Literature DB >> 35291777

Origin of thiocyanate spectral shifts in water and organic solvents.

Ruoqi Zhao1, Joseph C Shirley2, Euihyun Lee2, Adam Grofe1, Hui Li1, Carlos R Baiz2, Jiali Gao3.   

Abstract

Vibrational spectroscopy is a useful technique for probing chemical environments. The development of models that can reproduce the spectra of nitriles and azides is valuable because these probes are uniquely suited for investigating complex systems. Empirical vibrational spectroscopic maps are commonly employed to obtain the instantaneous vibrational frequencies during molecular dynamics simulations but often fail to adequately describe the behavior of these probes, especially in its transferability to a diverse range of environments. In this paper, we demonstrate several reasons for the difficulty in constructing a general-purpose vibrational map for methyl thiocyanate (MeSCN), a model for cyanylated biological probes. In particular, we found that electrostatics alone are not a sufficient metric to categorize the environments of different solvents, and the dominant features in intermolecular interactions in the energy landscape vary from solvent to solvent. Consequently, common vibrational mapping schemes do not cover all essential interaction terms adequately, especially in the treatment of van der Waals interactions. Quantum vibrational perturbation (QVP) theory, along with a combined quantum mechanical and molecular mechanical potential for solute-solvent interactions, is an alternative and efficient modeling technique, which is compared in this paper, to yield spectroscopic results in good agreement with experimental FTIR. QVP has been used to analyze the computational data, revealing the shortcomings of the vibrational maps for MeSCN in different solvents. The results indicate that insights from QVP analysis can be used to enhance the transferability of vibrational maps in future studies.

Entities:  

Year:  2022        PMID: 35291777      PMCID: PMC8923707          DOI: 10.1063/5.0082969

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  61 in total

1.  On the physical origin of blue-shifted hydrogen bonds.

Authors:  Xiaosong Li; Lei Liu; H Bernhard Schlegel
Journal:  J Am Chem Soc       Date:  2002-08-14       Impact factor: 15.419

2.  Nitrile and thiocyanate IR probes: molecular dynamics simulation studies.

Authors:  Kwang-Im Oh; Jun-Ho Choi; Joo-Hyun Lee; Jae-Beom Han; Hochan Lee; Minhaeng Cho
Journal:  J Chem Phys       Date:  2008-04-21       Impact factor: 3.488

3.  Molecular-level mechanisms of vibrational frequency shifts in a polar liquid.

Authors:  Christine M Morales; Ward H Thompson
Journal:  J Phys Chem B       Date:  2011-05-24       Impact factor: 2.991

4.  Nanosecond protein dynamics in a red/green cyanobacteriochrome revealed by transient IR spectroscopy.

Authors:  David Buhrke; Kerstin T Oppelt; Philipp J Heckmeier; Ricardo Fernández-Terán; Peter Hamm
Journal:  J Chem Phys       Date:  2020-12-28       Impact factor: 3.488

5.  FTIR investigation of the secondary structure of type I collagen: New insight into the amide III band.

Authors:  Chiaramaria Stani; Lisa Vaccari; Elisa Mitri; Giovanni Birarda
Journal:  Spectrochim Acta A Mol Biomol Spectrosc       Date:  2019-12-28       Impact factor: 4.098

6.  Enhanced vibrational solvatochromism and spectral diffusion by electron rich substituents on small molecule silanes.

Authors:  Courtney M Olson; Adam Grofe; Christopher J Huber; Ivan C Spector; Jiali Gao; Aaron M Massari
Journal:  J Chem Phys       Date:  2017-09-28       Impact factor: 3.488

7.  Vibrational dynamics and solvatochromism of the label SCN in various solvents and hemoglobin by time dependent IR and 2D-IR spectroscopy.

Authors:  Luuk J G W van Wilderen; Daniela Kern-Michler; Henrike M Müller-Werkmeister; Jens Bredenbeck
Journal:  Phys Chem Chem Phys       Date:  2014-09-28       Impact factor: 3.676

8.  An Empirical IR Frequency Map for Ester C═O Stretching Vibrations.

Authors:  Sean C Edington; Jennifer C Flanagan; Carlos R Baiz
Journal:  J Phys Chem A       Date:  2016-05-31       Impact factor: 2.781

9.  Empirical maps for the calculation of amide I vibrational spectra of proteins from classical molecular dynamics simulations.

Authors:  Edyta Małolepsza; John E Straub
Journal:  J Phys Chem B       Date:  2014-04-11       Impact factor: 2.991

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