丝氨酸蛋白酶中催化三元组内氢键的作用（英文）

为了探究丝氨酸蛋白酶催化效率的来源,本文分别研究了丝氨酸酶催化水解多肽CI2、MCTI-A和六肽(SUB)的过程中催化三元组内的氢键所起的作用.首先采用QM/MM-MD方法计算了在酶-底物复合物和过渡态下组氨酸和天冬氨酸之间质子转移的自由能曲线.结果表明低能垒氢键仅在CI2酰化反应的过渡态区域形成,而在MCTIA和SUB酰化反应中均是正常氢键.与MCTI-A相比,CI2和SUB体系中氢键强度在过渡态时显著增强,因此相应的酰化反应能垒明显降低.过渡态区域形成的低能垒氢键显然有助于加速酰化反应,同时研究也表明正常氢键也有可能降低能垒.氢键降低能垒的关键则在于过渡态下氢键强度的增加程度,而不是其是否生成了低能垒氢键.本文为研究催化三元组间的氢键在丝氨酸蛋白酶中的作用提供了新思路,并有助于理解丝氨酸蛋白酶中催化三元组的催化机制.     

钴络合物催化甲醇羰基化制甲酸甲酯反应的理论研究

本文运用密度泛函理论B3LYP方法,对C、O、H采用6-311+G(2d,p)基组,计算研究了钴络合物催化甲醇羰基化制甲酸甲酯反应的微观机理,优化了各反应物、中间体和过渡态的构型特征,用频率分析方法和内禀反应坐标方法对过渡态进行了验证,同时对各中间体进行电荷分析.对比了催化过程与非催化过程的能垒.结果表明,有催化剂参与后反应活化能明显降低.     

铂表面甘油脱除羟基的从头算分子动力学研究

随着生物质能源的开发,从生物柴油制备中大量获取的甘油成为热门的工业原材料. 甘油可以通过氢解生成1,2-丙二醇和1,3-丙二醇两种丙二醇,这两种丙二醇都具有十分广泛的用途. 实验上报道的众多相关金属催化剂中,铂具有性质稳定、不易失活、可活化氢分子提供氢原子等优点. 此外甘油在铂上氢解生成1,2-丙二醇的选择性高于1,3-丙二醇. 本文主要利用从头算分子动力学对甘油在Pt(111)和Pt(211)表面上发生的羟基解离过程进行了模拟计算,并对比分析了其自由能的变化和表面物种结构参数的变化,得出了以下结论：(i)密度泛函理论优化气相甘油分子结构的结果显示,氢键对于气相中分子的结构与能量有较大贡献,三个羟基形成三个分子内氢键结构时甘油分子能量最低;(ii)通过比较从头算分子动力学模拟得到的自由能能垒和反应自由能,可以得出,在Pt(111)和Pt(211)表面,末端碳上的羟基比中间碳上的羟基更容易发生解离. 这表明在类似的条件下,铂作为催化剂可以为1,2-丙二醇的生产提供更高的选择性,这与文献中报道的实验结果一致;(iii)通过对从头算分子动力学模拟得到的初始吸附态和过渡态结构参数的分析,发现在羟基解离的过程中,C-C键的键长没有明显变化,而氧原子的相对位置以及氢键的长度有明显变化,且氢键长度的变化更加剧烈;(iv)通过比较从头算分子动力学研究所得的自由能能垒和结构参数的相关趋势发现,自由能能垒与初始吸附态和过渡态的氧原子间位置的变化量之间存在线性关系,而分子内氢键对自由能能垒的贡献可以忽略不计. 氧原子间位置的变化越大,自由能能垒越高.     

中性循环中铱催化甲醇羰基化合成乙酸的理论研究

采用密度泛函理论研究了中性循环中Ir(CO)_3I催化甲醇羰基化制乙酸的反应机理,计算得到了反应路径上各驻点的几何构型与频率,通过能量和振动分析证实了过渡态的真实性.结果表明,Ir(CO)_2I与CH_3I作用后,亲核加成过程出现反应路径中最大能垒(40. 3 kJ/mol),使用能量跨度模型分析了反应过程的动力学信息,确定了反应的能量跨度和决速中间体和决速过渡态分别为IM1和TS12,亲核加成过程为反应的决速步骤,得到了298 K催化剂的转化频率3. 2×10~(-6)s~(-1).     

取代基对2-(2-羟基苯基)苯并噻唑分子内氢键及质子转移的影响:密度泛函理论研究

运用密度泛函(DFT)和含时密度泛函(TD DFT)理论方法研究了在2-(2-羟基苯基)苯并噻唑(HBT)苯环羟基的邻位或对位分别引入羟基和醛基后的衍生物分子内质子转移过程,考察了取代基的电子效应及取代位置对分子内氢键和质子转移反应的影响,模拟计算了各分子的IR振动光谱和电子光谱.研究发现,HBT及其衍生物分子可以形成分子内氢键,且激发态时氢键增强.基态时以醇式构型稳定存在,激发态时酮式结构为优势构象.分子的最大吸收峰和发射峰主要源于电子从前线分子轨道HOMO到LUMO之间的跃迁.基态分子内质子转移需要越过较高的能垒因而难以发生,而激发态时只需越过较低能垒就很容易发生激发态分子内质子转移.取代基的电子效应和取代位置对HBT分子氢键强度、互变异构体的相对稳定性、电子光谱及质子转移反应的能垒均有一定影响.     

ClONO2异构化反应和分解反应的理论研究

用B3LYP/6 31+G(d)和MP2 (Full) /6 31+G(d)优化ClONO2 及其分解反应和异构化反应的过渡态和产物的分子结构 .在B3LYP/6 31+G(d)水平上计算了相关分子的振动频率 .ClONO2 的几何结构、振动频率和红外强度与实验测量值符合得很好 .找到了未曾报道的立体异构体 .对这一立体异构体进行了高级别理论方法CCSD(T) /6 311G(d)和QCISD(T) /6 311G(d)的几何结构优化和振动频率计算 ,表明它是一个稳定的立体异构体 .在所研究的几种反应中 ,ClONO2 分解为NO2 +ClO是最容易进行的反应 .而ClONO2 异构为立体异构体的反应是最难进行的反应 .其所需克服的过渡态的能垒为 4 81.5 2kJ/mol,而反应吸收能量为 2 99.85kJ/mol.次难进行的是ClONO2 经TS1到反应中间体M1,再经TS12而分解为ClNO +O2 的反应 .这个反应通道所需克服过渡态的能垒为 4 2 1.5 5kJ/mol,反应吸收能量为 15 7.98kJ/mol.从以上分析可知 ,和ClO +NO2 反应生成ClONO2 比较 ,ClONO2 具有较好的稳定性 .     

取代基对2-(2-羟基苯基)苯并噻唑分子内氢键及质子转移的影响:密度泛函理论研究

运用密度泛函(DFT)和含时密度泛函(TD DFT)理论方法研究了在2-(2-羟基苯基)苯并噻唑(HBT)苯环羟基的邻位或对位分别引入羟基和醛基后的衍生物分子内质子转移过程，考察了取代基的电子效应及取代位置对分子内氢键和质子转移反应的影响，模拟计算了各分子的IR振动光谱和电子光谱.研究发现，HBT及其衍生物分子可以形成分子内氢键，且激发态时氢键增强.基态时以醇式构型稳定存在，激发态时酮式结构为优势构象.分子的最大吸收峰和发射峰主要源于电子从前线分子轨道HOMO到LUMO之间的跃迁.基态分子内质子转移需要越过较高的能垒因而难以发生，而激发态时只需越过较低能垒就很容易发生激发态分子内质子转移.取代基的电子效应和取代位置对HBT分子氢键强度、互变异构体的相对稳定性、电子光谱及质子转移反应的能垒均有一定影响.     

重离子位垒下熔合——多维位垒透射及动力学过程的研究

前言入射能量接近和低于库仑位垒能区的重离子熔合反应是当前重离子反应研究中一个十分活跃的前沿领域。实验和理论的探索已经证实并描述了高于位垒的低能区重离子(轻核到中重核)反应主要经历的全熔合反应机制。两个硬球在一维(径向距离)库仑+核势相互作用下碰撞、并越过熔合位垒熔合的图像给出了对于垒上低能区全熔合截面的相当好的拟合。然而,相当简化的一维位垒模型的成功是由于垒上低能区全熔合截面一般说来并不灵敏于其它自由度。     

孤立条件下布洛芬分子手性转变过程的理论研究

基于密度泛函理论的B3LYP方法,采用6-31+g(d,p)基组,对孤立条件下布洛芬分子的手性转变过程进行研究.通过寻找反应过程中包括过渡态和中间体的各极值点结构,绘制了布洛芬分子手性转变路径反应势能面,分析了各极值点的几何和电子结构特性.结果表明:布洛芬实现从S型到R型手性转变的反应路径有两条.路径1包括三个过渡态和两个中间体,路径2包括四个过渡态和三个中间体.反应路径上最大的能垒是73.54 Kcal/mol,来源于手性碳上的氢向羧基上的氧转移.这一研究为进一步实现一些有重要应用价值的点手性分子手性转变反应调控提供了理论参考.     

硫酸催化乙二醛气体相水化反应机理和速率常数理论计算研究

采用M06-2X和CCSD(T)高阶量化计算和传统过渡态理论研究硫酸催化乙二醛气体相水化反应.对HCOCHO+H₂O, HCOCHO+H₂O+H₂O, HCOCHO+H₂O+H₂O, HCOCHO+H₂O...H₂SO₄和HCOCHO+H₂O+H₂SO₄五个路径的反应机理和速率常数进行了研究.计算结果表明硫酸具有较强的催化能力,能显著减小乙二醛水化反应的能垒,在CCSD(T)/6-311++G(3df,3pd)//M06-2X/6-311++G(3df,3pd)理论水平,当硫酸分子参与乙二醛水化反应时,反应能垒从37.15 kcal/mol减少至7.08 kcal/mol.在室温条件下,硫酸催化乙二醛水化反应的反应速率1.34×10^-11 cm³/(molecule.s),是等量水分子参与乙二醛水化反应的速率的10¹²倍,大于乙二醛与OH自由基反应的反应速率1.10×10^-11 cm³/(molecule.s).这表明大气条件下,硫酸催化乙二醛水化反应可以发生,同乙二醛与OH自由基反应相竞争.     

Impact of Mercury(II) on proteinase K catalytic center: investigations via classical and Born-Oppenheimer molecular dynamics

Mercury(II) has a strong affinity for the thiol groups in proteins often resulting in the disruption of their biological functions. In this study we present classical and first-principles, DFT-based molecular dynamics (MD) simulations of a complex of Hg(II) and proteinase K, a well-known serine protease with a very broad and diverse enzymatic activity. It contains a catalytic triad formed by Asp39, His69, and Ser224, which is responsible for its biological activity. It was found previously by X-ray diffraction experiments that the presence of Hg(II) inhibits the enzymatic action of proteinase K by affecting the stereochemistry of the triad. Our simulations predict that (i) the overall structure as well as the protein backbone dynamics are only slightly affected by the mercury cation, (ii) depending on the occupied mercury site, the hydrogen bonds of the catalytic triad are either severely disrupted (both bonds for mercury at site 1, and the His69–Ser224 contact for mercury at site 2) or slightly strengthened (the Asp39–His69 bond when mercury is at site 2), (iii) the network of hydrogen bonds of the catalytic triad is not static but undergoes constant fluctuations, which are significantly modified by the presence of the Hg(II) cation, influencing in turn the triad’s ability to carry out the enzymatic function—these facts explain the experimental findings on the inhibition of proteinase K by Hg(II).     

HNCO+HCO→NCO+CH2O氢转移反应的从头算及动力学研究

在UMP2 (Full) /6 311G(d ,p)计算水平上 ,优化了标题反应的反应物、过渡态、产物的几何结构 ,沿最小能量途径讨论了异氰酸 (HNCO)和甲酰自由基 (HCO)发生氢转移反应位能面上驻点的结构以及相互作用分子结构变化 .指出该反应是一个N -H键断裂和C -H键生成的协同反应 .进一步采用UQCISD(T ,Full)方法对反应途径上的驻点进行了单点能量校正 ,得出该反应的计算位垒是 91.4 7kJ/mol,与实验值 10 8.92kJ/mol接近 .在5 0 0～ 2 5 0 0K实验温度范围内 ,运用变分过渡态理论 (CVT)计算得到的速率常数与实验观测值进行了比较 .     

过氧硝酸分解势能面的理论研究

使用密度泛函理论B3LYP/6-311+ G(2d,2p)研究了过氧硝酸的最低能量结构．采用耦合簇方法CCSD(T)/aug-cc-pVDZ首次分别扫描了过氧硝酸沿氧-氮和氧-氧键的分解势能面．计算结果表明在氧-氮势能面上,当O3—N4键长是2.82 ?时,对应的疏松过渡态的能垒是25.6 kcal/mol;在氧$-$氧键的势能面上,当O2—O3键长是2.35 ?时,对应的疏松过渡态的能垒是37.4 kcal/mol．这表明过氧硝酸更容易分解为HO₂和NO₂．     

Theoretical investigation on the excited‐state intramolecular proton transfer mechanism of 2‐(2′‐benzofuryl)‐3‐hydroxychromone

Spectroscopic studies on excited‐state proton transfer of a new chromophore 2‐(2′‐benzofuryl)‐3‐hydroxychromone (BFHC) have been reported recently. In the present work, based on the time‐dependent density functional theory (TD‐DFT), the excited‐state intramolecular proton transfer (ESIPT) of BFHC is investigated theoretically. The calculated primary bond lengths and angles involved in hydrogen bond demonstrate that the intramolecular hydrogen bond is strengthened. In addition, the phenomenon of hydrogen bond reinforce has also been testified based on infrared (IR) vibrational spectra as well as the calculated hydrogen bonding energies. Further, hydrogen bonding strengthening manifests the tendency of excited state proton transfer. Our calculated results reproduced absorbance and fluorescence emission spectra of experiment, which verifies that the TD‐DFT theory we used is reasonable and effective. The calculated Frontier Molecular Orbitals (MOs) further demonstrate that the excited state proton transfer is likely to occur. According to the calculated results of potential energy curves along O―H coordinate, the potential energy barrier of about 14.5 kcal/mol is discovered in the S₀ state. However, a lower potential energy barrier of 5.4 kcal/mol is found in the S₁ state, which demonstrates that the proton transfer process is more likely to happen in the S₁ state than the S₀ state. In other words, the proton transfer reaction can be facilitated based on the photo‐excitation effectively. Moreover, the phenomenon of fluorescence quenching could be explained based on the ESIPT mechanism. Copyright © 2015 John Wiley & Sons, Ltd.     

Hydrogen bonding and excited state properties of the photoexcited hydrogen‐bonded (E)‐S‐(2‐aminopropyl) 3‐(4‐hydroxyphenyl)prop‐2‐enethioate complexes

The time‐dependent density functional theory (TDDFT) method has been performed to investigate the excited state and hydrogen bonding dynamics of a series of photoinduced hydrogen‐bonded complexes formed by (E)‐S‐(2‐aminopropyl) 3‐(4‐hydroxyphenyl)prop‐2‐enethioate with water molecules in vacuum. The ground state geometric optimizations and electronic transition energies as well as corresponding oscillator strengths of the low‐lying electronic excited states of the (E)‐S‐(2‐aminopropyl) 3‐(4‐hydroxyphenyl)prop‐2‐enethioate monomer and its hydrogen‐bonded complexes O₁‐H₂O, O₂‐H₂O, and O₁O₂‐(H₂O)₂ were calculated by the density functional theory and TDDFT methods, respectively. It is found that in the excited states S₁ and S₂, the intermolecular hydrogen bond formed with carbonyl oxygen is strengthened and induces an excitation energy redshift, whereas the hydrogen bond formed with phenolate oxygen is weakened and results in an excitation energy blueshift. This can be confirmed based on the excited state geometric optimizations by the TDDFT method. Furthermore, the frontier molecular orbital analysis reveals that the states with the maximum oscillator strength are mainly contributed by the orbital transition from the highest occupied molecular orbital to the lowest unoccupied molecular orbital. These states are of locally excited character, and they correspond to single‐bond isomerization while the double bond remains unchanged in vacuum.     

The ESIPT mechanism of dibenzimidazolo diimine sensor: a detailed TDDFT study

Spectroscopic investigations on excited state proton transfer of a new dibenzimidazolo diimine sensor (DDS) were reported by Goswami et al. recently. In our present work, based on the time‐dependent density functional theory (TDDFT), the excited‐state intramolecular proton transfer (ESIPT) mechanism of DDS is studied theoretically. Our calculated results reproduced absorption and fluorescence emission spectra of the previous experiment, which verifies that the TDDFT method we adopted is reasonable and effective. The calculated dominating bond lengths and bond angles involved in hydrogen bond demonstrate that the intramolecular hydrogen bond is strengthened. In addition, the phenomenon of hydrogen bond reinforce has also been testified based on infrared vibrational spectra. Further, hydrogen bonding strengthening manifests the tendency of ESIPT process. The calculated frontier molecular orbitals further demonstrate that the excited state proton transfer is likely to occur. According to the calculated results of potential energy curves along O–H coordinate, the potential energy barrier of about 5.02 kcal/mol is discovered in the S₀ state. However, a lower potential energy barrier of 0.195 kcal/mol is found in the S₁ state, which demonstrates that the proton transfer process is more likely to happen in the S₁ state than the S₀ state. In other words, the proton transfer reaction can be facilitated based on the photo‐excitation effectively. Moreover, the phenomenon of fluorescence quenching could be explained based on the ESIPT mechanism. Copyright © 2015 John Wiley & Sons, Ltd.     

Comparative study of the nucleophilic attack step in the proteases catalytic activity: A theoretical study

ABSTRACT

The nucleophilic attack step of the hydrolysis reaction mechanism of the glycine-glycine peptide bond mediated by the enzymatic action of various proteases was elucidated by means of DFT calculations. Five different protease models were considered; namely: cysteine (Cys), threonine (Thr), serine (Ser), aspartyl (Asp) proteases, and a metalloprotease containing zinc (Zn). The model was simplified in order to gain information about the nucleophilic attack in this type of reaction. As a comparative study, this work is focused on the trend in the reactivity of the models. According to the computed activation energies, the reactivity order was determined as follows Cys?<?Thr?<?Ser?<?Zn?<?Asp, being in all cases faster than the uncatalysed spontaneous hydrolysis. A further analysis of the reactions by means of the reaction force approach showed that the structural changes accounts for 65–90% of the total activation energy. Moreover, a natural bond orbital analysis allows the reactions to be classified as synchronous with a late transition state for all cases. Systems analogous to the Cys-protease can be proposed as a promising candidate for the design of mimetic systems capable to cleavage amide bonds.     

Rotation of hydrogen molecules during the dissociative adsorption on the Mg(0001) surface: a first-principles study

Using first-principles calculations,we systematically study the potential energy surfaces and dissociation processes of the hydrogen molecule on the Mg(0001) surface.It is found that during the dissociative adsorption process with the minimum energy barrier,the hydrogen molecule first orients perpendicularly,and then rotates tobecome parallel to the surface.It is also found that the orientation of the hydrogen molecule in the transition state is neither perpendicular nor parallel to the surface.Most importantly,we find that the rotation causes a reduction of the calculated dissociation energy barrier for the hydrogen molecule.The underlying electronic mechanism for the rotation of the hydrogen molecule is also discussed in the paper.     

A theoretical study on the ESPT mechanism for a novel Bis‐HPBT fluorophore

In this work, based on the density functional theory and time‐dependent density functional theory methods, the properties of the 2 intramolecular hydrogen bonds (O1‐H2···N3 and O4‐H5···N6) of a new photochemical sensor 4‐(3‐(benzo[d]thiazol‐2‐yl)‐5‐tert‐butyl‐4‐hydroxybenzyl)‐2‐(benzo[d]thiazol‐2‐yl)‐6‐tert‐butyl phenol (Bis‐HPBT) have been investigated in detail. The calculated dominating bond lengths and bond angles about these 2 hydrogen bonds (O1‐H2···N3 and O4‐H5···N6) demonstrate that the intramolecular hydrogen bonds should be strengthened in the S₁ state. In addition, the variations of hydrogen bonds of Bis‐HPBT have been also testified based on infrared vibrational spectra. Our theoretical results reproduced absorption and emission spectra of the experiment, which verifies that the theoretical level we used is reasonable and effective in this work. Further, hydrogen bonding strengthening manifests the tendency of excited state intramolecular proton transfer (ESIPT) process. Frontier molecular orbitals depict the nature of electronically excited state and support the ESIPT reaction. According to the calculated results of potential energy curves along stepwise and synergetic O1‐H2 and O4‐H5 coordinates, the potential energy barrier of approximately 1.399 kcal/mol is discovered in the S₁ state, which supports the single ESIPT process along with 1 hydrogen bond of Bis‐HPBT. In other words, the proton transfer reaction can be facilitated based on the electronic excitation effectively. In turn, through the process of radiative transition, the proton‐transfer Bis‐HPBT‐SPT form regresses to the ground state with the fluorescence of 539 nm.