Contributions of vibrational spectroscopy to virology: A review

Chaudhary, Iqra Ishtiaq; Jackson, Naomi; Denning, Denise; O’Neill, Luke A.J.; Byrne, Hugh J.

doi:10.1016/j.clispe.2022.100022

Cited by 6 publications

(4 citation statements)

References 188 publications

(200 reference statements)

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“…Vibrational spectroscopy includes two major techniques, infrared and Raman, and their own varieties, which measure the transitions among quantified vibrational states of solids or molecules. [ 175 ] The principal mechanism of vibrational spectroscopy is based on the scattering or absorption of irradiated radiation and collecting the spectrum of spectroscopic responses. The acquired spectrum contains contributions from any molecular bond and is considered as the signature to characterize and identify the variations attributed with physical or chemical processes in materials of interest.…”

Section: Nanoscale Visualization and Characterization Tools For Mpxvmentioning

confidence: 99%

Addressing the Silent Spread of Monkeypox Disease with Advanced Analytical Tools

Bhalla

Payam

2022

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Section: Nanoscale Visualization and Characterization Tools For Mpxvmentioning

confidence: 99%

Addressing the Silent Spread of Monkeypox Disease with Advanced Analytical Tools

Bhalla

Payam

2022

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“…For IR inactive compounds the inelastic scattering of light (Raman scattering) provides a powerful alternative. Of late, the experimental applications of probing vibrational modes with Raman spectroscopy has been expanded from food, condensed phases, textile, , catalysts, and biomedical purposes. , Some advances that go beyond standard Raman methods include the surface-enhanced Raman spectroscopy (SERS), photoinduced enhanced Raman spectroscopy (known as PIERS), low-frequency Raman spectroscopy (LFR) and tip-enhanced Raman spectroscopy (TERS). This list is not meant to be exhaustive, but cover a basic overview of techniques that have been generally more favored in the scientific community.…”

Section: Introductionmentioning

confidence: 99%

“…Most of these enhanced instrumentations have been able to describe vibrational motions (with normal modes), and some have even been used to characterize structural configurations, such as enantiomers . Understanding and modeling protein conformational dynamics is a critical area of interest for both clinical and computational sectors, , where both Raman and IR spectroscopy have been used to elicit the dynamic behaviors of proteins. ,, …”

Section: Introductionmentioning

confidence: 99%

The Local Vibrational Mode Theory and Its Place in the Vibrational Spectroscopy Arena

et al. 2022

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This Feature Article starts highlighting some recent experimental and theoretical advances in the field of IR and Raman spectroscopy, giving a taste of the breadth and dynamics of this striving field. The local mode theory is then reviewed, showing how local vibrational modes are derived from fundamental normal modes. New features are introduced that add to current theoretical efforts: (i) a unique measure of bond strength based on local mode force constants ranging from bonding in single molecules in different environments to bonding in periodic systems and crystals and (ii) a new way to interpret vibrational spectra by pinpointing and probing interactions between particular bond stretching contributions to the normal modes. All of this represents a means to work around the very nature of normal modes, namely that the vibrational motions in polyatomic molecules are delocalized. Three current focus points of the local mode analysis are reported, demonstrating how the local mode analysis extracts important information hidden in vibrational spectroscopy data supporting current experiments: (i) metal−ligand bonding in heme proteins, such as myoglobin and neuroglobin; (ii) disentanglement of DNA normal modes; and (iii) hydrogen bonding in water clusters and ice. Finally, the use of the local mode analysis by other research groups is summarized. Our vision is that in the future local mode analysis will be routinely applied by the community and that this Feature Article serves as an incubator for future collaborations between experiment and theory.

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“…Vibrational spectroscopy can reveal in-depth information on the electronic structure and bonding of chemical systems, where its applications and improvements have been of recent interest. − Nevertheless, the very nature of a normal vibrational mode (NVM) in polyatomic systems is generally marked by delocalization in the form of collective motion of fragments, which makes it difficult to extract intrinsic bond properties and/or assigning contributions of a particular molecular fragment to a specific normal vibrational mode. The local vibrational mode (LVM) theory, , originally introduced by Konkoli and Cremer is a powerful tool to approach these complications by deriving local vibrations and associated local mode properties from NVMs, and to provide the foundation for the characterization of normal mode (CNM) procedure and the adiabatic connection scheme (ACS). − …”

Section: Introductionmentioning

confidence: 99%

Automatic Generation of Local Vibrational Mode Parameters: From Small to Large Molecules and QM/MM Systems

et al. 2022

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LModeAGen, a new protocol for the automatic determination of a nonredundant, complete set of local vibrational modes is reported, which is based on chemical graph concepts. Whereas local mode properties can be calculated for a selection of parameters targeting specific local modes of interest, a complete set of nonredundant local mode parameters is requested for the adiabatic connection scheme (ACS), relating each local vibrational mode with a normal mode counterpart, and for the decomposition of normal modes (CNM) in terms of local mode contributions, a unique way to analyze vibrational spectra. So far, nonredundant parameter sets have been generated manually following chemical intuition or from a set of redundant parameters in a trial-and-error fashion, which has hampered the study of larger systems with hundreds of parameters. LModeAGen was successfully applied for a test set of 11 systems, ranging from small molecules to the large QM (>100 atoms) subsystem of carbomonoxy-neuroglobin protein, described with a hybrid QM/MM method. The ωB97X-D/aug-cc-pVDZ, M06L/def2-TZVP, and QM/MM ωB97X-D/6-31G(d,p)/AMBER model chemistries were adopted for the description of the molecules in the test set. Our new protocol is an important step forward for a routine ACS and CNM analysis of the vibrational spectra of complex and large systems with hundreds of atoms, providing new access to important encoded electronic structure information.

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Contributions of vibrational spectroscopy to virology: A review

Cited by 6 publications

References 188 publications

Addressing the Silent Spread of Monkeypox Disease with Advanced Analytical Tools

Addressing the Silent Spread of Monkeypox Disease with Advanced Analytical Tools

The Local Vibrational Mode Theory and Its Place in the Vibrational Spectroscopy Arena

Automatic Generation of Local Vibrational Mode Parameters: From Small to Large Molecules and QM/MM Systems

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