The orbital-product expansion method for the evaluation of two-electron integrals applied to a calculation on MnO4

A previously described method for the evaluation of multi-centre integrals using gaussian function expansions of orbital products is rigorously tested. The ground state of the permanganate ion was studied by an ab initio SCF MO calculation using a minimal basis set of contracted gaussian functions of near Hartree-Fock accuracy. The two-electron integrals were estimated with considerable accuracy from moment-constrained expansions of the unique orbital products. The effect of errors in the integral estimation was considered.     

Weighted small gaussian expansions of Slater-type atomic orbitals

Small gaussian expansions of Slater-type atomic orbitals are generated under a wide range of radial weighting conditions by full least-squares procedures, and the quality of the wave functions obtained is examined for a particular expectation value, electron density at the nucleus.     

Another criterion for gaussian approximations of slater-type orbitals

An alternative criterion, which enforces gaussian expansions of Slater-type atomic orbitals to have similar shortrange and long-range suitabilities, is used. Such an approximation is deduced from weighted expansions recently proposed by Ehrenson in this journal. These new expansions should clarify scaling in molecular calculations.     

Hybrid HDMR method with an optimized hybridity parameter in multivariate function representation

High Dimensional Model Representation (HDMR) based methods are used to generate an approximation for a given multivariate function in terms of less variate functions. This paper focuses on Hybrid HDMR which is composed of Plain HDMR and Logarithmic HDMR. The Plain HDMR method works well for representing multivariate functions having additive nature. If the function under consideration has a multiplicative nature, then the Logarithmic HDMR method produces better approximation. Hybrid HDMR method aims to successfully represent a multivariate function having neither purely additive nor purely multiplicative nature under a hybridity parameter. The performance of the Hybrid HDMR method strongly depends on the value of this hybridity parameter because this parameter manages the contribution level of Plain and Logarithmic HDMR expansions. The main purpose of this work is to optimize the hybridity parameter to get the best approximations. Fluctuationlessness Approximation Theorem is used in this optimization process and in evaluating the multiple integrals appearing in HDMR based methods. A number of numerical implementations are given at the end of the paper to show the performance of our proposed method.     

From secondary structure to three-dimensional structure: Improved dihedral angle probability distribution function for use with energy searches for native structures of polypeptides and proteins

An improved scheme to help in the prediction of protein structure is presented. This procedure generates improved starting conformations of a protein suitable for energy minimization. Trivariate gaussian distribution functions for the π, ψ, and χ¹ dihedral angles have been derived, using conformational data from high resolution protein structures selected from the Protein Data Bank (PDB). These trivariate probability functions generate initial values for the π, ψ, and χ¹ dihedral angles which reflect the experimental values found in the PDB. These starting structures speed the search of the conformational space by focusing the search mainly in the regions of native proteins. The efficiency of the new trivariate probability distributions is demonstrated by comparing the results for the α-class polypeptide fragment, the mutant Antennapedia (C39 → S) homeodomain (2HOA), with those from two reference probability functions. The first reference probability function is a uniform or flat probability function and the second is a bivariate probability function for π and ψ. The trivariate gaussian probability functions are shown to search the conformational space more efficiently than the other two probability functions. The trivariate gaussian probability functions are also tested on the binding domain of Streptococcal protein G (2GB1), an α/β class protein. Since presently available energy functions are not accurate enough to identify the most native-like energy-minimized structures, three selection criteria were used to identify a native-like structure with a 1.90-Å rmsd from the NMR structure as the best structure for the Antennapedia fragment. Each individual selection criterion (ECEPP/3 energy, ECEPP/3 energy-plus-free energy of hydration, or a knowledge-based mean field method) was unable to identify a native-like structure, but simultaneous application of more than one selection criterion resulted in a successful identification of a native-like structure for the Antennapedia fragment. In addition to these tests, structure predictions are made for the Antennapedia polypeptide, using a Pattern Recognition-based Importance-Sampling Minimization (PRISM) procedure to predict the backbone conformational state of the mutant Antennapedia homeodomain. The ten most probable backbone conformational state predictions were used with the trivariate and bivariate gaussian dihedral angle probability distributions to generate starting structures (i.e., dihedral angles) suitable for energy minimization. The final energy-minimized structures show that neither the trivariate nor the bivariate gaussian probability distributions are able to overcome the inaccuracies in the backbone conformational state predictions to produce a native-like structure. Until highly accurate predictions of the backbone conformational states become available, application of these dihedral angle probability distributions must be limited to problems, such as homology modeling, in which only a limited portion of the backbone (e.g., surface loops) must be explored. © 1996 John Wiley & Sons, Inc.     

Polynomial expansion of basis sets: Alternatives to fully optimized exponents

Alternatives based on polynomial expansions of gaussian basis set exponents are introduced and evaluated. The formulas presented here outperform methods based upon the even-tempered formula or combinations of it. They closely match the performance of other methods based upon larger polynomial expansions of the logarithm of the exponents using the same or one less parameter per orbital angular symmetry.     

Incorporating specificity into optimization: evaluation of SPA using CSAR 2014 and CASF 2013 benchmarks

Scoring functions of protein–ligand interactions are widely used in computationally docking software and structure-based drug discovery. Accurate prediction of the binding energy between the protein and the ligand is the main task of the scoring function. The accuracy of a scoring function is normally evaluated by testing it on the benchmarks of protein–ligand complexes. In this work, we report the evaluation analysis of an improved version of scoring function SPecificity and Affinity (SPA). By testing on two independent benchmarks Community Structure-Activity Resource (CSAR) 2014 and Comparative Assessment of Scoring Functions (CASF) 2013, the assessment shows that SPA is relatively more accurate than other compared scoring functions in predicting the interactions between the protein and the ligand. We conclude that the inclusion of the specificity in the optimization can effectively suppress the competitive state on the funnel-like binding energy landscape, and make SPA more accurate in identifying the “native” conformation and scoring the binding decoys. The evaluation of SPA highlights the importance of binding specificity in improving the accuracy of the scoring functions.     

Auxiliary functions for molecular integrals with Slater‐type orbitals. II. Gauss transform methods

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     

Molecular electric polarizabilities. CI and explicitly correlated electric-field-variant functions. Calculation of the polarizability of H2

The concept of the so-called electric-field-variant (EFV) functions (functions with explicit dependence on the external electric field strength) is applied within the CI method. A similar treatment of the electric-field perturbation is also proposed for gaussian geminals. Both methods are illustrated by calculation of the static electric dipole polarizability of H₂. With variation of a single parameter, which enters both the perturbed function and the second-order perturbed energy, accurate polarizability values can be obtained without any explicit extension of the set of functions employed for the unperturbed system.     

Calculation of molecular integrals for systems confined by hard spherical walls: Use of the single‐center expansion of floating spherical gaussians

Assuming a gaussian basis set representation of atomic and molecular wave functions, the single‐center expansion of off‐centered spherical gaussian orbitals is exploited to calculate the one and two‐electron integrals for multielectronic atoms and molecules confined within hard spherical walls. As a validating test, the ground‐state energy of a helium atom positioned off‐center in a spherical box is calculated by applying the simplest form of the floating spherical gaussian orbital (FSGO) scheme, i.e., the use of a primitive basis set consisting of a single FSGO per electron pair. Comparison with corresponding recent accurate calculations gives supporting evidence of the adequacy of the method for its application to more elaborate gaussian‐type basis set representations for confined atoms and molecules. © 2001 John Wiley & Sons, Inc. Int J Quant Chem 83: 271–278, 2001     

A comparative study of semiempirical, ab initio, and DFT methods in evaluating metal-ligand bond strength, proton affinity, and interactions between first and second shell ligands in Zn-biomimetic complexes

Although theoretical methods are now available which give very accurate results, often comparable to the experimental ones, modeling chemical or biological interesting systems often requires less demanding and less accurate theoretical methods, mainly due to computer limitations. Therefore, it is crucial to know the precision of such less reliable methods for relevant models and data. This has been done in this work for small zinc-active site models including O- (H(2)O and OH(-)) and N-donor (NH(3) and imidazole) ligands. Calculations using a number of quantum mechanical methods were carried out to determine their precision for geometries, coordination number relative stability, metal-ligand bond strengths, proton affinities, and interaction energies between first and second shell ligands. We have found that obtaining chemical accuracy can be as straightforward as HF geometry optimization with a double-zeta plus polarization basis followed by a B3LYP energy calculation with a triple-zeta quality basis set including diffuse and polarization functions. The use of levels as low as PM3 geometry optimization followed by a B3LYP single-point energy calculation with a double-zeta quality basis including polarization functions already yields useful trends in bond length, proton affinities or bond dissociation energies, provided that appropriate caution is taken with the optimized structures. The reliability of these levels of calculation has been successfully demonstrated for real biomimetic cases.     

On the representation of coupled adiabatic potential energy surfaces using quasi-diabatic Hamiltonians: a distributed origins expansion approach

In two previous papers we have introduced a method to generate coupled quasi-diabatic Hamiltonians (H(d)) that are capable of representing adiabatic energies, energy gradients, and derivative couplings over a wide range of geometries including seams of conical intersection. In this work, two new synergistic features are introduced. Firstly, the functional form of H(d) is generalized. Rather than requiring there to be a low energy point of high symmetry to serve as the unique origin, functions centered on points distributed in nuclear coordinate space are used in the polynomials that comprise the matrix elements in H(d). The use of functions with distributed origins, allows reproduction of the ab initio data with lower order expansions, and offers the possibility of describing multichannel dissociation. The fitting algorithm is combined with a three-step procedure in which the domain of H(d) is extended from a core set of nuclear configurations to a region of nuclear coordinate space appropriate for nuclear dynamics, with a prescribed accuracy. This significant extension of the domain of definition compared to our original work, which is facilitated by the distributed origin approach, is achieved largely through the use of surface hopping trajectories. The 1,2(1)A states of NH(3), which provide an archetypical example of nonadiabatic dynamics, are used to demonstrate the utility of this approach. The representation describes 21 points on the 1(1)A-2(1)A seam of conical intersection and their local topography flawlessly and on the entire domain, the electronic structure data is represented to an accuracy of 77.00 (46.90) cm(-1), as measured by the root mean square (mean unsigned) error for energies lower than 50 000 cm(-1). This error is a factor of 10 lower than that of the most accurate representation of high quality ab initio data, on a comparable domain, previously reported for this system.     

Bessel-zernike discrete variable representation basis

The connection between the Bessel discrete variable basis expansion and a specific form of an orthogonal set of Jacobi polynomials is demonstrated. These so-called Zernike polynomials provide alternative series expansions of suitable functions over the unit interval. Expressing a Bessel function in a Zernike expansion provides a straightforward method of generating series identities. Furthermore, the Zernike polynomials may also be used to efficiently evaluate the Hankel transform for rapidly decaying functions or functions with finite support.     

Overlap Integrals Between Irregular Solid Harmonics and STOs Via the Fourier Transform Methods

In this paper, a unified analytical and numerical treatment of overlap integrals between Slater type orbitals (STOs) and irregular Solid Harmonics (ISH) with different screening parameters is presented via the Fourier transform method. Fourier transform of STOs is probably the simplest to express of overlap integrals. Consequently, it is relatively easy to express the Fourier integral representations of the overlap integrals as finite sums and infinite series of STOs, ISHs, Gegenbauer, and Gaunt coefficients. The another mathematical tools except for Fourier transform have used partial-fraction decomposition and Taylor expansions of rational functions. Our approach leads to considerable simplification of the derivation of the previously known analytical representations for the overlap integrals between STOs and ISHs with different screening parameters. These overlap integrals have also been calculated for extremely large quantum numbers using Gegenbauer, Clebsch-Gordan and Binomial coefficients. The accuracy of the numerical results is quite high for the quantum numbers of Slater functions, irregular solid harmonic functions and for arbitrary values of internuclear distances and screening parameters of atomic orbitals.     

Gaussian expansions of orbital products for the evaluation of two-electron integrals

A method is described for evaluating multicenter integrals over contracted gaussian-type orbitals by the use of gaussian expansion of orbital products. The expansions are determined by the method of non-linear least squares with constraints. There is no restriction upon the symmetry of the orbital product and the method is applicable to all products arising from s, p and d-type orbitals. Results are given to indicate the accuracy of the method.     

One-particle correlation function in evanescent wave dynamic light scattering

In order to interpret measured intensity autocorrelation functions obtained in evanescent wave scattering, their initial decay rates have been analyzed recently [P. Holmqvist, J. K. G. Dhont, and P. R. Lang, Phys. Rev. E 74, 021402 (2006); B. Cichocki, E. Wajnryb, J. Blawzdziewicz, J. K. G. Dhont, and P. R. Lang, J. Chem. Phys. 132, 074704 (2010); J. W. Swan and J. F. Brady, ibid. 135, 014701 (2011)]. A theoretical analysis of the longer time dependence of evanescent wave autocorrelation functions, beyond the initial decay, is still lacking. In this paper we present such an analysis for very dilute suspensions of spherical colloids. We present simulation results, a comparison to cumulant expansions, and experiments. An efficient simulation method is developed which takes advantage of the particular mathematical structure of the time-evolution equation of the probability density function of the position coordinate of the colloidal sphere. The computer simulation results are compared with analytic, first and second order cumulant expansions. The only available analytical result for the full time dependence of evanescent wave autocorrelation functions [K. H. Lan, N. Ostrowsky, and D. Sornette, Phys. Rev. Lett. 57, 17 (1986)], that neglects hydrodynamic interactions between the colloidal spheres and the wall, is shown to be quite inaccurate. Experimental results are presented and compared to the simulations and cumulant expansions.     

Parametric signal fitting by gaussian peak adjustment: A new multivariate curve resolution method for non-bilinear voltammetric measurements

A new methodology based on the fitting of signals to parametric functions is proposed for the multivariate curve resolution (MCR) analysis of overlapping and peak-shaped voltammetric signals which progressively get broader or narrower and move along the potential axis, thus causing a dramatic loss of linearity. The method is based on the least squares fitting of gaussian functions at both sides of the peaks by using adjustable parameters for the peak height, position and symmetry. It consists of several home-made programs written in Matlab environment, which are freely available as supplementary material of the present work. The application to the systems Zn(II)–oxalate, and to the phytochelatin PC₅ in a wide pH range provides excellent results as compared to these of more conventional linear methods, which raises good expectations about future application to electrochemical and even non-electrochemical data.     

Strategies for an efficient implementation of the Gauss-Bessel quadrature for the evaluation of multicenter integral over STFs

In a previous work, a new Gauss quadrature was introduced with a view to evaluate multicenter integrals over Slater-type functions efficiently. The complexity analysis of the new approach, carried out using the three-center nuclear integral as a case study, has shown that for low-order polynomials its efficiency is comparable to the SD. The latter was developed in connection with multi-center integrals evaluated by means of the Fourier transform of B functions. In this work we investigate the numerical properties of the Gauss-Bessel quadrature and devise strategies for an efficient implementation of the numerical algorithms for the evaluation of multi-center integrals in the framework of the Gaussian transform/Gauss-Bessel approach. The success of these strategies are essential to elaborate a fast and reliable algorithm for the evaluation of multi-center integrals over STFs.     

Economical geometry optimization in first row molecules with bond function augmented basis sets

Ab initio MO geometry optimization studies on a number of molecules containing first row atoms show that the use of gaussian bond functions in conjunction with the standard 4-31G basis sets enables geometry calculations closely approaching the accuracy of calculations using more extensive basis sets.