Density functional calculations of large systems containing heavy elements by means of the regionalization algorithm

The compounds containing transition metals orother heavy elements play important roles in chemistry.They possess diverse properties which have been util-ized in numerous functional materials. Some of theseproperties are also involved in biological processes.However, it is very difficult to study these compoundsdeeply by means of quantum chemical methods, be-cause in these systems usually there are a large amountof electrons, the distribution of the frontier orbitals isdense, the correlation be…     

Improving the efficiency and reliability of free energy perturbation calculations using overlap sampling methods

A challenge in free energy calculation for complex molecular systems by computer simulation is to obtain a reliable estimate within feasible computational time. In this study, we suggest an answer to this challenge by exploring a simple method, overlap sampling (OS), for producing reliable free-energy results in an efficient way. The formalism of the OS method is based on ensuring sampling of important overlapping phase space during perturbation calculations. This technique samples both forward and reverse free energy perturbation (FEP) to improve the free-energy calculation. It considers the asymmetry of the FEP calculation and features an ability to optimize both the precision and the accuracy of the measurement without affecting the simulation process itself. The OS method is tested at two optimization levels: no optimization (simple OS), and full optimization (equivalent to Bennett's method), and compared to conventional FEP techniques, including the widely used direct FEP averaging method, on three alchemical mutation systems: (a) an anion transformation in water solution, (b) mutation between methanol and ethane, and (c) alchemical change of an adenosine molecule. It is consistently shown that the reliability of free-energy estimates can be greatly improved using the OS techniques at both optimization levels, while the performance of Bennett's method is particularly striking. In addition, the efficiency of a calculation can be significantly improved because the method is able to (a) converge to the right answer quickly, and (b) work for large perturbations. The basic two-stage OS method can be extended to admit additional stages, if needed. We suggest that the OS method can be used as a general perturbation technique for computing free energy differences in molecular simulations.     

Equilibrium structures of isolated (halogenated) fluorolithiomethanes

Equilibrium structures of isolated fluorolithiomethanes (1-3), chlorofluorolithiomethanes (4-6), bromofluorolithiomethanes (7-9), and bromochlorofluorolithiomethane (10) have been calculated at the HF/6-31+G(d,p) and MP2/6-31+G(d,p) levels. Depending on the number of halogens and the computational method employed, five distinct minimum structures could be recognized, viz. normal tetrahedral without coordination of halogen (T), trigonal bidentate with coordination of carbon and halogen to lithium (BCX), tetrahedral tridentate with coordination of carbon and two halogens to lithium (TCX2), quadrilateral bidentate with coordination of two halogens to lithium (BX2), and bipyramidal tridentate with coordination of three halogens to lithium (TX3).     

The absolute sign of J coupling constants determined using the order matrix calculation

A novel methodology using the order matrix calculation to determine the absolute sign of spin-spin couplings based on the structure of organic compounds is presented. The sign of the residual dipolar coupling (RDC) depends on the sign of corresponding scalar spin-spin coupling constant and the sign of the RDC has a dramatic influence on the order matrix calculation. Therefore, the sign of the spin-spin coupling constant can be obtained by an order matrix calculation through the corresponding RDC. Six types of spin-spin coupling constants, including 2J(H,H), 1J(C,F), 2J(C,F), 3J(C,F), 2J(F,H) and 3J(F,H), were obtained simultaneously. Except for 3J(C,F) where the measured RDCs have very small magnitudes, the signs were determined unambiguously.     

聚合物{[CuII(Hpb) (mal)]H2O}n :单体的量子化学计算和磁性研究

{[Cu^Ⅱ（Hpb）（mal）]H=O}n （Hpb=2-2＇-pyridylbenzimidazole, mal=maleic acid） is a helical chain-like polymer complex. In order to investigate the electronic structure of the complex, the monomer Cu^Ⅱ（Hpb）（mal） was obturated with different functional groups respectively. For these selective segments, the geometry optimizations were conducted by using hybrid DFT （B3LYP）methods to find that the structure obturated with H2O was better consistent with the experiment, and then this model would be used to latter calculations, such as the frontier molecular orbital and the NBO charge population analysis. In addition the magnetic behaviors of this complex were analyzed by experiments and the weak antiferromagnetic couple between copper（Ⅱ） ions was observed. The exchange coupling constant was calculated by DFT based on the spin broken symmetry formalism. The calculated coupling constants were in good agreement with the experimental data.     

Crystal Structure, Thermal Analysis and Theoretical Calculation of a One-dimensional Chain Complex [Zn（dafo）2（H2O）2]（NO3）2

Introduction Molecular recognition and molecular self-assemblycarried out by cooperation of the weak interactions(electrostatic reaction, hydrogen bonds, van der Waalsforce, short-range repulsive force, etc) are the commonphenomena in nature. In recent years, the research onsupramolecular complex has been a crossing focus ofseveral subjects such as chemistry, physics, biology,material and information.1 Supramolecular complex hasa wide application foreground in material, catalysis,conductor,…     

Erratum: Separability between valence and conduction bands in transition metal clusters

Density Functional Theory (DFT) and direct ab initio molecular dynamics (MD) calculations were applied to the hydrogen molecule trapped in a water cluster composed of 12 water molecules (H₂O)₁₂. The static DFT calculation showed that the H₂ molecule is trapped in the center of mass of (H₂O)₁₂. The vibrational frequency of the H–H stretching mode of the H₂ molecule trapped in the water cluster was blueshifted from that in vacuo. On the other hand, the vibrational frequency of H₂ in water‐hydrogen 1:1 complex (H₂O–H₂) was redshifted. A direct ab initio MD calculation of H₂(H₂O)₁₂ at 50 K indicated that the H₂ molecule is rotated freely around the center of mass of the water cluster. The origin of the spectral shift of H₂ in water ice is discussed on the basis of the theoretical results. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

质子化硼烷正离子体系电子结构的理论研究

本文用a b initio计算法和近似a b initio计算法(PRDDO)研究了质子化硼烷正离子体系的电子结构,给出了一些正离子体系的优化几何构型并讨论了它们的成键情况。计算的硼烷分子质子亲和势与实验值相当吻合。     

Origin of visible-light-driven photocatalysis: A comparative study on N/F-doped and N-F-codoped TiO2 powders by means of experimental characterizations and theoretical calculations

An overall comparative study was carried out on N-doped, F-doped, and N-F-codoped TiO₂ powders (NTO, FTO, NFTO) synthesized by spray pyrolysis in order to elucidate the origin of their visible-light-driven photocatalysis. The comparisons in their experimentally obtained characteristics were based on the analysis of XPS, UV-Vis, PL, NH₃-TPD and ESR spectra. The comparisons in their theoretically predicted properties were based on the analysis of the calculated electronic structures. As the results, N-doping into TiO₂ resulted in not only the improvement in visible-light absorption but also the creation of surface oxygen vacancies. F-doping produced several beneficial effects including the creation of surface oxygen vacancies, the enhancement of surface acidity and the increase of Ti³⁺ ions. Doped N atoms formed a localized energy state above the valence band of TiO₂, whereas doped F atoms themselves had no influence on the band structure. The photocatalytic tests indicated that the NFTO demonstrated the highest visible-light activity for decompositions of both acetaldehyde and trichloroethylene. This high activity was ascribed to a synergetic consequence of several beneficial effects induced by the N-F-codoping.     

铂配位的腺嘌呤质子化的理论研究

用量子化学从头算研究一系列平面四方金属配体作用于腺嘌呤N₇位点对其质子化的影响。计算结果表明气相中，配合物质子化能力主要受长程静电效应影响，不同金属离子的影响差别甚微。综合考虑极性溶剂影响后长程静电效应影响显著降低。NBO电荷布居分析表明质子化位点电子云密度的变化直接影响该位点质子化能力。