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Local Structures and Chemical Properties of Deprotonated Arginine
KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.ORCID iD: 0000-0003-0007-0394
2012 (English)In: Chinese Journal of Chemical Physics, ISSN 1674-0068, Vol. 25, no 6, 681-686 p.Article in journal (Refereed) Published
Abstract [en]

The potential energy surface of gaseous deprotonated arginine has been systematically investigated by first principles calculations. At the B3LYP/6-31G(d) level, apart from the identification of several stable local structures, a new global minimum is located which is about 6.56 kJ/mol more stable than what has been reported. The deprotonated arginine molecule has two distinct forms with the deprotonation at the carboxylate group (COO-). These two forms are bridged by very high energy barrier and possess very different IR spectral profiles. Our calculated proton dissociation energy and gas-phase acidity of arginine molecule are found to be in good agreement with the corresponding experimental results. The predicted geometries, dipole moments, rotational constants, vertical ionization energies and IR spectra of low energy conformers will be useful for future experimental measurements.

Place, publisher, year, edition, pages
2012. Vol. 25, no 6, 681-686 p.
Keyword [en]
Deprotonated arginine, Energy barrier, IR spectrum, Gas-phase acidity
National Category
Other Natural Sciences
Identifiers
URN: urn:nbn:se:kth:diva-119757DOI: 10.1088/1674-0068/25/06/681-686ISI: 000315663700010Scopus ID: 2-s2.0-84875692441OAI: oai:DiVA.org:kth-119757DiVA: diva2:612315
Note

QC 20130321

Available from: 2013-03-21 Created: 2013-03-21 Last updated: 2014-05-22Bibliographically approved
In thesis
1. Conformations of amino acids characterized by theoretical spectroscopy
Open this publication in new window or tab >>Conformations of amino acids characterized by theoretical spectroscopy
2014 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Amino acids are the basic building blocks of proteins. The determinationof their structures plays an important role in correctly describing the functionsof the proteins. This thesis is devoted to theoretical studies on the potentialenergy surface of amino acids, in particular the infrared and soft X-ray spectralfingerprints of their most stable conformers.The stable structures of amino acids can be explored by different methods.We have used a full space systematic search strategy to determine the potentialenergy surface of deprotonated arginine and revealed several new conformers.With that, the calculated thermodynamic parameters are finally in good agreementwith their experimental counterparts. We have also proposed a molecularfragment based step-by-step strategy to search for the most stable conformers oflarge biomolecules. The high efficiency and good accuracy of this strategy havebeen firmly illustrated by the modeling of several polypeptides.Infrared (IR) spectroscopy has become one of the most applied techniques tocharacterize the structures of gas-phase amino acids. A direct comparison betweenexperimental and calculated infrared spectra provides an efficient way to describethe conformation exchanges of the amino acids. It is found that the conformersof an amino acid are not always necessary to reach the thermal equilibrium undercertain experimental conditions. The local minima could be responsible for theappearance of the measured spectra. This important point has been highlightedby the calculations of deprotonated tyrosine and cysteine, as well as the arginine.The near-edge X-ray absorption fine structure (NEXAFS) spectra and X-rayphotoelectron spectra (XPS) have also been simulated for neutral, deprotonatedand protonated arginine. The influences of intra-, and intermolecular hydrogenbonds on the electronic structure of the arginine have been carefully examined. Itis suggested that the XPS is capable of distinguishing the canonical and zwitterinicisomers of arginine, and works much better than any other tools available.

Place, publisher, year, edition, pages
Stockholm: KTH Royal Institute of Technology, 2014. xiv, 82 p.
Series
TRITA-BIO-Report, ISSN 1654-2312 ; 2014:11
Keyword
amino acids, spectroscopy
National Category
Theoretical Chemistry
Research subject
Theoretical Chemistry and Biology
Identifiers
urn:nbn:se:kth:diva-145208 (URN)978-91-7595-175-1 (ISBN)
Public defence
2014-06-09, FA32, AlbaNova University Center, Roslagstullsbacken 21, Stockholm, 14:30 (English)
Opponent
Supervisors
Note

QC 20140522

Available from: 2014-05-22 Created: 2014-05-14 Last updated: 2014-05-22Bibliographically approved

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