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Structure Solution from Powder Data-II: Real Space Methods

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Structure Solution from Powder Data-II: Real Space Methods Structure Solution from Powder Data-II: Powder from Solution Structure Real Space Methods Space Real Bangalore, India - Crystallographic Computing School (15th-20th August 2017) Crystal structure can be described as a combination of building blocks Spectroscopic can be usefultechniques NMR) (MS, It is necessaryknow the to connectivity. molecular atom Building starting model Building starting model molecule polyhedron Bangalore, India - Crystallographic Computing School (15th-20th August 2017) Password: IUCR2017 Password: Login: CCS2017 http://www.ba.ic.cnr.it/ochemdb/ programs Optimize molecular geometry Check for similar molecules Building starting model Building starting model by computational chemistry in databases orin the literature Bangalore, India - Crystallographic Computing School (15th-20th August 2017) Non-commercial database are in arein database Non-commercial Database Other databases File format: http://www.crystallography.net/ COD (inorganics, intermetallics):elements, minerals & ICSD http://www.ccdc.cam.ac.uk/ CSD (Cambridge Structural (Cambridge Database)(organics organometallics):& (Crystallography Database) Open (general database): (Inorganic Crystal Structure Database) , MINCRYST CIF (Crystallographic Information File) CIF (Crystallographic Crystal Structure Databases :ICDD PDF-4+, Crystal Structure Databases , , Zeolite StructuresDatabase red AmericanMineralogist Crystal Structure , ... ... , http://icsd.ill.fr/ Bangalore, India - Crystallographic Computing School (15th-20th August 2017) Otherdatabases Chemical Chemical file formats 2D molecular structures molecular must2D be optimized beingbefore Drugbank: Drugbank: Chemistry WebBook: NIST PubChem: http://www.drugbank.ca/ https://pubchem.ncbi.nlm.nih.gov/ Free Chemistry Databases Free Chemistry Databases : ZINC, : eMolecules, ChEBI, NMRShiftDB, ... used for used solutionstructure : sdf, mol, mol2, cml, SMILES http://webbook.nist.gov/chemistry/ Bangalore, India - Crystallographic Computing School (15th-20th August 2017) Three levelsThree of theory ORCA, Q-Chem,ORCA, Molpro, etc. octopus, Programs: Strategy: functional theory ( Ab initio Semi-empirical methods ( Molecular-mechanics force fields ( MM → SI →DFT methods: Hartree–Fock methods, density MOPAC, Gamess, NWChem, Gaussian, ABINIT, ABINIT, Gamess, Gaussian, NWChem, MOPAC, Geometry optimization Geometry optimization DFT ) SE ) MM ) ) Bangalore, India - Crystallographic Computing School (15th-20th August 2017) Some free available software Some free available A molecule editor allows editor molecule A Gabedit: Gabedit: - MarvinSketch - Avogadro - ACD/ChemSketch Create input file for the quantum-chemistry calculations file input for the Create quantum-chemistry calculations Optimize the geometry forceby method field or format2D 3D in Sketch molecules Read output files of the most common computational packages of files the output mostpackages Read computational common http://gabedit.sourceforge.net/ http://avogadro.openmolecules.net/wiki/Main_Page http://www.chemaxon.com/products/marvin/ Molecule editor Molecule editor http://www.acdlabs.com Bangalore, India - Crystallographic Computing School (15th-20th August 2017) 2-(4-Hydroxy-2-oxo-2,3-dihydro-1,3-benzothiazol-7-yl) ethylammonium chloride P 21/a P 3D structure optimization structure 3D Building starting model Building starting model N N dof frag = + 6 3 2 + = 2 .cif, .frac .pdb, .fhz, .mop, .mol, .mol2, Save as Save Bangalore, India - Crystallographic Computing School (15th-20th August 2017) program example4 ! ! Crystal structure solution of paracetamol (form I) by real space method. ! use iso_fortran_env, only: stdout => OUTPUT_UNIT,ERROR_UNIT use crystal_phase use gen_frm use errormod use datasetmod use prog_constants ) use variables, only: cryst,dataset 7 1 use general, only: lo 0 2 use molcom, only: kscreen t s u use sannel g u implicit none A type(error_type) :: err Paracetamol (form I polymorph) h t type(dataset_type) :: datas 0 C H NO 2 integer :: ier 8 9 2 - h t 5 type(SimAnn_Conditions_type) :: sc 1 ( type(bb_bc_condition) :: bcond l ! o o ! Initialize libexpo h c S call InitExpo2002(0) g n lo = stdout i t u kscreen = 0 p call load_chemical_tables('../files/',err) m o if (err%signal) then C c write(ERROR_UNIT,'(a)')' Message: '//err%msg() i h stop 1 p a r endif g o l ! l a t ! Set up crystal phase s y r call new_phases(cryst,1) C - call cryst(1)%set_symmetry(init_spaceg_type('P 21/n'), set_cell_type([7.100,9.380,11.708,90.0,97.42,90.0])) a i d call crystal_file_import(cryst(1),'paracetamol.mol',has_symmetry=.true.,err=err) n I , if (err%signal) stop 2 e r o ! l a ! Set up XRPD data set g n a call datas%open_file('paracetamol.xy',ier,wavel=CU_WAVE) B if (ier /= 0) stop 3 call push_back_dataset(dataset,datas) call dataset_to_expo(dataset(1)) ! ! Run global optimization call sa_prelim(goptim,sc,bcond,.true.,saerr=err); if (err%signal) stop 4 call sa_run(goptim,sc,bcond) ! end program example4 decreasing the to evaluatetime for CF each trial structure Eliminating the H atoms reduces the number of atoms and DoFs, ignored during the structure solution H atoms do not contribute significantly to X-ray diffraction, they can be subroutine Delete H atoms Delete Add H atoms at X-ray distances Add atX-ray H atoms subroutine e.g. e.g. call remove_atoms_from_list(atoms,atoms%z(),H_at,bonds) add_hydrogens(atoms,bonds,elem,cell,spg,[vat],[htype],ier) remove_atoms_from_list(atoms,veta,val,[bonds],[iord]) H atoms H atoms X-H(X-ray) < X-H (neutrons) 0.95 0.95 0.82 Å Å (neutrons) (X-ray) Bangalore, India - Crystallographic Computing School (15th-20th August 2017) Hydrogen atoms are atomsare Hydrogen positioned geometrically Hydrogen calculation Hydrogen Hydrogen calculation Hydrogen Bangalore, India - Crystallographic Computing School (15th-20th August 2017) Parameters are adjusted adjusted are Parameters Parameters are adjusted areadjusted Parameters Random displacement of displacement Random displacement of displacement Random Random individually and sequentially simultaneously Program Program organization contributes of parameter parameter of contributes In the calculation of the structure factors only the evaluation evaluation x i will be update be will displacement of displacement Random Random ... ... Bangalore, India - Crystallographic Computing School (15th-20th August 2017) Centrosymmetric crystal structure: crystal Centrosymmetric contributes of the displaced atoms will beupdate. will atoms displaced the of contributes In the calculation of the structure factors only the Program Program organization Rotated atoms are circled in blue Bangalore, India - Crystallographic Computing School (15th-20th August 2017) ! Runglobaloptimization ! call sc%nt goptim%nrun call Random seed Random Number of moves of Number Resolution function Cost Temperature reduction factor Temperature Starting temperature runs SA of Number sa_run(goptim,sc,bcond) =100 sa_prelim(goptim,sc,bcond,.true.,saerr ; sc%autont = 100 Simulated annealingoptionsSimulated Simulated annealingoptionsSimulated = .false. ● ● ● ● Theflexibility molecule the of No. internalof DoFs No. externalof DoFs No. molecularof fragments = err); if (err% signal ) stop 4 Bangalore, India - Crystallographic Computing School (15th-20th August 2017) FLEX=0 0 1 2 0 1 3 2 4 1 3 FLEX=7 2 1 FLEXparameter FLEXparameter 1 0 0 FLEX = 9 + (0 +++ ==+ 12 43+25 FLEX 9(0 + +3 10) + 2 FLEX = 6 +(0 + = 1 +1 +11 + + 1 0) +(0 2 = 6 FLEX f nDoF i = number of coupled = number = number of internal DoFs of =internal number FLEX=64 H-atoms were ignored internalin the DoF famotidine. In red the values of DoFs f for each Bangalore, India - Crystallographic Computing School (15th-20th August 2017) Other cost Other functions:cost Integratedintensities Rfactors: Wholeprofile Rfactors: Cost Functions Cost Bangalore, India - Crystallographic Computing School (15th-20th August 2017) Paracetamol(formIpolymorph) (C 8 H 9 NO 2 )* Molecular compounds Molecular compounds * Nichols, C. & Frampton, C. S. (1998). J. Pharm. Sci. 87, 684–693 . Bangalore, India - Crystallographic Computing School (15th-20th August 2017) * Jouanneaux, A., Verbaere, A., Guyomard, D., Piffard, Y., Oyetola, S. & Fitch, A. N. (1991). Oyetola,S. & Fitch, Y., A., Guyomard, D., Piffard, A.,Verbaere, Jouanneaux, Non-molecular compounds Non-molecular compounds Crystalstructure of Eur. J. Solid StateInorg. Eur. Chem. Sb 2 (PO4) 28 3 , , 755-765. * Bangalore, India - Crystallographic Computing School (15th-20th August 2017) N dof 51= Non-molecular Non-molecular compounds Non-molecular Non-molecular compounds Sb 2 (PO 4 ) 3 N dof 24= N dof 30= Bangalore, India - Crystallographic Computing School (15th-20th August 2017) program example5 ! ! Crystal structure solution of Sb2(PO4)3 by real space method. ! use iso_fortran_env, only: stdout => OUTPUT_UNIT,ERROR_UNIT use crystal_phase use gen_frm use errormod use datasetmod use prog_constants use variables, only: cryst,dataset ) use general, only: lo,alambda 7 1 use molcom, only: kscreen 0 2 use sannel t implicit none s u type(error_type) :: err g u type(dataset_type) :: datas A integer :: ier h t 0 type(SimAnn_Conditions_type) :: sc 2 - type(bb_bc_condition) :: bcond h ! t 5 1 ! Initialize libexpo ( l o call InitExpo2002(0) o lo = stdout h c kscreen = 0 S g call load_chemical_tables('../files/',err) n i if (err%signal) then t u write(ERROR_UNIT,'(a)')' Message: '//err%msg() p m stop 1 o endif C c ! i h ! Set up crystal phase p a r g call new_phases(cryst,1) o l l call cryst(1)%set_symmetry(init_spaceg_type('P 21/n'),set_cell_type([11.936,8.7354,8.3185,90.0,91.12,90.0]))
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