Similarity of atoms in molecules

Similarity of atoms in molecules is quantitatively assessed with a measure that employs electron densities within respective atomic basins. This atomic similarity measure does not rely on arbitrary assumptions concerning basis functions or 'atomic orbitals', is relatively inexpensive to compute, and has straightforward interpretation. Inspection of similarities between pairs of carbon, hydrogen, and fluorine atoms in the CH[sub 4], CH[sub 3]F, CH[sub 2]F[sub 2], CHF[sub 3], CF[sub 4], C[sub 2]H[sub 2], C[sub 2]H[sub 4], and C[sub 2]H[sub 6] molecules, calculated at the MP2/6-311G[sup **] level of theory, reveals that the atomic similarity is greatly reduced by a change in the number or the character of ligands (i.e. the atoms with nuclei linked through bond paths to the nucleus of the atom in question). On the other hand, atoms with formally identical (i.e. having the same nuclei and numbers of ligands) ligands resemble each other to a large degree, with the similarity indices greater than 0.95 for hydrogens and 0.99 for non-hydrogens. 19 refs., 6 tabs.

[1]  R. Bader,et al.  Quantum Topology: Theory of Molecular Structure and its Change , 1980 .

[2]  Cheng Chang,et al.  Properties of atoms in molecules: atomic volumes , 1987 .

[3]  D. Goldfarb.  A family of variable-metric methods derived by variational means , 1970 .

[4]  R. Fletcher,et al.  A New Approach to Variable Metric Algorithms , 1970, Comput. J..

[5]  R. Bader,et al.  On the presence of non-nuclear attractors in the charge distributions of Li and Na clusters , 1987 .

[6]  G. Pacchioni,et al.  Charge density topological study of bonding in lithium clusters , 1987 .

[7]  R. Carbó,et al.  Molecular quantum similarity measures and N-dimensional representation of quantum objects. I. Theoretical foundations† , 1992 .

[8]  Jerzy Cioslowski,et al.  Covalent bond orders in the topological theory of atoms in molecules , 1991 .

[9]  D. Shanno.  Conditioning of Quasi-Newton Methods for Function Minimization , 1970 .

[10]  Todd A. Keith,et al.  Properties of atoms in molecules: additivity and transferability of group polarizabilities , 1992 .

[11]  Richard F. W. Bader.  A quantum theory of molecular structure and its applications , 1991 .

[12]  C. G. Broyden.  Quasi-Newton methods and their application to function minimisation , 1967 .

[13]  R. Bader.  Properties of atoms and bonds in carbocations , 1986 .

[14]  Jerzy Cioslowski,et al.  Topological properties of electron density in search of steric interactions in molecules : electronic structure calculations on ortho-substituted biphenyls , 1992 .

[15]  Friedrich Biegler-König,et al.  Calculation of the average properties of atoms in molecules. II , 1982 .

[16]  R. Bader,et al.  Theoretical construction of a polypeptide , 1992 .

[17]  M. Challacombe,et al.  Rapid evaluation of atomic properties with mixed analytical/numerical integration , 1993 .

[18]  R. Bader,et al.  Properties of atoms in molecules : magnetic susceptibilities , 1993 .

[19]  Eugene D. Fleischmann,et al.  Assessing molecular similarity from results of ab initio electronic structure calculations , 1991 .

[20]  R. Bader,et al.  Transferability of atomic properties and the theorem of Hohenberg and Kohn , 1988 .

[21]  Kenneth B. Wiberg,et al.  Properties of atoms in molecules: Dipole moments and transferability of properties , 1987 .

[22]  Ramon Carbo,et al.  How similar is a molecule to another? An electron density measure of similarity between two molecular structures , 1980 .

[23]  J. Cioslowski,et al.  Electronegativities in situ, bond hardnesses, and charge-transfer components of bond energies from the topological theory of atoms in molecules , 1993 .