Energy matters!

Crystallography Reviews

Volumn 16, Issue 3, 2010, Pages 169-195

  Allen, Frank H ^a   Galek, Peter T A ^a   Wood, Peter A ^a  

^a CAMBRIDGE CRYSTALLOGRAPHIC DATA CENTRE   (United Kingdom)

Author keywords

ab initio energy calculations; Cambridge Structural Database; conformational analysis; intermolecular interactions

Indexed keywords

AB INITIO ENERGY CALCULATIONS; CAMBRIDGE STRUCTURAL DATABASES; CONFORMATIONAL ANALYSIS; CRYSTALLINE STATE; DRUG DISCOVERY; ENERGETIC FACTORS; ENERGY RELATIONSHIPS; INTERMOLECULAR INTERACTIONS; MATERIALS DEVELOPMENT; MOLECULAR AGGREGATION; OTHER APPLICATIONS; TORSION ANGLE; X-RAY DIFFRACTION METHOD;

CRYSTALLINE MATERIALS; X RAY DIFFRACTION;

CONFORMATIONS;

EID: 77954681986     PISSN: 0889311X     EISSN: 14763508     Source Type: Journal    
DOI: 10.1080/08893110903476919     Document Type: Conference Paper

References (80)

1. Buergi, H.-B., Dunitz, J.D., Eds.; Structure Correlation, Volumes 1 & 2; VCH: Weinheim, Germany, 1994.
2. Allen, F.H. The Cambridge Structural Database: A Quarter of a Million Crystal Structures and Rising. Acta Crystallogr. 2002, B58, 380-388.
3. Duax, W.L., Norton, D.A., Eds.; Atlas of Steroid Structure; Plenum: New York, 1975.
4. Murray-Rust, P.; Motherwell, W.D.S. Computer Retrieval and Analysis of Molecular Geometry. I. General Principles and Methods. Acta Crystallogr. 1978, B34, 2518-2526.
5. Murray-Rust, P.; Bland, R. Computer Retrieval and Analysis of Molecular Geometry. II. Variance and its Interpretation. Acta Crystallogr. 1978, B34, 2527-2533.
6. Murray-Rust, P.; Motherwell, W.D.S. Computer Retrieval and Analysis of Molecular Geometry. III. Geometry of the β-10-aminofuranoside Fragment. Acta Crystallogr. 1978, B34, 2534-2546.
7. Taylor, R. The Cambridge Structural Database in Molecular Graphics: Techniques for the Rapid Identification of Conformational Minima. J. Mol. Graphics 1986, 4, 123-131.
8. Allen, F.H.; Doyle, M.J.; Taylor, R. Automated Conformational Analysis from Crystallographic Data. 1. A Symmetry-Modified Single-Linkage Clustering Algorithm for 3D Pattern Recognition. Acta Crystallogr. 1991, B47, 29-40.
9. Allen, F.H.; Doyle, M.J.; Taylor, R. Automated Conformational Analysis from Crystallographic Data. 2. Symmetry-Modified Jarvis-Patrick and Complete-Linkage Clustering Algorithms for 3D Pattern Recognition. Acta Crystallogr. 1991, B47, 41-49.
10. Allen, F.H.; Doyle, M.J.; Taylor, R. Automated Conformational Analysis from Crystallographic Data. 3. 3D Pattern Recognition within the Cambridge Structural Database System: Implementation and Practical Examples. Acta Crystallogr. 1991, B47, 60-67.
11. Allen, F.H.; Taylor, R. Automated Conformational Analysis from Crystallographic Data. 5. Recognition of Special Positions in Conformational Space in Symmetry-Modified Clustering Algorithms. Acta Crystallogr. 1991, B47, 404-412.
12. Allen, F.H.; Doyle, M.J.; Auf der Heyde, T.P.E. Automated Conformational Analysis from Crystallographic Data. 6. Principal Component Analysis for n-membered Carbocyclic Rings (n=4, 5, 6). Symmetry Considerations and Correlations with Ring-Puckering Parameters. Acta Crystallogr. 1991, B47, 412-424.
13. Allen, F.H.; Howard, J.A.K.; Pitchford, N.A. Symmetry-Modified Conformational Mapping and Classification of the Medium Rings from Crystallographic Data. I. Cycloheptane. Acta Crystallogr. 1993, B49, 910-928.
14. Allen, F.H.; Howard, J.A.K.; Pitchford, N.A. Symmetry-Modified Conformational Mapping and Classification of the Medium Rings from Crystallographic Data. II. exo-Unsaturated and Heterocyclic Seven-Membered Rings. Acta Crystallogr. 1994, B50, 382-395.
15. Allen, F.H.; Howard, J.A.K.; Pitchford, N.A. Symmetry-Modified Conformational Mapping and Classification of the Medium Rings from Crystallographic Data. IV. Cyclooctane and Related Unsaturated and Heterocyclic Rings. Acta Crystallogr. 1996, B52, 882-891.
16. Cremer, D.; Pople, J.A. General Definition of Ring Puckering Coordinates. J. Am. Chem. Soc. 1975, 97, 1354-1358.
17. Zimmer, M. Molecular Mechanics, Data and Conformational Analysis of First-Row Transition Metal Complexes in the Cambridge Structural Database. Coord. Chem. Rev. 2001, 212, 133-163.
18. Conklin, D.; Fortier, S.; Glasgow, J.I.; Allen, F.H. Conformational Analysis from Crystallographic Data Using Conceptual Clustering. Acta Crystallogr. 1996, B52, 535-549.
19. Nolsoe, K.; Kessler, M.; Perez, J.; Madsen, H. Bayesian Conformational Analysis of Ring Molecules through Reversible Jump MCMC. J. Chemom. 2005, 19, 412-426.
20. Perez, J.; Nolsoe, K.; Kessler, M.; Garcia, L.; Perez, E.; Serrano, J.L. Bayesian Methods for the Conformational Classification of Eight-Membered Rings. Acta Crystallogr. 2005, 61, 585-594.
21. Kessler, M.; Perez, J.; Bueso, M.C.; Garcia, L.; Perez, E.; Serrano, J.L.; Carrascosa, R. Probabilistic Model-Based Methodology for the Conformational Study of Cyclic Systems: Application to Copper Complexes Double-Bridged by Phosphate and Related Ligands. Acta Crystallogr. 2007, 63, 869-878.
22. Barr, G.; Dong, W.; Gilmore, C.J.; Parkin, A.; Wilson, C.C. dSNAP: A Computer Program to Cluster and Classify Cambridge Structural Database Searches. J. Appl. Crystallogr. 2005, 38, 833-841.
23. Parkin, A.; Collins, A.; Gilmore, C.J.; Wilson, C.C. Using Small Molecule Crystal Structure Data to Obtain Information About Sulfonamide Conformation. Acta Crystallogr. 2008, B64, 66-71.
24. Collins, A.; Parkin, A.; Barr, G.; Dong, W.; Gilmore, C.J.; Wilson, C.C. Configurational and Conformational Classification of Pyranose Sugars. Acta Crystallogr. 2008, B64, 57-65.
25. Parkin, A. Uses of the dSNAP Cluster Analysis Software for Studying Geometric Information Extracted from the Cambridge Structural Database. Crystallogr. Rev. 2008, 14, 117-141.
26. Collins, A.; Parkin, A.; Barr, G.; Dong, W.; Gilmore, C.J.; Wilson, C.C. Identifying Structural Motifs in Intermolecular Contacts Using Cluster Analysis. CrystEngComm. 2007, 9, 245-253.
27. Barr, G.; Dong, W.; Gilmore, C.J. High-Throughput Powder Diffraction. II. Applications of Clustering Methods and Multivariate Data Analysis. J. Appl. Crystallogr. 2004, 37, 243-252.
28. Taylor, R.; Allen, F.H. Statistical and Numerical Methods of Data Analysis. In Structure Correlation Volumes 1 & 2: Buergi, H.-B., Dunitz, J.D., Eds.; VCH: Weinheim, Germany, 1994; pp 111-161.
29. Schweizer, W.B. Conformational Analysis. In Structure Correlation Volumes 1 & 2: Buergi, H.-B., Dunitz, J.D., Eds.; VCH: Weinheim, Germany, 1994; pp 367-404.
30. Murray-Rust, P. How Useful are X-ray Conformations? In Molecular Structure and Biological Activity: Griffin, J.T., Duax, W.L., Eds.; Elsevier: New York, 1982; pp 117-135.
31. Buergi, H.-B.; Dunitz, J.D. Can Statistical Analysis of Structural Parameters from Different Crystal Environments Lead to Quantitative Energy Relationships? Acta Crystallogr. 1988, B44, 445-448.
32. Rappoport, Z.; Biali, S.E.; Kaftory, M. Application of the Structural Correlation Method to ring-Flip Processes in Benzophenones. J. Am. Chem. Soc. 1990, 112, 7742-7748.
33. Klebe, G. Mapping Common Molecular Fragments in Crystal Structures to Explore Conformation and Configuration Space under the Conditions of Molecular Environment. J. Mol. Struct. (Theochem) 1994, 308, 53-89.
34. Klebe, G.; Meitzner, T. A Fast and Efficient Method to Generate Biologically Relevant Conformations. J. Comput. Aided Mol. Des. 1994, 8, 583-606.
35. Boehm, H.-J.; Klebe, G. What Can We Learn from Molecular Recognition in Protein-Ligand Complexes for the Design of New Drugs? Angew. Chem. Int. Ed. Engl. 1996, 35, 2588-2614.
36. Brameld, K.A.; Kuhn, B.; Reuter, D.C.; Stahl, M. Small Molecule Conformational P Derived from Crystal Structure Data. A Medicinal Chemistry Focused Analysis. J. Chem. Inf. Model. 2008, 48, 1-24.
37. Berman, H.M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T.N.; Weissig, H.; Shindyalov, I.N.; Bourne, P.E. The Protein Data Bank. Nucleic Acids Res. 2000, 28, 235-242.
38. Brock, C.P.; Minton, R.P. Systematic Effects of Crystal Packing Forces: Biphenyl Fragments with H Atoms in all Four Ortho Positions. J. Am. Chem. Soc. 1989, 111, 4586-4593.
39. Almenningen, A.; Bastiansen, O.; Fernholt, L.; Cyvin, B.N.; Cyvin, S.J.; Samdal, S. Structure and Barrier of Internal Rotation of Biphenyl Derivatives in the Gaseous State: Part 1. The Molecular Structure and Normal Coordinate Analysis of Normal Biphenyl and Perdeuterated Biphenyl. J. Mol. Struct. 1985, 128, 59-76.
40. Bastiansen, O.; Samdal, S. Structure and Barrier of Internal Rotation of Biphenyl Derivatives in the Gaseous State: Part 4. Barrier of Internal Rotation in Biphenyl, Perdeuterated Biphenyl and Seven Non-Ortho-Substituted Halogen Derivatives. J. Mol. Struct. 1985, 128, 115-125.
41. Almenningen, A.; Bastiansen, O.; Skancke, P.N. Preliminary Results of an Electron Diffraction Reinvestigation of the Structures of Cyclobutane and Cyclopentane. Acta Chem. Scand. 1961, 15, 711-712.
42. Stone, J.M.R.; Mills, I.M. Puckering Structure in the Infra-Red Spectrum of Cyclobutane. Mol. Phys. 1970, 18, 631-652.
43. Allen, F.H.; Harris, S.E.; Taylor, R. Comparison of Conformer Distributions in the Crystalline State with Conformational Energies Calculated by Ab Initio Techniques. J. Comput. Aided Mol. Des. 1996, 10, 247-254.
44. Weng, Z.F.; Motherwell, W.D.S.; Allen, F.H.; Cole, J.M. Conformational Variability of Molecules in Different Crystal Environments: A Database Study. Acta Crystallogr. 2008, B64, 348-362.
45. Bruno, I.J.; Cole, J.C.; Kessler, M.; Luo, J.; Motherwell, W.D.S.; Purkis, L.H.; Smith, B.R.; Taylor, R.; Cooper, R.I.; Harris, S.E.; Orpen, A.G. Retrieval of Crystallographically-Derived Molecular Geometry Information. J. Chem. Inf. Comput. Sci. 2004, 44, 2133-2144.
46. Cooper, R.I.; Watkin, D.J. Validation during Structure Refinement Using 'CRYSTALS'. Acta Crystallogr. 2002, A58 (Suppl), C58.
47. David, W.I.F.; Shankland, K.; van de Streek, J.; Pidcock, E.; Motherwell, W.D.S.; Cole, J.C. DASH: A Program for Crystal Structure Determination from Powder Diffraction Data. J. Applied Crystallogr. 2006, 39, 910-915.
48. Jeffrey, G.A.; Saenger, W. Hydrogen Bonding in Biological Structures; Springer-Verlag: Berlin, Germany, 1991.
49. Desiraju, G.R.; Steiner, T. The Weak Hydrogen Bond; Oxford University Press: Oxford, UK, 1999.
50. Hayes, I.C.; Stone, A.J. An Intermolecular Perturbation Theory for the Region of Moderate Overlap. Mol. Phys. 1984, 53, 83-105.
51. Amos, R.D.; Alberts, I.L.; Andrews, J.S.; Cohen, A.J.; Colwell, S.M.; Handy, N.C.; Jayatilaka, D.; Knowles, P.J.; Kobayashi, R.; Laming, G.J.; Lee, A.M.; Maslen, P.E.; Murray, C.W.; Palmieri, P.; Rice, J.E.; Simandiras, E.D.; Stone, A.J.; Su, M.-D.; Tozer, D.J. CADPAC 6.5. The Cambridge Analytical Derivatives Package: A Suite of Quantum Chemistry Programs; Chemistry Department, Cambridge University: Cambridge, UK, 1998.
52. Stone, A.J. Computation of Charge-Transfer Energies by Perturbation Theory. Chem. Phys. Lett. 1993, 211, 101-109.
53. Pauling, L. The Nature of the Chemical Bond, 3rd ed.; Cornell University Press: New York, 1960.
54. Allen, F.H.; Bird, C.M.; Rowland, R.S.; Raithby, P.R. Resonance-Induced Hydrogen-Bonding at Sulphur Acceptors in R1, R2C=S and R1CS 2 Systems. Acta Crystallogr. 1997, B53, 680-695.
55. Gilli, P.; Bertolasi, V.; Ferretti, V.; Gilli, G. Evidence for Resonance-Assisted Hydrogen Bonding. 4. Covalent Nature of the Strong Homonuclear Hydrogen Bond. Study of the O-H-O System by Crystal Structure Correlation Methods. J. Am. Chem. Soc. 1994, 116, 909-915.
56. Guest, M.F.; van Lenthe, J.H.; Kendrick, J.; Schoeffel, K.; Sherwood, P.; Harrison, R.J. GAMESS-UK User's Guide and Reference Manual; Computing for Science Ltd.; Daresbury Laboratory: Warrington, UK, 1993.
57. Wood, P.A.; Pidcock, E.; Allen, F.H. Interaction Geometries and Energies of Hydrogen Bonds to C=O and C=S Acceptors: A Comparative Study. Acta Crystallogr. 2008, B64, 491-496.
58. Infantes, L.; Motherwell, W.D.S. Hydrogen Bond Competition between Chemical Groups: New Methodology and the Cambridge Structural Database. Z. Kristallogr. 2005, 220, 333-339.
59. Nobeli, I.; Price, S.L.; Lommerse, J.P.M.; Taylor, R. Hydrogen Bonding Properties of Oxygen and Nitrogen Acceptors in Aromatic Heterocycles. J. Comput. Chem. 1997, 18, 2060-2074.
60. Lommerse, J.P.M.; Price, S.L.; Taylor, R. Hydrogen Bonding of Carbonyl, Ether and Ester Oxygen Atoms with Alkanol Hydroxyl Groups. J. Comput. Chem. 1997, 18, 757-780.
61. Nobeli, I.; Yeoh, S.L.; Price, S.L.; Taylor, R. On the Hydrogen Bonding Abilities of Phenols and Anisoles. Chem. Phys. Lett. 1997, 280, 196-202.
62. Wood, P.A.; Allen, F.H.; Pidcock, E. Hydrogen-Bond Directionality at the Donor H Atom: Analysis of Interaction Energies and Database Statistics. CrystEngComm. 2009, 11, 1563-1571.
63. Brammer, L.; Bruton, E.A.; Sherwood, P. Understanding the Behaviour of Halogens as Hydrogen Bond Acceptors. Cryst. Growth Des. 2001, 1, 277-290.
64. Brammer, L. Developments in Inorganic Crystal Engineering. Chem. Soc. Rev. 2004, 33, 476-489
65. Galek, P.T.A.; Fábián, L.; Motherwell, W.D.S.; Allen, F.H.; Feeder, N. A Knowledge-Based Model of Hydrogen Bonding Propensity in Organic Crystals. Acta Crystallogr. 2007, B63, 768-782.
66. Galek, P.T.A.; Allen, F.H.; Fábián, L.; Feeder, N. Knowledge-Based H-Bond Prediction to Aid Experimental Polymorph Screening. CrystEngComm. 2009, 11, 2634-2639.
67. Bauer, J.; Spanton, S.; Henry, R.; Quick, J.; Dziki, W.; Porter, W.; Morris, J. Ritonavir: An Extraordinary Example of Conformational Polymorphism. Pharm. Res. 2001, 18, 859-866.
68. Bent, H.A. Structural Chemistry of Donor-Acceptor Interactions. Chem. Rev. 1968, 68, 588-648.
69. Paulini, R.; Muller, K.; Diederich, F. Orthogonal Multipolar Interactions in Structural Chemistry and Biology. Angew. Chem. Int. Ed. Engl. 2005, 44, 1788-1805.
70. Allen, F.H.; Baalham, C.A.; Lommerse, J.P.M.; Raithby, P.R. Carbonyl-Carbonyl Interactions can be Competitive with Hydrogen Bonds. Acta Crystallogr. 1998, B54, 320-329.
71. Macullum, P.H.; Poet, R.; Milner-White, E.J. Coulombic Interactions Between Partially Charged Main-Chain Atoms not Hydrogen-Bonded to Each Other Influence the Conformations of -helices and Antiparallel sheet. A New Method for Analysing Forces between Hydrogen Bonding Groups in Proteins Includes all the Coulombic Interactions. J. Mol. Biol. 1995, 248, 361-373.
72. Deane, C.M.; Allen, F.H.; Taylor, R.; Blundell, T.L. Carbonyl-Carbonyl Interactions Stabilise the Partially Allowed Ramachandran Conformations of Asparagine and Aspartic Acid. Protein Eng. 1999, 12, 1025-1028.
73. Sparkes, H.A.; Raithby, P.R.; Clot, E.; Shields, G.P.; Chisholm, J.A.; Allen, F.H. Carbonyl Carbonyl Interactions in First-Row Transition Metal Complexes. CrystEngComm. 2006, 8, 563-570.
74. Wood, P.A.; Borwick, S.J.; Watkin, D.J.; Motherwell, W.D.S.; Allen, F.H. Dipolar C N C N Interactions in Organic Crystal Structures: Database Analysis and Calculation of Interaction Energies. Acta Crystallogr. 2008, B64, 393-396.
75. Bolton, W. The Crystal Structure Of Alloxan. Acta Crystallogr. 1964, 17, 147-152.
76. Bolton, W. The Crystal Structure of Triketoindane (Anhydrous Ninhydrin). A Structure Showing Close CO CO interactions. Acta Crystallogr. 1965, 18, 5-10.
77. Davies, D.R.; Blum, J.J. The Crystal Structure of Parabanic Acid. Acta Crystallogr. 1955, 8, 129-136.
78. Bolton, W. The Crystal Structure of Anhydrous Barbituric Acid. Acta Crystallogr. 1963, 16, 166-173.
79. Dunitz, J.D.; Schweizer, W.B. Alloxan: Is it Really a Problem Structuré CrystEngComm. 2007, 9, 266-269.
80. Bruno, I.J.; Cole, J.C.; Lommerse, J.P.M.; Rowland, R.S.; Taylor, R.; Verdonk, M.L. IsoStar: A Library of Information about Intermolecular Interactions. J. Comput. Aided Mol. Des. 1997, 11, 525-537.