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...
Synthesis of selenophene substituted benzodithiophene and fluorinated benzothiadiazole based conjugated polymers for organic solar cell applications
Cevher, Duygu; Taşkaya Aslan, Sultan; Bolayır, Eda; Hizalan Ozsoy, Gonul; UDUM, YASEMİN; Yıldırım, Erol; Toppare, Levent Kamil; Çırpan, Ali (2021-12-01)
A series of alternating conjugated copolymers which contain selenophene modified benzodithiophene and fluorine bearing benzothiadiazole have been synthesized via Stille polycondensation reaction to investigate the effect of the number of fluorine atoms substituted to the benzothiadiazole. Three different polymers, PBDTSe-BT, PBDTSe-FBT and PBDTSe-FFBT, were reported and their electrochemical, spectroelectrochemical, and photovoltaic behaviors were examined. Density functional theory calculations were perfor...
Design rules for suspending concentrated mixtures of solids in stirred tanks
Ayrancı Tansık, İnci (2011-10-01)
This study examines complete off-bottom suspension conditions for slurries containing mixtures of solids at a wide range of concentrations. Binary combinations of five different particles; bronze, two sizes of glass beads, ion exchange resin, and nickel were tested with two impellers: the Lightnin A310 and the down pumping 45 degrees PBT. The effect of particle size ratio and density ratio of the two solid phases on N(js) was investigated. Solids loadings were varied from 3 to 56 wt% (weight percent) with w...
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.