Intrinsic structure of pentapeptide Leu-enkephalin: geometry optimization and validation by comparison of VSCF-PT2 calculations with cold ion spectroscopy

Physical Chemistry Chemical Physics : PCCP
Tapta Kanchan RoyOleg V Boyarkin

Abstract

The intrinsic structure of an opioid peptide [Ala2, Leu5]-leucine enkephalin (ALE) has been investigated using first-principles based vibrational self-consistent field (VSCF) theory and cold ion spectroscopy. IR-UV double resonance spectroscopy revealed the presence of only one highly abundant conformer of the singly protonated ALE, isolated and cryogenically cooled in the gas phase. High-level quantum mechanical calculations of electronic structures in conjunction with a systematic conformational search allowed for finding a few low-energy candidate structures. In order to identify the observed structure, we computed vibrational spectra of the candidate structures and employed the theory at the semi-empirically scaled harmonic level and at the first-principles based anharmonic VSCF levels. The best match between the calculated "anharmonic" and the measured spectra appeared, indeed, for the most stable candidate. An average of two spectra calculated with different quantum mechanical potentials is proposed for the best match with experiment. The match thus validates the calculated intrinsic structure of ALE and demonstrates the predictive power of first-principles theory for solving structures of such large molecules.

References

Dec 21, 2006·Journal of the American Chemical Society·Sébastien R MercierThomas R Rizzo
Feb 13, 2007·Annual Review of Physical Chemistry·Mattanjah S de Vries, Pavel Hobza
Nov 6, 2007·The Journal of Chemical Physics·Yohann Scribano, David M Benoit
Mar 26, 2010·Physical Chemistry Chemical Physics : PCCP·Marie-Pierre Gaigeot
Mar 12, 2011·The Journal of Physical Chemistry. a·Brina BrauerR Benny Gerber
Apr 2, 2011·Journal of Computational Chemistry·Moshe GoldsteinR Benny Gerber
Nov 23, 2012·The Journal of Physical Chemistry. B·Sucismita ChutiaVolker Blum
Apr 6, 2013·The Journal of Chemical Physics·Nitzan MayorkasIlana Bar
May 17, 2013·Physical Chemistry Chemical Physics : PCCP·Tapta Kanchan Roy, R Benny Gerber
Jul 11, 2013·Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy·Roie KnaanieR Benny Gerber
Jul 16, 2013·Chemistry : a European Journal·Carsten BaldaufMatthias Scheffler
Jun 21, 2014·Journal of the American Chemical Society·Vladimir KopysovOleg V Boyarkin
Dec 4, 2014·Topics in Current Chemistry·Thomas R Rizzo, Oleg V Boyarkin
Feb 28, 2015·Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry·Tapta Kanchan RoyR Benny Gerber
Jun 10, 2015·Physical Chemistry Chemical Physics : PCCP·Jérôme MahéMarie-Pierre Gaigeot
Apr 3, 2014·The Journal of Physical Chemistry Letters·Géraldine FéraudTakayuki Ebata
Mar 13, 2012·Journal of Chemical Theory and Computation·Julien BloinoVincenzo Barone
Apr 14, 2009·Journal of Chemical Theory and Computation·A CimasM-P Gaigeot
Dec 18, 2015·Physical Chemistry Chemical Physics : PCCP·Tapta Kanchan RoyR Benny Gerber
Jul 2, 2016·Journal of the American Chemical Society·Liudmila VoroninaThomas Rizzo
Jul 30, 2016·The Journal of Physical Chemistry Letters·Paweł T Panek, Christoph R Jacob
Sep 15, 2016·The Journal of Physical Chemistry. B·Hiroki OtakiYuji Sugita
Jan 21, 2017·Physical Chemistry Chemical Physics : PCCP·A Y Pereverzev, O V Boyarkin
Oct 19, 2017·Angewandte Chemie·Aleksandr Y PereverzevOleg V Boyarkin
Nov 2, 2017·The Journal of Physical Chemistry. a·Tapta Kanchan RoyR Benny Gerber
Feb 6, 2018·Accounts of Chemical Research·Cristina Puzzarini, Vincenzo Barone

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Citations

Oct 4, 2019·Physical Chemistry Chemical Physics : PCCP·Aleksandr Y PereverzevOleg V Boyarkin
Mar 30, 2019·Angewandte Chemie·Erik SaparbaevOleg V Boyarkin
Dec 6, 2020·Annual Review of Physical Chemistry·Robert Benny Gerber
Sep 30, 2020·Journal of Chemical Theory and Computation·Tapta Kanchan Roy, R Benny Gerber
Oct 24, 2020·The Journal of Physical Chemistry. a·Hrishit Mitra, Tapta Kanchan Roy

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Methods Mentioned

BETA
X-ray
FRET

Software Mentioned

Spartan14
DEEPSAM
GAMESS
VSCF
ALE
TINKER

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