Quantum chemical studies of a model for peptide bond formation. 3. Role of magnesium cation in formation of amide and water from ammonia and glycine

The SN2 reaction between glycine and ammonia molecules with magnesium cation Mg2+ as a catalyst has been studied as a model reaction for Mg(2+)-catalyzed peptide bond formation using the ab initio Hartree-Fock molecular orbital method. As in previous studies of the uncatalyzed and amine-catalyzed reactions between glycine and ammonia, two reaction mechanisms have been examined, i.e., a two-step and a concerted reaction. The stationary points of each reaction including intermediate and transition states have been identified and free energies calculated for all geometry-optimized reaction species to determine the thermodynamics and kinetics of each reaction. Substantial decreases in free energies of activation were found for both reaction mechanisms in the Mg(2+)-catalyzed amide bond formation compared with those in the uncatalyzed and amine-catalyzed amide bond formation. The catalytic effect of the Mg2+ cation is to stabilize both the transition states and intermediate, and it is attributed to the neutralization of the developing negative charge on the electrophile and formation of a conformationally flexible nonplanar five-membered chelate ring structure.     

An excited state paired interacting orbital method

A new method for analyzing and visualizing the molecular excited states, named "excited state paired interacting orbital (EPIO)," is proposed. The method is based both on the paired interacting orbital (PIO) proposed by Fujimoto and Fukui [J. Chem. Phys. 60, 572 (1974)] and the natural transition orbital (NTO) by Martin [J. Chem. Phys. 118, 4775 (2003)]. Within the PIO method, orbital interactions between the two fragmented molecules are represented practically only by a few pairs of fragment orbitals. The NTO method is a means of finding a compact orbital representation for the electronic transitions in the excited states. With the method, electronic transitions are expressed by a few particle-hole orbital pairs and a clear picture on the electronic transitions is obtained. EPIO method is designed to have both properties of the preceding two methods: electronic transitions in composite molecular systems can be expressed with a few pairs of EPIOs which are constructed with fragmented molecular orbitals (MOs). Excited state characters, such as charge transfer and local excitations, are analyzed by using EPIOs with their generation probabilities. Thus, the present method gives us clear information on the composition of MOs which play an important role in the molecular excitation processes, e.g., optical processes.     

Studies on the 1,4-oxazepine ring formation reaction using the molecular orbital method

1,4-Oxazepine formation reactions of 1,8-naphthyridine derivatives (1-4) with peroxy acid have been studied using a semiempirical MO method (AM1) and an ab initio molecular orbital method (Gaussian 94). The energies of molecules involved in the reaction paths were calculated and the transition states related to experimental products were obtained. For the reactions of 1-3, the calculated energies of the transition states predicted the previously obtained products. However, the calculated values for the reaction of 4 suggested a different type of oxazepine compound, which was verified in further experiments.     

乙酰胆碱水解反应的从头算研究

本文对乙酰胆碱水解反应历程进行了从头算分子轨道研究。首先, 我们在RHF/6-31G级别上研究了乙酰胆碱的水解反应的势能面, 找到了反应过程中的两个过渡态和连接这两个过渡态的中间体。然后进行了RHF/6-31G**级别上的单点能量计算。优化结果表明在两个过渡态中都包含有四元环状结构, 而且, 两个过渡态的四元环中存在着不同的分子内氢键。计算结果还表明,乙酰胆碱最终分解成胆碱和乙酸盐部分时, 酯键的断裂发生在羰基碳和酯基氧之间。最后, 进一步考虑溶剂化效应, 我们还运用量子Onsager模型, 在RHF/6-31G**级别上对整个水解反应的反应物、产物、中间体和过渡态分别进行了从头算自洽反应场能量计算, 求出了包含溶剂化效应在内的反应的能垒及总反应热。     

A theoretical study of neighboring-group participation in thione-to-thiol rearrangement of xanthates. molecular orbital calculation using a conductor-like screening model (COSMO) approach.

The transition structures of the thione-to-thiol rearrangement of O-(2-dimethylaminoethyl and 2-methylthio-) S-methyl xanthates in several solvents were located by semiempirical molecular orbital method (PM3) using the conductor-like screening model (COSMO) approach. Each transition state transforms into the ion-pair intermediate with a three-membered ring structure (aziridinium or thiiranium), indicating that the rearrangement proceeds through an ionic intermediate with the anchimeric assistance of the neighboring group. The intermediary structures in gas phase are also analyzed by ab initio and density functional theory calculations.     

Theoretical study of free-radical migrations

Free-radical migrations have been investigated by ab initio molecular orbital theory to account for the facts that 1,2-migrations are observed for Cl-atoms, aryl or vinyl groups, whereas for H atoms only 1,5- and 1,6-migrations have been seen in contrast to the easy 1,2-hydride shifts in cations. The optimum geometry and energy models of the transition states of 1,2- and 1,5-migrations, and of their corresponding initial states have been determined using the Gaussian 70 STO-3G RHF method. The calculated activation energies ΔE are in agreement with experimental observations. The main features of the 1,2-migration reactions are (i) ΔE is more important for elements of the first and second row of the periodic classification than for those belonging to the third row; (ii) protonation strongly reduces ΔE. For both 1,2- and 1,5-migrations a correlation exists between ΔE and the energetic change of the frontier orbital, Δ?_somo: the reactions are under frontier orbital control.     

氟硼二吡咯类pH荧光探针PET光谱特性的理论计算

氟硼二吡咯(BODIPY)类pH荧光探针分子是基于光诱导电子转移(PET)的荧光探针分子, 识别基团氮原子上引入不同取代基可呈现不同的光学灵敏度. 本文应用密度泛函理论(DFT)及含时密度泛函理论(TD-DFT)方法对六种含不同取代基的探针分子进行了几何构型优化及激发态计算, 探讨了不同取代基对PET效应影响. 计算结果表明: 基态时这些探针分子的最高占有分子轨道(HOMO)和最低未占有分子轨道(LUMO)都在荧光母体BODIPY的π, π^*轨道, 而识别基团上氮原子孤对电子所在的轨道为HOMO-1轨道. 但是在激发态, 当氮原子上有两个取代基时, HOMO-1→LUMO跃迁的激发能都小于荧光团的HOMO→LUMO跃迁, 这将有可能产生PET效应并导致荧光熄灭, 而当氮原子上有一个取代基时不会出现这种现象. 通过激发态结构优化可以发现, 无论识别基团氮原子上有一个还是两个取代基, N原子的轨道对称性都发生变化, 由sp³→sp², 孤对电子占据在p轨道上, 其轨道能级升高至荧光团的HOMO和LUMO轨道之间, 将导致不同程度的PET效应, 与实验结果一致.     

苯酚羟基化制备苯二酚反应机理的理论研究

采用密度泛函理论(DFT)在UB3LYP/6-311G^**//UB3LYP/6-31G^*水平上研究了水溶液中羟基自由基进攻苯酚的邻位和对位生成邻苯二酚和对苯二酚的反应机理.结果表明,2个反应都存在3个过渡态,3个中间体,并通过振动分析对过渡态进行了确认.电荷密度的拓扑分析发现,邻位反应中羟基自由基的氧原子和苯酚环上的2个氢原子之间形成了氢键,并相应地形成了六元环和五元环结构.经单点能校正后,2个反应的主反应活化能十分接近,说明邻位和对位产物会同时存在,这与实验观测的结果一致.     

Single molecule charge transport: from a quantum mechanical to a classical description

This paper explores charge transport at the single molecule level. The conductive properties of both small organic molecules and conjugated polymers (molecular wires) are considered. In particular, the reasons for the transition from fully coherent to incoherent charge transport and the approaches that can be taken to describe this transition are addressed in some detail. The effects of molecular orbital symmetry, quantum interference, static disorder and molecular vibrations on charge transport are discussed. All of these effects must be taken into account (and may be used in a functional way) in the design of molecular electronic devices. An overview of the theoretical models employed when studying charge transport in small organic molecules and molecular wires is presented.     

烯酮及取代烯酮与环戊二烯环加成反应机理的理论研究

利用半经验分子轨道理论AM1方法,研究了烯酮及取代烯酮与环戊二烯环加成反应机理。采用Berny梯度法优化得到各反应的过渡态和中间体,并进行了振动分析确认。计算结果表明,该环加成反应是按照协同的非同步途径进行的,经过一个四元环发生扭曲的过渡态,并有部分电荷从环戊二烯迁移到烯酮或取代烯酮上,前线轨道分析表明反应机理为“2×[1+1]”机理;而氯甲基取代的烯酮与环戊二烯的环加成反应是按照分步途径发生的。计算结果可以很好地说明实验所观察到的立体选择性,并根据烯酮上取代基的电子效应和位阻效应对反应机理的影响进行了分析。     

Reactions of the phenylium cation with small oxygen- and nitrogen-containing molecules

The reactions of phenylium with water and ammonia and their methyl homologs have been investigated using a quadrupole ion trap and semiempirical molecular orbital calculations. The results indicate that both types of molecules react with phenylium through lone pair electrons even though, for methyl-containing compounds, insertion into a C-H bond would lead to more stable products. For the excited adducts formed by reaction with methyl-containing reactant neutrals, the only dissociation observed is loss of a methyl radical. Neutral losses of H₂ or CH₄, which are more thermodynamically stable, are not observed, which indicates that these reactions are either not kinetically competitive or have high energy transition states due to the fact that the reactions would need to occur via orbital symmetry forbidden 1,2 eliminations.     

An MNDO molecular orbital study of the reactions of protonated oxirane derivatives (XCHCH2OH+, X = CN,Cl, CH3, Ph) with simple nucleophiles. Implications for regioselectivity in the reactions of electrophiles with nucleic acid bases

The gas-phase analogs of the classical S_N1 and S_N2 reactions of nucleophiles with a series of protonated oxiranes bearing the substituents CN, Cl, Me, and Ph were studied using MNDO semiempirical molecular orbital theory. The transition states for nucleophilic attack on the intact rings are calculated to become progressively more “S_N1-like,” as the ability of the substituent group to stabilize the corresponding ring opened carbenium ion increases. At the same time the activation barriers become progressively smaller and their relative values for different nucleophiles approach the order expected on the basis of a purely electrostatic attraction between the reacting moieties. Exactly the opposite trends are calculated for the transition states for nucleophilic attack on the intermediate carbenium ions. As the stabilities of the latter increase the extent of bond formation, and transfer of charge to the incoming nucleophile also increase. Here, the relative barriers for attack by different nucleophiles approach the order expected on the basis of a superposition of both covalent and electrostatic interactions in which the former dominate. These results support a previously suggested rationalization for the enhanced reactivities of certain alkylating agents towards the exocyclic oxygen atoms, rather than the ring nitrogens, of the nucleic acid bases. They also suggest a new explanation for the tendencies of aralkylating electrophiles to modify the exocyclic amino groups of the nucleic acid bases: sites which are unreactive towards simple alkylating agents.     

Configuration-dependent interface charge transfer at a molecule-metal junction

The role of the molecule-metal interface is a key issue in molecular electronics. Interface charge transfer processes for 4-fluorobenzenethiol monolayers with different molecular orientations on Au(111) were studied by resonant photoemission spectroscopy. The electrons excited into the LUMO or LUMO+1 are strongly localized for the molecules standing up on Au(111). In contrast, an ultrafast charge transfer process was observed for the molecules lying down on Au(111). This configuration-dependent ultrafast electron transfer is dominated by an adiabatic mechanism and directly reflects the delocalization of the molecular orbitals for molecules lying down on Au(111). Theoretical calculations confirm that the molecular orbitals indeed experience a localization-delocalization transition resulting from hybridization between the molecular orbitals and metal surface. Such an orientation-dependent transition could be harnessed in molecular devices that switch via charge transfer when the molecular orientation is made to change.     

Mass spectral fragmentations of aminoketones in which charge is not localized exclusively on nitrogen

The low resolution mass spectra of α-dimethylaminoacetophenone and γ-dimethylaminobutyrophenone are compared to those of δ-methylhexanophenone and dimethyl n-butylamine as well as to those of α-dimethylaminoacetonitrile and γ-dimethylaminobutyronitrile. Analysis indicates that significant fractions of the fragmentations of the aminoketones are directed by the carbonyl. In particular, McLafferty rearrangement of the γ-aminoketone is favored over α-cleavage from nitrogen at ionizing voltages below 15 eV. Although the overall fragmentation patterns are presumably determined both by the distribution of charge and by the relative rates of the fragmentation processes available to the two ionized groups, the intrinsic rates for α-cleavage at ionized nitrogen and at ionized carbonyls appear to be very similar. Kinetic analysis suggests that 26% of the charge resides on the carbonyl in the γ-aminoketone molecular ion. The extent of delocalization of charge in any aminoketone may be partially controlled by the extent of spatial overlap of the two groups. Correlations of mass spectral behavior with photochemical behavior are thus limited because electronic excitation is more localized in the lowest excited states of molecules than charge is in electron-impact produced molecular ions.     

CuCl2催化（2-甲基辛烷-2，3-二烯-4-基）磷酸乙酯氯代环化反应机理理论研究

采用密度泛函理论（DFT）中的B3LYP方法对CuCl2催化的（2-甲基辛烷-2,3-二烯-4-基）磷酸乙酯氯代环化反应机理进行了理论研究．在6-31＋G（d）基组水平上对反应机理中所有反应物、过渡态、中间体和产物进行了优化,通过能量和振动频率分析以及IRC计算证实了中间体和过渡态的合理性．在相同基组水平上应用自然键轨道（NBO）理论和分子中的原子（AIM）理论分析了复合物的成键特征和轨道间相互作用．反应物R和催化剂CuCl2可通过IA和IB两条可行反应通道生成中间体IM9,控制步骤活化能分别是129．61和142．10kJ／m01．中间体IM9到产物P也有两条反应路径PA和PB,控制步骤活化能分别是179．55和9．83kJ／m01．整个反应机理中IA—PB和IB—PB反应通道可能同时发生,反应控制步骤活化能最低反应通道为IA→PB．     

Generation of initial trajectories for transition path sampling of chemical reactions with ab initio molecular dynamics

Transition path sampling is an innovative method for focusing a molecular dynamics simulation on a reactive event. Although transition path sampling methods can generate an ensemble of reactive trajectories, an initial reactive trajectory must be generated by some other means. In this paper, the authors have evaluated three methods for generating initial reactive trajectories for transition path sampling with ab initio molecular dynamics. The authors have tested each of these methods on a set of chemical reactions involving the breaking and making of covalent bonds: the 1,2-hydrogen elimination in the borane-ammonia adduct, a tautomerization, and the Claisen rearrangement. The first method is to initiate trajectories from the potential energy transition state, which was effective for all reactions in the test set. Assigning atomic velocities found using normal mode analysis greatly improved the success of this method. The second method uses a high temperature molecular dynamics simulation and then iteratively reduces the total energy of the simulation until a low temperature reactive trajectory is found. This was effective in generating a low temperature trajectory from an initial trajectory run at 3000 K of the tautomerization reaction, although it failed for the other two. The third uses an orbital based bias potential to find a reactive trajectory and uses this trajectory to initiate an unbiased trajectory. The authors found that a highest occupied molecular orbital-lowest unoccupied molecular orbital bias could be used to find a reactive trajectory for the Claisen rearrangement, although it failed for the other two reactions. These techniques will help make it practical to use transition path sampling to study chemical reaction mechanisms that involve bond breaking and forming.     

水助酮和烯醇类化合物互变异构反应机理的理论研究

采用MP2方法研究了水助MeC(＝O)(CH2R)与MeC(OH)(＝CHR)之间的异构化反应, 确定了相应的过渡态结构并计算了反应势垒. 研究结果表明, 常温下MeC(＝O)(CH2R)与MeC(OH)(＝CHR)之间的异构化反应容易通过2个水分子的参与而实现. 研究结果还表明, 发生质子转移的碳原子在过渡态中采取近sp3杂化. 凡是能够稳定该sp3轨道上的孤对电子的取代基, 都将使质子转移反应的势垒降低, 使异构化反应易于进行.     

Isotope effects in the reaction of benzo[h]quinoline N-oxides with methylsulfinyl carbanion examined by ab initio molecular orbital methods

The reactions of benzo[h]quinoline N-oxide with methylsulfinyl carbanion and deuterated methylsulfinyl carbanion, respectively, were studied theoretically. Differences in yield between these reactions were explained using ab initio molecular orbital methods by considering the zero-point energy correction and the barrier penetration effect. In these reactions, two transition states affected the total reaction rate. The hydrogen- or deuterium-transfer step played a significant role, accounting for the difference in reaction rates.     

A Computational Study of the Wallach Rearrangement

Treatment of azoxybenzene and its derivatives with acids is known to result in the Wallach rearrangement, which leads to 2- or4-hydroxyazobenzenes. Starting in the 1960s, experimental findings have lead to the proposal of several mechanisms for this rearrangement. In this work, molecular orbital theory employing the semiempirical AM1 method is used to locate and discuss the energetics of the intermediates and the transition states for this rearrangement. Based on the results of AM1 calculations in vacuum and in solution, the most plausible mechanistic pathways are proposed and discussed.     

Potassium-intercalated H(2)Pc films: Alkali-induced electronic and geometrical modifications

X-ray spectroscopy studies of potassium intercalated metal-free phthalocyanine multilayers adsorbed on Al(110) have been undertaken. Photoelectron spectroscopy measurements show the presence of several charge states of the molecules upon K intercalation, due to a charge transfer from the alkali. In addition, the comparison of valence band photoemission spectra with the density functional theory calculations of the density of states of the H(2)Pc(-) anion indicates a filling of the formerly lowest unoccupied molecular orbital by charge transfer from the alkali. This is further confirmed by x-ray absorption spectroscopy (XAS) studies, which show a decreased density of unoccupied states. XAS measurements in different experimental geometries reveal that the molecules in the pristine film are standing upright on the surface or are only slightly tilted away from the surface normal but upon K intercalation, the molecular orientation is changed in that the tilt angle of the molecules increases.