Pseudospin symmetric solutions of the Dirac equation with the modified Rosen-Morse potential using Nikiforov-Uvarov method and supersymmetric quantum mechanics approach

Employing the Pekeris-type approximation to deal with the pseudo-centrifugal term,we analytically study the pseudospin symmetry of a Dirac nucleon subjected to equal scalar and vector modified Rosen-Morse potential including the spin-orbit coupling term by using the Nikiforov-Uvarov method and supersymmetric quantum mechanics approach.The complex eigenvalue equation and the total normalized wave functions expressed in terms of Jacobi polynomial with arbitrary spin-orbit coupling quantum number k are presented under the condition of pseudospin symmetry.The eigenvalue equations for both methods reproduce the same result to affirm the mathematical accuracy of analytical calculations.The numerical solutions obtained for different adjustable parameters produce degeneracies for some quantum number.

A molecular mechanics approach for analyzing tensile nonlinear deformation behavior of single-walled carbon nanotubes

In this paper, by capturing the atomic information and reflecting the behaviour governed by the nonlinear potential function, an analytical molecular mechanics approach is proposed. A constitutive relation for single-walled carbon nanotubes （SWCNT＇s） is established to describe the nonlinear stress-strain curve of SWCNT＇s and to predict both the elastic properties and breaking strain of SWCNT＇s during tensile deformation. An analysis based on the virtual internal bond （VIB） model proposed by P. Zhang et al. is also presented for comparison. The results indicate that the proposed molecular mechanics approach is indeed an acceptable analytical method for analyzing the mechanical behavior of SWCNT＇s.

Simulation of Tensile Behaviors of Bamboo-like Carbon Nanotubes Based on Molecular Structural Mechanics Approach Combining with Finite Element Analysis

A molecular structural mechanics approach combining with finite element analysis(MSM/FEA) was applied to study the microstructure and tensile behaviors of bamboo-like carbon nanotubes(BCNTs). The mathematical model of tensile behaviors of BCNTs was established based on molecular structural mechanics theory. The deformations of BCNTs, with different diameters and compartments set based on the experimental investigation on BCNT structures synthesized by chemical vapor depositon, under tensile load, were analyzed with ANSYS programmed. Results show that the BCNTs have good tensile properties, and those Young's modulus can reach 0.84 Tpa. Through the analysis, it can be found that the Young's modulus of BCNTs depends on the diameters and the length of compartment, which is in good agreement with our experimental tests for the tensile performances of individual BCNT.

Surprising New Bohr Models for H2and H2+

Niels Bohr constructed the first version of quantum mechanics. It has been called “old quantum mechanics” with a connotation of being obsolete. It is logically consistent, however, and deserves the name of simple quantum mechanics (SQM). It differs only from the semiclassical approximation by assuming that the average position and average velocity of an electron can be sharply defined on closed orbits. This assumption does not contradict Heisenberg’s uncertainty relations, since the quantization rule means that the electron can be anywhere on this orbit when it allows for stationary waves. This approach was remarkably efficient for one electron in hydrogen atoms and even for the electron pair in hydrogen molecules. However, dissociation of H2 and determination of the orbit of the single electron in H2+led to problems that remained unsolved for more than 100 years. Their solution, presented here, yields more physical insight and reveals, for instance, that mutual polarization of two hydrogen atoms can yield a metastable state.

Molecular Simulation Study on Intrinsic Order of Interaction between Single Slab of Active Phase and Al-Si Support in HDS Catalysts

Molecular mechanics and quantum mechanics simulations, as molecular simulation methods, were performed to investigate the effects of different surfaces, the promoter Co/Ni, the active phase of MoS2 or WS2, the content of Si and other factors on the order of interaction between the MoS2 （WS2） single slab and the support surface. The influence of Si content was studied by molecular mechanics, and an advantageous Si content was found. Various surfaces, promoters and active phases also played an important role in the interaction between the support surfaces and active phases, and some significant trends were found out. Quantum mechanics simulation was performed to study the possible effect of electrostatic interaction between the support and the active phase, upon which the calculations suggested that the existence of a favorable Si content was possible. The electronic effects of Co/Ni promoter and the intensity of Co/Mo/Ni/W/Li/AI/Si species bonded to the alumina support were also investigated by quantum mechanics, and it was found that the different electronic effects of Co and Ni might bring forth some obvious influences on the interaction between the support and the active phase. And the results of comparing the intensity of Co/Mo/Ni/W/Li/AI/Si species bonded to the support can also explain the different interaction intensity in various catalyst systems.

Microwave-assisted synthesis,anticonvulsant activity and quantum mechanical modelling of N-(4-bromo-3-methylphenyl) semicarbazones

Objective: To study the effect of halo substitution on disubstituted aryl semicarbazones on the anticonvulsant potential and model the activity based on quantum mechanics. Methods: A series of twenty-six compounds of N4-(4-bromo-3-methylphenyl) semicarbazones were synthesized and evaluated for the anticonvulsant activity in the maximal electroshock seizure (MES) and subcutaneous pentylenetetrazole (scPTZ) seizure threshold tests. Some potential compounds were also tested in the subcutaneous strychnine (scSTY) and subcutaneous picrotoxin (scPIC) seizure threshold tests. The synthesized compounds were tested for behavioral impairment and CNS (central nervous system) depression in mice. Quantum mechanical modelling was carried out on these compounds to gain understanding on the structural features essential for activity. Results: Some compounds possessed broad spectrum anticonvulsant activity as indicated by their effect in pentylenetetrazole, strychnine, picrotoxin and maximal electro- shock seizures models in resemblance to other aryl semicarbazone derivatives reported earlier. The higher the difference in HOMO (highest occupied molecular orbital) and LUMO (lowest unoccupied molecular orbital) energy levels was, the greater was the activity profile. Conclusion: The pharmacophoric requirements for compounds to exhibit anticonvulsant activity that includes one aryl unit in proximity to a hydrogen donor-acceptor domain and an electron donor have been justified with the molecular orbital surface analysis of the synthesized compounds.

Molecular Dynamics Study on Mechanical Properties in the Structure of Self-Assembled Quantum Dot

Stress and strain in the structure of self-assembled quantum dots constructed in the Ge/Si(001) system is calculated by using molecular dynamics simulation. Pyramidal hut cluster composed of Ge crystal with {105} facets surfaces observed in the early growth stage are computationally modeled. We calculate atomic stress and strain in relaxed pyramidal structure. Atomic stress for triplet of atoms is approximately defined as an average value of pairwise (virial) quantity inside triplet, which is the product of vectors between each two atoms. Atomic strain by means of atomic strain measure (ASM) which is formulated on the Green’s definition of continuum strain. We find the stress (strain) relaxation in pyramidal structure and stress (strain) concentration in the edge of pyramidal structure. We discuss size dependency of stress and strain distribution in pyramidal structure. The relationship between hydrostatic stress and atomic volumetric strain is basically linear for all models, but for the surface of pyramidal structure and Ge-Si interface. This means that there is a reasonable correlation between atomic stress proposed in the present study and atomic strain measure, ASM.

A computational toolbox for molecular property prediction based on quantum mechanics and quantitative structure-property relationship

Chemical industry is always seeking opportunities to efficiently and economically convert raw materials to commodity chemicals and higher value-added chemicalbased products.The life cycles of chemical products involve the procedures of conceptual product designs,experimental investigations,sustainable manufactures through appropriate chemical processes and waste disposals.During these periods,one of the most important keys is the molecular property prediction models associating molecular structures with product properties.In this paper,a framework combining quantum mechanics and quantitative structure-property relationship is established for fast molecular property predictions,such as activity coefficient,and so forth.The workflow of framework consists of three steps.In the first step,a database is created for collections of basic molecular information;in the second step,quantum mechanics-based calculations are performed to predict quantum mechanics-based/derived molecular properties(pseudo experimental data),which are stored in a database and further provided for the developments of quantitative structure-property relationship methods for fast predictions of properties in the third step.The whole framework has been carried out within a molecular property prediction toolbox.Two case studies highlighting different aspects of the toolbox involving the predictions of heats of reaction and solid-liquid phase equilibriums are presented.

非血红素铁酶中动态配位变化对C-H键选择性胺化反应的调控机制

氮杂环丙烷结构广泛存在于天然生物碱中,具有杀菌、抗癌等作用.然而,目前关于生物体系在合成氮杂环丙烷结构过程中如何克服氮杂环丙烷高环张力带来的热力学不利因素,以及如何避免形成热力学更稳定的羟基化副产物的报道较少.TqaL_(NC)酶是目前非血红素酶家族中唯一一种能够依赖α-酮戊二酸活化C-H键,进而生成氮杂环丙烷结构的酶.深入探究TqaL_(NC)酶选择性生成氮杂环丙烷结构并避免羟基化副产物的机制,有助于深入理解非血红素铁酶家族在C-H键活化及官能化过程中的选择性调控机理.本文以TqaL_(NC)酶的晶体结构为基础,采用分子动力学(MD)模拟以及量子力学-分子力学(QM/MM)等多尺度模拟方法对TqaL_(NC)酶与L-缬氨酸(L-Val)、TqaL_(NC)酶与L-异亮氨酸(L-Ile)和F345A-TqaL_(NC)酶与L-异亮氨酸(L-Ile)三个反应过程进行了详细的机理研究.结果表明,TqaL_(NC)酶在反应过程中生成的直立式构象的Fe(Ⅳ)=O物种会通过构象异构化获得赤道面式构象,为底物(L-Val、L-Ile、L-homoalaine)上NH_(3)^(+)与Fe的配位提供结构基础.在水和关键酸性残基的介导下,底物NH_(3)^(+)两次脱去质子与Fe(Ⅳ)=O物种配位,生成HN-Fe(Ⅳ)=O结构.随后,Fe(Ⅳ)=O物种攫取底物H原子,生成HN-Fe(Ⅲ)-OH中间体.此时NH回弹反应比传统的OH回弹反应在动力学上更有优势,因此选择性地生成了氮杂环丙烷产物.在反应过程中,底物侧链与周围氨基酸的位阻效应是影响NH回弹反应能垒的重要因素.通过改变底物侧链大小(L-Val→L-Ile)以及附近氨基酸的突变(F345A)实验,证实了该结论.本文还通过理论计算预测了TqaL_(NC)酶与L-高丙氨酸的反应产物为羟基化产物,并通过新的实验证据进一步支持了理论预测的机理.此外,在HN-Fe(Ⅲ)-OH结构中,通过前线轨道理论分析发现,dπ*Fe-N,dπ*Fe-OH轨道的能量差是影响NH/OH回弹反应能垒的另一重要因素.当底物NH与Fe配位时,其配位作用能够使得dπ*Fe-N以及dπ*Fe-OH轨道有效分裂,这种分裂进而影响了反应路径的选择性,确保氮杂环丙烷产物的生成.综上,本文提出了依赖α-酮戊二酸酶催化合成氮杂环丙烷结构的新机理.研究发现,Fe中心的动态配位效应在实现C-H键选择性胺化反应并避免C-H键羟基化反应中起到了关键作用.该理论为非血红素Fe酶催化的非羟基化反应提供了新的见解,并为探索包括C-N/C-S/C-O等重要生物合成反应新机理的探究提供了新思路.

含Cl反应力场ReaxFF的评估

为考察反应分子力场ReaxFF对高氯酸铵(AP)推进剂材料模拟的适应性,从文献中选取了两种含C/H/O/N/Cl有机反应力场,对AP系统中含Cl的典型小分子进行结构和能量扫描计算,并对AP高温裂解过程进行了反应分子动力学模拟。通过对比反应力场与量子力学计算结果发现,现有的含Cl有机反应力场在计算HCl以及部分含H、Cl元素的小分子能量时表现较好,但无法合理描述含高价Cl小分子以及含N、O元素小分子的化学键形成和断裂行为。根据力场分子动力学模拟结果的物种分析,现有的反应力场模拟获得了H_(2)O、O_(2)、NH_(3)、HCl等产物小分子,但未能复现ClO_(2)、HClO 4等高价Cl产物以及NO_(2)、N_(2)O的生成,与实验观测有显著差距。

环保型缓蚀剂壳寡糖对304不锈钢化学机械抛光的影响

为研究环保型缓蚀剂壳寡糖对304不锈钢化学机械抛光过程和抛光效果的影响,探讨其在抛光过程中与金属表面的作用方式及吸附机制,采用化学机械抛光试验、接触角测量、扫描电子显微镜(SEM)和X-射线色散能谱仪(EDS)分析等方法,研究壳寡糖有机分子对304不锈钢化学机械抛光的影响,采用量子化学计算研究壳寡糖分子的全局反应参数,分析计算反应活性位点,采用分子动力学模拟有机分子在金属表面的吸附并分析活性原子的径向分布。结果表明:CMP抛光过程中添加壳寡糖能够通过吸附作用在304不锈钢表面形成一层疏水性的薄膜,抑制氧化剂对不锈钢表面的刻蚀,提高抛光后的表面质量;在壳寡糖质量浓度为400 mg/L时得到表面粗糙度为1.65 nm的最佳表面质量。量子化学研究表明,壳寡糖的活性反应位点主要为O原子,能够在金属表面形成多中心吸附。分子动力学模拟表明,壳寡糖有机分子能够平行吸附在金属表面,有机分子中的O原子能够与铁原子形成配位键,在吸附中占据主导地位。

量子化学计算研究自由基相互作用的双稳态轮烷的穿梭机理

设计了一种氧化还原驱动的可切换的双稳态轮烷。以双百草枯-对苯双自由基双阳离子环(CBPQT^(2(·+)))作为大环分子,主链分子上有2个结合位点,即4,4′-联吡啶自由基阳离子BIPY^(·+)和2,6-二氧亚萘基(DOP)位点。运用密度泛函理论对大环分子在主链分子上的运动机理进行研究,并通过量子力学理论计算分析大环分子CBPQT^(2(·+))与主链分子上2个结合位点BIPY^(·+)和DOP之间的弱相互作用,证明了氧化还原反应控制自由基络合物的形成和解离可以驱动CBPQT^(2(·+))环沿着主链分子的2个结合位点间实现往复运动。

Molecular Modeling of the Chain Structures of Polybenzoxazines

The structures and properties of benzoxazines were investigated by virtue of molecular modeling at a molecular level. By means of Cerius software(version 4.0) supplied by Molecular Simulations Inc., the molecular mechanics and the molecular dynamics were performed under a PCFF force field. Five kinds of the polymeric chains of benzoxazines were created by using polymer builder and energy minimization. The relaxation process was conducted with both energy minimization and molecular dynamics.

THE COUPLED EFFECTS OF MECHANICAL DEFORMATION AND ELECTRONIC PROPERTIES IN CARBON NANOTUBES

Coupled effects of mechanical and electronic behavior in single walled carbon nanotubes are investigated by using quantum mechanics and quantum molecular dynamics.It is found that external applied electric fields can cause charge polarization and significant geometric deformation in metallic and semi-metallic carbon nanotubes.The electric induced axial tension ratio can be up to 10% in the armchair tube and 8.5% in the zigzag tube.Pure external applied load has little effect on charge distribution,but indeed influences the energy gap.Tensile load leads to a narrower energy gap and compressive load increases the gap.When the CNT is tensioned under an external electric field,the effect of mechanical load on the electronic structures of the CNT becomes significant,and the applied electric field may reduce the critical mechanical tension load remarkably.Size effects are also discussed.

Implementing a Multi-Qubit Quantum Phase Gate Encoded by Photonic Qubit

A protocol is proposed to implement a three-qubit phase gate for photonic qubits in a three-mode cavity. The idea can be extended to directly implement a N-qubit phase gate. We also show that the interaction time remains unchanged with the increasing number of qubits. In addition, the influence of cavity decay and atomic spontaneous emission on the gate fidelity and photon loss probability is also discussed by numerical calculation.

Mechanistic, Energetic and Structural Aspects of the Adsorption of Carmustine on the Functionalized Carbon Nanotubes

Using density functional theory, noncovalent interactions and two mechanisms of covalent functionalization of drug carmustine with functionalized carbon nanotube（CNT） have been investigated. Quantum molecular descriptors of noncovalent configurations were studied. It was specified that binding of drug carmustine with functionalized CNT is thermodynamically suitable. NTCOOH and NTCOCl can bond to the NH group of carmustine through OH（COOH mechanism） and Cl（COCl mechanism） groups, respectively. The activation energies, activation enthalpies and activation Gibbs free energies of two pathways were calculated and compared with each other. The activation parameters related to COOH mechanism are higher than those related to COCl mechanism, and therefore COCl mechanism is suitable for covalent functionalization. COOH functionalized CNT（NTCOOH） has more binding energy than COCl functionalized CNT（NTCOCl） and can act as a favorable system for carmustine drug delivery within biological and chemical systems（noncovalent）. These results could be generalized to other similar drugs.

Lee Pedersen's work in theoretical and computational chemistry and biochemistry

Nature at the lab level in biology and chemistry can be described by the application of quantum mechanics.In many cases,a reasonable approximation to quantum mechanics is classical mechanics realized through Newton's equations of motion.Dr.Pedersen began his career using quantum mechanics to describe the properties of small molecular complexes that could serve as models for biochemical systems.To describe large molecular systems required a drop-back to classical means and this led surprisingly to a major improvement in the classical treatment of electrostatics for all molecules,not just biological molecules.Recent work has involved the application of quantum mechanics for the putative active sites of enzymes to gain greater insight into the key steps in enzyme catalysis.

Solvent effects and potential of mean force study of the SN2 reaction of CH3F+CN-in water

We used a combined quantum mechanics and molecular mechanics （QM/MM） method to investigate the solvent effects and potential of mean force of the CH3F＋CN- reaction in water. Comparing to gas phase, the water solution substantially affects the structures of the stationary points along the reaction path. We quantitatively obtained the solvent effects＇ contributions to the reaction： 1.7 kcal/mol to the activation barrier and -26.0 kcal/mol to the reaction free energy. The potential mean of force calculated with the density functional theory/MM theory has a barrier height at 19.7 kcal/mol, consistent with the experimental result at 23.0 kcal/mol; the calculated reaction free energy at -43.5 kcal/mol is also consistent with the one estimated based on the gas-phase data at -39.7 kcal/mol.

The application of molecular simulation in ash chemistry of coal

One of the crucial issues in modern ash chemistry is the realization of efficient and clean coal conversion.Industrially,large-scale coal gasification technology is well known as the foundation to improve the atom economy.In practice,the coal ash fusibility is a critical factor to determine steady operation standards of the gasifier,which is also the significant criterion to coal species selection for gasification.Since coal behaviors are resultant from various evolutions in different scales,the multi-scale understanding of the ash chemistry is of significance to guide the fusibility adjustment for coal gasification.Considering important roles of molecular simulation in exploring ash chemistry,this paper reviews the recent studies and developments on modeling of molecular systems for fusibility related ash chemistry for the first time.The discussions are emphasized on those performed by quantum mechanics and molecular mechanics,the two major simulation methods for microscopic systems,which may provide various insights into fusibility mechanism.This review article is expected to present comprehensive information for recent molecular simulations of coal chemistry so that new clues to find strategies controlling the ash fusion behavior can be obtained.

Molecular Simulation Studies on Basicity of Nitrogen-containing Compounds

The DFT-based （density fimctional theory） ab initio quantum mechanical methods have been applied to study the basicity of the nitrogen-containing compounds in petroleum. The results have indicated that there is a distinct relationship between the protonation energy of nitrogen-containing compounds and their basicity. The more negative the protonation energy, the stronger the basicity is. It has been also found that aliphatic amines are more basic than pyridines or aromatic amines, and all these compounds are more basic than pyrroles. The addition of the aromatic rings can influence the basicity of anilines, while the 5- and 6-membered heterocyclic compounds function differently. The solvent properties may affect the basicity of these nitrogen-containing compounds.