Microsolvation of 2-thiouracil: Molecular structure and spectroscopic parameters of the thiouracil-water complex

Journal of Physical Chemistry A

Volumn 119, Issue 21, 2015, Pages 5386-5395

  Puzzarini, Cristina ^a   Biczysko, Malgorzata ^b,c  

^a UNIVERSITY OF BOLOGNA   (Italy)

^b SCUOLA NORMALE SUPERIORE   (Italy)

^c CNR   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATION THEORY; MOLECULAR STRUCTURE; NUMERICAL METHODS; PERTURBATION TECHNIQUES; QUANTUM CHEMISTRY; QUANTUM THEORY; WATER VAPOR;

COMPUTATIONAL APPROACH; EQUILIBRIUM STRUCTURES; MOLECULAR DIPOLE MOMENT; PLESSET PERTURBATION THEORY; QUANTUM CHEMICAL COMPUTATIONS; SPECTROSCOPIC PARAMETERS; SPECTROSCOPIC PROPERTY; STRUCTURE EVALUATIONS;

COMPUTATIONAL CHEMISTRY;

SOLVENT; THIOURACIL; WATER;

CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; SPECTROSCOPY;

COMPUTER SIMULATION; MODELS, MOLECULAR; MOLECULAR STRUCTURE; SOLVENTS; SPECTRUM ANALYSIS; THIOURACIL; WATER;

EID: 84928961707     PISSN: 10895639     EISSN: 15205215     Source Type: Journal    
DOI: 10.1021/jp510511d     Document Type: Article

References (86)

1. Puzzarini et al. Phys. Chem. Chem. Phys. 2013, 15, 16965 - 16975
2. Roscioli, J. R.; Pratt, D. W. Base pair analogs in the gas phase Proc. Natl. Acad. Sci. 2003, 100, 13752-13754
3. Giuliano, B. M.; Caminati, W. Isotopomeric conformational change in anisole-water Angew. Chem., Int. Ed. 2004, 44, 603-606
4. de Vries, M. S.; Hobza, P. Gas-phase spectroscopy of biomolecular building blocks Annu. Rev. Phys. Chem. 2007, 58, 585-612
5. Reha, D.; Valdes, H.; Vondrasek, J.; Hobza, P.; Abu-Riziq, A.; Crews, B.; de Vries, M. S. Structure and IR spectrum of phenylalanyl-glycyl-glycine tripetide in the gas-phase: IR/UV experiments, ab initio quantum chemical calculations, and molecular dynamic simulations Chem.-Eur. J. 2005, 11, 6803-6817
6. Alonso, J.; Cocinero, E.; Lesarri, A.; Sanz, M.; Lopez, J. The glycine-water complex Angew. Chem., Int. Ed. 2006, 45, 3471-3474
7. Blanco, S.; Sanz, M. E.; López, J. C.; Alonso, J. L. Revealing the multiple structures of serine Proc. Natl. Acad. Sci. U. S. A. 2007, 104, 20183-20188
8. Häber, T.; Seefeld, K.; Engler, G.; Grimme, S.; Kleinermanns, K. IR/UV spectra and quantum chemical calculations of Trp-Ser: Stacking interactions between backbone and indole side-chain Phys. Chem. Chem. Phys. 2008, 10, 2844-2851
9. Fricke, H.; Funk, A.; Schrader, T.; Gerhards, M. Investigation of secondary structure elements by IR/UV double resonance spectroscopy: Analysis of an isolated beta-sheet model system J. Am. Chem. Soc. 2008, 130, 4692-4698
10. López, J. C.; Alonso, J. L.; Peña, I.; Vaquero, V. Hydrogen bonding and structure of uracil-water and thymine-water complexes Phys. Chem. Chem. Phys. 2010, 12, 14128-14134
11. Peña, I.; Sanz, M. E.; López, J. C.; Alonso, J. L. Preferred conformers of proteinogenic glutamic acid J. Am. Chem. Soc. 2012, 134, 2305-2312
12. Clarkson, J. R.; Baquero, E.; Shubert, V. A.; Myshakin, E. M.; Jordan, K. J.; Zwier, T. S. Laser-initiated shuttling of a water molecule between H-bonding sites Science 2005, 307, 1443-1446
13. Becucci, M.; Pietraperzia, G.; Pasquini, M.; Piani, G.; Zoppi, A.; Chelli, R.; Castellucci, E.; Demtroeder, W. A study on the anisole-water complex by molecular beam-electronic spectroscopy and molecular mechanics calculations J. Chem. Phys. 2004, 120, 5601
14. Piani, G.; Pasquini, M.; Pietraperzia, G.; Becucci, M.; Schiccheri, N.; Biczysko, M.; Pavone, M.; Barone, V. Isotopomeric conformational changes in the anisole-water complex: New insights from HR-UV spectroscopy and theoretical studies J. Phys. Chem. A 2007, 111, 12363-12371
15. Biczysko, M.; Piani, G.; Pasquini, M.; Schiccheri, N.; Pietraperzia, G.; Becucci, M.; Pavone, M.; Barone, V. On the properties of microsolvated molecules in the ground (S0) and excited (S1) states: The anisole-ammonia 1:1 complex J. Chem. Phys. 2007, 127, 144303
16. Pietraperzia, G.; Pasquini, M.; Schiccheri, N.; Piani, G.; Becucci, M.; Castellucci, E.; Biczysko, M.; Bloino, J.; Barone, V. The gas phase anisole dimer: A combined high-resolution spectroscopy and computational study of a stacked molecular system J. Phys. Chem. A 2009, 113, 14343-14351
17. Schmitt, M.; Bhom, M.; Ratzer, C.; Vu, C.; Kalkman, I.; Meerts, W. L. Structural selection by microsolvation: A conformational locking of tryptamine J. Am. Chem. Soc. 2005, 127, 10356-10364
18. Melandri, S. "Union is strength": How weak hydrogen bonds become strong Phys. Chem. Chem. Phys. 2011, 13, 13901-13911
19. Snoek, L. C.; Kroemer, R. T.; Hockridge, M. R.; Simons, J. P. Conformational landscapes of aromatic amino acids in the gas phase: Infrared and ultraviolet ion dip spectroscopy of tryptophan Phys. Chem. Chem. Phys. 2001, 3, 1819
20. Reimann, B.; Buchold, K.; Barth, H. D.; Brutschy, B.; Tarakeshwar, P.; Kim, K. S. Anisole-(H2O)n (n=1,3) complexes: An experimental and theoretical investigation of the modulation of optimal structures, binding energies, and vibrational spectra in both the ground and first excited states J. Chem. Phys. 2002, 117, 8805
21. Ribblett, J. W.; Sinclair, W. E.; Borst, D. R.; Yi, J. T.; Pratt, D. W. High Resolution electronic spectra of anisole and anisole-water in the gas phase: Hydrogen bond switching in the S1 state J. Phys. Chem. A 2006, 110, 1478-1483
22. Gordy, W.; Cook, R. L. In Microwave Molecular Spectra, 3 rd ed.; Weissberger, A., Ed.; Wiley: New York, 1984.
23. Puzzarini, C.; Stanton, J. F.; Gauss, J. Quantum-chemical calculation of spectroscopic parameters for rotational spectroscopy Int. Rev. Phys. Chem. 2010, 29, 273-367
24. Demaison, J.; Boggs, J. E.; Császár, A. G., Eds. Equilibrium Molecular Structures: From Spectroscopy to Quantum Chemistry; CRC Press: Boca Raton, FL, 2011.
25. Lesarri, A.; Mata, S.; López, J. C.; Alonso, J. L. A laser-ablation molecular-beam Fourier transform microwave spectrometer: The rotational spectrum of organic solids Rev. Sci. Instrum. 2003, 74, 4799-4804
26. Brown, G. G.; Dian, B. C.; Douglass, K. O.; Geyer, S. M.; Shipman, S. T.; Pate, B. H. A broadband Fourier transform microwave spectrometer based on chirped pulse excitation Rev. Sci. Instrum. 2008, 79, 053103/1-13
27. Barone, V., Ed. Computational Strategies for Spectroscopy, from Small Molecules to Nano Systems; John Wiley & Sons, Inc.: New York, 2011.
28. Grunenberg, J., Ed. Computational Spectroscopy; Wiley-VCHVerlag GmbH & Co. KGaA: Weinheim, 2010.
29. Quack, M.; Merkt, F., Eds. Handbook of High-Resolution Spectroscopy; John Wiley & Sons, Inc.: New York, 2011.
30. Senn, H. M.; Thiel, W. QM/MM methods for biomolecular systems Angew. Chem., Int. Ed. 2009, 48, 1198-1229
31. Brooks, B. R.; Brooks, C. L.; Mackerell, A. D.; Nilsson, L.; Petrella, R. J.; Roux, B.; Won, Y.; Archontis, G.; Bartels, C.; Boresch, S.; Caflisch, A.; Caves, L.; Cui, Q.; Dinner, A. R.; Feig, M.; Fischer, S.; Gao, J.; Hodoscek, M.; Im, W.; Kuczera, K.; Lazaridis, T.; Ma, J.; Ovchinnikov, V.; Paci, E.; Pastor, R. W.; Post, C. B.; Pu, J. Z.; Schaefer, M.; Tidor, B.; Venable, R. M.; Woodcock, H. L.; Wu, X.; Yang, W.; York, D. M.; Karplus, M. CHARMM: The biomolecular simulation program J. Comput. Chem. 2009, 30, 1545-1614
32. Pronk, S.; Páll, S.; Schulz, R.; Larsson, P.; Bjelkmar, P.; Apostolov, R.; Shirts, M. R.; Smith, J. C.; Kasson, P. M.; van der Spoel, D.; Hess, B.; Lindahl, E. GROMACS 4.5: A high-throughput and highly parallel open source molecular simulation toolkit Bioinformatics 2013, 29, 845-854
33. Grubisic, S.; Brancato, G.; Pedone, A.; Barone, V. Extension of the AMBER force field to cyclic α,α dialkylated peptides Phys. Chem. Chem. Phys. 2012, 14, 15308-15320
34. Maple, J. R.; Dinur, U.; Hagler, A. T. Derivation of force fields for molecular mechanics and dynamics from ab initio energy surfaces Proc. Natl. Acad. Sci. U. S. A. 1988, 85, 5350-5354
35. Dasgupta, S.; Yamasaki, T.; Goddard, W. A. The Hessian biased singular value decomposition method for optimization and analysis of force fields J. Chem. Phys. 1996, 104, 2898-2920
36. Biczysko, M.; Bloino, J.; Brancato, G.; Cacelli, I.; Cappelli, C.; Ferretti, A.; Lami, A.; Monti, S.; Pedone, A.; Prampolini, G.; Puzzarini, C.; Santoro, F.; Trani, F.; Villani, G. Integrated computational approaches for spectroscopic studies of molecular systems in the gas phase and in solution: Pyrimidine as a test case Theor. Chem. Acc. 2012, 131, 1201
37. Barone, V.; Cacelli, I.; De Mitri, N.; Licari, D.; Monti, S.; Prampolini, G. Joyce and Ulysses: integrated and user-friendly tools for the parametrization of intramolecular force fields from quantum mechanical data Phys. Chem. Chem. Phys. 2013, 15, 3736-3751
38. Grimme, S.; Steinmetz, M. Effects of London dispersion correction indensity functional theory on the structures of organic molecules in the gas phase Phys. Chem. Chem. Phys. 2013, 15, 16031-16042
39. Risthaus, T.; Steinmetz, M.; Grimme, S. Implementation of nuclear gradients of range-separated hybrid density functionals and benchmarking on rotational constants for organic molecules J. Comput. Chem. 2014, 35, 1509-1516
40. Lehninger, A. L. Biochemistry: The Molecular Basis of CellStructure and Function; Worth Publisher: New York, 2 nd ed., 1978.
41. Saenger, W. Springer Advanced Texts in Chemistry, Principles of Nucleic Acid Structure; Springer-Verlag: New York, 1984.
42. Puzzarini, C.; Biczysko, M.; Barone, V.; Peña, I.; Cabezas, C.; Alonso, J. L. Accurate molecular structure and spectroscopic properties of nucleobases: A combined computational-microwave investigation of 2-thiouracil as a case study Phys. Chem. Chem. Phys. 2013, 15, 16965-16975
43. Raghavachari, K.; Trucks, G. W.; Pople, J. A.; Head-Gordon, M. A fifth-order perturbation comparison of electron correlation theories Chem. Phys. Lett. 1989, 157, 479-483
44. Møller, C.; Plesset, M. S. Note on an approximation treatment for many-electron systems Phys. Rev. 1934, 46, 618-622
45. Dunning, T. H., Jr. Gaussian basis sets for use in correlated molecular calculations. I. The atoms boron through neon and hydrogen J. Chem. Phys. 1989, 90, 1007-1023
46. Kendall, A.; Dunning, T. H., Jr.; Harrison, R. J. Electron affinities of the first-row atoms revisited. Systematic basis sets and wave functions J. Chem. Phys. 1992, 96, 6796-6806
47. Woon, D. E.; Dunning, T. H., Jr. Gaussian basis sets for use in correlated molecular calculations. V. Core-valence basis sets for boron through neon J. Chem. Phys. 1995, 103, 4572-4585
48. Peterson, K. A.; Dunning, T. H., Jr. Accurate correlation consistent basis sets for molecular core-valence correlation effects. The second row atoms Al-Ar, and the first row atoms B-Ne revisited J. Chem. Phys. 2002, 117, 10548-10560
49. Stanton, J. F.; Gauss, J.; Harding, M. E.; Szalay, P. G. CFour A quantum chemical program package. 2011; with contributions from A. A. Auer, R. J. Bartlett, U. Benedikt, C. Berger, D. E. Bernholdt, Y. J. Bomble, O. Christiansen, M. Heckert, O. Heun, C. Huber et al. and the integral packages MOLECULE (J. Almloef and P. R. Taylor), PROPS (P. R. Taylor), ABACUS (T. Helgaker, H. J. Aa. Jensen, P. Jørgensen, and J. Olsen), and ECP routines by A. V. Mitin and C. van Wuellen. For the current version, see http://www.cfour.de (accessed September 13, 2012).
50. Stanton, J. F.; Gauss, J. Analytic second derivatives in high-order many-body perturbation and coupled-cluster theories: Computational considerations and applications Int. Rev. Phys. Chem. 2000, 19, 61-95
51. Becke, D. Density-functional thermochemistry. III. The role of exact exchange J. Chem. Phys. 1993, 98, 5648-5652
52. Grimme, S. Semiempirical hybrid density functional with perturbative second-order correlation J. Chem. Phys. 2006, 124, 034108
53. Schwabe, T.; Grimme, S. Double-hybrid density functionals with long-range dispersion corrections: higher accuracy and extended applicability Phys. Chem. Chem. Phys. 2007, 9, 3397-3406
54. Biczysko, M.; Panek, P.; Scalmani, G.; Bloino, J.; Barone, V. Harmonic and Anharmonic Vibrational frequency calculations with the double-hybrid B2PLYP method: Analytic second derivatives and benchmark studies J. Chem. Theory Comput. 2010, 6, 2115-2125
55. Double and triple-ζ basis sets of SNS and N07 families, are available for download. 2012; visit http://compchem.sns.it (accessed February 1, 2014).
56. Barone, V.; Biczysko, M.; Bloino, J. Fully anharmonic IR and Raman spectra of medium-size molecular systems: Accuracy and interpretation Phys. Chem. Chem. Phys. 2014, 16, 1759-1787
57. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Scalmani, G.; Barone, V.; Mennucci, B.; Petersson, G. A.; Gaussian 09, Revision D.01; Gaussian Inc.: Wallingford, CT, 2009.
58. Choi, M. Y.; Miller, R. E. Multiple isomers of uracil-water complexes: infrared spectroscopy in helium nanodroplets Phys. Chem. Chem. Phys. 2005, 7, 3565-3573
59. Puzzarini, C.; Barone, V. Extending the molecular size in accurate quantum-chemical calculations: the equilibrium structure and spectroscopic properties of uracil Phys. Chem. Chem. Phys. 2011, 13, 7189-7197
60. Barone, V.; Biczysko, M.; Bloino, J.; Puzzarini, C. Characterization of the elusive conformers of Glycine from state-of-the-art structural, thermodynamic and spectroscopic computations: theory complements experiment J. Chem. Theory Comput. 2013, 9, 1533-1547
61. Barone, V.; Biczysko, M.; Bloino, J.; Puzzarini, C. The performance of composite schemes and hybrid CC/DFT model in predicting structure, thermodynamic and spectroscopic parameters: the challenge of the conformational equilibrium in glycine Phys. Chem. Chem. Phys. 2013, 15, 10094-10111
62. Barone, V.; Biczysko, M.; Bloino, J.; Puzzarini, C. Accurate molecular structures and infrared spectra of trans-2,3-dideuterooxirane, methyloxirane, and trans-2,3-dimethyloxirane J. Chem. Phys. 2014, 141, 034107/1-17
63. Helgaker, T.; Klopper, W.; Koch, H.; Noga, J. Basis-set convergence of correlated calculations on water J. Chem. Phys. 1997, 106, 9639-9646
64. Puzzarini, C. Extrapolation to the complete basis set limit of structural parameters: Comparison of different approaches J. Phys. Chem. A 2009, 113, 14530-14535
65. Mills, I. M. In Molecular Spectroscopy: Modern Research; Rao, K. N.; Mathews, C. W., Eds.; Academic: New York, 1972.
66. Aliev, M. R.; Watson, J. K. G. In Molecular Spectroscopy: Modern Research, Vol. III; Rao, K. N.; Mathews, C. W., Eds.; Academic: New York, 1982; pp 1-67.
67. Watson, J. K. G. A planarity relation for sextic centrifugal distortion constants J. Mol. Spectrosc. 1977, 65, 123-133
68. Mort, B. C.; Autschbach, J. Magnitude of zero-point vibrational corrections of optical rotation in rigid organic molecules J. Phys. Chem. A 2005, 109, 8617-8623
69. Barone, V. Vibrational zero-point energies and thermodynamic functions beyond the harmonic approximation J. Chem. Phys. 2004, 120, 3059-3065
70. Barone, V. Anharmonic vibrational properties by a fully automated second-order perturbative approach J. Chem. Phys. 2005, 122, 014108
71. Bloino, J.; Barone, V. A second-order perturbation theory route to vibrational averages and transition properties of molecules: General formulation and application to infrared and vibrational circular dichroism spectroscopies J. Chem. Phys. 2012, 136, 124108
72. Puzzarini, C. A theoretical investigation on the HCCS radical and its ions Chem. Phys. 2008, 346, 45-52
73. Mentel, L. M.; Baerends, E. J. Can the counterpoise correction for basis set superposition effect be justified? J. Chem. Theory Comput. 2014, 10, 252-267
74. Boys, S.; Bernardi, F. The calculation of small molecular interactions by the differences of separate total energies. Some procedures with reduced errors Mol. Phys. 1970, 19, 553-566
75. Schuurman, M. S.; Allen, W. D.; von Ragué Schleyer, P.; Schaefer, H. F., III. The highly anharmonic BH5 potential energy surface characterized in the ab initio limit J. Chem. Phys. 2005, 122, 104302
76. Bloino, J.; Biczysko, M.; Barone, V. General perturbative approach for spectroscopy, thermodynamics, and kinetics: Methodological background and benchmark studies J. Chem. Theory Comput. 2012, 8, 1015-1036
77. Helgaker, T.; Gauss, J.; Jørgensen, P.; Olsen, J. The prediction of molecular equilibrium structures by the standard electronic wave functions J. Chem. Phys. 1997, 106, 6430-6440
78. Helgaker, T.; Jørgensen, P.; Olsen, J. Electronic-Structure Theory; Wiley: Chichester, U.K., 2000.
79. Demaison, J. Experimental, semi-experimental and ab initio equilibrium structures Mol. Phys. 2007, 105, 3109-3138
80. Puzzarini, C.; Biczysko, M.; V, B.; Largo, L.; Peña, I.; Cabezas, C.; Alonso, J. L. Accurate characterization of the peptide linkage in the gas phase: A joint quantum-chemical and rotational spectroscopy study of the glycine dipeptide analogue J. Phys. Chem. Lett. 2014, 5, 534-540
81. Sponer, J.; Jurecka, P.; Hobza, P. Accurate interaction energies of hydrogen-bonded nucleic acid base pairs J. Am. Chem. Soc. 2004, 126, 10142-10151
82. Jurecka, P.; Sponer, J.; Cerny, J.; Hobza, P. Benchmark database of accurate (MP2 and CCSD(T) complete basis set limit) interaction energies of small model complexes, DNA base pairs, and amino acid pairs Phys. Chem. Chem. Phys. 2006, 8, 1985-1993
83. Rezac, J.; Riley, K. E.; Hobza, P. S66: A well-balanced database of benchmark interaction energies relevant to biomolecular structures J. Chem. Theory Comput. 2011, 7, 2427-2438
84. Morgado, C. A.; Jurecka, P.; Svozil, D.; Hobza, P.; Sponer, J. Reference MP2/CBS and CCSD(T) quantum-chemical calculations on stacked adenine dimers. Comparison with DFT-D, MP2.5, SCS(MI)-MP2, M06-2X, CBS(SCS-D) and force field descriptions Phys. Chem. Chem. Phys. 2010, 12, 3522-3534
85. Pulay, P.; Meyer, W.; Boggs, J. E. Cubic force constants and equilibrium geometry of methane from Hartree-Fock and correlated wavefunctions J. Chem. Phys. 1978, 68, 5077-5085
86. Pawlowski, F.; Jørgensen, P.; Olsen, J.; Hegelund, F.; Helgaker, T.; Gauss, J.; Bak, K. L.; Stanton, J. F. Molecular equilibrium structures from experimental rotational constants and calculated vibration-rotation interaction constants J. Chem. Phys. 2002, 116, 6482-6496