Basis Set Orbital Relaxation in Atomic and Molecular Hydrogen Systems

Orbital relaxation (OR) amounts to variation of the orbital exponents in hydrogen molecules and ions relative to the exponents of the isolated atom; it is represented as the sum of the one- and two-center contributions depending on the effective atomic charge and on the presence of other atoms in the molecule. The procedure for isolating the contributions of the exponent includes treatment of the OR of hydrogen in a special set of neutral and charged atoms and molecules with certain multiplicities of their electronic states. Within the framework of the spin-unrestricted Hartree-Fock method, we found and discussed the optimal values of the exponents of the basis orbitals of hydrogen atoms and molecules using the minimal split valence-shell basis set, the basis set that includes the polarization function, and the expanded set of grouped natural orbitals. A simple energy model is suggested for OR. Expressions are derived for evaluating the exponents of the relaxed orbitals in hydrogen-containing systems.Original Russian Text Copyright © 2004 by A. I. Ermakov, A. E. Merkulov, A. A. Svechnikova, and V. V. Belousov__________Translated from Zhurnal Strukturnoi Khimii, Vol. 45, No. 6, pp. 973–978, November–December, 2004.     

Improving (Q)SAR predictions by examining bias in the selection of compounds for experimental testing

ABSTRACT

Existing data on structures and biological activities are limited and distributed unevenly across distinct molecular targets and chemical compounds. The question arises if these data represent an unbiased sample of the general population of chemical-biological interactions. To answer this question, we analyzed ChEMBL data for 87,583 molecules tested against 919 protein targets using supervised and unsupervised approaches. Hierarchical clustering of the Murcko frameworks generated using Chemistry Development Toolkit showed that the available data form a big diffuse cloud without apparent structure. In contrast hereto, PASS-based classifiers allowed prediction whether the compound had been tested against the particular molecular target, despite whether it was active or not. Thus, one may conclude that the selection of chemical compounds for testing against specific targets is biased, probably due to the influence of prior knowledge. We assessed the possibility to improve (Q)SAR predictions using this fact: PASS prediction of the interaction with the particular target for compounds predicted as tested against the target has significantly higher accuracy than for those predicted as untested (average ROC AUC are about 0.87 and 0.75, respectively). Thus, considering the existing bias in the data of the training set may increase the performance of virtual screening.     

微视频技术在基础化学实验教学中的实践应用

以高校基础化学实验"从海带中提取碘""三草酸合铁（Ⅲ）酸钾的制备"为例，分别探讨了微视频技术在化学基本操作实验和综合设计型实验中的具体应用；此外，举例说明利用Flash软件制作的虚拟微视频可以在仪器分析实验中清晰地再现仪器真实操作中的每一个步骤，弥补了学生在实验前无法实际操作仪器的不足。实践证明，微视频技术的应用，丰富了基础化学实验教学模式，增强了学生自主学习的能力和动手能力，提高了实验成功率和实验教学效果。     

Lewis碱性混合萃取剂碱度的测定

提出一种利用萃取法间接测定Lewis碱性萃取剂碱度的简便方法, 选择常用的Lewis碱性萃取剂TOA/正辛醇和TRPO/煤油, 测定了其碱度, 为今后络合萃取剂的选择及其机理的研究提供理论指导.     

无烟煤结构的高分辨电镜研究

镜质组不仅是煤结构变化最具规律性，也是影响煤质的主要微成分。用点分辨率为２．１Ａ的高分辨电镜对几种不同煤化程度的无烟煤大分子结构进行了研究。结果表明：电镜图像直接表征了无烟煤分子的非均匀性孔隙结构。京西煤分子方向化程度强，主要以芳层平行堆或有序化前结构为主；晋城煤方向化程度弱，主要以粒状嵌晶结构为主。高分辨电镜技术是研究煤分子结构和煤化作用实质的有效方法。     

Static electric properties of LiH: explicitly correlated coupled cluster calculations

Explicitly correlated MBPT-R12 and coupled cluster [up to CCSD(T)-R12] methods have been used in calculations of various (vibrationless) electrical properties for the LiH molecule, including the dipole and quadrupole moments, dipole and quadrupole polarizability tensors, dipole hyperpolarizability tensors, and the second dipole hyperpolarizability tensors. Generally, with extension of the basis set the R12 method did not lead to faster convergence for the calculated properties towards the basis limit. Nevertheless, R12 calculations serve as useful indicators to judge the reliability of the results, and substantially help in determining the accuracy. Results obtained with the 11s8p6d5f/9s8p6d5f basis and CCSD(T)-R12 calculated within this work should be close to the basis set limit. Received: 8 June 1998 / Accepted: 23 July 1998 / Published online: 7 October 1998     

[Bi6O4.5(OH)3.5]2(NO3)11: a new anhydrous bismuth basic nitrate. Synthesis and structure determination from twinned crystals

The bismuth basic nitrate [Bi₆O_4.5(OH)_3.5]₂(NO₃)₁₁ crystallizes in the monoclinic space group P2₁ with , , , β=107.329(17)° and . Its structure has been determined from , twinned crystal X-ray data (16 781 reflections, 683 parameters, R=0.0703). It is built upon [Bi₆O_x(OH)_8−x]^(10−x)+, x=4 and x=5 hexanuclear complexes and nitrate groups. The polycationic entities are linked to the nitrate anions either by hydrogen bonds or through bismuth-oxygen coordination. Even at , the [Bi₆O₄(OH)₄]⁶⁺ and [Bi₆O₅(OH)₃]⁵⁺ polycations could not be observed as such, the crystal structure refinement only detecting an average [Bi₆O_4.5(OH)_3.5]^5.5+ polycation. To prove the presence of both hexanuclear complexes in the structure, we report the existence of a correlation between the bismuth-linked oxygen bond-valence parameters and the presence, or not, of hydroxyl groups. Moreover, the Raman spectrum of the new anhydrous bismuth basic nitrate is compared to those of [Bi₆O₅(OH)₃](NO₃)₅·3H₂O, [Bi₆O₄(OH)₄](NO₃)₆·4H₂O, and two yet uncharacterized bismuth nitrates.     

Complete basis set ab initio computational study of ionization potential, electron affinity and the C-F bond dissociation energy for perfluorinated methane derivatives

A computational study of perfluorinated methane derivatives was performed with complete basis set ab initio methods. The total energies for their neutral, cation, and anionic states were computed. From these values, the energy gaps between different electronic states, ionization potentials, electron affinities, and C-F bond dissociation energies were calculated. The computed values are compared with experimental data and the reliability of complete basis set ab initio methods is discussed. New values for C-F bond dissociation energies are suggested. Received: 12 January 1998 / Accepted: 2 April 1998 / Published online: 29 July 1998     

HCN(HNC)与NH3, H2O和HF分子间相互作用的理论研究

在MP2/aug-cc-pVTZ水平上, 对HCN(HNC)与NH3, H2O和HF分子间可能存在的氢键型复合物进行了全自由度能量梯度优化, 通过在相同水平上的频率验证分析发现了稳定的分子间相互作用形式是HCN(HNC)作为质子供体或作为质子受体形成的复合物. 基组重叠误差对总相互作用能的影响均小于3.34 kJ/mol. 通过自然键轨道(NBO)分析, 研究了单体和复合物中的原子电荷和电荷转移对分子间相互作用的影响. 对称性匹配微扰理论(SAPT, Symmetry Adapted Perturbation Theory)能量分解结果表明, 在分子间相互作用中, 静电作用与诱导作用占主导地位, 而诱导作用与复合物的电荷转移之间具有良好的正相关性.     

Simultaneous determination of acidic,basic and alcoholic substances relating to monoamine hormones and metabolites in biological material by mass fragmentography (GC/MF)

A method is described for the simultaneous quantitative determination of monoamines and related compounds from urine and brain tissue samples in the pg-range, using a GC/MF instrument LKB-2091 provided with a multiple ion detection (MID) system and capillary columns. The simultaneous detection of “fingerprints” with fourteen and more compounds during one single GC run was achieved after the intoduction of “time gates” for the detection of the different characteristic masses. Several modifications to the LKB equipment permitted exact reproducibility of retention times, which is essential for the use of “time gates”. The detection of “fingerprints” with these acidic, basic and alcoholic substances was achieved by the extraction of the dried biological samples with silylating agents.