Atomic charges derived from electrostatic potentials: A detailed study

A new algorithm for fitting atomic charges to molecular electrostatic potentials is presented. This method is non-iterative and rapid compared to previous work. Results from a variety of gaussian basis sets, including STO-3G, 3-21G and 6-31G*, are presented. Charges for a representative collection of molecules, comprising both first and second row atoms and anions are tabulated. The effects of using experimental and optimized geometries are explored. Charges derived from these fits are found to adequately reproduce SCF dipole moments. A small split valence representation, 3-21G, appears to yield consistently good results in a reasonable amount of time.     

VESPA: A new,fast approach to electrostatic potential-derived atomic charges from semiempirical methods

An improved semiempirical method for computing electrostatic potential-derived atomic charges is described. It includes a very fast algorithm for the generation of the grid points around the molecule and the calculation of the electrostatic potential at these points. The dependency of the atomic point charges obtained on the number of grid points used in the fitting procedure is examined. For “buried” atoms a high density grid is necessary. It is possible to obtain 6–31G*-quality atom-centered point charges, even for phosphorus compounds, using AM1 or PM3. This approach can therefore be recommended for general use in QSAR or molecular mechanics for any organic and bioorganic system up to about 200 atoms. © 1997 by John Wiley & Sons, Inc. J Comput Chem 18: 744–756, 1997     

Atomic charges of cerbinal

The mol­ecule of the title compound, methyl 1-formyl-6-oxa-6H-indene-4-carboxyl­ate, C₁₁H₈O₄, is planar. There are weak C—H⋯O intramolecular interactions and an intermolecular hydrogen bond in the structure, and these influence the crystal packing.     

Atomic charges derived from a fast and accurate method for electrostatic potentials based on modified AM1 calculations

Atomic charges derived from a recently described approach to the very rapid computation of AM1 electrostatic potentials (ESP) accurately parallel, but are ca. 20% smaller than, the corresponding HF/6-31G* values. The dipole moments computed from the AM1 charges are virtually identical to those derived directly from the wave function and in rather better agreement with the experimental values than those computed using the HF/6-31G* charges. Unlike other approaches to the semiempirical calculation of ESP-derived charges, the present method also yields near HF/6-31G* quality potentials close to the molecular periphery. For medium-sized organic molecules (40-100 basis functions), the method is approximately two orders of magnitude faster than those involving prior deorthogonalization of AM1 wave function and explicit computation of the full ESP integral matrix. © 1994 by John Wiley & Sons, Inc.     

Faster gradients for semiempirical methods

A new algorithm for the numerical evaluation of gradients in semiempirical methods is described. The method is approximately twice as fast as the schemes currently employed and produces gradients of comparable accuracy. This method has been tested by comparing the results obtained by the new method with those of the previous numerical scheme, and also with those calculated analytically. The results of using the new gradients in geometry optimizations are also presented. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 629–635, 1999     

Atomic charges for molecular dynamics calculations

Atomic charges obtained with the fit of the ab initio electrostatic potential suffers of several defects, for instance, chemical meaning is not insured. We have employed a method recently put forward for deriving atomic charges which addresses the issue of chemical meaning and conformational transferability to N,N-dibutylacetamide and ethylenediaminetetraacetate. The charges have been used in molecular dynamics calculations where the interaction with a metallic cation is considered. We found structural parameters for the complexes in good agreement with the available experimental results.     

Consistent parametrization of semiempirical MO methods

The parametrization of semiempirical molecular orbital methods is reviewed. The parametrization procedures are classified in three categories. The newly proposed category of consistency of parameters in a row of elements is applied in SINDO 1 to the Si atom. The calculations on test molecules and silicon clusters demonstrate that significant improvements in accuracy can be obtained in this way. © 1992 John Wiley & Sons, Inc.     

Improved methods for semiempirical solvation models

We present improved algorithms for the SMx (x = 1, 1a, 2, 3) solvation models presented previously [see the overview in C. J. Cramer and D. G. Truhlar, J. Comp.-Aided Mol. Design, 6 , 629 (1992)]. These models estimate the free energy of solvation by augmenting a semiempirical Hartree-Fock calculation on the solute with the generalized Born (GB) model for electric polarization of the solvent and a surface tension term based on solvent-accessible surface area. This article presents three improvements in the algorithms used to carry out such calculations, namely (1) an analytical accessible surface area algorithm, (2) a more efficient radial integration scheme for the dielectric screening computation in the GB model, and (3) a damping algorithm for updating the GB contribution to the Fock update during the iterations to achieve a self-consistent field. Improvements (1) and (2) decrease the computer time, and improvement (3) leads to more stable convergence. Improvement (2) removes a small systematic numerical error that was explicitly absorbed into the parameterization in the SMx models. Therefore, we have adjusted the parameters for one of the previous models to yield essentially identical performance as was obtained originally while simultaneously taking advantage of improvement (2). The resulting model is called SM2.1. The fact that we obtain similar results after removing the systematic quadrature bias attests to the robustness of the original parameterization. © 1995 by John Wiley & Sons, Inc.     

Atomic charges from IR intensity parameters: theory,implementation and application

Abstract  

A computational method to extract atomic charges (IR charges) from DFT/ab initio-computed atomic polar tensors is presented and compared with commonly available population schemes. The procedure adopted and its implementation in a (freely available) code are also reported and commented. Thanks to the procedure developed, infrared charges can be now readily gathered also by non-experts, provided that Cartesian dipole derivatives from a quantum chemical calculation of the IR spectrum are available. The method has been applied for the calculation of IR charges of about 50 molecules: It performs well in describing peculiar intramolecular interactions, providing a picture of the molecular charge distribution coherent with the chemical intuition. A nice agreement is also found with charges obtained from Hirshfeld algorithm and from the fitting of the electrostatic potential (CHELPG and MK schemes). On this basis, we propose IR charges as a reliable, physically sound and easily accessible alternative to other charge parameters currently adopted.     

Potential energy integrals in semiempirical MO methods

The two-center core-electron attraction integral V_AB in zero-differential overlap semiempirical MO methods is examined. It is concluded that core-valence orthogonality and valence symmetrical orthogonalization effects must be considered, and that these effects provide justification for the CNDO /2 approximation V_AB = Z_BγAB.     

Comparison of various semiempirical MO LCAO methods

In an orthogonalized basis, the diagonal element F of the Fock operator, for a number of semiempirical MO LCAO methods, can be represented by a trinomial which is quadratic with respect to the Mulliken charge. The coefficients differ for different methods, depending on the manner in which the interelectronic interaction is taken into account. From a study, in general form, of the influence of change in the coefficients of the trinomial F on the bond order matrix, an explanation has been given for certain familiar calculation results: the equalization of the -charges on going from the Hückel method to the more advanced techniques, and the decrease in the covalent character of metal-ligand bonds when allowance is made for the interelectronic interaction in the calculations for complexes.In conclusion, we wish to thank V. D. Sutula and L. I. Chernyavskii for much valuable discussion.     

Circular dichroism of helical structures using semiempirical methods

A general semiempirical scheme has been elaborated to simulate circular dichroism (CD) spectra of supramolecular systems. This approach adopts the analytical method of Beck and Hohlneicher [Theor. Chem. Acc. 101, 297 (1999).] to evaluate the one- and two-center integrals over Slater atomic orbitals. The performance of the method, employing INDO/S and CNDO/S semiempirical parametrizations, has been assessed by considering (i) the effect of the size of the singly excited states manifold, (ii) the origin invariance, and (iii) comparisons with the experimental and other theoretical spectra of several helicenes as well as pyridine-pyrimidine oligomers, which can adopt helical conformations. The main results are (i) the INDO/S parametrization with rather small excitation manifolds is able to reproduce, at low computational costs, the experimental CD spectra of several helicenes as well as CD simulations performed at ab initio and time-dependent density functional theory level of approximation; (ii) in the series of homohelicenes, the rotatory strength of the lowest-energy band increases almost linearly with the size of the helix; (iii) as evidenced by the study of tetradodecyloxy helicene bisquinone, packing effects can change the sign of remarkable CD bands, which are used to assign the structure configuration.     

Comparison of semiempirical MO methods for open-shell systems

The use of AM1, MNDO, and MNDOC semiempirical MO methods for calculation of heats of formation and ionization potentials of a series of 38 radicals are described. AM1 and MNDO calculations are reported using both half-electron (HE) and Unrestricted Hartree Fock (UHF) wavefunctions. Results show the MNDOC method to give lowest overall errors, being slightly better than the HE-AM1 method. In all cases, the AM1 method shows considerable improvement over MNDO.     

Study of reaction mechanisms by semiempirical methods I

The author suggests a procedure offering the possibility to determine, with the use of a double iteration technique, the equilibrium geometry within the framework of a single calculation of the energy function. The method is used for the ground state and the lowest excited singlet state of formaldehyde and for the formyl radical. The individual contributions of the potential energy are discussed in brief.

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Zusammenfassung Der Autor schlÄgt ein Verfahren vor, das erlaubt, mittels einer Doppeliterationstechnik die Gleichgewichtsgeometrie im Laufe einer einzigen Berechnung der Energiefunktion zu bestimmen. Das Verfahren wird auf den Grund- und den ersten angeregten Zustand von Formaldehyd und auf das Formylradikal angewendet. Die einzelnen BeitrÄge zur potentiellen Energie werden kurz diskutiert.

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Résumé L'auteur propose une méthode par laquelle il est possible de déterminer par une technique iterative double la géométrie d'équilibre dans le cadre d'un seul calcul de la fonction énergétique. On a appliqué la méthode pour l'état fondamental et l'état excité le plus bas singulet de formaldehyde et pour HCO. On discute brevement les contributions singulaires de l'énergie potentielle.

     

Calculations of molecular vibrational frequencies using semiempirical methods

MINDO/3, MNDO, AM1, and PM3 calculations of molecular vibrational frequencies are reported for 61 molecules. All techniques were applied to both well-behaved and badly behaved systems. Overall, MINDO/3 and MNDO were found to contain rather large errors whereas AM1 and PM3 were relatively accurate. Since no technique does well for all molecules, the technique used should be chosen based on the molecular vibration of interest. In general, AM1 and PM3 together provide fairly accurate results.     

Extension of semiempirical methods to simulation of surfaces

Various approaches for surface simulation are described. They are based on free, saturated, and embedded clusters, as well as periodic models. The features of semiempirical methods are reviewed and ideas for their improvement are discussed. Special features of the structure and stability of clusters are presented which are suitable for the transition to the solid state. Linear and nonlinear relationships for binding energies and bond lengths in dependence of the average coordination number are discussed. Finally, a systematic way for the simulation of adsorption at ion crystal surfaces by model clusters is suggested. © 1996 John Wiley & Sons, Inc.     

Atomic charges in the multiple scattering molecular orbital method

The concept of atomic charges in molecular orbital theory is discussed. A definition which pays special attention to the behaviour of the orbitals close to the atomic nuclei, is suggested. This new definition is particularly simple to apply in the multiple scattering method. Some transition metal complexes are considered as examples. The existence of the back donation effect is demonstrated for a series of octahedral cyanides.Supported by NFR, the Swedish Natural Science Research Council.