determined that the 2D hexagonal p6 mm structure is preserved for SBA-15 with thiourea groups at maximal TEOS:trifunctional silane ratio (mol) = 10:2, which was confirmed by TEM and by the presence of an intense reflex in the small-angle region of diffractograms of the final product. It was shown that the obtained sorbents possess high kinetic characteristics. The experimental data fit pseudo-second-order kinetic equation, but the rate constants depend on the content of functional groups in the surface layer. Template Pluronic P-123 defines the porosity of functional mesoporous silica materials even at increasing content of trifunctional silane in the initial solution. Infrared spectroscopy analysis showed that thione form of thiourea ligand is prevalent on the surface of pores of mesoporous samples. However, during the sorption of silver(I) ions, there are both thione and thiol forms on the surface. Thione form is transformed into thiol with increasing concentration of mercury(II) ions in the sorption solution. Adsorption experiments showed that the SBA-15 silicas functionalized with ethylthiocarbamidepropyl groups had high selectivity for silver(I) ions and could concentrate Ag(I) ions from metal ions mixture at pH 2.

Structural dualism in the zwitterionic 7-RR ' NH-nido-7,8,9-C3B8H10 tricarbollide series: An example of absolute tautomerism

Czech Academy of Sciences Publication Activity Database

Bakardjiev, Mario; Holub, Josef; Hnyk, Drahomír; Císařová, I.; Londesborough, Michael Geoffrey Stephen; Perelakin, D.S.; Štíbr, Bohumil

2005-01-01

Roč. 44, č. 38 (2005), s. 6222-6226 ISSN 1433-7851 R&D Projects: GA MŠk(CZ) LC523; GA ČR GA203/05/2646 Institutional research plan: CEZ:AV0Z40320502 Keywords : boron * carboranes * structural dualism Subject RIV: CA - Inorganic Chemistry Impact factor: 9.596, year: 2005

Validation of tautomeric and protomeric binding modes by free energy calculations. A case study for the structure based optimization of d-amino acid oxidase inhibitors

Science.gov (United States)

Orgován, Zoltán; Ferenczy, György G.; Steinbrecher, Thomas; Szilágyi, Bence; Bajusz, Dávid; Keserű, György M.

2018-02-01

Optimization of fragment size d-amino acid oxidase (DAAO) inhibitors was investigated using a combination of computational and experimental methods. Retrospective free energy perturbation (FEP) calculations were performed for benzo[d]isoxazole derivatives, a series of known inhibitors with two potential binding modes derived from X-ray structures of other DAAO inhibitors. The good agreement between experimental and computed binding free energies in only one of the hypothesized binding modes strongly support this bioactive conformation. Then, a series of 1-H-indazol-3-ol derivatives formerly not described as DAAO inhibitors was investigated. Binding geometries could be reliably identified by structural similarity to benzo[d]isoxazole and other well characterized series and FEP calculations were performed for several tautomers of the deprotonated and protonated compounds since all these forms are potentially present owing to the experimental pKa values of representative compounds in the series. Deprotonated compounds are proposed to be the most important bound species owing to the significantly better agreement between their calculated and measured affinities compared to the protonated forms. FEP calculations were also used for the prediction of the affinities of compounds not previously tested as DAAO inhibitors and for a comparative structure-activity relationship study of the benzo[d]isoxazole and indazole series. Selected indazole derivatives were synthesized and their measured binding affinity towards DAAO was in good agreement with FEP predictions.

Solution interactions of diclofenac sodium and meclofenamic acid sodium with hydroxypropyl methylcellulose (HPMC).

Science.gov (United States)

Pygall, Samuel R; Griffiths, Peter C; Wolf, Bettina; Timmins, Peter; Melia, Colin D

2011-02-28

Many pharmaceutical agents require formulation in order to facilitate their efficacious delivery. However, the interaction between the active species and the formulation additives has the potential to significantly influence the pharmocokinetics of the active. In this study, the solution interactions between hydroxypropyl methylcellulose (HPMC) with two non-steroidal anti-inflammatories - the sodium salts of diclofenac and meclofenamate - were investigated using tensiometric, rheological, NMR, neutron scattering and turbidimetric techniques. The two drugs behaved very differently-meclofenamate addition to HPMC solutions led to substantial increases in viscosity, a depression of the gel point and a marked reduction in the self-diffusion coefficient of the drug, whereas diclofenac did not induce these changes. Collectively, these observations are evidence of meclofenamate forming self-assembled aggregates on the HPMC, a phenomenon not observed with diclofenac Na. Any process that leads to aggregation on a nonionic polymer will not be strongly favoured when the aggregating species is charged. Thus, it is hypothesised that the distinction between the two drugs arises as a consequence of the tautomerism present in meclofenamate that builds electron density on the carbonyl group that is further stabilised by hydrogen bonding to the HPMC. This mechanism is absent in the diclofenac case and thus no interaction is observed. These studies propose for the first time a molecular basis for the observed often-unexpected, concentration-dependant changes in HPMC solution properties when co-formulated with different NSAIDs, and underline the importance of characterising such fundamental interactions that have the potential to influence drug release in solid HPMC-based dosage forms. Copyright © 2010 Elsevier B.V. All rights reserved.

RP-UHPLC-UV-ESI-MS/MS analysis of LPMO generated C4-oxidized gluco-oligosaccharides after non-reductive labeling with 2-aminobenzamide.

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Frommhagen, Matthias; van Erven, Gijs; Sanders, Mark; van Berkel, Willem J H; Kabel, Mirjam A; Gruppen, Harry

2017-08-07

Lytic polysaccharide monooxygenases (LPMOs) are able to cleave recalcitrant polysaccharides, such as cellulose, by oxidizing the C1 and/or C4 atoms. The analysis of the resulting products requires a variety of analytical techniques. Up to now, these techniques mainly focused on the identification of non-oxidized and C1-oxidized oligosaccharides. The analysis of C4-oxidized gluco-oligosaccharides is mostly performed by using high pressure anion exchange chromatography (HPAEC). However, the alkaline conditions used during HPAEC analysis lead to tautomerization of C4-oxidized gluco-oligosaccharides, which limits the use of this technique. Here, we describe the use of reverse phase-ultra high performance liquid chromatography (RP-UHPLC) in combination with non-reductive 2-aminobenzamide (2-AB) labeling. Non-reductive 2-AB labeling enabled separation of C4-oxidized gluco-oligosaccharides from their non-oxidized counterparts. Moreover, RP-UHPLC does not require buffered mobile phases, which reduce mass spectrometry (MS) sensitivity. The latter is seen as an advantage over other techniques such as hydrophilic interaction liquid chromatography and porous graphitized carbon coupled to MS. RP-UHPLC coupled to UV detection and mass spectrometry allowed the identification of both labeled non-oxidized and C4-oxidized oligosaccharides. Non-reductive labeling kept the ketone at the C4-position of LPMO oxidized oligosaccharides intact, while selective reducing agents such as sodium triacetoxyborohydride (STAB) reduced this ketone group. Our results show that RP-UHPLC-UV-ESI-MS in combination with non-reductively 2-AB labeling is a suitable technique for the separation and identification of LPMO-generated C4-oxidized gluco-oligosaccharides. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Collision induced dissociation of protonated N-nitrosodimethylamine by ion trap mass spectrometry: Ultimate carcinogens in gas phase

Science.gov (United States)

Kulikova, Natalia; Baker, Michael; Gabryelski, Wojciech

2009-12-01

Collision induced dissociation of protonated N-nitrosodimethylamine (NDMA) and isotopically labeled N-nitrosodimethyl-d6-amine (NDMA-d6) was investigated by sequential ion trap mass spectrometry to establish mechanisms of gas phase reactions leading to intriguing products of this potent carcinogen. The fragmentation of (NDMA + H+) occurs via two dissociation pathways. In the alkylation pathway, homolytic cleavage of the N-O bond of N-dimethyl, N'-hydroxydiazenium ion generates N-dimethyldiazenium distonic ion which reacts further by a CH3 radical loss to form methanediazonium ion. Both methanediazonium ion and its precursor are involved in ion/molecule reactions. Methanediazonium ion showed to be capable of methylating water and methanol molecules in the gas phase of the ion trap and N-dimethyldiazenium distonic ion showed to abstract a hydrogen atom from a solvent molecule. In the denitrosation pathway, a tautomerization of N-dimethyl, N'-hydroxydiazenium ion to N-nitrosodimethylammonium intermediate ion results in radical cleavage of the N-N bond of the intermediate ion to form N-dimethylaminium radical cation which reacts further through [alpha]-cleavage to generate N-methylmethylenimmonium ion. Although the reactions of NDMA in the gas phase are different to those for enzymatic conversion of NDMA in biological systems, each activation method generates the same products. We will show that collision induced dissociation of N-nitrosodiethylamine (NDEA) and N-nitrosodipropylamine (NDPA) is also a feasible approach to gain information on formation, stability, and reactivity of alkylating agents originating from NDEA and NDPA. Investigating such biologically relevant, but highly reactive intermediates in the condensed phase is hampered by the short life-times of these transient species.

Structures of the Class D Carbapenemase OXA-24 from Acinetobacter baumannii in Complex with Doripenem

Energy Technology Data Exchange (ETDEWEB)

Schneider, Kyle D.; Ortega, Caleb J.; Renck, Nicholas A.; Bonomo, Robert A.; Powers, Rachel A.; Leonard, David A. (Case Western); (Grand Valley)

2012-02-08

The emergence of class D {beta}-lactamases with carbapenemase activity presents an enormous challenge to health practitioners, particularly with regard to the treatment of infections caused by Gram-negative pathogens such as Acinetobacter baumannii. Unfortunately, class D {beta}-lactamases with carbapenemase activity are resistant to {beta}-lactamase inhibitors. To better understand the details of the how these enzymes bind and hydrolyze carbapenems, we have determined the structures of two deacylation-deficient variants (K84D and V130D) of the class D carbapenemase OXA-24 with doripenem bound as a covalent acyl-enzyme intermediate. Doripenem adopts essentially the same configuration in both OXA-24 variant structures, but varies significantly when compared to the non-carbapenemase class D member OXA-1/doripenem complex. The alcohol of the 6a hydroxyethyl moiety is directed away from the general base carboxy-K84, with implications for activation of the deacylating water. The tunnel formed by the Y112/M223 bridge in the apo form of OXA-24 is largely unchanged by the binding of doripenem. The presence of this bridge, however, causes the distal pyrrolidine/sulfonamide group to bind in a drastically different conformation compared to doripenem bound to OXA-1. The resulting difference in the position of the side-chain bridge sulfur of doripenem is consistent with the hypothesis that the tautomeric state of the pyrroline ring contributes to the different carbapenem hydrolysis rates of OXA-1 and OXA-24. These findings represent a snapshot of a key step in the catalytic mechanism of an important class D enzyme, and might be useful for the design of novel inhibitors.

Solution structure of the parvulin-type PPIase domain of Staphylococcus aureus PrsA – Implications for the catalytic mechanism of parvulins

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Koskela Harri

2009-03-01

Full Text Available Abstract Background Staphylococcus aureus is a Gram-positive pathogenic bacterium causing many kinds of infections from mild respiratory tract infections to life-threatening states as sepsis. Recent emergence of S. aureus strains resistant to numerous antibiotics has created a need for new antimicrobial agents and novel drug targets. S. aureus PrsA is a membrane associated extra-cytoplasmic lipoprotein which contains a parvulin-type peptidyl-prolyl cis-trans isomerase domain. PrsA is known to act as an essential folding factor for secreted proteins in Gram-positive bacteria and thus it is a potential target for antimicrobial drugs against S. aureus. Results We have solved a high-resolution solution structure of the parvulin-type peptidyl-prolyl cis-trans isomerase domain of S. aureus PrsA (PrsA-PPIase. The results of substrate peptide titrations pinpoint the active site and demonstrate the substrate preference of the enzyme. With detailed NMR spectroscopic investigation of the orientation and tautomeric state of the active site histidines we are able to give further insight into the structure of the catalytic site. NMR relaxation analysis gives information on the dynamic behaviour of PrsA-PPIase. Conclusion Detailed structural description of the S. aureus PrsA-PPIase lays the foundation for structure-based design of enzyme inhibitors. The structure resembles hPin1-type parvulins both structurally and regarding substrate preference. Even though a wealth of structural data is available on parvulins, the catalytic mechanism has yet to be resolved. The structure of S. aureus PrsA-PPIase and our findings on the role of the conserved active site histidines help in designing further experiments to solve the detailed catalytic mechanism.

Identification of ligand efficient, fragment-like hits from an HTS library: structure-based virtual screening and docking investigations of 2H- and 3H-pyrazolo tautomers for Aurora kinase A selectivity.

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Sarvagalla, Sailu; Singh, Vivek Kumar; Ke, Yi-Yu; Shiao, Hui-Yi; Lin, Wen-Hsing; Hsieh, Hsing-Pang; Hsu, John T A; Coumar, Mohane Selvaraj

2015-01-01

Furanopyrimidine 1 (IC50 = 273 nM, LE = 0.36, LELP = 10.28) was recently identified by high-throughput screening (HTS) of an in-house library (125,000 compounds) as an Aurora kinase inhibitor. Structure-based hit optimization resulted in lead molecules with in vivo efficacy in a mouse tumour xenograft model, but no oral bioavailability. This is attributed to "molecular obesity", a common problem during hit to lead evolution during which degradation of important molecular properties such as molecular weight (MW) and lipophilicity occurs. This could be effectively tackled by the right choice of hit compounds for optimization. In this regard, ligand efficiency (LE) and ligand efficiency dependent lipophilicity (LELP) indices are more often used to choose fragment-like hits for optimization. To identify hits with appropriate LE, we used a MW cut-off library. Next, structure-based virtual screening using software (Libdock and Glide) in the Aurora A crystal structure (PDB ID: 3E5A) was carried out, and the top scoring 18 compounds tested for Aurora A enzyme inhibition. This resulted in the identification of a novel tetrahydro-pyrazolo-isoquinoline hit 7 (IC50 = 852 nM, LE = 0.44, LELP = 8.36) with fragment-like properties suitable for further hit optimization. Moreover, hit 7 was found to be selective for Aurora A (Aurora B IC50 = 35,150 nM) and the possible reasons for selectivity investigated by docking two tautomeric forms (2H- and 3H-pyrazole) of 7 in Auroras A and B (PDB ID: 4AF3) crystal structures. This docking study shows that the major 3H-pyrazole tautomer of 7 binds in Aurora A stronger than in Aurora B.

Site-selective 13C labeling of proteins using erythrose

International Nuclear Information System (INIS)

Weininger, Ulrich

2017-01-01

NMR-spectroscopy enables unique experimental studies on protein dynamics at atomic resolution. In order to obtain a full atom view on protein dynamics, and to study specific local processes like ring-flips, proton-transfer, or tautomerization, one has to perform studies on amino-acid side chains. A key requirement for these studies is site-selective labeling with 13 C and/or 1 H, which is achieved in the most general way by using site-selectively 13 C-enriched glucose (1- and 2- 13 C) as the carbon source in bacterial expression systems. Using this strategy, multiple sites in side chains, including aromatics, become site-selectively labeled and suitable for relaxation studies. Here we systematically investigate the use of site-selectively 13 C-enriched erythrose (1-, 2-, 3- and 4- 13 C) as a suitable precursor for 13 C labeled aromatic side chains. We quantify 13 C incorporation in nearly all sites in all 20 amino acids and compare the results to glucose based labeling. In general the erythrose approach results in more selective labeling. While there is only a minor gain for phenylalanine and tyrosine side-chains, the 13 C incorporation level for tryptophan is at least doubled. Additionally, the Phe ζ and Trp η2 positions become labeled. In the aliphatic side chains, labeling using erythrose yields isolated 13 C labels for certain positions, like Ile β and His β, making these sites suitable for dynamics studies. Using erythrose instead of glucose as a source for site-selective 13 C labeling enables unique or superior labeling for certain positions and is thereby expanding the toolbox for customized isotope labeling of amino-acid side-chains.

Fast automated placement of polar hydrogen atoms in protein-ligand complexes

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Lippert Tobias

2009-08-01

Full Text Available Abstract Background Hydrogen bonds play a major role in the stabilization of protein-ligand complexes. The ability of a functional group to form them depends on the position of its hydrogen atoms. An accurate knowledge of the positions of hydrogen atoms in proteins is therefore important to correctly identify hydrogen bonds and their properties. The high mobility of hydrogen atoms introduces several degrees of freedom: Tautomeric states, where a hydrogen atom alters its binding partner, torsional changes where the position of the hydrogen atom is rotated around the last heavy-atom bond in a residue, and protonation states, where the number of hydrogen atoms at a functional group may change. Also, side-chain flips in glutamine and asparagine and histidine residues, which are common crystallographic ambiguities must be identified before structure-based calculations can be conducted. Results We have implemented a method to determine the most probable hydrogen atom positions in a given protein-ligand complex. Optimality of hydrogen bond geometries is determined by an empirical scoring function which is used in molecular docking. This allows to evaluate protein-ligand interactions with an established model. Also, our method allows to resolve common crystallographic ambiguities such as as flipped amide groups and histidine residues. To ensure high speed, we make use of a dynamic programming approach. Conclusion Our results were checked against selected high-resolution structures from an external dataset, for which the positions of the hydrogen atoms have been validated manually. The quality of our results is comparable to that of other programs, with the advantage of being fast enough to be applied on-the-fly for interactive usage or during score evaluation.

Analysis of the enzymatic formation of citral in the glands of sweet basil.

Science.gov (United States)

Iijima, Yoko; Wang, Guodong; Fridman, Eyal; Pichersky, Eran

2006-04-15

Basil glands of the Sweet Dani cultivar contain high levels of citral, a mixture of geranial and its cis-isomer neral, as well as low levels of geraniol and nerol. We have previously reported the identification of a cDNA from Sweet Dani that encodes an enzyme responsible for the formation of geraniol from geranyl diphosphate in the glands, and that these glands cannot synthesize nerol directly from geranyl diphosphate. Here, we report the identification of two basil cDNAs encoding NADP+-dependent dehydrogenases that can use geraniol as the substrate. One cDNA, designated CAD1, represents a gene whose expression is highly specific to gland cells of all three basil cultivars examined, regardless of their citral content, and encodes an enzyme with high sequence similarity to known cinnamyl alcohol dehydrogenases (CADs). The enzyme encoded by CAD1 reversibly oxidizes geraniol to produce geranial (which reversibly isomerizes to neral via keto-enol tautomerization) at half the efficiency compared with its activity with cinnamyl alcohol. CAD1 does not use nerol and neral as substrates. A second cDNA, designated GEDH1, encodes an enzyme with sequence similarity to CAD1 that is capable of reversibly oxidizing geraniol and nerol in equal efficiency, and prolonged incubation of geraniol with GEDH1 in vitro produces not only geranial and neral, but also nerol. GEDH1 is also active, although at a lower efficiency, with cinnamyl alcohol. However, GEDH1 is expressed at low levels in glands of all cultivars compared with its expression in leaves. These and additional data presented indicate that basil glands may contain additional dehydrogenases capable of oxidizing geraniol.

Using a Fluorescent Cytosine Analogue tC[superscript o] To Probe the Effect of the Y567 to Ala Substitution on the Preinsertion Steps of dNMP Incorporation by RB69 DNA Polymerase

Energy Technology Data Exchange (ETDEWEB)

Xia, Shuangluo; Beckman, Jeff; Wang, Jimin; Konigsberg, William H. (Yale)

2012-10-10

Residues in the nascent base pair binding pocket (NBP) of bacteriophage RB69 DNA polymerase (RB69pol) are responsible for base discrimination. Replacing Tyr567 with Ala leads to greater flexibility in the NBP, increasing the probability of misincorporation. We used the fluorescent cytosine analogue, 1,3-diaza-2-oxophenoxazine (tC{sup o}), to identify preinsertion step(s) altered by NBP flexibility. When tC{sup o} is the templating base in a wild-type (wt) RB69pol ternary complex, its fluorescence is quenched only in the presence of dGTP. However, with the RB69pol Y567A mutant, the fluorescence of tC{sup o} is also quenched in the presence of dATP. We determined the crystal structure of the dATP/tC{sup o}-containing ternary complex of the RB69pol Y567A mutant at 1.9 {angstrom} resolution and found that the incoming dATP formed two hydrogen bonds with an imino-tautomerized form of tC{sup o}. Stabilization of the dATP/tC{sup o} base pair involved movement of the tC{sup o} backbone sugar into the DNA minor groove and required tilting of the tC{sup o} tricyclic ring to prevent a steric clash with L561. This structure, together with the pre-steady-state kinetic parameters and dNTP binding affinity, estimated from equilibrium fluorescence titrations, suggested that the flexibility of the NBP, provided by the Y567 to Ala substitution, led to a more favorable forward isomerization step resulting in an increase in dNTP binding affinity.

Human tRNA^Lys3_UUU Is Pre-Structured by Natural Modifications for Cognate and Wobble Codon Binding through Keto-Enol Tautomerism

Energy Technology Data Exchange (ETDEWEB)

Vendeix, Franck A.P.; Murphy, IV, Frank V.; Cantara, William A.; Leszczy,; #324; ska, Gra; #380; yna,; Gustilo, Estella M.; Sproat, Brian; Malkiewicz, Andrzej; Agris, Paul F. [Cornell; (NCSU); (Poland); (Integrated DNA); (SUNYA)

2013-09-27

Human tRNA^Lys3_UUU (htRNA^Lys3_UUU) decodes the lysine codons AAA and AAG during translation and also plays a crucial role as the primer for HIV-1 (human immunodeficiency virus type 1) reverse transcription. The posttranscriptional modifications 5-methoxycarbonylmethyl-2-thiouridine (mcm⁵s²U₃₄), 2-methylthio-N⁶-threonylcarbamoyladenosine (ms²t⁶A₃₇), and pseudouridine (Ψ₃₉) in the tRNA's anticodon domain are critical for ribosomal binding and HIV-1 reverse transcription. To understand the importance of modified nucleoside contributions, we determined the structure and function of this tRNA's anticodon stem and loop (ASL) domain with these modifications at positions 34, 37, and 39, respectively (hASL^Lys3_UUU-mcm⁵s²U₃₄;ms²t⁶A₃₇;Ψ₃₉). Ribosome binding assays in vitro revealed that the hASL^Lys3_UUU-mcm⁵s²U₃₄;ms²t⁶A₃₇;Ψ₃₉ bound AAA and AAG codons, whereas binding of the unmodified ASL^Lys3_UUU was barely detectable. The UV hyperchromicity, the circular dichroism, and the structural analyses indicated that Ψ₃₉ enhanced the thermodynamic stability of the ASL through base stacking while ms²t⁶A₃₇ restrained the anticodon to adopt an open loop conformation that is required for ribosomal binding. The NMR-restrained molecular-dynamics-derived solution structure revealed that the modifications provided an open, ordered loop for codon binding. The crystal structures of the hASL^Lys3_UUU-mcm⁵s²U₃₄;ms²t⁶A₃₇;Ψ₃₉ bound to the 30S ribosomal subunit with each codon in the A site showed that the modified nucleotides mcm⁵s²U₃₄ and ms²t⁶A₃₇ participate in the stability of the anticodon–codon interaction. Importantly, the mcm⁵s²U₃₄·G₃ wobble base pair is in the Watson–Crick geometry, requiring unusual hydrogen bonding to G in which mcm⁵s²U₃₄ must shift from the keto to the enol form. The results unambiguously demonstrate that modifications pre-structure the anticodon as a key prerequisite for efficient and accurate recognition of cognate and wobble codons.

InChIKey collision resistance: an experimental testing

Directory of Open Access Journals (Sweden)

Pletnev Igor

2012-12-01

Full Text Available Abstract InChIKey is a 27-character compacted (hashed version of InChI which is intended for Internet and database searching/indexing and is based on an SHA-256 hash of the InChI character string. The first block of InChIKey encodes molecular skeleton while the second block represents various kinds of isomerism (stereo, tautomeric, etc.. InChIKey is designed to be a nearly unique substitute for the parent InChI. However, a single InChIKey may occasionally map to two or more InChI strings (collision. The appearance of collision itself does not compromise the signature as collision-free hashing is impossible; the only viable approach is to set and keep a reasonable level of collision resistance which is sufficient for typical applications. We tested, in computational experiments, how well the real-life InChIKey collision resistance corresponds to the theoretical estimates expected by design. For this purpose, we analyzed the statistical characteristics of InChIKey for datasets of variable size in comparison to the theoretical statistical frequencies. For the relatively short second block, an exhaustive direct testing was performed. We computed and compared to theory the numbers of collisions for the stereoisomers of Spongistatin I (using the whole set of 67,108,864 isomers and its subsets. For the longer first block, we generated, using custom-made software, InChIKeys for more than 3 × 1010 chemical structures. The statistical behavior of this block was tested by comparison of experimental and theoretical frequencies for the various four-letter sequences which may appear in the first block body. From the results of our computational experiments we conclude that the observed characteristics of InChIKey collision resistance are in good agreement with theoretical expectations.

Structural basis for the enzymatic formation of the key strawberry flavor compound 4-hydroxy-2,5-dimethyl-3(2H)-furanone.

Science.gov (United States)

Schiefner, André; Sinz, Quirin; Neumaier, Irmgard; Schwab, Wilfried; Skerra, Arne

2013-06-07

The last step in the biosynthetic route to the key strawberry flavor compound 4-hydroxy-2,5-dimethyl-3(2H)-furanone (HDMF) is catalyzed by Fragaria x ananassa enone oxidoreductase (FaEO), earlier putatively assigned as quinone oxidoreductase (FaQR). The ripening-induced enzyme catalyzes the reduction of the exocyclic double bond of the highly reactive precursor 4-hydroxy-5-methyl-2-methylene-3(2H)-furanone (HMMF) in a NAD(P)H-dependent manner. To elucidate the molecular mechanism of this peculiar reaction, we determined the crystal structure of FaEO in six different states or complexes at resolutions of ≤1.6 Å, including those with HDMF as well as three distinct substrate analogs. Our crystallographic analysis revealed a monomeric enzyme whose active site is largely determined by the bound NAD(P)H cofactor, which is embedded in a Rossmann-fold. Considering that the quasi-symmetric enolic reaction product HDMF is prone to extensive tautomerization, whereas its precursor HMMF is chemically labile in aqueous solution, we used the asymmetric and more stable surrogate product 2-ethyl-4-hydroxy-5-methyl-3(2H)-furanone (EHMF) and the corresponding substrate (2E)-ethylidene-4-hydroxy-5-methyl-3(2H)-furanone (EDHMF) to study their enzyme complexes as well. Together with deuterium-labeling experiments of EDHMF reduction by [4R-(2)H]NADH and chiral-phase analysis of the reaction product EHMF, our data show that the 4R-hydride of NAD(P)H is transferred to the unsaturated exocyclic C6 carbon of HMMF, resulting in a cyclic achiral enolate intermediate that subsequently becomes protonated, eventually leading to HDMF. Apart from elucidating this important reaction of the plant secondary metabolism our study provides a foundation for protein engineering of enone oxidoreductases and their application in biocatalytic processes.

Synthesis of azo pyridone dyes

Directory of Open Access Journals (Sweden)

Mijin Dušan Ž.

2011-01-01

Full Text Available Over 50% of all colorants which are used nowdays are azo dyes and pigments, and among them arylazo pyridone dyes (and pigments have became of interest in last several decades due to the high molar extinction coefficient, and the medium to high light and wet fastness properties. They find application generally as disperse dyes. The importance of disperse dyes increased in the 1970s and 1980s due to the use of polyester and nylon as the main synthetic fibers. Also, disperse dyes were used rapidly since 1970 in inks for the heat-transfer printing of polyester. The main synthetic route for the preparation of azo dyes is coupling reaction between an aromatic diazo compound and a coupling component. Of all dyes manufactured, about 60% are produced by this reaction. Arylazo pyridone dyes can be prepared from pyridone moiety as a coupling component, where substituent can be on nitrogen, and diazonim salts which can be derived from different substituted anilines or other heterocyclic derivatives. In addition, arylazo dyes containing pyridone ring can be prepared from arylazo diketones or arylazo ketoesters (obtained by coupling β-diketones or β-ketoesters with diazonim salts by condensation with cyanoacetamide. Disazo dyes can be prepared by tetrazotizing a dianiline and coupling it with a pyridone or by diazotizing aniline and coupling it with a dipyridone. Trisazo dyes can be also prepared by diazotizing of aniline and coupling it with a tripyridone or by hexazotizing a trianiline and coupling it with a pyridone. The main goal of this paper is to give a brief review on the synthesis of arylazo pyridone dyes due to the lack of such reviews. In addition, some properties of arylazo pyridone dyes as light fastness and azo-hydrazon tautomerism are disccused.

The PARP inhibitor PJ-34 sensitizes cells to UVA-induced phototoxicity by a PARP independent mechanism.

Science.gov (United States)

Lakatos, Petra; Hegedűs, Csaba; Salazar Ayestarán, Nerea; Juarranz, Ángeles; Kövér, Katalin E; Szabó, Éva; Virág, László

2016-08-01

A combination of a photosensitizer with light of matching wavelength is a common treatment modality in various diseases including psoriasis, atopic dermatitis and tumors. DNA damage and production of reactive oxygen intermediates may impact pathological cellular functions and viability. Here we set out to investigate the role of the nuclear DNA nick sensor enzyme poly(ADP-ribose) polymerase 1 in photochemical treatment (PCT)-induced tumor cell killing. We found that silencing PARP-1 or inhibition of its enzymatic activity with Veliparib had no significant effect on the viability of A431 cells exposed to 8-methoxypsoralen (8-MOP) and UVA (2.5J/cm(2)) indicating that PARP-1 is not likely to be a key player in either cell survival or cell death of PCT-exposed cells. Interestingly, however, another commonly used PARP inhibitor PJ-34 proved to be a photosensitizer with potency equal to 8-MOP. Irradiation of PJ-34 with UVA caused changes both in the UV absorption and in the 1H NMR spectra of the compound with the latter suggesting UVA-induced formation of tautomeric forms of the compound. Characterization of the photosensitizing effect revealed that PJ-34+UVA triggers overproduction of reactive oxygen species, induces DNA damage, activation of caspase 3 and caspase 8 and internucleosomal DNA fragmentation. Cell death in this model could not be prevented by antioxidants (ascorbic acid, trolox, glutathione, gallotannin or cell permeable superoxide dismutase or catalase) but could be suppressed by inhibitors of caspase-3 and -8. In conclusion, PJ-34 is a photosensitizer and PJ-34+UVA causes DNA damage and caspase-mediated cell death independently of PARP-1 inhibition. Copyright © 2016 Elsevier B.V. All rights reserved.

Liquid-crystalline dendrimer Cu(II) complexes and Cu(0) nanoclusters based on the Cu(II) complexes: An electron paramagnetic resonance investigation

Science.gov (United States)

Domracheva, N. E.; Mirea, A.; Schwoerer, M.; Torre-Lorente, L.; Lattermann, G.

2007-07-01

New nanostructured materials, namely, the liquid-crystalline copper(II) complexes that contain poly(propylene imine) dendrimer ligands of the first (ligand 1) and second (ligand 2) generations and which have a columnar mesophase and different copper contents (x = Cu/L), are investigated by EPR spectroscopy. The influence of water molecules and nitrate counterions on the magnetic properties of complex 2 (x = 7.3) is studied. It is demonstrated that water molecules can extract some of the copper ions from dendrimer complexes and form hexaaqua copper complexes with free ions. The dimer spectra of fully hydrated complex 2 (x = 7.3) are observed at temperatures T dendrimer copper(II) complex. The temperature-induced valence tautomerism attended by electron transport is revealed for the first time in blue dendrimer complexes 1 (x = 1.9) with a dimer structure. The activation energy for electron transport is estimated to be 0.35 meV. The coordination of the copper ion site (NO4) and the structural arrangement of green complexes 1 (x = 1.9) in the columnar mesophase are determined. Complexes of this type form linear chains in which nitrate counterions serve as bridges between copper centers. It is revealed that green complexes 1 (x = 1.9) dissolved in isotropic inert solvents can be oriented in the magnetic field (B 0 = 8000 G). The degree of orientation of these complexes is rather high (S z = 0.76) and close to that of systems with a complete ordering (S z = 1) in the magnetic field. Copper(0) nanoclusters prepared by reduction of complex 2 (x = 7.3) in two reducing agents (NaBH4, N2H4 · H2O) are examined. A model is proposed for a possible location of Cu(0) nanoclusters in a dendrimer matrix.

Oscillatory transenantiomerization of the selected 2-arylpropionic acid (2-APAs) in vitro as a spontaneous phenomenon

International Nuclear Information System (INIS)

Sajewicz, M.; Alska, T.K.

2006-01-01

In this paper, we summarize the results of our earlier investigations on an attempted enantioseparation of the selected 2-arylpropionic acids (2-APAs) by means of the chiral thin layer chromatography (TLC). These results have been originally presented in a series of the research papers published in several chromatography journals. In the current article it was reminded that the prolonged storage of the investigated 2-APAs in the aqueous and the non-aqueous solutions results in an oscillatory change of the respective retardation factor (RF) and the specific rotation (alfa)/sub P/) values. An assumption is introduced as to the chemical nature of the observed phenomenon. It is assumed that the observed oscillations are due to the repeated structural inversion (in our study labelled as oscillatory transenantiomerization) of one enantiomer to its respective antimer. One attempts to at least roughly explain the molecular mechanism of transenantiomerization either by keto-enol tautomerism, or by formation of an intermediate enolic anion, any of these two reaction mechanisms possible only in the basic environment. Then one reflects on the most probable mechanism responsible for the oscillatory nature of the observed structural inversion. It is concluded that the oscillations could be due to an enhanced viscosity of the investigated 2-APA solutions (as compared with those of the respective pure solvents) and/or due to the molecular self-organization within these solutions, resulting in anisotropic properties thereof. Finally, it is concluded that an ultimate explanation of the observed oscillatory transenantiomerization of the selected 2-APAs could probably be offered by the Brusselator-type kinetic model implemented with the diffusion term. In the last section of this paper, argumentation is presented strongly in favour of this particular model and against any alternative speculation as to the supramolecular nature of the observed oscillatory phenomena. (author)

Providing theoretical data for detection of four formamidic acid isomers in astrophysical media

Science.gov (United States)

Vichietti, R. M.; da Silva, A. B. F.; Haiduke, R. L. A.

2018-03-01

We present a theoretical study, so that molecular data (geometrical parameters, vibrational frequencies, infrared intensities, electronic energies, enthalpies, and Gibbs energies) of four formamidic acid (FA) isomers (labeled here as FA1, FA2, FA3, and FA4) and formamide (HCONH2) are obtained from CCSD/cc-pVTZ, CCSD/aug-cc-pVTZ, CCSD/cc-pVQZ, and CCSD(T)/cc-pVTZ calculations. Furthermore, on the basis of insufficient or even lacking theoretical and experimental results in the literature, we employed the aforementioned theory levels to determine benchmark values of dipole moments and rotational constants for these four FA isomers in order to contribute for their detection in astrophysical environments. Besides, we provide for the first time data about forward and reverse rate constants (200-4000 K) and Arrhenius' parameters for each interconversion reaction between pairs of FA isomers as well as for the tautomeric process involving FA4 and formamide, which were calculated from a Complete Basis Set (CBS) extrapolation equation obtained at CCSD/cc-pVTZ optimized geometries. Our kinetic analysis indicated a faster interconversion between the FA structures in comparison with the FA4 ↔ HCONH2 process, suggesting that these isomers could co-exist in astrophysical media. Finally, we estimated that these isomers may be detected with relative abundances, [FAx]/[HCONH2] (x = 1, 2, 3, and 4), between ∼0.01 and ∼0.1% in astrophysical sources at chemical equilibrium conditions and temperatures around 1000 K. However, these ratios can become as high as ∼1, ∼3, and ∼5%, respectively, in hotter regions with temperatures around 2000, 3000, and 4000 K (expected, for example, in massive star-forming regions).

Integrated preservation and sample clean up procedures for studying water ingestion by recreational swimmers via urinary biomarker determination.

Science.gov (United States)

Cantú, Ricardo; Shoemaker, Jody A; Kelty, Catherine A; Wymer, Larry J; Behymer, Thomas D; Dufour, Alfred P; Magnuson, Matthew L

2017-08-22

The use of cyanuric acid as a biomarker for ingestion of swimming pool water may lead to quantitative knowledge of the volume of water ingested during swimming, contributing to a better understanding of disease resulting from ingestion of environmental contaminants. When swimming pool water containing chlorinated cyanurates is inadvertently ingested, cyanuric acid is excreted quantitatively within 24 h as a urinary biomarker of ingestion. Because the volume of water ingested can be quantitatively estimated by calculation from the concentration of cyanuric acid in 24 h urine samples, a procedure for preservation, cleanup, and analysis of cyanuric acid was developed to meet the logistical demands of large scale studies. From a practical stand point, urine collected from swimmers cannot be analyzed immediately, given requirements of sample collection, shipping, handling, etc. Thus, to maintain quality control to allow confidence in the results, it is necessary to preserve the samples in a manner that ensures as quantitative analysis as possible. The preservation and clean-up of cyanuric acid in urine is complicated because typical approaches often are incompatible with the keto-enol tautomerization of cyanuric acid, interfering with cyanuric acid sample preparation, chromatography, and detection. Therefore, this paper presents a novel integration of sample preservation, clean-up, chromatography, and detection to determine cyanuric acid in 24 h urine samples. Fortification of urine with cyanuric acid (0.3-3.0 mg/L) demonstrated accuracy (86-93% recovery) and high reproducibility (RSD urine suggested sufficient cyanuric acid stability for sample collection procedures, while longer holding times suggested instability of the unpreserved urine. Preserved urine exhibited a loss of around 0.5% after 22 days at refrigerated storage conditions of 4 °C. Published by Elsevier B.V.

The fate of benzotriazole pollutants in an urban oxic intergranular aquifer.

Science.gov (United States)

Trček, Branka; Žigon, Dušan; Zidar, Vlasta Kramarič; Auersperger, Primož

2017-12-26

Benzotriazoles (BTs) are considered as Contaminants of Emerging Concern (CECs); however, information about their fate in aquifers continues to be absent. This was the focus of the present study, which provides the first evidence for relevant BTs' degradation products (BTTPs) in urban aquifers that may impact the groundwater quality. The mechanisms and biotransformation pathways of BTs were investigated in an oxic intergranular medium. The BTs and BTTPs were identified and quantified by gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-mass spectrometry (LC-MS) analytical techniques based on reference standards and internal materials. The major transformation products were identified as 2-methyl-2H-benzotriazole (2-MeBT) for the degradation of 1H-benzotriazole (BT) and as 2,4-dimethyl-2H-benzotriazole (2,4-dMeBT) and 1,4-dimethyl-1H-benzotriazole (1,4-dMeBT) for the degradation of 4-methyl-1H-benzotriazole (4-MeBT), and most probably also 5-methyl-1H-benzotriazole (5-MeBT). The leakage of wastewater pipelines is most probably the source of BTs. Sediments with a lower hydraulic conductivity give rise to perched aquifer conditions that lead to the temporal storage of leaking effluents and presumably the majority of BTs' transformation processes via methylation and tautomerization. The most stable BTTPs entered the saturated zone of the aquifer, where they prevailed. Concentrations up to 1500 ng L -1 were measured for the 2,4-dMeBT, which suggest a contamination risk for groundwater that is or may be used as a source for drinking water in the case of a constant input of pollutant loads from sewer systems. Copyright © 2017 Elsevier Ltd. All rights reserved.

Site-selective {sup 13}C labeling of proteins using erythrose

Energy Technology Data Exchange (ETDEWEB)

Weininger, Ulrich, E-mail: ulrich.weininger@physik.uni-halle.de [Lund University, Department of Biophysical Chemistry, Center for Molecular Protein Science (Sweden)

2017-03-15

NMR-spectroscopy enables unique experimental studies on protein dynamics at atomic resolution. In order to obtain a full atom view on protein dynamics, and to study specific local processes like ring-flips, proton-transfer, or tautomerization, one has to perform studies on amino-acid side chains. A key requirement for these studies is site-selective labeling with {sup 13}C and/or {sup 1}H, which is achieved in the most general way by using site-selectively {sup 13}C-enriched glucose (1- and 2-{sup 13}C) as the carbon source in bacterial expression systems. Using this strategy, multiple sites in side chains, including aromatics, become site-selectively labeled and suitable for relaxation studies. Here we systematically investigate the use of site-selectively {sup 13}C-enriched erythrose (1-, 2-, 3- and 4-{sup 13}C) as a suitable precursor for {sup 13}C labeled aromatic side chains. We quantify {sup 13}C incorporation in nearly all sites in all 20 amino acids and compare the results to glucose based labeling. In general the erythrose approach results in more selective labeling. While there is only a minor gain for phenylalanine and tyrosine side-chains, the {sup 13}C incorporation level for tryptophan is at least doubled. Additionally, the Phe ζ and Trp η2 positions become labeled. In the aliphatic side chains, labeling using erythrose yields isolated {sup 13}C labels for certain positions, like Ile β and His β, making these sites suitable for dynamics studies. Using erythrose instead of glucose as a source for site-selective {sup 13}C labeling enables unique or superior labeling for certain positions and is thereby expanding the toolbox for customized isotope labeling of amino-acid side-chains.

Theoretical investigation of the photophysics of methyl salicylate isomers

Science.gov (United States)

Massaro, Richard D.; Blaisten-Barojas, Estela

2011-10-01

The photophysics of methyl salicylate (MS) isomers has been studied using time-dependent density functional theory and large basis sets. First electronic singlet and triplet excited states energies, structure, and vibrational analysis were calculated for the ketoB, enol, and ketoA isomers. It is demonstrated that the photochemical pathway involving excited state intramolecular proton transfer (ESIPT) from the ketoB to the enol tautomer agrees well with the dual fluorescence in near-UV (from ketoB) and blue (from enol) wavelengths obtained from experiments. Our calculation confirms the existence of a double minimum in the excited state pathway along the O-H-O coordinate corresponding to two preferred energy regions: (1) the hydrogen belongs to the OH moiety and the structure of methyl salicylate is ketoB; (2) the hydrogen flips to the closest carboxyl entailing electronic rearrangement and tautomerization to the enol structure. This double well in the excited state is highly asymmetric. The Franck-Condon vibrational overlap is calculated and accounts for the broadening of the two bands. It is suggested that forward and backward ESIPT through the barrier separating the two minima is temperature-dependent and affects the intensity of the fluorescence as seen in experiments. When the enol fluoresces and returns to its ground state, a barrier-less back proton transfer repopulates the ground state of methyl salicylate ketoB. It is also demonstrated that the rotamer ketoA is not stable in an excited state close to the desired emission wavelength. This observation eliminates the conjecture that the near-UV emission of the dual fluorescence originates from the ketoA rotamer. New experimental results for pure MS in the liquid state are reported and theoretical results compared to them.

Theoretical studies of the tautomerism in 3-(2-R-Phenylhydrazono)-naphthalene- 1,2,4-triones: synthesis of copper(II) complexes and studies of antibacterial and antitumor activities

Energy Technology Data Exchange (ETDEWEB)

Francisco, Acacio I.; Vargas, Maria D.; Fragoso, Thais P.; Carneiro, J. Walkimar de M.; Silva, Fernando de C. da; Ferreira, Vitor F., E-mail: mdvargas@vm.uff.b [Universidade Federal Fluminense (UFF), Niteroi, RJ (Brazil). Inst. de Quimica; Casellato, Annelise [Universidade Federal do Rio de Janeiro (UFRJ), RJ (Brazil). Inst. de Quimica; Barbosa, Jussara P. [Instituto Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, RJ (Brazil); Pessoa, Claudia; Costa-Lotufo, Leticia V.; Marinho Filho, Jose D.B.; Moraes, Manoel O. de [Universidade Federal do Ceara (UFC), Fortaleza, CE (Brazil). Dept. de Fisiologia e Farmacologia; Mangrich, Antonio S. [Universidade Federal do Parana (UFPR), Curitiba, PR (Brazil). Dept. de Quimica

2010-07-01

DFT calculations using the B3LYP and PBE1PBE functionals with the standard 6-31G(d) and 6-311+G(2d,p) basis sets were carried out for the 3-(2-phenylhydrazone)-naphthalene-1,2,4-trione system in solution (dmso) and in the gas phase, and showed the keto-hydrazone forms (rotamers Ia and Ib) to be more stable than the enol-azo forms (rotamers IIa and IIb, by about 14 kcal mol-1) and III (by approximately 6 kcal mol-1), independently of the nature of the substituent in the phenylene ring. These results were confirmed by spectroscopic data on the derivatives HL1-HL13, obtained from 2-hydroxy-1,4-naphthoquinone and arylamines (R = 4-OMe, 4-N{sub 2}-C{sub 6}H{sub 5}, 4-Cl, 4-I, 3-I, 2-I, 4-COOH, 3-COOH, 4-CN, 3-CN, 4-NO{sub 2}, 3-NO{sub 2}, 2-NO{sub 2}). The in vitro antitumor (against SF-295, HCT-8, MDAMB-435 and HL-60 cancer cell lines) and antibacterial activities (Bacillus cereus, Bacillus subtilis, Enterococcus faecalis, Staphylococcus aureus, Escherichia coli, Klebsiella pneumonia and Pseudomonas aeruginosa) of compounds HL1-HL13 and of their respective copper(II) complexes, [Cu(L1-13){sub 2}], were tested. In general, these compounds exhibited low antibacterial activity, except for HL5 (R 3-I), more active than the control; however, the corresponding complex was inactive. In contrast, increased cytotoxicity was observed upon complexation. Complex [Cu(L13){sub 2}] (R = 3-NO{sub 2}) presented moderate cytotoxicity against human leukemia (HL-60). (author)

Reversible conversion of valence-tautomeric copper metal-organic frameworks dependent single-crystal-to-single-crystal oxidation/reduction: a redox-switchable catalyst for C-H bonds activation reaction.

Science.gov (United States)

Huang, Chao; Wu, Jie; Song, Chuanjun; Ding, Ran; Qiao, Yan; Hou, Hongwei; Chang, Junbiao; Fan, Yaoting

2015-06-28

Upon single-crystal-to-single-crystal (SCSC) oxidation/reduction, reversible structural transformations take place between the anionic porous zeolite-like Cu(I) framework and a topologically equivalent neutral Cu(I)Cu(II) mixed-valent framework. The unique conversion behavior of the Cu(I) framework endowed it as a redox-switchable catalyst for the direct arylation of heterocycle C-H bonds.

Theoretical studies of the tautomerism in 3-(2-R-Phenylhydrazono)-naphthalene- 1,2,4-triones: synthesis of copper(II) complexes and studies of antibacterial and antitumor activities

International Nuclear Information System (INIS)

Francisco, Acacio I.; Vargas, Maria D.; Fragoso, Thais P.; Carneiro, J. Walkimar de M.; Silva, Fernando de C. da; Ferreira, Vitor F.; Pessoa, Claudia; Costa-Lotufo, Leticia V.; Marinho Filho, Jose D.B.; Moraes, Manoel O. de; Mangrich, Antonio S.

2010-01-01

DFT calculations using the B3LYP and PBE1PBE functionals with the standard 6-31G(d) and 6-311+G(2d,p) basis sets were carried out for the 3-(2-phenylhydrazone)-naphthalene-1,2,4-trione system in solution (dmso) and in the gas phase, and showed the keto-hydrazone forms (rotamers Ia and Ib) to be more stable than the enol-azo forms (rotamers IIa and IIb, by about 14 kcal mol-1) and III (by approximately 6 kcal mol-1), independently of the nature of the substituent in the phenylene ring. These results were confirmed by spectroscopic data on the derivatives HL1-HL13, obtained from 2-hydroxy-1,4-naphthoquinone and arylamines (R = 4-OMe, 4-N 2 -C 6 H 5 , 4-Cl, 4-I, 3-I, 2-I, 4-COOH, 3-COOH, 4-CN, 3-CN, 4-NO 2 , 3-NO 2 , 2-NO 2 ). The in vitro antitumor (against SF-295, HCT-8, MDAMB-435 and HL-60 cancer cell lines) and antibacterial activities (Bacillus cereus, Bacillus subtilis, Enterococcus faecalis, Staphylococcus aureus, Escherichia coli, Klebsiella pneumonia and Pseudomonas aeruginosa) of compounds HL1-HL13 and of their respective copper(II) complexes, [Cu(L1-13) 2 ], were tested. In general, these compounds exhibited low antibacterial activity, except for HL5 (R 3-I), more active than the control; however, the corresponding complex was inactive. In contrast, increased cytotoxicity was observed upon complexation. Complex [Cu(L13) 2 ] (R = 3-NO 2 ) presented moderate cytotoxicity against human leukemia (HL-60). (author)

FT-IR and FT-Raman spectra of 5-chlorocytosine: Solid state simulation and tautomerism. Effect of the chlorine substitution in the Watson-Crick base pair 5-chlorodeoxycytidine-deoxyguanosine

Science.gov (United States)

Alcolea Palafox, M.; Rastogi, V. K.; Singh, S. P.

2018-01-01

The laser Raman and IR spectra of 5-chlorocytosine have been recorded and accurately assigned in the solid state using Density functional calculations (DFT) together with the linear scaling equation procedure (LSE) and the solid state simulation of the crystal unit cell through a tetramer form. These results remarkably improve those reported previously by other authors. Several new scaling equations were proposed to be used in related molecules. The six main tautomers of the biomolecule 5-chlorocytosine were determined and optimized at the MP2 and CCSD levels, using different basis sets. The relative stabilities were compared with those obtained in cytosine and their 5-halo derivatives. Several relationships between energies, geometric parameters and NBO atomic charges were established. The effect of the chlorine substitution in the fifth position was evaluated through the stability of the Watson-Crick (WC) base pair of 5-chlorodeoxycytidine with deoxyguanosine, and through their vibrational spectra.

Surface enhancement Raman scattering of tautomeric thiobarbituric acid. Natural bond orbitals and B3LYP/6-311+G (d, p) assignments of the Fourier Infrared and Fourier Raman Spectra.

Science.gov (United States)

Soto, C A Téllez; Ramos, J M; Costa Junior, A C; Vieira, Laís S; Rangel, João L; Raniero, L; Fávero, Priscila P; Lemma, Tibebe; Ondar, Grisset F; Versiane, Otavio; Martin, A A

2013-10-01

Surface enhancement Raman scattering (SERS) of two tautomer of thiobarbituric acid was obtained using silver and gold nanoparticles. Large band enhancement in the region of the ν(C=S), ν(C=C), δ(CH2), and δ(CNH) vibrational modes was found. Natural bond analysis of the tautomer species revealed expressive values of charge transfer, principally from lone pair electron orbitals of the S, N, and O atoms. Complete vibrational assignment was done for the two tautomers using the B3LYP/6-311+G (d, p) procedure, band deconvolution analysis, and from a rigorous interpretation of the normal modes matrix. The calculated spectra agree well with the experimental ones. Copyright © 2013 Elsevier B.V. All rights reserved.

Tautomerism in quinoxalines derived from the 1,4-naphthoquinone nucleus: acid mediated synthesis, X-ray molecular structure of 5-chlorobenzo[f]quinoxalin-6-ol and density functional theory calculations

International Nuclear Information System (INIS)

Gomez, Javier A.G.; Lage, Mateus R.; Carneiro, Jose Walkimar de M.; Resende, Jackson A.L.C.; Vargas, Maria D.

2013-01-01

The reaction of tert-butyl 2-(3-chloro-1,4-dioxo-1,4-dihydronaphthalen-2-ylamino) ethylcarbamate with CF 3 COOH/CH 2 Cl 2 yields 5-chloro-3,4-dihydrobenzo[f]quinoxalin-6(2H)-one which undergoes acid-promoted dehydrogenation in the presence of water to give novel 5-chlorobenzo[f]quinoxalin-6-ol. The molecular structure of 5-chlorobenzo[f]quinoxalin-6-ol in the solid state, determined by an X-ray diffraction (XRD) study, and the solution data confirm that it exists as the enol-imine tautomer, both in the solid state and in solution, differently from 5-chloro-3,4-dihydrobenzo[f]quinoxalin-6(2H)-one, which exhibits the keto-amine arrangement. Density functional theory (DFT) calculations confirmed the preference of 5-chlorobenzo[f]quinoxalin-6-ol and of the derivatives containing H and CH 3 groups in place of the Cl atom for the enol-imine tautomer. It is suggested that the enol-imine structure is preferred for 5-chlorobenzo[f]quinoxalin-6-ol as a consequence of the higher aromatic character of this structure in comparison with the keto-amine form. DFT calculations carried out on the two tautomers of the benzo[a]phenazin-5(7H)-ones analogous to the benzo[f]quinoxalin-6(4H)-ones showed that the relative stabilities are dominated by solvation effects in the first case and the degree of aromaticity, in the latter. (author)

Tautomerism in quinoxalines derived from the 1,4-naphthoquinone nucleus: acid mediated synthesis, X-ray molecular structure of 5-chlorobenzo[f]quinoxalin-6-ol and density functional theory calculations

Energy Technology Data Exchange (ETDEWEB)

Gomez, Javier A.G.; Lage, Mateus R.; Carneiro, Jose Walkimar de M.; Resende, Jackson A.L.C.; Vargas, Maria D., E-mail: mdvargas@vm.uff.br, E-mail: walk@vm.uff.br [Universidade Federal Fluminense (UFF), Niteroi, RJ (Brazil). Instituto de Quimica

2013-02-15

The reaction of tert-butyl 2-(3-chloro-1,4-dioxo-1,4-dihydronaphthalen-2-ylamino) ethylcarbamate with CF{sub 3}COOH/CH{sub 2}Cl{sub 2} yields 5-chloro-3,4-dihydrobenzo[f]quinoxalin-6(2H)-one which undergoes acid-promoted dehydrogenation in the presence of water to give novel 5-chlorobenzo[f]quinoxalin-6-ol. The molecular structure of 5-chlorobenzo[f]quinoxalin-6-ol in the solid state, determined by an X-ray diffraction (XRD) study, and the solution data confirm that it exists as the enol-imine tautomer, both in the solid state and in solution, differently from 5-chloro-3,4-dihydrobenzo[f]quinoxalin-6(2H)-one, which exhibits the keto-amine arrangement. Density functional theory (DFT) calculations confirmed the preference of 5-chlorobenzo[f]quinoxalin-6-ol and of the derivatives containing H and CH{sub 3} groups in place of the Cl atom for the enol-imine tautomer. It is suggested that the enol-imine structure is preferred for 5-chlorobenzo[f]quinoxalin-6-ol as a consequence of the higher aromatic character of this structure in comparison with the keto-amine form. DFT calculations carried out on the two tautomers of the benzo[a]phenazin-5(7H)-ones analogous to the benzo[f]quinoxalin-6(4H)-ones showed that the relative stabilities are dominated by solvation effects in the first case and the degree of aromaticity, in the latter. (author)

Spectroscopic and theoretical study of the "azo"-dye E124 in condensate phase: evidence of a dominant hydrazo form.

Science.gov (United States)

Almeida, Mariana R; Stephani, Rodrigo; Dos Santos, Hélio F; de Oliveira, Luiz Fernando C

2010-01-14

Spectroscopic techniques, including Raman, IR, UV/vis, and NMR were used to characterize the samples of the azo dye Ponceau 4R (also known as E124, New Coccine; Cochineal Red; C.I. no. 16255; Food Red No. 102), which is 1,3-naphthalenedisulfonic acid, 7-hydroxy-8-[(4-sulfo-1-naphthalenyl) azo] trisodium salt in aqueous solution and solid state. In addition, first principle calculations were carried out for the azo (OH) and hydrazo (NH) tautomers in order to assist in the assignment of the experimental data. The two intense bands observed in the UV/vis spectrum, centered at 332 and 507 nm, can be compared to the calculated values at 296 and 474 nm for azo and 315 and 500 nm for hydrazo isomer, with the latter in closer agreement to the experiment. The Raman spectrum is quite sensitive to tautomeric equilibrium; in solid state and aqueous solution, three bands were observed around 1574, 1515, and 1364 cm(-1), assigned to mixed modes including deltaNH + betaCH + nuCC, deltaNH + nuC horizontal lineO + nuC horizontal lineN + betaCH and nuCC vibrations, respectively. These assignments are predicted only for the NH species centered at 1606, 1554, and 1375 cm(-1). The calculated Raman spectrum for the azo (OH) tautomer showed two strong bands at 1468 (nuN = N + deltaOH) and 1324 cm(-1) (nuCC + nuC-N), which were not obtained experimentally. The (13)C NMR spectrum showed a very characteristic peak at 192 ppm assigned to the carbon bound to oxygen in the naphthol ring; the predicted values were 165 ppm for OH and 187 for NH isomer, supporting once again the predominance of NH species in solution. Therefore, all of the experimental and theoretical results strongly suggest the food dye Ponceau 4R or E124 has a major contribution of the hydrazo structure instead of the azo form as the most abundant in condensate phase.

The PARP inhibitor PJ-34 sensitizes cells to UVA-induced phototoxicity by a PARP independent mechanism

International Nuclear Information System (INIS)

Lakatos, Petra; Hegedűs, Csaba; Salazar Ayestarán, Nerea; Juarranz, Ángeles; Kövér, Katalin E.; Szabó, Éva; Virág, László

2016-01-01

Highlights: • PARP-1 is not a key regulator of photochemotherapy. • The PARP inhibitor PJ-34 sensitizes cells to UVA-induced phototoxicity by a PARP independent mechanism. • Photosensitization by PJ-34 is associated with increased ROS production and DNA damage. • Cells sensitized by PJ-34 undergo caspase-mediated apoptosis. - Abstract: A combination of a photosensitizer with light of matching wavelength is a common treatment modality in various diseases including psoriasis, atopic dermatitis and tumors. DNA damage and production of reactive oxygen intermediates may impact pathological cellular functions and viability. Here we set out to investigate the role of the nuclear DNA nick sensor enzyme poly(ADP-ribose) polymerase 1 in photochemical treatment (PCT)-induced tumor cell killing. We found that silencing PARP-1 or inhibition of its enzymatic activity with Veliparib had no significant effect on the viability of A431 cells exposed to 8-methoxypsoralen (8-MOP) and UVA (2.5 J/cm"2) indicating that PARP-1 is not likely to be a key player in either cell survival or cell death of PCT-exposed cells. Interestingly, however, another commonly used PARP inhibitor PJ-34 proved to be a photosensitizer with potency equal to 8-MOP. Irradiation of PJ-34 with UVA caused changes both in the UV absorption and in the 1H NMR spectra of the compound with the latter suggesting UVA-induced formation of tautomeric forms of the compound. Characterization of the photosensitizing effect revealed that PJ–34 + UVA triggers overproduction of reactive oxygen species, induces DNA damage, activation of caspase 3 and caspase 8 and internucleosomal DNA fragmentation. Cell death in this model could not be prevented by antioxidants (ascorbic acid, trolox, glutathione, gallotannin or cell permeable superoxide dismutase or catalase) but could be suppressed by inhibitors of caspase-3 and −8. In conclusion, PJ-34 is a photosensitizer and PJ–34 + UVA causes DNA damage and caspase

Biochemical and Structural Characterization of Mycobacterium tuberculosis beta-Lactamase with the Carbapenems Ertapenem and Doripenem

Energy Technology Data Exchange (ETDEWEB)

L Tremblay; F Fan; J Blanchard

2011-12-31

Despite the enormous success of {beta}-lactams as broad-spectrum antibacterials, they have never been widely used for the treatment of tuberculosis (TB) due to intrinsic resistance that is caused by the presence of a chromosomally encoded gene (blaC) in Mycobacterium tuberculosis. Our previous studies of TB BlaC revealed that this enzyme is an extremely broad-spectrum {beta}-lactamase hydrolyzing all {beta}-lactam classes. Carbapenems are slow substrates that acylate the enzyme but are only slowly deacylated and can therefore act also as potent inhibitors of BlaC. We conducted the in vitro characterization of doripenem and ertapenem with BlaC. A steady-state kinetic burst was observed with both compounds with magnitudes proportional to the concentration of BlaC used. The results provide apparent K{sub m} and k{sub cat} values of 0.18 {micro}M and 0.016 min{sup -1} for doripenem and 0.18 {micro}M and 0.017 min{sup -1} for ertapenem, respectively. FTICR mass spectrometry demonstrated that the doripenem and ertapenem acyl-enzyme complexes remain stable over a time period of 90 min. The BlaC-doripenem covalent complex obtained after a 90 min soak was determined to 2.2 {angstrom}, while the BlaC-ertapenem complex obtained after a 90 min soak was determined to 2.0 {angstrom}. The 1.3 {angstrom} diffraction data from a 10 min ertapenem-soaked crystal revealed an isomerization occurring in the BlaC-ertapenem adduct in which the original {Delta}2-pyrroline ring was tautomerized to generate the {Delta}1-pyrroline ring. The isomerization leads to the flipping of the carbapenem hydroxyethyl group to hydrogen bond to carboxyl O2 of Glu166. The hydroxyethyl flip results in both the decreased basicity of Glu166 and a significant increase in the distance between carboxyl O2 of Glu166 and the catalytic water molecule, slowing hydrolysis.

High-resolution studies of tropolone in the S0 and S1 electronic states: isotope driven dynamics in the zero-point energy levels.

Science.gov (United States)

Keske, John C; Lin, Wei; Pringle, Wallace C; Novick, Stewart E; Blake, Thomas A; Plusquellic, David F

2006-02-21

Rotationally resolved microwave (MW) and ultraviolet (UV) spectra of jet-cooled tropolone have been obtained in S(0) and S(1) electronic states using Fourier-transform microwave and UV-laser/molecular-beam spectrometers. In the ground electronic state, the MW spectra of all heavy-atom isotopomers including one (18)O and four (13)C isotopomers were observed in natural abundance. The OD isotopomer was obtained from isotopically enriched samples. The two lowest tunneling states of each isotopomer except (18)O have been assigned. The observed inversion splitting for the OD isotopomer is 1523.227(5) MHz. For the asymmetric (13)C structures, the magnitudes of tunneling-rotation interactions are found to diminish with decreasing distance between the heavy atom and the tunneling proton. In the limit of closest approach, the 0(+) state of (18)O was well fitted to an asymmetric rotor Hamiltonian, reflecting significant changes in the tautomerization dynamics. Comparisons of the substituted atom coordinates with theoretical predictions at the MP2/aug-cc-pVTZ level of theory suggest the localized 0(+) and 0(-) wave functions of the heavier isotopes favor the C-OH and C=O forms of tropolone, respectively. The only exception occurs for the (13)C-OH and (13)C[Double Bond]O structures which correlate to the 0(-) and 0(+) states, respectively. These preferences reflect kinetic isotope effects as quantitatively verified by the calculated zero-point energy differences between members of the asymmetric atom pairs. From rotationally resolved data of the 0(+) <--0(+) and 0(-) <--0(-) bands in S(1), line-shape fits have yielded Lorentzian linewidths that differ by 12.2(16) MHz over the 19.88(4) cm(-1) interval in S(1). The fluorescence decay rates together with previously reported quantum yield data give nonradiative decay rates of 7.7(5) x 10(8) and 8.5(5) x 10(8) s(-1) for the 0(+) and 0(-) levels of the S(1) state of tropolone.

On the solubility advantage of a pharmaceutical’s glassy state over the crystal state, and of its crystal polymorphs

International Nuclear Information System (INIS)

Johari, G.P.; Shanker, Ravi M.

2014-01-01

Highlights: • Heat capacity data do not yield the solubility advantage of amorphous and metastable crystal pharmaceuticals. • There is no reversible equilibrium of an amorphous solid with its saturated solution. • Solubility advantage of an amorphous solid depends upon the solvent and other interactions. - Abstract: At equilibrium, the saturation solubility and vapor pressure of a material in a state of high free energy are greater than in its state of low free energy. This knowledge from classical thermodynamics is currently used for increasing the solubility of crystalline pharmaceuticals by producing them in their glassy state, or in other solid states of high free energy. The ratio of the apparent saturation solubility of these solids to that of a crystal, calculated from the thermodynamic data of the pure solute, ϕ cal , is called the solubility advantage, and it is used as a guide for increasing the solubility of a pharmaceutical. We argue that the ϕ cal differs from the measured solubility ratio, ϕ meas , because, (i) ϕ cal is independent of the solvent, but ϕ meas is not so, (ii) ϕ cal would increase with the dissolution time monotonically to a constant value, but ϕ meas would first reach a maximum and then decrease, and (iii) approximations are made in estimating ϕ cal and the effect of thermal history on high free energy solids is ignored. On the other hand, ϕ meas is affected by, (a) another chemical equilibrium in the solution, e.g., hydrogen-bond formation and ionic dissociation, (b) the production method and thermal history of a glass or an amorphous samples, and (c) mutarotation in the solution, isomerization or tautomeric conversion in the solid. We also discuss the effects of structural relaxation and crystallization on ϕ meas . The ϕ meas value of a (crystal) polymorph would be affected by all the three, and further if the polymorph is orientationally disordered. We provide evidence for these effects from analysis of the known

Exceptionally High Proton and Lithium Cation Gas-Phase Basicity of the Anti-Diabetic Drug Metformin.

Science.gov (United States)

Raczyńska, Ewa D; Gal, Jean-François; Maria, Pierre-Charles; Michalec, Piotr; Zalewski, Marcin

2017-11-16

Substituted biguanides are known for their biological effect, and a few of them are used as drugs, the most prominent example being metformin (1,1-dimethylbiguanide, IUPAC name: N,N-dimethylimidodicarbonimidic diamide). Because of the presence of hydrogen atoms at the amino groups, biguanides exhibit a multiple tautomerism. This aspect of their structures was examined in detail for unsubstituted biguanide and metformin in the gas phase. At the density functional theory (DFT) level {essentially B3LYP/6-311+G(d,p)}, the most stable structures correspond to the conjugated, push-pull, system (NR 2 )(NH 2 )C═N-C(═NH)NH 2 (R = H, CH 3 ), further stabilized by an internal hydrogen bond. The structural and energetic aspects of protonation and lithium cation adduct formation of biguanide and metformin was examined at the same level of theory. The gas-phase protonation energetics reveal that the more stable tautomer is protonated at the terminal imino C═NH site, still with an internal hydrogen bond maintaining the structure of the neutral system. The calculated proton affinity and gas-phase basicity of the two molecules reach the domain of superbasicity. By contrast, the lithium cation prefers to bind the less stable, not fully conjugated, tautomer (NR 2 )C(═NH)-NH-C(═NH)NH 2 of biguanides, in which the two C═NH groups are separated by NH. This less stable form of biguanides binds Li + as a bidentate ligand, in agreement with what was reported in the literature for other metal cations in the solid phase. The quantitative assessment of resonance in biguanide, in metformin and in their protonated forms, using the HOMED and HOMA indices, reveals an increase in electron delocalization upon protonation. On the contrary, the most stable lithium cation adducts are less conjugated than the stable neutral biguanides, because the metal cation is better coordinated by the not-fully conjugated bidentate tautomer.

The PARP inhibitor PJ-34 sensitizes cells to UVA-induced phototoxicity by a PARP independent mechanism

Energy Technology Data Exchange (ETDEWEB)

Lakatos, Petra; Hegedűs, Csaba [Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, Debrecen (Hungary); Salazar Ayestarán, Nerea; Juarranz, Ángeles [Department of Biology, Faculty of Sciences, Universidad Autónoma of Madrid, 28049-Madrid (Spain); Kövér, Katalin E. [Department of Inorganic and Analytical Chemistry, Faculty of Sciences, University of Debrecen, Debrecen (Hungary); Szabó, Éva [Department of Dermatology, Faculty of Medicine, University of Debrecen, Debrecen (Hungary); Virág, László, E-mail: lvirag@med.unideb.hu [Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, Debrecen (Hungary); MTA-DE Cell Biology and Signaling Research Group, Debrecen (Hungary)

2016-08-15

Highlights: • PARP-1 is not a key regulator of photochemotherapy. • The PARP inhibitor PJ-34 sensitizes cells to UVA-induced phototoxicity by a PARP independent mechanism. • Photosensitization by PJ-34 is associated with increased ROS production and DNA damage. • Cells sensitized by PJ-34 undergo caspase-mediated apoptosis. - Abstract: A combination of a photosensitizer with light of matching wavelength is a common treatment modality in various diseases including psoriasis, atopic dermatitis and tumors. DNA damage and production of reactive oxygen intermediates may impact pathological cellular functions and viability. Here we set out to investigate the role of the nuclear DNA nick sensor enzyme poly(ADP-ribose) polymerase 1 in photochemical treatment (PCT)-induced tumor cell killing. We found that silencing PARP-1 or inhibition of its enzymatic activity with Veliparib had no significant effect on the viability of A431 cells exposed to 8-methoxypsoralen (8-MOP) and UVA (2.5 J/cm{sup 2}) indicating that PARP-1 is not likely to be a key player in either cell survival or cell death of PCT-exposed cells. Interestingly, however, another commonly used PARP inhibitor PJ-34 proved to be a photosensitizer with potency equal to 8-MOP. Irradiation of PJ-34 with UVA caused changes both in the UV absorption and in the 1H NMR spectra of the compound with the latter suggesting UVA-induced formation of tautomeric forms of the compound. Characterization of the photosensitizing effect revealed that PJ–34 + UVA triggers overproduction of reactive oxygen species, induces DNA damage, activation of caspase 3 and caspase 8 and internucleosomal DNA fragmentation. Cell death in this model could not be prevented by antioxidants (ascorbic acid, trolox, glutathione, gallotannin or cell permeable superoxide dismutase or catalase) but could be suppressed by inhibitors of caspase-3 and −8. In conclusion, PJ-34 is a photosensitizer and PJ–34 + UVA causes DNA damage and caspase

Nonequimolar Mixture of Organic Acids and Bases: An Exception to the Rule of Thumb for Salt or Cocrystal.

Science.gov (United States)

Pratik, Saied Md; Datta, Ayan

2016-08-04

Formation of salt and/or cocrystal from organic acid-base mixtures has significant consequences in the pharmaceutical industry and its related intellectual property rights (IPR). On the basis of calculations using periodic dispersion corrected DFT (DFT-D2) on formic acid-pyridine adduct, we have demonstrated that an equimolar stoichiometric ratio (1:1) exists as a neutral cocrystal. On the other hand, the nonequimolar stoichiometry (4:1) readily forms an ionic salt. While the former result is in agreement with the ΔpKa rule between the base and the acid, the latter is not. Calculations reveal that, within the equimolar manifold (n:n; n = 1-4), the mixture exists as a hydrogen bonded complex in a cocrystal-like environment. However, the nonequimolar mixture in a ratio of 5:1 and above readily forms salt-like structures. Because of the cooperative nature of hydrogen bonding, the strength of the O-H···N hydrogen bond increases and eventually transforms into O(-)···H-N(+) (complete proton transfer) as the ratio of formic acid increases and forms salt as experimentally observed. Clearly, an enhanced polarization of formic acid on aggregation increases its acidity and, hence, facilitates its transfer to pyridine. Motion of the proton from formic acid to pyridine is shown to follow a relay mechanism wherein the proton that is far away from pyridine is ionized and is subsequently transferred to pyridine via hopping across the neutral formic acid molecules (Grotthuss type pathway). The dynamic nature of protons in the condensed phase is also evident for cocrystals as the barrier of intramolecular proton migration in formic acid (leading to tautomerism), ΔH(⧧)tautomer = 17.1 kcal/mol in the presence of pyridine is half of that in free formic acid (cf. ΔH(⧧)tautomer = 34.2 kcal/mol). We show that an acid-base reaction can be altered in the solid state to selectively form a cocrystal or salt depending on the strength and nature of aggregation.

Effect of deuteration on the vibrational spectra of organic molecules

International Nuclear Information System (INIS)

Billes, Ferenc; Endredi, Henrietta; Varady, Balazs

2001-01-01

The stable isotope substitution of organic compounds deforms their vibrational spectra. The modifications of the spectra appear as band shifts and changes in intensities and shapes of the bands. The magnitude of the effect depends on the ratio of the masses of the new and old isotopes and on the atom active position. According to these mentioned reasons large effects can be observed only if hydrogen atoms are substituted. With the effect of the substitution we dealt already in a former lecture. In this lecture we concentrate on the effect of the change of hydrogen to deuterium. We investigate the changes both experimentally and theoretically. There are two possibilities: - the hydrogen atom is in an active position, its interaction with the environment is strong, either it can dissociate or move on the skeleton of the molecule (tautomerism, resonance) and it can build hydrogen bond, (e.g. it is connected to nitrogen and oxygen atoms); - the hydrogen atom is in an indifferent position in the molecule, its interaction with the environment is weak (e.g. it joins carbon atom). When building the hydrogen bond besides the hydrogen donors also acceptors exist, namely, oxygen and nitrogen atoms having non-bonded electron pairs. When comparing the experimental and theoretical (calculated) effects of this type of isotope changes one must take into account that the calculations refer to the isolated molecule while the experimental spectra characterize the compound. The hydrogen bond is a very strong intermolecular interaction and produces tremendous changes in the infrared spectrum of the molecule in comparison to the imagined theoretical spectrum of the molecule. Some bands disappear, appear, or shift and deform drastically. The H/D change diminishes these effects. Of course, these changes entail the shift of several bands. The Raman spectrum is less sensitive to the large dipole moment changes therefore the deuteration effect is there less dramatic. Deuteration of hydrogen

Theoretical Kinetic Study of the Unimolecular and H-Assisted Keto-Enol Tautomerism Propen-2-ol ↔Acetone. Pressure Effects and Implications in the Pyrolysis and Oxidation of tert- And 2-Butanol

KAUST Repository

Grajales Gonzalez, Edwing Javier

2018-01-01

and variational transition state theory were considered in a wide temperature and pressure range (200 K – 3000 K, 0.1 kPa – 108 kPa). It was observed that decreasing pressure leads to a decrease in rate constants, describing the expected falloff behavior for both

Photoelectron spectrum of valence anions of uracil and first-principles calculations of excess electron binding energies.

Science.gov (United States)

Bachorz, Rafał A; Klopper, Wim; Gutowski, Maciej; Li, Xiang; Bowen, Kit H

2008-08-07

The photoelectron spectrum (PES) of the uracil anion is reported and discussed from the perspective of quantum chemical calculations of the vertical detachment energies (VDEs) of the anions of various tautomers of uracil. The PES peak maximum is found at an electron binding energy of 2.4 eV, and the width of the main feature suggests that the parent anions are in a valence rather than a dipole-bound state. The canonical tautomer as well as four tautomers that result from proton transfer from an NH group to a C atom were investigated computationally. At the Hartree-Fock and second-order Moller-Plesset perturbation theory levels, the adiabatic electron affinity (AEA) and the VDE have been converged to the limit of a complete basis set to within +/-1 meV. Post-MP2 electron-correlation effects have been determined at the coupled-cluster level of theory including single, double, and noniterative triple excitations. The quantum chemical calculations suggest that the most stable valence anion of uracil is the anion of a tautomer that results from a proton transfer from N1H to C5. It is characterized by an AEA of 135 meV and a VDE of 1.38 eV. The peak maximum is as much as 1 eV larger, however, and the photoelectron intensity is only very weak at 1.38 eV. The PES does not lend support either to the valence anion of the canonical tautomer, which is the second most stable anion, and whose VDE is computed at about 0.60 eV. Agreement between the peak maximum and the computed VDE is only found for the third most stable tautomer, which shows an AEA of approximately -0.1 eV and a VDE of 2.58 eV. This tautomer results from a proton transfer from N3H to C5. The results illustrate that the characteristics of biomolecular anions are highly dependent on their tautomeric form. If indeed the third most stable anion is observed in the experiment, then it remains an open question why and how this species is formed under the given conditions.

Syntheses of New Unsymmetrical and Symmetrical Diarylsulphides and Diarylsulphones Containing Thiazolinyl and Thiazolidinonyl Moieties Using 4,4'-Diacetyldiphenylsulphide

Directory of Open Access Journals (Sweden)

M. I. Abdel-Monem

2003-07-01

Full Text Available Condensation of 4,4’-diacetyldiphenyl sulphide (2 with variable amounts of thiosemicarbazide (3 in refluxing ethanol and in the presence of catalytic amounts of dry piperidine afforded only 4-acetylthiosemicarbazone-4’-acetyldiphenyl sulphide (5. Condensation of 2 with excess semicarbazide hydrochloride (4 in the presence of fused sodium acetate and/or piperidine yielded 4,4’-diacetylsemicarbazone diphenyl sulphide (6, whereas use of equimolar amounts of 2 and 4 afforded 4-acetyl-semicarbazone-4’-acetyldiphenyl sulphide (7. 4-Acetylsemicarbazone-4’-acetylthiosemicarbazone diphenyl sulphide (8 was also obtained via two different routes. The effect of tautomeric structure 5d is discussed. 4-(4"-phenyl-Δ3-thiazoline-2"-acetylazino-4’-acetyldiphenyl sulphide (9, 4-(5"-carboxyethyl-4"-thiazolidinone-2"-acetylazino-4’-acetyldiphenyl sulphide (10, 4-(4"-thiazolidinone-2’-acetylazino-4’-acetyldiphenyl sulphide (11 and 4-(4"-methyl-Δ3-thiazoline-2"-acetylazino-4’-acetyldiphenyl sulphide (12 were prepared by interaction of 5 with phenacylbromide, bromodiethylmalonate, chloro ethylacetate and chloroacetone, respectively. Sulphides 9-12 were easily condensed with 3 to afford the corresponding 4-(heterocyclic moiety-2"-acetylazino-4’-acetylthiosemicarbazone diphenyl sulphides 23-26. Oxidation of the prepared sulphides 5-7, 9-12, 23 and 25-26 using H2O2/glacial AcOH mixtures yielded only 4,4’-diacetyldiphenyl sulphone (13 as the main product in every case, besides 3 and 4 in certain cases. Unsymmetrical and symmetrical sulphones 14-22 were obtained starting from 13. The structures of the synthesized compounds are based on IR, 1H-NMR, 13C-NMR and mass spectral data. A theoretical study on some of the prepared compounds using molecular modeling was carried out.

Differential stabilities and sequence-dependent base pair opening dynamics of Watson-Crick base pairs with 5-hydroxymethylcytosine, 5-formylcytosine, or 5-carboxylcytosine.

Science.gov (United States)

Szulik, Marta W; Pallan, Pradeep S; Nocek, Boguslaw; Voehler, Markus; Banerjee, Surajit; Brooks, Sonja; Joachimiak, Andrzej; Egli, Martin; Eichman, Brandt F; Stone, Michael P

2015-02-10

5-Hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC) form during active demethylation of 5-methylcytosine (5mC) and are implicated in epigenetic regulation of the genome. They are differentially processed by thymine DNA glycosylase (TDG), an enzyme involved in active demethylation of 5mC. Three modified Dickerson-Drew dodecamer (DDD) sequences, amenable to crystallographic and spectroscopic analyses and containing the 5'-CG-3' sequence associated with genomic cytosine methylation, containing 5hmC, 5fC, or 5caC placed site-specifically into the 5'-T(8)X(9)G(10)-3' sequence of the DDD, were compared. The presence of 5caC at the X(9) base increased the stability of the DDD, whereas 5hmC or 5fC did not. Both 5hmC and 5fC increased imino proton exchange rates and calculated rate constants for base pair opening at the neighboring base pair A(5):T(8), whereas 5caC did not. At the oxidized base pair G(4):X(9), 5fC exhibited an increase in the imino proton exchange rate and the calculated kop. In all cases, minimal effects to imino proton exchange rates occurred at the neighboring base pair C(3):G(10). No evidence was observed for imino tautomerization, accompanied by wobble base pairing, for 5hmC, 5fC, or 5caC when positioned at base pair G(4):X(9); each favored Watson-Crick base pairing. However, both 5fC and 5caC exhibited intranucleobase hydrogen bonding between their formyl or carboxyl oxygens, respectively, and the adjacent cytosine N(4) exocyclic amines. The lesion-specific differences observed in the DDD may be implicated in recognition of 5hmC, 5fC, or 5caC in DNA by TDG. However, they do not correlate with differential excision of 5hmC, 5fC, or 5caC by TDG, which may be mediated by differences in transition states of the enzyme-bound complexes.

Differential Stabilities and Sequence-Dependent Base Pair Opening Dynamics of Watson–Crick Base Pairs with 5-Hydroxymethylcytosine, 5-Formylcytosine, or 5-Carboxylcytosine

Science.gov (United States)

2016-01-01

5-Hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC) form during active demethylation of 5-methylcytosine (5mC) and are implicated in epigenetic regulation of the genome. They are differentially processed by thymine DNA glycosylase (TDG), an enzyme involved in active demethylation of 5mC. Three modified Dickerson–Drew dodecamer (DDD) sequences, amenable to crystallographic and spectroscopic analyses and containing the 5′-CG-3′ sequence associated with genomic cytosine methylation, containing 5hmC, 5fC, or 5caC placed site-specifically into the 5′-T8X9G10-3′ sequence of the DDD, were compared. The presence of 5caC at the X9 base increased the stability of the DDD, whereas 5hmC or 5fC did not. Both 5hmC and 5fC increased imino proton exchange rates and calculated rate constants for base pair opening at the neighboring base pair A5:T8, whereas 5caC did not. At the oxidized base pair G4:X9, 5fC exhibited an increase in the imino proton exchange rate and the calculated kop. In all cases, minimal effects to imino proton exchange rates occurred at the neighboring base pair C3:G10. No evidence was observed for imino tautomerization, accompanied by wobble base pairing, for 5hmC, 5fC, or 5caC when positioned at base pair G4:X9; each favored Watson–Crick base pairing. However, both 5fC and 5caC exhibited intranucleobase hydrogen bonding between their formyl or carboxyl oxygens, respectively, and the adjacent cytosine N4 exocyclic amines. The lesion-specific differences observed in the DDD may be implicated in recognition of 5hmC, 5fC, or 5caC in DNA by TDG. However, they do not correlate with differential excision of 5hmC, 5fC, or 5caC by TDG, which may be mediated by differences in transition states of the enzyme-bound complexes. PMID:25632825

Chemistry of the oxophosphinidene ligand. 2. Reactivity of the anionic complexes [MCp{P(O)R*}(CO)(2)](-) (M = Mo, W; R* = 2,4,6-C(6)H(2)(t)Bu(3)) toward electrophiles based on elements different from carbon.

Science.gov (United States)

Alonso, María; Alvarez, M Angeles; García, M Esther; Ruiz, Miguel A; Hamidov, Hayrullo; Jeffery, John C

2010-12-20

The anionic oxophosphinidene complexes (H-DBU)[MCp{P(O)R*}(CO)(2)] (M = Mo, W; R* = 2,4,6-C(6)H(2)(t)Bu(3); Cp = η(5)-C(5)H(5), DBU = 1,8-diazabicyclo [5.4.0] undec-7-ene) displayed multisite reactivity when faced with different electrophilic reagents. The reactions with the group 14 organochloride compounds ER(4-x)Cl(x) (E = Si, Ge, Sn, Pb) led to either phosphide-like, oxophosphinidene-bridged derivatives [MCp{P(OE')R*}(CO)(2)] (E' = SiMe(3), SiPh(3), GePh(3), GeMe(2)Cl) or to terminal oxophosphinidene complexes [MCp{P(O)R*}(CO)(2)(E')] (E' = SnPh(3), SnPh(2)Cl, PbPh(3); Mo-Pb = 2.8845(4) Å for the MoPb compound). A particular situation was found in the reaction with SnMe(3)Cl, this giving a product existing in both tautomeric forms, with the phosphide-like complex [MCp{P(OSnMe(3))R*}(CO)(2)] prevailing at room temperature and the tautomer [MCp{P(O)R*}(CO)(2)(SnMe(3))] being the unique species present below 203 K in dichloromethane solution. The title anions also showed a multisite behavior when reacting with transition-metal based electrophiles. Thus, the reactions with the complexes [M'Cp(2)Cl(2)] (M' = Ti, Zr) gave phosphide-like derivatives [MCp{P(OM')R*}(CO)(2)] (M = Mo, M' = TiCp(2)Cl, ZrCp(2)Cl; M = W, M' = ZrCp(2)Cl), displaying a bridging κ(1),κ(1)-P,O- oxophosphinidene ligand connecting MCp(CO)(2) and M'Cp(2)Cl metal fragments (W-P = 2.233(1) Å, O-Zr = 2.016(4) Å for the WZr compound]. In contrast, the reactions with the complex [AuCl{P(p-tol)(3)}] gave the metal-metal bonded derivatives trans-[MCp{P(O)R*}(CO)(2){AuP(p-tol)(3)}] (M = Mo, W; Mo-Au = 2.7071(7) Å). From all the above results it was concluded that the terminal oxophosphinidene complexes are preferentially formed under conditions of orbital control, while charge-controlled reactions tend to give derivatives with the electrophilic fragment bound to the oxygen atom of the oxophosphinidene ligand (phosphide-like, oxophosphinidene-bridged derivatives).

Molecular Recognition Involving Anthraquinone Derivatives and Molecular Clips

Science.gov (United States)

Alaparthi, Madhubabu

In the past, we have demonstrated that 1,8-anthraquinone-18-crown-5 (1) and its heterocyclic derivatives act as luminescent hosts for a variety of cations of environmental and clinical concern. We report here a series of heteroatom-substituted macrocycles containing an anthraquinone moiety as a fluorescent signaling unit and a cyclic polyheteroether chain as the receptor. Sulfur, selenium, and tellurium derivatives of 1,8-anthraquinone-18-crown-5 (1) were synthesized by reacting sodium sulfide (Na2S), sodium selenide (Na2Se) and sodium telluride (Na2Te) with 1,8-bis(2-bromoethylethyleneoxy)anthracene - 9,10-dione in a 1:1 ratio (2,3, and 6). These sensors bind metal ions in a 1:1 ratio (7 and 8), and the optical properties of the new complexes were examined and the sulfur and selenium analogues show that selectivity for Pb(II) is markedly improved as compared to the oxygen analogue 1 which was competitive for Ca(II) ion. Selective reduction of 1 yields secondary alcohols where either one or both of the anthraquinone carbonyl groups has been reduced ( 15 and 9). A new mechanism for the fluorescence detection of metal cations in solution is introduced involving a unique keto-enol tautomerization. Reduction of 1 yields the doubly reduced secondary alcohol, 9. 9 acts as a chemodosimeter for Al(III) ion producing a strong blue emission due to the formation of the anthracene fluorophore, 10, via dehydration of the internal secondary alcohol in DMSO/aqueous solution. The enol form is not the most thermodynamically stable form under these conditions however, and slowly converts to the keto form 11.. Currently we are focusing on cucurbituril derivatives, also described as molecular clips due to their folded geometry used as molecular recognition hosts. We first investigated the synthesis and characterization of aromatic methoxy/catechol terminated cucurbituril units that act as hosts for small solvent molecules, such as CH2Cl2, CH3CN, DMF, and MeOH, through dual pi...H-C T

Prototropic tautomerism of 5-nitrobenzimidazole derivatives in {sup 1}H, {sup 13}C and {sup 15}N NMR spectra; Tautomeria prototropowa pochodnych 5-nitrobenzimidazolu w widmach {sup 1}H, {sup 13}C, {sup 15}N NMR

Energy Technology Data Exchange (ETDEWEB)

Wiench, J W; Bocian, W; Stefaniak, L [Inst. Chemii Organicznej, Polska Akademia Nauk, Warsaw (Poland)

1994-12-31

NMR spectra of 5-nitrobenzimidazole derivatives in DMSO solution show the fast exchange of protons. The line broadening in {sup 1}H,{sup 13}C and {sup 15}N spectra have been observed. The interpretation of the spectra has been done basing on chemical shifts values and couplings between nuclei in the investigated derivatives. 3 refs, 2 figs, 3 tabs.

Mechanism of Prototropy. V. Arrhenius parameters of the tautomerization of Benzylidene Benzylamine and its {alpha}-{alpha}-alkyl derivatives; Mecanismo de la prototropia V. Parametros de Arrhenius de la toutomerizacion de benciliden-bencilamina y sus {alpha}- y {alpha}-alquilderivados

Energy Technology Data Exchange (ETDEWEB)

Perez Ossorio, R; Gomez Herrera, F; Utrilla, R M; Hidalgo, A; Gamboa, J M

1961-07-01

The reactions were conducted in ethyl alcohol-dioxan, in the presence of EtONa, as catalyst. Rates were followed by a radioactive tracer method when R=H and by spectroscopic method when R= alkyl as described in previous papers. The results suggest that polar effects alone cannot account for the relative Arrhenius parameters obtained. (Author) 3 refs.

Unusual C-C bond cleavage in the formation of amine-bis(phenoxy) group 4 benzyl complexes: Mechanism of formation and application to stereospecific polymerization

KAUST Repository

Gowda, Ravikumar R.

2014-08-11

Group 4 tetrabenzyl compounds MBn4 (M = Zr, Ti), upon protonolysis with an equimolar amount of the tetradentate amine-tris(phenol) ligand N[(2,4-tBu2C6H2(CH 2)OH]3 in toluene from -30 to 25 °C, unexpectedly lead to amine-bis(phenoxy) dibenzyl complexes, BnCH2N[(2,4- tBu2C6H2(CH2)O] 2MBn2 (M = Zr (1), Ti (2)) in 80% (1) and 75% (2) yields. This reaction involves an apparent cleavage of the >NCH2-ArOH bond (loss of the phenol in the ligand) and formation of the >NCH 2-CH2Bn bond (gain of the benzyl group in the ligand). Structural characterization of 1 by X-ray diffraction analysis confirms that the complex formed is a bis(benzyl) complex of Zr coordinated by a newly derived tridentate amine-bis(phenoxy) ligand arranged in a mer configuration in the solid state. The abstractive activation of 1 and 2 with B(C6F 5)3·THF in CD2Cl2 at room temperature generates the corresponding benzyl cations {BnCH2N[(2,4- tBu2C6H2(CH2)O] 2MBn(THF)}+[BnB(C6F5) 3]- (M = Zr (3), Ti, (4)). These cationic complexes, along with their analogues derived from (imino)phenoxy tri- and dibenzyl complexes, [(2,6-iPr2C6H3)N=C(3,5- tBu2C6H2)O]ZrBn3 (5) and [2,4-Br2C6H2(O)(6-CH2(NC 5H9))CH2N=CH(2-adamantyl-4-MeC 6H2O)]ZrBn2 (6), have been found to effectively polymerize the biomass-derived renewable β-methyl-α-methylene- γ-butyrolactone (βMMBL) at room temperature into the highly stereoregular polymer PβMMBL with an isotacticity up to 99% mm. A combined experimental and DFT study has yielded a mechanistic pathway for the observed unusual C-C bond cleavage in the present protonolysis reaction between ZrBn4 and N[(2,4-tBu2C 6H2(CH2)OH]3 for the formation of complex 1, which involves the benzyl radical and the Zr(III) species, resulting from thermal and photochemical decomposition of ZrBn4, followed by a series of reaction sequences consisting of protonolysis, tautomerization, H-transfer, oxidation, elimination, and radical coupling. © 2014 American Chemical Society.

Direct Functionalization of Nitrogen Heterocycles via Rh-Catalyzed C-H Bond Activation

Energy Technology Data Exchange (ETDEWEB)

Lewis, Jared; Bergman, Robert; Ellman, Jonathan

2008-02-04

Nitrogen heterocycles are present in many compounds of enormous practical importance, ranging from pharmaceutical agents and biological probes to electroactive materials. Direct funtionalization of nitrogen heterocycles through C-H bond activation constitutes a powerful means of regioselectively introducing a variety of substituents with diverse functional groups onto the heterocycle scaffold. Working together, our two groups have developed a family of Rh-catalyzed heterocycle alkylation and arylation reactions that are notable for their high level of functional-group compatibility. This Account describes their work in this area, emphasizing the relevant mechanistic insights that enabled synthetic advances and distinguished the resulting transformations from other methods. They initially discovered an intramolecular Rh-catalyzed C-2-alkylation of azoles by alkenyl groups. That reaction provided access to a number of di-, tri-, and tetracyclic azole derivatives. They then developed conditions that exploited microwave heating to expedite these reactions. While investigating the mechanism of this transformation, they discovered that a novel substrate-derived Rh-N-heterocyclic carbene (NHC) complex was involved as an intermediate. They then synthesized analogous Rh-NHC complexes directly by treating precursors to the intermediate [RhCl(PCy{sub 3}){sub 2}] with N-methylbenzimidazole, 3-methyl-3,4-dihydroquinazolein, and 1-methyl-1,4-benzodiazepine-2-one. Extensive kinetic analysis and DFT calculations supported a mechanism for carbene formation in which the catalytically active RhCl(PCy{sub 3}){sub 2} fragment coordinates to the heterocycle before intramolecular activation of the C-H bond occurs. The resulting Rh-H intermediate ultimately tautomerizes to the observed carbene complex. With this mechanistic information and the discovery that acid co-catalysts accelerate the alkylation, they developed conditions that efficiently and intermolecularly alkylate a variety of

Carbapenems and SHV-1 β-Lactamase Form Different Acyl-Enzyme Populations in Crystals and Solution

Science.gov (United States)

Kalp, Matthew; Carey, Paul R.

2009-01-01

The reactions between single crystals of the SHV-1 β-lactamase enzyme and the carbapenems, meropenem, imipenem and ertapenem, have been studied by Raman microscopy. Aided by quantum mechanical calculations, major populations of two acyl-enzyme species, a labile Δ2-pyrroline and a more tightly bound Δ1-pyrroline, have been identified for all three compounds. These isomers differ only in the position of the double bond about the carbapenem nucleus. This discovery is consonant with X-ray crystallographic findings that also identified two populations for meropenem bound in SHV-1: one with the acyl C=O group in the oxyanion hole and the second with the acyl group rotated 180 degrees compared to its expected position [Nukaga, M., Bethel, C. R., Thomson, J. M., Hujer, A. M., Distler, A. M., Anderson, V. E., Knox, J. R., and Bonomo, R. A. (2008) Journal of the American Chemical Society]. When crystals of the Δ1 and Δ2 containing acyl-enzymes were exposed to solutions with no carbapenem, rapid deacylation of the Δ2 species was observed by kinetic Raman experiments. However, no change in the Δ1 population was observed over 1 hour, the effective lifetime of the crystal. These observations lead to the hypothesis that the stable Δ1 species is due to the form seen by X-ray with the acyl carbonyl outside the oxyanion hole, while the Δ2 species corresponds to the form with the carbonyl inside the oxyanion hole. Soak-in and soak-out Raman experiments also demonstrated that tautomeric exchange between the Δ1 and Δ2 forms does not occur on the crystalline enzyme. When meropenem or ertapenem were reacted with SHV-1 in solution, the Raman difference spectra demonstrated that only a major population corresponding to the Δ1 acyl-enzyme could be detected. The 1003 cm-1 mode of the phenyl ring positioned on the C3 side chain of ertapenem acts as an effective internal Raman intensity standard and the ratio of its intensity to that of the 1600 cm-1 feature of Δ1 provides an

Synthesis and reactions of cyclovalence isomers of azo-keto-carbenes

International Nuclear Information System (INIS)

Rettenbacher, A.S.

2001-09-01

Novel types of cycloaddition products with an azomethine imine functionality have been prepared from ω-azo-α'-diazo ketones with a carbon chain of variable length between the azo- and the keto-group; the reaction is induced by catalytical amounts of rhodium(II) acetate and occurs with the concomitant extrusion of dinitrogen. The synthesis of these cyclic azomethine imines succeeded in the course of the intramolecular reaction of the azo nitrogen atoms with a carbene/carbenoid carbon atom, in situ generated from the α-diazoketone functionality; this is a novel cyclization reaction. Some of the resulting cyclization products are stable and have been isolated, others could only be trapped with dipolarophiles as [3+2] cycloadducts. The ring-size of the heterocyclic products depends on the one hand on the length of the carbon-chain (for n = 0, 1, 2) between the carbonyl carbon atom and the quaternary aliphatic or aromatic carbon atom that blocks the tautomerization of the azo-group in the starting material. On the other hand, the ring size depends on which of the two nitrogen atoms of the azo-group undergoes the ring closure with the carbene/carbenoid carbon atom generated from the α-diazoketon functionality in the course of the reaction. By far the most serious problem in the preparation of the cyclic azomethine imines is the synthesis of the required ω-azo-α'-diazo ketones. A so far unknown property of the azo-group is its intramolecularly directed nucleophilicity toward ketenes, which emerge from acid chlorides and anhydrides, or from α-diazo ketones in the course of the Wolff rearrangement. This complicated the approach to the required ω-azo-α'-diazo ketones via these functionalities as precursors and with the desired chain length between the azo- and diazo-keto-groups. Nevertheless, these problems could be overcome by using alternative strategies. Utilizing ω-azo-α'-diazo ketones a largely commonly applicable approach to endocyclic and N

Dimeric Fe (II, III) complex of quinoneoxime as functional model of PAP enzyme: Mössbauer, magneto-structural and DNA cleavage studies

Science.gov (United States)

Salunke-Gawali, Sunita; Ahmed, Khursheed; Varret, François; Linares, Jorge; Zaware, Santosh; Date, Sadgopal; Rane, Sandhya

2008-07-01

Purple acid phosphatase, ( PAP), is known to contain dinuclear Fe2 + 2, + 3 site with characteristic Fe + 3 ← Tyr ligand to metal charge transfer in coordination. Phthiocoloxime (3-methyl-2-hydroxy-1,4-naphthoquinone-1-oxime) ligand L, mimics (His/Tyr) ligation with controlled and unique charge transfers resulting in valence tautomeric coordination with mixed valent diiron site in model compound Fe-1: [μ-OH-Fe2 + 2, + 3 ( o-NQCH3ox) ( o-NSQCH3ox)2 (CAT) H2O]. Fe-2: [Fe + 3( o-NQCH3ox) ( p-NQCH3ox)2]2 a molecularly associated dimer of phthiocoloxime synthesized for comparison of charge transfer. 57Fe Mössbauer studies was used to quantitize unusual valences due to ligand in dimeric Fe-1 and Fe-2 complexes which are supported by EPR and SQUID studies. 57Fe Mössbauer spectra for Fe-1 at 300 K indicates the presence of two quadrupole split asymmetric doublets due to the differences in local coordination geometries of [Fe + 3]A and [Fe + 2]B sites. The hyperfine interaction parameters are δ A = 0.152, (Δ E Q)A = 0.598 mm/s with overlapping doublet at δ B = 0.410 and (Δ E Q)B = 0.468 mm/s. Due to molecular association tendency of ligand, dimer Fe-2 possesses 100% Fe + 3(h.s.) hexacoordinated configuration with isomer shift δ = 0.408 mm/s. Slightly distorted octahedral symmetry created by NQCH3ox ligand surrounding Fe + 3(h.s.) state generates small field gradient indicated by quadrupole split Δ E Q = 0.213 mm/s. Decrease of isomer shifts together with variation of quadrupole splits with temperature in Fe-1 dimer compared to Fe-2 is result of charge transfers in [Fe2 + 2, + 3 SQ] complexes. EPR spectrum of Fe-1 shows two strong signals at g 1 = 4.17 and g 2 = 2.01 indicative of S = 3/2 spin state with an intermediate spin of Fe + 3(h.s.) configuration. SQUID data of χ _m^{corr} .T were best fitted by using HDVV spin pair model S = 2, 3/2 resulting in antiferromagnetic exchange ( J = -13.5 cm - 1 with an agreement factor of R = 1.89 × 10 - 5). The lower J

Solid-state molecular organometallic chemistry. Single-crystal to single-crystal reactivity and catalysis with light hydrocarbon substrates.

Science.gov (United States)

Chadwick, F Mark; McKay, Alasdair I; Martinez-Martinez, Antonio J; Rees, Nicholas H; Krämer, Tobias; Macgregor, Stuart A; Weller, Andrew S

2017-08-01

Single-crystal to single-crystal solid/gas reactivity and catalysis starting from the precursor sigma-alkane complex [Rh(Cy 2 PCH 2 CH 2 PCy 2 )(η 2 η 2 -NBA)][BAr F 4 ] (NBA = norbornane; Ar F = 3,5-(CF 3 ) 2 C 6 H 3 ) is reported. By adding ethene, propene and 1-butene to this precursor in solid/gas reactions the resulting alkene complexes [Rh(Cy 2 PCH 2 CH 2 PCy 2 )(alkene) x ][BAr F 4 ] are formed. The ethene ( x = 2) complex, [Rh(Cy 2 PCH 2 CH 2 PCy 2 )(ethene) 2 ][BAr F 4 ]-Oct , has been characterized in the solid-state (single-crystal X-ray diffraction) and by solution and solid-state NMR spectroscopy. Rapid, low temperature recrystallization using solution methods results in a different crystalline modification, [Rh(Cy 2 PCH 2 CH 2 PCy 2 )(ethene) 2 ][BAr F 4 ]-Hex , that has a hexagonal microporous structure ( P 6 3 22). The propene complex ( x = 1) [Rh(Cy 2 PCH 2 CH 2 PCy 2 )(propene)][BAr F 4 ] is characterized as having a π-bound alkene with a supporting γ-agostic Rh···H 3 C interaction at low temperature by single-crystal X-ray diffraction, variable temperature solution and solid-state NMR spectroscopy, as well as periodic density functional theory (DFT) calculations. A fluxional process occurs in both the solid-state and solution that is proposed to proceed via a tautomeric allyl-hydride. Gas/solid catalytic isomerization of d 3 -propene, H 2 C 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111

PubChem atom environments.

Science.gov (United States)

Hähnke, Volker D; Bolton, Evan E; Bryant, Stephen H

2015-01-01

procedure for atom types, functional groups, and tautomeric/resonance forms based on atom environments is possible. The complete sets of atom types and atom environments are supplied as supporting information.