Investigation of biologically important small molecules: quantum chemical and molecular dynamics calculations

Tekin, Emine Deniz
In this thesis, six small molecules (S-allylcysteine, S-allyl mercaptocysteine, allicin, methyl propyl disulfide, allyl methyl sulfide and dipropylsulfide) that are found in garlic and onion, and are known to be beneficial for human health were studied using molecular mechanics, semi-empirical methods, ab-initio (Restricted Hartree Fock), and density functional theory. Using the same methods, a synthetic pyrethroid pesticide molecule, called cyfluthrin, was also studied. Structural, vibrational and electronic properties of these molecules were found. These theoretical studies could clarify the role of these molecules on human health before they are commercially developed and used. In addition, unfolding dynamics of small peptide sequences (DDATKTFT and its variants) in immunoglobulin G-binding protein G was investigated. Protein folding and unfolding is one of the most important unsolved problems in molecular biology. Because of the large number of atoms involved in protein folding, it is a massive computational problem. The hope is that, one could understand this mechanism with the help of molecular dynamics simulation on small peptides. One of our findings is that the location of the hydrogen bonds is important for the stability of the peptide.


Applications of terahertz spectroscopy in biosystems
Plusquellic, David F.; SİEGRİST, Karen; Heilweil, Edwin J.; Esentürk, Okan (Wiley, 2007-12-03)
Terahertz (THz) spectroscopic investigations of condensed-phase biological samples are reviewed ranging from the simple crystalline forms of amino acids, carbohydrates and polypeptides to the more complex aqueous forms of small proteins, DNA and RNA. Vibrationally resolved studies of crystalline samples have revealed the exquisite sensitivity of THz modes to crystalline order, temperature, conformational form, peptide sequence and local solvate environment and have given unprecedented measures of the bindin...
Calculation of the thermodynamic and spectroscopic quantities in molecular crystals close to the phase transitons
Kavruk, Dilan; Yurtseven, Hasan Hamit; Department of Physics (2011)
We study in this thesis work the spectroscopic and thermodynamic quantities of some substances such as ammonium halides (NH4Cl, NH4I), ferroelectric crystals of tris-sarcosine calcium chloride (TSCC), tris-sarcosine calcium bromide (TSCB), organic compounds of carbon tetrachloride (CCl4) and s-triazine (C3N3H3) close to the phase transitions. Various physical and chemical properties of those materials have been measured near the critical points and have been reported in the literature. In this study, the sp...
Chemoselective Immobilization of Proteins by Microcontact Printing and Bio-orthogonal Click Reactions
Tolstyka, Zachary P.; Richardson, Wade; Bat, Erhan; Stevens, Caitlin J.; Parra, Dayanara P.; Dozier, Jonathan K.; Distefano, Mark D.; Dunn, Bruce; Maynard, Heather D. (Wiley, 2013-12-16)
Herein, a combination of microcontact printing of functionalized alkanethiols and site-specific modification of proteins is utilized to chemoselectively immobilize proteins onto gold surfaces, either by oxime- or copper-catalyzed alkyne-azide click chemistry. Two molecules capable of click reactions were synthesized, an aminooxy-functionalized alkanethiol and an azide-functionalized alkanethiol, and self-assembled monolayer (SAM) formation on gold was confirmed by IR spectroscopy. The alkanethiols were then...
Evaluation of adsorbents with passive sampling and their analytical methods to determine volatile organic compounds emitted from vehicular exhaust
CİVAN, MİHRİBAN; Tuncel, Süleyman Gürdal (2012-04-01)
In order to accurate and precise determination of Volatile Organic Compounds (VOCs) from vehicular emissions were developed method including a) adsorption of VOCs on different adsorbents followed by thermal desorption and gas chromatography (GC) with flame ionization detector (FID) quantification, b) validation of the sampling and analytical method. The adsorption efficiency of Tenax and Chromosorb 106 adsorbents were eveluated for 104 VOCs to select of adequate sorbent for passive sampling. Since most of t...
Production of an acetone-butanol-ethanol mixture from Clostridium acetobutylicum and its conversion to high-value biofuels
Sreekumar, Sanil; Baer, Zachary C.; Pazhamalai, Anbarasan; Günbaş, Emrullah Görkem; Grippo, Adam; Blanch, Harvey W.; Clark, Douglas S.; Toste, F. Dean (Springer Science and Business Media LLC, 2015-03-01)
Clostridium acetobutylicum is a bacterial species that ferments sugar to a mixture of organic solvents (acetone, butanol and ethanol). This protocol delineates a methodology to combine solventogenic clostridial fermentation and chemical catalysis via extractive fermentation for the production of biofuel blendstocks. Extractive fermentation of C. acetobutylicum is operated in fed-batch mode with a concentrated feed solution (500 grams per liter glucose and 50 grams per liter yeast extract) for 60 h, producin...
Citation Formats
E. D. Tekin, “ Investigation of biologically important small molecules: quantum chemical and molecular dynamics calculations,” Ph.D. - Doctoral Program, Middle East Technical University, 2010.