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James WH, Baquero EE, Choi SH, Gellman SH, Zwier TS. Laser Spectroscopy of Conformationally Constrained α/β-Peptides: Ac-ACPC-Phe-NHMe and Ac-Phe-ACPC-NHMe. J Phys Chem A 2009; 114:1581-91. [PMID: 20039717 DOI: 10.1021/jp9090975] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- William H. James
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - Esteban E. Baquero
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - Soo Hyuk Choi
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - Samuel H. Gellman
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - Timothy S. Zwier
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706
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53
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Minenkov Y, Occhipinti G, Jensen VR. Metal−Phosphine Bond Strengths of the Transition Metals: A Challenge for DFT. J Phys Chem A 2009; 113:11833-44. [DOI: 10.1021/jp902940c] [Citation(s) in RCA: 118] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yury Minenkov
- Department of Chemistry, University of Bergen, Allégaten 41, N-5007 Bergen, Norway
| | - Giovanni Occhipinti
- Department of Chemistry, University of Bergen, Allégaten 41, N-5007 Bergen, Norway
| | - Vidar R. Jensen
- Department of Chemistry, University of Bergen, Allégaten 41, N-5007 Bergen, Norway
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Shimizu A, Mori T, Inoue Y, Yamada S. Combined Experimental and Quantum Chemical Investigation of Chiroptical Properties of Nicotinamide Derivatives with and without Intramolecular Cation−π Interactions. J Phys Chem A 2009; 113:8754-64. [DOI: 10.1021/jp904243w] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Akinori Shimizu
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita 565-0871, Japan, and Department of Chemistry, Graduate School of Science, Ochanomizu University, Tokyo 112-8610, Japan
| | - Tadashi Mori
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita 565-0871, Japan, and Department of Chemistry, Graduate School of Science, Ochanomizu University, Tokyo 112-8610, Japan
| | - Yoshihisa Inoue
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita 565-0871, Japan, and Department of Chemistry, Graduate School of Science, Ochanomizu University, Tokyo 112-8610, Japan
| | - Shinji Yamada
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita 565-0871, Japan, and Department of Chemistry, Graduate School of Science, Ochanomizu University, Tokyo 112-8610, Japan
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James WH, Baquero EE, Shubert VA, Choi SH, Gellman SH, Zwier TS. Single-Conformation and Diastereomer Specific Ultraviolet and Infrared Spectroscopy of Model Synthetic Foldamers: α/β-Peptides. J Am Chem Soc 2009; 131:6574-90. [PMID: 19366210 DOI: 10.1021/ja901051v] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- William H. James
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - Esteban E. Baquero
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - V. Alvin Shubert
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - Soo Hyuk Choi
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - Samuel H. Gellman
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - Timothy S. Zwier
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706
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56
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Raju RK, Ramraj A, Hillier IH, Vincent MA, Burton NA. Carbohydrate-aromatic pi interactions: a test of density functionals and the DFT-D method. Phys Chem Chem Phys 2009; 11:3411-6. [PMID: 19421542 DOI: 10.1039/b822877a] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The performance of a number of computational approaches based upon density functional theory (DFT) for the accurate description of carbohydrate-pi interactions is described. A database containing interaction energies of a small number of representative complexes, computed at a high ab initio level, is described, and is used to judge 18 different density functionals including the M05 and M06 families as well as the DFT method augmented with empirical dispersive corrections (DFT-D). The DFT-D method and the M06 functionals are found to perform particularly well, whilst traditional functionals such as B3LYP perform poorly. The interaction energies for 23 sugar-aromatic complexes calculated by the DFT-D method are compared with the values from the 18 functionals. Again, the M06 class of functional is found to be superior.
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Affiliation(s)
- Rajesh K Raju
- School of Chemistry, University of Manchester, Oxford Road, M13 9PL, Manchester, UK
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Danilov VI, van Mourik T, Kurita N, Wakabayashi H, Tsukamoto T, Hovorun DM. On the Mechanism of the Mutagenic Action of 5-Bromouracil: A DFT Study of Uracil and 5-Bromouracil in a Water Cluster. J Phys Chem A 2009; 113:2233-5. [DOI: 10.1021/jp811007j] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Victor I. Danilov
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Zabolotny Street, Kyiv-143, 03143, Ukraine, School of Chemistry, University of St Andrews, North Haugh, St. Andrews, Fife, KY16 9ST, Scotland, U.K., and Department of Knowledge-based Information Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi 441-8580, Japan
| | - Tanja van Mourik
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Zabolotny Street, Kyiv-143, 03143, Ukraine, School of Chemistry, University of St Andrews, North Haugh, St. Andrews, Fife, KY16 9ST, Scotland, U.K., and Department of Knowledge-based Information Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi 441-8580, Japan
| | - Noriyuki Kurita
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Zabolotny Street, Kyiv-143, 03143, Ukraine, School of Chemistry, University of St Andrews, North Haugh, St. Andrews, Fife, KY16 9ST, Scotland, U.K., and Department of Knowledge-based Information Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi 441-8580, Japan
| | - Hajime Wakabayashi
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Zabolotny Street, Kyiv-143, 03143, Ukraine, School of Chemistry, University of St Andrews, North Haugh, St. Andrews, Fife, KY16 9ST, Scotland, U.K., and Department of Knowledge-based Information Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi 441-8580, Japan
| | - Takayuki Tsukamoto
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Zabolotny Street, Kyiv-143, 03143, Ukraine, School of Chemistry, University of St Andrews, North Haugh, St. Andrews, Fife, KY16 9ST, Scotland, U.K., and Department of Knowledge-based Information Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi 441-8580, Japan
| | - Dmytro M. Hovorun
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Zabolotny Street, Kyiv-143, 03143, Ukraine, School of Chemistry, University of St Andrews, North Haugh, St. Andrews, Fife, KY16 9ST, Scotland, U.K., and Department of Knowledge-based Information Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi 441-8580, Japan
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58
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Gloaguen E, Pollet R, Piuzzi F, Tardivel B, Mons M. Gas phase folding of an (Ala)4 neutral peptide chain: spectroscopic evidence for the formation of a β-hairpin H-bonding pattern. Phys Chem Chem Phys 2009; 11:11385-8. [DOI: 10.1039/b918670k] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Bjornsson R, Arnason I. Conformational properties of six-membered heterocycles: accurate relative energy differences with DFT, the importance of dispersion interactions and silicon substitution effects. Phys Chem Chem Phys 2009; 11:8689-97. [PMID: 20449011 DOI: 10.1039/b910016d] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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60
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Vaden TD, Gowers SAN, Snoek LC. Infrared spectroscopy of ‘forbidden’ peptide sequences. Phys Chem Chem Phys 2009; 11:5843-50. [DOI: 10.1039/b903039e] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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61
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Picot D, Ohanessian G, Frison G. Thermodynamic Stability Versus Kinetic Lability of ZnS4Core. Chem Asian J 2008; 5:1445-54. [DOI: 10.1002/asia.200900624] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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