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Nachaki EO, Leonik FM, Kuroda DG. Effect of the N-Alkyl Side Chain on the Amide-Water Interactions. J Phys Chem B 2022; 126:8290-8299. [PMID: 36219826 DOI: 10.1021/acs.jpcb.2c04988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Amide-water interactions influence the structure and functions of amide-based systems, such as proteins and homopolymers. In particular, the N-alkylation of the amide unit appears to play a critical role in defining the interactions of the amide group. Previous studies have linked the thermal behavior of amide-based polymers to the nature of their N-alkyl side chain. However, the connection between the chemical structure of the N-alkyl and the hydration of the amide remains elusive. In this study, the solvation structure and dynamics of amides, having differing N-alkyl groups, are investigated using a combination of linear and nonlinear infrared spectroscopies and computational methods. Interestingly, the dynamics of the amide local environment do not slow down as the N-alkyl side chain becomes bulkier, but rather speeds up. Computational calculations confirm the hydration dynamics and assign the effect to smaller amplitude and faster rotations of the bulkier group. It is also observed experimentally that the hydrogen-bond making and breaking between water and the amide carbonyl do not directly relate to the size of the N-alkyl side chain. The bulkier N-isopropyl substituent presents significantly slower chemical exchange dynamics than smaller chains (ethyl and methyl), but the two small groups do not present a major difference. The hydrogen-bond making and breaking disparities and similarities among groups are well modeled by the theory demonstrating that the N-alkyl group affects the amide hydration structure and dynamics via a steric effect. In summary, the results presented here show that the size of the N-substituted alkyl group significantly influences the hydration dynamics of amides and stress the importance of considering this effect on much larger systems, such as polymers.
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Affiliation(s)
- Ernest O Nachaki
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana70803, United States
| | - Fedra M Leonik
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana70803, United States
| | - Daniel G Kuroda
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana70803, United States
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2
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Limits in the Enhancement Factor in Near-Brewster Angle Reflection Pump-Probe Two-Dimensional Infrared Spectroscopy. CHINESE J CHEM PHYS 2022. [DOI: 10.1063/1674-0068/cjcp2111234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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3
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Cai K, Zheng X, Du F. Electrostatic frequency maps for amide-I mode of β-peptide: Comparison of molecular mechanics force field and DFT calculations. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 183:150-157. [PMID: 28448953 DOI: 10.1016/j.saa.2017.04.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 04/09/2017] [Accepted: 04/16/2017] [Indexed: 06/07/2023]
Abstract
The spectroscopy of amide-I vibrations has been widely utilized for the understanding of dynamical structure of polypeptides. For the modeling of amide-I spectra, two frequency maps were built for β-peptide analogue (N-ethylpropionamide, NEPA) in a number of solvents within different schemes (molecular mechanics force field based, GM map; DFT calculation based, GD map), respectively. The electrostatic potentials on the amide unit that originated from solvents and peptide backbone were correlated to the amide-I frequency shift from gas phase to solution phase during map parameterization. GM map is easier to construct with negligible computational cost since the frequency calculations for the samples are purely based on force field, while GD map utilizes sophisticated DFT calculations on the representative solute-solvent clusters and brings insight into the electronic structures of solvated NEPA and its chemical environments. The results show that the maps' predicted amide-I frequencies present solvation environmental sensitivities and exhibit their specific characters with respect to the map protocols, and the obtained vibrational parameters are in satisfactory agreement with experimental amide-I spectra of NEPA in solution phase. Although different theoretical schemes based maps have their advantages and disadvantages, the present maps show their potentials in interpreting the amide-I spectra for β-peptides, respectively.
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Affiliation(s)
- Kaicong Cai
- College of Chemistry and Chemical Engineering, Fujian Normal University, Fuzhou, Fujian 350007, PR China; Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen, Fujian 361005, PR China.
| | - Xuan Zheng
- College of Chemistry and Chemical Engineering, Fujian Normal University, Fuzhou, Fujian 350007, PR China; Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen, Fujian 361005, PR China
| | - Fenfen Du
- College of Chemistry and Chemical Engineering, Fujian Normal University, Fuzhou, Fujian 350007, PR China; Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen, Fujian 361005, PR China
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4
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Simulation of the T-jump triggered unfolding and thermal unfolding vibrational spectroscopy related to polypeptides conformation fluctuation. Sci China Chem 2017. [DOI: 10.1007/s11426-016-9055-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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5
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Wang J. Ultrafast two-dimensional infrared spectroscopy for molecular structures and dynamics with expanding wavelength range and increasing sensitivities: from experimental and computational perspectives. INT REV PHYS CHEM 2017. [DOI: 10.1080/0144235x.2017.1321856] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Jianping Wang
- Beijing National Laboratory for Molecular Sciences, Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, The Chinese Academy of Sciences, Beijing, P.R. China
- College of Chemistry, University of Chinese Academy of Sciences, Beijing, P.R. China
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6
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Jeon J, Cho M. An Accurate Classical Simulation of a Two-Dimensional Vibrational Spectrum: OD Stretch Spectrum of a Hydrated HOD Molecule. J Phys Chem B 2014; 118:8148-61. [DOI: 10.1021/jp501182d] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jonggu Jeon
- Department
of Chemistry, Korea University, Seoul 136-701, Korea
| | - Minhaeng Cho
- Department
of Chemistry, Korea University, Seoul 136-701, Korea
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7
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Healion D, Wang H, Mukamel S. Simulation and visualization of attosecond stimulated x-ray Raman spectroscopy signals in trans-N-methylacetamide at the nitrogen and oxygen K-edges. J Chem Phys 2011; 134:124101. [PMID: 21456639 PMCID: PMC4108684 DOI: 10.1063/1.3557057] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2010] [Accepted: 02/01/2011] [Indexed: 01/14/2023] Open
Abstract
The stimulated Raman component of the pump-probe spectrum of trans-N-methylacetamide obtained in response to two soft x-ray pulses is calculated by treating the core excitations at the Hartree-Fock static-exchange level. The signal reveals the dynamics of valence-electron wave packets prepared and detected in the vicinity of a selected atom (either nitrogen or oxygen). The evolving electronic charge density as well as electronic coherence of the doorway and the window created by the two pulses are visualized using a time-dependent basis set of natural orbitals, which reveals that the wave packets consist of several entangled valence particle-hole pairs.
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Affiliation(s)
- Daniel Healion
- Department of Chemistry, University of California, Irvine, California 92697-2025, USA
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8
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Hanna G, Geva E. Computational study of the signature of hydrogen-bond strength on the infrared spectra of a hydrogen-bonded complex dissolved in a polar liquid. Chem Phys 2010. [DOI: 10.1016/j.chemphys.2010.01.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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9
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Lee H, Choi JH, Cho M. Vibrational solvatochromism and electrochromism of cyanide, thiocyanate, and azide anions in water. Phys Chem Chem Phys 2010; 12:12658-69. [DOI: 10.1039/c0cp00214c] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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10
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Candelaresi M, Pagliai M, Lima M, Righini R. Chemical Equilibrium Probed by Two-Dimensional IR Spectroscopy: Hydrogen Bond Dynamics of Methyl Acetate in Water. J Phys Chem A 2009; 113:12783-90. [DOI: 10.1021/jp906072w] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Marco Candelaresi
- European Laboratory for Nonlinear Spectroscopy (LENS), Via Nello Carrara 1, and Dipartimento di Chimica, Università di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino (Fi), Italy
| | - Marco Pagliai
- European Laboratory for Nonlinear Spectroscopy (LENS), Via Nello Carrara 1, and Dipartimento di Chimica, Università di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino (Fi), Italy
| | - Manuela Lima
- European Laboratory for Nonlinear Spectroscopy (LENS), Via Nello Carrara 1, and Dipartimento di Chimica, Università di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino (Fi), Italy
| | - Roberto Righini
- European Laboratory for Nonlinear Spectroscopy (LENS), Via Nello Carrara 1, and Dipartimento di Chimica, Università di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino (Fi), Italy
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11
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Calculations of intermode coupling constants and simulations of amide I, II, and III vibrational spectra of dipeptides. Chem Phys 2009. [DOI: 10.1016/j.chemphys.2009.05.016] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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12
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Kim YS, Hochstrasser RM. Applications of 2D IR spectroscopy to peptides, proteins, and hydrogen-bond dynamics. J Phys Chem B 2009; 113:8231-51. [PMID: 19351162 PMCID: PMC2845308 DOI: 10.1021/jp8113978] [Citation(s) in RCA: 238] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Following a survey of 2D IR principles, this article describes recent experiments on the hydrogen-bond dynamics of small ions, amide-I modes, nitrile probes, peptides, reverse transcriptase inhibitors, and amyloid fibrils.
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Affiliation(s)
- Yung Sam Kim
- Department of Chemistry, University of Pennsylvania Philadelphia, Pennsylvania 19104-6323, U.S.A
| | - Robin M. Hochstrasser
- Department of Chemistry, University of Pennsylvania Philadelphia, Pennsylvania 19104-6323, U.S.A
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Bagchi S, Charnley AK, Smith AB, Hochstrasser RM. Equilibrium exchange processes of the aqueous tryptophan dipeptide. J Phys Chem B 2009; 113:8412-7. [PMID: 19459617 PMCID: PMC2929808 DOI: 10.1021/jp811168x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The tryptophan dipeptide (NATMA) in D2O shows two conformers having distinctive acetyl end amide-I' transition frequencies. In 2D echo spectroscopy, cross peaks between these conformer transitions are used to show that they are undergoing exchange on the 1.5 ps time scale. Simulations suggest that the accessibility of the amide group to water is restricted in one of the conformations.
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Affiliation(s)
- Sayan Bagchi
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, U. S. A
| | - Adam K. Charnley
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, U. S. A
| | - Amos B. Smith
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, U. S. A
| | - Robin M. Hochstrasser
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, U. S. A
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14
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Hanna G, Geva E. Multidimensional Spectra via the Mixed Quantum-Classical Liouville Method: Signatures of Nonequilibrium Dynamics. J Phys Chem B 2009; 113:9278-88. [DOI: 10.1021/jp902797z] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Gabriel Hanna
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055
| | - Eitan Geva
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055
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15
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Zhuang W, Hayashi T, Mukamel S. Kohärente mehrdimensionale Schwingungsspektroskopie von Biomolekülen: Konzepte, Simulationen und Herausforderungen. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200802644] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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16
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17
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Zhuang W, Hayashi T, Mukamel S. Coherent multidimensional vibrational spectroscopy of biomolecules: concepts, simulations, and challenges. Angew Chem Int Ed Engl 2009; 48:3750-81. [PMID: 19415637 PMCID: PMC3526115 DOI: 10.1002/anie.200802644] [Citation(s) in RCA: 125] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The response of complex molecules to sequences of femtosecond infrared pulses provides a unique window into their structure, dynamics, and fluctuating environments. Herein we survey the basic principles of modern two-dimensional infrared (2DIR) spectroscopy, which analogous to those of multidimensional NMR spectroscopy. The perturbative approach for computing the nonlinear optical response of coupled localized chromophores is introduced and applied to the amide backbone transitions of proteins, liquid water, membrane lipids, and amyloid fibrils. The signals are analyzed using classical molecular dynamics simulations combined with an effective fluctuating Hamiltonian for coupled localized anharmonic vibrations whose dependence on the local electrostatic environment is parameterized by an ab initio map. Several simulation methods, (cumulant expansion of Gaussian fluctuation, quasiparticle scattering, the stochastic Liouville equations, direct numerical propagation) are surveyed. Chirality-induced techniques which dramatically enhance the resolution are demonstrated. Signatures of conformational and hydrogen-bonding fluctuations, protein folding, and chemical-exchange processes are discussed.
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Affiliation(s)
- Wei Zhuang
- Department of Chemistry, University of California at Irvine, CA 92697-2025, USA
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18
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Hanna G, Geva E. Computational Study of the One and Two Dimensional Infrared Spectra of a Vibrational Mode Strongly Coupled to Its Environment: Beyond the Cumulant and Condon Approximations. J Phys Chem B 2008; 112:12991-3004. [DOI: 10.1021/jp804120v] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Gabriel Hanna
- Department of Chemistry and FOCUS center, University of Michigan, Ann Arbor, Michigan 48109-1055
| | - Eitan Geva
- Department of Chemistry and FOCUS center, University of Michigan, Ann Arbor, Michigan 48109-1055
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19
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20
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Hayashi T, Mukamel S. Two-Dimensional Vibrational Lineshapes of Amide III, II, I and A Bands in a Helical Peptide. J Mol Liq 2008; 141:149-154. [PMID: 20613971 DOI: 10.1016/j.molliq.2008.02.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
An effective exciton Hamiltonian for all amide bands is used to calculate the linear absorption and photon echo spectra of a 17 residue helical peptide (YKKKH17). The cross peak bandshapes are sensitive to the inter-band couplings. Fluctuations of the local amide frequencies of the all amide fundamental and their overtone and combination states are calculated using the multipole electric field induced by environment employing the electrostatic DFT map of N-methyl acetamide. Couplings between neighboring peptide units are obtained using the anharmonic vibrational Hamiltonian of glycine dipeptide (GLDP) at the BPW91/6-31G(d,p) level. Electrostatic couplings between non-neighboring units are calculated by the fourth rank transition multipole coupling (TMC) expansion including 1/R(3) (dipole-dipole), 1/R(4) (quadrupole-dipole), and 1/R(5) (quadrupole-quadrupole and octapole-dipole) interactions.
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Affiliation(s)
- Tomoyuki Hayashi
- Department of Chemistry, University of California, Irvine, California 92697-2025, USA
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21
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Oh KI, Choi JH, Lee JH, Han JB, Lee H, Cho M. Nitrile and thiocyanate IR probes: Molecular dynamics simulation studies. J Chem Phys 2008; 128:154504. [DOI: 10.1063/1.2904558] [Citation(s) in RCA: 112] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
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22
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Choi JH, Oh KI, Lee H, Lee C, Cho M. Nitrile and thiocyanate IR probes: Quantum chemistry calculation studies and multivariate least-square fitting analysis. J Chem Phys 2008; 128:134506. [DOI: 10.1063/1.2844787] [Citation(s) in RCA: 155] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
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23
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Hasegawa T, Tanimura Y. Nonequilibrium molecular dynamics simulations with a backward-forward trajectories sampling for multidimensional infrared spectroscopy of molecular vibrational modes. J Chem Phys 2008; 128:064511. [DOI: 10.1063/1.2828189] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
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24
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Dijkstra AG, la Cour Jansen T, Bloem R, Knoester J. Vibrational relaxation in simulated two-dimensional infrared spectra of two amide modes in solution. J Chem Phys 2007; 127:194505. [DOI: 10.1063/1.2786455] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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25
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Woutersen S. Simultaneous photon absorption as a probe of molecular interaction and hydrogen-bond cooperativity in liquids. J Chem Phys 2007; 127:154517. [DOI: 10.1063/1.2779033] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Affiliation(s)
- Sander Woutersen
- Van’t Hoff Institute for Molecular Sciences, University of Amsterdam, Nieuwe Achtergracht 127-129, 1018 WV Amsterdam, The Netherlands
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