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PREDICCIÓN DE ESTRUCTURAS DE CRISTALES CON MOLÉCULAS FLEXIBES EN SU CELDA

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PREDICCIÓN DE ESTRUCTURAS DE CRISTALES CON MOLÉCULAS FLEXIBES EN SU CELDA. V. Bazterra, M. B. Ferraro, J. C. Facelli. Departamento de Física Facultad de Ciencias Exactas y Naturales Universidad de Buenos Aires. 2007. AIM OF THE APPLICATION. Crystal engeneering. Pharmaceutical design.

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PREDICCIÓN DE ESTRUCTURAS DE CRISTALES CON MOLÉCULAS FLEXIBES EN SU CELDA

V. Bazterra, M. B. Ferraro,

J. C. Facelli

Departamento de Física

Facultad de Ciencias Exactas y Naturales

Universidad de Buenos Aires

2007

slide2

AIM OF THE APPLICATION

  • Crystal engeneering
  • Pharmaceutical design
  • Polymorphism
  • Application in materials.
slide3

Why GENETIC ALGORITHMS?

  • Difficult crystal prediction from first principles.
  • Polymorphic forms in organic crystals
  • Useful to model atomic and molecular clusters.
slide4

MGAC Crystal Structure Prediction CapabilitiesVictor E. Bazterra, Matthew Thorley, Marta B. Ferraro, and Julio C. FacelliJ. Chem. Theory Comput. 2007, 3, 201-209

  • Search for crystal structures within any symmetry group and with an arbitrary number of molecules and molecular types per asymmetric unit.
  • Search structures using either the rigid or flexible molecule models.
  • Automatically generate the molecule’s force field using existing force field libraries.
  • Increase the sampling power and the complexity of molecules amenable to CSP studies using the parallel and distributed computing capabilities of the system.
  • Automatically compare, sort and archive the most relevant structures in a user database.
genetic coding

Molecular center of mass  {R1, R2,…Rn} 

Its orientations  {1 , 2 ,…\n }

Relevant dihedral angles  {1 , 2 , …..n }

Space group and lattice parameters  {a,b,c,,,}

GENETIC CODING

(Rigid bodies)

semi rigid approximation
SEMI-RIGID APPROXIMATION

-Crystallographic group

DATA

-Number of molecules in the cell

MOLECULES:

-center of mass positions

-relative orientations

PARAMETERS

-Lattice axis a, b, c

-Lattice angles, , , 

-AMBER FORCE FIELD

-CHARMm FORCE FIELD

in CHARMM code

APTITUDE FUNCTION

semirigid approximation
SEMIRIGID APPROXIMATION

-crystallographic cell axes and angles.

-positions of the center of masss of each molecule.

-Euler angles respect to the unit cell.

-Ndihe molecular angles.

Rigid bodies with flexible chains

K=6+Z(6+Ndihed.)

Parameters to be optimized

population analysis
Population analysis

Evolution of the

population energy

Hystogram of the evolution

csp2007 methodology
CSP2007 Methodology
  • Local optimization using CHARMM 6, 7 with the GAFF 14 parameters. cutoff of 14 Å, and the electrostatic interactions were calculated using the Ewald technique.
  • Atomic charges, , using the restrained electrostatic potential approach implemented on the RESP program. Gaussian03 32 package at HF/6-31G* level.
  • Restricted searches using 30 individuals in the population for up to 130 generations, for the 14 most common symmetry groups for organic molecules, P1, P-1, P21, C2, Pc, Cc, P21/c, C2/c, P212121, Pca21, Pna21, Pbcn, Pbca and Pnma.
  • For each molecule we performed between 150 and 200 runs leading to at least 100 complete runs with 130 generations.
  • From these short lists we manually detected clearly unphysical structures and duplicated ones that were not eliminated in the previous step that were identified by comparison of their XRPD spectra
molecule xii
Molecule XII

ACRY02

Space group: Pbca

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  • Test predictions of benchmark crystals
  • Prediction of experimental data
  • Incorporation of additional pseudopotentials
  • Cosmetics and website.
slide24

Marta Ferraro

Víctor Bazterra

Departamento de Física

University of Buenos Aires

Argentina

Center for High

Performance Computing

University of Utah

Julio C. Facelli

Martin Cuma

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