Nitrile groups as vibrational probes of biomolecular structure and dynamics: an overview

Lindquist, Beth A.; Furse, Kristina E.; Corcelli, Steven A.

doi:10.1039/b908588b

Cited by 148 publications

(173 citation statements)

References 220 publications

(237 reference statements)

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“…In addition, the effect of the local electric field and hydration on the C≡N stretching frequency has also been extensively studied by means of theoretical and computational approaches (98–100). Due to space limitations, we are unable to describe these studies in detail and would like to refer the interested reader to relevant literature and two of the most recent reviews on nitrile probes (78, 98).…”

Section: Sidechain-based Ir Probesmentioning

confidence: 99%

Site-Specific Infrared Probes of Proteins

Pazos²,

Zhang³

et al. 2015

Annu. Rev. Phys. Chem.

161

189

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Infrared spectroscopy has played an instrumental role in studying a wide variety of biological questions. However, in many cases it is impossible or difficult to rely on the intrinsic vibrational modes of biological molecules of interest, such as proteins, to reveal structural and/or environmental information in a site-specific manner. To overcome this limitation, many recent efforts have been dedicated to the development and application of various extrinsic vibrational probes that can be incorporated into biological molecules and used to site-specifically interrogate their structural and/or environmental properties. In this Review, we highlight some recent advancements of this rapidly growing research area.

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Section: Sidechain-based Ir Probesmentioning

confidence: 99%

Site-Specific Infrared Probes of Proteins

Pazos²,

Zhang³

et al. 2015

Annu. Rev. Phys. Chem.

161

189

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“…There are a few reports 25,30,34,39 showing that the parameters of this kind can be solvent and solute transferable. Additionally, it was shown [40][41][42][43] that, by using semiempirical quantum mechanical approach involving reparameterization of the original semi-empirical PM3 44 Hamiltonian and its bath-coupling parameters specifically to the problem of interest, it becomes possible to make the solvent and solute parameters transferable to other systems. A few rigorous theoretical models of both vibrational solvatochromism and electrochromism have been developed throughout the years.…”

Section: Introductionmentioning

confidence: 99%

Vibrational solvatochromism: Towards systematic approach to modeling solvation phenomena

Lee¹,

Cho²

2013

The Journal of Chemical Physics

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Vibrational solvatochromic frequency shift of IR probe is an effect of interaction between local electric field and IR probe in condensed phases. Despite prolonged efforts to develop empirical maps for vibrational frequency shifts and transition dipoles of IR probes, a systematic approach to ab initio calculation of vibrational solvatochromic charges and multipoles has not been developed. Here, we report on density functional theory (DFT) calculations of N-methylacetamide (NMA) frequency shifts using implicit and coarse-grained models. The solvatochromic infrared spectral shifts are estimated based on the distributed multipole analysis of electronic densities calculated for gas-phase equilibrium structure of NMA. Thus obtained distributed solvatochromic multipole parameters are used to calculate the amide I vibrational frequency shifts of NMA in water clusters that mimic the instantaneous configurations of the liquid water. Our results indicate that the spectral shifts are primarily electrostatic in nature and can be quantitatively reproduced using the proposed model with semi-quantitative accuracy when compared to the corresponding DFT results.

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“…Organic nitriles have been used in a variety of protein and peptide studies. [33][34][35][36] Unfortunately, the nitrile stretching vibration exhibits a relatively weak transition moment making it a less than ideal probe. Recently, cyanylated cysteine, in which the cysteine thiol has been converted into a thiocyanate, has been the subject of several studies.…”

Section: Introductionmentioning

confidence: 99%

Two-dimensional infrared study of 3-azidopyridine as a potential spectroscopic reporter of protonation state

Nydegger

Dutta

Cheatum

2010

The Journal of Chemical Physics

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The lack of general spectroscopic probes that can be used in a range of systems to probe kinetics and dynamics is a major obstacle to the widespread application of two-dimensional infrared (2D IR) spectroscopy. We have studied 3-azidopyridine to characterize its potential as a probe of the protonation state of the pyridine ring. We find that the azido-stretching vibration is split by accidental Fermi resonance interactions with one or more overtones and combination states. Using 2D IR spectroscopy, we determine the state structure of the resulting eigenstates for complexes of 3-azidopyridine with formic acid and trifluoroacetic acid in which the pyridine ring is unprotonated and protonated, respectively. Based on the measurements, we develop a two-oscillator depurturbation model to determine the energies and couplings of the zeroth-order azido-stretching state and the perturbing dark state that couples to it. Based on these results, we conclude that the azido-stretching vibration is, in fact, sensitive to the protonation state of the pyridine shifting up in frequency by 8 cm(-1) in the complex with trifluoroacetic acid relative to the formic acid complex. These results suggest that, although 3-azidopyridine is not suitable as a spectroscopic probe, the approach of employing an organic azide as a remote probe of protonation state holds significant promise.

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Nitrile groups as vibrational probes of biomolecular structure and dynamics: an overview

Cited by 148 publications

References 220 publications

Site-Specific Infrared Probes of Proteins

Site-Specific Infrared Probes of Proteins

Vibrational solvatochromism: Towards systematic approach to modeling solvation phenomena

Two-dimensional infrared study of 3-azidopyridine as a potential spectroscopic reporter of protonation state

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