Theoretical investigation on isomer formation probability and free energy of small C clusters

Molecular dynamics simulations and free energy calculations are employed to investigate the evolution, formation probability, detailed balance, and isomerization rate of small C cluster isomer at 2500 K. For C10, the isomer formation probability predicted by free energy is in good agreement with molecular dynamics simulation. However, for C20, C3o, and C36, the formation probabilities predicted by free energy are not in agreement with molecular dynamics simulations. Although the cluster systems are in equilibrium, detailed balance is not reached. Such results may be attributed to high transformation barriers between cage, bowl, and sheet isomers. In summary, for mesoscopic nanosystems the free energy criterion, which commonly holds for macroscopic systems in dynamic equilibrium, may not provide a good prediction for isomer formation probability. New theoretical criterion should be further investigated for predicting the isomer formation probability of a mesoscopic nanosystem.

DFT Study on Two C_4N_(12)O_4 Isomers with Pagodane- and Isopagodane-like Structures

Geometries, energies, and vibrational frequencies for two C4N12O4 isomers with pagodane- and isopagodane-like structures have been calculated at the B3LYP/6-31G＊ level.Isomers 1 and 2 are of D2h and D2d symmetry, respectively. Heats of formation for the two C4N12O4 isomers have been estimated in this paper, indicating they would be reasonable candidates for high energy density materials.

水液相下Eda酮式异构体与超氧化氢自由基反应的DFT理论计算

在M06-2X/SMD/6-311+G(d,p)理论水平下,研究水液相1个大气压、 310.15 K温度下依达拉奉(Eda)酮式异构体与超氧化氢自由基(·HO_(2))的反应机理.结果表明:Eda酮式异构体与·HO_(2)的反应有抽H、加成和单电子转移3个过程;抽H反应主要通过·HO_(2)抽取杂环H和甲基H实现,反应的自由能垒为77.1~78.7 kJ/mol;加成反应可通过·HO_(2)加成不饱和C的过程实现,加成自由能垒为48.2~95.0 kJ/mol;加成到杂环上与甲基相连的C原子的放热反应最具优势,自由能垒为48.2 kJ/mol;单电子转移的自由能垒为141.1 kJ/mol,该过程不能实现.可见,水液相下Eda酮式异构体可通过抽H和加成反应消除·HO_(2).

锝化学研究 Ⅵ.^(99)Tc^m-HM-PAO异构体稳定性的研究

根据^(99)Tc标记HM-PAO的晶体结构数据,采用三种不同判断尺度对^(99)Tc^m-HM-PAO异构体进行模拟计算与构象分析。可看出这种向心配体配合物存在三种(d、l-,meso 1,meso 2)不同立体结构,找到了影响该类异构体稳定性的本质因素,探讨了d、l-CB-PAO稳定异构体的立体构型,验证了前文提出的物理模型与计算方法的可靠性,为促进药物设计和搞清有关Tc放射性药物脑代动力学的立体构象打下基础。

Lys分子的旋光异构及羟自由基致损伤机理

采用密度泛函理论的B3LYP方法和微扰理论的MP2方法,研究了具有氨基和羧基间单氢键的赖氨酸分子的旋光异构、水分子簇的催化、羟基自由基致赖氨酸损伤机理及水溶剂化效应。反应通道研究发现:标题反应有2个通道a和b。分别是分步机理和协同机理。势能面计算表明:羧基异构和质子迁移分步进行的a通道为主反应通道,决速步裸反应吉布斯自由能垒为259.90 kJ·mol^(-1);2个水分子簇的催化使a通道决速步能垒降为145.80 kJ·mol^(-1),水溶剂效应使该能垒进一步降到111.22 kJ·mol^(-1);羟自由基与水分子链作氢迁移媒介可导致赖氨酸损伤,在水汽相环境下的能垒是134.12 kJ·mol^(-1),水溶剂效应使该能垒骤降到32.62 kJ·mol^(-1)。

水环境下氢氧根水分子团簇催化赖氨酸旋光异构及羟自由基致损伤的机理

在MP2/6-311++G(2df,pd)∥B3LYP/6-31+G(d,p)双理论水平,研究了氢氧根水分子团簇催化2种稳定构象的赖氨酸分子旋光异构及羟基自由基致其损伤的机理。反应通道研究发现:赖氨酸旋光异构有2个通道a与b,a是氢氧根水分子团簇与α-氢和氨基氮通过氢键作用形成底物,氢氧根拔α-氢,然后α-碳再拔另一侧2个水分子簇的氢;b是氢氧根水分子团簇与α-氢和羰基氧通过氢键作用形成底物,氢氧根拔α-氢,而后α-碳再拔另一侧2个水分子簇的氢。羟自由基拔氢致赖氨酸损伤可在b通道实现。势能面计算表明:水液相环境下,构象1(氨基羧基间为单氢键)和构象2(氨基羧基间为双氢键)旋光异构的优势通道均为b,决速步能垒分别是49.94和60.41 k J·mol^(-1),羟自由基在b通道致构象1和2赖氨酸分子的损伤为低或无势垒放热反应。

Solvation effects on brain uptakes of isomers of ^(99m)Tc brain imaging agents

Analysis of electrostatic hydration free energies of the isomers of the 99mTc-BAT and 99mTc-DADT complexes is carried out using the computer simulation technique. The results show that not only a correlation exists between the logarithm of the brain uptake and the electrostatic hydration free energy for the isomers of 99mTc-brain radiopharmaceu-ticals, but also a linear relationship exists between the logarithm of the ratio of the brain uptake of the syn isomer to that of the anti one and the difference between the electrostatic hydration free energy of the syn-isomer and that of the anti one. Furthermore, the investigation on the important factors influencing the brain uptakes of 99mTc-radiophar-maceuticals and the reasons of the different biodistribution of the isomers of the 99mTc-complexes is explored at the molecular level. The results may provide a reference for the rational drug design of brain imaging agents.

水液相环境下赖氨酸旋光异构及羟自由基致其损伤的机理

在MP2/6-311++G(2df,pd)//B3LYP/6-31+G(d,p)双理论下,采用自洽反应场(SCRF)理论的SMD模型方法,研究水液相环境下,两种稳定构象赖氨酸分子基于氨基氮为氢迁移桥梁的旋光异构过程及羟自由基致其损伤的机理.势能面计算结果表明:在水液相环境下,当2个和3个水分子簇作为氢迁移媒介时,构象1旋光异构的决速步骤Gibbs自由能垒分别为116.02,112.71kJ/mol,构象2旋光异构的决速步骤Gibbs自由能垒分别为110.27,114.29kJ/mol;当羟自由基与水分子链作为氢迁移媒介时,羟自由基抽氢致赖氨酸分子构象1和构象2损伤的Gibbs自由能垒分别为-53.06,-56.05kJ/mol,均为无势垒反应.即在水液相环境下,赖氨酸分子可缓慢地旋光异构,羟自由基可迅速致赖氨酸损伤.

互为同分异构体的植物雌激素与ER_(α)及ER_(β)结合亲和力的分子动力学研究

本研究采用分子动力学模拟方法探究了互为同分异构体的2种植物雌激素芹菜素和染料木素与雌激素受体ER_(α)及ER_(β)之间的结合亲和力,选择内源性激素17β-雌二醇进行对比研究.研究结果表明,配体中官能团的位置、配体和受体之间形成的氢键数目、范德华能、静电能及溶剂化能等相互作用影响复合物的稳定性,进而影响结合能力.