Ab initio quality one‐electron properties of large molecules: Development and testing of molecular tailoring approach

The development of a linear‐scaling method, viz. “molecular tailoring approach” with an emphasis on accurate computation of one‐electron properties of large molecules is reported. This method is based on fragmenting the reference macromolecule into a number of small, overlapping molecules of similar size. The density matrix (DM) of the parent molecule is synthesized from the individual fragment DMs, computed separately at the Hartree–Fock (HF) level, and is used for property evaluation. In effect, this method reduces the O(N3) scaling order within HF theory to an n·O(N′3) one, where n is the number of fragments and N′, the average number of basis functions in the fragment molecules. An algorithm and a program in FORTRAN 90 have been developed for an automated fragmentation of large molecular systems. One‐electron properties such as the molecular electrostatic potential, molecular electron density along with their topography, as well as the dipole moment are computed using this approach for medium and large test chemical systems of varying nature (tocopherol, a model polypeptide and a silicious zeolite). The results are compared qualitatively and quantitatively with the corresponding actual ones for some cases. This method is also extended to obtain MP2 level DMs and electronic properties of large systems and found to be equally successful. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 484–495, 2003

[1]  W. G. Richards,et al.  Rapid evaluation of shape similarity using Gaussian functions , 1993, J. Chem. Inf. Comput. Sci..

[2]  Li,et al.  Density-matrix electronic-structure method with linear system-size scaling. , 1993, Physical review. B, Condensed matter.

[3]  Gustavo E. Scuseria,et al.  A quantitative study of the scaling properties of the Hartree–Fock method , 1995 .

[4]  Paul G. Mezey,et al.  Ab Initio Quality Electron Densities for Proteins: A MEDLA Approach , 1994 .

[5]  R. Mcweeny.  Perturbation Theory for the Fock-Dirac Density Matrix , 1962 .

[6]  Yang,et al.  Direct calculation of electron density in density-functional theory. , 1991, Physical review letters.

[7]  S. Goedecker.  Linear scaling electronic structure methods , 1999 .

[8]  Darrin M. York,et al.  Electronic structure properties of solvated biomolecules: A quantum approach for macromolecular characterization , 2000 .

[9]  R. Bader.  Atoms in molecules : a quantum theory , 1990 .

[10]  S. L. Dixon,et al.  Semiempirical molecular orbital calculations with linear system size scaling , 1996 .

[11]  Shridhar R. Gadre,et al.  Molecular Tailoring Approach for Simulation of Electrostatic Properties , 1994 .

[12]  Mark S. Gordon,et al.  General atomic and molecular electronic structure system , 1993, J. Comput. Chem..

[13]  Michael J. Frisch,et al.  Achieving Linear Scaling for the Electronic Quantum Coulomb Problem , 1996, Science.

[14]  Paul G. Mezey,et al.  Ab initio quality properties for macromolecules using the ADMA approach , 2003, J. Comput. Chem..

[15]  Alistair P. Rendell,et al.  The Potassium Ion Channel: Comparison of Linear Scaling Semiempirical and Molecular Mechanics Representations of the Electrostatic Potential , 2001 .

[16]  Weitao Yang,et al.  A density‐matrix divide‐and‐conquer approach for electronic structure calculations of large molecules , 1995 .

[17]  Shridhar R. Gadre,et al.  Development of a restricted Hartree—Fock program INDMOL on PARAM: A highly parallel computer , 1993, J. Comput. Chem..

[18]  Paul G. Mezey,et al.  Macromolecular density matrices and electron densities with adjustable nuclear geometries , 1995 .

[19]  Daw.  Model for energetics of solids based on the density matrix. , 1993, Physical review. B, Condensed matter.

[20]  C. Carter,et al.  Active Species for the Ground-State Complex of Cytidine Deaminase: A Linear-Scaling Quantum Mechanical Investigation , 1998 .

[21]  Warren J. Hehre,et al.  AB INITIO Molecular Orbital Theory , 1986 .

[22]  S. R. Gadre,et al.  Molecular electrostatics. A comprehensive topographical approach , 1992 .

[23]  C. F. Matta.  Theoretical Reconstruction of the Electron Density of Large Molecules from Fragments Determined as Proper Open Quantum Systems: The Properties of the Oripavine PEO, Enkephalins, and Morphine , 2001 .

[24]  Kenneth M. Merz,et al.  Fully Quantum Mechanical Description of Proteins in Solution. Combining Linear Scaling Quantum Mechanical Methodologies with the Poisson−Boltzmann Equation , 1999 .

[25]  Paul G. Mezey,et al.  Ab Initio-Quality Electrostatic Potentials for Proteins: An Application of the ADMA Approach , 2002 .

[26]  David L. Beveridge,et al.  Approximate molecular orbital theory , 1970 .

[27]  K. Merz,et al.  Implementation and Testing of a Frozen Density Matrix−Divide and Conquer Algorithm , 1999 .

[28]  Gustavo E. Scuseria,et al.  Linear Scaling Density Functional Calculations with Gaussian Orbitals , 1999 .

[29]  Matt Challacombe,et al.  A simplified density matrix minimization for linear scaling self-consistent field theory , 1999 .

[30]  S. L. Dixon,et al.  Fast, accurate semiempirical molecular orbital calculations for macromolecules , 1997 .

[31]  F. Escudero,et al.  Atoms in molecules , 1982 .

[32]  P. Schleyer.  Encyclopedia of computational chemistry , 1998 .

[33]  Kenneth M. Merz,et al.  Divide and Conquer Interaction Energy Decomposition , 1999 .

[34]  J. Almlöf,et al.  Principles for a direct SCF approach to LICAO–MOab‐initio calculations , 1982 .

[35]  Michael J. Frisch,et al.  Achieving linear scaling in exchange-correlation density functional quadratures , 1996 .