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Volumn 5, Issue 3, 2012, Pages 415-431

Template-based geometric simulation of flexible frameworks

Author keywords

Flexibility; Framework; Geometric simulation; Perovskite; Rigid unit; Zeolite

Indexed keywords

COMPUTER SOFTWARE; GEOMETRY; PEROVSKITE; RIGID STRUCTURES;

EID: 84874055051     PISSN: None     EISSN: 19961944     Source Type: Journal    
DOI: 10.3390/ma5030415     Document Type: Article
Times cited : (15)

References (48)
  • 1
    • 40549086337 scopus 로고    scopus 로고
    • Pure silica zeolite-type frameworks: A structural analysis
    • Wragg, D.S.; Morris, R.S.; Burton, A.W. Pure silica zeolite-type frameworks: A structural analysis. Chem. Mater. 2008, 20, 1561-1570.
    • (2008) Chem. Mater. , vol.20 , pp. 1561-1570
    • Wragg, D.S.1    Morris, R.S.2    Burton, A.W.3
  • 2
    • 0000510951 scopus 로고
    • Straight Si-O-Si bridging bonds do exist in silicates and silicon dioxide polymorphs
    • Baur, W.H. Straight Si-O-Si bridging bonds do exist in silicates and silicon dioxide polymorphs. Acta Crystallogr. 1980, B36, 2198-2202.
    • (1980) Acta Crystallogr , vol.B36 , pp. 2198-2202
    • Baur, W.H.1
  • 3
    • 0001629501 scopus 로고
    • Rigid unit modes in framework silicates
    • Dove, M.T.; Heine, V.; Hammonds, K.D. Rigid unit modes in framework silicates. Mineral. Mag. 1995, 59, 629-639.
    • (1995) Mineral. Mag. , vol.59 , pp. 629-639
    • Dove, M.T.1    Heine, V.2    Hammonds, K.D.3
  • 4
    • 34547247838 scopus 로고    scopus 로고
    • Exotic distributions of rigid unit modes in the reciprocal spaces of framework aluminosilicates
    • Dove, M.T.; Pryde, A.K.A.; Heine, V.; Hammonds, K.D. Exotic distributions of rigid unit modes in the reciprocal spaces of framework aluminosilicates. J. Phys. Condens. Matter 2007, 19, 275209.
    • (2007) J. Phys. Condens. Matter , vol.19 , pp. 275209
    • Dove, M.T.1    Pryde, A.K.A.2    Heine, V.3    Hammonds, K.D.4
  • 5
    • 0001224931 scopus 로고
    • CRUSH: A FORTRAN program for the analysis of the rigid unit mode spectrum of a framework structure
    • Hammonds, K.D.; Dove, M.T.; Giddy, A.P.; Heine, V. CRUSH: A FORTRAN program for the analysis of the rigid unit mode spectrum of a framework structure. Am. Mineral. 1994, 79, 1297-1209.
    • (1994) Am. Mineral. , vol.79 , pp. 1297-1209
    • Hammonds, K.D.1    Dove, M.T.2    Giddy, A.P.3    Heine, V.4
  • 6
    • 0001678815 scopus 로고
    • The determination of rigid unit modes as potential soft modes for displacive phase transitions in framework crystal structures
    • Giddy, A.P.; Dove, M.T.; Pawley, G.S.; Heine, V. The determination of rigid unit modes as potential soft modes for displacive phase transitions in framework crystal structures. Acta Crystallogr. 1993, A49, 697-703.
    • (1993) Acta Crystallogr , vol.A49 , pp. 697-703
    • Giddy, A.P.1    Dove, M.T.2    Pawley, G.S.3    Heine, V.4
  • 7
    • 0037071346 scopus 로고    scopus 로고
    • Real-space rigid-unit-mode analysis of dynamic disorder in quartz, cristobalite and amorphous silica
    • Wells, S.A.; Dove, M.T.; Tucker, M.G.; Trachenko, K. Real-space rigid-unit-mode analysis of dynamic disorder in quartz, cristobalite and amorphous silica. J. Phys. Condens. Matter 2002, 14, 4645.
    • (2002) J. Phys. Condens. Matter , vol.14 , pp. 4645
    • Wells, S.A.1    Dove, M.T.2    Tucker, M.G.3    Trachenko, K.4
  • 8
    • 33748616559 scopus 로고
    • GULP:A computer program for the symmetry-adapted simulation of solids
    • Gale, J.D. GULP: A computer program for the symmetry-adapted simulation of solids. J. Chem. Soc. Faraday Trans. 1995, 93, 629-637.
    • (1995) J. Chem. Soc. Faraday Trans. , vol.93 , pp. 629-637
    • Gale, J.D.1
  • 10
    • 0037029641 scopus 로고    scopus 로고
    • Finding best-fit polyhedral rotations with geometric algebra
    • Wells, S.A.; Dove, M.T.; Tucker, M.G. Finding best-fit polyhedral rotations with geometric algebra. J. Phys. Condens. Matter 2002, 14, 4567-4584.
    • (2002) J. Phys. Condens. Matter , vol.14 , pp. 4567-4584
    • Wells, S.A.1    Dove, M.T.2    Tucker, M.G.3
  • 11
    • 9944225170 scopus 로고    scopus 로고
    • + ion motion in quartz and β-eucryptite studied by dielectric spectroscopy and atomistic simulations
    • + ion motion in quartz and β-eucryptite studied by dielectric spectroscopy and atomistic simulations. J. Phys. Condens. Matter 2004, 16, 8173-8189.
    • (2004) J. Phys. Condens. Matter , vol.16 , pp. 8173-8189
    • Sartbaeva, A.1    Wells, S.A.2    Redfern, S.A.T.3
  • 12
    • 14544276367 scopus 로고    scopus 로고
    • Ionic diffusion in quartz studied by transport measurements SIMS and atomistic simulations
    • Sartbaeva, A.; Wells, S.A.; Redfern, S.A.T.; Hinton, R.W.; Reed, S.J.B. Ionic diffusion in quartz studied by transport measurements, SIMS and atomistic simulations. J. Phys. Condens. Matter 2005, 17, 1099-1112.
    • (2005) J. Phys. Condens. Matter , vol.17 , pp. 1099-1112
    • Sartbaeva, A.1    Wells, S.A.2    Redfern, S.A.T.3    Hinton, R.W.4    Reed, S.J.B.5
  • 13
    • 0035022953 scopus 로고    scopus 로고
    • Intensities of the vibrational spectra of siliceous zeolites by molecular dynamics calculations II-Raman spectra
    • Bornhauser, J.B.; Bougeard, D. Intensities of the vibrational spectra of siliceous zeolites by molecular dynamics calculations II-Raman spectra. J. Raman Spectrosc. 2001, 32, 279-285.
    • (2001) J. Raman Spectrosc. , vol.32 , pp. 279-285
    • Bornhauser, J.B.1    Bougeard, D.2
  • 14
    • 85176342171 scopus 로고
    • DLS-76, A FORTRAN Program for the Simulation of Crystal Structures by Geometric Refinement; Institut fur Kristallographie and Petrographie ETH: Zurich
    • Baerlocher, C.; Hepp, A.; Meier, W.M. DLS-76, A FORTRAN Program for the Simulation of Crystal Structures by Geometric Refinement; Institut fur Kristallographie and Petrographie ETH: Zurich, Switzerland, 1978.
    • (1978) Switzerland
    • Baerlocher, C.1    Hepp, A.2    Meier, W.M.3
  • 16
    • 80053986273 scopus 로고    scopus 로고
    • Density of mechanisms within the flexibility window of zeolites
    • Kapko, V.; Dawson, C.; Rivin, I.; Treacy, M.M.J. Density of mechanisms within the flexibility window of zeolites. Phys. Rev. Lett. 2011, 107, 164304.
    • (2011) Phys. Rev. Lett. , vol.107 , pp. 164304
    • Kapko, V.1    Dawson, C.2    Rivin, I.3    Treacy, M.M.J.4
  • 17
    • 0036205277 scopus 로고    scopus 로고
    • Neutron total scattering method: Simultaneous determination of long-range and short-range order in disordered materials
    • Dove, M.T.; Tucker, M.G.; Keen, D.A. Neutron total scattering method: Simultaneous determination of long-range and short-range order in disordered materials. Eur. J. Mineral. 2002, 14, 331-348.
    • (2002) Eur. J. Mineral. , vol.14 , pp. 331-348
    • Dove, M.T.1    Tucker, M.G.2    Keen, D.A.3
  • 18
    • 4043067843 scopus 로고    scopus 로고
    • Reverse Monte Carlo with geometric analysis-RMC + GA
    • Wells, S.A.; Dove, M.T.; Tucker, M.G. Reverse Monte Carlo with geometric analysis-RMC + GA. J. Appl. Crystallogr. 2004, 37, 536-544.
    • (2004) J. Appl. Crystallogr. , vol.37 , pp. 536-544
    • Wells, S.A.1    Dove, M.T.2    Tucker, M.G.3
  • 20
    • 0037222475 scopus 로고    scopus 로고
    • Molecular-dynamics study of the high-temperature elasticity of quartz above the alpha-beta phase transition
    • Kimizuka, H.; Kaburaki, H.; Kogue, Y. Molecular-dynamics study of the high-temperature elasticity of quartz above the alpha-beta phase transition. Phys. Rev. B 2003, 167, 024105.
    • (2003) Phys. Rev. B , vol.167 , pp. 024105
    • Kimizuka, H.1    Kaburaki, H.2    Kogue, Y.3
  • 21
    • 36649003091 scopus 로고    scopus 로고
    • Ferroelectric nanoscale domains and the 905 K phase transition in SrSnO3: A neutron total-scattering study
    • Goodwin, A.L.; Redfern, S.A.T.; Dove, M.T.; Keen, D.A.; Tucker, M.G. Ferroelectric nanoscale domains and the 905 K phase transition in SrSnO3: A neutron total-scattering study. Phys. Rev. B 2007, 76, 174114.
    • (2007) Phys. Rev. B , vol.76 , pp. 174114
    • Goodwin, A.L.1    Redfern, S.A.T.2    Dove, M.T.3    Keen, D.A.4    Tucker, M.G.5
  • 22
    • 13644273976 scopus 로고    scopus 로고
    • Total scattering and reverse Monte Carlo study of the 105 K displacive phase transition in strontium titanate
    • Hui, Q.; Tucker, M.G.; Dove, M.T.; Wells, S.A.; Keen, D.A. Total scattering and reverse Monte Carlo study of the 105 K displacive phase transition in strontium titanate. J. Phys. Condens. Matter 2005, 17, S111-S124.
    • (2005) J. Phys. Condens. Matter , vol.17
    • Hui, Q.1    Tucker, M.G.2    Dove, M.T.3    Wells, S.A.4    Keen, D.A.5
  • 23
    • 29144444420 scopus 로고    scopus 로고
    • Negative thermal expansion in ZrW2O8: Mechanisms, rigid unit modes, and neutron total scattering
    • Tucker, M.G.; Goodwin, A.L.; Dove, M.T.; Keen, D.A.; Wells, S.A.; Evans, J.S.O. Negative thermal expansion in ZrW2O8: Mechanisms, rigid unit modes, and neutron total scattering. Phys. Rev. Lett. 2005, 95, 255501.
    • (2005) Phys. Rev. Lett. , vol.95 , pp. 255501
    • Tucker, M.G.1    Goodwin, A.L.2    Dove, M.T.3    Keen, D.A.4    Wells, S.A.5    Evans, J.S.O.6
  • 25
    • 84863113120 scopus 로고    scopus 로고
    • The crystallography of flexibility: Local structure and dynamics in framework materials
    • Goodwin, A.L. The crystallography of flexibility: Local structure and dynamics in framework materials. Z. Krist. 2009, 30, 1-11.
    • (2009) Z. Krist. , vol.30 , pp. 1-11
    • Goodwin, A.L.1
  • 26
    • 3342900222 scopus 로고    scopus 로고
    • A neutron diffraction and Rietveld analysis of cooperative Li motion in beta-eucryptite
    • Sartbaeva, A.; Redfern, S.A.T.; Lee, W.T. A neutron diffraction and Rietveld analysis of cooperative Li motion in beta-eucryptite. J. Phys. Condens. Matter 2004, 16, 5267-5278.
    • (2004) J. Phys. Condens. Matter , vol.16 , pp. 5267-5278
    • Sartbaeva, A.1    Redfern, S.A.T.2    Lee, W.T.3
  • 27
    • 79953721143 scopus 로고    scopus 로고
    • Direct observation of catalyst behaviour under real working conditions with X-ray diffraction: Comparing SAPO-18 and SAPO-34 methanol to olefin catalysts
    • Wragg, D.S.; Akporiaye, D.; Fjellvag, H. Direct observation of catalyst behaviour under real working conditions with X-ray diffraction: Comparing SAPO-18 and SAPO-34 methanol to olefin catalysts. J. Catal. 2011, 279, 397-402.
    • (2011) J. Catal. , vol.279 , pp. 397-402
    • Wragg, D.S.1    Akporiaye, D.2    Fjellvag, H.3
  • 28
    • 30744437653 scopus 로고    scopus 로고
    • Cation substitution and strain screening in framework structures: The role of rigid unit modes
    • Goodwin, A.L.; Wells, S.A.; Dove, M.T. Cation substitution and strain screening in framework structures: The role of rigid unit modes. Chem. Geol. 2006, 225, 213-221.
    • (2006) Chem. Geol. , vol.225 , pp. 213-221
    • Goodwin, A.L.1    Wells, S.A.2    Dove, M.T.3
  • 29
    • 7744244225 scopus 로고    scopus 로고
    • Rigid unit modes at high pressure: An explorative study of a fibrous zeolite-like framework with EDI topology
    • Gatta, G.D.; Wells, S.A. Rigid unit modes at high pressure: An explorative study of a fibrous zeolite-like framework with EDI topology. Phys. Chem. Miner. 2004, 31, 1-10.
    • (2004) Phys. Chem. Miner. , vol.31 , pp. 1-10
    • Gatta, G.D.1    Wells, S.A.2
  • 30
    • 33751574827 scopus 로고    scopus 로고
    • Structural evolution of zeolite levyne under hydrostatic and non-hydrostatic pressure: Geometric modelling
    • Gatta, G.D.; Wells, S.A. Structural evolution of zeolite levyne under hydrostatic and non-hydrostatic pressure: Geometric modelling. Phys. Chem. Miner. 2006, 33, 1-10.
    • (2006) Phys. Chem. Miner. , vol.33 , pp. 1-10
    • Gatta, G.D.1    Wells, S.A.2
  • 31
    • 23844512264 scopus 로고    scopus 로고
    • Tetrahedral distortion and energetic packing penalty in "zeolite" frameworks: Linked phenomena?
    • Zwijnenburg, M.A.; Simperler, A.; Wells, S.A.; Bell, R.G. Tetrahedral distortion and energetic packing penalty in "zeolite" frameworks: Linked phenomena? J. Phys. Chem. B 2005, 109, 14783-14785.
    • (2005) J. Phys. Chem. B , vol.109 , pp. 14783-14785
    • Zwijnenburg, M.A.1    Simperler, A.2    Wells, S.A.3    Bell, R.G.4
  • 34
    • 0028552884 scopus 로고
    • Framework silica structures generated using simulated annealing with a potential energy function based on an H6Si2O7 molecule
    • Boisen, M.B.; Gibbs, G.V.; Bukowinski, M.S.T. Framework silica structures generated using simulated annealing with a potential energy function based on an H6Si2O7 molecule. Phys. Chem. Miner. 1994, 21, 269-284.
    • (1994) Phys. Chem. Miner. , vol.21 , pp. 269-284
    • Boisen, M.B.1    Gibbs, G.V.2    Bukowinski, M.S.T.3
  • 35
    • 33745642276 scopus 로고    scopus 로고
    • A simple geometric structure optimizer for accelerated detection of infeasible zeolite graphs
    • Wells, S.A.; Foster, M.D.; Treacy, M.M.J. A simple geometric structure optimizer for accelerated detection of infeasible zeolite graphs. Microporous Microporous Mater. 2007, 93, 151-157.
    • (2007) Microporous Microporous Mater , vol.93 , pp. 151-157
    • Wells, S.A.1    Foster, M.D.2    Treacy, M.M.J.3
  • 37
    • 33746924840 scopus 로고    scopus 로고
    • Geometric simulation of perovskite frameworks with Jahn-Teller distortions: Applications to the cubic manganites
    • Sartbaeva, A.; Wells, S.A.; Thorpe, M.F.; Bozin, E.S.; Billinge, S.J.L. Geometric simulation of perovskite frameworks with Jahn-Teller distortions: Applications to the cubic manganites. Phys. Rev. Lett. 2006, 97, 065501.
    • (2006) Phys. Rev. Lett. , vol.97 , pp. 065501
    • Sartbaeva, A.1    Wells, S.A.2    Thorpe, M.F.3    Bozin, E.S.4    Billinge, S.J.L.5
  • 38
    • 52649163377 scopus 로고    scopus 로고
    • Nanoscale structural order from the atomic pair distribution function (PDF): There's plenty of room in the middle
    • Billinge, S.J.L. Nanoscale structural order from the atomic pair distribution function (PDF): There's plenty of room in the middle. J. Solid State Chem. 2008, 181, 1695-1700.
    • (2008) J. Solid State Chem. , vol.181 , pp. 1695-1700
    • Billinge, S.J.L.1
  • 40
    • 33751575657 scopus 로고    scopus 로고
    • Geometric simulations: A lesson from virtual zeolites
    • Rivin, I. Geometric simulations: A lesson from virtual zeolites. Nat. Mater. 2006, 5, 931-932.
    • (2006) Nat. Mater. , vol.5 , pp. 931-932
    • Rivin, I.1
  • 41
    • 79051469466 scopus 로고    scopus 로고
    • Flexibility window controls pressure-induced phase transition in analcime
    • Sartbaeva, A.; Gatta, G.D.; Wells, S.A. Flexibility window controls pressure-induced phase transition in analcime. Europhys. Lett. 2008, 83, 26002.
    • (2008) Europhys. Lett. , vol.83 , pp. 26002
    • Sartbaeva, A.1    Gatta, G.D.2    Wells, S.A.3
  • 42
    • 67749099685 scopus 로고    scopus 로고
    • Compression behaviour and flexibility window of the analcime-like feldspathoids: Experimental and theoretical findings
    • Gatta, G.D.; Sartbaeva, A.; Wells, S.A. Compression behaviour and flexibility window of the analcime-like feldspathoids: Experimental and theoretical findings. Eur. J. Mineral. 2009, 21, 571-580.
    • (2009) Eur. J. Mineral. , vol.21 , pp. 571-580
    • Gatta, G.D.1    Sartbaeva, A.2    Wells, S.A.3
  • 43
    • 79959278046 scopus 로고    scopus 로고
    • Flexibility windows and phase transitions of ordered and disordered ANA framework zeolites
    • Wells, S.A.; Sartbaeva, A.; Gatta, G.D. Flexibility windows and phase transitions of ordered and disordered ANA framework zeolites. Europhys. Lett. 2011, 94, 56001.
    • (2011) Europhys. Lett. , vol.94 , pp. 56001
    • Wells, S.A.1    Sartbaeva, A.2    Gatta, G.D.3
  • 44
    • 27744471408 scopus 로고    scopus 로고
    • Constrained geometric simulation of diffusive motion in proteins
    • Wells, S.A.; Menor, S.; Hespenheide, B.M.; Thorpe, M.F. Constrained geometric simulation of diffusive motion in proteins. Phys. Biol. 2005, 2, S127-S136.
    • (2005) Phys. Biol. , vol.2
    • Wells, S.A.1    Menor, S.2    Hespenheide, B.M.3    Thorpe, M.F.4
  • 47
    • 79960718392 scopus 로고    scopus 로고
    • A normal mode-based geometric simulation approach for exploring biologically relevant conformational transitions in proteins
    • Ahmed, A.; Rippmann, F.; Barnickel, G.; Gohlke, H. A normal mode-based geometric simulation approach for exploring biologically relevant conformational transitions in proteins. J. Chem. Inform. Model. 2011, 51, 1604-1622.
    • (2011) J. Chem. Inform. Model. , vol.51 , pp. 1604-1622
    • Ahmed, A.1    Rippmann, F.2    Barnickel, G.3    Gohlke, H.4
  • 48
    • 84856954623 scopus 로고    scopus 로고
    • Protein flexibility explored with normal modes and geometric simulation
    • Jimenez-Roldan, J.E.; Freedman, R.B.; Roemer, R.A.; Wells, S.A. Protein flexibility explored with normal modes and geometric simulation. Phys. Biol. 2012, 9, 016008.
    • (2012) Phys. Biol. , vol.9 , pp. 016008
    • Jimenez-Roldan, J.E.1    Freedman, R.B.2    Roemer, R.A.3    Wells, S.A.4


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