G型含氟有机磷神经毒剂醇解反应机理研究

含氟有机磷神经毒剂毒性强,危害大,给实验研究带来不便。本文采用B3LYP/6-311G**和MP2/6-311G**方法及一个简化计算模型,探讨了G型含氟有机磷神经毒剂在中性和碱性条件下的醇解反应机理。结果显示,中性环境下G型含氟有机磷神经毒剂的醇解,不管是气相还是液相反应,3个甲醇分子参与的分步路径(Path C)都是最优路径;而1个甲醇阴离子参与的碱性条件下的分步路径(Path A'),其气相和液相反应决速步骤的吉布斯自由能垒分别为14.6和31.4 k J/mol,比Path C分别低87.0和59.8 k J/mol。因此,强碱催化下的G型含氟有机磷神经毒剂的醇解更高效。     

大肠杆菌中高丝氨酸琥珀酰基转移酶的同源模建与对接研究

利用同源模建和分子动力学模拟方法,模建了大肠杆菌中高丝氨酸琥珀酰基转移酶的三维结构.分析了活性位点的组成,从结构上佐证了Cys142而不是Lys47为亲核进攻的残基,并通过与其天然底物琥珀酰-辅酶A的对接研究,从理论上确认了对复合物形成起到重要作用的氨基酸残基.     

人工设计逆醛缩酶RA95.5-8F催化β-羟基酮C—C裂解的理论研究

采用量子力学与分子力学组合(QM/MM)方法对人工设计逆醛缩酶RA95.5-8F催化β-羟基酮化合物裂解反应的机理进行了研究.结果表明,裂解反应主要包括赖氨酸Lys1083对底物的亲核进攻、Schiff碱形成、烯胺水解及C—N断裂等过程, C—N键裂解生成丙酮为整个反应的决速步骤,能垒为106.27 kJ/mol;活性中心的赖氨酸Lys1083、酪氨酸Tyr1051、天冬酰胺Asn1110和酪氨酸Tyr1180构成一个催化四联体, Lys1083通过与底物形成席夫碱对底物进行活化, Tyr1051作为催化酸碱参与质子转移过程,催化四联体的氢键网络有利于反应过渡态的稳定并使R-构型的底物更容易结合在活性位点,导致RA95.5-8F对R构型底物具有高的选择性和催化活性.     

铑催化去对称氢酰化机制理论研究

本文运用密度泛函理论(DFT)计算,研究了手性双膦络合Rh(I)催化去对称性烯烃氢酰基化反应机理.计算确定了该反应最优反应路径包括醛基C–H键活化、第一个烯基插入Rh–H键、β-H消除、第二个烯基插入Rh–H键以及还原消除.计算结果表明,第一个烯基插入Rh–H键是立体选择性决定步,还原消除反应是整个反应的决速步.我们还通过理论计算研究了可能的烯烃碳酰基化副反应机理.计算预测反应主产物是S构型——季碳环戊酮,与实验报道一致.我们通过非共价弱相互作用分析研究配体对反应化学选择性的影响,结果表明,当使用位阻大的双膦配体(R)-DTBM-MeOBIPHEP时,由于配体与底物的排斥较大,不利于碳酰化反应发生,反应优势产物是烯烃氢酰化产物;而当用空间位阻小的双膦配体BzDPPB时,碳酰化反应变得更加有利,反应主产物为碳酰化产物双环[2.2.1]庚酮.因此,配体的空间位阻决定了Rh(I)催化烯烃酰基化反应的化学选择性.     

停流法研究Cu(Ser)2及Cu(Gly-Gly)2催化O2·-歧化反应动力学

采用停流法对pH=7.8的磷酸盐缓冲液体系中丝氨酸铜Cu(ser)2和甘氨酰甘氨酸铜Cu(Gly-Gly)2催化超氧阴离子自由基O2-歧化反应的动力学进行了研究,求得不同温度下的催化速率常数Kcat、反应级数n、活化能Ea及指前因子A,初步探讨了Cu(Ser)2和Cu(Gly-Gly)2催化O2-歧化反应机理,证实了第一步反应为整体反应过程的速控步骤.     

Li+粘贴CHnCl3-nO2和CFnCl3-nO2( n = 1~3 )自由基：Li+–CHnCl3-nO2和 Li+–CFnCl3-nO2的结构与性质的研究

The structures and stabilities of these still experimentally unknown CH_nCl_(3-n)O_(2-)Li~ and CF_nCl_(3-n)O_(2-)Li~ ionshave been theoretically investigated by ab initio molecular orbital theory and density functional theory(DFT)inconjunction with the 6-311G(d,p),6-311 G(d,p),6-311 G(2d,p)and 6-311 G(2df,2p)basis sets.The optimizedgeometries,chemical bonding and NBO analysis indicate that these complexes of CH_nCl_(3-n)O_(2-)Li~ and CF_nCl_(3-n)O_(2-)Li~ exist as ion-dipole molecules.The calculated affinity energies of these species exceed 41.9 kJ/mol,which arelarge enough to suggest the possibility that these title complexes could be detected as stable species in gas phase byLi~ ion attachment mass spectrometry.     

以氰甲基亚磷酸酯为含膦试剂的铜催化膦酰化异喹啉酮类化合物的高效合成

报道了一种铜催化"一锅法"高效合成膦酰化异喹啉酮类化合物的新方法.该反应是第一例基于铜催化Ullmann偶联策略以氰甲基亚磷酸酯为含膦试剂制备含膦取代氮杂环化合物的新方法.     

3-甲基环状乙撑磷酸二酯醇解的反应途径的理论研究

采用密度泛函理论和MP2方法研究了3-甲基环状乙撑磷酸二酯(MEP)与甲醇的反应途径:(Ⅰ)CH3O-+MEP;(Ⅱ)CH3OH+MEP;(Ⅲ)CH3O-+HMEP(MEP的质子化形式);(Ⅳ)CH3OH+HMEP.在B3LYP/6-31++G(d,p)水平上优化了四条反应途径的反应物、中间体、过渡态及产物的几何构型,并在同水平上进行了自然电荷分析,然后在MP2/6-311++G(3df,2p)水平上计算了各驻点的单点能.采用极化连续介质模型(PCM)研究了各途径在苯、甲醇和水溶液中的溶剂化效应.计算结果表明,溶剂效应使途径(Ⅰ)的自由能垒降低,而使途径(Ⅱ)和(Ⅳ)的决速步骤的自由能垒升高.在气相和苯溶剂中途径(Ⅳ)是反应的优势途径,在甲醇和水溶剂中途径(Ⅰ)则成为最优.研究结果进一步表明实验条件下途径(Ⅱ)与(Ⅳ)对总醇解反应的贡献相当.     

4-乙酰苯胺磺酸酯类化合物的合成研究

本文合成了新型离子负载双(三氟乙酰氧基)碘苯(BTI)试剂,并将其用于催化乙酰苯胺的磺酰化反应,以较高产率选择性合成了对甲苯磺酸4-乙酰氨基-苯基酯化合物。考察了氧化剂、溶剂、添加剂、温度等条件对乙酰苯胺的磺酰化反应的影响。反应完全后离子负载的BTI试剂可回收,经再生并循环利用三次后,其反应活性几乎保持不变。     

CM⁃Phos配体在钯催化交叉偶联反应中的应用

本文综合评述了近年来2-[2-(二环己膦基)苯基]-1-甲基-1H-吲哚(CM-Phos)膦配体及其衍生物在钯催化的交叉偶联反应中的应用, 主要根据不同种类的交叉偶联反应进行系统性分述, 并对该领域的发展前景进行了展望.     

Elucidation of hydrolysis mechanisms for fatty acid amide hydrolase and its Lys142Ala variant via QM/MM simulations

Fatty acid amide hydrolase (FAAH) is a serine hydrolase that degrades anandamide, an endocannabinoid, and oleamide, a sleep-inducing lipid, and has potential applications as a therapeutic target for neurological disorders. Remarkably, FAAH hydrolyzes amides and esters with similar rates; however, the normal preference for esters reemerges when Lys142 is mutated to alanine. To elucidate the hydrolysis mechanisms and the causes behind this variation of selectivity, mixed quantum and molecular mechanics (QM/MM) calculations were carried out to obtain free-energy profiles for alternative mechanisms for the enzymatic hydrolyses. The methodology features free-energy perturbation calculations in Monte Carlo simulations with PDDG/PM3 as the QM method. For wild-type FAAH, the results support a mechanism, which features proton transfer from Ser217 to Lys142, simultaneous proton transfer from Ser241 to Ser217, and attack of Ser241 on the substrate's carbonyl carbon to yield a tetrahedral intermediate, which subsequently undergoes elimination with simultaneous protonation of the leaving group by a Lys142-Ser217 proton shuttle. For the Lys142Ala mutant, a striking multistep sequence is proposed with simultaneous proton transfer from Ser241 to Ser217, attack of Ser241 on the carbonyl carbon of the substrate, and elimination of the leaving group and its protonation by Ser217. Support comes from the free-energy results, which well reproduce the observation that the Lys142Ala mutation in FAAH decreases the rate of hydrolysis for oleamide significantly more than for methyl oleate.     

Theoretical modeling study for the phosphonylation mechanisms of the catalytic triad of acetylcholinesterase by sarin

Potential energy surfaces for the process of phosphonylation of the catalytic triad of acetylcholinesterase by sarin have been explored at the B3LYP/6-311G(d,p) level of theory through a computational study. It is concluded that the phosphonylation process involves a critical addition-elimination mechanism. The first nucleophilic addition process is the rate-determining step. The following elimination process of the fluoride ion comprises a composite reaction that includes several steps, and it occurs rapidly by comparison with the rate-determining step. The mobility characteristics of histidine play an important role in the reaction. A double proton-transfer mechanism is proposed for the catalytic triad during the phosphonylation process of sarin on AChE. The effect of aqueous solvation has been considered via the polarizable continuum model (PCM). One concludes that the energy barriers are generally lowered in solvent, compared to the gas-phase reactions.     

Phosphonylation mechanisms of sarin and acetylcholinesterase: a model DFT study

Potential energy surfaces for the phosphonylation of sarin and acetylcholinesterase (AChE) have been theoretically studied at the B3LYP/6-311G(d,p) level of theory. The obtained results show that the phosphonylation process involves a two-step addition-elimination mechanism, with the first step (addition process) being the rate-determining step, while by comparison, the ensuing steps are very rapid. Stable trigonal bipyramidal intermediates are formed in the studied pathways. It is also revealed that the catalytic triad of acetylcholinesterase plays the catalytic role in the reaction by speeding up the phosphonylation process, as it does in the acylation reaction of ACh and AChE. The effect of aqueous solvation was accounted for via the polarizable continuum model. It is concluded that the enzymatic reaction here is influenced strongly by the solvent environment.     

Direct ab‐initio molecular dynamics study on the radiation effects on catalytic triad composed of Ser‐His‐Glu residues

High energy irradiation to the hydrogen bonded system is important in relevance with the initial process of DNA and enzyme damages. In the present study, the effects of radiation to catalytic triad have been investigated by means of direct ab‐initio molecular dynamics (AIMD) calculation. As a model of the catalytic triad, Ser‐His‐Glu residue, which is one of the important enzymes in the acylation reaction, was examined. The ionization and electron attachment processes in Ser‐His‐Glu were investigated as the radiation effects. The direct AIMD calculation showed that a proton of His is spontaneously transferred to carbonyl oxygen of Glu after the ionization. However, the whole structure of catalytic triad was essentially kept after the ionization. On the other hand, in the case of the electron capture in the model catalytic triad Ser‐His‐Glu, the dissociation of Glu residue from [Ser‐His]^? was found as a product channel. The mechanism of ionization and electron capture process in the catalytic triad was discussed on the basis of theoretical results. © 2015 Wiley Periodicals, Inc.     

Fluoride-mediated capture of a noncovalent bound state of a reversible covalent enzyme inhibitor: X-ray crystallographic analysis of an exceptionally potent α-ketoheterocycle inhibitor of fatty acid amide hydrolase

Two cocrystal X-ray structures of the exceptionally potent α-ketoheterocycle inhibitor 1 (K(i) = 290 pM) bound to a humanized variant of rat fatty acid amide hydrolase (FAAH) are disclosed, representing noncovalently and covalently bound states of the same inhibitor with the enzyme. Key to securing the structure of the noncovalently bound state of the inhibitor was the inclusion of fluoride ion in the crystallization conditions that is proposed to bind the oxyanion hole precluding inhibitor covalent adduct formation with stabilization of the tetrahedral hemiketal. This permitted the opportunity to detect important noncovalent interactions stabilizing the binding of the inhibitor within the FAAH active site independent of the covalent reaction. Remarkably, noncovalently bound 1 in the presence of fluoride appears to capture the active site in the same "in action" state with the three catalytic residues Ser241-Ser217-Lys142 occupying essentially identical positions observed in the covalently bound structure of 1, suggesting that this technique of introducing fluoride may have important applications in structural studies beyond inhibiting substrate or inhibitor oxyanion hole binding. Key insights to emerge from the studies include the observations that noncovalently bound 1 binds in its ketone (not gem diol) form, that the terminal phenyl group in the acyl side chain of the inhibitor serves as the key anchoring interaction overriding the intricate polar interactions in the cytosolic port, and that the role of the central activating heterocycle is dominated by its intrinsic electron-withdrawing properties. These two structures are also briefly compared with five X-ray structures of α-ketoheterocycle-based inhibitors bound to FAAH recently disclosed.     

The Molecular Basis of Catalysis by SDR Family Members Ketoacyl-ACP Reductase FabG and Enoyl-ACP Reductase FabI in Type-II Fatty Acid Biosynthesis

The short-chain dehydrogenase/reductase (SDR) superfamily members acyl-ACP reductases FabG and FabI are indispensable core enzymatic modules and catalytic orientation controllers in type-II fatty acid biosynthesis. Herein, we report their distinct substrate allosteric recognition and enantioselective reduction mechanisms. FabG achieves allosteric regulation of ACP and NADPH through ACP binding across two adjacent FabG monomers, while FabI follows an irreversible compulsory order of substrate binding in that NADH binding must precede that of ACP on a discrete FabI monomer. Moreover, FabG and FabI utilize a backdoor residue Phe187 or a “rheostat” α8 helix for acyl chain length selection, and their corresponding triad residues Ser142 or Tyr145 recognize the keto- or enoyl-acyl substrates, respectively, facilitating initiation of nucleophilic attack by NAD(P)H. The other two triad residues (Tyr and Lys) mediate subsequent proton transfer and (R)-3-hydroxyacyl- or saturated acyl-ACP production.     

Inhibition Mechanism of Cholinesterases by Carbamate: A Theoretical Study

The density functional theory at the B3LYP/6-311G（d, p） level was applied to exploring the inhibition mechanism of cholinesterases by carbamate. The results indicate that the inhibition reactions with or without the catalytic effect of the catalytic triad in eholinesterases underwent a two-step addition-elimination mechanism, which is in good agreement with the proposed mechanism. The solvent has a strong effect on the inhibition reactions and the reaction with the catalytic triad in the solvent phase is close to the real reaction under biological condition.     

Understanding the role of carbamate reactivity in fatty acid amide hydrolase inhibition by QM/MM mechanistic modelling

QM/MM modelling of FAAH inactivation by O-biphenyl-3-yl carbamates identifies the deprotonation of Ser241 as the key reaction step, explaining why FAAH is insensitive to the electron-donor effect of conjugated substituents; this may aid design of new inhibitors with improved selectivity and in vivo potency.     

Ab initio model study on acetylcholinesterase catalysis: potential energy surfaces of the proton transfer reactions

Ab initio molecular orbital (MO) and hybrid density functional theory (DFT) calculations have been applied to the initial step of the acylation reaction catalyzed by acetylcholinesterase (AChE), which is the nucleophiric addition of Ser200 in catalytic triads to a neurotransmitter acetylcholine (ACh). We focus our attention mainly on the effects of oxyanion hole and Glu327 on the potential energy surfaces (PESs) for the proton transfer reactions in the catalytic triad Ser200-His440-Glu327. The activation barrier for the addition reaction of Ser200 to ACh was calculated to be 23.4 kcal/mol at the B3LYP/6-31G(d)//HF/3-21G(d) level of theory. The barrier height under the existence of oxyanion hole, namely, Ser200-His440-Glu327-ACh-(oxyanion hole) system, decreased significantly to 14.2 kcal/mol, which is in reasonable agreement with recent experimental value (12.0 kcal/mol). Removal of Glu327 from the catalytic triad caused destabilization of both energy of transition state for the reaction and tetrahedral intermediate (product). PESs calculated for the proton transfer reactions showed that the first proton transfer process is the most important in the stabilization of tetrahedral intermediate complex. The mechanism of addition reaction of ACh was discussed on the basis of theoretical results.     

Photochemical nucleophile mapping: identification of Tyr311 within the catalytic domain of rabbit muscle glyceraldehyde-3-phosphate dehydrogenase

Photochemical mapping of nucleophiles in close proximity to the active site Cys149 of rabbit glyceraldehyde-3-phosphate dehydrogenase (GAPDH) was demonstrated based on the nucleophilic aromatic photosubstitution reaction using two regioisomers of alkoxy-fluoro-nitro-substituted benzenes. Two photophores were covalently attached to the active site SH group of GAPDH and the protein was subjected to photolysis then to the cyanogen bromide cleavage reaction. The advantage of this method is the capability to chase labeled products by monitoring absorption at 380 nm because of the chromogenic property of photophore. HPLC separation identified a large labeled peptide fragment that was further digested by V8 protease for Edman sequence analysis. From the recent X-ray crystallography of rabbit GAPDH, Tyr311, His176, Ser238 and Lys183 are closely located to catalytic Cys149. Among these nucleophiles, Tyr311 was preferentially labeled with 2-fluoro-4-nitrophenoxy photophore and no label was identified with the isomeric 4-fluoro-2-nitrophenoxy photophore. The result clearly reflects the distance between Cys149 and nucleophiles to distinguish the nearest Tyr311. As photophores show great reactivity even with water under neutral conditions, the distance between nucleophiles and photophores is important for photoinduced nucleophilic aromatic substitution. The method will provide a useful technique to survey nucleophiles within the catalytic domain.