New approach for the synthesis of 1-aryl- and 1-heteroaryl-5-nitrouracil derivatives

1-(2,4-Dinitrophenyl)-5-nitrouracil and its 3-methyl derivatives were synthesized and used as substrates in reaction with aromatic amines and amino pyridines. In the reaction of aniline with 1-(2,4-dinitrophenyl)-5-nitrouracil, only the acyclic adduct was isolated. When 1-(2,4-dinitrophenyl)-3-methyl-5-nitrouracil was treated with aniline and other aromatic amines or amino pyridines, the desired 1-aryl-5-nitrouracil derivatives were obtained in satisfactory yield. The influence of the free H-3 proton present in the uracil ring on the course of the reaction is discussed.     

Intriguing roles of reactive intermediates in dissociation chemistry of N-phenylcinnamides

In mass spectrometry of protonated N-phenylcinnamides, the carbonyl oxygen is the thermodynamically most favorable protonation site and the added proton is initially localized on it. Upon collisional activation, the proton transfers from the carbonyl oxygen to the dissociative protonation site at the amide nitrogen atom or the α-carbon atom, leading to the formation of important reactive intermediates. When the amide nitrogen atom is protonated, the amide bond is facile to rupture to form ion/neutral complex 1, [RC(6)H(4)CH[double bond, length as m-dash]CHCO(+)/aniline]. Besides the dissociation of the complex, proton transfer reaction from the α-carbon atom to the nitrogen atom within the complex takes place, leading to the formation of protonated aniline. The presence of electron-withdrawing groups favored the proton transfer reaction, whereas electron-donating groups strongly favored the dissociation (aniline loss). When the proton transfers from the carbonyl oxygen to the α-carbon atom, the cleavage of the C(α)-CONHPh bond results in another ion/neutral complex 2, [PhNHCO(+)/RC(6)H(4)CH[double bond, length as m-dash]CH(2)]. However, in this case, electron-donating groups expedited the proton transfer reaction from the charged to the neutral partner to eliminate phenyl isocyanate. Besides the cleavage of the C(α)-CONHPh bond, intramolecular nucleophilic substitution (a nucleophilic attack of the nitrogen atom at the β-carbon) and stepwise proton transfer reactions (two 1,2-H shifts) also take place when the α-carbon atom is protonated, resulting in the loss of ketene and RC(6)H(5), respectively. In addition, the H/D exchanges between the external deuterium and the amide hydrogen, vinyl hydrogens and the hydrogens of the phenyl rings were discovered by D-labeling experiments. Density functional theory-based (DFT) calculations were performed to shed light on the mechanisms for these reactions.     

Rate constants for 1,5- and 1,6-hydrogen atom transfer reactions of mono-, di-, and tri-aryl-substituted donors, models for hydrogen atom transfers in polyunsaturated fatty acid radicals

Rate constants for 1,5- and 1,6-hydrogen atom transfer reactions in models of polyunsaturated fatty acid radicals were measured via laser flash photolysis methods. Photolyses of PTOC (pyridine-2-thioneoxycarbonyl) ester derivatives of carboxylic acids gave primary alkyl radicals that reacted by 1,5-hydrogen transfer from mono-, di-, and tri-aryl-substituted positions or 1,6-hydrogen transfer from di- and tri-aryl-substituted positions to give UV-detectable products. Rate constants for reactions in acetonitrile at room temperature ranged from 1 x 10(4) to 4 x 10(6) s(-1). The activation energies for a matched pair of 1,5- and 1,6-hydrogen atom transfers giving tri-aryl-substituted radicals were approximately equal, as were the primary kinetic isotope effects, but the 1,5-hydrogen atom transfer reaction was 1 order of magnitude faster at room temperature than the 1,6-hydrogen atom transfer reaction due to a less favorable entropy of activation for the 1,6-transfer reaction. Solvent effects on the rate constants for the 1,5-hydrogen atom transfer reaction of the 2-[2-(diphenylmethyl)phenyl]ethyl radical at ambient temperature were as large as a factor of 2 with the reaction increasing in rate in lower polarity solvents. Hybrid density functional theory computations for the 1,5- and 1,6-hydrogen atom transfers of the tri-aryl-substituted donors were in qualitative agreement with the experimental results.     

甲苯-2,4-二异氰酸酯与仲胺类化合物反应中的质子转移过程

采用密度泛函理论B3LYP/6-31+G(d,p)方法研究了甲苯-2,4-二异氰酸酯(2,4-TDI)与仲胺类化合物反应过程中的质子转移效应. 研究发现甲醇分子对反应有显著的催化效应,可使反应能垒大幅降低,这表明含活泼氢的化合物会加速质子转移过程,从而加快反应速率. 2,4-TDI与甲基-N-甲基氨基甲酸酯的催化加成反应为一步反应,其反应过渡态呈六元环结构;而2,4-TDI与N-甲基对硝基苯胺、二苯胺、1,2-二氢-2,2,4-三甲基喹啉等芳香胺类化合物的催化加成反应经历了两步反应,其中第一步为速率控制步骤. 研究表明,在与2,4-TDI的反应中,芳胺化合物的活性高于甲基-N-甲基氨基甲酸酯的活性,计算的反应活性顺序与实验结果一致.     

Interaction of dimethyl carbonate with anilines in the presence of potassium methylate: Kinetics and the role of the base

The kinetic patterns of the reaction between dimethyl carbonate and anilines in the presence of a potassium methylate as a catalyst were studied. The mechanism of aminolysis was clarified, which includes the detachment of the proton from the amino group of aniline and the subsequent attack of the resulting anion on the carbonyl group of dimethyl carbonate. It is shown that when the reaction occurs in the dimethyl carbonate-methanol 3:1 system, the process can be described as an irreversible first-order reaction in the aniline though the target reaction is complicated by side interaction between potassium methylate and dimethyl carbonate. The rate constants of the target reaction with substituted anilines and of the side reaction in the temperature range of 70-90°C were determined. It is shown that the influence of the substituent on the reaction rate is described by the Hammett equation, with the constant of the reaction series being positive and the best correlation being achieved for σ-scale. The results obtained are consistent with the proposed mechanism of the reaction and are explained by the facilitation of the aniline deprotonation with increasing acceptor properties of the substituent. Effective activation energies for the reaction of various anilines with dimethyl carbonate are found.     

The reaction mechanism of the hydroamination of alkenes catalyzed by gold(I)-phosphine: the role of the counterion and the N-nucleophile substituents in the proton-transfer step

The reaction mechanism of the gold(I)-phosphine-catalyzed hydroamination of 1,3-dienes was analyzed by means of density functional methods combined with polarizable continuum models. Several mechanistic pathways for the reaction were considered and evaluated. It was found that the most favorable series of reaction steps include the ligand substitution reaction in the catalytically active Ph3PAuOTf species between the triflate and the substrate, subsequent nucleophile attack of the N-nucleophile (benzyl carbamate) on the activated double bond, which is followed by proton transfer from the NH2 group to the unsaturated carbon atom. The latter step, the most striking one, was analyzed in detail, and a novel pathway involving tautomerization of benzyl carbamate nucleophile assisted by triflate anion acting as a proton shuttle was characterized by the lowest barrier, which is consistent with experimental findings.     

The Interaction of Ground and Excited States of Lumichrome with Aliphatic and Aromatic Amines in Methanol

The reaction of the ground and excited states of lumichrome (=7,8‐dimethylalloxazine=7,8‐dimethylbenzo[g]pteridine‐2,4(1H,3H)‐dione) with aliphatic and aromatic amines was investigated in MeOH. In the presence of aliphatic amines of high basicity, new bands are observed in the absorption and fluorescence spectra. These bands arise in a proton‐transfer reaction from lumichrome, in the ground and in the singlet excited states, to the amine. On the other hand, amines with lower basicity such as triethanolamine (=2,2′,2″‐nitrilotris[ethanol]) and aromatic amines are not able to deprotonate lumichrome, and hence a quenching of the fluorescent emission takes place without changes in the spectral shape. In this case, bimolecular‐quenching rate constants were determined for the excited singlet and triplet states. Based on laser‐flash‐photolysis experiments, an electron‐transfer mechanism is proposed. Aliphatic amines yield lower rate constants than the aromatic ones for the same driving force. A notable difference arises in the limiting value reached by the singlet and triplet quenching rate constants by aromatic amines. For the singlet quenching, the limit is coincident with a diffusion‐controlled reaction, while those for triplet quenching reach a lower constant value, independent of the driving force. This is explained by an electron‐transfer mechanism, with a lower frequency factor for the triplet‐state process.     

Regioselectivity and the nature of the reaction mechanism in nucleophilic substitution reactions of 2,4-dinitrophenyl X-substituted benzenesulfonates with primary amines

Second-order rate constants have been measured for the reaction of 2,4-dinitrophenyl X-substituted benzenesulfonates with a series of primary amines. The nucleophilic substitution reaction proceeds through competitive S-O and C-O bond fission pathways. The S-O bond fission occurs dominantly for reactions with highly basic amines or with substrates having a strong electron-withdrawing group in the sulfonyl moiety. On the other hand, the C-O bond fission occurs considerably for the reactions with low basic amines or with substrates having a strong electron-donating group in the sulfonyl moiety, emphasizing that the regioselectivity is governed by both the amine basicity and the electronic effect of the sulfonyl substituent X. The apparent second-order rate constants for the S-O bond fission have resulted in a nonlinear Br?nsted-type plot for the reaction of 2,4-dinitrophenyl benzenesulfonate with 10 different primary amines, suggesting that a change in the rate-determining step occurs upon changing the amine basicity. The microscopic rate constants (k(1) and k(2)/k(-)(1) ratio) associated with the S-O bond fission pathway support the proposed mechanism. The second-order rate constants for the S-O bond fission result in good linear Yukawa-Tsuno plots for the aminolyses of 2,4-dinitrophenyl X-substituted benzenesulfonates. However, the second-order rate constants for the C-O bond fission show no correlation with the electronic nature of the sulfonyl substituent X, indicating that the C-O bond fission proceeds through an S(N)Ar mechanism in which the leaving group departure occurs rapidly after the rate-determining step.     

黄嘌呤异构体质子转移异构化反应机理的理论研究

采用量子化学密度泛函B3LYP/6-31G(d,p)和M06-2X/6-311++G(d,p)方法对黄嘌呤两种酮式异构体X(1,3,7)与X(1,3,9)间质子转移引起的互变异构反应机理进行了计算研究,获得了异构化反应过程的反应焓﹑活化吉布斯自由能和质子转移反应的速率常数等参数。水相计算采用极化连续(PCM)模型。结果表明,由于可能的氢迁移顺序差异,分子内由X(1,3,7)向X(1,3,9)异构化可能共有16条反应通道,涉及11个中间体和20个过渡态,其主反应通道速控步骤的活化吉布斯自由能为183.10k J/mol,速率常数为5.17×10-20s-1,其余各通道速控步骤活化吉布斯自由能均较高,而且整体水溶剂效应不利于质子转移的发生。     

Antioxidant activity of trans-resveratrol toward hydroxyl and hydroperoxyl radicals: a quantum chemical and computational kinetics study

In this work, we have carried out a systematic study of the antioxidant activity of trans-resveratrol toward hydroxyl ((?)OH) and hydroperoxyl ((?)OOH) radicals in aqueous simulated media using density functional quantum chemistry and computational kinetics methods. All possible mechanisms have been considered: hydrogen atom transfer (HAT), proton-coupled electron transfer (PCET), sequential electron proton transfer (SEPT), and radical adduct formation (RAF). Rate constants have been calculated using conventional transition state theory in conjunction with the Collins-Kimball theory. Branching ratios for the different paths contributing to the overall reaction, at 298 K, are reported. For the global reactivity of trans-resveratrol toward (?)OH radicals, in water at physiological pH, the main mechanism of reaction is proposed to be the sequential electron proton transfer (SEPT). However, we show that trans-resveratrol always reacts with (?)OH radicals at a rate that is diffusion-controlled, independent of the reaction pathway. This explains why trans-resveratrol is an excellent but very unselective (?)OH radical scavenger that provides antioxidant protection to the cell. Reaction between trans-resveratrol and the hydroperoxyl radical occurs only by phenolic hydrogen abstraction. The total rate coefficient is predicted to be 1.42 × 10(5) M(-1) s(-1), which is much smaller than the ones for reactions of trans-resveratrol with (?)OH radicals, but still important. Since the (?)OOH half-life time is several orders larger than the one of the (?)OH radical, it should contribute significantly to trans-resveratrol oxidation in aqueous biological media. Thus, trans-resveratrol may act as an efficient (?)OOH, and also presumably (?)OOR, radical scavenger.     

2,6-二巯基嘌呤质子转移异构化的密度泛函理论研究

采用密度泛函B3LYP方法, 在6-311＋G(d,p)基组水平上对2,6-二巯基嘌呤质子转移引起的硫醇式与硫酮式互变异构反应进行了计算研究, 获得了互变异构过程的反应焓、活化能、活化吉布斯自由能和质子转移反应的速率常数等性质. 计算结果表明, 2,6-二巯基嘌呤无论是孤立分子还是一水合物, 其二硫酮式R是最稳定异构体. 由二硫酮式通过分子内质子转移向二硫醇式异构化共有6条反应通道, 其主通道(1)速控步骤的活化能为139.1 kJ•mol^－1, 速率常数为2.16×10^－12 s^－1; 当水分子参与反应以双质子转移机理异构化时, 活化能显著降低, 有利于硫酮式向硫醇式转变, 其主通道(7)速控步骤的活化能为61.3 kJ•mol^－1, 速率常数为1.33×10 s^－1. 计算结果还表明, 氢键作用在增大2,6-二巯基嘌呤氢键一水合物稳定性、降低质子转移异构化反应活化能等方面起着重要的作用.     

Theoretical study on the mechanism of a ring-opening reaction of oxirane by the active-site aspartic dyad of HIV-1 protease

Two possible mechanisms of the irreversible inhibition of HIV-1 protease by epoxide inhibitors are investigated on an enzymatic model using ab initio (MP2) and density functional theory (DFT) methods (B3LYP, MPW1K and M05-2X). The calculations predict the inhibition as a general acid-catalyzed nucleophilic substitution reaction proceeding by a concerted SN2 mechanism with a reaction barrier of ca. 15-21 kcal mol(-1). The irreversible nature of the inhibition is characterized by a large negative reaction energy of ca. -17-(-24) kcal mol(-1). A mechanism with a direct proton transfer from an aspartic acid residue of the active site onto the epoxide ring has been shown to be preferred compared to one with the proton transfer from the acid catalyst facilitated by a bridging catalytic water molecule. Based on the geometry of the transition state, structural data important for the design of irreversible epoxide inhibitors of HIV-1 protease were defined. Here we also briefly discuss differences between the epoxide ring-opening reaction in HIV-1 protease and epoxide hydrolase, and the accuracy of the DFT method used.     

Relative reactivity and kinetic pattern of aniline and N‐methylaniline as nucleophiles in aromatic substitution (SNAr) reactions

Kinetic results are reported for the reactions of 4‐nitrophenyl‐2,4,6‐trinitrophenyl ether 3 with aniline and N‐methylaniline in dimethyl sulphoxide, acetonitrile, methanol, and benzene. The reactions gave the expected 2,4,6‐trinitrodiphenylamine and were base catalyzed in all the solvents. Both nucleophiles showed the same kinetic pattern under the same reaction conditions but aniline was found to be considerably more reactive than N‐methylaniline. The greater catalytic efficiency of aniline over N‐methylaniline is consistent with the proton transfer mechanism of the base‐catalyzed step. Dichotomy of amine effects in aromatic substitution (S_NAr) reactions is discussed. © 2004 Wiley Periodicals, Inc. Int J Chem Kinet 36: 188–196, 2004     

DFT/B3LYP study of the substituent effect on the reaction enthalpies of the individual steps of single electron transfer-proton transfer and sequential proton loss electron transfer mechanisms of phenols antioxidant action

The reaction enthalpies related to the individual steps of two phenolic antioxidants action mechanisms, single electron transfer-proton transfer (SET-PT) and sequential proton loss electron transfer (SPLET), for 30 meta and para-substituted phenols (ArOH) were calculated using DFT/B3LYP method. These mechanisms represent the alternative ways to the extensively studied hydrogen atom transfer (HAT) mechanism. Except the comparison of calculated reaction enthalpies with available experimental and/or theoretical values, obtained enthalpies were correlated with Hammett constants. We have found that electron-donating substituents induce the rise in the enthalpy of proton dissociation (PDE) from ArOH+* radical cation (second step in SET-PT) and in the proton affinities of phenoxide ions ArO- (reaction enthalpy of the first step in SPLET). Electron-withdrawing groups cause the increase in the reaction enthalpies of the processes where electron is abstracted, i.e., in the ionization potentials of ArOH (first step in SET-PT) and in the enthalpy of electron transfer from ArO- (second step in SPLET). Found results indicate that all dependences of reaction enthalpies on Hammett constants of the substituents are linear. The calculations of liquid-phase reaction enthalpies for several para-substituted phenols indicate that found trends hold also in water, although substituent effects are weaker. From the thermodynamic point of view, entering SPLET mechanism represents the most probable process in water.     

5-氟胞嘧啶气相及水助质子转移异构化的理论研究

采用密度泛函B3LYP/6-311G**方法,对6种5-氟胞嘧啶异构体孤立分子的稳定性及质子转移引起的酮式-烯醇式、氨基式-亚胺式互变异构反应机理进行了计算研究,获得了零点能、吉布斯自由能及质子转移过程的反应焓、活化能、活化吉布斯自由能和速率常数等参数.计算结果表明,气相中烯醇-氨基式FC4是最稳定的异构体.分子内质子转移设计了FC1→FC2和FC1→FC6两条通道,分别标记为P(1)和P(2),各通道速控步骤的活化能和速率常数分别为155.9 kJ·mol-1,4.70×10-15 s-1和173.1 kJ·mol-1,1.41×10-18 s-1.水助催化时,相应通道P(3) 和P(4) 速控步骤的活化能和速率常数分别为51.0 kJ·mol-1,1.41×103 s-1和88.2 kJ·mol-1,4.53×10-3 s-1.可见,水分子的加入极大地降低了质子转移的活化能垒.另外发现,水分子参与形成协同的双质子转移机理比水助单质子转移机理更利于降低活化能垒.     

Effect of the Structure of 1- and 3-Methylpyrimidin-4-ones on the Rate of Nucleophilic Substitution of the 2-Methylsylfanyl Group

Rate constants for substitution of the 2-methylsulfanyl group in 1- and 3-methyl-2-methylsulfanyl-pyrimidin-4-ones and their 5-fluoro analogs were measured in the reaction with butylamine, alkaline hydrolysis, and methanolysis. The rate of substitution in 1-methyl isomers having a zwitterionic structure is greater by a factor of ~2 than the rate of substitution in 3-methyl isomers with conjugated double bonds in the ring. The presence of a fluorine atom in position 5 accelerates nucleophilic substitution in 1-methyl isomers, while 5-fluoro-3-methyl-2-methylsulfanylpyrimidin-4-ones react at a lower rate than their 5-unsubstituted analogs. According to the NMR data, the reactions involve formation of a tetrahedral intermediate. Anchimeric effect of the methyl group on N¹ hampersattack by basic reagent on the C⁶atom.     

胞嘧啶一水复合物质子转移异构化反应机理的理论研究

采用密度泛函B3LYP方法,在6-311＋G＊＊基组水平上对胞嘧啶一水复合物质子转移引起的氨-酮式、氨-烯醇式与亚胺-酮式互变异构反应机理进行了计算研究,获得了互变异构过程的反应焓、活化能、活化吉布斯自由能和质子转移反应速率常数等参数。将Onsager反应场溶剂模型用于水相的计算,结果表明,胞嘧啶一水复合物无论在气相中...     

Theoretical investigations on the stereoselectivity of the proline catalyzed Mannich reaction in DMSO

The stereocontrol steps of the (S)-proline catalyzed Mannich reaction of cyclohexanone, formaldehyde, and aniline were theoretically investigated. The geometries of reactants, products, and transition states were optimized using density functional theory using the B3LYP functional with the 6-31++G(d,p) basis set. The energies of these compounds were then more accurately determined at the MP2 level, and the effect of DMSO as the solvent was included using a polarizable continuum model (PCM). The reaction was modeled from the previously proposed mechanism that cyclohexanone reacts with (S)-proline to generate an enamine, while formaldehyde reacts with aniline to produce an imine, and that the conformation around the C-N bond of the enamine 1 is crucial for the further enantioselective step. The formation of two conformations of the enamine via a proton transfer process was examined, revealing activation barriers for syn- and anti-enamine proton transfer of 10.2 and 17.9 kcal/mol, respectively. The transformation of syn- to anti-enamine through C-N bond rotation, however, was predicted to require only 4.2 kcal/mol, while the (S)- and (R)-intermediates could be obtained from subsequent reactions between enamine and imine with energy barriers of 8.5 and 12.4 kcal/mol, respectively. The difference between these barriers, but not the C-N rotation energy, becomes larger at the MP2 level and when DMSO as a solvent is included. This predicted enantioselective reaction, through the kinetic and thermodynamic favoring of the (S)-pathway, is in agreement with experimental results, which have reported the (S)-configuration as the major product.     

Hydrogen atom transfer reactions of a ruthenium imidazole complex: hydrogen tunneling and the applicability of the Marcus cross relation

The reaction of Ru(II)(acac)2(py-imH) (Ru(II)imH) with TEMPO(*) (2,2,6,6-tetramethylpiperidine-1-oxyl radical) in MeCN quantitatively gives Ru(III)(acac)2(py-im) (Ru(III)im) and the hydroxylamine TEMPO-H by transfer of H(*) (H(+) + e(-)) (acac = 2,4-pentanedionato, py-imH = 2-(2'-pyridyl)imidazole). Kinetic measurements of this reaction by UV-vis stopped-flow techniques indicate a bimolecular rate constant k(3H) = 1400 +/- 100 M(-1) s(-1) at 298 K. The reaction proceeds via a concerted hydrogen atom transfer (HAT) mechanism, as shown by ruling out the stepwise pathways of initial proton or electron transfer due to their very unfavorable thermochemistry (Delta G(o)). Deuterium transfer from Ru(II)(acac)2(py-imD) (Ru(II)imD) to TEMPO(*) is surprisingly much slower at k(3D) = 60 +/- 7 M(-1) s(-1), with k(3H)/k(3D) = 23 +/- 3 at 298 K. Temperature-dependent measurements of this deuterium kinetic isotope effect (KIE) show a large difference between the apparent activation energies, E(a3D) - E(a3H) = 1.9 +/- 0.8 kcal mol(-1). The large k(3H)/k(3D) and DeltaE(a) values appear to be greater than the semiclassical limits and thus suggest a tunneling mechanism. The self-exchange HAT reaction between Ru(II)imH and Ru(III)im, measured by (1)H NMR line broadening, occurs with k(4H) = (3.2 +/- 0.3) x 10(5) M(-1) s(-1) at 298 K and k(4H)/k(4D) = 1.5 +/- 0.2. Despite the small KIE, tunneling is suggested by the ratio of Arrhenius pre-exponential factors, log(A(4H)/A(4D)) = -0.5 +/- 0.3. These data provide a test of the applicability of the Marcus cross relation for H and D transfers, over a range of temperatures, for a reaction that involves substantial tunneling. The cross relation calculates rate constants for Ru(II)imH(D) + TEMPO(*) that are greater than those observed: k(3H,calc)/k(3H) = 31 +/- 4 and k(3D,calc)/k(3D) = 140 +/- 20 at 298 K. In these rate constants and in the activation parameters, there is a better agreement with the Marcus cross relation for H than for D transfer, despite the greater prevalence of tunneling for H. The cross relation does not explicitly include tunneling, so close agreement should not be expected. In light of these results, the strengths and weaknesses of applying the cross relation to HAT reactions are discussed.     

Photoinduced Electron and H-atom Transfer Reactions of Xanthone by Laser Flash Photolysis

The property of the lowest excited triplet states of xanthone in acetonitrile was investigated using time-resolved laser °ash photolysis at 355 nm. The transient absorption spectra and the quenching rate constants(kq) of the excited xanthone with several amines were determined. Good correlation between lgkq and the driving force of the reactions suggests the electron transfer mechanism, except aniline and 3-nitroaniline (3-NO2-A) which showed energy transfer mechanism. With the appearance of ketyl radical, hydrogen atom transfer also happened between xanthone and dimethyl-p-toluidine, 3,5,N,N-tetramethylaniline, N,N-dimethylaniline, and triethylamine. Therefore, both electron transfer and H-atom transfer occured in these systems. Great discrepancies of kq values were discovered in H-atom abstraction reactions for alcohols and phenols, which can be explained by di?erent abstraction mechanisms. The quenching rate constants between xanthone and alcohols correlate well with the ?-C?H bonding energy of alcohols.