| Quantum Interpretative Techniques and Force
fields packages |
Softwares Development
You can find here links to various software projects
I. Quantum Interpretative Techniques
- EPLF (Electron Pair Localization Function)
The Electron Pair Localization Function is a function defined in the three-dimensional space. It measures the degree of pairing of electrons in a molecule, with an increasing
value as the electron pairing increases. Therefore chemical bonds, core domains and lone pairs can be visualized.
The new EPLF code can be downloaded
here:
Link
If you use it, please cite:
"Electron Pair Localization Function (EPLF) for Density Functional Theory and
ab initio wave function-based methods : a new tool for chemical
interpretation"
A. Scemama, R. Chaudret, M. Caffarel, J-P. Piquemal, J. Chem. Theor. Comput., 2011, 7, 618
DOI: 10.1021/ct1005938
- NCI (Non Covalent interaction)
This code enables graphical visualization of inter and intramolecular non-covalent interactions (i.e. hydrogen bonds, steric clashes and van der Waals) in systems ranging from
small molecules to large biosystems
The NCI code can be downloaded here:
Link
If you use it, please cite:
"NCIPLOT: a program for plotting non-covalent interaction regions"
J. Contreras-Garcia, E. R. Johnson, S. Keinan, R. Chaudret, J-P. Piquemal, D.
Beratan and W. Yang, J. Chem. Theory. Comput., 2011, 7, 625.
DOI: 10.1021/ct100641a
- TopMod
TopMod is a software which enables to carry out the ELF and AIM topological analyses for molecular wave functions expressed in terms of
Gaussian primitives.
You can download the current TopMod 09 version by Bernard Silvi here:
Link
If you use it, please cite:
-->S. Noury, X. Krokidis, F. Fuster and B. Silvi, Comput. Chem.,
1999, 23, 597.
I am currently working on the 2012 release of the code. Please contact me
concerning the 2012 version. An updated version of the pop90 code is already available (see DEMEP analysis below)
For a review concerning the applications of the Electron Localization Function
to biological systems:
"What can be learnt on biological or biomimetic systems with the topological
analysis of the electron localization function?"
J-P Piquemal, J. Pilmé, O. Parisel, H. Gérard, I. Fourré, J. Bergès,
C. Gourlaouen, A. de la Lande, M. C. van Severen and B. Silvi,
Int. J. Quant. Chem., 2008, 108, 1951.
DOI: 10.1002/qua.21711
- DEMEP Analysis (Distributed Multipoles analysis from ELF Partition)
To use it you'll need to download also Topmod. This version is a modified Pop90 code (from TopMod) allowing the evaluation of
local ELF or AIM electrostatic moments.ELF moments allow the evaluation of non atomic electrostatic quantities on bond, lone pairs, pi systems giving access to chemically
intuitive new analyses.
The latest version of the DEMEP code can be downloaded here:
Link
If you use it, please cite:
"Advancing beyond Charge Analysis using the Electronic Localization Function:
Chemically Intuitive Distribution of Electrostatic Moments."
J. Pilme and J-P Piquemal, 2008, J. Comput. Chem., 29, 1440
DOI: 10.1002/jcc.20904
II. New generation Force Fields
SCOPE OF THE SIBFA POLARIZABLE FORCE FIELD
SIBFA (Sum of Interactions Between Fragments Ab initio computed) is
a polarizable fore field formulated and calibrated on the basis of
ab initio supermolecule computations (1). Using distributed multipoles and
, its purpose is to enable the
simultaneous and reliable computations of both intermolecular and conformational
energies governing the binding specificities of biologically and pharmacologically
relevant molecules.
The intermolecular interaction energy is computed as a sum of five separate
contributions:
DEtot = EMTP + Erep + Epol + Ect + Edisp
EMTP is the electrostatic (multipolar) contribution, computed with distributed
multipoles derived from the ab initio Hartree-Fock wave function of the constitutive
fragments. The multipoles (up to quadrupoles) are located on the atoms and
bond barycenters (2). Erep is the short-range repulsion energy, computed as a sum
of bond-bond, bond-lone pair, and lone pair-lone pair interactions. Epol is the
polarization energy contribution, computed with distributed, anisotropic polarizabilities
. These are located on the centroids of the localized orbitals, heteroatoms
and bond barycenters (3). Ect is the charge-transfer energy, in which a coupling
with the polarization is introduced, and Edisp is the dispersion energy
contribution.
The intra-molecular energy in a flexible molecule is computed as a sum of inter-
fragment interaction energies between the fragments making up the molecule and
using a similar formulation.
The calculation of solvation energies (DH and DG) can be done using a Continuum
reaction field procedure (4) in which the potential exerted by the solute on the
solvent is computed with the same set of distributed multipoles as for DE.
Energy-minimization is done using the 'Merlin' software (5). A 'Generalized Simulated
Anneling Procedure' (6) was recently integrated to assist in searches for
other minima in the potential energy surface.
SIBFA is a joint project of René Descartes (Paris V) and
Pierre et Marie Curie (Paris VI) Universities.
To test SIBFA : contact us !!
Nohad Gresh (at Univ. Paris V)
Jean-Philip Piquemal (at Univ. Paris VI)
New Release includes :
New Intermolecular and intramolecular potentials (for flexible macromolecules)
- advanced multipolar electrostatic including generalized penetration effects (7)
- new short range repulsion.(8)
- DFT based correlated potentials.(8a)
- open shell cation treatment.(9)
- Molecular Dynamics
- Particle Mesh Ewald (in progress)
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A review paper is available:
Anisotropic, polarizable molecular mechanics studies of inter-, intra-molecular interactions, and ligand-macromolecule complexes. A bottom-up strategy.
N. Gresh, G. A. Cisneros, T. A. Darden and J-P Piquemal, J. Chem.
Theo. Comput., 2007, 3, 1960. DOI: 10.1021/ct700134r
REFERENCES :
updating
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RECENT SUPPLEMENTARY MATERIALS :
Antony, Piquemal, Gresh, J. Comp. Chem. 2005, 26, 1147
Download (WORD format .doc)
Roux, Gresh, Perera, Piquemal, Salmon, J. Comp. Chem. 2007,
Download (format .pdb)
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|
| Gaussian Electrostatic Model (GEM) |
GEM is a force field based on density fitting developed in
collaboration with G. Andres Cisneros
at Wayne State
The figure above shows the electrostatic potential (ESP) of a water molecule
calculated with Merz-Kollman point charges (MK), GEM (P1 auxiliary basis set)
and a quantum approach (B3LYP DFT functional).
More details soon ! (see Publications page)
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