Method and algorithm of obtaining the molecular intrinsic characteristic contours (MICCs) of organic molecules

The molecular intrinsic characteristic contour (MICC) is defined as the set of all the classical turning points of electron movement in a molecule. Studies on the MICCs of some medium organic molecules, such as dimethylether, acetone, and some homologues of alkanes, alkenes, and alkynes, as well as the electron density distributions on the MICCs, are shown for the first time. Results show that the MICC is an intrinsic approach to shape and size of a molecule. Unlike the van der Waals hard‐sphere model, the MICC is a smooth contour, and it has a clear physical meaning. Detailed investigations on the cross‐sections of MICCs have provided a kind of important information about atomic size changing in the process of forming molecules. Studies on electron density distribution on the MICC not only provide a new insight into molecular shape, but also show that the electron density distribution on the boundary surface relates closely with molecular properties and reactivities. For the homologues of alkanes, R  outH , Dmin, and Dmax (the minimum and maximum of electron density on the MICC), all have very good linear relationships with minus of the molecular ionization potential. This work may serve as a basis for exploring a new reactivity indicator of chemical reactions and for studying molecular shape properties of large organic and biological molecules. © 2004 Wiley Periodicals, Inc. J Comput Chem 26: 35–47, 2005

[1]  K. D. Gibson,et al.  Exact calculation of the volume and surface area of fused hard-sphere molecules with unequal atomic radii , 1987 .

[2]  Armin A. Weiser,et al.  Neighbor‐list reduction: Optimization for computation of molecular van der Waals and solvent‐accessible surface areas , 1998 .

[3]  R. J. Boyd.  The relative sizes of atoms. , 1977 .

[4]  Iñaki Tuñón,et al.  GEPOL: An improved description of molecular surfaces. III. A new algorithm for the computation of a solvent‐excluding surface , 1994, J. Comput. Chem..

[5]  Zhong-Zhi Yang,et al.  The changing features of the molecular intrinsic characteristic contours of H2 molecule in the ground and first excited states calculated by an ab initio method , 2002 .

[6]  Modeling hydrophobic solvation of nonspherical systems: Comparison of use of molecular surface area with accessible surface area , 1997 .

[7]  Zhong-Zhi Yang,et al.  Molecular intrinsic characteristic contours of small organic molecules containing oxygen atom , 2003 .

[8]  M. L. Connolly.  Solvent-accessible surfaces of proteins and nucleic acids. , 1983, Science.

[9]  Zhong-Zhi Yang,et al.  Theoretical study on characteristic ionic radii , 1998 .

[10]  C. Chothia,et al.  Principles of protein–protein recognition , 1975, Nature.

[11]  J. Tomasi,et al.  Effective generation of molecular cavities in polarizable continuum model by DefPol procedure , 1999, J. Comput. Chem..

[12]  Jacopo Tomasi,et al.  DefPol: New procedure to build molecular surfaces and its use in continuum solvation methods , 1998 .

[13]  F M Richards,et al.  Areas, volumes, packing and protein structure. , 1977, Annual review of biophysics and bioengineering.

[14]  Y. Marcus.  The sizes of molecules—revisited , 2003 .

[15]  Zhong-Zhi Yang,et al.  Exploration of the potential acting on an electron within diatomic molecules , 2002 .

[16]  Zhong-Zhi Yang,et al.  A characteristic molecular contour evaluated by a theoretical method , 1998 .

[17]  Enrico O. Purisima,et al.  Molecular surface generation using marching tetrahedra , 1998, J. Comput. Chem..

[18]  A. Y. Meyer.  The size of molecules , 1987 .

[19]  Michel Petitjean,et al.  On the analytical calculation of van der Waals surfaces and volumes: Some numerical aspects , 1994, J. Comput. Chem..

[20]  C. Chothia,et al.  Hydrophobic bonding and accessible surface area in proteins , 1974, Nature.

[21]  Jan B. F. N. Engberts,et al.  STRUCTURE AND REACTIVITY IN AQUEOUS SOLUTION , 1994 .

[22]  Zhong-Zhi Yang,et al.  Theory on the molecular characteristic contour (II) —— Molecular intrinsic characteristic contours of several typical organic molecules , 2005 .

[23]  Oleg V. Tsodikov,et al.  Novel computer program for fast exact calculation of accessible and molecular surface areas and average surface curvature , 2002, J. Comput. Chem..

[24]  B. Lee,et al.  The interpretation of protein structures: estimation of static accessibility. , 1971, Journal of molecular biology.

[25]  Emil Alexov,et al.  Rapid grid‐based construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: Applications to the molecular systems and geometric objects , 2002, J. Comput. Chem..

[26]  Graham J. L. Kemp,et al.  Fast computation, rotation, and comparison of low resolution spherical harmonic molecular surfaces , 1999, J. Comput. Chem..

[27]  W. C. Still,et al.  Approximate atomic surfaces from linear combinations of pairwise overlaps (LCPO) , 1999 .

[28]  P. Laug,et al.  Generation of finite element meshes on molecular surfaces , 2003 .

[29]  A. Olson,et al.  Approximation and characterization of molecular surfaces , 1993, Biopolymers.

[30]  P. Ayers.  Strategies for computing chemical reactivity indices , 2001 .

[31]  J. Andrew Grant,et al.  A smooth permittivity function for Poisson–Boltzmann solvation methods , 2001, J. Comput. Chem..

[32]  J. Murray,et al.  Molecular electrostatic potentials : concepts and applications , 1996 .

[33]  Werner Braun,et al.  Exact and efficient analytical calculation of the accessible surface areas and their gradients for macromolecules , 1998 .

[34]  Zhong-Zhi Yang,et al.  The molecular intrinsic characteristic contours (MICCs) of some small organic molecules , 2003 .

[35]  B. Bush,et al.  Macromolecular shape and surface maps by solvent exclusion. , 1978, Proceedings of the National Academy of Sciences of the United States of America.

[36]  Thanh N. Truong,et al.  Optimized atomic radii for quantum dielectric continuum solvation models , 1995 .

[37]  Goran Krilov,et al.  On characterization of molecular surfaces , 1997 .

[38]  Matthias Keil,et al.  Pattern recognition strategies for molecular surfaces. I. Pattern generation using fuzzy set theory , 2002, J. Comput. Chem..

[39]  Richard M. Jackson,et al.  Protein surface area defined , 1993, Nature.

[40]  Wensheng Cai,et al.  New approach for representation of molecular surface , 1998, J. Comput. Chem..

[41]  E. Paci,et al.  On the volume of macromolecules , 1997 .

[42]  M. Spackman,et al.  Molecular surfaces from the promolecule: A comparison with Hartree–Fock ab initio electron density surfaces , 2000 .

[43]  J. A. Grant,et al.  A Gaussian Description of Molecular Shape , 1995 .

[44]  Estanislao Silla,et al.  GEPOL: An improved description of molecular surfaces. I. Building the spherical surface set , 1990 .

[45]  Christian Silvio Pomelli,et al.  A Symmetry adapted tessellation of the GEPOL surface: applications to molecular properties in solution , 2001, Journal of Computational Chemistry.

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

[47]  Peter Politzer,et al.  Electrostatic potentials and covalent radii , 2003, J. Comput. Chem..

[48]  Jörg Weiser,et al.  Optimization of Gaussian surface calculations and extension to solvent‐accessible surface areas , 1999, J. Comput. Chem..

[49]  J. Crabbe,et al.  Molecular modelling: Principles and applications , 1997 .

[50]  E. Davidson,et al.  Evaluation of a characteristic atomic radius by an ab initio method , 1997 .

[51]  F. Richards.  The interpretation of protein structures: total volume, group volume distributions and packing density. , 1974, Journal of molecular biology.

[52]  Iñaki Tuñón,et al.  GEPOL: An improved description of molecular surfaces II. Computing the molecular area and volume , 1991 .

[53]  Roberto Cammi,et al.  Analytical first derivatives of molecular surfaces with respect to nuclear coordinates , 1996, J. Comput. Chem..

[54]  Brian J. Smith,et al.  Atomic radii: Incorporation of solvation effects , 1998 .

[55]  Zhong-Zhi Yang,et al.  Polarization and bonding of the intrinsic characteristic contours of hydrogen and fluorine atoms of forming a hydrogen fluoride molecule based on an ab initio study. , 2004, The Journal of chemical physics.

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

[57]  Charles L. Brooks,et al.  New analytic approximation to the standard molecular volume definition and its application to generalized Born calculations , 2003, J. Comput. Chem..

[58]  Matthias Keil,et al.  Pattern recognition strategies for molecular surfaces. II. Surface complementarity , 2002, J. Comput. Chem..