CheckDen, a program to compute quantum molecular properties on spatial grids.

CheckDen, a program to compute quantum molecular properties on a variety of spatial grids is presented. The program reads as unique input wavefunction files written by standard quantum packages and calculates the electron density rho(r), promolecule and density difference function, gradient of rho(r), Laplacian of rho(r), information entropy, electrostatic potential, kinetic energy densities G(r) and K(r), electron localization function (ELF), and localized orbital locator (LOL) function. These properties can be calculated on a wide range of one-, two-, and three-dimensional grids that can be processed by widely used graphics programs to render high-resolution images. CheckDen offers also other options as extracting separate atom contributions to the property computed, converting grid output data into CUBE and OpenDX volumetric data formats, and perform arithmetic combinations with grid files in all the recognized formats.

[1]  Chérif F. Matta,et al.  The Quantum Theory of Atoms in Molecules , 2007 .

[2]  James F. Harrison,et al.  On the role of the electron density difference in the interpretation of molecular properties , 2003 .

[3]  Axel D. Becke,et al.  A Simple Measure of Electron Localization in Atomic and Molecular-Systems , 1990 .

[4]  Hanno Essén,et al.  The characterization of atomic interactions , 1984 .

[5]  Á. M. Pendás,et al.  Electron-electron interactions between ELF basins , 2008 .

[6]  L. Pacios Changes of Electron Properties in the Formation of Hydrogen Bonds , 2006 .

[7]  Thomas Williams,et al.  Gnuplot 4.4: an interactive plotting program , 2010 .

[8]  Paul L. A. Popelier,et al.  Atoms in Molecules: An Introduction , 2000 .

[9]  E. Molins,et al.  Retrieving interaction potentials from the topology of the electron density distribution: The case of hydrogen bonds , 2000 .

[10]  E. Molins,et al.  About the evaluation of the local kinetic, potential and total energy densities in closed-shell interactions , 2001 .

[11]  R. Bader Atoms in molecules , 1990 .

[12]  Vladimir Tsirelson,et al.  Analyzing experimental electron density with the localized-orbital locator. , 2002, Acta crystallographica. Section B, Structural science.

[13]  Axel D. Becke,et al.  Chemical content of the kinetic energy density , 2000 .

[14]  S. J. Grabowski,et al.  Hydrogen Bonding—New Insights , 2006 .

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

[16]  A numerical study of molecular information entropies , 1994 .

[17]  L. Pacios,et al.  Approximate kinetic energy density for intermolecular regions in hydrogen bond dimers , 2001 .

[18]  Reinhard Nesper,et al.  A New Look at Electron Localization , 1991 .

[19]  A. Becke,et al.  Two functions of the density matrix and their relation to the chemical bond , 2002 .

[20]  K Schulten,et al.  VMD: visual molecular dynamics. , 1996, Journal of molecular graphics.

[21]  Ronald J. Gillespie,et al.  Chemical Bonding and Molecular Geometry: From Lewis to Electron Densities , 1972 .

[22]  Paul L. A. Popelier,et al.  MORPHY, a program for an automated “atoms in molecules” analysis , 1996 .

[23]  A. Savin,et al.  Classification of chemical bonds based on topological analysis of electron localization functions , 1994, Nature.

[24]  C. Gatti Chemical bonding in crystals: new directions , 2005 .

[25]  Peter Politzer,et al.  The fundamental nature and role of the electrostatic potential in atoms and molecules , 2002 .

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

[27]  R. Bader,et al.  Calculation of the average properties of atoms in molecules. II , 1981 .

[28]  Peter Politzer,et al.  Chemical Applications of Atomic and Molecular Electrostatic Potentials: "Reactivity, Structure, Scattering, And Energetics Of Organic, Inorganic, And Biological Systems" , 2013 .

[29]  Mark S. Gordon,et al.  Chapter 41 – Advances in electronic structure theory: GAMESS a decade later , 2005 .

[30]  Wilfried Langenaeker,et al.  Atomic charges, dipole moments, and Fukui functions using the Hirshfeld partitioning of the electron density , 2002, J. Comput. Chem..

[31]  P. Politzer,et al.  Calculation of electrostatic and polarization energies from electron densities. , 2004, The Journal of chemical physics.

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

[33]  Ramon Carbó-Dorca,et al.  Modeling Large Macromolecular Structures Using Promolecular Densities , 2002, J. Chem. Inf. Comput. Sci..

[34]  Density-difference maps in quantum chemistry , 1982 .

[35]  Y. Abramov On the Possibility of Kinetic Energy Density Evaluation from the Experimental Electron-Density Distribution , 1997 .

[36]  L. Pacios A theoretical study of the intramolecular interaction between proximal atoms in planar conformations of biphenyl and related systems , 2007 .

[37]  Amount of information present in the one-particle density matrix and the charge density , 1998 .

[38]  L. Pacios,et al.  Conformational changes of the electrostatic potential of biphenyl: A theoretical study , 2006 .

[39]  I. Good,et al.  The Maximum Entropy Formalism. , 1979 .

[40]  Kwang S. Kim,et al.  Theory and applications of computational chemistry : the first forty years , 2005 .

[41]  R. Parr,et al.  Information theory, atoms in molecules, and molecular similarity. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[42]  Rodolfo O. Esquivel,et al.  Molecular similarity based on information entropies and distances , 1998 .

[43]  Bernard Silvi,et al.  Computational Tools for the Electron Localization Function Topological Analysis , 1999, Comput. Chem..

[44]  Shubin Liu,et al.  On the relationship between densities of Shannon entropy and Fisher information for atoms and molecules. , 2007, The Journal of chemical physics.

[45]  Heiko Jacobsen,et al.  Localized-orbital locator (LOL) profiles of chemical bonding , 2008 .

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

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

[48]  G. A. Jeffrey,et al.  An Introduction to Hydrogen Bonding , 1997 .

[49]  B. Silvi How topological partitions of the electron distributions reveal delocalization , 2004 .

[50]  Luis Fernández Pacios,et al.  Check Den: a computer program to generate 1D, 2D and 3D grids of functions dependent on the molecular ab initio electron density , 2003, Comput. Biol. Chem..

[51]  Conrad C. Huang,et al.  UCSF Chimera—A visualization system for exploratory research and analysis , 2004, J. Comput. Chem..