The embedded ion method: A new approach to the electrostatic description of crystal lattice effects in chemical shielding calculations

Concepts in Magnetic Resonance Part A: Bridging Education and Research

Volumn 28, Issue 5, 2006, Pages 347-368

  Stueber, Dirk ^a  

^a WASHINGTON UNIVERSITY   (United States)

Author keywords

Crystal lattice effects; Electrostatic; Embedded ion method (eim); Ewald method; Intermolecular interactions; NMR; Nuclear magnetic shielding tensor; Point charge arrays; Quantum mechanical shielding calculations

Indexed keywords

EID: 33749420995     PISSN: 15466086     EISSN: 15525023     Source Type: Journal    
DOI: 10.1002/cmr.a.20061     Document Type: Article

References (123)

1. Grant DM. 1996. Chemical shift tensors. In: Grant DM, Harris RK, editors. Encyclopedia of NMR. Volume 2. Chichester: John Wiley. p 1298-1312.
2. Facelli JC, Grant DM. 1989. Molecular structure and carbon-13 chemical shielding tensors obtained from nuclear magnetic resonance. Top Stereochem 19:1-62.
3. Facelli JC, Grant DM. 1993. Determination of molecular symmetry in crystalline naphthalene using solid-state NMR. Nature 365:325-327.
4. Veeman WS. 1984. Carbon-13 chemical shift anisotropy. Prog Nucl Magn Reson Spectrosc 16:193-235.
5. Facelli JC, de Dios AC, editors. 1999. Modeling NMR chemical shifts: gaining insights into structure and environment. Volume 732. Washington, DC: American Chemical Society.
6. 13C solid-state NMR spectroscopy. J Am Chem Soc 123(8):1713-1722.
7. 15N chemical shift tensors in nucleic acid bases. J Am Chem Soc 120(38):9863-9869.
8. 15N chemical shift principal values in nitrogen heterocycles. J Am Chem Soc 119(41):9804-9809.
9. Harper KJ, Mulgrew AE, Li JY, Barich DH, Strobel GA, Grant DM. 2001. Characterization of stereochemistry and molecular conformation using solid-state NMR tensors. J Am Chem Soc 123(40):9837-9842.
10. 13C chemical shift tensors in terpenes. Magn Reson Chem 36:135-134.
11. 13C shielding tensors in condensed aromatic hydrocarbons. Theor Chim Acta 71:277-288.
12. 13C chemical shift tensors in terpenes. 3. Structural characterization of polymorphous verbanol. J Am Chem Soc 122(15): 3708-3714.
13. Seminario JM, Politzer P, editors. 1995. Modern density functional theory: a tool for chemistry. Volume 2. New York: Elsevier.
14. Helgaker T, Jaszunski M, Ruud K. 1999. Ab initio methods for the calculation of NMR shielding and indirect spin-spin coupling constants. Chem Rev 99: 293-352.
15. Keith T, Bader RFW. 1992. Calculation of magnetic response properties using atoms in molecules. Chem Phys Lett 194(1-2):1-8.
16. Keith TA, Bader RFW. 1993. Calculation of magnetic response properties using a continuous set of gauge transformations. Chem Phys Lett 210(1-3):223-231.
17. Ditchfield R. 1974. Self-consistent perturbation theory of diamagnetism I. A gauge-invariant LCAO method for NMR chemical shifts. Mol Phys 27:789-807.
18. Ditchfield R. 1972. Molecular orbital theory of magnetic shielding and magnetic susceptibility. J Chem Phys 56(11):5688-5691.
19. 13C chemical shift tensors in purine. In: Facelli JC, de Dios AC, editors. Modeling NMR chemical shifts. Volume 732. Gaining insights into structure and environment. ACS Symposium Series. Washington, DC: American Chemical Society. p 162-176.
20. Facelli JC. 1998. Nitrogen-15 chemical shifts in at (adenosine-thymine) and cg (cytosine-guanine) nucleic acid base pairs. J Biomol Struct Dyn 16:619-629.
21. Facelli JC. 2003. Calculations of chemical shieldings: theory and applications. Concepts Magn Reson 20A(1):42-69.
22. Jameson CJ. 1987. The chemical shift. In: Mason J, editor. Multinuclear NMR. New York: Plenum Press.
23. Witanowski M, Stefaniak L, Webb GA. 1986. Nitrogen NMR spectroscopy. Annual reports on NMR spectroscopy. Volume 18. New York: Academic Press.
24. 15N chemical shift tensors of β-HMX. J Phys Chem A 106(26):6352-6357.
25. 13C chemical shift tensors in terpenes. 2. NMR characterization of distinct molecules in the asymmetric unit and steric influences on shift in parthenolide. J Am Chem Soc 121(27):6488-6496.
26. Liu F, Phung CG, Alderman DW, Grant DM. 1996. Analyzing and assigning carbon-13 chemical-shift tensors in fructose, sorbose, and xylose single crystal. J Magn Reson A 120:231-241.
27. Liu F, Phung CG, Alderman DW, Grant DM. 1996. Analyzing and assigning carbon-13 chemical-shift tensors in α-L-rhamnose monohydrate single crystals. J Magn Reson Series A 120:242-248.
28. Liu F, Phung CG, Alderman DW, Grant DM. 1996. Carbon-13 chemical shift tensors in methyl glycosides, comparing diffraction and optimized structures with single-crystal NMR. J Am Chem Soc 118(43): 10629-10634.
29. 13C. Chem Phys Lett 134(5):461-466.
30. 15N nuclear magnetic shielding scale from gas phase studies. J Chem Phys 74(1):81-88.
31. Carter CM, Facelli JC, Alderman DW, Dalley NK, Wilson BE, Grant DM. 1988. Carbon-13 chemical-shift tensors in single-crystal methoxybenzenes. J Chem Soc Faraday Trans 1 84:3673-3690.
32. Carter CM, Alderman DW, Facelli JC, Grant DM. 1987. Carbon-13 chemical shielding tensors in polycyclic aromatic compounds. 1. Single-crystal study of pyrene. J Am Chem Soc 109(9):2639-2644.
33. Sherwood MH, Facelli JC, Alderman DW, Grant DM. 1991. Carbon-13 chemical shift tensors in polycyclic aromatic compounds. 2. Single-crystal study of naphthalene. J Am Chem Soc 113(3):750-753.
34. Soderquist A, Hughes CD, Horton WJ, Facelli JC, Grant DM. 1992. Carbon-13 chemical shift tensors in aromatic compounds. 3. Phenanthrene and triphenylene. J Am Chem Soc 114:2826-2832.
35. Orendt AM, Sethi NK, Facelli JC, Horton WJ, Pugmire RJ, Grant DM. 1992. Carbon-13 chemical shift tensors in aromatic compounds. 4. Substituted naphthalenes. J Am Chem Soc 114(8):2832-2836.
36. Iuliucci RJ, Facelli JC, Alderman DW, Grant DM. 1995. Carbon-13 chemical shift tensors in polycyclic aromatic compounds. 5. Single-crystal study of acenaphthene. J Am Chem Soc 117(8):2336-2343.
37. Iuliucci RJ, Phung CG, Facelli JC, Grant DM. 1996. Carbon-13 chemical shift tensors in polycyclic aromatic compounds. 6. Single-crystal study of perylene. J Am Chem Soc 118(20):4880-4888.
38. Iuliucci RJ, Phung CG, Facelli JC, Grant DM. 1998. Carbon-13 chemical shift tensors in polycyclic aromatic compounds. 7. Symmetry augmented chemical shift-chemical-shift correlation spectroscopy and single crystal study of triphenylene. J Am Chem Soc 120(36):9305-9311.
39. 13C NMR, X-ray, and quantum mechanical studies of the carbon chemical shift tensors of p-tolyl ether. J Phys Chem 98(47): 12186-12190.
40. Solum MS, Facelli JC, Grant DM, Michl J. 1986. Low-temperature carbon-13 magnetic resonance in solids. 7. Methyl carbons. J Am Chem Soc 108(21): 6464-6470.
41. 13C chemical shift tensor in cadmium acetate dihydrate. Chem Phys Lett 302:499-504.
42. 15N chemical shift tensors: benzamide. J Am Chem Soc 118(23): 5488-5489.
43. Facelli JC. 2000. Nitrogen-15 chemical shift in the pyridine-methanol complex. Chem Phys Lett 322:91-96.
44. Liu F, Orendt AM, Alderman DW, Grant DM. 1997. Carbon-13 chemical shift tensors on pentaerythritol. J Am Chem Soc 119(38):8981-8984.
45. 13C dipolar NMR spectroscopy. J Am Chem Soc 99(26):10454-10458.
46. Facelli JC, Gu Z, McDermott AE. 1995. Carbon-13 chemical shift tensors of carboxylic acids: GIAO calculations in acetic acid + methylamine dimer. Mol Physics 86(4):865-872.
47. 13C chemical shielding tensors in ionic compounds using point charge arrays obtained from Ewald lattice sums. J Chem Phys 114:9236-9243.
48. de Dios AC, Pearson JG, Oldfield E. 1993. Secondary and tertiary structural effects on protein NMR chemical shifts: an ab initio approach. Science 260:1491-1496.
49. de Dios AC, Laws DD, Oldfield E. 1994. Predicting carbon-13 nuclear magnetic resonance chemical shielding tensors in Zwitterionic L-threonine and L-tyrosine via quantum chemistry. J Am Chem Soc 116(17):7784-7786.
50. Ewald PP. 1921. Die Berechnung optischer und elektrischer Gitterpotentiale. Ann Phys 64:253-287.
51. Derenzo SE, Klintenberg MK, Weber MJ. 2000. Determining point charge arrays that produce accurate ionic crystal lattice fields for atomic cluster calculations. J Chem Phys 112(5):2074-2081.
52. Klintenberg M, Derenzo SE, Weber MJ. 2000. Accurate crystal fields for embedded cluster calculations. J Comput Phys Commun 131:120-128.
53. 13C chemical shift tensors in potassium carbonate, bicarbonate and related monomethyl derivatives. Solid State NMR 22:29-49.
54. 13C chemical shift tensor principal values and orientations in dialkyl carbonates and trithiocarbonates. Solid State NMR.
55. 15N Chemical shift tensors in adenosine, guanosine dihydrate, 2′-deoxythymidine, and cytidine. J Am Chem Soc 124(35):10359-10551.
56. 14N quadrupolar coupling constant calculations in amino acid crystals: zwitterionic, hydrogen-bonded systems. J Phys Chem A 107(38):7629-7642.
57. Barich DH, Clawson JS, Stueber D, Strohmeier M, Pugmire RJ, Grant DM. 2002. Determination of 13C chemical shift tensors in the presence of hydrogen bonding and 14N quadrupolar coupling: p-aminosalicylic acid, isaniazid, and pyrazinamide. J Phys Chem A 106(46):11375-11379.
58. 15N chemical shifts in energetic materials: CP/MAS and ab initio studies of aminonitropyridines, aminonitropyrimidines, and their N-oxides. Int J Mol Sci 3:858-872.
59. Weiner SJ, Kollman PA, Nguyen DT, Case DA. 1986. An all atom force field for simulations of proteins and nucleic acids. J Comput Chem 7(2):230-252.
60. Stefanovich EV, Truong TN. 1998. A simple method for incorporating Madelung field effects into ab initio embedded cluster calculations of crystals and macromolecules. J Phys Chem B 102(16):3018-3022.
61. 19F solid state NMR chemical shifts. J Mol Struct 602/603:159-164.
62. Di Fiori N, Orendt AM, Caputo MC, Ferraro MB. Facelli JC. 2004. Modeling solid-state effects on NMR chemical shifts using electrostatic models. Magn Reson Chem 42:S41-S47.
63. Chipot C, Maigret B, Rivail J-L. 1992. Modeling amino acid side chains. 1. Determination of net atomic charges from ab initio self-consistent-field molecular electrostatic properties. J Chem Phys 96(25): 10276-10284.
64. Spackman MA. 1996. Potential derived charges using a geodesic point selection scheme. J Comput Chem 17(1):1-18.
65. Schmidt MW, Baldridge KK, Boatz JA. Elbert ST, Gordon MS, Jensen JH, et al. 1993. General atomic and molecular electronic structure system. J Comput Chem 14(11):1347-1363.
66. 15N chemical shift tensors. Solid State Nucl Magn Res 10(4):185-189.
67. 2 oxidative addition. J Phys Chem 100(50).
68. Karadakov PB, Morokuma K. 2000. ONIOM as an efficient tool for calculating NMR chemical shielding constants in large molecules. Chem Phys Lett 317: 589-596.
69. Rickard GA, Karadakov PB, Webb AW, Morokuma K. 2003. Calculation of NMR chemical shifts in carbohydrates with ONIOM: a study of the conformera of β-D-glucopyranose. J Phys Chem A 107(2):292-300.
70. Warshel A, Karplus M. 1972. Calculation of ground and excited state potential surfaces of conjugated molecules. I. Formulation and parameterization. J Am Chem Soc 94(16):5612-5625.
71. Field MJ, Bash PA, Karplus M. 1990. A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations. J Comput Chem 11(6):700-733.
72. Cui Q, Karplus M. 2000. Molecular properties from combined QM/MM methods. 2. Chemical shifts in large molecules. J Phys Chem B 104(15):3721-3743.
73. Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M. 1983. CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem 4(2): 187-217.
74. Cui Q, Karplus M. 2000. Molecular properties from combined QM/MM methods. I. Analytical second derivative and vibrational calculations. J Chem Phys 112(3):1133-1149.
75. Mauri F, Pfrommer BG, Louie SG. 1996. Ab initio theory of NMR chemical shifts in solids and liquids. Phys Rev Lett 77(26):5300-5303.
76. Mauri F, Louie SG. 1996. Magnetic susceptibility of insulators from first principles. Phys Rev Lett 76(22): 4246-4249.
77. Mauri F, Pfrommer BG, Louie SG. 1997. Ab initio NMR chemical shift of diamond, chemical-vapor-deposited diamond, and amorphous carbon. Phys Rev Lett 79(12):2340-2343.
78. Yoon Y-G, Pfrommer BG, Mauri F, Louie SG. 1998. NMR chemical shifts in hard carbon nitride compounds. Phys Rev Lett 80(15):3388-3391.
79. Mauri F, Pfrommer BG, Louie SG. 1999. Signature of surface states on NMR chemical shifts: a theoretical prediction. Phys Rev B 60(4):2941-2945.
80. 13C chemical shifts of retinylidene iminium salts. J Phys Chem B 104(38):9048-9053.
81. Pfrommer BG, Mauri F, Louie SG. 2000. NMR chemical shifts of ice and liquid water: the effect of condensation. J Am Chem Soc 122(1):123-129.
82. 29Si analysis. Phys Rev B 62(8):R4786-R4789.
83. Cheeseman JR, Trucks GW, Keith T, Frisch MJ. 1996. A comparison of models for calculating nuclear magnetic resonance shielding tensors. J Chem Phys 104(14):5497-5509.
84. Pickard CJ, Mauri F. 2001. All-electron magnetic response with pseudopotentials: NMR chemical shifts. Phys Rev B 63:245101.
85. Sebastiani D, Parrinello M. 2001. A new ab-initio approach for NMR chemical shifts in periodic systems. J Phys Chem A 105(10):1951-1958.
86. Car R, Parrinello M. 1985. Unified approach for molecular dynamics and density-functional theory. Phys Rev Lett 55(22):2471-2474.
87. Hutter J, Alavi A, Deutsch T, Bernasconi M, Goedecker D, Marx M, et al. Computer Code CPMD, Version 3.8. Max-Planck-Institut für Festkörperforschung Stuttgart and IBM Research Laboratory. Available at: http://www.cpmd.org
88. Sebastiani D, Goward G, Schnell I, Spiess HW. 2003. NMR chemical shifts in proton conducting crystals from first principles. J Mol Struct (Theochem) 625(1-3):283-288.
89. Sebastiani D, Rothlisberger U. 2004. Nuclear magnetic resonance chemical shifts from hybrid DFT QM/MM calculations. J Phys Chem B 108(9):2807-2815.
90. Kittel C. 1996. Introduction to solid state physics. New York: Wiley.
91. Toukmaji AY, John JAB. 1996. Ewald summation techniques in perspective: a survey. Comp Phys Commun 95:73-92.
92. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, et al. 2001. Gaussian 98. Revision A. 10. Pittsburgh: Gaussian, Inc.
93. Klooster WT, Ruble JR, Craven BM. 1991. Structure and thermal vibrations of adenosine from neutron diffraction data at 123K. Acta Cryst B 47:376-383.
94. Storer JW, Giesen DJ, Cramer CJ, Truhlar DG. 1995. Class IV charge models: a new semiempirical approach in quantum chemistry. J Comput Aided Mol Des 9:87-110.
95. Straatsma TP, McCammon JA. 1992. Computational alchemy. Annu Rev Phys Chem 43:407-435.
96. Wiberg KB, Rablen PR. 1993. Comparison of atomic charges derived via different procedures. J Comput Chem 14(12):1504-1518.
97. Dewar MJS, Zoebisch EG, Healy EF, Stewart JJP. 1985. Development and use of quantum mechanical molecular models. 76. AMI: a new general purpose quantum mechanical molecular model. J Am Chem Soc 107(13):3902-3909.
98. Stewart JJP. 1989. Optimization of parameters for semiempirical methods I. Method. J Comput Chem 10(2):209-220.
99. Stewart JJP. 1989. Optimization of parameters for semiempirical methods II. Applications. J Comput Chem 10(2):221-264.
100. Foster JP, Weinhold F. 1980. Natural hybrid orbitals. J Am Chem Soc 102(24):7211-7218.
101. Reed AE, Weinhold F. 1983. Natural bond orbital analysis of near-Hartree-Fock water dimer. J Chem Phys 78(6):4066-4073.
102. Reed AE, Weinhold F. 1985. Natural localized molecular orbitals. J Chem Phys 83(4):1736-1740.
103. Reed AE, Curtiss LA, Weinhold F. 1988. Intermolecular interactions from a natural bond orbital, donor-acceptor viewpoint. Chem Rev 88(6):899-926.
104. Weinhold F, Carpenter JE. 1988. The structure of small molecules and ions. In: Naaman R, Vager Z, editors. New York: Plenum Press. p 227-236.
105. Pacios LF, Gomez PC. 2001. Atomic charges in confomers of gaseous glycine. J Mol Struct (Theochem) 544:237-251.
106. Breneman CM, Wiberg KB. 1990. Determining atom-centered monopoles from molecular electrostatic potentials. The need for high sampling density in formamide conformational analysis. J Comput Chem 11(3):361-373.
107. Carpenter JE. 1987. Extension of Lewis structure concepts to open-shell and excited-state molecular species. Ph.D. thesis. University of Wisconsin-Madison, Madison, WI.
108. Becke AD. 1988. Density-functional exchange-energy approximation with correct asymptotic behavior. Phys Rev A 38:3098-3100.
109. Becke AD. 1993. Density-functional thermochemistry. III. The role of exact exchange. J Chem Phys 98(7):5648-5652.
110. Lee C, Yang W, Parr RG. 1988. Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. Phys Rev B 37: 785-789.
111. Miehlich B, Savin A, Stoll H, Preuss H. 1989. Results obtained with the correlation energy density functionals of Becke and Lee, Yang and Parr. Chem Phys Lett 157(3):200-206.
112. Kendall RA, Dunning Jr. TH, Harrison RJ. 1992. Electron affinities of the first-row atoms revisited. Systematic basis set and wave functions. J Chem Phys 96(9):6796-6806.
113. Dunning TH Jr, Hay PG. 1977. Methods of electronic structure theory. In: Schaefer HF, editor. New York: Plenum Press.
114. Jeffrey GA. 1997. An introduction to hydrogen bonding. Oxford: Oxford University Press.
115. Gu Z, Zambrano R, McDermott AE. 1994. Hydrogen bonding of carboxyl groups in solid-state amino acids and peptides: comparison of carbon chemical shielding, infrared frequencies, and structures. J Am Chem Soc 116(14):6368-6372.
116. Stueber D. 2001. The measurement and interpretation of carbon-13 and nitrogen-15 chemical shift tensors in selected ionic and polar systems [Ph.D. thesis]. University of Utah, Salt Lake City, UT.
117. Joensson P-G, Kvick A. 1972. Precision neutron diffraction structure determination of protein and nucleic acid components. III. The crystal structure of amino acid α-glycine. Acta Cryst B 28:1827-1833.
118. Kvick A. 1980. Experimental study of the influence of temperature on a hydrogen-bonded system: the crystal structure of γ-glycine at 83 K and 298 K by neutron diffraction. Acta Cryst B 36:115-120.
119. Lehmann MS, Koetzle TF, Hamilton WC. 1972. Precision neutron diffraction structure determination of protein and nucleic acid components. I. The crystal structure of the amino acid 1-alanine. J Am Chem Soc 94(8):2657-2660.
120. Ramanadham M, Sikka SK, Chidambaram R. 1972. Structure of L-asparagine monohydrate by neutron diffraction. Acta Cryst B 28:3000-3005.
121. Fuess H, Hohlwein D, Mason SA. 1977. Neutron diffraction study of 1-histidine hydrochloride monohydrate. Acta Cryst B 33:654-659.
122. McLean AD, Chandler GS. 1980. Contracted Gaussian basis sets for molecular calculations. I. Second row atoms, Z = 11-18. J Chem Phys 72(10): 5639-5648.
123. Krishnan R, Binkley JS, Seeger R, Pople JA. 1980. Self-consistent molecular orbital methods. XX. A basis set for correlated wave functions. J Chem Phys 72(1):650-654.