Maximum Overlap Symmetry Molecular Orbital Calculation under CNDO／2 Approximation

A basic calculation procedure for the MOSMO method under CNDO/2 approximation is presented in this paper,and performed by using the same parameters as those used in the ordinary CNDO/2 LCAO-MO calculation.The calculated results on the whole are close to those obtained by use of the ordinary CNDO/2 LCAO-MO calculation,illustrating that the presented procedure is reasonable.Due to its simplicity,the presented calculation procedure may be feasible even in very large molecular s ystems.

Infrared Spectra and Pyrolysis of Selected Molecular Models of Coal: Insight from Density Functional Calculations

Equilibrium structures and infrared spectra of four typical molecular models of coal have been studied by density functional calculations. Combining theoretical calculations on the coal models with experimental FT-IR spectra of selected low rank perhydrous coals, a plausible molecular representation for this kind of coals was proposed, and its predicted IR spectra reasonably match the experimental observation. Calculations indicate that the cleavage of the C-C bridge bond for the coal structures considered here occurs at about 540 ℃ and the C-O ether bridge bond may break under temperature ranging from 500 to 600 ℃for the aryl-CH2-O-CH2-aryl ether bond or from 200 to 300 ℃ for the aryl-CH2-O-aryl ether bond, showing remarkable effect of the local structural environment. The coal model containing the carboxyl group may release CO2 at about 300 ℃ through the decarboxylation with a barrier of 69 kcal/mol.

Free energy calculation of single molecular interaction using Jarzynski's identity method:the case of HIV-1 protease inhibitor system

Jarzynski＇ identity （JI） method was suggested a promising tool for reconstructing free energy landscape of biomolecular interactions in numerical simulations and ex- periments. However, JI method has not yet been well tested in complex systems such as ligand-receptor molecular pairs. In this paper, we applied a huge number of steered molec- ular dynamics （SMD） simulations to dissociate the protease of human immunodeficiency type I virus （HIV-1 protease） and its inhibitors. We showed that because of intrinsic com- plexity of the ligand-receptor system, the energy barrier pre- dicted by JI method at high pulling rates is much higher than experimental results. However, with a slower pulling rate and fewer switch times of simulations, the predictions of JI method can approach to the experiments. These results sug- gested that the JI method is more appropriate for reconstruct- ing free energy landscape using the data taken from experi- ments, since the pulling rates used in experiments are often much slower than those in SMD simulations. Furthermore, we showed that a higher loading stiffness can produce higher precision of calculation of energy landscape because it yields a lower mean value and narrower bandwidth of work distri- bution in SMD simulations.

Free Energy Change of Micelle Formation for Sodium Dodecyl Sulfate from a Dispersed State in Solution to Complete Micelles along Its Aggregation Pathways Evaluated by Chemical Species Model Combined with Molecular Dynamics Calculations

Surfactant molecules, when dispersed in solution, have been shown to spontaneously form aggregates. Our previous studies on molecular dynamics(MD) calculations have shown that ionic sodium dodecyl sulfate molecules quickly aggregated even when the aggregation number is small. The aggregation rate, however, decreased for larger aggregation numbers. In addition, studies have shown that micelle formation was not completed even after a 100 ns-long MD run(Chem. Phys. Lett. 2016, 646, 36). Herein, we analyze the free energy change of micelle formation based on chemical species model combined with molecular dynamics calculations. First, the free energy landscape of the aggregation, ?G_(i+j)^+, where two aggregates with sizes i and j associate to form the(i + j)-mer, was investigated using the free energy of micelle formation of the i-mer, G_i^+, which was obtained through MD calculations. The calculated ?G_(i+j)^+ was negative for all the aggregations where the sum of DS ions in the two aggregates was 60 or less. From the viewpoint of chemical equilibrium, aggregation to the stable micelle is desired. Further, the free energy profile along possible aggregation pathways was investigated, starting from small aggregates and ending with the complete thermodynamically stable micelles in solution. The free energy profiles, G(l, k), of the aggregates at l-th aggregation path and k-th state were evaluated by the formation free energy ∑_in_i( l,k)G_i^+ and the free energy of mixing ∑_in_i( l,k)k_BTln( n_i( l,k)/n( l,k)), where ni(l, k) is the number of i-mer in the system at the l-th i aggregation path and k-th state, with n(l,k)= ∑_n_i( l,k). All the aggregation pathways were obtained from the initial i state of 12 pentamers to the stable micelle with i = 60. All the calculated G(l, k) values monotonically decreased with increasing k. This indicates that there are no free energy barriers along the pathways. Hence, the slowdown is not due to the thermodynamic stability of the aggregates, but rather the kinetics that inhibit the association of the fragments. The time required for a collision between aggregates, one of the kinetic factors, was evaluated using the fast passage time, t_(FPT). The calculated t_(FPT) was about 20 ns for the aggregates with N = 31. Therefore, if aggregation is a diffusion-controlled process, it should be completed within the 100 ns-simulation. However, aggregation does not occur due to the free energy barrier between the aggregates, that is, the repulsive force acting on them. This may be caused by electrostatic repulsions produced by the overlap of the electric double layers, which are formed by the negative charge of the hydrophilic groups and counter sodium ions on the surface of the aggregates.

Molecular engineering binuclear copper catalysts for selective CO_(2) reduction to C_(2) products

Molecular copper catalysts serve as exemplary models for correlating the structure-reaction-mechanism relationship in the electrochemical CO_(2) reduction(eCO_(2)R),owing to their adaptable environments surrounding the copper metal centres.This investigation,employing density functional theory calculations,focuses on a novel family of binuclear Cu molecular catalysts.The modulation of their coordination configuration through the introduction of organic groups aims to assess their efficacy in converting CO_(2) to C_(2)products.Our findings highlight the crucial role of chemical valence state in shaping the characteristics of binuclear Cu catalysts,consequently influencing the eCO_(2)R behaviour,Notably,the Cu(Ⅱ)Cu(Ⅱ)macrocycle catalyst exhibits enhanced suppression of the hydrogen evolution reaction(HER),facilitating proton trans fer and the eCO_(2)R process.Fu rthermore,we explo re the impact of diverse electro n-withdrawing and electron-donating groups coordinated to the macrocycle(R=-F,-H,and-OCH_3)on the electron distribution in the molecular catalysts.Strategic placement of-OCH_3 groups in the macrocycles leads to a favourable oxidation state of the Cu centres and subsequent C-C coupling to form C_(2) products.This research provides fundamental insights into the design and optimization of binuclear Cu molecular catalysts for the electrochemical conversion of CO_(2) to value-added C_(2) products.

X-ray Crystal Structure and Molecular Mechanics Calculations of (2,6-iso-dipropyl-phcnylamidc) Dimethyl (tetra-methylecyclopenta- dienyl)Silane Titanium Dichloride

Crystal and molecular structure of (2.6-dipropylphenylamidc) dimethyl (tetra-methyl cyclopentadienyl) silane titanium dichloride (I) was fully characterized by X-ray diffraction. The crystal is obtained tyom a mixture of ether/hexane as orthorhombic, with a = 12.658 (3 ) A. b = 16.62 (3) A. c = 11 .760 (2) A. V = 2474,2 (9) A. Z = 4. space group Pnma. R = 0.0399. Compound I compose of the R -bounded ring with its dimethylsilyl-dipropyl phenyl amido group and the two terminal chloride atoms coordinated to central metal to form a so-called constrained geometry catalyst (CGC) structure. The result of molecular mechanics (MM) calculations on compound I shows that bond lengths and bond angles from the MM calculation are comparable to the data obtained from the X-ray diffraction study. The relation of the structure of CGCs and their catalytic activity by MM calculations is also discussed.

Comparison of Fungicidal Difference of Two Arylpyrazoles Based on the Crystal Structures, Density Functional Theory Calculation and Molecular Docking

Two arylpyrazoles I andⅡwere synthesized and characterized by NMR and single-crystal X-ray diffraction.Compound I displayed 71.4%fungicidal inhibition rate against Rhizoctonia solani at 0.1 ppm,better than the control pyraclostrobin,whereasⅡhad little activity.Their fungicidal difference was discussed from theoretic level based on the crystal structure,density functional theory(DFT)calculation and molecular docking.The B3 LYP/6-31G^**level was employed to explore the HOMO-LUMO energy gap and charge distribution.Molecular docking was performed on the probable target protein bc1-enzyme complex.DFT calculation and docking studies supported the in vitro findings.

Crystal Structure and Molecular Orbital Calculation of(1R,2S)-N-Methylephedine Benzoate Hydrochloride

The title compound was synthesized and its crystal structure was determined. C_(13)H(21)NO_2·HCl, orthorhombic, space group P2_12_12_1 with dimensions:a =10. 635(2), b=26.942(6), c=6.193(2), V=1774.5(8),Z=4,Mr=319. 83 and Dc=1.20g/cm￣3. The final residual factor R=0.048, Rw=0.062. The C atoms except those in rings has a distorted tetrahedron structure.The dihedral angle between the phenyl rings in the molecule is 74. 56°. There is no bond between HCl and ester.The molecules join each other by van der Waals force. Its molecular orbital calculations were carried out by means of extended Huckel molecular orbital method.

FULLERENE GEOMETRY PREDICTION WITH MOLECULAR MECHANICS CALCULATIONS

A serial of fullerenes had been built and the optimized geome- tries had been obtained with the energy minimization of molecular mechanics calculations according to the fact that the pentagonal number is exactly 12 in the fullerenes which consist of pentagons and hexagons.The fullerene geometry prediction could facilitate further theoretical and synthetical studies in the near future.

MM CALCULATIONS OF THE METAL-PROTEIN MODEL COMPLEXES Ⅰ.MOLECULAR FORCE FIELD FOR COBALT COMPEXES

Cobalt-protein complexes play an important role in biochemical processes.The structure of the model molecule,Co(H_2O)_3SO_4(phen) has been studied by molecular mechanics.The molecular force field (MM2) parameters have been developed for the particular class of the complexes.

Structural and Vibrational Study of 2-（Quinolin-8-yloxy）-Acetic Acid based on FT-IR-Raman Spectroscopy and DFT Calculations

We have prepared the 2-（quinolin-8-yloxy）-acetic acid and characterized it by infrared and Raman spectroscopies in the solid phase. The Density Functional Theory （DFT） method, together with the 6-31G^＊ and 6-311＋＋ G^＊＊ basis sets, show that three stable molecules, for the anhydrous and monohydrated compounds were theoretically determined in the gas phase, and that probably the two more stable conformations are present in the solid phase of the monohydrated compound. The harmonic vibrational wavenumbers for the optimized geometries were calculated at B3LYP/6-31G^＊and B3LYP/6-311＋＋G^＊＊ levels. For a complete assignment of all the observed bands in the vibrational spectra the DFT calculations were combined with Pulay＇s scaled quantum mechanical force field （SQMFF） methodology in order to fit the theoretical Wavenumber values to the experimental ones. The characteristics of the electronic delocalization of all structures of both forms were performed by using natural bond orbital （NBO）, while the corresponding topological properties of electronic charge density are analysed by employing Bader＇s atoms in molecules theory （AIM）.

Effect of the alkali metal(Li, Na, K) substitution on the geometric,electronic and optical properties of the smallest diamondoid: First principles calculations

In this study we employed the B3LYP/6-311++G(d,p) method combined with the CIS/6-311++G(d,p) calculation to investigate the effects of the type and the number of alkali metal atoms(Li, Na, K) on the geometric, electronic, and optical properties of alkali metals substituted into adamantanes. Substituting alkali metal(Li, Na, K)atoms caused significant changes in the electronic and optical properties of adamantane. The Ad-1Li, Ad-1Na,and Ad-1K structures showed a dramatically decreased energy gap and ionization potential, while adding more alkali metal atoms slightly decreased these properties. Substituting more alkali metals led to a shift in the maximum absorption wavelength from the visible to the infrared region, depending on the type of alkali metal atom substituted. The magnitude of shift occurred in the following order: Li b Na b K. These characteristics suggest the possibility of tunable electronic structures of this material for optoelectronic device applications.

First Oxidation Product of Vitamin C, the Dehydro-L-Ascorbic Acid Dimer： A Study Based on FTIR-Raman and DFT Calculations

We studied the first oxidation product of vitamin C, the dehydro-L-ascorbic acid dimer and characterized it by infrared and Raman spectroscopies in the solid phase. The Density functional theory was used to study its structure and vibrational properties. These calculations gave us a precise knowledge of the normal modes of vibration taking into account that the molecule comprises a system of five fused rings; non planar γ-lactone and furonose rings are attached to a central dioxan ring in the twisted boat conformation. The calculated harmonic vibrational frequencies are consistent with the experimental vibrational spectra. An assignment of the observed spectral features is proposed. The shift of the band located in the infrared spectrum of the ascorbic acid from 3409 cm^-1 to 3299 cml and the remarkable increase in the band intensity at 1784 cm^-1 evidences the acid decomposition into its first product, the dehydro-L-ascorbic acid. The theoretical vibrational calculations allowed us to obtain a set of scaled force constants. The nature of the different -γ-lactone, furanose and dioxan rings and their topological properties were investigated by means of natural bond orbital and Bader＇s atoms in the molecule theory, respectively.

富含双键咪唑啉在饱和CO_(2)盐水中缓蚀行为研究

目的合成含有两个双键的亚油酸咪唑啉,与传统的含有单个双键油酸咪唑啉对比,研究其结构对其缓蚀性能的影响。方法在60℃下将Q235钢浸泡于饱和CO_(2)的3%(w)NaCl溶液中,通过失重、电化学测试和缓蚀效率测试,并通过表面分析方法观察腐蚀后钢片形貌变化,最后通过理论计算对合成缓蚀剂进行性能研究。结果电化学与失重结果显示在加入质量浓度为200 mg/L的亚油酸咪唑啉后,缓蚀效率能达到90%,缓蚀性能优于常见的油酸咪唑啉。在结构上,由于亚油酸咪唑啉分子比油酸咪唑啉多了一个双键,增加了咪唑啉缓蚀剂的吸附位点,使其能更好地吸附于金属的表面。结论亚油酸咪唑啉对碳钢有很好的缓蚀性能;在同等实验条件下,缓蚀性能优于油酸咪唑啉;其吸附满足Langmuir吸附等温线;吸附过程中主要通过N—Fe键吸附在Fe表面。

飞秒激光作用TATB的大尺寸分子动力学模拟

深入认识炸药在飞秒激光作用下的快速化学反应机制和热力响应特征,是发展飞秒激光加工炸药技术的基础。采用分子动力学方法,基于ReaxFF/lg反应力场,对不同飞秒激光能量作用于三氨基三硝基苯(TATB)炸药的过程进行亚微米级大尺寸反应分子动力学模拟,考虑炸药对飞秒激光的非线性吸收过程,分析炸药烧蚀去除机制、产物演化和热力响应规律。计算结果表明:不同强度的飞秒激光对TATB的烧蚀去除机制不同,当激光强度为6.79×10^(17) W/m^(2)时,TATB发生等离子体烧蚀,产物以小分子或等离子体为主;当激光强度为3.39×10^(17) W/m^(2)时,TATB发生不完全反应,产物以大分子或团簇为主;当激光强度为1.69×10^(17) W/m^(2)时,TATB发生光机械烧蚀,以完整分子形式被剥离去除;激光强度越高,烧蚀产物的温度和粒子速度越高,对烧蚀区周围的热力响应越严重,有引发点火的风险。

新型高温酸化缓蚀剂的制备及性能评价

为了更好地减缓油气田高温酸化下金属的腐蚀,研究出一种耐高温且配方简单的复合酸化缓蚀剂。以喹啉和氯化苄为原料,采用“一锅法”制备得到了一种新型稠杂环季铵盐(BQD)缓蚀主剂。通过添加甲酸、乌洛托品等复配剂,经过单因素失重法优选,得到一种配方简单的新型高温酸化缓蚀剂GS-1,通过电化学测试、表面形貌分析研究其缓蚀性能,采用分子模拟的方法研究BQD的缓蚀机理。结果表明,GS-1缓蚀剂在添加量为3%时,在160℃下盐酸与土酸的酸化环境中,N80钢片的腐蚀速率分别降低至41.63g/(m^(2)·h)、31.94g/(m^(2)·h),均可达行业标准要求;GS-1缓蚀剂可在N80钢片表面形成一层吸附保护层,属于兼具抑制阳极和阴极反应的混合型缓蚀剂;量子化学计算及分子动力学模拟表明,BQD的缓蚀活性优于常见的苄基喹啉季铵盐缓蚀剂(BQC),同时BQD分子是以共轭平面为基准,与金属基底平行的角度被吸附于界面上,具有更加高效的缓蚀性能。

Materials Studio软件在计算化学和计算材料学课程教学中的应用

将Materials Studio软件使用引入计算化学和计算材料学等课程教学,采取“计算理论方法讲解+计算软件实践操作科研案例”模式进行高效课程教学,实现科研反哺高质量教学。让学生在软件实践操作中运用、巩固理论知识概念,实现理论方法水平和软件操作技能的双重提升。同时使课程教学内容变得形象具体,激发学生对计算化学和计算材料学课程的学习兴趣,培养学生的科研思维和探索能力,实现教学支撑高水平科研。

理论计算在药物制剂设计中的研究进展

药物制剂不仅关系国计民生,而且也是国家安全和科技竞争的战略重点。理论计算在药物制剂设计过程中发挥了重要作用,有关药物制剂设计中的现代理论计算方法一直备受关注。近年来,随着人工智能等新兴技术的飞速发展,药物制剂的研发模式也逐渐向大数据驱动的智能设计模式转变。首先,阐述了理论计算在药物制剂设计中的重要性。然后,重点探讨了药物制剂设计中理论计算的研究现状,分别对分子模拟、热力学计算和人工智能等方法进行了归纳和总结,深入分析了各类方法的优缺点。在此基础上,讨论了理论计算在药物制剂设计中面临的挑战,并对其未来发展方向提出了展望,有望为药物制剂的智能设计提供参考与指导。

第一性原理计算约束宏观地质现象的微观机制

微观尺度物理化学机制随着时间推移和空间尺度放大,逐步累积形成在地球系统中能够被直观观测到的大规模地质过程。揭示地质作用过程中隐藏在宏观表象下的微观机制一直是地球科学研究的重要内容。近年来,随着计算能力的提高和计算方法的进步,基于量子力学原理的理论计算方法——第一性原理计算,以精度高、效率高、应用灵活且所得结果可以媲美实验等优势,为构建宏观与微观之间的桥梁提供了一个有力途径。本文归纳总结了第一性原理计算的基本原理,梳理了使用第一性原理计算在研究宏观地质现象的微观机制领域取得的新认识,侧重论述了第一性原理计算在研究矿物物理化学性质、深部熔体性质、同位素分馏机理、元素地球化学行为等方面的应用,并展望了第一性原理计算在未来可能遇到的挑战和发展趋势,为微观机制的计算模拟研究提供帮助。第一性原理计算的发展和应用,增强了人们对地球系统微观机制的理解,为未来地球科学的研究提供了新思路。