Modeling and analysing thermal motion in experimental charge density studies

Modern Charge-Density Analysis

Volumn , Issue , 2012, Pages 133-163

  Madsen, Anders Ø ^a  

^a UNIVERSITY OF COPENHAGEN   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

MOTION ANALYSIS;

ATOMIC MOTION; BACK-GROUND KNOWLEDGE; EXPERIMENTAL CHARGE DENSITY; MOLECULAR MOTIONS; THERMAL MOTION;

CHARGE DENSITY;

EID: 84872871870     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-90-481-3836-4_3     Document Type: Chapter

References (77)

1. Stewart RF, Feil D (1980) A theoretical study of elastic X-ray scattering. Acta Crystallogr A 36(4):503-509.
2. Willis BTM, Pryor AW (1975) Thermal vibrations in crystallography. Cambridge University Press, London/New York.
3. Born M, Huang K (1954) Dynamical theory of crystal lattices. Clarendon, Oxford.
4. Lefebvre J, More M, Fouret R, Hennion B, Currat R (1975) Lattice-vibrations in deuterated urea. J Phys C 8(13):2011-2021.
5. Madsen A, Civalleri B, Ferrabone M, Pascale F, Dovesi R (2011) Anisotropic displacement parameters for molecular crystals from periodic HF and DFT calculations. Acta Crystallogr B (submitted).
6. Willis BTM, Howard JAK (1975) Do the ellipsoids of thermal vibration mean anything?-analysis of neutron diffraction measurements on hexamethylenetetramine. Acta Crystallogr A 31:514-520.
7. Flensburg C, Stewart RF (1999) Lattice dynamical Debye-Waller factor for silicon. Phys Rev B 60(1):284-290.
8. Born M, Sarginson K (1941) The effect of thermal vibrations on the scattering of X-rays. Proc R Soc Lond A 179:69-93.
9. Trueblood KN, Burgi HB, Burzlaff H, Dunitz JD, Gramaccioli CM, Schulz HH, Shmueli U, Abrahams SC (1996) Atomic displacement parameter nomenclature. Report of a subcommittee on atomic displacement parameter nomenclature. Acta Crystallogr A 52(5):770-781.
10. Kuhs WF (1992) Generalized atomic displacements in crystallographic structure analysis. Acta Crystallogr A 48:80-98.
11. Sprensen HO, Stewart RF, Mc Intyre GJ, Larsen S (2003) Simultaneous variation of multipole parameters and Gram-Charlier coefficients in a charge-density study of tetrafluorotereph- thalonitrile based on X-ray and neutron data. Acta Crystallogr A 59(6):540-550.
12. Swaminathan S, Craven BN, Mc Mullanrk (1984) The crystal structure and molecular thermal motion of urea at 12, 60 and 123 k from neutron diffraction. Acta Crystallogr B 40:300-306.
13. Hummel W, Hauser J, Buergi HB (1990) PEANUT: computer graphics program to represent atomic displacement parameters. J Mol Graph 8:214-220.
14. Johnson CK (1976) ORTEPII. Report ORNL-5138. Technical report. Oak Ridge National Laboratory, Tennessee.
15. Hirshfeld FL (1976) Can X-ray data distinguish bonding effects from vibrational smearing? Acta Crystallogr A 32:239-244.
16. Rosenfield RE Jr, Trueblood KN, Dunitz JD (1978) A test for rigid-body vibrations, based on a generalization of Hirshfeld’s ‘rigid-bond’ postulate. Acta Crystallogr A 34:828-829.
17. Cruickshank DWJ (1956) The analysis of the anisotropic thermal motion of molecules in crystals. Acta Crystallogr 9:754.
18. Cruickshank DWJ (1956) The entropy of crystalline naphthalene. Acta Crystallogr 9(12): 1010-1011.
19. Schomaker V, Trueblood KN (1998) Correlation of internal torsional motion with overall molecular motion in crystals. Acta Crystallogr B 54:507-514.
20. Dunitz JD, Maverick EF, Trueblood KN (1988) Atomic motions in molecular crystals from diffraction measurements. Angew Chem Int Ed Engl 27:880-895.
21. Trueblood KN, Dunitz JD (1983) Internal molecular motions in crystals. The estimation of force constants, frequencies and barriers from diffraction data. A feasibility study. Acta Crystallogr B Acta Cryst. B 39:120-133.
22. Dunitz JD, White DNJ (1973) Non-rigid-body thermal-motion analysis. Acta Crystallogr A 29:93.
23. He XM, Craven BM (1993) Internal vibrations of a molecule consisting of rigid segments. I. Non-interacting internal vibrations. Acta Crystallogr A 49:10-22.
24. He XM, Craven BM (1985) Internal molecular vibrations from crystal diffraction data by quasinormal mode analysis. Acta Crystallogr A 41:244-251.
25. Schomaker V, Trueblood KN (1968) On the rigid-body motion of molecules in crystals. Acta Crystallogr B 24:63-76.
26. Burgi HB, Capelli SC (2000) Dynamics of molecules in crystals from multi-temperature anisotropic displacement parameters. I. Theory. Acta Crystallogr A 56:403-412.
27. Capelli SC, Fortsch M, Burgi HB (2000) Dynamics of molecules in crystals from multitemperature anisotropic displacement parameters. II. Application to benzene (C6D6) and urea [OC(NH)2]. Acta Crystallogr A 56:413-424.
28. Burgi HB, Capelli SC, Goeta AE, Howard JAK, Spackman MA, Yufit DS (2002) Electron distribution and molecular motion in crystalline benzene: an accurate experimental study combining CCD X-ray data on C6H6 with multitemperature neutron-diffraction results on C6H6. Chem Eur J 8(15):3512-3521.
29. Spek AL (1990) PLATON, an integrated tool for the analysis of the results of a single crystal structure determination. Acta Crystallogr A 46:C34.
30. Capelli SC, Hauser J (2004) NKA user manual, 16.2.2004 edn. Universitat Bern, Bern.
31. Johnson CK (1970) Thermal neutron diffraction, Chap. 9. Oxford University Press, New York.
32. Hamilton WC, Edmonds JW, Tippe A, Rush JJ (1969) Methyl group rotation and low temperature transition in hexamethylbenzene-a neutron diffraction study. Discuss Faraday Soc 48:192-204.
33. Aree T, Buergi HB (2006) Specific heat of molecular crystals from atomic mean square displacements with the Einstein, Debye, and Nernst-Lindemann models. J Phys Chem B 110(51):26, 129-26, 134.
34. Madsen A0, Larsen S (2007) Insights into solid state thermodynamics from diffraction data. Angew Chem Int Ed 46:8609-8613.
35. Madsen A0, Mattson R, Larsen S (2011) Understanding thermodynamic properties at the molecular level: multiple temperature charge density study of ribitol and xylitol. J Phys Chem 115(26):7794-7804.
36. Coppens P (1968) Evidence for systematic errors in X-ray temperature parameters resulting from bonding effects. Acta Crystallogr B 24(9):1272-1274.
37. Blessing RH (1995) On the differences between X-ray and neutron thermal vibration parameters. Acta Crystallogr B 51:816-823.
38. Becker PJ, Coppens P (1975) Extinction within the limit of validity of the Darwin transfer equations. I. General formalisms for primary and secondary extinction and their application to spherical crystals. Acta Crystallogr A 31:129-147.
39. Rossmanith E (2003) UMWEG: a program for the calculation and graphical representation of multiple-diffraction patterns. J Appl Cryst 36(Part 6):1467-1474.
40. Merritt E (1999) Comparing anisotropic displacement parameters in protein structures. Acta Crystallogr D 55:1997-2004.
41. Whitten AE, Spackman MA (2006) Anisotropic displacement parameters for H atoms using an ONIOM approach. Acta Crystallogr B 62:875-888.
42. Munshi P, Madsen AO, Spackman MA, Larsen S, Destro R (2008) Estimated H-atom anisotropic displacement parameters: a comparison between different methods and with neutron diffraction results. Acta Crystallogr A 64(Part 4):465-475.
43. Gramaccioli CM, Filippini G, Simonetta M (1982) Lattice-dynamical evaluation of temperature factors for aromatic hydrocarbons, including internal molecular motion: a straightforward systematic procedure. Acta Crystallogr A 38:350-356.
44. Gramaccioli CM, Filippini G (1983) Lattice-dynamical evaluation of temperature factors in non-rigid molecular crystals: a first application to aromatic hydrocarbons. Acta Crystallogr A 39:784-791.
45. Lee C, Gonze X (1995) Ab initio calculation of the thermodynamic properties and atomic temperature factors of SiO2a-quarts and stishovite. Phys Rev B 51(13):8610-8613.
46. Parlinski K, Li ZQ, Kawazoe Y (1997) First-principles determination of the soft mode in cubic ZrO2. Phys Rev Lett 78(21):4063-4066.
47. Schowalter M, Rosenauer A, Titantah JT, Lamoen D (2009) Temperature-dependent Debye- Waller factors for semiconductors with the wurtzite-type structure. Acta Crystallogr A 65: 227-231.
48. Dovesi R, Saunders VR, Roetti C, Orlando R, Zicovich-Wilson CM, Pascale F, Civalleri B, Doll K, Harrison NM, Bush IJ, D’Arco P, Llunell M (2009) CRYSTAL09 user’s manual. Universita di Torino, Torino.
49. Stewart RF, Davidson ER, Simpson WT (1965) Coherent X-ray scattering for the hydrogen atom in the hydrogen molecule. J Chem Phys 42(9):3175-3187.
50. Roversi P, Destro M (2004) Approximate anisotropic displacement parameters for H atoms in molecular crystals. Chem Phys Lett 386:472-478.
51. Madsen A, S0rensen HO, Stewart RF, Flensburg C, Larsen S (2004) Modeling of nuclear parameters for hydrogen atoms in X-ray charge density studies. Acta Crystallogr A 60: 550-561.
52. Hoser AA, Dominiak PM, WoZniak K (2009) Towards the best model for H atoms in experimental charge-density refinement. Acta Crystallogr A 65(4):300-311.
53. Chandler GS, Spackman MA (1982) Pseudoatom expansions of the first-row diatomic hydride electron densities. Acta Crystallogr A 38:225-239.
54. Mata I, Espinosa E, Molins E, Veintemillas S, Maniukiewicz W, Lecomte C, Cousson A, Paulus W (2006) Contributions to the application of the transferability principle and the multipolar modeling of H atoms: electron-density study of L-histidinium dihydrogen orthophosphate orthophosphoric acid. I. Acta Crystallogr A 62(5):365-378.
55. Jayatilaka D, Dittrich B (2008) X-ray structure refinement using aspherical atomic density functions obtained from quantum-mechanical calculations. Acta Crystallogr A 64(Part 3): 383-393.
56. Hirshfeld F (1977) Bonded-atom fragments for describing molecular charge-densities. Theor Chim Acta 44(2):129-138.
57. Destro R, Roversi P, Barzaghi M, Marsh RE (2000) Experimental charge density of a-glycine at 23 K. J Phys Chem A 104:1047-1054.
58. May E, Destro R, Gatti C (2001) The unexpected and large enhancement of the dipole moment in the 3,4-bis(dimethylamino)-3-cyclobutene-1,2-dione (DMACB) molecule upon crystallization: a new role of the intermolecular CH- • • O interactions. J Am Chem Soc 123(49):12248-12254.
59. Forni A, Destro R (2003) Electron density investigation of a push-pull ethylene (C14H12NO2 • • • H2O) by x-ray diffraction at T = 21 K. Chem Eur J 9(22):5528-5537.
60. Destro R, Soave R, Barzaghi M, Lo Presti L (2005) Progress in the understanding of drug- receptor interactions, part 1: experimental charge-density study of an angiotensin II receptor antagonist (C30H30N6O3S) at T = 17 K. Chem Eur J 11(16):4621-4634.
61. Soave R, Barzaghi M, Destro R (2007) Progress in the understanding of drug-receptor interactions, part 2: experimental and theoretical electrostatic moments and interaction energies of an angiotensin II receptor antagonist C30H30N6O3S. Chem Eur J 13(24):6942-6956.
62. Allen FH, Watson DG, Brammer L, Orpen AG, Taylor R (1999) Typical interatomic distances: organic compounds. In: Wilson AJC, Prince E (eds) International tables for crystallography, vol C. Kluwer Academic Publishers, Dordrecht/Boston/London, pp 782-803.
63. Weber HP, Craven BM, Sawzip P, Mc Mullan RK (1991) Crystal structure and thermal vibrations of cholesteryl acetate from neutron diffraction at 123 and 20 K. Acta Crystallogr B 47:116-127.
64. Gao Q, Weber HP, Craven BM, Mc Mullan RK (1994) Structure of suberic acid at 18.4, 75 and 123 K from neutron diffraction data. Acta Crystallogr B 50(6):695-703.
65. Kampermann SP, Sabine TM, Craven BM, Mc Mullan RK (1995) Hexamethylenetetramine: extinction and thermal vibrations from neutron diffraction at six temperatures. Acta Crystallogr A 51:489-497.
66. Luo J, Ruble JR, Craven BM, Mc Mullan RK (1996) Effects of H/D substitution on thermal vibrations in piperazinium hexanoate-H1 1, D1 1. Acta Crystallogr B 52(2):357-368.
67. Madsen A0, Mason S, Larsen S (2003) A neutron diffraction study of xylitol: derivation of mean square internal vibrations for hydrogen atoms from a rigid-body description. Acta Crystallogr B 59:653-663.
68. Madsen A0 (2006) SHADE web server for estimation of hydrogen anisotropic displacement parameters. J Appl Cryst 39:757-758.
69. Hall SR, Allen FH, Brown ID (1991) The crystallographic information file (CIF): a new standard archive file for crystallography. Acta Crystallogr A 47:655-685.
70. Volkov A, Macchi P, Farrugia LJ, Gatti C, Mallinson P, Richter T, Koritsanszky T. (2006) XD2006-A computer program package for multipole refinement, topological analysis of charge densities and evaluation of intermolecular energies from experimental and theoretical structure factors.
71. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Montgomery Jr JA, Vreven T, Kudin KN, Burant JC, Millam JM, Iyengar SS, Tomasi J, Barone V, Mennucci B, Cossi M, Scalmani G, Rega N, Petersson GA, Nakatsuji H, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Klene M, Li X, Knox JE, Hratchian HP, Cross JB, Bakken V, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin AJ, Cammi R, Pomelli C, Ochterski JW, Ayala PY, Morokuma K, Voth GA, Salvador P, Dannenberg JJ, Zakrzewski VG, Dapprich S, Daniels AD, Strain Mc, Farkas O, Malick DK, Rabuck AD, Raghavachari K, Foresman JB, Ortiz JV, Cui Q, Baboul AG, Clifford S, Cioslowski J, Stefanov BB, Liu G, Liashenko A, Piskorz P, Komaromi I, Martin RL, Fox DJ, Keith T, Al-Laham MA, Peng CY, Nanayakkara A, Challacombe M, Gill PMW, Johnson B, Chen W, Wong MW, Gonzalez C, Pople JA (2004) Gaussian 03, revision C.02 (2003). Gaussian, Inc, Wallingford.
72. Williams RV, Gadgil VR, Luger P, Koritsanszky T, Weber M (1999) The search for homoaromatic semibullvalenes. 6. X-ray structure and charge density studies of 1,5-dimethyl- 2,4,6,8-semibullvalenetetracarboxylic dianhydride in the temperature range 123-15 K. J Org Chem 64:1180-1190.
73. Buschmann J, Koritsanszky T, Lentz D, Luger P, Nickelt N, Willemsen S (2000) Structure and charge density studies on 1,1-difluoroallene and tetrafluoroallene. Z Kristallogr 215:487-494.
74. Koritsanszky T, Buschmann J, Lentz D, Luger P, Perpetuo G, Rottger M (1999) Topological analysis of the experimental electron density of diisocyanomethane at 115 k. Chem Eur J 5:3413-3420.
75. Koritsanszky T, Zobel D, Luger P (2000) Topological analysis of experimental electron densities. 3. potassium hydrogen(C)-tartrate at 15 K. J Phys Chem A 104:1549-1556.
76. Flaig R, Koritsanszky T, Zobel D, Luger P (1998) Topological analysis of the experimental electron densities of amino acids. 1. D, L-Aspartic acid at 20 K. J Am Chem Soc 120: 2227-2238.
77. Oddershede J, Larsen S (2004) Charge density study of naphthalene based on X-ray diffraction data at four different temperatures and theoretical calculations. J Phys Chem A 108:1057-1063.