Literature DB >> 22990297

Geometry determination of complexes in a molecular liquid mixture using electron-vibration-vibration two-dimensional infrared spectroscopy with a vibrational transition density cube method.

Rui Guo1, Shaul Mukamel, David R Klug.   

Abstract

We demonstrate the use of a new vibrational transition density cube (VTDC) method for determining the geometry of complexes in a molecular liquid mixture from electron-vibration-vibration two-dimensional infrared (pan class="Chemical">EVV 2DIR) spectra. The VTDC method was used to calculate the electrically-mediated intermolecular vibrational coupling and thereby the EVV 2DIR spectra. Using the 1:1 benzonitrile-phenylacetylene (BN-PA) liquid mixture as a test case, the new method leads to a distance of 3.60 Å between the interacting BN-PA pair, a much more accurate value than the distance previously obtained using a dipolar approximation for the electrical coupling. We also show that molecular dynamics simulations of the liquid mixture predict a modal geometry of complexation which agrees well with the geometry determined from the 2DIR data via VTDC analysis. We therefore conclude the combination of VTDC and EVV 2DIR data is a useful approach for the determination of the geometry of molecular complexes in the condensed phase.

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Year:  2012        PMID: 22990297      PMCID: PMC3596003          DOI: 10.1039/c2cp42593a

Source DB:  PubMed          Journal:  Phys Chem Chem Phys        ISSN: 1463-9076            Impact factor:   3.676


  10 in total

1.  The origin of vibrational mode couplings in various secondary structural motifs of polypeptides.

Authors:  Andrew Moran; Shaul Mukamel
Journal:  Proc Natl Acad Sci U S A       Date:  2004-01-02       Impact factor: 11.205

2.  Potential for the detection of molecular complexes and determination of interaction geometry by 2DIR: application to protein sciences.

Authors:  Rui Guo; Margherita Miele; Elizabeth M Gardner; Frederic Fournier; Kathryn M Kornau; Ian R Gould; David R Klug
Journal:  Faraday Discuss       Date:  2011       Impact factor: 4.008

3.  Direct identification and decongestion of Fermi resonances by control of pulse time ordering in two-dimensional IR spectroscopy.

Authors:  Paul M Donaldson; Rui Guo; Frederic Fournier; Elizabeth M Gardner; Laura M C Barter; Chris J Barnett; Ian R Gould; David R Klug; D Jason Palmer; Keith R Willison
Journal:  J Chem Phys       Date:  2007-09-21       Impact factor: 3.488

4.  PACKMOL: a package for building initial configurations for molecular dynamics simulations.

Authors:  L Martínez; R Andrade; E G Birgin; J M Martínez
Journal:  J Comput Chem       Date:  2009-10       Impact factor: 3.376

Review 5.  Biological and biomedical applications of two-dimensional vibrational spectroscopy: proteomics, imaging, and structural analysis.

Authors:  Frederic Fournier; Rui Guo; Elizabeth M Gardner; Paul M Donaldson; Christian Loeffeld; Ian R Gould; Keith R Willison; David R Klug
Journal:  Acc Chem Res       Date:  2009-09-15       Impact factor: 22.384

6.  Protein identification and quantification by two-dimensional infrared spectroscopy: implications for an all-optical proteomic platform.

Authors:  Frédéric Fournier; Elizabeth M Gardner; Darek A Kedra; Paul M Donaldson; Rui Guo; Sarah A Butcher; Ian R Gould; Keith R Willison; David R Klug
Journal:  Proc Natl Acad Sci U S A       Date:  2008-10-01       Impact factor: 11.205

7.  Detection of complex formation and determination of intermolecular geometry through electrical anharmonic coupling of molecular vibrations using electron-vibration-vibration two-dimensional infrared spectroscopy.

Authors:  Rui Guo; Frederic Fournier; Paul M Donaldson; Elizabeth M Gardner; Ian R Gould; David R Klug
Journal:  Phys Chem Chem Phys       Date:  2009-07-22       Impact factor: 3.676

8.  VMD: visual molecular dynamics.

Authors:  W Humphrey; A Dalke; K Schulten
Journal:  J Mol Graph       Date:  1996-02

9.  Optical fingerprinting of peptides using two-dimensional infrared spectroscopy: proof of principle.

Authors:  Frédéric Fournier; Elizabeth M Gardner; Rui Guo; Paul M Donaldson; Laura M C Barter; D Jason Palmer; Chris J Barnett; Keith R Willison; Ian R Gould; David R Klug
Journal:  Anal Biochem       Date:  2007-11-13       Impact factor: 3.365

Review 10.  Coherent multidimensional vibrational spectroscopy of biomolecules: concepts, simulations, and challenges.

Authors:  Wei Zhuang; Tomoyuki Hayashi; Shaul Mukamel
Journal:  Angew Chem Int Ed Engl       Date:  2009       Impact factor: 15.336

  10 in total
  1 in total

1.  Photon echoes and two dimensional spectra of the amide I band of proteins measured by femtosecond IR - Raman spectroscopy.

Authors:  Paul M Donaldson
Journal:  Chem Sci       Date:  2020-07-27       Impact factor: 9.825

  1 in total

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