Hybrid QM/MM study of thio effects in transphosphorylation reactions

Results of a series of hybrid quantum mechanical/molecular mechanical (QM/MM) activated dynamics simulations of thio effects in the transphosphorylation (methanolysis) of a 2'-ribose, 5'-methyl phosphate-diester under basic conditions are presented. Single and double substitutions in the nonbridging oxygen positions exhibit thio effects in accord with experimental data and show the existence of a stable intermediate. Thio substitution at the 2' and 5' positions resulted in reactions having a single transition state with increased and decreased free energy barriers, respectively, relative to the unsubstituted reaction. In all of the reactions except for the 5' substitution, the rate-limiting step corresponds to exocyclic cleavage. In the 5' substitution reaction, the rate-limiting step corresponds to endocyclic cleavage and shows a considerable reverse thio effect, in accord with experimental observations of phosphates with enhanced leaving groups. Thio substitution at the 3' position results in a mild reverse thio effect that arises from electronic stabilization of the dianionic transition state. The results presented here provide an important step toward the development and application of new hybrid QM/MM methods that, combined with experiment, may provide a detailed picture of the molecular mechanisms of RNA catalysis.     

Hybrid QM/MM study of thio effects in transphosphorylation reactions: the role of solvation

Transphosphorylation thio effects in solution are studied using hybrid QM/MM calculations with a d-orbital semiempirical Hamiltonian. Activated dynamics simulations were performed for a 3' ribose-phosphate model in an explicit 20 A sphere of TIP3P water surrounded by a solvent boundary potential, and free energy analysis was performed using the weighted histogram analysis method. Single thio-substitutions at all of the phosphoryl oxygen positions and a double thio-substitution at the nonbridging positions were considered. The reaction free energy profiles are compared with available experimental data, and the role of solvation on the barrier heights and reaction coordinate is discussed. These results provide an important step in the characterization of thio effects in reactions of biological phosphates that may aid in the interpretation of kinetic data and ultimately help to unravel the catalytic mechanisms of ribozymes.     

Organocatalysis mediated by (thio)urea derivatives

Over the last decade the potential for N,N-dialkyl(thio)urea derivatives to serve as active metal-free organocatalysts for a wide range of synthetically useful reactions susceptible to the influence of general acid catalysis has begun to be realised. This article charts the development of these catalysts (with emphasis on the design principles involved), from early "proof-of-concept" materials to contemporary active chiral (bifunctional) promoters of highly selective asymmetric transformations.     

Smooth solvation method for d-orbital semiempirical calculations of biological reactions. 2. Application to transphosphorylation thio effects in solution

Density-functional and semiempirical quantum methods and continuum dielectric and explicit solvation models are applied to study the role of solvation on the stabilization of native and thio-substituted transphosphorylation reactions. Extensive comparison is made between results obtained from the different methods. For the semiempirical methods, explicit solvation was treated using a hybrid quantum mechanical/molecular mechanical (QM/MM) approach and the implicit solvation was treated using a recently developed smooth solvation model implemented into a d-orbital semiempirical framework (MNDO/d-SCOSMO) within CHARMM. The different quantum and solvation methods were applied to the transesterification of a 3'-ribose,5'-methyl phosphodiester that serves as a nonenzymatic model for the self-cleavage reaction catalyzed by the hammerhead and hairpin ribozymes. Thio effects were studied for a double sulfur substitution at the nonbridging phosphoryl oxygen positions. The reaction profiles of both the native and double sulfur-substituted reactions from the MNDO/d-SCOSMO calculations were similar to the QM/MM results and consistent with the experimentally observed trends. These results underscore the need for a d-orbital semiempirical representation for phosphorus and sulfur for the study of experimentally observed thio effects in enzymatic and nonenzymatic phosphoryl transfer reactions. One of the major advantages of the present approach is that it can be applied to model chemical reactions at a significantly lower computational cost than either the density-functional calculations with implicit solvation or the semiempirical QM/MM simulations with explicit solvent.     

Density functional study of the in-line mechanism of methanolysis of cyclic phosphate and thiophosphate esters in solution: insight into thio effects in RNA transesterification

Density functional calculations of thio effects on the in-line mechanism of methanolysis of ethylene phosphate (a reverse reaction model for RNA phosphate transesterification) are presented. A total of 12 reaction mechanisms are examined using the B3LYP functional with large basis sets, and the effects of solvation were treated using the PCM, CPCM, and SM5 solvation models. Single thio substitutions at all of the distinct phosphoryl oxygen positions (2', 3', 5', pro-R) and a double thio substitution at the nonbridging (pro-R/pro-S) positions were considered. Profiles for each reaction were calculated in the dianionic and monoanionic/monoprotic states, corresponding to reaction models under alkaline and nonalkaline conditions, respectively. These models provide insight into the mechanisms of RNA transesterification thio effects and serve as a set of high-level quantum data that can be used in the design of new semiempirical quantum models for hybrid quantum mechanical/molecular mechanical simulations and linear-scaling electronic structure calculations.     

The interplay of thio(seleno)amide/vinylogous thio(seleno)amide "resonance" and the anisotropic effect of thiocarbonyl and selenocarbonyl functional groups

Amino-substituted thio(seleno)acrylamides 1-4 were synthesized and their 1H and 13C NMR spectra assigned. Both the NMR data and the results of theoretical calculations at the ab initio level of theory were employed to elucidate the adopted structures of the compounds in terms of E/Z isomerism and s-cis/s-trans configuration. In the case of the asymmetrically N(Me)Ph-substituted compounds, ab initio GIAO-calculated ring current effects of the N-phenyl group were applied to successfully determine the preferred conformer bias. The restricted rotations about the two C-N partial double bonds were studied by DNMR and the barriers to rotation (DeltaG(c)++) determined at the coalescence temperatures, and these were discussed with respect to the structural differences between the compounds. The barriers to rotation were also calculated at the ab initio level of theory where the best results (R(2) = 0.8746) were obtained only with inclusion of the solvent at the SCIPCM-HF/6-31G* level of theory. The calculations also provided means of assessing structural influences which were not available due to inaccessible rotation barriers. By means of natural bond orbital (NBO) analysis of 1-4, the occupation numbers of nitrogen lone pairs and bonding/antibonding pi/pi orbitals were shown to quantitatively describe thio(seleno)amide/vinylogous thio(seleno)amide "resonance". Finally, the thio(seleno)carbonyl anisotropic effect was quantitatively calculated by the GIAO method and visualized by isochemical shielding surfaces (ICSS). Only marginal differences between the two anisotropic effects were calculated and are therefore of questionable utility for previous and future applications with respect to stereochemical assignments.     

Synthesis and Biological Importance of 2-(thio)ureabenzothiazoles

The (thio)urea and benzothiazole (BT) derivatives have been shown to have a broad spectrum of biological activities. These groups, when bonded, result in the 2-(thio)ureabenzothizoles (TBT and UBT), which could favor the physicochemical and biological properties. UBTs and TBTs are compounds of great importance in medicinal chemistry. For instance, Frentizole is a UBT derivative used for the treatment of rheumatoid arthritis and systemic lupus erythematosus. The UBTs Bentaluron and Bethabenthiazuron are commercial fungicides used as wood preservatives and herbicides in winter corn crops. On these bases, we prepared this bibliography review, which covers chemical aspects of UBTs and TBTs as potential therapeutic agents as well as their studies on the mechanisms of a variety of pharmacological activities. This work covers synthetic methodologies from 1935 to nowadays, highlighting the most recent approaches to afford UBTs and TBTs with a variety of substituents as illustrated in 42 schemes and 13 figures and concluded with 187 references. In addition, this interesting review is designed on chemical reactions of 2-aminobenzothiazoles (2ABTs) with (thio)phosgenes, iso(thio)cyanates, 1,1′-(thio)carbonyldiimidazoles [(T)CDI]s, (thio)carbamoyl chlorides, and carbon disulfide. This topic will provide information of utility for medicinal chemists dedicated to the design and synthesis of this class of compounds to be tested with respect to their biological activities and be proposed as new pharmacophores.     

Computational study on vapor phase coupling reaction between diiso(thio)cyanates with diamines,diols, and dithiols

Coupling between iso(thio)cyanates and amines, alcohols, and thiols to yield (thio)urea/urethane in the gas phase is important for the vacuum deposition processes of functional organic thin films such as molecular layer deposition or chemical vapor deposition. In this study, the kinetics and thermodynamics of 12 reactions between bifunctional reactants containing ? NCO/? NCS and ? NH₂/? OH/? SH moieties were calculated using double‐hybrid density functional theory to find systematic structure–reactivity relationships. The activation energy for the proton‐transfer step was correlated with the basicity of the nucleophile/Brønsted acid reactants, while the exothermicity of the coupling reaction depends on whether the other functionality is ? NCO or ? NCS. Analysis of the transition states revealed that the location of the transition state is affected by the basicity of the reactants. Vibrational and electronic spectra of the product were obtained to help future experimental investigations.     

Ammonium-chlor(thio)phosphat-Betaine,eine Klasse koordinationsstabilisierter Chlor(thio)metaphosphate

Ammonium Chloro(thio)phosphate Betaines, a Class of Coordination-stabilized Chloro(thio)metaphosphates Ammonium chloro(thio)phosphate betaines behave like systems being in equilibrium with tert. amine and monomeric chloro(thio)metaphosphate. In solution at room temperature the amine component can be displaced by stronger donors. Mass spectra reveal the presence of ClPS₂ as monomer and dimer, of ClPO₂ by fragment ions of the dimer, trimer, and tetramer before reorganization takes place to form PXCl₃ and P₄X₁₀ (X = O, S). Detection of ClPOS fails owing to fast equilibration into ClPO₂ and ClPS₂.     

One-pot synthesis of thia-Michael products from thio acids, epoxides, and electron-deficient alkenes promoted by a silica gel/Et3N combined catalyst

An efficient method for the one-pot production of thia-Michael adducts using thio acids, epoxides, and electron-deficient alkenes is described. Epoxides quickly underwent nucleophilic ring-opening with thio acids on the silica gel surface at room temperature under solvent-free conditions to yield β-hydroxy thioester intermediates. After addition of an electron-deficient alkene and a catalytic amount of Et₃N to the reaction mixture, the β-acyloxy mercaptans were generated in situ and subsequently underwent thia-Michael addition reactions to produce the corresponding adducts in good to excellent yields.     

(Aza,thio)xanthenylated amines and imines: synthesis,properties, and biological activity

Russian Chemical Bulletin - The review addresses the synthetic potential of cations or hydrols of (aza,thio)xanthenes in reactions with primary and secondary amines and imines. The diversity of...     

Ab initio calculations of effect of (thio)xanthenyl and dibenzosuberenyl substituents on dehydrogenation of N-Benzylanilines

Higher values of the energies of the highest occupied molecular orbitals for N-benzyl-4-[9-(thio)-xanthenyl]aniline, N-benzyl-4-(5-dibenzosuberenyl)aniline molecules and their zwitterions and the electron density increase on the reaction center (carbon atom in the CH₂-group) for the latter were obtained in the quantum-chemical calculations by RHF/6-31G(d) method. This explains the possibility and the ease of dehydrogenation of N-benzyl-4-[9-(thio)xanthenyl]aniline with imines in trifluoroacetic acid due to effect of the substituents. The calculated data suggest the same possibility for N-benzyl-4-(5-dibenzosuberenyl)aniline: it is dehydrogenated already in the synthesis from N-benzylaniline and dibenzosuberenol in acetic acid.     

Design and synthesis of novel indoline-(thio)urea hybrids

Abstract

A series of novel indoline-(thio)urea were designed and prepared using indoline(s) as a new platform and tested as organocatalysts in the Michael and Morita–Baylis–Hillman reactions. Most of the compounds were found to be very active catalysts although they did not promote the enantioselectivity. As agents for the conversion of thiocarbonyl compounds into carbonyl compounds, potentials of PIFA and DDQ were also displayed. Furthermore, DFT calculations rationalized the experimentally observed non-enantioselectivity of the catalysts.     

Synthesis,spectroscopic studies,and antioxidant activities of novel thio/carbohydrazones and bis-isatin derivatives from terephthalaldehyde

New bis(isatins-thio/carbohydrazones) based on Schiff bases were prepared from terephthalaldehyde biscarbohydrazone and 5-substituted isatins in the presence of a drop of sulfuric acid under reflux in ethanol. Terephthalaldehyde bis(thio/carbohydrazone) was synthesized by the reaction of (thio)/carbohydrazide and terephthalaldehyde in the presence of a few drops of acetic acid under reflux in ethanol. The structures of these synthesized compounds were determined using IR, ¹H NMR, and ¹³C NMR spectroscopy and elemental analysis. The in vitro antioxidant activity of all the compounds was determined by the 1,1-diphenyl-2-picryl hydrazyl (DPPH.) free radical scavenging method. Compound 2 showed the best antioxidant activity.     

Reaction of chloromethyliso(thio)cyanato(thio)phosphonates(-phosphinates) with phenol,ethanol, and thiols

(Chloromethyl)isocyanatophosphonates(-phosphinates) take up phenol to form carbamates whose -cleavage gives rise to phenyl (chloromethyl)phosphonates(-phosphinates). (Chloromethyl)(thio)phosphinic-(phosphonic) isothiocyanates react with phenol at 20°C in the absence of catalyst to afford phenyl phosphinates(-phosphonates). (Alkylsulfanyl)carbamates formed by addition of thiols to (chloromethyl)iso(thio)cyanastophosphonates(-phosphinates) under the action of an equimolar amount of triethylamine undergo cyclization into 1,3,4-oxaza(thiaza)phospholines.Translated from Zhurnal Obshchei Khimii, Vol. 74, No. 9, 2004, pp. 1441–1446.Original Russian Text Copyright © 2004 by Khailova, Bagautdinova, Shaimardanova, Krepysheva, M. Pudovik, Chmutova, Azancheev, Musin, A. Pudovik.This revised version was published online in April 2005 with a corrected cover date.     

5-(色酮基-3-次甲基)(硫代)巴比妥酸的合成

将巴比妥酸或硫代巴比妥酸、3-甲酰基色酮在乙酸-乙酸酐溶液(含乙酸酐10%)中进行缩合反应,制备了5-(色酮基-3-次甲基)(硫代)巴比妥酸.并经元素分析,IR,1H NMR及13C NMR确证了产物的结构.     

Chiral enantiopure bis(thio)ureas derived from TADDOL and their carboxylate complexation capacity

New chiral enantiopure ureas and thioureas with (R,R)-TADDOL backbone were synthesized. Bis-(thio)ureas with C2 symmetry were obtained from TADDOL iso(thio)cyanates and bifunctional amino-(thio)ureas from TADDAMINE, respectively. These were tested for carboxylate recognition capacity and the association constant was determined for the most stable complex.      

Synthesis of novel pyrimidine derivatives with (pyridin-3-ylmethyl)thio and phenylamino moieties and evaluation of their antifungal activity

A series of novel pyrimidine derivatives with (pyridin-3-ylmethyl)thio and phenylamino moieties were synthesized from ethyl acetoacetate, thiourea, 3-pyridinylmethyl chloride hydrochloride, and substituted anilines by multi-step reactions. The structures of the target compounds were characterized by IR, ¹H NMR, ¹³C NMR and elemental analysis. The in vitro antifungal activities against Botrytis cinerea and Sclerotinia sclerotiorum were evaluated. The result showed that N-phenyl-6-methyl-2- ((pyridin-3-ylmethyl)thio) pyrimidin-4-amine (4a) displayed high inhibition activity against Botrytis cinerea with 87.5%inhibition at 100 µg/mL; 4a, and N-(4-isopropylphenyl)-6-methyl-2-((pyridin-3-ylmethyl)thio)pyrimidin-4-amine (4c), N-(4-methoxyphenyl)-6-methyl-2-((pyridin-3-ylmethyl)thio)pyrimidin-4-amine (4d) and N-(2-hydroxy-5-chloro)-6-methyl-2-((pyridin-3-ylmethyl)thio)pyrimidin- 4-amine (4h) exhibited sufficient activities against Sclerotinia sclerotiorum with 86.6% –93.7% inhibitions at the same concentration.     

Structure and intramolecular lability of N-(thio)phosphoryl(thio)amides: XIV. Electronic structure and spatial arrangement of N-[diisopropoxy(thio)phosphoryl](thio)benzamides

Semiempirical quantum-chemical calculations of the spatial arrangement and electronic structure of the tautomeric forms of N-[diisopropoxy(thio)phosphoryl](thio)benzamides were carried out by the PM3 method. The most energetically favorable forms were revealed, and the reasons for their stabilization were discussed.     

Theoretical studies of dissociative phosphoryl transfer in interconversion of phosphoenolpyruvate to phosphonopyruvate: solvent effects, thio effects, and implications for enzymatic reactions

The conversion of phosphoenolpyruvate (PEP) to phosphonopyruvate (P-pyr) is catalyzed by PEP mutase via a dissociative mechanism. In this work, we investigate the uncatalyzed reaction using ab initio methods, density functional theory, and the semiempirical MNDO/d method. Comparisons of geometries and relative energies of stationary points (minima and transition states) with density functional results indicate that the semiempirical method is reasonably accurate. Solvent effects are examined using implicit solvent models, including the recently extended smooth conductor-like screening model. Due to the large negative charge carried by the system, solvation is found to drastically alter the location and energy of stationary points along the dissociative reaction pathways. The influence of substituting a nonbridging phosphoryl oxygen by sulfur (thio effects) was also investigated. Implications of these results for the enzymatic reaction are discussed.