DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

This content will become publicly available on July 2, 2023

Title: The effect of hydrogen-bonding on flavin’s infrared absorption spectrum

Authors:
; ; ;
Publication Date:
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES)
OSTI Identifier:
1805079
Resource Type:
Publisher's Accepted Manuscript
Journal Name:
Spectrochimica Acta. Part A. Molecular and Biomolecular Spectroscopy (Print)
Additional Journal Information:
Journal Name: Spectrochimica Acta. Part A. Molecular and Biomolecular Spectroscopy (Print) Journal Volume: 262 Journal Issue: C; Journal ID: ISSN 1386-1425
Publisher:
Elsevier
Country of Publication:
United Kingdom
Language:
English

Citation Formats

Kabir, Mohammad Pabel, Orozco-Gonzalez, Yoelvis, Hastings, Gary, and Gozem, Samer. The effect of hydrogen-bonding on flavin’s infrared absorption spectrum. United Kingdom: N. p., 2021. Web. doi:10.1016/j.saa.2021.120110.
Kabir, Mohammad Pabel, Orozco-Gonzalez, Yoelvis, Hastings, Gary, & Gozem, Samer. The effect of hydrogen-bonding on flavin’s infrared absorption spectrum. United Kingdom. https://doi.org/10.1016/j.saa.2021.120110
Kabir, Mohammad Pabel, Orozco-Gonzalez, Yoelvis, Hastings, Gary, and Gozem, Samer. Wed . "The effect of hydrogen-bonding on flavin’s infrared absorption spectrum". United Kingdom. https://doi.org/10.1016/j.saa.2021.120110.
@article{osti_1805079,
title = {The effect of hydrogen-bonding on flavin’s infrared absorption spectrum},
author = {Kabir, Mohammad Pabel and Orozco-Gonzalez, Yoelvis and Hastings, Gary and Gozem, Samer},
abstractNote = {},
doi = {10.1016/j.saa.2021.120110},
journal = {Spectrochimica Acta. Part A. Molecular and Biomolecular Spectroscopy (Print)},
number = C,
volume = 262,
place = {United Kingdom},
year = {2021},
month = {12}
}

Journal Article:
Free Publicly Available Full Text
This content will become publicly available on July 2, 2023
Publisher's Version of Record

Save / Share:

Works referenced in this record:

The Chemical and Biological Versatility of Riboflavin
journal, August 2000


HY4 gene of A. thaliana encodes a protein with characteristics of a blue-light photoreceptor
journal, November 1993

  • Ahmad, Margaret; Cashmore, Anthony R.
  • Nature, Vol. 366, Issue 6451
  • DOI: 10.1038/366162a0

Formation of an unusual glutamine tautomer in a blue light using flavin photocycle characterizes the light-adapted state
journal, October 2020

  • Goings, Joshua J.; Li, Pengfei; Zhu, Qiwen
  • Proceedings of the National Academy of Sciences, Vol. 117, Issue 43
  • DOI: 10.1073/pnas.2016719117

In situ ftir thin-layer reflectance spectroscopy of flavin adenine dinucleotide at a mercury/gold electrode
journal, November 1994


Electronic spectra of flavin in different redox and protonation states: a computational perspective on the effect of the electrostatic environment
journal, January 2019

  • Kabir, Mohammad Pabel; Orozco-Gonzalez, Yoelvis; Gozem, Samer
  • Physical Chemistry Chemical Physics, Vol. 21, Issue 30
  • DOI: 10.1039/C9CP02230A

Comparison between Optimized Geometries and Vibrational Frequencies Calculated by the DFT Methods
journal, January 1996

  • El-Azhary, A. A.; Suter, H. U.
  • The Journal of Physical Chemistry, Vol. 100, Issue 37
  • DOI: 10.1021/jp960618o

Ultrafast 2D-IR spectroelectrochemistry of flavin mononucleotide
journal, June 2015

  • El Khoury, Youssef; Van Wilderen, Luuk J. G. W.; Bredenbeck, Jens
  • The Journal of Chemical Physics, Vol. 142, Issue 21
  • DOI: 10.1063/1.4916916

Local vibrational modes of the water dimer – Comparison of theory and experiment
journal, December 2012


Blue-Light-Induced Changes in Arabidopsis Cryptochrome 1 Probed by FTIR Difference Spectroscopy
journal, February 2006

  • Kottke, Tilman; Batschauer, Alfred; Ahmad, Margaret
  • Biochemistry, Vol. 45, Issue 8
  • DOI: 10.1021/bi051964b

Infrared Difference Spectroscopy of Proteins: From Bands to Bonds
journal, March 2020


Molecular properties from combined QM/MM methods. I. Analytical second derivative and vibrational calculations
journal, January 2000

  • Cui, Qiang; Karplus, Martin
  • The Journal of Chemical Physics, Vol. 112, Issue 3
  • DOI: 10.1063/1.480658

BLUF: a novel FAD-binding domain involved in sensory transduction in microorganisms
journal, October 2002


Infrared spectrum and absorption coefficient of the cofactor flavin in water
journal, November 2011


Electrostatic Spectral Tuning Maps for Biological Chromophores
journal, March 2019

  • Orozco-Gonzalez, Yoelvis; Kabir, Mohammad Pabel; Gozem, Samer
  • The Journal of Physical Chemistry B, Vol. 123, Issue 23
  • DOI: 10.1021/acs.jpcb.9b00489

Flavin coenzymes: at the crossroads of biological redox chemistry
journal, May 1980


Local vibrational modes of the formic acid dimer – the strength of the double hydrogen bond
journal, May 2013


Flavoenzymes that catalyse reactions with no net redox change
journal, September 2002

  • Bornemann, Stephen
  • Natural Product Reports, Vol. 19, Issue 6
  • DOI: 10.1039/b108916c

A new way of analyzing vibrational spectra. I. Derivation of adiabatic internal modes
journal, January 1998


A comprehensive analysis of hydrogen bond interactions based on local vibrational modes
journal, April 2012

  • Freindorf, Marek; Kraka, Elfi; Cremer, Dieter
  • International Journal of Quantum Chemistry, Vol. 112, Issue 19
  • DOI: 10.1002/qua.24118

Photoenzymic repair of UV-damaged DNA: a chemist's perspective
journal, January 1995

  • Heelis, Paul F.; Hartman, Rosemarie F.; Rose, Seth D.
  • Chemical Society Reviews, Vol. 24, Issue 4
  • DOI: 10.1039/cs9952400289

Reaction-induced infrared difference spectroscopy for the study of protein function and reaction mechanisms
journal, June 1993


Calculated vibrational properties of pigments in protein binding sites
journal, June 2011

  • Lamichhane, H. P.; Hastings, G.
  • Proceedings of the National Academy of Sciences, Vol. 108, Issue 26
  • DOI: 10.1073/pnas.1104046108

Protonated triplet-excited flavin resolved by step-scan FTIR spectroscopy: implications for photosensory LOV domains
journal, January 2013

  • Thöing, Christian; Pfeifer, Anna; Kakorin, Sergej
  • Physical Chemistry Chemical Physics, Vol. 15, Issue 16
  • DOI: 10.1039/c3cp43881c

Spectroscopy in Complex Environments from QM–MM Simulations
journal, February 2018

  • Morzan, Uriel N.; Alonso de Armiño, Diego J.; Foglia, Nicolás O.
  • Chemical Reviews, Vol. 118, Issue 7
  • DOI: 10.1021/acs.chemrev.8b00026

Density Functional Theory Combined with Molecular Mechanics: The Infrared Spectra of Flavin in Solution†
journal, December 2010


Decoding chemical information from vibrational spectroscopy data: Local vibrational mode theory
journal, May 2020

  • Kraka, Elfi; Zou, Wenli; Tao, Yunwen
  • WIREs Computational Molecular Science, Vol. 10, Issue 5
  • DOI: 10.1002/wcms.1480

On the performance of eleven DFT functionals in the description of the vibrational properties of aluminosilicates: Performance of Eleven DFT Functionals
journal, July 2009

  • Demichelis, Raffaella; Civalleri, Bartolomeo; Ferrabone, Matteo
  • International Journal of Quantum Chemistry, Vol. 110, Issue 2
  • DOI: 10.1002/qua.22301

DFT/MM Description of Flavin IR Spectra in BLUF Domains
journal, September 2011

  • Rieff, Benjamin; Bauer, Sebastian; Mathias, Gerald
  • The Journal of Physical Chemistry B, Vol. 115, Issue 38
  • DOI: 10.1021/jp2043637

Coupled-cluster Raman intensities: Assessment and comparison with multiconfiguration and density functional methods
journal, November 2002

  • Neugebauer, Johannes; Reiher, Markus; Hess, Bernd A.
  • The Journal of Chemical Physics, Vol. 117, Issue 19
  • DOI: 10.1063/1.1506919

Efficient Analytic Second Derivative of Electrostatic Embedding QM/MM Energy: Normal Mode Analysis of Plant Cryptochrome
journal, April 2020

  • Schwinn, Karno; Ferré, Nicolas; Huix-Rotllant, Miquel
  • Journal of Chemical Theory and Computation, Vol. 16, Issue 6
  • DOI: 10.1021/acs.jctc.9b01145

LOV (light, oxygen, or voltage) domains of the blue-light photoreceptor phototropin (nph1): Binding sites for the chromophore flavin mononucleotide
journal, July 1999

  • Christie, J. M.; Salomon, M.; Nozue, K.
  • Proceedings of the National Academy of Sciences, Vol. 96, Issue 15
  • DOI: 10.1073/pnas.96.15.8779

Efficient Calculation of QM/MM Frequencies with the Mobile Block Hessian
journal, December 2010

  • Ghysels, An; Woodcock, H. Lee; Larkin, Joseph D.
  • Journal of Chemical Theory and Computation, Vol. 7, Issue 2
  • DOI: 10.1021/ct100473f

Hydrogen Bonding Environments in the Photocycle Process around the Flavin Chromophore of the AppA-BLUF domain
journal, August 2018

  • Iwata, Tatsuya; Nagai, Takashi; Ito, Shota
  • Journal of the American Chemical Society, Vol. 140, Issue 38
  • DOI: 10.1021/jacs.8b05123

Harmonic frequency scaling factors for Hartree-Fock, S-VWN, B-LYP, B3-LYP, B3-PW91 and MP2 with the Sadlej pVTZ electric property basis set
journal, May 2001

  • Halls, Mathew D.; Velkovski, Julia; Schlegel, H. Bernhard
  • Theoretical Chemistry Accounts, Vol. 105, Issue 6
  • DOI: 10.1007/s002140000204

C 2 in a Box: Determining Its Intrinsic Bond Strength for the X 1 Σ g + Ground State
journal, January 2016


Mechanisms of flavoprotein-catalyzed reactions
journal, April 1989


Structure and function of DNA photolyase
journal, January 1994


Infrared Spectrum of p -Benzoquinone in Water Obtained from a QM/MM Hybrid Molecular Dynamics Simulation
journal, October 2003

  • Nonella, Marco; Mathias, Gerald; Tavan, Paul
  • The Journal of Physical Chemistry A, Vol. 107, Issue 41
  • DOI: 10.1021/jp027747r

A new way of analyzing vibrational spectra. II. Comparison of internal mode frequencies
journal, January 1998


Same Substrate, Many Reactions: Oxygen Activation in Flavoenzymes
journal, January 2018


Redox-Triggered FTIR Difference Spectra of FAD in Aqueous Solution and Bound to Flavoproteins
journal, November 2003

  • Wille, Georg; Ritter, Michaela; Friedemann, Rudolf
  • Biochemistry, Vol. 42, Issue 50
  • DOI: 10.1021/bi035219f

Spectroscopic Properties of Lumiflavin: A Quantum Chemical Study
journal, October 2018

  • Kar, Rajiv Kumar; Borin, Veniamin A.; Ding, Yonghong
  • Photochemistry and Photobiology, Vol. 95, Issue 2
  • DOI: 10.1111/php.13023

The Diverse Roles of Flavin CoenzymesNature's Most Versatile Thespians
journal, August 2007

  • Mansoorabadi, Steven O.; Thibodeaux, Christopher J.; Liu, Hung-wen
  • The Journal of Organic Chemistry, Vol. 72, Issue 17
  • DOI: 10.1021/jo0703092

Molecular Models Predict Light-Induced Glutamine Tautomerization in BLUF Photoreceptors
journal, May 2008

  • Domratcheva, Tatiana; Grigorenko, Bella L.; Schlichting, Ilme
  • Biophysical Journal, Vol. 94, Issue 10
  • DOI: 10.1529/biophysj.107.124172

Analytical Harmonic Vibrational Frequencies for the Green Fluorescent Protein Computed with ONIOM: Chromophore Mode Character and Its Response to Environment
journal, January 2014

  • Thompson, Lee M.; Lasoroski, Aurélie; Champion, Paul M.
  • Journal of Chemical Theory and Computation, Vol. 10, Issue 2
  • DOI: 10.1021/ct400664p

Strengthening of hydrogen bonding with the push-pull effect
journal, October 2017


Flavogenomics - a genomic and structural view of flavin-dependent proteins: Flavin-dependent proteins
journal, July 2011