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Conformations of amino acids characterized by theoretical spectroscopy
KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
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 [en]
amino acids, spectroscopy
National Category
Theoretical Chemistry
Research subject
Theoretical Chemistry and Biology
Identifiers
URN: urn:nbn:se:kth:diva-145208ISBN: 978-91-7595-175-1 (print)OAI: oai:DiVA.org:kth-145208DiVA: diva2:717264
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
List of papers
1. Local Structures and Chemical Properties of Deprotonated Arginine
Open this publication in new window or tab >>Local Structures and Chemical Properties of Deprotonated Arginine
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.

Keyword
Deprotonated arginine, Energy barrier, IR spectrum, Gas-phase acidity
National Category
Other Natural Sciences
Identifiers
urn:nbn:se:kth:diva-119757 (URN)10.1088/1674-0068/25/06/681-686 (DOI)000315663700010 ()2-s2.0-84875692441 (Scopus ID)
Note

QC 20130321

Available from: 2013-03-21 Created: 2013-03-21 Last updated: 2014-05-22Bibliographically approved
2. A Fragment Based Step-by-Step Strategy for Determining the Most Stable Conformers of Biomolecules
Open this publication in new window or tab >>A Fragment Based Step-by-Step Strategy for Determining the Most Stable Conformers of Biomolecules
2014 (English)In: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 610, 303-309 p.Article in journal (Refereed) Published
Abstract [en]

For biomolecules of increased size and flexibility, more efficient and reliable strategiesare always needed to determine their stable low-energy conformers. Here, we propose a fragment basedstep-by-step strategy to search for the full conformational space of biomolecules. In this strategy, themolecule is divided into several fragments and each of them is systematically optimized in a step-bystepfashion. It can significantly reduce the computational cost without losing any accuracy asdemonstrated by the conformer search of several representative di-/tri-/tetra- peptides. Such an approachwill be very useful for finding the stable conformers of large biomolecules.

Keyword
Fragment Based Step-by-Step Strategy
National Category
Natural Sciences
Identifiers
urn:nbn:se:kth:diva-145198 (URN)10.1016/j.cplett.2014.07.054 (DOI)000342527500056 ()2-s2.0-84905725347 (Scopus ID)
Note

Updated from submitted to published.

20141104

Available from: 2014-05-14 Created: 2014-05-14 Last updated: 2017-12-05Bibliographically approved
3. Gas-phase IR spectroscopy of deprotonated amino acids: Global or Local minima?
Open this publication in new window or tab >>Gas-phase IR spectroscopy of deprotonated amino acids: Global or Local minima?
2014 (English)In: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 598, 86-90 p.Article in journal (Refereed) Published
Abstract [en]

Density functional theory calculations for the structure and IR spectroscopy of deprotonated tyrosine and cysteine molecules in gas phase have been carried out to resolve the on-going debate about the global minimum of deprotonated amino acids. It is found that the global minimum of the deprotonated specie is not always directly produced from the most stable neutral conformer. Depending on the setup, the experimental IR spectroscopy of deprotonated amino acids could only give the information of the local minima of the deprotonated species.

Keyword
Mass-Spectrometry, Carboxyl Groups, Protein, Conformers, Cysteine, Computations, Dissociation, Acidities, Tyrosine, Sites
National Category
Chemical Sciences Physical Sciences
Research subject
Theoretical Chemistry and Biology
Identifiers
urn:nbn:se:kth:diva-145203 (URN)10.1016/j.cplett.2014.02.059 (DOI)000334294900017 ()2-s2.0-84897043220 (Scopus ID)
Note

QC 20140515

Available from: 2014-05-14 Created: 2014-05-14 Last updated: 2017-12-05Bibliographically approved
4. The Role of Dimerization on the Structure Transformation of Arginine in Gas Phase
Open this publication in new window or tab >>The Role of Dimerization on the Structure Transformation of Arginine in Gas Phase
2014 (English)In: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 608, 398-403 p.Article in journal (Refereed) Published
Abstract [en]

The equilibrium distribution of arginine molecules in canonical and zwitterionicforms predicted by the theory failed to correctly reproduce the double-peak feature observedin the IR experiment. We have shown from first principles calculations that the energeticallyfavorable dimerization of zwitterions can effectively eliminate the pathway for the structureconversion between two distinct canonical forms and reduce the probability for thesecanonical forms to reach their thermal equilibrium. The role of dispersion effect is discussed.It suggests that the experimental IR spectrum is determined by the way how the conformersof arginine are initially generated.

Place, publisher, year, edition, pages
Elsevier: , 2014
Keyword
dimerization
National Category
Chemical Sciences Physical Sciences
Identifiers
urn:nbn:se:kth:diva-145199 (URN)10.1016/j.cplett.2014.06.019 (DOI)000340202600071 ()2-s2.0-84903942607 (Scopus ID)
Note

Updated from submitted to published.

QC 20140912

Available from: 2014-05-14 Created: 2014-05-14 Last updated: 2017-12-05Bibliographically approved
5. First-Principles Study on Core-Level Spectroscopy of Arginine in Gas and Solid Phases
Open this publication in new window or tab >>First-Principles Study on Core-Level Spectroscopy of Arginine in Gas and Solid Phases
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.

Keyword
X-Ray-Absorption, Photoelectron Binding-Energies, Amino-Acids, Fine-Structure, Liquid Water, Electron Spectroscopy, Chemical Analysis, Hydrogen-Bonds, Glycine, Spectra
National Category
Physical Chemistry
Identifiers
urn:nbn:se:kth:diva-106131 (URN)10.1021/jp302309u (DOI)000310120900001 ()2-s2.0-84867819204 (Scopus ID)
Note

QC 20121203

Available from: 2012-12-03 Created: 2012-11-29 Last updated: 2017-12-07Bibliographically approved

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