Computational vibrational spectroscopy of peptides and proteins in one and two dimensions

Jonggu Jeon, Seongeun Yang, Jun H O Choi, Minhaeng Cho

Research output: Contribution to journalArticle

65 Citations (Scopus)

Abstract

Vibrational spectroscopy provides direct information on molecular environment and motions but, its interpretation is often hampered by band broadening. Over the past decade, two-dimensional (2D) vibrational spectroscopy has emerged as a promising technique to overcome a number of difficulties associated with linear spectroscopy and provided significantly detailed information on the structure and dynamics of complex molecules in condensed phases. This Account reviews recently developed computational methods used to simulate ID and 2D vibrational spectra. The central quantity to calculate in computational spectroscopy is the spectroscopic response function, which is the product of many contributing factors such as vibrational transition energies, transition moments, and their modulations by fluctuating local environment around a solute. Accurate calculations of such linear and nonlinear responses thus require a concerted effort employing a wide range of methods including electronic structure calculation (ESC) and molecular dynamics (MD) simulation. The electronic structure calculation can provide fundamental quantities such as normal-mode frequencies and transition multipole strengths. However, since the treatable system size is limited with this method, classical MD simulation has also been used to account for the dynamics of the solvent environment. To achieve chemical accuracy, these two results are combined to generate time series of fluctuating transition frequencies and transition moments with the distributed multipole analysis, and this particular approach has been known as the hybrid ESC/MD method. For coupled multichromophore systems, vibrational properties of each chromophore such as a peptide are individually calculated by electronic structure methods and the Hessian matrix reconstruction scheme was used to obtain local mode frequencies and couplings of constituting anharmonic oscillators. The spectra thus obtained, especially for biomolecules including polypeptides and proteins, have proven to be reliable and in good agreement with experimental spectra. An alternative to the hybrid method has also been developed, where the classical limit of the vibrational response function was considered. Its main attraction is the capability to obtain the spectra directly from a set of MD trajectories. A novel development along this direction has been achieved by using quantum mechanical/molecular mechanical (QM/MM) force fields for the accurate description of vibrational anharmonicity and chromophore polarization effects. The latter aspects are critical in the 2D case because classical force fields employing harmonic intramolecular potential cannot produce reliable 2D signal. We anticipate that the computational methods presented here will continue to evolve along with experimental advancements and will be of use to further elucidate ultrafast dynamics of chemical and biological systems.

Original languageEnglish
Pages (from-to)1280-1289
Number of pages10
JournalAccounts of Chemical Research
Volume42
Issue number9
DOIs
Publication statusPublished - 2009 Sep 15

Fingerprint

Vibrational spectroscopy
Electronic structure
Molecular dynamics
Peptides
Chromophores
Computational methods
Proteins
Spectroscopy
Computer simulation
Biomolecules
Vibrational spectra
Biological systems
Time series
Trajectories
Modulation
Polarization
Molecules

ASJC Scopus subject areas

  • Chemistry(all)

Cite this

Computational vibrational spectroscopy of peptides and proteins in one and two dimensions. / Jeon, Jonggu; Yang, Seongeun; Choi, Jun H O; Cho, Minhaeng.

In: Accounts of Chemical Research, Vol. 42, No. 9, 15.09.2009, p. 1280-1289.

Research output: Contribution to journalArticle

Jeon, Jonggu ; Yang, Seongeun ; Choi, Jun H O ; Cho, Minhaeng. / Computational vibrational spectroscopy of peptides and proteins in one and two dimensions. In: Accounts of Chemical Research. 2009 ; Vol. 42, No. 9. pp. 1280-1289.
@article{0f67374a71b644b2b66334956b170740,
title = "Computational vibrational spectroscopy of peptides and proteins in one and two dimensions",
abstract = "Vibrational spectroscopy provides direct information on molecular environment and motions but, its interpretation is often hampered by band broadening. Over the past decade, two-dimensional (2D) vibrational spectroscopy has emerged as a promising technique to overcome a number of difficulties associated with linear spectroscopy and provided significantly detailed information on the structure and dynamics of complex molecules in condensed phases. This Account reviews recently developed computational methods used to simulate ID and 2D vibrational spectra. The central quantity to calculate in computational spectroscopy is the spectroscopic response function, which is the product of many contributing factors such as vibrational transition energies, transition moments, and their modulations by fluctuating local environment around a solute. Accurate calculations of such linear and nonlinear responses thus require a concerted effort employing a wide range of methods including electronic structure calculation (ESC) and molecular dynamics (MD) simulation. The electronic structure calculation can provide fundamental quantities such as normal-mode frequencies and transition multipole strengths. However, since the treatable system size is limited with this method, classical MD simulation has also been used to account for the dynamics of the solvent environment. To achieve chemical accuracy, these two results are combined to generate time series of fluctuating transition frequencies and transition moments with the distributed multipole analysis, and this particular approach has been known as the hybrid ESC/MD method. For coupled multichromophore systems, vibrational properties of each chromophore such as a peptide are individually calculated by electronic structure methods and the Hessian matrix reconstruction scheme was used to obtain local mode frequencies and couplings of constituting anharmonic oscillators. The spectra thus obtained, especially for biomolecules including polypeptides and proteins, have proven to be reliable and in good agreement with experimental spectra. An alternative to the hybrid method has also been developed, where the classical limit of the vibrational response function was considered. Its main attraction is the capability to obtain the spectra directly from a set of MD trajectories. A novel development along this direction has been achieved by using quantum mechanical/molecular mechanical (QM/MM) force fields for the accurate description of vibrational anharmonicity and chromophore polarization effects. The latter aspects are critical in the 2D case because classical force fields employing harmonic intramolecular potential cannot produce reliable 2D signal. We anticipate that the computational methods presented here will continue to evolve along with experimental advancements and will be of use to further elucidate ultrafast dynamics of chemical and biological systems.",
author = "Jonggu Jeon and Seongeun Yang and Choi, {Jun H O} and Minhaeng Cho",
year = "2009",
month = "9",
day = "15",
doi = "10.1021/ar900014e",
language = "English",
volume = "42",
pages = "1280--1289",
journal = "The BMJ",
issn = "0730-6512",
publisher = "Kluwer Academic Publishers",
number = "9",

}

TY - JOUR

T1 - Computational vibrational spectroscopy of peptides and proteins in one and two dimensions

AU - Jeon, Jonggu

AU - Yang, Seongeun

AU - Choi, Jun H O

AU - Cho, Minhaeng

PY - 2009/9/15

Y1 - 2009/9/15

N2 - Vibrational spectroscopy provides direct information on molecular environment and motions but, its interpretation is often hampered by band broadening. Over the past decade, two-dimensional (2D) vibrational spectroscopy has emerged as a promising technique to overcome a number of difficulties associated with linear spectroscopy and provided significantly detailed information on the structure and dynamics of complex molecules in condensed phases. This Account reviews recently developed computational methods used to simulate ID and 2D vibrational spectra. The central quantity to calculate in computational spectroscopy is the spectroscopic response function, which is the product of many contributing factors such as vibrational transition energies, transition moments, and their modulations by fluctuating local environment around a solute. Accurate calculations of such linear and nonlinear responses thus require a concerted effort employing a wide range of methods including electronic structure calculation (ESC) and molecular dynamics (MD) simulation. The electronic structure calculation can provide fundamental quantities such as normal-mode frequencies and transition multipole strengths. However, since the treatable system size is limited with this method, classical MD simulation has also been used to account for the dynamics of the solvent environment. To achieve chemical accuracy, these two results are combined to generate time series of fluctuating transition frequencies and transition moments with the distributed multipole analysis, and this particular approach has been known as the hybrid ESC/MD method. For coupled multichromophore systems, vibrational properties of each chromophore such as a peptide are individually calculated by electronic structure methods and the Hessian matrix reconstruction scheme was used to obtain local mode frequencies and couplings of constituting anharmonic oscillators. The spectra thus obtained, especially for biomolecules including polypeptides and proteins, have proven to be reliable and in good agreement with experimental spectra. An alternative to the hybrid method has also been developed, where the classical limit of the vibrational response function was considered. Its main attraction is the capability to obtain the spectra directly from a set of MD trajectories. A novel development along this direction has been achieved by using quantum mechanical/molecular mechanical (QM/MM) force fields for the accurate description of vibrational anharmonicity and chromophore polarization effects. The latter aspects are critical in the 2D case because classical force fields employing harmonic intramolecular potential cannot produce reliable 2D signal. We anticipate that the computational methods presented here will continue to evolve along with experimental advancements and will be of use to further elucidate ultrafast dynamics of chemical and biological systems.

AB - Vibrational spectroscopy provides direct information on molecular environment and motions but, its interpretation is often hampered by band broadening. Over the past decade, two-dimensional (2D) vibrational spectroscopy has emerged as a promising technique to overcome a number of difficulties associated with linear spectroscopy and provided significantly detailed information on the structure and dynamics of complex molecules in condensed phases. This Account reviews recently developed computational methods used to simulate ID and 2D vibrational spectra. The central quantity to calculate in computational spectroscopy is the spectroscopic response function, which is the product of many contributing factors such as vibrational transition energies, transition moments, and their modulations by fluctuating local environment around a solute. Accurate calculations of such linear and nonlinear responses thus require a concerted effort employing a wide range of methods including electronic structure calculation (ESC) and molecular dynamics (MD) simulation. The electronic structure calculation can provide fundamental quantities such as normal-mode frequencies and transition multipole strengths. However, since the treatable system size is limited with this method, classical MD simulation has also been used to account for the dynamics of the solvent environment. To achieve chemical accuracy, these two results are combined to generate time series of fluctuating transition frequencies and transition moments with the distributed multipole analysis, and this particular approach has been known as the hybrid ESC/MD method. For coupled multichromophore systems, vibrational properties of each chromophore such as a peptide are individually calculated by electronic structure methods and the Hessian matrix reconstruction scheme was used to obtain local mode frequencies and couplings of constituting anharmonic oscillators. The spectra thus obtained, especially for biomolecules including polypeptides and proteins, have proven to be reliable and in good agreement with experimental spectra. An alternative to the hybrid method has also been developed, where the classical limit of the vibrational response function was considered. Its main attraction is the capability to obtain the spectra directly from a set of MD trajectories. A novel development along this direction has been achieved by using quantum mechanical/molecular mechanical (QM/MM) force fields for the accurate description of vibrational anharmonicity and chromophore polarization effects. The latter aspects are critical in the 2D case because classical force fields employing harmonic intramolecular potential cannot produce reliable 2D signal. We anticipate that the computational methods presented here will continue to evolve along with experimental advancements and will be of use to further elucidate ultrafast dynamics of chemical and biological systems.

UR - http://www.scopus.com/inward/record.url?scp=70349233964&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=70349233964&partnerID=8YFLogxK

U2 - 10.1021/ar900014e

DO - 10.1021/ar900014e

M3 - Article

VL - 42

SP - 1280

EP - 1289

JO - The BMJ

JF - The BMJ

SN - 0730-6512

IS - 9

ER -