共查询到20条相似文献，搜索用时 15 毫秒
1.
De Proft F Van Alsenoy C Peeters A Langenaeker W Geerlings P 《Journal of computational chemistry》2002,23(12):1198-1209
In the Hirshfeld partitioning of the electron density, the molecular electron density is decomposed in atomic contributions, proportional to the weight of the isolated atom density in the promolecule density, constructed by superimposing the isolated atom electron densities placed on the positions the atoms have in the molecule. A maximal conservation of the information of the isolated atoms in the atoms-in-molecules is thereby secured. Atomic charges, atomic dipole moments, and Fukui functions resulting from the Hirshfeld partitioning of the electron density are computed for a large series of molecules. In a representative set of organic and hypervalent molecules, they are compared with other commonly used population analysis methods. The expected bond polarities are recovered, but the charges are much smaller compared to other methods. Condensed Fukui functions for a large number of molecules, undergoing an electrophilic or a nucleophilic attack, are computed and compared with the HOMO and LUMO densities, integrated over the Hirshfeld atoms in molecules. 相似文献
2.
《Journal of computational chemistry》2018,39(22):1728-1737
Partition coefficients serve in various areas as pharmacology and environmental sciences to predict the hydrophobicity of different substances. Recently, they have also been used to address the accuracy of force fields for various organic compounds and specifically the methylated DNA bases. In this study, atomic charges were derived by different partitioning methods (Hirshfeld and Minimal Basis Iterative Stockholder) directly from the electron density obtained by electronic structure calculations in a vacuum, with an implicit solvation model or with explicit solvation taking the dynamics of the solute and the solvent into account. To test the ability of these charges to describe electrostatic interactions in force fields for condensed phases, the original atomic charges of the AMBER99 force field were replaced with the new atomic charges and combined with different solvent models to obtain the hydration and chloroform solvation free energies by molecular dynamics simulations. Chloroform–water partition coefficients derived from the obtained free energies were compared to experimental and previously reported values obtained with the GAFF or the AMBER‐99 force field. The results show that good agreement with experimental data is obtained when the polarization of the electron density by the solvent has been taken into account, and when the energy needed to polarize the electron density of the solute has been considered in the transfer free energy. These results were further confirmed by hydration free energies of polar and aromatic amino acid side chain analogs. Comparison of the two partitioning methods, Hirshfeld‐I and Minimal Basis Iterative Stockholder (MBIS), revealed some deficiencies in the Hirshfeld‐I method related to the unstable isolated anionic nitrogen pro‐atom used in the method. Hydration free energies and partitioning coefficients obtained with atomic charges from the MBIS partitioning method accounting for polarization by the implicit solvation model are in good agreement with the experimental values. © 2018 Wiley Periodicals, Inc. 相似文献
3.
Thomas A. Manz 《Journal of computational chemistry》2013,34(5):418-421
In recent years, several methods have been developed that partition the electron density among atoms using spherically symmetric atomic weights. D. E. P. Vanpoucke, P. Bultinck, and I. Van Driessche (J. Comput. Chem. 2012, doi: 10.1002/jcc.23088) recently reported a periodic implementation of the Hirshfeld‐I method that uses a combination of Becke‐style and uniform integration grids and modified atomic reference densities to compute net atomic charges in periodic materials. Herein, this method is discussed in the context of earlier periodic implementations of the Hirshfeld‐I method, the Iterated Stockholder Atoms method, and the density derived electrostatic and chemical method. 相似文献
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Araz Jakalian Bruce L. Bush David B. Jack Christopher I. Bayly 《Journal of computational chemistry》2000,21(2):132-146
The AM1‐BCC method quickly and efficiently generates high‐quality atomic charges for use in condensed‐phase simulations. The underlying features of the electron distribution including formal charge and delocalization are first captured by AM1 atomic charges for the individual molecule. Bond charge corrections (BCCs), which have been parameterized against the HF/6‐31G* electrostatic potential (ESP) of a training set of compounds containing relevant functional groups, are then added using a formalism identical to the consensus BCI (bond charge increment) approach. As a proof of the concept, we fit BCCs simultaneously to 45 compounds including O‐, N‐, and S‐containing functionalities, aromatics, and heteroaromatics, using only 41 BCC parameters. AM1‐BCC yields charge sets of comparable quality to HF/6‐31G* ESP‐derived charges in a fraction of the time while reducing instabilities in the atomic charges compared to direct ESP‐fit methods. We then apply the BCC parameters to a small “test set” consisting of aspirin, d ‐glucose, and eryodictyol; the AM1‐BCC model again provides atomic charges of quality comparable with HF/6‐31G* RESP charges, as judged by an increase of only 0.01 to 0.02 atomic units in the root‐mean‐square (RMS) error in ESP. Based on these encouraging results, we intend to parameterize the AM1‐BCC model to provide a consistent charge model for any organic or biological molecule. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 132–146, 2000 相似文献
7.
The variation of atomic charges upon proton transfer in hydrogen bonding complexes of 4-methylimidazole, in both neutral and protonated cationic forms, and acetate anion, is investigated. These complexes model the histidine (neutral and protonated)-aspartate pair present in active sites of proteases where strong N--H...O hydrogen bonds are formed. Three procedures (Merz-Kollman scheme, Natural Population Analysis, and Atoms in Molecules Method) are used to compute atomic charges and explore their variation upon H-transfer in the gas phase and in the presence of two continuum media with dielectric constants 5 (protein interiors) and 78.39 (water). The effect of electron correlation was also studied by comparing Hartree-Fock and MP2 results for both complexes in the gas phase. Greater net charge interchanged upon H-transfer is observed in the anionic complex with respect to the neutral complex. Raising the polarity of the medium increases the amount of net charge transfer in both complexes, although the neutral system exhibits a larger sensitivity to the presence of solvent. Charge transfer associated to N--H...O and N...H--O bonds reveal the ionic contribution to the interaction depending on the number of charged subunits but the presence of solvent affects little this quantity. The lack of electron correlation overestimates all the charges as well as their variations and so uncorrelated calculations should be avoided. 相似文献
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Prof. Dr. Wolfgang Scherer M. Sc. Petra Meixner Dr. José Enrique Barquera‐Lozada Dipl.‐Phys. Christoph Hauf Dr. Andreas Obenhuber Dr. Andreas Brück Dr. David J. Wolstenholme Prof. Dr. Klaus Ruhland Dr. Dirk Leusser Prof. Dr. Dietmar Stalke 《Angewandte Chemie (International ed. in English)》2013,52(23):6092-6096
9.
Natthaya Meundaeng Timothy John Prior Apinpus Rujiwatra 《Acta Crystallographica. Section C, Structural Chemistry》2019,75(9):1319-1326
The crystal structures of five new transition‐metal complexes synthesized using thiazole‐2‐carboxylic acid (2‐Htza), imidazole‐2‐carboxylic acid (2‐H2ima) or 1,3‐oxazole‐4‐carboxylic acid (4‐Hoxa), namely diaquabis(thiazole‐2‐carboxylato‐κ2N,O)cobalt(II), [Co(C4H2NO2S)2(H2O)2], 1 , diaquabis(thiazole‐2‐carboxylato‐κ2N,O)nickel(II), [Ni(C4H2NO2S)2(H2O)2], 2 , diaquabis(thiazole‐2‐carboxylato‐κ2N,O)cadmium(II), [Cd(C4H2NO2S)2(H2O)2], 3 , diaquabis(1H‐imidazole‐2‐carboxylato‐κ2N3,O)cobalt(II), [Co(C4H2N2O2)2(H2O)2], 4 , and diaquabis(1,3‐oxazole‐4‐carboxylato‐κ2N,O4)cobalt(II), [Co(C4H2NO3)2(H2O)2], 5 , are reported. The influence of the nature of the heteroatom and the position of the carboxyl group in relation to the heteroatom on the self‐assembly process are discussed based upon Hirshfeld surface analysis and used to explain the observed differences in the single‐crystal structures and the supramolecular frameworks and topologies of complexes 1 – 5 . 相似文献
10.
Jack Halpern 《Angewandte Chemie (International ed. in English)》1985,24(4):274-282
Stable organometallic compounds, notably of the later transition metals (groups VI–VIII), usually are characterized by closed shell electron configurations (typically 18-electron valence shells) which are destabilized by electron addition or removal. One-electron oxidation of such compounds results in the formation of unstable radical ions, whose characteristic reactivity patterns include susceptibility to nucleophilic attack, disproportionation, and metal-carbon bond dissociation. Two-electron oxidation may result in dissociation or oxidation of the organic ligand. In this review studies on the chemical and electrochemical oxidations of metal carbonyls, metal-olefin complexes, and alkyl transition-metal compounds are described. The studies encompass the following themes: (1) The kinetics and thermodynamics of the initial redox steps; (2) The characterization and reactivity patterns of the resulting oxidation products; (3) The synthetic and catalytic applications of organometallic redox processes. 相似文献
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《Journal of computational chemistry》2017,38(20):1811-1818
An analytical method is presented that provides quantitative insight into light‐driven electron density rearrangement using the output of standard time‐dependent density functional theory (TD‐DFT) computations on molecular compounds. Using final and initial electron densities for photochemical processes, the subtraction of summed electron density in each atom‐centered Voronoi polyhedron yields the electronic charge difference, Q VECD. This subtractive method can also be used with Bader, Mulliken and Hirshfeld charges. A validation study shows Q VECD to have the most consistent performance across basis sets and good conservation of charge between electronic states. Besides vertical transitions, relaxation processes can be investigated as well. Significant electron transfer is computed for isomerization on the excited state energy surface of azobenzene. A number of linear anilinepyridinium donor‐bridge‐acceptor chromophores was examined using Q VECD to unravel the influence of its pi‐conjugated bridge on charge separation. Finally, the usefulness of the presented method as a tool in optimizing charge transfer is shown for a homologous series of organometallic pigments. The presented work allows facile calculation of a novel, relevant quantity describing charge transfer processes at the atomic level. © 2017 The Authors Journal of Computational Chemistry Published by Wiley Periodicals, Inc. 相似文献
12.
利用配体 5-(二甲基氨基)间苯二甲酸(H2dia)和咪唑(mdz)分别与锌(Ⅱ)和铜(Ⅱ)金属盐反应,制备了 3 例过渡金属配合物[Zn(dia)(mdz)2]·2H2O (1)、[Cu(dia)(mdz)2(DMF)] (2)和[Cu(dia)(mdz)2]·H2O (3)。利用单晶 X射线衍射、元素分析、红外光谱、热重和Hirshfeld表面分析对其进行了结构表征。结果表明配合物1和2为一维线状链,1中每个四配位的Zn(Ⅱ)处于变形四面体中心,2中Cu(Ⅱ)中心拥有五配位的三角双锥几何构型。改变合成溶剂条件得到锯齿形一维链状配合物3,其四配位Cu(Ⅱ)中心展现出对称平面四边形构型。上述结果说明,金属离子几何构型以及合成溶剂可能对配合物结构具有重要影响。丰富的分子间氢键帮助3例配合物形成稳定的三维超分子结构。热重分析表明,3例配合物均具有良好的热稳定性。固体荧光分析表明配合物1具有较强荧光性,而配合物2和3荧光强度均远低于配体。 相似文献
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利用配体 5-(二甲基氨基)间苯二甲酸(H2dia)和咪唑(mdz)分别与锌(Ⅱ)和铜(Ⅱ)金属盐反应,制备了 3 例过渡金属配合物[Zn(dia)(mdz)2]·2H2O (1)、[Cu(dia)(mdz)2(DMF)] (2)和[Cu(dia)(mdz)2]·H2O (3)。利用单晶 X射线衍射、元素分析、红外光谱、热重和Hirshfeld表面分析对其进行了结构表征。结果表明配合物1和2为一维线状链,1中每个四配位的Zn(Ⅱ)处于变形四面体中心,2中Cu(Ⅱ)中心拥有五配位的三角双锥几何构型。改变合成溶剂条件得到锯齿形一维链状配合物3,其四配位Cu(Ⅱ)中心展现出对称平面四边形构型。上述结果说明,金属离子几何构型以及合成溶剂可能对配合物结构具有重要影响。丰富的分子间氢键帮助3例配合物形成稳定的三维超分子结构。热重分析表明,3例配合物均具有良好的热稳定性。固体荧光分析表明配合物1具有较强荧光性,而配合物2和3荧光强度均远低于配体。 相似文献
14.
Priyadarshi Satpati 《International journal of quantum chemistry》2011,111(15):4241-4246
We propose that complexation of all metal antiaromatic Al4Li with C2H4 may lead to stable C2H4Al4Li species [II(b)]. Complexation leads to the electron transfer from Al4Li moiety to C2H4 and development of aromatic character in the Al4 ring. Our proposed compound C2H4Al4Li [II(b)] is very similar to the existing organic compound bicyclo[2.2.0]hex‐2‐ene [I(b)]. The complex C2H4Al4Li [II(b)] can be imagined as an analogue of bicyclo[2.2.0]hex‐2‐ene [I(b)] achieved by a simple replacement of C4H4 in the later with π‐isoelectronic Al4Li moiety in the former. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2010 相似文献
15.
Udier-Blagović M Morales De Tirado P Pearlman SA Jorgensen WL 《Journal of computational chemistry》2004,25(11):1322-1332
Absolute free energies of hydration (DeltaGhyd) have been computed for 25 diverse organic molecules using partial atomic charges derived from AM1 and PM3 wave functions via the CM1 and CM3 procedures of Cramer, Truhlar, and coworkers. Comparisons are made with results using charges fit to the electrostatic potential surface (EPS) from ab initio 6-31G* wave functions and from the OPLS-AA force field. OPLS Lennard-Jones parameters for the organic molecules were used together with the TIP4P water model in Monte Carlo simulations with free energy perturbation theory. Absolute free energies of hydration were computed for OPLS united-atom and all-atom methane by annihilating the solutes in water and in the gas phase, and absolute DeltaGhyd values for all other molecules were computed via transformation to one of these references. Optimal charge scaling factors were determined by minimizing the unsigned average error between experimental and calculated hydration free energies. The PM3-based charge models do not lead to lower average errors than obtained with the EPS charges for the subset of 13 molecules in the original study. However, improvement is obtained by scaling the CM1A partial charges by 1.14 and the CM3A charges by 1.15, which leads to average errors of 1.0 and 1.1 kcal/mol for the full set of 25 molecules. The scaled CM1A charges also yield the best results for the hydration of amides including the E/Z free-energy difference for N-methylacetamide in water. 相似文献
16.
The metal dinitrogen bonding in a wide series of terminal end-on dinitrogen complexes is investigated with the charge displacement analysis based on natural orbitals of chemical valence (CD-NOCV). The effect of the σ donation and π backdonation on the N N bond are discussed and compared with the observations for a series of carbonyl complexes, published in 2016 by Tarantelli et al. The σ donation is relative invariant over the series of dinitrogen complexes and has no significant effect on the N N bond strength, whereas the π backdonation causes a considerable elongation of the N N bond. Some uncommon examples of weakly bound dinitrogen with blue-shifted stretching frequency compared to free N2 (ν = 2330 cm−1) are known. The dinitrogen bonding in these complexes is simulated with a point charge. Apparently, electrostatics account for the shortened N─N bond in these systems. 相似文献
17.
Cortlandt G. Pierpont 《Journal of Chemical Sciences》2002,114(4):247-254
The properties of transition metal complexes containing catecholate and radical semiquinonate ligands have often been found
to be unusual and unexpected. Crystals of Rh(CO)2(3,6-DBSQ), containing the 3,6-di-tert-butyl-1,2-semiquinonate ligand, form as long thin needles that are observed to bend
reversibly upon irradiation with NIR light. Crystallographic characterization reveals a stacked solid state lattice with planar
molecules aligned with metal atoms atop one another. Electronic spectra recorded in the solid state and in solution show an
intense band at 1600 nm that maps the energy dependence of crystal bend angle. The transition is a property of the stacked
assembly, rather than of an individual complex molecule, and appears associated with an MLCT process that transfers charge
from an antibonding band formed by interacting Rhd
z
2
orbitals to the vacant quinone π* orbital. Related observations have been made on the [Co(μ-pyz)(3,6-DBSQ)(3,6-DBCat)]npolymer. Photomechanical properties appear associated with electronic transitions that lead to a physical change in axial
length of a linear polymer, coupled with a soft solid state lattice that permits axial contraction/expansion without crystal
fracture. 相似文献
18.
The electronegativity equalization method (EEM) was developed by Mortier et al. as a semiempirical method based on the density-functional theory. After parameterization, in which EEM parameters A(i), B(i), and adjusting factor kappa are obtained, this approach can be used for calculation of average electronegativity and charge distribution in a molecule. The aim of this work is to perform the EEM parameterization using the Merz-Kollman-Singh (MK) charge distribution scheme obtained from B3LYP/6-31G* and HF/6-31G* calculations. To achieve this goal, we selected a set of 380 organic molecules from the Cambridge Structural Database (CSD) and used the methodology, which was recently successfully applied to EEM parameterization to calculate the HF/STO-3G Mulliken charges on large sets of molecules. In the case of B3LYP/6-31G* MK charges, we have improved the EEM parameters for already parameterized elements, specifically C, H, N, O, and F. Moreover, EEM parameters for S, Br, Cl, and Zn, which have not as yet been parameterized for this level of theory and basis set, we also developed. In the case of HF/6-31G* MK charges, we have developed the EEM parameters for C, H, N, O, S, Br, Cl, F, and Zn that have not been parameterized for this level of theory and basis set so far. The obtained EEM parameters were verified by a previously developed validation procedure and used for the charge calculation on a different set of 116 organic molecules from the CSD. The calculated EEM charges are in a very good agreement with the quantum mechanically obtained ab initio charges. 相似文献
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The NDDO method has been extended to include elements withd-orbitals. A parametrization for the first-row transition metals is given, which has been worked out to describe structural properties of transition metal complexes. Applications of the method to the Jahn-Teller distortions of tetrachloro complexes are presented. The NDDO results are compared with those from CNDO and INDO calculations. It turns out that the NDDO method seems to be the most sensitive among the ZDO procedures. 相似文献