Vibrational cross-angles in condensed molecules: A structural tool

Journal of Physical Chemistry A

Volumn 117, Issue 35, 2013, Pages 8407-8415

  Chen, Hailong ^a   Zhang, Yufan ^a   Li, Jiebo ^a   Liu, Hongjun ^b   Jiang, De En ^b   Zheng, Junrong ^a  

^a RICE UNIVERSITY   (United States)

^b OAK RIDGE NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CHEMICAL AND BIOLOGICALS; MOLECULAR CONFORMATION; MOLECULAR DYNAMICS SIMULATIONS; MOLECULAR PHENOMENA; NUCLEAR MAGNETIC RESONANCE(NMR); THERMODYNAMIC INTERACTIONS; VIBRATIONAL SPECTROSCOPIC TECHNIQUES; VIBRATIONAL TRANSITIONS;

MOLECULAR DYNAMICS; MOLECULES; X RAY DIFFRACTION;

CONFORMATIONS;

EID: 84883658096     PISSN: 10895639     EISSN: 15205215     Source Type: Journal    
DOI: 10.1021/jp406304c     Document Type: Article

References (33)

1. Tian, P.; Keusters, D.; Suzaki, Y.; Warren, W. S. Femtosecond Phase-Coherent Two-Dimensional Spectroscopy Science 2003, 300, 1553-1555
2. DeFlores, L. P.; Ganim, Z.; Nicodemus, R. A.; Tokmakoff, A. Amide I′-II′ 2D IR Spectroscopy Provides Enhanced Protein Secondary Structural Sensitivity J. Am. Chem. Soc. 2009, 131, 3385-3391
3. Finkelstein, I. J.; Zheng, J. R.; Ishikawa, H.; Kim, S.; Kwak, K.; Fayer, M. D. Probing Dynamics of Complex Molecular Systems with Ultrafast 2D IR Vibrational Echo Spectroscopy Phys. Chem. Chem. Phys. 2007, 9, 1533-1549
4. Haleblian, J.; McCrone, W. Pharmaceutical Applications of Polymorphism J. Pharm. Sci. 1969, 58, 911-929
5. Haleblian, J. K. Characterization of Habits and Crystalline Modification of Solids and Their Pharmaceutical Applications J. Pharm. Sci. 1975, 64, 1269-1288
6. Borka, L.; Haleblian, J. K. Crystal Polymorphism of Pharmaceuticals Acta Pharm. Jugosl. 1990, 40, 71-94
7. Weissenhorn, W.; Dessen, A.; Calder, L.; Harrison, S.; Skehel, J.; Wiley, D. Structural Basis for Membrane Fusion by Enveloped Viruses Mol. Membr. Biol. 1999, 16, 3-9
8. Gibbons, D. L.; Vaney, M.-C.; Roussel, A.; Vigouroux, A.; Reilly, B.; Lepault, J.; Kielian, M.; Rey, F. A. Conformational Change and Protein-Protein Interactions of the Fusion Protein of Semliki Forest Virus Nature 2004, 427, 320-325
9. Zheng, J.; Kwac, K.; Xie, J.; Fayer, M. D. Ultrafast Carbon-Carbon Single Bond Rotational Isomerization in Room Temperature Solution Science 2006, 313, 1951-1955
10. Ernst, R. R.; Bodenhausen, G.; Wokaun, A. Nuclear Magnetic Resonance in One and Two Dimensions; Oxford University Press: Oxford, U.K., 1987.
11. Bifulco, G.; Dambruoso, P.; Gomez-Paloma, L.; Riccio, R. Determination of Relative Configuration in Organic Compounds by NMR Spectroscopy and Computational Methods Chem. Rev. 2007, 107, 3744
12. Chen, H. L.; Bian, H. T.; Li, J. B.; Wen, X. W.; Zheng, J. R. Relative Intermolecular Orientation Probed via Molecular Heat Transport J. Phys. Chem. A. 2013, 117, 6052-6065
13. Chen, H. L.; Bian, H. T.; Li, J. B.; Wen, X. W.; Zheng, J. R. Ultrafast Multiple-Mode Multiple-Dimensional Vibrational Spectroscopy Int. Rev. Phys. Chem. 2012, 31, 469-565
14. Rubtsov, I. V.; Kumar, K.; Hochstrasser, R. M. Dual-Frequency 2D IR Photon Echo of a Hydrogen Bond Chem. Phys. Lett. 2005, 402, 439-443
15. Khalil, M.; Demirdoven, N.; Tokmakoff, A. Coherent 2D IR Spectroscopy: Molecular Structure and Dynamics in Solution J. Phys. Chem. A. 2003, 107, 5258-5279
16. Dong, F.; Miller, R. E. Vibrational Transition Moment Angles in Isolated Biomolecules: A Structural Tool Science 2002, 298, 1227-1230
17. Bian, H. T.; Li, J. B.; Wen, X. W.; Sun, Z. G.; Song, J. A.; Zhuang, W.; Zheng, J. R. Mapping Molecular Conformations with Multiple-Mode Two-Dimensional Infrared Spectroscopy J. Phys. Chem. A 2011, 115, 3357-3365
18. Bian, H. T.; Li, J. B.; Chen, H. L.; Yuan, K. J.; Wen, X. W.; Li, Y. Q.; Sun, Z. G.; Zheng, J. R. Molecular Conformations and Dynamics on Surfaces of Gold Nanoparticles Probed with Multiple-Mode Multiple-Dimensional Infrared Spectroscopy J. Phys. Chem. C 2012, 116, 7913-7924
19. Petersen, P. B.; Tokmakoff, A. Source for Ultrafast Continuum Infrared and Terahertz Radiation Opt. Lett. 2010, 35, 1962-1964
20. Calabrese, C.; Stingel, A. M.; Shen, L.; Petersen, P. B. Ultrafast Continuum Mid-Infrared Spectroscopy: Probing the Entire Vibrational Spectrum in a Single Laser Shot with Femtosecond Time Resolution Opt. Lett. 2012, 37, 2265-2267
21. Fletton, R. A.; Lancaster, R. W.; Harris, R. K.; Kenwright, A. M.; Packer, K. J.; Waters, D. N.; Yeadon, A. A Comparative Spectroscopic Investigation of Two Polymorphs of 4′-Methyl-2′-nitroacetanilide Using Solid-State Infrared and High-Resolution Solid-State Nuclear Magnetic Resonance Spectroscopy J. Chem. Soc., Perkin Trans. 2 1986, 1705-1709
22. Wang, J. M.; Wolf, R. M.; Caldwell, J. W.; Kollman, P. A.; Case, D. A. Development and Testing of a General Amber Force Field J. Comput. Chem. 2004, 25, 1157-1174
23. Bayly, C. I.; Cieplak, P.; Cornell, W. D.; Kollman, P. A. A Well-Behaved Electrostatic Potential Based Method Using Charge Restraints for Deriving Atomic Charges: The Resp Model J. Phys. Chem. 1993, 97, 10269-10280
24. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Gaussian 09, revision A.02; Gaussian, Inc.: Wallingford, CT, 2009.
25. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. Comparison of Simple Potential Functions for Simulating Liquid Water J. Chem. Phys. 1983, 79, 926-935
26. Plimpton, S. Fast Parallel Algorithms for Short-Range Molecular-Dynamics J. Comput. Phys. 1995, 117, 1-19
27. Shinoda, W.; Shiga, M.; Mikami, M. Rapid estimation of elastic constants by molecular dynamics simulation under constant stress Phys. Rev. B 2004, 69, 134103
28. Gattermann, L. Ueber einige Derivate des m -Nitro- p -Toluidins Berichte der deutschen chemischen Gesellschaft 1885, 18, 1482-1488
29. Moore, J. C.; Yeadon, A.; Palmer, R. A. Crystal and Molecular Structures of Two Polymorphs of 4-Methyl-2-nitroacetanilide (MNA) J. Chem. Cryst. 1983, 13, 279-292
30. Fayer, M. D., Ed. Ultrafast Infrared and Raman Spectroscopy; Marcel Dekker, Inc: New York, 2001; Vol. 26.
31. Lakowicz, J. Principles of Fluorescence Spectroscopy, 3 rd ed.; Springer: New York, 2006.
32. Bernstein, J. Polymorphism in Molecular Crystals; Clarendon Press/International Union of Crystallography: Oxford, U.K., 2002; Vol. 14.
33. Alarco, P. J.; Abu-Lebdeh, Y.; Abouimrane, A.; Armand, M. The Plastic-Crystalline Phase of Succinonitrile As a Universal Matrix for Solid-State Ionic Conductors Nat. Mater. 2004, 3, 476-481