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First-Principles Study on Core-Level Spectroscopy of Arginine in Gas and Solid Phases
KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.ORCID iD: 0000-0002-6706-651X
KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.ORCID iD: 0000-0003-0007-0394
2012 (English)In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 116, no 42, 12641-12650 p.Article in journal (Refereed) Published
Abstract [en]

First-principles simulations have been performed for near-edge X-ray absorption fine-structure (NEXAFS) spectra of neutral arginine at different K-edges in the solid phase as well as X-ray photoelectron spectra (XPS) of neutral, deprotonated, and protonated arginines in the gas phase. Influences of the intra- and intermolecular hydrogen bonds (HBs) and different charge states have been carefully examined to obtain useful structure-property relationships. Our calculations show a noticeable difference in the NEXAFS/XPS spectra of the canonical and zwitterionic species that can be used for unambiguously identifying the dominant form in the gas phase. It is found that the deprotonation/protonation always results in red/blue shifts of several electronvolts for the core binding energies (BEs) at all edges. The normal hydrogen bond Y-H center dot center dot center dot X (X, Y = N, O) can cause a blue/red shift of ca. 1 eV to the core BEs of the proton acceptor X/donor Y, while the weak C-H center dot center dot center dot Y hydrogen bond may also lead to a weak red shift (less than 1 eV) of the C1s BEs. Moreover, the influence of intermolecular interactions in the solid state is reflected as a broadening in the sigma* region of the NEXAFS spectra at each edge, while in the pi* region, these interactions lead to a strengthening or weakening of individual transitions from different carbons, although no evident visual change is found in the resolved total spectra. Our results provide a better understanding of the influences of the intra- and intermolecular forces on the electronic structure of arginine.

Place, publisher, year, edition, pages
2012. Vol. 116, no 42, 12641-12650 p.
Keyword [en]
X-Ray-Absorption, Photoelectron Binding-Energies, Amino-Acids, Fine-Structure, Liquid Water, Electron Spectroscopy, Chemical Analysis, Hydrogen-Bonds, Glycine, Spectra
National Category
Physical Chemistry
URN: urn:nbn:se:kth:diva-106131DOI: 10.1021/jp302309uISI: 000310120900001ScopusID: 2-s2.0-84867819204OAI: diva2:573642

QC 20121203

Available from: 2012-12-03 Created: 2012-11-29 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.
TRITA-BIO-Report, ISSN 1654-2312 ; 2014:11
amino acids, spectroscopy
National Category
Theoretical Chemistry
Research subject
Theoretical Chemistry and Biology
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)

QC 20140522

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

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