The rate constants of the nucleophilic reactions between amines and benzhydrylium ions were calculated using first-principles theoretical methods. Solvation models including PCM, CPCM, and COSMORS, as well as differen...The rate constants of the nucleophilic reactions between amines and benzhydrylium ions were calculated using first-principles theoretical methods. Solvation models including PCM, CPCM, and COSMORS, as well as different types of atomic radii including UA0, UAKS, UAHF, Bondi, and UFF, and several single-point energy calculation methods （B3LYP, B3P86, B3PW91, BHANDH, PBEPBE, BMK, M06, MP2, and ONIOM method） were examined. By comparing the correlation between experimental rate constants and the calculated values, the ONIOM（CCSD（T）/6-311＋＋G（2df,2p）：B3LYP/6-311＋＋G（2df,2p））//B3LYP/6- 31G（d）/PCM/UFF） method was found to perform the best. This method was then employed to calculate the rate constants of the reactions between diverse amines and diarylcarbenium ions. The calculated rate constants for 65 reactions of amines with diarylcarbenium ions are in agreement with the experimental values, indicating that it is feasible to predict the rate constant of a reaction between an amine and a diarylcarbenium ion through ab initio calculation.展开更多
Ab initio calculations at the B3LYP/3-21G^(**), HF/3-21G>^(**) and ONIOM(HF/3-21G^(**): AM1) levels of the theory in combination with counterpoise procedure for BSSE correction were performed on HMX dimers. There e...Ab initio calculations at the B3LYP/3-21G^(**), HF/3-21G>^(**) and ONIOM(HF/3-21G^(**): AM1) levels of the theory in combination with counterpoise procedure for BSSE correction were performed on HMX dimers. There exist two O...H intermolecular contacts and the dispersion forces are dominant in the dimers. The corrected binding energies of the dimer are -15.10 and -17.81 kJ/mol at the HF/3-21G^(**) and \{ONIOM(HF/3-21G^(**): AM1) \}levels, respectively. The calculation by the B3LYP method gives irrational corrected binding energies though it produces similar intermolecular distances as those produced by the HF or \{ONIOM\} method. The geometrical parameters, the contact distances and the binding energies demonstrated, for the first time, the validity of the ONIOM method applied in the calculation of the parameters of intermolecular interactions.展开更多
Mycolactone molecules are responsible of Buruli ulcer disease. In this work, we are interested in the geometric, energetic and spectroscopic characterization of the hydrogen bonding interactions in mycolactone A/B, us...Mycolactone molecules are responsible of Buruli ulcer disease. In this work, we are interested in the geometric, energetic and spectroscopic characterization of the hydrogen bonding interactions in mycolactone A/B, using quantum chemical method, especially ONIOM(HF/6-311+G(d,p):AM1) and ONIOM (B3LYP/6-311+G(d,p):AM1) levels. ONIOM two layers method has been used because mycolactones compounds are very large, taking into account diffuse and polarization functions are important whenever the matter is intermolecular interactions. Geometric, energetic and spectroscopic parameters of hydrogen bonding reaction on each of the nine oxygen heteroatoms of mycolactone A/B have revealed that the O5sp2 heteroatom is far away the hydrogen bonding site. The identification of such a site constitutes a tool for working out a methodology for the annihilation of the destruction effects of mycolactones.展开更多
This work was undertaken to analyze intramolecular and intermolecular interactions of Manzamenones from natural bond orbitals (NBO method). For their use in the treatment of malaria, the results of these molecules are...This work was undertaken to analyze intramolecular and intermolecular interactions of Manzamenones from natural bond orbitals (NBO method). For their use in the treatment of malaria, the results of these molecules are compared to those of Artemisinin and Quinine. Manzamenones are a class of atypical fatty acids. They are isolated from a marine sponge of the genus Plakortis kenyensis. The analysis of intramolecular interactions compares the results of each molecule (Manzamenones, Artemisinin and Quinine) in the non-complexed state with those of its complex with a water molecule. Thus, for the same electron donors (i) and associated acceptors (j), the electron density (ED), stabilization energy E<sup>2</sup> related to the delocalization of i to j, the energies of the NBO orbitals ε<sub>i</sub> and ε<sub>j</sub> of the donor and acceptor, respectively, and element of the Fock matrix F<sub>i,j</sub> are determined and compared. The change in E<sup>2</sup> is used to deduce whether or not the molecule is stabilized after complex formation. These analyses allowed to match each Manzamenone to one of the two antimalarials. The intermolecular interactions were analyzed, for each molecule (Manzamenones, Artemisinin and Quinine), in two complexes. These complexes are obtained with a water molecule on the one hand and with an alanine molecule on the other hand. For these interactions, the electron donor and its electron density, the electron acceptor and its electron density as well as the donor—acceptor stabilization energy have been calculated. The ONIOM 2 method is used to study Manzamenones. Theoretical calculations were done using density functional theory (B3LYP) by combining one of the two function bases 6-31++G(d,p) and 6-31+G(d,p).展开更多
用量子化学ONIOM(B3LYP/6-311++G(3df,3pd):UFF)∥ONIOM(B3LYP/6-31+G(d,p):UFF)方法,研究α-Ala在SWBNNT(9,9)与水复合环境的手性转变。分子结构计算表明:反应物S型α-Ala和中间体INT1在SWBNNT(9,9)与水复合环境,与单体相比,氢转移断的...用量子化学ONIOM(B3LYP/6-311++G(3df,3pd):UFF)∥ONIOM(B3LYP/6-31+G(d,p):UFF)方法,研究α-Ala在SWBNNT(9,9)与水复合环境的手性转变。分子结构计算表明:反应物S型α-Ala和中间体INT1在SWBNNT(9,9)与水复合环境,与单体相比,氢转移断的O-H和C-H键都略长,H与其要转移到的目标原子O的距离均短很多。反应通道研究发现:在SWBNNT(9,9)与水复合环境下,α-Ala手性转变有4条路径,每条路径上氢转移都能以1个或2个水分子为媒介实现。势能面计算发现:手性转变反应的最高能垒来自H从手性C向羰基O转移的过渡态;在氨基先异构接着羧基H转移和H从手性C向羰基O转移顺次实现的路径,并以2H2O为氢转移媒介时最高能垒被降到最小值153.8 k J·mol-1。比只在SWBNNT(9,9)内的302.7 k J·mol-1明显降低,比只在水环境的167.8 k J·mol-1也有所降低。结果表明:SWBNNT(9,9)与水复合环境,对α-Ala手性转变有较好的催化作用。展开更多
用密度泛函理论和ONIOM(our own N-layer integrated molecular orbital molecular mechanics)方法研究磷改性的ZSM-5沸石中含磷基团的可能存在形态.计算的反应焓和自由能数据表明P-ZSM-5沸石中以磷进入骨架和在骨架外的形成磷酸根离子...用密度泛函理论和ONIOM(our own N-layer integrated molecular orbital molecular mechanics)方法研究磷改性的ZSM-5沸石中含磷基团的可能存在形态.计算的反应焓和自由能数据表明P-ZSM-5沸石中以磷进入骨架和在骨架外的形成磷酸根离子对是合理的稳定结构.而且,计算结果表明离子对模型F和G更适合在室温下存在,磷进入骨架的酸性结构C?在高温下更稳定,而磷进入骨架的结构C对温度变化不敏感.计算得到的27Al,31P,29Si化学位移、酸性的变化趋势和结构参数与相关实验数据吻合.展开更多
采用组合的量子化学ONIOM(our own n-layered integrated molecule orbit and molecule mechanics)(B3LYP/6-31++G(d,p):UFF)方法,研究了限域在SWBNNT(9,9)内α-丙氨酸的分子结构和手性转变通道.为得到高水平的能量,在ONIOM(B3LYP/6-311...采用组合的量子化学ONIOM(our own n-layered integrated molecule orbit and molecule mechanics)(B3LYP/6-31++G(d,p):UFF)方法,研究了限域在SWBNNT(9,9)内α-丙氨酸的分子结构和手性转变通道.为得到高水平的能量,在ONIOM(B3LYP/6-311++G(3df,3pd):UFF)水平,计算了各个包结物的单点能.分子结构分析表明:与单体α-丙氨酸相比,受限在SWBNNT(9,9)内时,骨架碳氮原子间的键长不同程度地缩短,骨架碳原子的键角及骨架碳氮原子的二面角略有增大.反应路径研究发现:α-丙氨酸分子在SWBNNT(9,9)内的手性转变有两条同单体情况大致相同的反应通道,不存在单体情况的含有羰基H和甲基H协同转移过程的反应通道.手性转变反应过程的势能面计算发现:与单体α-丙氨酸手性转变反应过程的主要能垒相比较,在纸外面的氢从手性碳直接到羰基氧的过渡态产生的能垒,从326.5kJ·mol-1降到319.7kJ·mol-1;氢首先在羧基内转移,而后手性碳的氢在纸面外转移到羰基,这两个过程的能垒从198.0kJ·mol-1和320.3kJ·mol-1降到135.5kJ·mol-1和302.7kJ·mol-1.结果表明:限域在SWBNNT(9,9)内的α-丙氨酸,其手性转变过程中不同的氢转移反应能垒被不同程度地降低.展开更多
文摘The rate constants of the nucleophilic reactions between amines and benzhydrylium ions were calculated using first-principles theoretical methods. Solvation models including PCM, CPCM, and COSMORS, as well as different types of atomic radii including UA0, UAKS, UAHF, Bondi, and UFF, and several single-point energy calculation methods （B3LYP, B3P86, B3PW91, BHANDH, PBEPBE, BMK, M06, MP2, and ONIOM method） were examined. By comparing the correlation between experimental rate constants and the calculated values, the ONIOM（CCSD（T）/6-311＋＋G（2df,2p）：B3LYP/6-311＋＋G（2df,2p））//B3LYP/6- 31G（d）/PCM/UFF） method was found to perform the best. This method was then employed to calculate the rate constants of the reactions between diverse amines and diarylcarbenium ions. The calculated rate constants for 65 reactions of amines with diarylcarbenium ions are in agreement with the experimental values, indicating that it is feasible to predict the rate constant of a reaction between an amine and a diarylcarbenium ion through ab initio calculation.
基金Supported by the National Natural Science Foundation of China(No.2 0 1730 2 8) and the Postdoctoral Foundation of theMinistry of Education of China
文摘Ab initio calculations at the B3LYP/3-21G^(**), HF/3-21G>^(**) and ONIOM(HF/3-21G^(**): AM1) levels of the theory in combination with counterpoise procedure for BSSE correction were performed on HMX dimers. There exist two O...H intermolecular contacts and the dispersion forces are dominant in the dimers. The corrected binding energies of the dimer are -15.10 and -17.81 kJ/mol at the HF/3-21G^(**) and \{ONIOM(HF/3-21G^(**): AM1) \}levels, respectively. The calculation by the B3LYP method gives irrational corrected binding energies though it produces similar intermolecular distances as those produced by the HF or \{ONIOM\} method. The geometrical parameters, the contact distances and the binding energies demonstrated, for the first time, the validity of the ONIOM method applied in the calculation of the parameters of intermolecular interactions.
文摘Mycolactone molecules are responsible of Buruli ulcer disease. In this work, we are interested in the geometric, energetic and spectroscopic characterization of the hydrogen bonding interactions in mycolactone A/B, using quantum chemical method, especially ONIOM(HF/6-311+G(d,p):AM1) and ONIOM (B3LYP/6-311+G(d,p):AM1) levels. ONIOM two layers method has been used because mycolactones compounds are very large, taking into account diffuse and polarization functions are important whenever the matter is intermolecular interactions. Geometric, energetic and spectroscopic parameters of hydrogen bonding reaction on each of the nine oxygen heteroatoms of mycolactone A/B have revealed that the O5sp2 heteroatom is far away the hydrogen bonding site. The identification of such a site constitutes a tool for working out a methodology for the annihilation of the destruction effects of mycolactones.
文摘This work was undertaken to analyze intramolecular and intermolecular interactions of Manzamenones from natural bond orbitals (NBO method). For their use in the treatment of malaria, the results of these molecules are compared to those of Artemisinin and Quinine. Manzamenones are a class of atypical fatty acids. They are isolated from a marine sponge of the genus Plakortis kenyensis. The analysis of intramolecular interactions compares the results of each molecule (Manzamenones, Artemisinin and Quinine) in the non-complexed state with those of its complex with a water molecule. Thus, for the same electron donors (i) and associated acceptors (j), the electron density (ED), stabilization energy E<sup>2</sup> related to the delocalization of i to j, the energies of the NBO orbitals ε<sub>i</sub> and ε<sub>j</sub> of the donor and acceptor, respectively, and element of the Fock matrix F<sub>i,j</sub> are determined and compared. The change in E<sup>2</sup> is used to deduce whether or not the molecule is stabilized after complex formation. These analyses allowed to match each Manzamenone to one of the two antimalarials. The intermolecular interactions were analyzed, for each molecule (Manzamenones, Artemisinin and Quinine), in two complexes. These complexes are obtained with a water molecule on the one hand and with an alanine molecule on the other hand. For these interactions, the electron donor and its electron density, the electron acceptor and its electron density as well as the donor—acceptor stabilization energy have been calculated. The ONIOM 2 method is used to study Manzamenones. Theoretical calculations were done using density functional theory (B3LYP) by combining one of the two function bases 6-31++G(d,p) and 6-31+G(d,p).
文摘用量子化学ONIOM(B3LYP/6-311++G(3df,3pd):UFF)∥ONIOM(B3LYP/6-31+G(d,p):UFF)方法,研究α-Ala在SWBNNT(9,9)与水复合环境的手性转变。分子结构计算表明:反应物S型α-Ala和中间体INT1在SWBNNT(9,9)与水复合环境,与单体相比,氢转移断的O-H和C-H键都略长,H与其要转移到的目标原子O的距离均短很多。反应通道研究发现:在SWBNNT(9,9)与水复合环境下,α-Ala手性转变有4条路径,每条路径上氢转移都能以1个或2个水分子为媒介实现。势能面计算发现:手性转变反应的最高能垒来自H从手性C向羰基O转移的过渡态;在氨基先异构接着羧基H转移和H从手性C向羰基O转移顺次实现的路径,并以2H2O为氢转移媒介时最高能垒被降到最小值153.8 k J·mol-1。比只在SWBNNT(9,9)内的302.7 k J·mol-1明显降低,比只在水环境的167.8 k J·mol-1也有所降低。结果表明:SWBNNT(9,9)与水复合环境,对α-Ala手性转变有较好的催化作用。
基金supported by the Program for New Century Excellent Talent in University, China (NCET-04-0268)Plan 111 Project of the Ministry of Education of ChinaHigh Performance Computing Department of Network and Information Center, Dalian University of Technology, China~~
文摘用密度泛函理论和ONIOM(our own N-layer integrated molecular orbital molecular mechanics)方法研究磷改性的ZSM-5沸石中含磷基团的可能存在形态.计算的反应焓和自由能数据表明P-ZSM-5沸石中以磷进入骨架和在骨架外的形成磷酸根离子对是合理的稳定结构.而且,计算结果表明离子对模型F和G更适合在室温下存在,磷进入骨架的酸性结构C?在高温下更稳定,而磷进入骨架的结构C对温度变化不敏感.计算得到的27Al,31P,29Si化学位移、酸性的变化趋势和结构参数与相关实验数据吻合.
文摘采用组合的量子化学ONIOM(our own n-layered integrated molecule orbit and molecule mechanics)(B3LYP/6-31++G(d,p):UFF)方法,研究了限域在SWBNNT(9,9)内α-丙氨酸的分子结构和手性转变通道.为得到高水平的能量,在ONIOM(B3LYP/6-311++G(3df,3pd):UFF)水平,计算了各个包结物的单点能.分子结构分析表明:与单体α-丙氨酸相比,受限在SWBNNT(9,9)内时,骨架碳氮原子间的键长不同程度地缩短,骨架碳原子的键角及骨架碳氮原子的二面角略有增大.反应路径研究发现:α-丙氨酸分子在SWBNNT(9,9)内的手性转变有两条同单体情况大致相同的反应通道,不存在单体情况的含有羰基H和甲基H协同转移过程的反应通道.手性转变反应过程的势能面计算发现:与单体α-丙氨酸手性转变反应过程的主要能垒相比较,在纸外面的氢从手性碳直接到羰基氧的过渡态产生的能垒,从326.5kJ·mol-1降到319.7kJ·mol-1;氢首先在羧基内转移,而后手性碳的氢在纸面外转移到羰基,这两个过程的能垒从198.0kJ·mol-1和320.3kJ·mol-1降到135.5kJ·mol-1和302.7kJ·mol-1.结果表明:限域在SWBNNT(9,9)内的α-丙氨酸,其手性转变过程中不同的氢转移反应能垒被不同程度地降低.
