On the efficiency of VBSCF algorithms,a comment on “An efficient algorithm for energy gradients and orbital optimization in valence bond theory”

We comment on the paper [Song et al., J. Comput. Chem. 2009, 30, 399]. and discuss the efficiency of the orbital optimization and gradient evaluation in the Valence Bond Self Consistent Field (VBSCF) method. We note that Song et al. neglect to properly reference Broer et al., who published an algorithm [Broer and Nieuwpoort, Theor. Chim. Acta 1988, 73, 405] to use a Fock matrix to compute a matrix element between two different determinants, which can be used for an orbital optimization. Further, Song et al. publish a misleading comparison with our VBSCF algorithm [Dijkstra and van Lenthe, J. Chem. Phys. 2000, 113, 2100; van Lenthe et al., Mol. Phys. 1991, 73, 1159] to enable them to favorably compare their algorithm with ours. We give detail timings in terms of different orbital types in the calculation and actual timings for the example cases. © 2012 Wiley Periodicals, Inc.     

ERKALE—A flexible program package for X‐ray properties of atoms and molecules

ERKALE is a novel software program for computing X‐ray properties, such as ground‐state electron momentum densities, Compton profiles, and core and valence electron excitation spectra of atoms and molecules. The program operates at Hartree–Fock or density‐functional level of theory and supports Gaussian basis sets of arbitrary angular momentum and a wide variety of exchange‐correlation functionals. ERKALE includes modern convergence accelerators such as Broyden and ADIIS and it is suitable for general use, as calculations with thousands of basis functions can routinely be performed on desktop computers. Furthermore, ERKALE is written in an object oriented manner, making the code easy to understand and to extend to new properties while being ideal also for teaching purposes. © 2012 Wiley Periodicals, Inc.     

Simple Method for Determination of Lead in Hair Dyes Using Slurry Sampling Graphite Furnace Atomic Absorption Spectrometry

A fast, simple and sensitive method for determining of lead in hair dyes using graphite furnace atomic absorption spectrometry with slurry sampling was developed. Multivariate optimization was used to establish optimal analytical parameters through a fractional factorial and a central composite design. The samples were submitted for direct analysis without prior digestion and were diluted in 2.5% v/v HNO₃ and 1.5% v/v H₂O₂. Palladium (chemical modifier) and rhodium (permanent modifier) were selected from several potential modifiers. The optimal conditions were a pyrolysis time of 10 s (liquid and dust dyes) 20 s (cream dyes), a pyrolysis temperature of 789°C (liquid dyes) or 750°C (cream and dust dyes) and an atomization temperature of 1800°C for all dyes. Under optimum conditions, the calibration graph is linear in the 1.50–50.0 µg L^?1 concentration range, with a detection limit of 0.33, 0.44, and 0.39 µg L^?1 for liquid, dust, and cream hair dyes, respectively. The relative standard deviation ranged from 1.63 to 4.56%. The recovery rate ranged from 85 to 108%, and no significant differences were found between the results obtained with the proposed method and the microwave decomposition analysis method of real samples. The concentration ranges obtained for lead in the hair dyes samples were 1.00–11.3 µg L^?1 for liquid dyes, 14.0–100 µg kg^?1 for dust dyes, and 19.9–187 µg kg^?1 for cream dyes.     

Counterpoise-corrected potential energy surfaces of simple H-bonded systems

Geometries and stabilization energies of various simple H-bonded complexes (water dimer, hydrogen fluoride dimer, formamide dimer, formic acid dimer) have been determined by a gradient optimization that eliminates the basis set superposition error (BSSE) by the counterpoise (CP) method in each gradient cycle as well as by the standard gradient optimization. Both optimization methods lead to different potential energy surfaces (PES). The difference depends on the theoretical level used and is larger if correlation energy is considered. Intermolecular distances from the CP-corrected PES are consistently longer, and this difference might be significant (∼0.1 ?); also angular characteristics determined from both surfaces differ significantly. Different geometries were obtained even when passing to larger basis sets (aug-cc-pVDZ). The standard optimization procedure can result in a completely wrong structure. For example, the “quasi-linear” structure of the (HF)₂ (global minimum) does not exist at the standard MP2/ 6-31G** PES (where only cyclic structure was detected) and is found only at the CP-corrected PES. Stabilization energies obtained from the CP-corrected PES are always larger than these from the standard PES where the BSSE is added only a posteriori for the final optimized structure; both energies converge only when passing to a larger basis set (aug-cc-pVDZ). Received: 11 March 1998 / Accepted: 19 June 1998 / Published online: 4 September 1998 RID=" ID=" <E6>Acknowledgements.</E6> The project was supported by the Grant Agency of the Czech Republic (Grant No. 203/98/1166). RID=" ID=" <E5>Correspondence to</E5>: P. Hobza     

自动化势能面搜索方法新进展

本文简要介绍了势能面搜索的两个主要问题,即过渡态搜索和全局势能面搜索,并针对这两个问题介绍了本研究组最近发展的3种方法,即限制最小化双子算法、偏置势函数辅助限制性最小化双子算法以及势能面随机行走方法．这3种方法均只需计算一阶梯度,能够用于快速自动化的搜索过渡态以及势能面．通过几个典型例子分别说明了3种方法的特点及优势．     

Chemometric analysis for optimizing derivatization in gas chromatography‐based procedures

This paper focuses on the application of principal component analysis (PCA) to facilitate the optimization of the derivatization of oestrogenic steroids—estrone, 17β‐estradiol, estriol, 17α‐ethinylestradiol and diethylstilbestrol—in order to achieve (1) the complete derivatization of all the hydroxyl groups contained in the structure of the compounds and (2) the greatest effectiveness of this reaction. Six different derivatization reagents were used in this study, whereas 2‐methyl‐anthracene was applied as the internal standard to evaluate the effectiveness of the reactions. The experimental data were subjected to PCA. With PCA, the dimensionality of the original multivariable data set could be reduced and the selection of optimum conditions for derivatization facilitated. The mixture of 99% N,O‐bis(trimethylsilyl)trifluoroacetamide + 1% trimethylchlorosilane and pyridine (1:1, v/v) at 60 °C for 30 min has been established as the most convenient and efficient means of derivatizing the aforementioned oestrogenic steroids and diethylstilbestrol; the N‐methyl‐N‐(trimethylsilyl)trifluoroacetamide + pyridine (1:1, v/v) mixture seems to be a promising alternative. The application of PCA for optimizing the derivatization procedure, proposed for the first time in this study, is particularly useful in the development of multicomponent methods across several chemical classes of compounds. Copyright © 2011 John Wiley & Sons, Ltd.     

柴胡舒肝丸的毛细管电泳指纹图谱及其黄芩苷含量的测定

建立了柴胡舒肝丸(Chaihu Shugan Pill, CHSGP)的毛细管区带电泳指纹图谱(capillary electrophoresis fingerprint, CEFP),并采用内标法测定了黄芩苷的含量。以50 mmol/L硼砂-150 mmol/L磷酸二氢钠-50 mmol/L磷酸氢二钠(1:1:1, v/v/v)(含5 mmol/L庚烷磺酸钠)为背景电解质(BGE)溶液,采用未涂层石英毛细管(总长度75 cm,有效分离长度63 cm,内径75 μm),以色谱指纹图谱分离量指数(RF)为目标函数优化实验条件,在紫外检测波长265 nm、运行电压11 kV条件下,以黄芩苷峰为参照物峰,确定了22个共有指纹峰,建立了CHSGP的CEFP,通过对20批样品聚类分析确定用其中13批生成对照CEFP(RCEFP),以此RCEFP为标准用系统指纹定量法鉴别20批柴胡舒肝丸质量。结果其中的4批化学成分数量和分布比例不合格,4批含量明显偏低,其他12批完全合格。采用内标法测定黄芩苷的含量,在5～200 mg/L范围内线性良好(r=0.9999),平均回收率(n=9)为98.2%。该法具有较好的精密度和重现性,为柴胡舒肝丸的质量控制提供了一种新的参考。     

Multiple ligand simultaneous docking: Orchestrated dancing of ligands in binding sites of protein

Present docking methodologies simulate only one single ligand at a time during docking process. In reality, the molecular recognition process always involves multiple molecular species. Typical protein–ligand interactions are, for example, substrate and cofactor in catalytic cycle; metal ion coordination together with ligand(s); and ligand binding with water molecules. To simulate the real molecular binding processes, we propose a novel multiple ligand simultaneous docking (MLSD) strategy, which can deal with all the above processes, vastly improving docking sampling and binding free energy scoring. The work also compares two search strategies: Lamarckian genetic algorithm and particle swarm optimization, which have respective advantages depending on the specific systems. The methodology proves robust through systematic testing against several diverse model systems: E. coli purine nucleoside phosphorylase (PNP) complex with two substrates, SHP2NSH2 complex with two peptides and Bcl‐xL complex with ABT‐737 fragments. In all cases, the final correct docking poses and relative binding free energies were obtained. In PNP case, the simulations also capture the binding intermediates and reveal the binding dynamics during the recognition processes, which are consistent with the proposed enzymatic mechanism. In the other two cases, conventional single‐ligand docking fails due to energetic and dynamic coupling among ligands, whereas MLSD results in the correct binding modes. These three cases also represent potential applications in the areas of exploring enzymatic mechanism, interpreting noisy X‐ray crystallographic maps, and aiding fragment‐based drug design, respectively. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Quantum control implemented as combinatorial optimization

Optimal control theory provides a general means for designing controls to manipulate quantum phenomena. Traditional implementation requires solving coupled nonlinear equations to obtain the optimal control solution, whereas this work introduces a combinatorial quantum control (CQC) algorithm to avoid this complexity. The CQC technique uses a predetermined toolkit of small time step propagators in conjunction with combinatorial optimization to identify a proper sequence for the toolkit members. Results indicate that the CQC technique exhibits invariance of search effort to the number of system states and very favorable scaling upon comparison to a standard gradient algorithm, taking into consideration that CQC is easily parallelizable. © 2009 Wiley Periodicals, Inc. J Comput Chem 2010     

Generation and characterization of low‐energy structures in atomic clusters

Factors relevant for controlling the structures determined in the local optimization of argon clusters are investigated. In particular, the role of volume and shape for the box where initial structures are generated is assessed. A thorough characterization of the optimization is also presented, based on a nearest‐neighbor analysis, in clusters ranging from 30 to 55 atoms. This includes the assessment of the degree of preservation of aspects of the initial randomly generated structure in the final optimized counterpart, and the correlation between optimized energy and the number of nearest neighbors and average departure from the diatomic reference distance. The usefulness of this analysis to explore the energy landscape of atomic clusters is also highlighted. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010