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Local Structures and Chemical Properties of Deprotonated Arginine
KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.ORCID-id: 0000-0003-0007-0394
2012 (engelsk)Inngår i: Chinese Journal of Chemical Physics, ISSN 1674-0068, Vol. 25, nr 6, s. 681-686Artikkel i tidsskrift (Fagfellevurdert) 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.

sted, utgiver, år, opplag, sider
2012. Vol. 25, nr 6, s. 681-686
Emneord [en]
Deprotonated arginine, Energy barrier, IR spectrum, Gas-phase acidity
HSV kategori
Identifikatorer
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, id: diva2:612315
Merknad

QC 20130321

Tilgjengelig fra: 2013-03-21 Laget: 2013-03-21 Sist oppdatert: 2014-05-22bibliografisk kontrollert
Inngår i avhandling
1. Conformations of amino acids characterized by theoretical spectroscopy
Åpne denne publikasjonen i ny fane eller vindu >>Conformations of amino acids characterized by theoretical spectroscopy
2014 (engelsk)Doktoravhandling, med artikler (Annet vitenskapelig)
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.

sted, utgiver, år, opplag, sider
Stockholm: KTH Royal Institute of Technology, 2014. s. xiv, 82
Serie
TRITA-BIO-Report, ISSN 1654-2312 ; 2014:11
Emneord
amino acids, spectroscopy
HSV kategori
Forskningsprogram
Teoretisk kemi och biologi
Identifikatorer
urn:nbn:se:kth:diva-145208 (URN)978-91-7595-175-1 (ISBN)
Disputas
2014-06-09, FA32, AlbaNova University Center, Roslagstullsbacken 21, Stockholm, 14:30 (engelsk)
Opponent
Veileder
Merknad

QC 20140522

Tilgjengelig fra: 2014-05-22 Laget: 2014-05-14 Sist oppdatert: 2014-05-22bibliografisk kontrollert

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