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Basis Set Dependence of Phosphate Frequencies in Density Functional Theory Calculations
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
2012 (English)In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 112, no 11, 2435-2439 p.Article in journal (Refereed) Published
Abstract [en]

The addition of extravalence, polarization and diffuse functions, were studied in order to conclude how they affect the PO stretching frequencies of several biological relevant phosphate molecules. The results show that the polarization and the diffuse functions have opposite effects on the frequencies: the polarization functions downshift while the diffuse functions upshift the frequencies. The effect of the valence functions was more difficult to interpret. The effect of the conductor-like screening model (CPCM)-continuum model was also studied. The results show that the CPCM-continuum model has a substantial effect on the frequencies for these small molecules. The continuum model's efficiency is mainly due to its effect on the geometries and not on the frequencies.

Place, publisher, year, edition, pages
2012. Vol. 112, no 11, 2435-2439 p.
Keyword [en]
phosphate, frequencies, B3LYP, basis set, DFT
National Category
Theoretical Chemistry
Research subject
Biophysics
Identifiers
URN: urn:nbn:se:su:diva-65012DOI: 10.1002/qua.23182ISI: 000303198100012OAI: oai:DiVA.org:su-65012DiVA: diva2:460511
Available from: 2011-12-01 Created: 2011-11-30 Last updated: 2017-12-08Bibliographically approved
In thesis
1. The Beauty of the Bitter Devils: A Theoretical Study on Phosphate Molecules
Open this publication in new window or tab >>The Beauty of the Bitter Devils: A Theoretical Study on Phosphate Molecules
2011 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Phosphate transfer reactions are catalyzed by a large number of enzymes comprising kinases, mutases and phosphatases. These enzymes play a fundamental role in controlling numerous life processes and it is therefore important to understand the origin of their potent catalytic power. An example is the Ca2+-ATPase. In the E2P-state, this enzyme hydrolyses the phosphorylated amino acid, Asp351, 106 to 107 fold faster than when the model compound, acetyl phosphate, is hydrolyzed in in water.This thesis explores the catalytic power of Ca2+-ATPase using theoretical method based on quantum mechanics. The studies of this protein were made by performing quantum chemical calculations on models of phosphoric monoesters as well as on the explicit reaction pathway of the hydrolysis. The studies show the importance of electrostatic interactions as well as the role of the specific active site residue Glu183, a residue that acts as a base in the catalytic pathway. Furthermore, based on the calculations, the interpretation of the experimental infrared spectrum of the E2P-state of Ca2+-ATPase, could be further elucidated as well as modified.The experimental infrared spectrum of phosphoenol pyruvate in water has also been elucidated through calculations. This molecule is converted into pyruvate in the last step of the glycolytic pathway, a reaction that is catalyzed by pyruvate kinase (PK). These results further enabled the interpretation of the experimental spectrum of the PK's catalytic reaction.These two processes, the transport of Ca2+ into the sarcoplasmatic reticulum against a concentration gradient and the glycolysis, are two important actions of a muscle cell.

Place, publisher, year, edition, pages
Stockholm: Department of Biochemistry and Biophysics, Stockholm University, 2011. 65 p.
National Category
Theoretical Chemistry
Research subject
Biophysics
Identifiers
urn:nbn:se:su:diva-65090 (URN)978-91-86071-80-6 (ISBN)
Public defence
2012-01-13, Magnélisalen, Kemiska övningslaboratoriet, Svante Arrhenius väg 16 B, Stockholm, 10:00 (English)
Opponent
Supervisors
Note
At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 2: Epub ahead of print. Paper 3: Submitted. Paper 4: Manuscript. Paper 5: Manuscript.Available from: 2011-12-15 Created: 2011-12-01 Last updated: 2011-12-20Bibliographically approved

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