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Twelve 4-benzoyl-1-dichlorobenzoylthiosemicarbazides have been tested as potential antibacterials. All the compounds had MICs between 0.49 and 15.63 µg/ml toward Micrococcus luteus, Bacillus cereus, Bacillus subtilis and Staphylococcus epidermidis indicating, in most cases, equipotent or even more effective action than cefuroxime. In order to clarify if the observed antibacterial effects are universal, further research were undertaken to test inhibitory potency of two most potent compounds 3 and 11 on clinical isolates of Staphylococcus aureus. Compound 11 inhibited the growth of methicillin-sensitive S. aureus (MSSA) at MICs of 1.95-7.81 µg/ml, methicillin-resistant S. aureus (MRSA) at MICs of 0.49-1.95 µg/ml and MDR-MRSA at MIC of 0.98 and 3.90 µg/ml, respectively. Finally, inhibitory efficacy of 3 and 11 on planktonic cells and biofilms formation in clinical isolates of S. aureus and Haemophilus parainfluenzae was tested. The majority of cells in biofilm populations of MSSA and MRSA were eradicated at low level of 3, with MBICs in the range of 7.82-15.63 µg/ml.

Rhabdomyosarcoma is the third most common solid tumor in children and the most common soft tissue sarcoma in this age group. However, 5-year survival is only observed in approximately 70% of cases, and the prognosis for patients with progressive disease is still poor. The authors hypothesize that the still unidentified differences in embryonal and alveolar tumor biology reflect the complex chemical reactions occurring during cell growth and metabolism and may be pursued in isotopic fractionation processes. Presented herein is the first evaluation of the nitrogen and carbon isotope ratio using isotope ratio mass spectrometry in the two major rhabdomyosarcoma histologic types. 15N enrichment was found in tumor tissues of embryonal histological type. The obtained result may indicate that individual patient considerations such as isotope ratio, in addition to widely accepted prognostic factors, may facilitate patient classification in terms of risk groups.

Thanks to proteomics and metabolomics, for the past several years there has been a real explosion of information on the biology of cancer, which has been achieved by spectroscopic methods, including mass spectrometry. These modern techniques can provide answers to key questions about tissue structure and mechanisms of its pathological changes. However, despite the thousands of spectroscopic studies in medicine, there is no consensus on issues ranging from the choice of research tools, acquisition and preparation of test material to the interpretation and validation of the results, which greatly reduces the possibility of transforming the achieved knowledge to progress in the treatment of individual patients. The aim of this study was to verify the utility of isotope ratio mass spectrometry in the evaluation of tumor tissues. Based on experimentation on animal tissues and human neoplasms, the first protocol of stable isotope ratio assessment of carbon and nitrogen isotopes in tumor tissues was established.

Using molecular modeling approach, potential antibacterial agents with triazole core were proposed. A moderate to weak level of antibacterial activity in most of the compounds have been observed, with best minimal inhibitory concentration (MIC) value of 0.003 mg/mL, as shown by the 15 against S. epidermidis. Studied compounds were also submitted to the antifungal assay. The best antifungal activity was detected for 16 with MIC at 0.125 and 0.25 mg/mL against C. albicans and C. parapsilosis, respectively.

Despite vigorous studies, effective nonnucleoside inhibitors of HIV-1 reverse transcriptase (NNRTIs) are still in demand, not only due to toxicity and detrimental side effects of currently used drugs but also because of the emergence of multidrug-resistant viral strains. In this contribution, we present results of docking of 47 inhibitors to 107 allosteric centers of HIV-1 reverse transcriptase. Based on the average binding scores, we have constructed QSAR equations to elucidate directions of further developments in the inhibitor design that come from this structural data. Electronic supplementary material The online version of this article (10.1007/s00894-017-3489-3) contains supplementary material, which is available to authorized users.

Approaches to determine chlorine kinetic isotope effects (Cl-KIEs) on enzymatic dehalogenations are discussed and illustrated by representative examples. Three aspects are considered. First methodology for experimental measurement of Cl-KIEs, with stress being on FAB-IRMS technique developed in our laboratory, is described. Subsequently, we concentrate our discussion on the consequences of reaction complexity in the interpretation of experimental values, a problem especially important in cases of polychlorinated reactants. The most fruitful studies of enzymatic dehalogenations by Cl-KIEs require their theoretical evaluation, hence the computational focus of the second part of this chapter.

This article describes the synthesis of six 4-aryl-(thio)semicarbazides (series a and b) linked with diphenylacetyl moiety along with their pharmacological evaluation on the central nervous system in mice and computational studies, including conformational analysis and electrostatic properties. All thiosemicarbazides (series b) were found to exhibit strong antinociceptive activity in the behavioural model. Among them, compound 1-diphenylacetyl-4-(4-methylphenyl)thiosemicarbazide 1b was found to be the most potent analgesic agent, whose activity is connected with the opioid system. For compounds from series a significant anti-serotonergic effect, especially for compound 1-diphenylacetyl-4-(4-methoxyphenyl)semicarbazide 2b was observed. The computational studies strongly support the obtained results.

The mechanism of cis-dihydroxylation of nitrobenzene and 2-nitrotoluene catalyzed by nitrobenzene 1,2-dioxygenase (NBDO), a member of the naphthalene family of Rieske non-heme iron dioxygenases, was studied by means of the density functional theory method using four models of the enzyme active site. Different possible reaction pathways for the substrate dioxygenation initiated either by the Fe(III)-OOH or HO-Fe(V)═O attack on the aromatic ring were considered and the computed activation barriers compared with the Gibbs free energy of activation for the oxygen-oxygen cleavage leading to the formation of the iron(V)-oxo species from its ferric hydroperoxo precursor. The mechanism of the substrate cis-dihydroxylation leading to the formation of a cis-dihydrodiol was then investigated, and the most feasible mechanism was found to be starting with the attack of the high-valent iron-oxo species on the substrate ring yielding a radical intermediate, which further evolves toward the final product.

A detailed description of the mechanism of C-H hydroxylation by Rieske non-heme iron dioxygenases remains elusive, as the nature of the oxidizing species is not definitively known. DFT calculations on cluster models of nitrobenzene 1,2-dioxygenase were done to explore possible mechanisms arising from oxidation by either the experimentally observed Fe(III)-OOH complex or the putative high-valent HO-Fe(V)=O intermediate formed through a heterolytic O-O bond cleavage. Hydrogen abstraction by HO-Fe(V)=O, followed by oxygen rebound, was found to be consistent with experimental studies. The findings from the quantum mechanical cluster approach were verified by accounting for the effect of the protein environment on transition state geometries and reaction barriers through ONIOM calculations.

International Symposium on Chromatography of Natural Products (ISCNP), Lublin, POLAND, 2016; During the biosynthesis of natural products, isotope fractionation occurs due to the selectivity of enzymes for the heavier or lighter isotopomers. As only some of the positions in the molecule are implicated in a given reaction mechanism, position-specific fractionation occurs. Thus, the position-specific C-13/C-12 ratios in these compounds can be related to their known precursors and to the known isotope effects of enzymes involved in their biosynthesis, or similar reaction mechanisms. This can be accessed by isotope ratio monitoring NMR spectrometry. In this short review, how isotope fractionation occurs and when it is manifest is described. Then, the way that C-13 NMR spectrometry has been applied to study certain aspects of the biosynthesis of the solanaceous alkaloids S-(-)-nicotine and tropine is outlined. Notably, it is shown how similar isotope fractionation is found in the steps of the pathway to the common intermediate, N-methyl-Delta(1)-pyrrolinium, but that in the moieties derived from different origins no such similarity is found, the isotopic composition of these atoms reflecting their specific metabolic ancestry. In a second example, tramadol, it is shown how this technique can be used in retro-biosynthesis to give direction as to what precursors and pathway intermediates are probable. It is shown how the observed fractionation in the site-specific C-13/C-12 ratios can be effectively explained by known metabolism and the properties of enzymes proposed for the pathway. Furthermore, it can give indications of possible mechanisms of those enzymes that are as yet to be described for a number of key steps. (C) 2016 Phytochemical Society of Europe. Published by Elsevier Ltd. All rights reserved.

International audience; Many O-methyl and N-methyl groups in natural products are depleted in C-13 relative to the rest of the molecule. These methyl groups are derived from the C-1 tetrahydrofolate pool via L-methionine, the principle donor of methyl units. Depletion could occur at a number of steps in the pathway. We have tested the hypothesis that methionine biosynthesis is implicated in this depletion by using a combined experimental and theoretical approach. By using isotope ratio monitoring C-13 NMR spectrometry to measure the position-specific distribution of C-13 within L-methionine of natural origin, it is shown that the S-methyl group is depleted in C-13 by similar to 20%o relative to the other positions in the molecule. In parallel, we have conducted a basic theoretical analysis of the reaction pathway of methionine synthase to assess whether the enzyme cobalamin-independent L-methionine synthase (EC 2.1.1.14) that catalyzes the synthesis of L-methionine from 5-methyl-tetrahydrofolate and homocysteine plays a role in causing this depletion. Calculation predicts a strong normal C-13 kinetic isotope effect (1.087) associated with this enzyme. Hence, depletion in C-13 in the S-methyl of L-methionine during biosynthesis can be identified as an important factor contributing to the general depletion seen in many O methyl and N-methyl groups of natural products.

Approaches to determine chlorine kinetic isotope effects (Cl-KIEs) on enzymatic dehalogenations are discussed and illustrated by representative examples. Three aspects are considered. First methodology for experimental measurement of Cl-KIEs, with stress being on FAB-IRMS technique developed in our laboratory, is described. Subsequently, we concentrate our discussion on the consequences of reaction complexity in the interpretation of experimental values, a problem especially important in cases of polychlorinated reactants. The most fruitful studies of enzymatic dehalogenations by Cl-KIEs require their theoretical evaluation, hence the computational focus of the second part of this chapter.

Reductive dehalogenation involvingcobalamin has been proved to be a promising strategy for decontamination of the polluted environment. However, cob(I)alamin can act both as a strong reductant and a powerful nucleophile, and thus, several competing dehalogenation pathways may be involved. This work uses experimentally calibrated density functional theory on a realistic cobalamin model to resolve controversies of cobalamin-mediated reduction of chloroethylenes by exploring mechanisms of electron transfer, nucleophilic substitution, and nucleophilic addition. The computational results provide molecular-level insight into the competing pathways for chloroethylenes reacting with cob(I)alamin: the computed ratios of inner-sphere to outer-sphere pathways for perchloroethylene and trichloroethylene are 17:1 and 3.5:1, respectively, in accord with the corresponding experimental ratios of >10:1 and >2.3:1,whilethe computed outer-sphere pathway for other less-chlorinated ethylenesis hampered by high barriers (>25 kcal/mol). Thus, a new mechanistic picture has been obtained in which the highly chlorinated ethylenes primarily react via an inner-sphere nucleophilic-substitution pathway, whereas the less-chlorinated ethylenes mainly react through an inner-spherenucleophilic-addition pathway. Especially, the quantitative comparison of standard reduction potentials between the formed chlorinated-cobalamin and cob(II)alamin/cob(I)alamin couple can be used to distinguish whether the inner-sphere pathway can proceed or not, and linear free-energy relationships have been developed to predict the reductive dehalogenation reactivity within a given mechanism. Finally, we propose new dual-isotope analyses for distinguishing the various environmental dehalogenation mechanisms.

Nucleophilic dechlorination of all 209 PCBs congeners by ethylene glycol anion has been studied theoretically at the DFT level. The obtained Gibbs free energies of activation are in the range 7–22 kcal/mol. The reaction Gibbs free energies indicate that all reactions are virtually irreversible. Due to geometric constrains these reactions undergo rather untypical attack with attacking oxygen atom being nearly perpendicular to the attacked C–Cl bond. The most prone to substitution are chlorine atoms that occupy ortho- (2, 2′, 6, 6′) positions. These results provide extensive information on the PEG/KOH dependent PCBs degradation. They can also be used in further developments of reaction class transition state theory (RC-TST) for description of complex reactive systems encountered for example in combustion processes.

Compound-specific isotope analysis (CSIA) is a promising approach for tracking biotransformation of organic pollutants, but isotope fractionation associated with aromatic oxygenations is only poorly understood. We investigated the dioxygenation of a series of nitroaromatic compounds to the corresponding catechols by two enzymes, namely, nitrobenzene and 2-nitrotoluene dioxygenase (NBDO and 2NTDO) to elucidate the enzyme- and substrate-specificity of C and H isotope fractionation. While the apparent C-13- and H-2-kinetic isotope effects of nitrobenzene, nitrotoluene isomers, 2,6-dinitrotoluene, and naphthalene dioxygenation by NBDO varied considerably, the correlation of C and H isotope fractionation revealed a common mechanism for nitrobenzene and nitrotoluenes. Similar observations were made for the dioxygenation of these substrates by 2NTDO. Evaluation of reaction kinetics, isotope effects, and commitment-to-catalysis based on experiment and theory showed that rates of dioxygenation are determined by the enzymatic O-2 activation and aromatic C oxygenation. The contribution of enzymatic O-2 activation to the reaction rate varies for different nitroaromatic substrates of NBDO and 2NTDO. Because aromatic dioxygenation by nonheme iron dioxygenases is frequently the initial step of biodegradation, O-2 activation kinetics may also have been responsible for the minor isotope fractionation reported for the oxygenation of other aromatic contaminants.

The preliminary cytotoxic effect of 4-ethoxycarbonylmethyl-1-(piperidin-4-ylcarbonyl)-thiosemicarbazide hydrochloride (1)—a potent topoisomerase II inhibitor—was measured using a MTT assay. It was found that the compound decreased the number of viable cells in both estrogen receptor-positive MCF-7 and estrogen receptor-negative MDA-MB-231breast cancer cells, with IC50 values of 146 ± 2 and 132 ± 2 μM, respectively. To clarify the molecular basis of the inhibitory action of 1, molecular docking studies were carried out. The results suggest that 1 targets the ATP binding pocket. Figure 4-ethoxycarbonylmethyl-1-(piperidin-4-ylcarbonyl)-thiosemicarbazide hydrochloride Electronic supplementary material The online version of this article (doi:10.1007/s00894-012-1679-6) contains supplementary material, which is available to authorized users.

The oxidation of (2'S)-nicotine in the active site of human cytochrome P450 2A6 has been subjected to a detailed analysis by theoretical quantum mechanical/molecular mechanical (QM/MM) calculations linked with a theoretical and experimental study of the associated isotope effects. The study has focused on seeking an explanation as to why oxidation at the 5'-carbon position (A) is favored over oxidation at the methyl carbon (CMe) position (B). It is deduced that the choice of hydrogen for abstraction is not determined by geometric features of the active site, but by the lower energy barrier associated with 5' oxidation. N-Demethylation leading to N-hydroxymethylnornicotine requires ca. 6.5 kcal/mol more energy to transfer a hydrogen atom than is required for oxidation on the carbon 5'. Neither protonation of the pyrrolidine nitrogen (N1') nor inclusion of a water molecule in the reaction process influences the balance between the two oxidation pathways. In both cases, the hydrogen transfer step is rate limiting. An analysis of the calculated kinetic isotope effects indicates that the presence of a (2)H in either the C5' or the CMepositions has a significant effect on the reaction kinetics. However, the experimental values of around 2.2-2.6 are considerably lower than those predicted by theoretical calculations (9.3 and 6.9 for C5' or the CMe positions, respectively, in the LS state of Cpd I), typical of the masking commonly found for CYP450 reactions. The fact that similar values are found for cotinine formation from both substrates, however, may indicate that the measured value is not that for H-abstraction but, rather, is a combined value for (2)H influence on electronic redistribution between iminium states of the pyrrolidine ring. This is the first time that oxidation at the C5' or the CMe positions has been directly compared and that isotope effects have been obtained for this reaction in a human cytochrome P450 reaction.

Ever since the recognition of strong pharmaceutical activities of triazoles and thiadiazoles, these scaffolds have been the subject of vigorous studies. One of the best strategies for synthesis of these azoles is dehydrocyclization of 1,4-disubstituted thiosemicarbazides, which leads to s-triazoles in alkaline media, whereas in strong acidic media 1,3,4-thiadiazoles are formed. However, the literature is riddled with contradictory communications regarding the nature of the products of such reactions under mild acidic conditions. As these compounds are not amenable to X-ray analysis, we have resorted to NMR and theoretical modelling to resolve this discrepancy. In this article, we present arguments indicating that dehydrocyclization of 4-benzoylthiosemicarbazides in glacial acetic acid leads to thiadiazole derivatives. These structural findings are augmented by studies of bioactivity of a few members of the studied class of compounds.

An approach combining experimental kinetic isotope effects (KIEs) and quantum chemistry calculations at the DFT level was used to explore the mechanism by which the C?N bond of the bicyclic amine nortropine (2) was cleaved during the catabolism of tropine (1) by Pseudomonas bacteria. The working model is that the ring opening involves the oxidation of nortropine at one bridgehead carbon position by cytochrome P450 monooxygenase, followed by the protonation of the nitrogen, which leads to heterolytic bond cleavage. 15N and 2H heavy-atom KIEs for the reaction were determined both experimentally and theoretically (DFT). Transition states were described for both oxidation and ring cleavage. Calculation of the heavy-atom KIE values indicated a high 2H, a moderate 13C, and a negligible 15N effect for the oxidation and a strong inverse 15N and normal 13C KIEs at N and 1C for the 1C?N bond cleavage. Experimental KIE values for the overall reaction were a strongly inverse 15N and negligible 2H effect, which indicated that the catalytic rate depended on the bond-breaking part of the reaction. Thus, from the experimental and calculated results, it could be proposed that the enzyme-dependent activation of the 1C position to destabilize the structure is a prerequisite for bond cleavage, but the driving force behind the carbonnitrogen bond fission is the simultaneous protonation of the nitrogen of the intermediate species [3] and sp3 to sp2 transition at the 1C position. Thus, a mechanism that satisfactorily fits both the experimental and theoretical results could be proposed. It is unusual in that it indicates that the cytochrome P450 monooxygenase-catalyzed hydrogen abstractionthough essential for the overall reaction to occuris not the kinetically limiting partial reaction.

(15)N heavy isotope effects are especially useful when detail is sought pertaining to the reaction mechanism for the cleavage of a C-N bond. Their potential in assisting to describe the mechanism of N-demethylation of tertiary amines by the action of cytochrome P450 monooxygenase has been investigated. As a working model for the first step, oxidation of the N-methyl group to N-methoxyl, tropine and a cytochrome P450 monooxygenase reaction centre composed of a truncated heme with sulfhydryl as the axial ligand were used. It is apparent that this first step of the reaction proceeds via a hydrogen atom transfer mechanism. Transition states for this step are described for both the high spin ((4)TS(H)) and low spin ((2)TS(H)) pathways in both gas and solvation states. Hence, overall normal secondary (15)N KIE could be calculated for the reaction path modeled in the low spin state, and inverse for the reaction modeled in the high spin state. This partial reaction has been identified as the probable rate limiting step. The model for the second step, fission of the C-N bond, consisted of N-methoxylnortropine and two molecules of water. A transition state described for this step, TS(CN), gives a strongly inverse overall theoretical (15)N KIE.

The mechanism of the environmentally important reaction between permanganate anion and trichloroethene (TCE) has been studied theoretically using modern DFT functional. It has been shown that IEFPCM/M05-2X/aug-cc-pVDZ theory level yields activation parameters and carbon isotopic fractionation factor in excellent agreement with the experimental data. Obtained results indicate that this reaction proceeds via the 3+2 mechanism with a very early transition state, in which the new C-O bonds are formed only in about 20%. An alternative, stepwise mechanism that involves initial formation of a single new C-O bond and a C-Mn bond, followed by rearrangement to the permanganate-TCE adduct, has been found to be more energetically demanding and in disagreement with the experimental isotopic fractionation.

We present QM/MM calculations that show differences in geometries of active sites of M 4 and H 4 isoforms of human LDH ligated with oxamate, pyruvate or l -lactate. As the consequence of these differences, binding isotope effects of the methyl hydrogen atoms of pyruvate and l -lactate may be used to experimentally distinguish these isoforms. Based on the FEP calculations we argue that l -lactate is a better candidate for the experimental studies. Our calculations of energies of interactions of ligands with the active site residues provide explanation for the observed experimentally sensitivity to inhibition of the M 4 isoenzyme isoform and pinpoint the differences to interactions of the ligand with the histidine residue. We conclude that pyruvate interacts much stronger in the active site of H 4 than M 4 isoform and that the latter interactions are weaker than with water molecules in the aqueous solution.

This article reports anti- Toxoplasma gondii activity of 3-(thiophen-2-yl)-1,2,4-triazole-5-thione. The compound displayed significant and reproducible antiparasitic effects at nontoxic concentrations for the host cells, with an experimentally determined 50% inhibitory concentration (IC 50 ) at least 30 times better than that of the known chemotherapeutic agent sulfadiazine. Purine nucleoside phosphorylase was defined as the probable target for anti- Toxoplasma activity of the tested compound. These results provide the foundation for future work to develop a new class of medicines to better treat toxoplasmosis.

4-Benzoyl-1-(4-methyl-imidazol-5-yl)-carbonylthiosemicarbazide (1) was synthesized, and its antibacterial and type IIA topoisomerase (DNA gyrase and topoisomerase IV) activity evaluated. (1) was found to have high therapeutic potential against opportunistic Gram-positive bacteria, and inhibitory activity against topoisomerase IV (IC(50)=90 μM) but not against DNA gyrase. An increase in activity against topoisomerase IV (IC(50)=14 μM) was observed when the imidazole moiety of (1) was replaced with the indole group in 4-benzoyl-1-(indol-2-yl)-carbonylthiosemicarbazide (2). However, (2) showed only weak antibacterial activity. Although the results of the bacterial type IIA topoisomerases inhibition study did not parallel antibacterial activities, our observations strongly imply that a 4-benzoylthiosemicarbazide scaffold can be developed into an efficient Gram-positive antibacterial targeting topoisomerase IV. The difference in activity against type IIA topoisomerases between (1) and (2) was further investigated by docking studies, which suggested that these compounds target the ATP binding pocket.

Using the example of lactate dehydrogenase, we show that enzyme quaternary structure has an important influence on the structure of the active site and that models that comprise all amino acids in the vicinity of an active site, but are missing this structural information, can lead to incorrect results. We also show that binding isotope effects are very sensitive to the geometric parameters, and thus one should be very cautious when interpreting results obtained with models that are too coarse. In terms of the type of hydrogen bonds, our results indicate that binding isotope effects are pronounced only when a hydrogen bond exhibits some covalent character.

Four 4-aryl-3-(2-methyl-furan-3-yl)-Δ2-1,2,4-triazole-5-thiones were synthesized by intramolecular cyclization of 4-aryl-1-[(2-methyl-furan-3-yl)carbonyl]thiosemicarbazides in alkaline medium. The antimicrobial activity of the synthesized triazoles was evaluated. Semiempirical calculations of geometries, energies, and QSAR parameters have been determined in the hope of gaining insight into different biological activities of closely related isomers. New RM1 parameterization has been shown to perform very well for this class of compounds.

Five iridium Ir(III) complexes have been studied using B3P86, B3LYP, M05, M06, M05-2X, and M06-2X functionals within configuration interaction singles (CIS) and time dependent density functional theory (TDDFT) formalisms with the aim of finding theory level that would allow for reliable prediction of emission properties. Knowledge of these properties prior to synthesis may significantly facilitate rational design of organic light-emitting diodes (OLEDs). Our results indicate that the M05-2X functional gives excellent results in this respect for the class of complexes studied here with the exception of the (bsn)2Ir(acac) complex. We have shown that the discrepancy between the theoretical and experimental values for this complex is due to the presence of the sulfur atom. Copyright © 2009 John Wiley & Sons, Ltd.

We report the chromatographic behavior of the antitubercular drugs isoniazid (INH), pyrazinamide (PYR), ethambutol (ETB), and p -aminosalicylic acid (PAS) in reversed-phase TLC with organic aqueous mobile phases modified with Cu(II) chloride. The spectra of the free ligands and complexes formed during chromatography were measured densitometrically by use of a scanner equipped with a diode-array detector and compared in the range 200–700 nm. The complexes of Cu(II) with isoniazid and ethambutol were isolated on a micropreparative scale. The structures of the INH-Cu and EMB-Cu complexes were analyzed by electron paramagnetic resonance (EPR) spectroscopy and illustrated graphically by molecular modeling using GaussView software.

Kinetic isotope effects (KIEs) on the two alternative reactions, SN2 and E2, between hypochlorite anion and ethyl chloride in water have been studied theoretically using B3LYP and M06-2X functionals. It has been found that the latter one yields more correct geometries and energetics. Although, in the qualitative sense, KIEs obtained using both DFT functionals are in agreement, interpretation of some of them, like (18)O-KIE in the present case, leads to different mechanistic conclusions.

The primary and secondary deuterium kinetic isotope effects as well as leaving-group fluorine kinetic isotope effects have been calculated for the base-promoted elimination of hydrogen fluoride from 4-fluoro-4-(4'-nitrophenyl)butane-2-one in 75% aqueous methanol solution. The elimination was studied for both formate and imidazole as the catalytic base; and reactant and transition state structures and vibrational frequencies have been calculated by including the base explicitly and by including the solvent by an implicit solvation model that includes both electrostatics by class IV charges and first-solvation-shell effects by atomic surface tensions. We used the M06-L density functional for all calculations. The optimized stationary points, the geometry changes along the solution-phase minimum free energy path, and the solution-phase free energy profile indicate that the elimination reaction occurs concertedly but asynchronously via an E1cb-like transition state. Reaction rates were calculated by the equilibrium solvation path method, using variational transition state theory with multidimensional tunneling. The primary deuterium kinetic isotope effects are calculated to be large: 1.67 and 5.13 for formate and imidazole, respectively. The corresponding C4-secondary deuterium kinetic isotope effects are 1.044 and 1.044, and the leaving group fluorine kinetic isotope effects are respectively 1.020 and 1.015.

The cyclization of 2-(hydroxypropyl)-4-nitrophenyl phosphate (HpPNP) catalyzed by the dinuclear zinc complex of 1,3-bis(1,4,7-triazacyclonon-1-yl)-2-hydroxypropane (1) proceeds by a transition state that is different from that of the uncatalyzed reaction. Kinetic isotope effects (KIEs) measured in the nucleophilic atom and in the leaving group show that the uncatalyzed cyclization has a transition state (TS) with little phosphorus-oxygen bond fission to the leaving group ((18)k(lg) = 1.0064 +/- 0.0009 and (15)k = 1.0002 +/- 0.0002) and that nucleophilic bond formation occurs in the rate-determining step ((18)k(nuc) = 1.0326 +/- 0.0008). In the catalyzed reaction, larger leaving group isotope effects ((18)k(lg) = 1.0113 +/- 0.0005 and (15)k = 1.0015 +/- 0.0005) and a smaller nucleophile isotope effect ((18)k(nuc) = 1.0116 +/- 0.0010) indicate a later TS with greater leaving group bond fission and greater nucleophilic bond formation. These observed nucleophile KIEs are the combined effect of the equilibrium effect on deprotonation of the 2'-hydroxyl nucleophile and the KIE on the nucleophilic step. An EIE of 1.0245 for deprotonation of the hydroxyl group of HPpNP was obtained computationally. The different KIEs for the two reactions indicate that the effective catalysis by 1 is accompanied by selection for an altered transition state, presumably arising from the preferential stabilization by the catalyst of charge away from the nucleophile and toward the leaving group. These results demonstrate the potential for a catalyst using biologically relevant metal ions to select for an altered transition state for phosphoryl transfer.

Three 3-(thiophen-2-yl)-4-substituted-Δ 2 -1,2,4-triazoline-5-thiones were synthesized by intramolecular cyclization of 1-(thiophen-2-ylcarbonyl)-4-substituted thiosemicarbazides in alkaline medium. Their effects on the central nervous system (CNS) of mice in some behavioral tests were investigated. All investigated compounds displayed antinociceptive activity. The correlation between the structural features and bioactivity has been discussed.

In order to interpret the observed isotopic fractionation it is necessaryto understand its relationship with the isotope effect(s) on steps that occur during the conversion of the initial reactant to the final product. We examine this relationship from the biochemical point of view and elaborate on the consequences of the assumptions that it is based on. We illustrate the discrepancies between theoretical and experimental interpretation of kinetic isotope effects on examples of dehalogenation reactions that occur at an aromatic carbon atom. The examples include 4-chlorobenzoyl-CoA dehalogenase-catalyzed conversion of 4-chlorobenzoyl-CoA to 4-hydroxybenzoyl-CoA, dehaloperoxidase-catalyzed conversion of 2,4,6-trichlorophenol to 2,6-dichloroquinone, and spontaneous hydrolysis of atrazine at pH 12. For this latter reaction we have measured the chlorine kinetic isotope effect and estimated its value theoretically at the DFT level of theory. Results of chlorine kinetic isotope effects suggest that the studied dechlorination reactions proceed in a single step with significant weakening of the carbon-chlorine bond in the transition state.

The application of kinetic isotope effects and molecular modeling to characterize three enzyme-catalyzed reactions is presented; the mechanism of the chloroacid dehalogenase catalyzed reaction is approached using chlorine kinetic isotope effects and solvent kinetic isotope effects. The pre-steady-state phase of the reaction catalyzed by methylmalonyl-CoA mutase is approached by different QM/MM schemes and the results are validated by comparison with the experimental value of the deuterium kinetic isotope effect. Finally, a procedure for improving QM/MM calculations is illustrated by analysis of the trihydroxynaphthalene reductase-catalyzed reaction.

We have recently described theoretically the mechanism of the reaction between 4-methyl-1,2,4-triazol-3-thiol and formaldehyde that leads to the N-substituted product, N1-hydroxymethyl-4-methyl-1,2,4-triazol-3-thione. New experimental findings indicate that the thione tautomeric form in reaction with formaldehyde also yields this product. This observation could not be explained on the basis of previous calculations, which predicted that the thione tautomer undergoes nucleophilic substitution at the sulfur atom, leading to the S-substituted product. We present theoretical explanation of the observed reactivity. We show that under experimental conditions this reaction proceeds with the intervention of the anionic form of the triazole with the Gibbs free energy of activation of only 1.8 kcal/mol. Copyright © 2008 John Wiley & Sons, Ltd.

By the reaction of 2-methyl-furan-3-carboxylic acid hydrazide with isothiocyanates, 1-[(2-methyl-furan-3-yl)carbonyl]-4-substituted thiosemicarbazides 1 were obtained. Further cyclization with 2% NaOH led to the formation of 3-(2-methyl-furan-3-yl)-4-substituted-Δ2-1,2,4-triazoline-5-thiones 2. The pharmacological effects of 2 on the central nervous system in mice were investigated. Strong antinociceptive properties of the investigated derivatives were observed in a wide range of doses.

The synthesis of 4-[3-(2-methyl-furan-3-yl)-5-thioxo-1,2,4-triazolin-4-yl]acetic acid, its structural study in the solid state, and the thiol–thione tautomeric recognition on the basis of spectroscopic data and theoretical calculations are presented. It is shown that NMR spectra, especially 13C and 15N, are indicative of the actual tautomeric form whereas vibrational data can be ambiguous. © 2008 Wiley Periodicals, Inc. Heteroatom Chem 19:337–344, 2008; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/hc.20433

During the biosynthesis of natural products, isotopic fractionation occurs due to the selectivity of enzymes for the heavier or lighter isotopomers. As only some of the positions in the molecule are implicated in a given reaction mechanism, position-specific fractionation occurs, leading to a non-statistical distribution of isotopes. This can be accessed by isotope ratio monitoring (13)C NMR spectrometry. The solanaceous alkaloids S-(-)-nicotine and hyoscyamine (atropine) are related in having a common intermediate, but downstream enzymatic steps diverge, providing a relevant test case to: (a) elucidate the isotopic affiliation between carbon atoms in the alkaloids and those in the precursors; (b) obtain information about the kinetic isotope effects of as yet undescribed enzymes, thus to make predictions as to their possible mechanism(s). We show that the position-specific (13)C/(12)C ratios in the different moieties of these compounds can satisfactorily be related to their known precursors and to the known kinetic isotope effects of enzymes involved in their biosynthesis, or to similar reaction mechanisms. Thus, the pathway to the common intermediate, N-methyl-Δ(1)-pyrrolinium, is seen to introduce similar isotope distribution patterns in the two alkaloids independent of plant species, whereas the remaining atoms of each target compound, which are of different origins, reflect their specific metabolic ancestry. We further demonstrate that the measured (13)C distribution pattern can be used to deduce aspects of the reaction mechanism of enzymes still to be identified.

Contrary to the typical nucleophilic substitution, occurring on the sulfur atom of 4-methyl-1,2,4- triazol-3-thiole, the reaction with formaldehyde leads to the formation of the NC bond rather than the SC bond. The mechanism of this reaction has been characterized theoretically. Calculations indicate that the reaction proceeds via a cyclic transition state involving one solvent molecule with the Gibbs free activation energy of only 2 kcal/mol. The alternative pathway that leads to the SC bond formation is about 5 kcal/mol more energetically demanding. Copyright © 2007 John Wiley & Sons, Ltd.

1,3,8-Trihydroxynaphthalene is one of the substrates in the fungal melanin biosynthesis pathway. We present theoretical studies on energies of its tautomeric forms and their rotamers. Several theory levels and solvent models have been tested using experimental results obtained in water-acetone mixtures as the reference point. Our results indicate that the best agreement with these data is obtained with density functional theory levels when the continuum solvation model uses the united atom topological cavity. We also noticed a fairly good performance of the semiempirical AM1 method that makes it a promising alternative for studies of large systems.

Heavy-atom isotope effects for the N-demethylation of nicotine have been determined in vivo in static-phase biosynthetically incompetent plant cell cultures of Nicotiana species. A (2)H kinetic isotope effect of 0.587 and a (15)N kinetic isotope effect of 1.0028 were obtained. An identical (15)N kinetic isotope effect of 1.0032 was obtained for the nicotine analogue, N-methyl-2-phenylpyrrolidine. The magnitude of the (15)N heavy-atom isotope effect indicates that the fission of the CN bond is not rate limiting for demethylation. The theoretical calculation of heavy-atom isotope effects for a model of the reaction pathway based on cytochrome P450 best fits the measured kinetic isotope effect to the addition of hydroxyl ion to iminium to form N-hydroxymethyl, for which the computed (2)H- and (15)N kinetic isotope effects are 0.689 and 1.0081, respectively. This large inverse (2)H kinetic isotope effect is not compatible with the initial abstraction of the H from the methyl group playing a significant kinetic role in the overall kinetic limitation of the reaction pathway, since computed values for this step (4.54 and 0.9995, respectively) are inconsistent with the experimental data.

The assignment of the absolute configuration of hydroxy- and aminophosphonates by their double derivatization with commercially available naproxen is presented. The correlation between the spatial arrangement around the stereogenic carbon center and the signs of the DeltadeltaRS allows determination of the absolute configuration of hydroxy- and aminophosphonates by simple comparison of the 1H and 31P NMR spectra of the (R)- and (S)-naproxen ester or amide derivatives. Extensive conformational analysis (theoretical calculations, low-temperature experiments) supported by the NMR studies of structurally diverse naproxen esters and amides of hydroxy- and aminophosphonates proved that a simplified model can be successfully used.

Carbon and secondary deuterium kinetic isotope effect (KIE) for three types of SN2 methyl transfer reactions have been predicted theoretically at a DFT level in gas phase and in aqueous solution modelled by the PCM continuum solvent model. No correlation between these isotope effects and geometrical features of the corresponding transition states (TSs), force constants of the imaginary frequency or Gibbs free energies of the studied reactions has been found. These findings suggest that comparative analysis of the magnitudes of the studied KIEs should be constrained to interpretation of the TS localization on the reaction coordinate only in a series of very closely related reactions. Copyright # 2007 John Wiley & Sons, Ltd.

While typically cyclodehydration of thiosemicarbazides in acidic media leads to 1,3,4-thiadiazoles, we have recently shown that under reflux conditions in anhydrous acetic acid the cyclization yields an imidazolidine derivative. The mechanism of this reaction has been characterized theoretically. Calculations indicate that this direction, facilitated by the presence of the CH2CO2 moiety in the N4 substituent is favored over the direction leading toward the thiadiazole product. Formation of the CN bond that closes the five-member ring appears to be concerted with the departure of ethanol molecule, although the proton transfer from the nitrogen atom to oxygen atom is much more advanced in the transition state. Copyright © 2007 John Wiley & Sons, Ltd.

OH radicals generated by the photolysis of H2O2 can degrade aromatic contaminants by either attacking the aromatic ring to form phenolic products or oxidizing the substituent. We characterized these competing pathways by analyzing the carbon and hydrogen isotope fractionation (eC and eH) of various substituted benzenes. For benzene and halobenzenes that only undergo ring addition, low values of eC (-0.7‰ to -1.0‰) were observed compared with theoretical values (-7.2‰ to -8‰), possibly owing to masking effect caused by pre-equilibrium between the substrate and OH radical preceding the rate-limiting step. In contrast, the addition of OH radicals to nitrobenzene ring showed a higher eC (-3.9‰), probably due to the lower reactivity. Xylene isomers, anisole, aniline, N,N-dimethylaniline, and benzonitrile yielded normal eH values (-2.8‰ to -29‰) indicating the occurrence of side-chain reactions, in contrast to the inverse eH (11.7‰ to 30‰) observed for ring addition due to an sp(2) to sp(3) hybridization change at the reacting carbon. Inverse eH values for toluene (14‰) and ethylbenzene (30‰) were observed despite the formation of side-chain oxidation products, suggesting that ring addition has a larger contribution to isotope fractionation. Dual element isotope slopes (∆δ(2)H/∆δ(13)C) therefore allow identification of significant degradation pathways of aromatic compounds by photochemically induced OH radicals. Issues that should be addressed in future studies include quantitative determination of the contribution of each competing pathway to the observed isotope fractionation and characterization of physical processes preceding the reaction that could affect isotope fractionation.

Azoles are a promising class of the new generation of HIV-1 non-nucleoside reverse transcriptase inhibitors (NNRTIs). From thousands of reported compounds, many possess the same basic structure of an aryl substituted azole ring linked by a thioglycolamide chain with another aromatic ring. In order to find novel extensions for this basic scaffold, we explored the 5-position substitution pattern of triazole NNRTIs using molecular docking followed by the synthesis of selected compounds. We found that heterocyclic substituents in the 5-position of the triazole ring are detrimental to the inhibitory activity of compounds with four-membered thioglycolamide linker and this substitution seems to be viable only for compounds with shorter two-membered linker. Promising compound, N-(4-carboxy-2-chlorophenyl)-2-((4-benzyl-5-methyl-4H-1,2,4-triazol-3-yl)sulfanyl)acetamide, with potent inhibitory activity and acceptable aqueous solubility has been identified in this study that could serve as lead scaffold for the development of novel water-soluble salts of triazole NNRTIs.

In the present article, we describe the inhibitory potency of nine thiosemicarbazide derivatives against bacterial type IIA topoisomerases, their antibacterial profile and molecular modelling evaluation. We found that one of the tested compounds, compound 7, significantly inhibits activity of Staphylococcus aureus DNA gyrase with an IC50 below 15 μM. Besides, this compound displays antibacterial activity on reference Staphylococuss spp. and Enterococcus faecalis strains as well as clinical S. aureus isolates at non-cytotoxic concentrations in mammalian cells with MIC values ranging from 16 to 32 μg/mL thereby indicating, in some cases, equipotent or even more effective action than standard drugs such as vancomycin, ampicillin and nitrofurantoin. The computational studies showed that both molecular geometry and the electron density distribution have a great impact on antibacterial activity of thiosemicarbazide derivatives.

We report the influence of the substituent at the N atom of the ligands on the synthesis, biological activity, and stability of Pd(II) complexes of the general formula PdL(2). The compounds adopt a cis or trans configuration with respect to the substituent at the nitrogen atom. Sterically hindered substituents promote the formation of trans isomers, whereas when the nitrogen atom is unsubstituted, cis isomers are formed. The compounds were characterized by elemental analysis, infrared and 1H NMR spectroscopies, and electrospray mass spectrometry. The complexes were also studied using X-ray diffraction and computational DFT methods. Both complexes cis-3a and trans-3c exhibit square-planar geometries around the Pd(II) atom. The cytotoxic effects of these complexes were examined on two human leukemia cell lines, HL-60 and NALM-6. Pd complex cis-3a showed significant cytotoxic activity. The effects exhibited by this complex were comparable to those reported for carboplatin. Loigand 2a was not cytotoxic. Computational analysis carried out at the PB/B3LYP/LACVP**//mPW1PW91/LanL2DZ level showed excellent correlation between the energy difference of the cis and trans isomers and the cytotoxic activity, rendering computations a useful predictive tool for the design of new drugs.

ONIOM calculations have provided novel insights into the mechanism of homolytic Co-C5' bond cleavage in the 5'-deoxyadenosylcobalamin cofactor catalyzed by methylmalonyl-CoA mutase. We have shown that it is a stepwise process in which conformational changes in the 5'-deoxyadenosine moiety precede the actual homolysis step. In the transition state structure for homolysis, the Co-C5' bond elongates by approximately 0.5 Angstroms from the value found in the substrate-bound reactant complex. The overall barrier to homolysis is approximately 10 kcal/mol, and the radical products are approximately 2.5 kcal/mol less stable than the initial ternary complex of enzyme, substrate, and cofactor. The movement of the deoxyadenosine moiety during the homolysis step positions the resulting 5'-deoxyadenosyl radical for the subsequent hydrogen atom transfer from the substrate, methylmalonyl-CoA.