First-Principles Approach to Vibrational Spectroscopy of Biomolecules

Herrmann, Carmen; Reiher, Markus

doi:10.1007/128_2006_082

Cited by 65 publications

(69 citation statements)

References 218 publications

(243 reference statements)

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“…[37,52] Within this approximation, the normal modes Q p are obtained as eigenvectors of the mass-weighted molecular Hessian matrix H (m) , which contains the second derivatives of the total electronic energy of the considered molecule with respect to Cartesian nuclear coordinates. The corresponding eigenvalues equal the squared angular frequencies of the vibrations, w 2 p = 4p 2 n 2 p , in which n p is the vibrational frequency corresponding to the normal mode Q p .…”

Section: Resultsmentioning

confidence: 99%

Understanding the Signatures of Secondary‐Structure Elements in Proteins with Raman Optical Activity Spectroscopy

Jacob

Luber

Reiher

2009

Chemistry A European J

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110

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A prerequisite for the understanding of functional molecules like proteins is the elucidation of their structure under reaction conditions. Chiral vibrational spectroscopy is one option for this purpose, but provides only indirect access to this structural information. By first-principles calculations, we investigate how Raman optical activity (ROA) signals in proteins are generated and how signatures of specific secondary-structure elements arise. As a first target we focus on helical motifs and consider polypeptides consisting of twenty alanine residues to represent alpha-helical and 3(10)-helical secondary-structure elements. Although ROA calculations on such large molecules have not been carried out before, our main goal is the stepwise reconstruction of the ROA signals. By analyzing the calculated ROA spectra in terms of rigorously defined localized vibrations, we investigate in detail how total band intensities and band shapes emerge. We find that the total band intensities can be understood in terms of the reconstructed localized vibrations on individual amino acid residues. Two different basic mechanisms determining the total band intensities can be established, and it is explained how structural changes affect the total band intensities. The band shapes can be rationalized in terms of the coupling between the localized vibrations on different residues, and we show how different band shapes arise as a consequence of different coupling patterns. As a result, it is demonstrated for the chiral variant of Raman spectroscopy how collective vibrations in proteins can be understood in terms of well-defined localized vibrations. Based on our calculations, we extract characteristic ROA signatures of alpha helices and of 3(10)-helices, which our analysis directly relates to differences in secondary structure.

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Section: Resultsmentioning

confidence: 99%

Understanding the Signatures of Secondary‐Structure Elements in Proteins with Raman Optical Activity Spectroscopy

Jacob

Luber

Reiher

2009

Chemistry A European J

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110

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“…With the development of quantitatively improved functionals, DFT has received attention not only in the calculation of molecular structure but also in the vibrational spectroscopy of large molecules (Sousa et al 2007). Recent benchmark calculations on organic (Bento et al 2008) and organometallic reactions (Rayón et al 2008), as well as molecular properties of smaller polyatomic compounds (Mohn et al 2005), vibrational spectroscopy of biomolecules (Herrmann and Reiher 2007), and adiabatic ionization energies (Feller et al 2008), show undeniably that the accuracy of PESs is not better than 10 kJ mol −1 , typically, at critical points, which is far below the standard needed for a quantitative understanding of high-resolution vibrational spectroscopy.…”

Section: Ab Initio Calculations Of Potential Energy Surfacesmentioning

confidence: 99%

Global Analytical Potential Energy Surfaces for High‐resolution Molecular Spectroscopy and Reaction Dynamics

Marquardt¹,

Qüack²

2011

Handbook of High‐resolution Spectroscopy

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Analytical representations of potential energy hypersurfaces for the nuclear motion in polyatomic molecules from ab initio theory and experiment are discussed in a general way. The qualification of potential hypersurface representations from ab initio theory regarding the description of experimental data from rovibrational high-resolution spectroscopy and chemical reaction kinetics is analyzed in more detail for a restricted group of molecules including methane, CH 4 , ammonia, NH 3 , H 2 O 2 , and (HF) 2 . Current methods for the derivation of analytical representations of potential energy surfaces as well as some applications are reviewed.

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“…12 One is based on normal mode analysis ͑NMA͒, 13 with either a quantum mechanical ͑QM͒, 14 an empirical molecular mechanical ͑MM͒, 15 or a QM/MM ͑Ref. 16͒ potential function; to consider the effect of thermal fluctuation, it is possible to average the computed IR spectra over a large number of configurations sampled from equilibrium molecular dynamics simulations.…”

Section: Introductionmentioning

confidence: 99%

The vibrational spectra of protonated water clusters: A benchmark for self-consistent-charge density-functional tight binding

Cui

2007

The Journal of Chemical Physics

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The vibrational spectra of protonated water clusters: A benchmark for selfconsistent-charge density-functional tight binding AbstractProton transfers are involved in many chemical processes in solution and in biological systems. Although water molecules have been known to transiently facilitate proton transfers, the possibility that water molecules may serve as the "storage site" for proton in biological systems has only been raised in recent years. To characterize the structural and possibly the dynamic nature of these protonated water clusters, it is important to use effective computational techniques to properly interpret experimental spectroscopic measurements of condensed phase systems. Bearing this goal in mind, we systematically benchmark the self-consistent-charge density-functional tight-binding �SCC-DFTB� method for the description of vibrational spectra of protonated water clusters in the gas phase, which became available only recently with infrared multiphoton photodissociation and infrared predissociation spectroscopic experiments. It is found that SCC-DFTB qualitatively reproduces the important features in the vibrational spectra of protonated water clusters, especially concerning the characteristic signatures of clusters of various sizes. In agreement with recent ab initio molecular dynamics studies, it is found that dynamical effects play an important role in determining the vibrational properties of these water clusters. Considering computational efficiency, these benchmark calculations suggest that the SCC-DFTB/molecular mechanical approach can be an effective tool for probing the structural and dynamic features of protonated water molecules in biomolecular systems. The vibrational spectra of protonated water clusters: A benchmark for self-consistent-charge density-functional tight binding Proton transfers are involved in many chemical processes in solution and in biological systems. Although water molecules have been known to transiently facilitate proton transfers, the possibility that water molecules may serve as the "storage site" for proton in biological systems has only been raised in recent years. To characterize the structural and possibly the dynamic nature of these protonated water clusters, it is important to use effective computational techniques to properly interpret experimental spectroscopic measurements of condensed phase systems. Bearing this goal in mind, we systematically benchmark the self-consistent-charge density-functional tight-binding ͑SCC-DFTB͒ method for the description of vibrational spectra of protonated water clusters in the gas phase, which became available only recently with infrared multiphoton photodissociation and infrared predissociation spectroscopic experiments. It is found that SCC-DFTB qualitatively reproduces the important features in the vibrational spectra of protonated water clusters, especially concerning the characteristic signatures of clusters of various sizes. In agreement with recent ab initio molecular dynamics studies, it is found that dynamic...

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First-Principles Approach to Vibrational Spectroscopy of Biomolecules

Cited by 65 publications

References 218 publications

Understanding the Signatures of Secondary‐Structure Elements in Proteins with Raman Optical Activity Spectroscopy

Understanding the Signatures of Secondary‐Structure Elements in Proteins with Raman Optical Activity Spectroscopy

Global Analytical Potential Energy Surfaces for High‐resolution Molecular Spectroscopy and Reaction Dynamics

The vibrational spectra of protonated water clusters: A benchmark for self-consistent-charge density-functional tight binding

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