A study of the electronic structure of phenylsilanes by X-ray emission spectroscopy and quantum chemical calculation methods

The electronic structure of a series of phenylsilanes Ph_4?n SiH _n (n = 0?C3) is studied by X-ray emission spectroscopy and quantum chemical calculations by the density functional theory method. Based on the calculations theoretical X-ray emission SiK??₁ spectra of phenylsilanes Ph_4?n SiH _n (n = 0?C4) are constructed and their energy structure and shape turn out to be well consistent with experiment. The distribution of the electron density of states with different symmetry of Si, C, H atoms are also constructed. An analysis of the obtained X-ray fluorescent SiK??₁ spectra and the distribution of the electron density of states in Ph₄Si and Ph₃SiH compounds shows that their energy structure is mainly determined by a system of the energy levels of phenyl ligands weakly perturbed by interactions with valence AOs of silicon. In the energy structure of MOs of the PhSiH₃ compound, energy orbitals related to t ₂ and a ₁ levels of tetrahedral SiH₄ are mainly presented.     

Stabilization of boron clusters with classical fullerene structures by combined doping effect: a quantum chemical study

A combined approach (endohedral doping and exohedral environment) to stabilization of boron clusters with classical fullerene structures has been studied. The boron clusters with classical fullerene structures are stable when heteroatomic part of the complex (endohedral atom and exohedral environment) donates in total 18 electrons to the composite system, stability of which depends on the coordination capabilities and donor ability of the endohedral and surrounding atoms. The most effective stabilization is achieved in the case of the endohedral transition metals atoms, whereas the most effective environment is given by the lithium surrounding.

     

A new proposed model of aldose reductase enzyme inhibition on the basis of an artificial intelligence approach: A computer automated structure evaluation (case) study

A large number of inhibitors of aldose reductase enzyme were submitted to the CASE (computer automated structure evaluation) program in order to ascertain the topological features relevant to activity. On the basis of the twenty-six biophores (activating fragments) and one biophobe (inactivating fragment), a new proposed interaction model was suggested for an aldose reductase enzyme with the chemical inhibitors. The critical relationship between enzyme inhibition and the structure of inhibitors is believed to depend on the relative positions of subordinate regions within the inhibitor structure.     

DFT-calculated structures based on 1H NMR chemical shifts in solution vs. structures solved by single-crystal X-ray and crystalline-sponge methods: Assessing specific sources of discrepancies

DFT calculations of ¹H NMR chemical shifts, using various functionals and basis sets, the conductor-like polarizable continuum model and discrete solute-solvent hydrogen bond interactions have been used to derive the solution structures of methyl salicylate and methyl 2,5-dihydroxybenzoate. We demonstrate that very good agreement between experimental and computed ¹H NMR chemical shifts can be obtained for various basis sets. The DFT structures in solution were compared with the recently reported X-ray structure, solved by the crystalline-sponge method, of the methyl salicylate and the single-crystal X-ray structure of methyl 2,5-dihydroxybenzoate. It is demonstrated that the information provided by ¹H NMR chemical shifts about the solution structure is significantly more precise than that obtained by the single-crystal X-ray and the crystalline-sponge methods.     

偏最小二乘和量子化学参数预测酯类物质的闪点

基于化合物定量结构与性质的关系,对其中88个酯类化合物进行了B3LYP/6-31G*水平上的结构优化,并在优化结构基础上进行了量子化学结构参数的计算。应用偏最小二乘(PLS)方法对酯类化合物闪点温度这个理化性质与量子化学参数进行了关联。结果表明,分子热力学自由能(ΔG)结合偶极距(μ)可以很好地表达酯类化合物闪点温度与量子化学参数间的定量关系。所建立的QSPR模型具有较强的稳健性和预测能力。     

Structural and spectroscopic study of the excited electronic states of silver dihalides by quantum chemical methods

The structural and electronic properties of the excited electronic states of AgX(2) (X = F, Cl, Br, and I), have been calculated, taking electron correlation and spin-orbit coupling into account and employing improved relativistic-effective-core potentials for silver and the halogen atoms. The relative ordering of the excited states of these molecules has been discussed via molecular-orbital arguments. The spin-orbit splittings of three degenerate electronic states ((2)Pi(g), (2)Pi(u), and (2)Delta(g)) have been calculated and the spin-orbit induced inter-state (Sigma - Pi) coupling has been discussed. The composition of the spin-orbit eigenstates is analyzed in terms of scalar-relativistic electronic states. Finally, a theoretical prediction of the photodetachment bands of the title molecules has been accomplished.     

基于人工智能和互联网时代的化合物毒性预测综述

随着商品中所含各种化合物的不断使用,人们日益关注其对人类及生态环境的安全危害。在过去的几年里,通过计算方法预测化合物毒性已经显示出极大的潜力。在此,总结了常用的机器学习和深度学习算法在建立毒性预测模型上的优缺点,并系统回顾了近三年发表的可免费访问的毒性预测网络服务器。此外,还讨论了基于人工智能和互联网时代下毒性预测所面临的机遇和挑战。希望指导人们合理的选择算法和网络服务器进行建模及化合物毒性评估。     

X-ray and quantum chemical study of the electronic structure of glycine and its metal complexes

OK_α spectra of glycine and some transition metal complexes with glycine ligands were obtained. The electronic structure of the glycine zwitterion is calculated by a quantum chemical method, and a theoretical X-ray spectrum of the glycine molecule is constructed. The nature of the metal-ligand bond in the compounds is discussed on the basis of experimental spectra and theoretical calculations. Institute of Inorganic Chemistry, Siberian Branch, Russian Academy of Sciences. Moscow State Academy of Light Industry, Novosibirsk Branch. Moscow State Academy of Light Industry. Novosibirsk State University. Translated fromZhurnal Strukturnoi Khimii, Vol. 34, No. 4, pp. 112–116, July–August, 1994. Translated by L. Smolina     

Structure and spectroscopic aspects of water‐halide ion clusters: A study based on a conjunction of stochastic and quantum chemical methods

In this article, we propose a stochastic search based method, namely genetic algorithm in conjunction with density functional theory to evaluate structures of water‐halide microclusters, with the halide ion being Cl^?, Br^?, and I^?. Once the structures are established, we evaluate the infrared spectroscopic modes, vertical detachment energies and natural population analysis based charges. We compare our results with available experimental and theoretical results. © 2012 Wiley Periodicals, Inc.     

A study on the antipicornavirus activity of flavonoid compounds (flavones) by using quantum chemical and chemometric methods

The AM1 semiempirical method is employed to calculate a set of molecular properties (variables) of 45 flavone compounds with antipicornavirus activity, and 9 new flavone molecules are used for an activity prediction study. Principal Component Analysis (PCA), Hierarchical Cluster Analysis (HCA), Stepwise Discriminant Analysis (SDA), and K-Nearest Neighbor (KNN) are employed in order to reduce dimensionality and investigate which subset of variables should be more effective for classifying the flavone compounds according to their degree of antipicornavirus activity. The PCA, HCA, SDA, and KNN methods showed that the variables MR (molar refractivity), B(9) (bond order between C(9) and C(10) atoms), and B(25) (bond order between C(11) and R(7) atoms) are important properties for the separation between active and inactive flavone compounds, and this fact reveals that electronic and steric effects are relevant when one is trying to understand the interaction between flavone compounds with antipicornavirus activity and the biological receptor. In the activity prediction study, using the PCA, HCA, SDA, and KNN methodologies, three of the 9 new flavone compounds studied were classified as potentially active against picornaviruses.     

Structural and spectroscopic studies on some chloropyrimidine derivatives by experimental and quantum chemical methods

Ab initio quantum chemical and experimental spectroscopic studies in the infrared (4000-60 cm(-1)) and UV spectral regions are being reported on 4-chloro-2,6-dimethylsulfanyl pyrimidine-5-carbonitrile and 4-chloro-2-methylsulfanyl-6-(2-thienyl) pyrimidine-5-carbonitrile. Optimized geometries, electronic charge distribution, dipole moments and three-dimensional molecular electrostatic potential surfaces have been obtained. These have been used to understand the structure and spectral characteristics of the two compounds. A complete assignment of vibrational spectra on the basis of DFT/6-311G** and electronic spectra on the basis of TD-DFT/6-31+G* 5D calculations have been attempted for the two molecules.     

A study of the electronic structure of octavinylsilsesquioxane and dendron with chromium based compounds by X-ray photoelectron spectroscopy and quantum chemical modeling in the DFT approximation

The electronic structure and some features of octavinylsilsesquioxane interaction with sulfene chloride chromium acetylacetonate complex were studied by means of XPS and DFT. According to XPS, spectrum lines have close positions for all the studied compounds, half-width for dendrons not exceeding 2 eV. For octavinylsilsesquioxane, the broader lines appear due to the action of substrate atoms. Chemical composition of a dendron was determined by analyzing the concentrations of atoms in different chemical states and a residual content of chlorine atoms. Chemical bonding between the complex and octavinylsilsesquioxane is provided by the covalent interaction of carbon and sulfur atoms.     

Evolution detection of phenol by pristine BN nanocone: chemical quantum study

Structural Chemistry - In order to evaluate the electrical response of boron nitride nanocones (BNNCs) to phenol gas, density functional theory (DFT) calculations are employed. The sensitivity and...     

Steroid binding by antibodies and artificial receptors: Exploration of theoretical methods to determine the origins of binding affinities and specificities

Binding mode calculations for complexes between an artificial paracyclophane receptor and digoxins, cholic acids as well as cortisone steroids show encapsulation of different ring combinations. Docking experiments were performed between the 26-10 antibody and digoxins. Coordination affinity arises from hydrophobic desolvation and van der Waals interactions rather than from hydrogen bonds. The specificity and affinity arises mainly from shape complementarity. Computed binding free energies and Kohonen neural network computations both point to physicochemical and structural similarities of natural antibodies and artificial receptors.     

Molecular structures of phthalocyaninatozinc and hexadecafluorophthalocyaninatozinc studied by gas-phase electron diffraction and quantum chemical calculations

The molecular structures of phthalocyaninatozinc (HPc-Zn) and hexadecafluorophthalocyaninatozinc (FPc- Zn) are determined using the gas electron diffraction (GED) method and high-level density functional theory (DFT) quantum chemical calculations. Calculations at the B3LYP/6-311++G** level indicate that the equilibrium structures of HPc-Zn and FPc-Zn have D4h symmetry and yield structural parameters in good agreement with those obtained by GED at 480 and 523 degrees C respectively. The calculated force fields indicate that both molecules are flexible. Normal coordinate calculations on HPc-Zn yield five vibrational frequencies (one degenerate) in the range 22-100 cm(-1), and ten vibrational frequencies ranging from 13 to 100 cm(-1) (three degenerate) for FPc-Zn. The high-level force field calculations confirm most of the previous vibrational assignments, and some new ones are suggested. The out-of-plane vibration of the Zn atom in HPc-Zn was studied in detail optimizing models in which the distance from the Zn atom to the two symmetry equivalent diagonally opposed N atoms (h) was fixed. The calculations indicate that the vibrationally activated vertically displacement of the Zn atom is accompanied by distortion of the ligand from D4h to C2v symmetry. The average height, h, at the temperature of the GED experiment was calculated to be 14.5 pm. Small structural changes indicate that a full F substitution on the benzo-subunits do not significantly alter the geometry, however there are indications that the benzo-subunits may shrink slightly with perfluorination.     

Investigation of the structural units of germanium sulfide and selenide by quantum chemical methods

This article deals with the modeling of the structural units (clusters) of germanium sulfide and germanium selenide glasses by quantum chemical (ab initio Hartree–Fock) methods. Clusters of different sizes were investigated. Geometric parameters and vibrational frequencies of these structural units were calculated. The quantum chemical calculations were followed by normal coordinate analysis. Based on the yielded results, the vibrational spectra of the clusters were simulated. The results for germanium sulfide and germanium selenide were compared. It was concluded that in the spectral regions where germanium sulfide is not applicable for fiber optics, germanium selenide or different germanium sulfide–selenides are suitable to replace it. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001     

Structure and energetics of water-silanol binding on the surface of silicalite-1: quantum chemical calculations

Quantum mechanical calculations have been carried out to investigate the structural properties and the interaction between water molecules and silanol groups on the surface of silicalite-1. The (010) surface, which is perpendicular to the straight channel, has been selected and represented by three fragments taken from different parts of the surface. Calculations have been performed using different levels of accuracy: HF/6-31G(d,p), B3LYP/6-31G(d,p), HF/6-31++G(d,p), and B3LYP/6-31++G(d,p). The basis set superposition error has been taken into account. The geometry of the silanol groups and that of the water molecules have been fully optimized. The results show that the most stable conformation takes place when a water molecule forms two hydrogen bonds with two silanols, with only one silanol lying on the opening of the pore of the straight channel. The corresponding binding energy is -48.82 kJ/mol. These areas are supposed to be the first binding sites which have to be covered when the water molecule approaches the surface. When the water loading increases, the next favorable silanols are those of the opening of the pore in which the four possible complex conformations yield a binding energy between -25.62 and -37.41 kJ/mol. It was also found that the calculated O-H bond length of the silanol in the free form was slightly shorter than that in the complex. In terms of the stretching frequency, the complexation leads to a red shift of the O-H stretching of the silanol group.