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1.
The present work provides a detailed investigation on the use of singular value decomposition (SVD) to solve the linear least-squares problem (LLS) for the purposes of obtaining potential-derived atom-centered point charges (PD charges) from the ab initio molecular electrostatic potential (V(QM)). Given the SVD of any PD charge calculation LLS problem, it was concluded that (1) all singular vectors are not necessary to obtain the optimal set of PD charges and (2) the most effective set of singular vectors do not necessarily correspond to those with the largest singular values. It is shown that the efficient use of singular vectors can provide statistically well-defined PD charges when compared with conventional PD charge calculation methods without sacrificing the agreement with V(QM). As can be expected, the methodology outlined here is independent of the algorithm for sampling V(QM) as well as the basis set used to calculate V(QM). An algorithm is provided to select the best set of singular vectors used for optimal PD charge calculations. To minimize the subjective comparisons of different PD charge sets, we also provide an objective criterion for determining if two sets of PD charges are significantly different from one another. 相似文献
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Electronic structures and properties of several anions, metal cations, and their complexes with neutral molecules were investigated at the HF/6‐31G** and B3LYP/6‐31G** levels of theory. Charges shifted from atomic sites due to atomic orbital hybridization called hybridization displacement charges (HDC) were investigated in detail. It has been found that many components of HDC are associated with each atom of ion that are shifted from the atomic sites, those associated with metal cations being shifted by large distances as found previously in electrically neutral systems. It is shown that atomic orbitals are appreciably rehybridized in going from neutral molecules to anions and cations. Molecular dipole moments and surface molecular electrostatic potentials (MEP) are obtained satisfactorily using HDC for the various types of species mentioned above. In the OH?? H2O complex, reversal of direction of shift of an HDC component associated with the hydrogen atom of H2O involved in hydrogen bonding, indicates that the hydrogen bond between OH? and H2O would have some covalent character. Other atomic site‐based point charge models cannot provide such information about the nature of bonding. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem 2007 相似文献
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Alexander Kane Ren-Fan Shao Joseph E Maclennan Lixing Wang David M Walba Noel A Clark 《Chemphyschem》2007,8(1):170-174
We demonstrate, both theoretically and experimentally, that it is possible to use an electric field to drive the formation of macroscopic chiral (conglomerate) domains from an initially homogeneous fluid racemate. Field-induced segregation is exhibited in a fluid smectic liquid-crystal phase of a racemic mesogen, wherein enantiomerically-enriched domains are readily identifiable by their chiral electro-optical response. The sharp field-generated boundaries that form between opposite-handed domains broaden by diffusion in the absence of field, but reform rapidly if the field is switched on again, providing unambiguous evidence for the field-driven physical separation of enantiomers. A mean-field model successfully describes the steady-state and the dynamic evolution of conglomerate formation. 相似文献
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Salvador Cardona‐Serra Luis Escalera‐Moreno José J. Baldoví Alejandro Gaita‐Ariño Juan M. Clemente‐Juan Eugenio Coronado 《Journal of computational chemistry》2016,37(13):1238-1244
SIMPRE is a fortran77 code which uses an effective electrostatic model of point charges to predict the magnetic behavior of rare‐earth‐based mononuclear complexes. In this article, we present SIMPRE1.2, which now takes into account two further phenomena. First, SIMPRE now considers the hyperfine and quadrupolar interactions within the rare‐earth ion, resulting in a more complete and realistic set of energy levels and wave functions. Second, and to widen SIMPRE's predictive capabilities regarding potential molecular spin qubits, it now includes a routine that calculates an upper‐bound estimate of the decoherence time considering only the dipolar coupling between the electron spin and the surrounding nuclear spin bath. Additionally, SIMPRE now allows the user to introduce the crystal field parameters manually. Thus, we are able to demonstrate the new features using as examples (i) a Gd‐based mononuclear complex known for its properties both as a single ion magnet and as a coherent qubit and (ii) an Er‐based mononuclear complex. © 2016 Wiley Periodicals, Inc. 相似文献
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Bruce L. Bush Christopher I. Bayly Thomas A. Halgren 《Journal of computational chemistry》1999,20(14):1495-1516
Bond-charge increments (BCIs) are additive parameters used to assign atomic charges for the MMFF force field. BCI parameters are classified parsimoniously according to two atom types and the bond order. We show how BCIs may be fitted rapidly by linear least squares to the calculated ab initio electrostatic potential (ESP) or to the electrostatic field. When applied simultaneously to a set of compounds or conformations, the method yields consensus values of the BCIs. The method can also derive conventional “ESP-fit” atomic charges with improved numerical stability. The method may be generalized to determine atom multipoles, multicenter charge templates, or electronegativities, but not polarizability or hardness. We determine 65 potential-derived (PD) BCI parameters, which are classified as in MMFF, by fitting the 6-31G* ESP or the electrostatic field of the 45 compounds in the original MMFF94 training set. We compare the consensus BCIs with classified BCIs that were fit to each molecule individually and with “unique-bond” BCIs (ESP-derived atom charges). Consensus BCIs give a satisfactory representation for about half of the structures and are robust to the adjustment of the alkyl CH bond increment to the zero value employed in MMFF94. We highlight problems at three levels: Point approximation: the potential near lone pairs on sulfur and to some extent nitrogen cannot be represented just by atom charges. Bond classification: BCIs classified according to MMFF atom types cannot represent all delocalized electronic effects. The problem is especially severe for bonds between atoms of equivalent MMFF type, whose BCI must be taken as zero. Consensus: discrepancies that occur in forming the consensus across the training set indicate the need for a more detailed classification of BCIs. Contradictions are seen (e.g., between acetic acid and acetone and between guanidine and formaldehydeimine). We then test the three sets of PD-BCIs in energy minimizations of hydrogen-bonded dimers. Unique-bond BCIs used with the MMFF buffered 14–7 potential reproduce unscaled quantum chemical dimer interaction energies within 0.9 kcal/mol root mean square (or 0.5, omitting two N-oxides). These energies are on average 0.7 (or 0.5) kcal/mol too weak to reproduce the scaled quantum mechanical (SQM) results that are a benchmark for MMFF parameterization. Consensus BCIs tend to weaken the dimer energy by a further 0.4–0.6 kcal/mol. Thus, consensus PD-BCIs can serve as a starting point for MMFF parameterization, but they require both systematic and individual adjustments. Used with a “harder” AMBER-like Lennard–Jones potential, unique-bond PD-BCIs without systematic adjustment give dimer energies in fairly good agreement with SQM. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 1495–1516, 1999 相似文献
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J. J. Fernndez R. Lpez I. Ema G. Ramírez J. Fernndez Rico 《International journal of quantum chemistry》2006,106(9):1986-1997
Many types of molecular integrals involving Slater functions can be expressed, with the ζ‐function method in terms of sets of one‐dimensional auxiliary integrals whose integrands contain two‐range functions. After reviewing the properties of these functions (including recurrence relations, derivatives, integral representations, and series expansions), we carry out a detailed study of the auxiliary integrals aimed to facilitate both the formal and computational applications of the ζ‐function method. The usefulness of this study in formal applications is illustrated with an example. The high performance in numerical applications is proved by the development of a very efficient program for the calculation of two‐center integrals with Slater functions corresponding to electrostatic potential, electric field, and electric field gradient. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006 相似文献
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Umbilics in a nematic layer can be seen as topological defects of a complex order parameter. Being analogous to vortex lines in superfluids or superconductors, they are much easier to handle. We describe classroom experiments on controlled generation of umbilics in a nematic layer with homeotropic anchoring conditions submitted to an electric field. For this purpose we submit nematic samples to magnetic fields created by small NdFeB magnets. Umbilics induced by applied fields are unveiled by observation between crossed polarisers in monochromatic or white light. We report also on the winding action of rotating localised magnetic fields and on the winding reversal induced by Poiseuille flows. 相似文献
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《Journal of computational chemistry》2017,38(6):319-335
The electronic absorption spectra of pyridine and nicotine in aqueous solution have been computed using a multistep approach. The computational protocol consists in studying the solute solvation with accurate molecular dynamics simulations, characterizing the hydrogen bond interactions, and calculating electronic transitions for a series of configurations extracted from the molecular dynamics trajectories with a polarizable QM/MM scheme based on the fluctuating charge model. Molecular dynamics simulations and electronic transition calculations have been performed on both pyridine and nicotine. Furthermore, the contributions of solute vibrational effect on electronic absorption spectra have been taken into account in the so called vertical gradient approximation. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. 相似文献
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《International journal of quantum chemistry》2018,118(8)
Efficient quantum chemical calculations of electrostatic properties, namely, the electron density (EDN), electrostatic potential (ESP), and electric field (EFL), were performed using the fragment molecular orbital (FMO) method. The numerical errors associated with the FMO scheme were examined at the HF, MP2, and RI‐MP2 levels of theory using 4 small peptides. As a result, the FMO errors in the EDN, ESP, and EFL were significantly smaller than the magnitude of the electron correlation effects, which indicated that the FMO method provides sufficiently accurate values of electrostatic properties. In addition, an attempt to reduce the computational effort was proposed by combining the FMO scheme and a point charge approximation. The error due to this approximation was examined using 2 proteins, prion protein and human immunodeficiency virus type 1 protease. As illustrative examples, the ESP values at the molecular surface of these proteins were calculated at the MP2 level of theory. 相似文献
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The effect of isodensity surface sampling on ESP derived charges and the effect of adding bondcenters on DMA derived charges 总被引：2，自引：0，他引：2
The effect of sampling the electrostatic potential around a molecule on the quality of electrostatic potential derived charges is investigated. In addition, the effect of the number of expansion sites in a Distributed Multipole Analysis (DMA) on the quality of charges fitted to the DMA derived electrostatic potential is investigated. Sampling on constant electron density surfaces gives a better fit between the quantum mechanical potential and the potential derived from the fitted charges, compared to sampling on a van der Waals surface composed of intersecting spheres. The fit between the electrostatic potential derived from point charges and the quantum mechanical potential becomes poorer with increasing quality of the employed basis set. The inclusion of bondcenters into the calculations improves the fit between the Quantum Mechanical (QM) electrostatic potential and the DMA derived potential. The number of expansion sites needed for an accurate approximation of the QM electrostatic potential increases with increasing quality of the used basis set. 相似文献
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Duan Y Wu C Chowdhury S Lee MC Xiong G Zhang W Yang R Cieplak P Luo R Lee T Caldwell J Wang J Kollman P 《Journal of computational chemistry》2003,24(16):1999-2012
Molecular mechanics models have been applied extensively to study the dynamics of proteins and nucleic acids. Here we report the development of a third-generation point-charge all-atom force field for proteins. Following the earlier approach of Cornell et al., the charge set was obtained by fitting to the electrostatic potentials of dipeptides calculated using B3LYP/cc-pVTZ//HF/6-31G** quantum mechanical methods. The main-chain torsion parameters were obtained by fitting to the energy profiles of Ace-Ala-Nme and Ace-Gly-Nme di-peptides calculated using MP2/cc-pVTZ//HF/6-31G** quantum mechanical methods. All other parameters were taken from the existing AMBER data base. The major departure from previous force fields is that all quantum mechanical calculations were done in the condensed phase with continuum solvent models and an effective dielectric constant of epsilon = 4. We anticipate that this force field parameter set will address certain critical short comings of previous force fields in condensed-phase simulations of proteins. Initial tests on peptides demonstrated a high-degree of similarity between the calculated and the statistically measured Ramanchandran maps for both Ace-Gly-Nme and Ace-Ala-Nme di-peptides. Some highlights of our results include (1) well-preserved balance between the extended and helical region distributions, and (2) favorable type-II poly-proline helical region in agreement with recent experiments. Backward compatibility between the new and Cornell et al. charge sets, as judged by overall agreement between dipole moments, allows a smooth transition to the new force field in the area of ligand-binding calculations. Test simulations on a large set of proteins are also discussed. 相似文献
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I. Ema R. López J. J. Fernández G. Ramírez J. F. Rico 《International journal of quantum chemistry》2008,108(1):25-39
The Gauss transform of Slater‐type orbitals is used to express several types of molecular integrals involving these functions in terms of simple auxiliary functions. After reviewing this transform and the way it can be combined with the shift operator technique, a master formula for overlap integrals is derived and used to obtain multipolar moments associated to fragments of two‐center distributions and overlaps of derivatives of Slater functions. Moreover, it is proved that integrals involving two‐center distributions and irregular harmonics placed at arbitrary points (which determine the electrostatic potential, field and field gradient, as well as higher order derivatives of the potential) can be expressed in terms of auxiliary functions of the same type as those appearing in the overlap. The recurrence relations and series expansions of these functions are thoroughly studied, and algorithms for their calculation are presented. The usefulness and efficiency of this procedure are tested by developing two independent codes: one for the derivatives of the overlap integrals with respect to the centers of the functions, and another for derivatives of the potential (electrostatic field, field gradient, and so forth) at arbitrary points. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008 相似文献
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Wei-Hong Chen Hui-Min He Ying Li Hui Yang Jia-Yuan Liu Dan Yu Di Wu Zhong-Jun Zhou Wei-Ming Sun Feng-Long Gu Zhi-Ru Li 《International journal of quantum chemistry》2019,119(21):e26005
A small Janus molecular dimer, as external electric field (Fz) manipulated both a molecular clam switch and a novel electric information storage unit, is found by quantum chemical computations for the first time. The molecular clam switching is intriguing and reversible. A critical Fz value of 95 × 10−4 au causes a dramatically open change in conformation from Closed form to Open form. And a small reversed electric field of Fz = −10 × 10−4 au performs a close change from Open form to Closed form. In the switching process, owing to the existence of a great electric dipole moment (μ) contrast between 0 and 22.13 D, the molecular clam switch may serve as an electric information storage unit. Gratifyingly, the reading, writing, and erasing of binary information on the electric information storage unit are easy. And further calculations show that Janus graphene fragment dimer can also serve as a molecular clam switch. Thus, this work proposes a new molecular switch prototype in the invention of artificial molecular machines, and a novel electric information storage unit in the field of molecular electronics. 相似文献
17.
A systematic analysis was performed on the suitability of the molecular electrostatic potential (MEP) and MEP-derived properties determined by means of density functional (DFT) methods. Attention was paid to the electrostatic potential (ESP) derived charges, the ESP and exact quantum mechanical dipole moments, the depth of MEP minima, and the MEP distribution in layers around the molecule for a large series of molecules. The electrostatic properties were determined at either local or nonlocal DFT levels using different functionals. The results were compared with the values estimated from quantum mechanical calculations performed at Hartree–Fock, Møller–Plesset up to fourth order, and CIPSI levels. The suitability of the MEP-derived properties estimated from DFT methods is discussed for application in different areas of chemical interest. © 1997 John Wiley & Sons, Inc. J Comput Chem 18 : 980–991, 1997 相似文献
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Nicolas G. Martinelli Yoann Olivier Dr. Stavros Athanasopoulos Dr. Mari‐Carmen Ruiz Delgado Dr. Kathryn R. Pigg Demétrio A. da Silva Filho Dr. Roel S. Sánchez‐Carrera Dr. Elisabetta Venuti Raffaele G. Della Valle Prof. Jean‐Luc Brédas Prof. David Beljonne Dr. Jérôme Cornil Dr. 《Chemphyschem》2009,10(13):2265-2273
We have performed classical molecular dynamics simulations and quantum‐chemical calculations on molecular crystals of anthracene and perfluoropentacene. Our goal is to characterize the amplitudes of the room‐temperature molecular displacements and the corresponding thermal fluctuations in electronic transfer integrals, which constitute a key parameter for charge transport in organic semiconductors. Our calculations show that the thermal fluctuations lead to Gaussian‐like distributions of the transfer integrals centered around the values obtained for the equilibrium crystal geometry. The calculated distributions have been plugged into Monte‐Carlo simulations of hopping transport, which show that lattice vibrations impact charge transport properties to various degrees depending on the actual crystal structure. 相似文献
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Patricio N. Romero-Hasler Lynn K. Kurihara Lamar O. Mair Irving N. Weinberg E. A Soto-Bustamante 《Liquid crystals》2020,47(2):169-178
ABSTRACT We study a nanocomposite consisting of a ferroelectric liquid crystal and a magnetic nanoparticle in order to explore the possibility of using it as a magnetic resonant imaging contrast agent which will measure a field of 20 V/m. To achieve this we use the ferroic properties exhibited by the nanocomposite. We used the ferroelectric liquid crystal 2-(4-((2-fluorooctyl)oxy)phenyl)-5-(octyloxy)pyrimidine mixed with FeCo nanoparticles nominally 2–3 nm in diameter in concentrations of 0.56, 4.3 and 10.8 wt%. The 10.8 wt% sample was chosen for our study because the nanoparticles acted as a lubricant for the ferroelectric liquid crystal. This concentration yields nanoparticle clusters in about 5 ? 10 μm diameter spherulites. An electric field as low as 5V/cm is enough to turn and realign the spherulites where the particles are contained. We estimate the value of the magnetic in a spehrulite and associate it to the number of spherulites aligned as a function of electric field. We find thus that we can achieve low electric fields. 相似文献
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Nicolas G. Martinelli Yoann Olivier Dr. Stavros Athanasopoulos Dr. Mari‐Carmen Ruiz Delgado Dr. Kathryn R. Pigg Demétrio A. da Silva Filho Dr. Roel S. Sánchez‐Carrera Dr. Elisabetta Venuti Raffaele G. Della Valle Prof. Jean‐Luc Brédas Prof. David Beljonne Dr. Jérôme Cornil Dr. 《Chemphyschem》2009,10(13):2158-2158