Quantum mechanical free energy barrier for an enzymatic reaction

We discuss problems related to in silico studies of enzymes and show that accurate and converged free energy changes for complex chemical reactions can be computed if a method based on a thermodynamic cycle is employed. The method combines the sampling speed of molecular mechanics with the accuracy of a high-level quantum mechanics method. We use the method to compute the free energy barrier for a methyl transfer reaction catalyzed by the enzyme catechol O-methyltransferase at the level of density functional theory. The surrounding protein and solvent are found to have a profound effect on the reaction, and we show that energies can be extrapolated easily from one basis set and exchange-correlation functional to another. Using this procedure we calculate a barrier of 69 kJ/mol, in excellent agreement with the experimental value of 75 kJ/mol.     

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 .     

Kinetics,mechanism and thermodynamics of reactions of CH3NHNH2 with OOH

Reactions between CH₃NHNH₂ and OOH radical were studied using computational methods. The activation energies (E_a) and Gibbs free energies of activation (ΔG^#) were calculated at the MP2 and B3LYP levels of theory. The calculated activation energies of the hydrogen abstraction reactions were less than 100 kJ/mol and those for the substitution reactions were about 150–250 kJ/mol. The calculated activation energies for the intra-molecular hydrogen transfer reactions in CH₃NHNH, CH₂NNH₂ and CH₃NN molecules were 210–250 kJ/mol. Catalytic effect of the water molecule on the intra-molecular hydrogen transfer reactions was studied. It was found that the water molecule decreases the activation energies by about 70–100 kJ/mol. Rate constants of the reactions were calculated using transition state theory in the temperature range of 298–2000 K. Consecutive hydrogen abstraction reactions from CH₃NHNH₂ led to the formation of CH₂NN, which was a very stable molecule.     

Electron spin resonance spectra of nitrogen heterocyclic radical ions

Abstract

We introduce a representative benchmark database of 20 cycloreversion reaction energies obtained by means of the high-level W1 thermochemical protocol. We use these benchmark values to assess the performance of a variety of contemporary DFT, double-hybrid DFT (DHDFT), standard ab initio, and compound thermochemistry methods. We show that this set of reaction energies provides an extremely challenging test for nearly all of the considered DFT and DHDFT methods. For example, about 80% of the considered functionals result in root-mean-square deviations (RMSDs) above 10 kJ mol^?1. The best DFT and DHDFT procedures are ωB97X and DSD-PBEP86-D3, with RMSDs of 4.7 and 7.9 kJ mol^?1, respectively. Coupled with the fact that the barrier heights for these reactions also pose a significant challenge for many DFT methods, this work shows that only a handful of functionals can quantitatively describe all aspects of the potential energy surface of this important class of reactions. In addition, this work shows that London dispersion effects are particularly large for this class of reactions. For example, empirical D3 dispersion corrections reduce the RMSDs for the DFT and DHDFT procedures by amounts ranging from 3.5 (PBE and B2K-PLYP) to 22.0 (BLYP) kJ mol^?1.     

Adsorption and desorption behavior of NO on H-ZSM-5, Na-ZSM-5, and Na-A as studied by EPR

Nitric monoxide probe molecules are used to characterize the Lewis acid properties of sodium cations and aluminum defect centers in various zeolite materials. The adsorption-desorption behavior of NO probe molecules is studied at different temperatures for Na-A, Na-ZSM-5, H-ZSM-5, and silicalite. Adsorbed NO molecules form paramagnetic adsorption complexes with Lewis acid sites which can be examined by EPR transitions ((Delta)m(S)+/-1) at g approximately 2.0. Otherwise the desorption of NO into the gas phase can be monitored by the typical nine-line EPR spectrum ((Delta)m(J)+/-1) of the (2)Pi(3/2) state at g approximately 0.7776. This gas-phase signal is used to study the overall adsorption-desorption properties of the zeolites in the temperature range 150 K less than or approximately T less than or approximately 300 K. At lower temperatures the probe molecules are adsorbed at the Lewis acid sites inside the nanoporous materials and produce an intensive spectrum at T less than or approximately 110 K. But at intermediate temperatures 110 K less than or approximately T less than or approximately 150 K the NO molecules are adsorbed only for a few hundred picoseconds because the lifetime of the adsorption complexes is limited by the beginning desorption processes. The decreasing lifetime of the adsorption complex with rising temperature results in an increasing homogeneous line broadening of their EPR signals. An analysis of the line-broadening effects provides an opportunity for determining the specific desorption energies E(A)(H-ZSM-5)=(20.2+/-7.3) kJ/mol, E(A)(Na-ZSM-5)=(4.1+/-1.5) kJ/mol, and E(A)(Na-A)=(7.1+/-2.1) kJ/mol for NO probe molecules at sodium cations and aluminum defect centers just below the desorption temperature.     

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 .     

Theoretical Study on Mechanism of Cycloadditional Reaction Between Dichloro-Germylidene and Formaldehyde

用MP2/6-31G^*方法研究了单线态二氯亚甲基锗烯与甲醛环加成反应的反应机理,该反应有两条相互竞争的主反应通道,同时伴随着两中间体(INT3和INT4)副产物的生成. 第一条主反应通道所生成的物种为三员环中间体(INT1)和Ge-O顺位的四员环产物(P1);第二条主反应通道所生成的物种为Ge-O对位的扭曲四员环中间体(INT2)和氯迁移产物(P2);P1和INT2分别与甲醛(R2)的进一步作用而导致了两副产物的生成.     

Reaction mechanism of ammonia oxidation over RuO2(1 1 0): A combined theory/experiment approach

Combining state-of-the-art density functional theory (DFT) calculations with high resolution core level shift spectroscopy experiments we explored the reaction mechanism of the ammonia oxidation reaction over RuO₂(1 1 0). The high catalytic activity of RuO₂(1 1 0) is traced to the low activation energies for the successive hydrogen abstractions of ammonia by on-top O (less than 73 kJ/mol) and the low activation barrier for the recombination of adsorbed O and N (77 kJ/mol) to form adsorbed NO. The NO desorption is activated by 121 kJ/mol and represents therefore the rate determining step in the ammonia oxidation reaction over RuO₂ (1 1 0).     

紫外光辐照对偶氮苯光谱特性的影响

采用紫外可见吸收、稳态荧光光谱和荧光衰减测量技术,观察了4-硝基-4'-氨基偶氮苯(NAA)在氯仿溶液中的光致变色现象及分子的跃迁能级和能级寿命。结果表明:NAA分子的顺反异构化反应并非一级反应;分子处于反式异构体和顺式异构体的跃迁能分别为255.6,240.2 kJ/mol;分子处于反式异构体的能级寿命为0.02 ns,处于顺式异构体的能级寿命为3.54 ns。顺反异构体的含量、NAA分子之间及NAA分子与溶剂分子之间的相互作用影响NAA分子激发态的能级寿命。     

不同溶剂中番茄红素的荧光光谱及其特性研究

用970CRT荧光光度计测定了番茄红素在正己烷、乙酸乙酯、四氢呋喃、氯仿、丙酮和苯等6种溶剂中的荧光光谱以及番茄红素在四氢呋喃溶液中不同浓度下的荧光光谱。对所测光谱分析得出:6种溶剂中荧光光谱的最大峰值波长(λmax)分别为542.5 nm5、48.2 nm5、55.0 nm、555.7 nm、556.4 nm和565.7 nm,由于溶剂效应,随溶剂极性由小到大,荧光光谱的最大峰值波长(λmax)逐渐红移,由这些峰值波长计算得出相应的番茄红素分子在6种溶剂中的跃迁能ET分别为220.5 kJ/mol2、18.2 kJ/mol2、15.6 kJ/mol2、15.3 kJ/mol2、14.9 kJ/mol和211.5 kJ/mol,可见跃迁能ET也随溶剂极性增大而降低;当番茄红素在四氢呋喃溶液中的质量浓度低于50μg/ml时,溶液的荧光强度随溶液浓度增加而增大,当质量浓度高于50μg/ml时,由于番茄红素的激发态分子与基态分子相互作用,荧光强度反而减小;在浓度低于80μg/ml的溶液中,番茄红素的荧光光谱除最大峰值外还有三个较小峰值,据此计算得出相应的番茄红素分子的跃迁能分别为E(T1)=278.2 kJ/mol、E(T2)=260.2 kJ/mol和E(T3)=239.3 kJ/mol。     

抗癌药β-榄香烯分子内部运动的13C核自旋弛豫研究

首次应用变温实验方法和¹³C核自旋弛豫方法研究了抗癌药β-榄香烯小分子的内部运动状况。结果表明β-榄香烯分子的六元环在所研究的温度范围(298~318K)内几乎是刚性的。该分子的整体滚动自扩散活化能为14kJ/mol.其六元环外侧链基团CH₂=CCH₃-和CH₂=CH-的整体内旋转扩散活化能均为19kJ/mol.而与该六元环直接相连的甲基的内旋转扩散活化能为18kJ/mol.这个数值大大高于连在六元环上不同位置的两个侧链基团CH₂=CCH₃一中甲基的内旋转扩散活化能(其数值分别为了7kJ/mol和2.8KJ/mol).3个不同位置的甲基的内旋转扩散活化能有很大差别可能是由它们所处的分子空间环境不同而引起的。     

CH2Cl与OH自由基反应机理的理论研究

用量子化学从头算方法对CH2 Cl与OH自由基反应生成HCCl+H2 O、HCOCl+H2 和H2 CO +HCl的机理进行了研究 .在UMP2 (FC) / 6 311++G 水平上计算出了各物种的优化构型、振动频率 ;并在Gaussian 3(G3)水平上计算了他们的零点能 (ZPE)、相对能量及总能量 .结果表明 ,CH2 Cl和OH自由基反应首先经无垒过程生成一个富能中间体CH2 ClOH ,中间体再经过一系列原子转移、基团旋转和键断裂分别生成产物HCCl+H2 O、HCOCl+H2 和H2 CO +HCl;三者均为放热反应 ,放热量分别为 72 .81、338.5 4和 35 4 .0 8kJ/mol;生成H2 CO +HCl放出的热量比生成HCCl+H2 O放出的热量多 2 81.2 7kJ/mol,与实验结果吻合 .     

锐钛矿相纳米TiO2晶体生长动力学及生长过程控制

研究了采用溶胶-凝胶法经由前驱物钛酸四异丙酯水解制备纳米TiO₂结构相变及锐钛矿晶体生长动力学过程. 研究结果表明,在酸性条件下水解,由于高压热处理温度的变化导致锐钛矿向金红石相的结构相变,锐钛矿相纳米TiO₂生长活化能在250℃以下和以上分别为(15.8±4.5)kJ/mol和(80.2±1.0)kJ/mol;而在碱性条件下水解的活化能值为(3.5±0.4)kJ/mol. 在不发生结构相变的条件下,酸性水解条件下锐钛矿相纳米TiO₂生长速 关键词： 2')" href="#">纳米TiO₂ 锐钛矿 生长动力学 溶胶-凝胶法     

用扩散蒙特卡罗方法研究BH2, B(OH)2, BCl2和BCl的键离解能

采用扩散蒙特卡罗(DMC)方法计算了BH₂, B(OH)₂, BCl₂和BCl的HB-H和HOB-OH的键离解能, 同时也研究了轨道选择和Backflow变换对DMC计算结果的影响． 在Slater-Jastrow DMC(SJ-DMC)计算方法中,当采用B3PW91轨道时得到的HB-H和HOB-OH键离解能分别是359.1±0.12和98.2±0.12 kJ/mol;用B3LYP SJ-DMC计算键离解能得到了与用B3PW91 SJ-DMC方法类似的结果．通过BF-DMC(即在DMC中引入backflow修正)计算得到的HB?H键离解能为369.6±0.12 kJ/mol,也得到了更加接近实验值的HOB-OH键离解能为446.0±1.84 kJ/mol．由DMC的计算结果可以断定HB?H的键离解能的实验值为375.8 kJ/mol．另外还给出了BCl2和BCl的键离解能的计算结果.     

NAMI-A型钌配合物(HL)[trans-RuCl4L(dmso-S)] (L=1-methyl-1,2,4-triazole)水解机理的理论研究

用量子化学密度泛函方法结合导体极化连续模型研究了具有潜在抗肿瘤活性的NAMI-A型钌配合物(HL)[trans-RuCl₄L(dmso-S)](L=1-methyl-1,2,4-triazole,dmso-S=S-dimethyl sulfoxide) (1)的水解反应过程．计算得到该配合物水解反应过程中相应的结构特征和详细的反应势能面．对于第一步水解,液相中配合物1的活化能垒比已经报道的抗肿瘤药物(Him)[trans-RuCl₄(     

Adsorption of cyclohexadiene, cyclohexene and cyclohexane on Pt(1 1 1)

The adsorption of 1,3-cyclohexadiene, 1,4-cyclohexadiene, cyclohexene and cyclohexane on Pt(1 1 1) was studied using ab initio density functional theory. For 1,3-cyclohexadiene three adsorption modes were distinguished: bridge 1,2-di-σ/3,4-π, hollow 1,4-di-σ/2,3-π and bridge 1,4-di-σ/2,3-π with adsorption energies of −155, −147 and −75 kJ/mol, respectively. Three stable adsorption modes were also identified for 1,4-cyclohexadiene: bridge quadra-σ, hollow di-σ/π and bridge di-π with adsorption energies of −146 kJ/mol, −142 kJ/mol and −88 kJ/mol, respectively. Cyclohexene was found to adsorb in six modes: 4 di-σ and 2 π-adsorption modes. The preferred configuration was found to be boat di-σ with an adsorption energy of −81 kJ/mol. The three other di-σ adsorption modes have comparable adsorption energies, ranging from −64 to −69 kJ/mol. Molecular strain and CPt bonding energies are used to elucidate stability trends. Cyclohexane is found to adsorb only at the hollow site whereby the axial hydrogen atoms are positioned over surface Pt-atoms with an adsorption energy of −37 kJ/mol. The calculations correctly predict the weakening of the axial CH bonds and provide a possible explanation for the large shift in the vibrational frequencies.     

A computational exploration of the mechanisms for the acid‐catalytic urea–formaldehyde reaction: new insight into the old topic

Some initial acid‐catalytic reactions involved in the synthesis of the urea‐formaldehyde resin were theoretically investigated at B3LYP and MP2 levels with solvent effects included. The results suggest that the addition between urea and formaldehyde in neutral condition undergoes with a concerted mechanism represented by a four‐member ring transition state. For this reaction, a notable barrier (above 130 kJ/mol) was identified at all theoretical levels. The reactions between urea and different protonated forms of formaldehyde in acid solution were investigated. The reaction between protonated methanediol with urea can produce the methylol urea cation via an S_N2 transition state with a lower barrier of 54.8 kJ/mol. With the mediation of a water molecule, the intra‐molecular proton transfer produces the stable methylol carbonium (NH₂CONHCH₂⁺), which plays an important role in the following formation of methylene and methylene ether linkages. Copyright © 2011 John Wiley & Sons, Ltd.     

Free-radical copolymerisation of acrylamides,acrylates, and α-olefins

We report the results of a joint theoretical and experimental investigation into the copolymerisation of acrylamides and acrylates with α-olefins in free-radical processes. The transition-state structures of models for free-radical homo- and copolymerisation involving acrylamide, methylacrylamide, methacrylate, methyl methacrylate, and ethylene have been determined using density functional theory. The reaction energies and barrier heights comport with the experimentally observed properties, including the prevalence of monomer alternation, the realised stereospecificity, and the reaction yield. Continuum solvation models have been applied to determine the sensitivity of the relative energies to the bulk solvent properties. Experimentally, a Lewis acid catalyst is demonstrated to increase the incorporation of nonpolar 1-alkenes in copolymerisations with polar acrylamides and acrylates. In the presence of the Lewis acid, scandium (III) trifluoromethanesulfonate, the copolymerisation of 1-hexene and acrylamide results in an 8.5 mol % incorporation, up from 3.9 mol % in the absence of the Lewis acid. Computations incorporating Mg²⁺ as a model Lewis acid elucidate the mechanism of this catalysis. In the addition of methacrylate to a methyl methacrylate radical terminated polymer, the Lewis acid binds to the carbonyls on both promoting isotactic addition, while for the addition of an alkene to the same polymer, the Lewis acid binds to the polymer, reducing the barrier for alkenyl addition inductively by withdrawing electron density. We have demonstrated the ability of computational studies to aid experimentalists in the synthesis of new copolymers with desired properties.     

Theoretical study on the mechanism for NH3BH3 reduction of ketones and imines

In spite of a potential hydrogen storage material, ammonia borane (AB) was recently found to be a good hydrogenation reagent. It can reduce certain ketones to alcohols or borate esters, and imines to amines. The mechanisms of these reactions are not fully understood yet, and have been systematically studied using high-level CCSD(T) calculations in this work. We have validated theoretically that the forming of alcohols and amines undergoes concerted double-hydrogen transfer (DHT) mechanism. Furthermore, we predicted that the DHT process is facile for more general ketones and imines. For the borate ester formation, we found a pretty high barrier for the experimentally derived stepwise mechanism. Alternatively, we propose that the reaction starts with the DHT process to form alcohol and NH₂BH₂, followed by alcoholysis of NH₂BH₂ to form the first B–O bond. This mechanism is in good agreement with the current experimental facts, and also explains why ketone reduction affords different products at different conditions. For these reaction systems, the performances of M06-2x and MP2 (underestimate the barrier by 5–7 kcal/mol, but with right trends) are better than B3LYP and BLYP methods (underestimate the barrier by 0–5 kcal/mol).     

Kinetics of Isothermal and Nonisothermal Crystallization of Poly(ethylene oxide) (PEO) in PEO/Fatty Acid Blends

In this work, isothermal and nonisothermal crystallization kinetics of poly(ethylene oxide) (PEO) and PEO in PEO/fatty acid (lauric and stearic acid) blends, that are used as thermal energy storage materials, was studied using differential scanning calorimetry (DSC) data. The Avrami equation was adopted to describe isothermal crystallization of PEO and nonisothermal crystallization was analyzed using both the modified Avrami approach and Ozawa method. Avrami exponent (n) for PEO crystallization was in the range 1.08–1.32 (10–90% relative crystallinity), despite of spherulites formation, while for PEO in PEO/fatty acid blends n was between 1.61 and 2.13. Hoffman and Lauritzen theory was applied to calculate the activation energy of nucleation (K_g) – the lowest value of K_g was observed for pure PEO, despite of heterogeneous nucleation of fatty acid crystals in PEO/fatty acid blends. For nonisothermal crystallization of PEO in PEO/lauric acid (1:1 w/w) and PEO/stearic acid (1:3 w/w) blends, secondary crystallization occurred and values of the Avrami exponent were 2.8 and 2.0, respectively. The crystallization activation energies of PEO were determined to be ?260 kJ/mol for pure PEO, ?538 kJ/mol for PEO/lauric acid blend, and ?387 kJ/mol for PEO/stearic acid blend for isothermal crystallization and ?135,6 kJ/mol, ?114,5 kJ/mol, and ?92,8 kJ/mol, respectively, for nonisothermal crystallization.