Fitted electronic density functions from H to Rn for use in quantum similarity measures: cis-diamminedichloroplatinum(II) complex as an application example

A consistent set of fitted electronic density functions was generated for the elements from hydrogen to radon using an algorithm based on the elementary Jacobi rotations (EJR) technique. The main distinguishing attribute of this fitting procedure is the production of approximated electronic density functions with positive definite expansion coefficients; in this way, the statistical meaning of the probability distribution is preserved. The methodology, which was fully described previously, was modified in this work to improve and accelerate the fitting procedure. This variation concerns the optimization method employed to obtain the optimal angle of the EJR, implementing an algorithm based on a Taylor series expansion. Additionally, a new 1S-Type Gaussian basis set for atoms H to Rn is presented, that was fitted from a primitive basis set of Huzinaga. Fitted density functions facilitate theoretical calculations over large molecules and may be employed in many areas of computational chemistry, for example, in quantum similarity measures (QSM). To verify the basis set, a sound example related to QSM applications is given. This corresponds to the comparison of experimental structures obtained from X-ray determination for cis-diamminedichloroplatinum(II) complex with optimized molecular geometries using several theoretical methods to quantify the differences between the analyzed levels of theory. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 911–920, 1999     

The role of orbital products in the optimized effective potential method

The orbital products of occupied and virtual orbitals are employed as an expansion basis for the charge density generating the local potential in the optimized effective potential method thus avoiding the use of auxiliary basis sets. The high computational cost arising from the quadratic increase of the dimension of this product basis with system size can be greatly reduced by elimination of the linearly dependent products according to a procedure suggested by Beebe and Linderberg [Int. J. Quantum Chem. 12, 683 (1977)]. Numerical results from this approach show a very good agreement with those obtained from balancing the auxiliary basis for the expansion of the local potential with the orbital basis set.     

An intrinsic localization procedure for active CAS SCF orbitals

An intrinsic localization criterion for the active (valence) orbitals of a CAS SCF wavefunction is presented. The localization criterion is based on minimization of the energy of a “perfect pairing” configuration. Equations for carrying out the localization in terms of an exponential transformation are developed. The technique can easily be incorporated into any MC SCF program. The CAS SCF wavefunction obtained using these localized active orbitals corresponds to a full VB calculation where the VB structures are built from orthogonal “molecule adapted minimal basis set atomic orbitals” and thus offers an interpretational advantage over the use of canonical CAS SCF orbitals. The method is applied to the 1,3-dipole, nitrone.     

Molecule intrinsic minimal basis sets. I. Exact resolution of ab initio optimized molecular orbitals in terms of deformed atomic minimal-basis orbitals

A method is presented for expressing the occupied self-consistent-field (SCF) orbitals of a molecule exactly in terms of chemically deformed atomic minimal-basis-set orbitals that deviate as little as possible from free-atom SCF minimal-basis orbitals. The molecular orbitals referred to are the exact SCF orbitals, the free-atom orbitals referred to are the exact atomic SCF orbitals, and the formulation of the deformed "quasiatomic minimal-basis-sets" is independent of the calculational atomic orbital basis used. The resulting resolution of molecular orbitals in terms of quasiatomic minimal basis set orbitals is therefore intrinsic to the exact molecular wave functions. The deformations are analyzed in terms of interatomic contributions. The Mulliken population analysis is formulated in terms of the quasiatomic minimal-basis orbitals. In the virtual SCF orbital space the method leads to a quantitative ab initio formulation of the qualitative model of virtual valence orbitals, which are useful for calculating electron correlation and the interpretation of reactions. The method is applicable to Kohn-Sham density functional theory orbitals and is easily generalized to valence MCSCF orbitals.     

Extended floating spherical Gaussian basis sets for molecules. Alternative correlating orbitals for molecular energy calculations

A procedure previously described for representing large basis SCF results in terms of a smaller floating spherical Gaussian orbital (FSGO) basis set is generalized to apply to the virtual orbitals from the SCF calculation. This provides a method for systematically reducing the dimensions of the virtual space or replacing the virtual orbitals with a simpler, compact basis set. The method is illustrated by application to Lill.     

An ab initio method for approximation of the frozen molecular fragment

An ab initio method for calculation on many-electron molecular systems with the approximation of the inactive part of a molecule by frozen molecular fragment is presented. In the following method the SCF calculations are performed in two series. First the molecular orbitals resulting from the first SCF calculation (modest basis set) are localized. In the second SCF run, the basis set is extended for the active part of the molecule, while molecular orbitals of the inactive part, selected from the localized set, are kept frozen. The results are in good agreement with the extended basis set calculation.     

An efficient self-consistent field method for large systems of weakly interacting components

An efficient method for removing the self-consistent field (SCF) diagonalization bottleneck is proposed for systems of weakly interacting components. The method is based on the equations of the locally projected SCF for molecular interactions (SCF MI) which utilize absolutely localized nonorthogonal molecular orbitals expanded in local subsets of the atomic basis set. A generalization of direct inversion in the iterative subspace for nonorthogonal molecular orbitals is formulated to increase the rate of convergence of the SCF MI equations. Single Roothaan step perturbative corrections are developed to improve the accuracy of the SCF MI energies. The resulting energies closely reproduce the conventional SCF energy. Extensive test calculations are performed on water clusters up to several hundred molecules. Compared to conventional SCF, speedups of the order of (N/O)2 have been achieved for the diagonalization step, where N is the size of the atomic orbital basis, and O is the number of occupied molecular orbitals.     

On the suitability of strictly localized orbitals for hybrid QM/MM calculations

In the QM/MM method we have developed (LSCF/MM), the QM and the MM parts are held together by means of strictly localized bonding orbitals (SLBOs). Generally these SLBOs are derived from localized bond orbitals (LBOs) that undergo tails deletion, resulting in a nonpredictable change of their properties. An alternative set of SLBOs is provided by the extremely localized molecular orbitals (ELMOs) approach, where the orbitals are rigorously localized on some prefixed atoms without tails on the other atoms of the molecule. A comparative study of SLBOs arising from various localization schemes and ELMOs is presented to test the reliability and the transferability of these functions within the Local Self-Consistent Field (LSCF) framework. Two types of chemical bonds were considered: C--C and C--O single bonds. The localized functions are obtained on the ethane and the methanol molecules, and are tested on beta-alanine and diethyl ether molecules. Moreover, the various protonation forms of beta-alanine have been investigated to illustrate how well the polarity variation of the chemical bond can be handled throughout a chemical process. At last, rotation energy profiles around C--C and C--O bonds are reproduced for butane and fluoromethanol. Energetic, geometric, as well as electronic factors all indicate that ELMO functions are much more transferable from one molecule to another, leading to results closer to the usual SCF reference than any other calculations involving any other localized orbitals. When the shape of the orbital is the most important factor then ELMO functions will perform as well as any other localized orbital.     

Variationally optimized basis orbitals for biological molecules

Numerical atomic basis orbitals are variationally optimized for biological molecules such as proteins, polysaccharides, and deoxyribonucleic acid within a density functional theory. Based on a statistical treatment of results of a fully variational optimization of basis orbitals (full optimized basis orbitals) for 43 biological model molecules, simple sets of preoptimized basis orbitals classified under the local chemical environment (simple preoptimized basis orbitals) are constructed for hydrogen, carbon, nitrogen, oxygen, phosphorous, and sulfur atoms, each of which contains double valence plus polarization basis function. For a wide variety of molecules we show that the simple preoptimized orbitals provide well convergent energy and physical quantities comparable to those calculated by the full optimized orbitals, which demonstrates that the simple preoptimized orbitals possess substantial transferability for biological molecules.     

Calculations using a set of evenly spaced S-type gaussian functions

A basis set of evenly spaced S-type Gaussian functions with common exponents is examined. Formulas for common one- and two-electron integrals are derived. Because of thesymmetry of this basis set, a very compact two-electron integral list is produced. The number of two-electron integrals that must be stored is approximately eight times the number of basis functions. Use of this basis set in an SCF calculation is examined. Numerical results show that this approach works well for molecules containing only small atoms such as hydrogen, helium, or lithium, but that the method has problems with the core orbitals of heavier atoms. Procedures for augementing this basis set in calculations involving heavier atoms are examined.     

Ab initio calculations on large molecules: The multiplicative integral approximation

In the multiplicative integral approximation (MIA), two-electron integrals are evaluated using an expansion of a product of two Gaussians in terms of auxiliary functions. An estimator of the error introduced by the approximation is incorporated in the self-consistent field (SCF) calculations and the integrals for which the error estimate is larger than a preset value are systematically corrected. In this way the results of a MIA-assisted calculation have the same accuracy as a conventional calculation. The full exploitation of the expansion technique while constructing the Fock-matrix allows important time savings. Results are presented for a number of test cases.     

All-electron density functional calculation on insulin with quasi-canonical localized orbitals

An all-electron density functional (DF) calculation on insulin was performed by the Gaussian-based DF program, ProteinDF. Quasi-canonical localized orbitals (QCLOs) were used to improve the initial guess for the self-consistent field (SCF) calculation. All calculations were carried out by parallel computing on eight processors of an Itanium2 cluster (SGI Altix3700) with a theoretical peak performance of 41.6 GFlops. It took 35 h for the whole calculation. Insulin is a protein hormone consisting of two peptide chains linked by three disulfide bonds. The numbers of residues, atoms, electrons, orbitals, and auxiliary functions are 51, 790, 3078, 4439, and 8060, respectively. An all-electron DF calculation on insulin was successfully carried out, starting from connected QCLOs. Regardless of a large molecule with complicated topology, the differences in the total energy and the Mulliken atomic charge between initial and converged wavefunctions were very small. The calculation proceeded smoothly without any trial and error, suggesting that this is a promising method to obtain SCF convergence on large molecules such as proteins.     

Generalized hybrid-orbital method for combining density functional theory with molecular mechanicals.

The generalized hybrid orbital (GHO) method has previously been formulated for combining molecular mechanics with various levels of quantum mechanics, in particular semiempirical neglect of diatomic differential overlap theory, ab initio Hartree-Fock theory, and self-consistent charge density functional tight-binding theory. To include electron-correlation effects accurately and efficiently in GHO calculations, we extend the GHO method to density functional theory in the generalized-gradient approximation and hybrid density functional theory (denoted by GHO-DFT and GHO-HDFT, respectively) using Gaussian-type orbitals as basis functions. In the proposed GHO-(H)DFT formalism, charge densities in auxiliary hybrid orbitals are included to calculate the total electron density. The orthonormality constraints involving the auxiliary Kohn-Sham orbitals are satisfied by carrying out the hybridization in terms of a set of L?wdin symmetrically orthogonalized atomic basis functions. Analytical gradients are formulated for GHO-(H)DFT by incorporating additional forces associated with GHO basis transformations. Scaling parameters are introduced for some of the one-electron integrals and are optimized to obtain the correct charges and geometry near the QM/MM boundary region. The GHO-(H)DFT method based on the generalized gradient approach (GGA) (BLYP and mPWPW91) and HDFT methods (B3 LYP, mPW1PW91, and MPW1 K) is tested-for geometries and atomic charges-against a set of small molecules. The following quantities are tested: 1) the C--C stretch potential in ethane, 2) the torsional barrier for internal rotation around the central C--C bond in n-butane, 3) proton affinities for a set of alcohols, amines, thiols, and acids, 4) the conformational energies of alanine dipeptide, and 5) the barrier height of the hydrogen-atom transfer between n-C4H10 and n-C4H9, where the reaction center is described at the MPW1 K/6-31G(d) level of theory.     

Study on the maximum accuracy of the pseudopotential density functional method with localized atomic orbitals versus plane-wave basis sets

A detailed study on the accuracy attainable with numerical atomic orbitals in the context of pseudopotential first-principles density functional theory is presented. Dimers of first- and second-row elements are analyzed: bond lengths, atomization energies, and Kohn-Sham eigenvalue spectra obtained with localized orbitals and with plane-wave basis sets are compared. For each dimer, the cutoff radius, the shape, and the number of the atomic basis orbitals are varied in order to maximize the accuracy of the calculations. Optimized atomic orbitals are obtained following two routes: (i) maximization of the projection of plane wave results into atomic orbital basis sets and (ii) minimization of the total energy with respect to a set of primitive atomic orbitals as implemented in the OPENMX software package. It is found that by optimizing the numerical basis, chemical accuracy can be obtained even with a small set of orbitals.     

Bond orbital framework for rapid calculation of environmental effects on molecular potential surfaces

A procedure is outlined to calculate rapidly potential surfaces of very large (bio) molecules. Using strictly localized orbitals as a basis set, the molecule is divided into a central part, treated at the SCF level, and the environment where the strictly localized character of the orbitals is maintained. Conformation of the active serine sidechain in α-chymotrypsin is discussed.     

Use of promolecular ASA density functions as a general algorithm to obtain starting MO in SCF calculations

Atomic shell approximation (ASA) constitutes a way to fit first‐order density functions to a linear combination of spherical functions. The ASA fitting method makes use of positive definite expansion coefficients to ensure appropriate probability distribution features. The ASA electron density is sufficiently accurate for the practical implementation of quantum similarity measures, as was proved in previous published work. Here, a new application of the ASA density formalism is analyzed, and employed to obtain an initial guess of the density matrix for SCF procedures. The number of cycles needed to assess the convergence criterion in electronic energy calculations appears comparable to or less than those obtained by other means. Several molecular structures of different classes, including organic systems and metal complexes, were chosen as representative test cases. In addition, an ASA basis set for atoms Sc‐Kr fitted to an ab initio 6‐311G basis set is also presented. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001     

Kohn-Sham Density Matrix and the Kernel Energy MethodSCI北大核心CSCD

The kernel energy method(KEM) has been shown to provide fast and accurate molecular energy calculations for molecules at their equilibrium geometries.KEM breaks a molecule into smaller subsets,called kernels,for the purposes of calculation.The results from the kernels are summed according to an expression characteristic of KEM to obtain the full molecule energy.A generalization of the kernel expansion to density matrices provides the full molecule density matrix and orbitals.In this study,the kernel expansion for the density matrix is examined in the context of density functional theory(DFT) Kohn-Sham(KS) calculations.A kernel expansion for the one-body density matrix analogous to the kernel expansion for energy is defined,and is then converted into a normalizedprojector by using the Clinton algorithm.Such normalized projectors are factorizable into linear combination of atomic orbitals(LCAO) matrices that deliver full-molecule Kohn-Sham molecular orbitals in the atomic orbital basis.Both straightforward KEM energies and energies from a normalized,idempotent density matrix obtained from a density matrix kernel expansion to which the Clinton algorithm has been applied are compared to reference energies obtained from calculations on the full system without any kernel expansion.Calculations were performed both for a simple proof-of-concept system consisting of three atoms in a linear configuration and for a water cluster consisting of twelve water molecules.In the case of the proof-of-concept system,calculations were performed using the STO-3 G and6-31 G(d,p) bases over a range of atomic separations,some very far from equilibrium.The water cluster was calculated in the 6-31 G(d,p) basis at an equilibrium geometry.The normalized projector density energies are more accurate than the straightforward KEM energy results in nearly all cases.In the case of the water cluster,the energy of the normalized projector is approximately four times more accurate than the straightforward KEM energy result.The KS density matrices of this study are applicable to quantum crystallography.     

Molecule intrinsic minimal basis sets. II. Bonding analyses for Si4H6 and Si2 to Si10

The method, introduced in the preceding paper, for recasting molecular self-consistent field (SCF) or density functional theory (DFT) orbitals in terms of intrinsic minimal bases of quasiatomic orbitals, which differ only little from the optimal free-atom minimal-basis orbitals, is used to elucidate the bonding in several silicon clusters. The applications show that the quasiatomic orbitals deviate from the minimal-basis SCF orbitals of the free atoms by only very small deformations and that the latter arise mainly from bonded neighbor atoms. The Mulliken population analysis in terms of the quasiatomic minimal-basis orbitals leads to a quantum mechanical interpretation of small-ring strain in terms of antibonding encroachments of localized molecular-orbitals and identifies the origin of the bond-stretch isomerization in Si4H6. In the virtual SCF/DFT orbital space, the method places the qualitative notion of virtual valence orbitals on a firm basis and provides an unambiguous ab initio identification of the frontier orbitals.