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Abstract It is demonstrated that semiempirical methods give electrostatic potential (ESP) derived atomic point charges that are in reasonable agreement with ab initio ESP charges. Furthermore, we find that MNDO ESP charges are superior to AM1 ESP charges in correlating with ESP charges derived from the 6‐31G* basis set. Thus, it is possible to obtain 6‐31G* quality point charges by simply scaling MNDO ESP charges. The charges are scaled in a linear ( y = Mx ) manner to conserve charge. In this way researchers desiring to carry out force field simulations or minimizations can obtain charges by using MNDO, which requires much less computer time than the corresponding 6‐31G* calculation.
We present the first global parameterization and validation of a novel charge model, called AM1-BCC, which quickly and efficiently generates high-quality atomic charges for computer simulations of organic molecules in polar media. The goal of the charge model is to produce atomic charges that emulate the HF/6-31G* electrostatic potential (ESP) of a molecule. Underlying electronic structure features, including formal charge and electron delocalization, are first captured by AM1 population charges; simple additive bond charge corrections (BCCs) are then applied to these AM1 atomic charges to produce the AM1-BCC charges. The parameterization of BCCs was carried out by fitting to the HF/6-31G* ESP of a training set of >2700 molecules. Most organic functional groups and their combinations were sampled, as well as an extensive variety of cyclic and fused bicyclic heteroaryl systems. The resulting BCC parameters allow the AM1-BCC charging scheme to handle virtually all types of organic compounds listed in The Merck Index and the NCI Database. Validation of the model was done through comparisons of hydrogen-bonded dimer energies and relative free energies of solvation using AM1-BCC charges in conjunction with the 1994 Cornell et al. forcefield for AMBER.(13) Homo- and hetero-dimer hydrogen-bond energies of a diverse set of organic molecules were reproduced to within 0.95 kcal/mol RMS deviation from the ab initio values, and for DNA dimers the energies were within 0.9 kcal/mol RMS deviation from ab initio values. The calculated relative free energies of solvation for a diverse set of monofunctional isosteres were reproduced to within 0.69 kcal/mol of experiment. In all these validation tests, AMBER with the AM1-BCC charge model maintained a correlation coefficient above 0.96. Thus, the parameters presented here for use with the AM1-BCC method present a fast, accurate, and robust alternative to HF/6-31G* ESP-fit charges for general use with the AMBER force field in computer simulations involving organic small molecules.
We show that D-branes, extended objects defined by mixed Dirichlet-Neumann boundary conditions, break half the supersymmetries of the type II superstring and carry a complete set of electric and magnetic Ramond-Ramond charges. The product of the electric and magnetic charges is a single Dirac unit, and the quantum of charge is that required by string duality. This is strong evidence that D-branes are intrinsic to type II string theory and are the Ramond-Ramond sources needed for string duality. Also, we find in the IIa string a 9-form potential, which gives an effective cosmological constant.
ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP modelChristopher I. Bayly, Piotr Cieplak, Wendy Cornell, and Peter A. KollmanCite this: J. Phys. Chem. 1993, 97, 40, 10269–10280Publication Date (Print):October 1, 1993Publication History Published online1 May 2002Published inissue 1 October 1993https://pubs.acs.org/doi/10.1021/j100142a004https://doi.org/10.1021/j100142a004research-articleACS PublicationsRequest reuse permissionsArticle Views12411Altmetric-Citations6126LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access options Get e-Alerts
Abstract We present an approach for deriving net atomic charges from ab initio quantum mechanical calculations using a least squares fit of the quantum mechanically calculated electrostatic potential to that of the partial charge model. Our computational approach is similar to those presented by Momany [ J. Phys. Chem. , 82 , 592 (1978)], Smit, Derissen, and van Duijneveldt [ Mol. Phys. , 37 , 521 (1979)], and Cox and Williams [ J. Comput. Chem. , 2 , 304 (1981)], but differs in the approach to choosing the positions for evaluating the potential. In this article, we present applications to the molecules H 2 O, CH 3 OH, (CH 3 ) 2 O, H 2 CO, NH 3 , (CH 3 O) 2 PO , deoxyribose, ribose, adenine, 9‐CH 3 adenine, thymine, 1‐CH 3 thymine, guanine, 9‐CH 3 guanine, cytosine, 1‐CH 3 cytosine, uracil, and 1‐CH 3 uracil. We also address the question of inclusion of “lone pairs,” their location and charge.
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We outline details about an extension of the tight-binding (TB) approach to improve total energies, forces, and transferability. The method is based on a second-order expansion of the Kohn-Sham total energy in density-functional theory (DFT) with respect to charge density fluctuations. The zeroth order approach is equivalent to a common standard non-self-consistent (TB) scheme, while at second order a transparent, parameter-free, and readily calculable expression for generalized Hamiltonian matrix elements may be derived. These are modified by a self-consistent redistribution of Mulliken charges (SCC). Besides the usual ``band structure'' and short-range repulsive terms the final approximate Kohn-Sham energy additionally includes a Coulomb interaction between charge fluctuations. At large distances this accounts for long-range electrostatic forces between two point charges and approximately includes self-interaction contributions of a given atom if the charges are located at one and the same atom. We apply the new SCC scheme to problems where deficiencies within the non-SCC standard TB approach become obvious. We thus considerably improve transferability.
Abstract This paper addresses the issues of charging, rate control and routing for a communication network carrying elastic traffic, such as an ATM network offering an available bit rate service. A model is described from which max‐min fairness of rates emerges as a limiting special case; more generally, the charges users are prepared to pay influence their allocated rates. In the preferred version of the model, a user chooses the charge per unit time that the user will pay; thereafter the user's rate is determined by the network according to a proportional fairness criterion applied to the rate per unit charge. A system optimum is achieved when users' choices of charges and the network's choice of allocated rates are in equilibrium.
The so-called D4 model is presented for the accurate computation of London dispersion interactions in density functional theory approximations (DFT-D4) and generally for atomistic modeling methods. In this successor to the DFT-D3 model, the atomic coordination-dependent dipole polarizabilities are scaled based on atomic partial charges which can be taken from various sources. For this purpose, a new charge-dependent parameter-economic scaling function is designed. Classical charges are obtained from an atomic electronegativity equilibration procedure for which efficient analytical derivatives with respect to nuclear positions are developed. A numerical Casimir-Polder integration of the atom-in-molecule dynamic polarizabilities then yields charge- and geometry-dependent dipole-dipole dispersion coefficients. Similar to the D3 model, the dynamic polarizabilities are precomputed by time-dependent DFT and all elements up to radon (Z = 86) are covered. The two-body dispersion energy expression has the usual sum-over-atom-pairs form and includes dipole-dipole as well as dipole-quadrupole interactions. For a benchmark set of 1225 molecular dipole-dipole dispersion coefficients, the D4 model achieves an unprecedented accuracy with a mean relative deviation of 3.8% compared to 4.7% for D3. In addition to the two-body part, three-body effects are described by an Axilrod-Teller-Muto term. A common many-body dispersion expansion was extensively tested, and an energy correction based on D4 polarizabilities is found to be advantageous for larger systems. Becke-Johnson-type damping parameters for DFT-D4 are determined for more than 60 common density functionals. For various standard energy benchmark sets, DFT-D4 slightly but consistently outperforms DFT-D3. Especially for metal containing systems, the introduced charge dependence of the dispersion coefficients improves thermochemical properties. We suggest (DFT-)D4 as a physically improved and more sophisticated dispersion model in place of DFT-D3 for DFT calculations as well as other low-cost approaches like semi-empirical models.
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ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTConversion of light to electricity by cis-X2bis(2,2'-bipyridyl-4,4'-dicarboxylate)ruthenium(II) charge-transfer sensitizers (X = Cl-, Br-, I-, CN-, and SCN-) on nanocrystalline titanium dioxide electrodesM. K. Nazeeruddin, A. Kay, I. Rodicio, R. Humphry-Baker, E. Mueller, P. Liska, N. Vlachopoulos, and M. GraetzelCite this: J. Am. Chem. Soc. 1993, 115, 14, 6382–6390Publication Date (Print):July 1, 1993Publication History Published online1 May 2002Published inissue 1 July 1993https://doi.org/10.1021/ja00067a063RIGHTS & PERMISSIONSArticle Views26519Altmetric-Citations5393LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (2 MB) Get e-Alertsclose Get e-Alerts
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peer reviewed
SUPERFLIP is a computer program that can solve crystal structures from diffraction data using the recently developed charge-flipping algorithm. It can solve periodic structures, incommensurately modulated structures and quasicrystals from X-ray and neutron diffraction data. Structure solution from powder diffraction data is supported by combining the charge-flipping algorithm with a histogram-matching procedure. SUPERFLIP is written in Fortran90 and is distributed as a source code and as precompiled binaries. It has been successfully compiled and tested on a variety of operating systems.
An improvement to the grid-based algorithm of Henkelman et al. for the calculation of Bader volumes is suggested, which more accurately calculates atomic properties as predicted by the theory of Atoms in Molecules. The CPU time required by the improved algorithm to perform the Bader analysis scales linearly with the number of interatomic surfaces in the system. The new algorithm corrects systematic deviations from the true Bader surface, calculated by the original method and also does not require explicit representation of the interatomic surfaces, resulting in a more robust method of partitioning charge density among atoms in the system. Applications of the method to some small systems are given and it is further demonstrated how the method can be used to define an energy per atom in ab initio calculations.
The galvanostatic charge and discharge of a lithium anode/solid polymer separator/insertion cathode cell is modeled using concentrated solution theory. The model is general enough to include a wide range of polymeric separator materials, lithium salts, and composite insertion cathodes. Insertion of lithium into the active cathode material is simulated using superposition, thus greatly simplifying the numerical calculations. Variable physical properties are permitted in the model. The results of a simulation of the charge/discharge behavior of the system are presented. Criteria are established to assess the importance of diffusion in the solid matrix and transport in the electrolyte. Consideration is also given to various procedures for optimization of the utilization of active cathode material.
ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStructural Changes Accompanying Intramolecular Electron Transfer: Focus on Twisted Intramolecular Charge-Transfer States and StructuresZbigniew R. Grabowski, Krystyna Rotkiewicz, and Wolfgang RettigView Author Information Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw, Poland, and Institute of Chemistry, Akademia Świȩtokrzyska, Chȩcińska 5, 25-020 Kielce, Poland Institute of Chemistry, Humboldt University, Brook-Taylor-Strasse 2, D-12489 Berlin, Germany Cite this: Chem. Rev. 2003, 103, 10, 3899–4032Publication Date (Web):September 17, 2003Publication History Received20 June 2001Published online17 September 2003Published inissue 1 October 2003https://pubs.acs.org/doi/10.1021/cr940745lhttps://doi.org/10.1021/cr940745lresearch-articleACS PublicationsCopyright © 2003 American Chemical SocietyRequest reuse permissionsArticle Views35683Altmetric-Citations3094LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Fluorescence,Molecules,Polarity,Reaction products,Solvents Get e-Alerts
A systematic study of metal ion doping in quantum (Q)-sized (2-4 nm) TiO_2 colloids is performed by measuring their photoreactivities and the transient charge carrier recombination dynamics. The presence of metal ion dopants in the TiO_2 crystalline matrix significantly influences photoreactivity, charge carrier recombination rates, and interfacial electron-transfer rates. The photoreactivities of 21 metal ion-doped colloids are quantified in terms of both the conduction band electron reduction of an electron acceptor (CCl_4 dechlorination) and the valence band hole oxidation of an electron donor (CHCl_3 degradation). Doping with Fe^(3+), Mo^(5+), Ru^(3+), Os^(3+), Re^(5+), V^(4+), and Rh^(3+) at 0.1-0.5 at.% significantly increases the photoreactivity for both oxidation and reduction while Co^(3+) and Al^(3+) doping decreases the photoreactivity. The transient absorption signals upon laser flash photolysis (λ_(ex) = 355 nm) at λ = 600 nm are extended up to 50 ms for Fe^(3+)-, V^(4+)-, Mo^(5+)-, and Ru^(3+)-doped TiO_2 while the undoped Q-sized TiO_2 shows a complete "blue electron" signal decay within 200 μs. Co^(3+)- and Al^(3+)-doped TiO_2 are characterized by rapid signal decays with a complete loss of absorption signals within 5 μs. The quantum yields obtained during CW photolyses are quantitatively correlated with the measured transient absorption signals of the charge carriers. Photoreactivities \nare shown to increase with the relative concentration of trapped charge carriers. The photoreactivity of doped TiO_2 appears to be a complex function of the dopant concentration, the energy level of dopants within the TiO_2 lattice, their d electronic configuration, the distribution of dopants, the electron donor concentration, and the light intensity.