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Articles 1 - 9 of 9
Full-Text Articles in Computational Chemistry
Novel Chiral Interstellar Molecules: Quantum Anharmonic Ir And Vcd Predictions, Meredith Paik
Novel Chiral Interstellar Molecules: Quantum Anharmonic Ir And Vcd Predictions, Meredith Paik
Dissertations, Master's Theses and Master's Reports
The 2016 discovery of the chiral molecule propylene oxide (C3H6O) in the interstellar medium (ISM) has opened new avenues into explaining the origin of biomolecular homochirality on Earth. Thus, studies of chiral molecules in the ISM may be able to reveal more about the mechanism behind homochirality. However, while the search for chiral molecules in space has become an active field of study, astrochemical researchers have yet to detect other chiral molecules in the ISM. For this purpose, numerous characteristics for detectability have been outlined that may facilitate the discovery of other interstellar chiral molecules. With …
Multiscale Computational Chemistry Studies Of The Catalytic Mechanisms Of Non-Heme Fe(Ii)/2-Oxoglutarate-Dependent Oxygenases, Simahudeen Bathir Jaber Sathik Rifayee
Multiscale Computational Chemistry Studies Of The Catalytic Mechanisms Of Non-Heme Fe(Ii)/2-Oxoglutarate-Dependent Oxygenases, Simahudeen Bathir Jaber Sathik Rifayee
Dissertations, Master's Theses and Master's Reports
Enzymes catalyze complex biological transformations. Non-heme Fe(II)/2-oxoglutarate (2OG)–dependent enzymes are highly versatile catalysts capable of selective C–H oxidation, enabling transformations such as hydroxylation, halogenation, desaturation, demethylation, ring rearrangements, epoxidation, and electrophilic aromatic substitution. These enzymes are involved in various biological processes, including fatty acid metabolism, hypoxic signaling, collagen maturation, and transcriptional regulation. Computational Modeling provides detailed knowledge of the enzymes including atomistic details of the important catalytic species, conformational and electronic effects, which are crucial to enzyme engineering and drug design efforts. This dissertation implements advanced multi-scale molecular modelling techniques including Molecular dynamics and Quantum Mechanic / Molecular Mechanics calculations …
Towards Developing Glut2 Specific Probes For Biochemical And Biomedical Applications, Abdelrahman Ismail
Towards Developing Glut2 Specific Probes For Biochemical And Biomedical Applications, Abdelrahman Ismail
Dissertations, Master's Theses and Master's Reports
Facilitated Glucose transporters (GLUTs) are membrane proteins responsible for the uptake of simple sugars and other structurally similar metabolites in all mammalian cells. One of the hallmarks of cancer is dysfunctional sugar metabolism, known as the Warburg effect, and one of the manifestations of that effect is abnormal GLUT expression. There are 14 known GLUT proteins with different expression patterns in different tissues, and tumors tend to express certain GLUTs that are not present in surrounding healthy tissue. Therefore, selective targeting of GLUTs presents a potentially powerful tool for diagnostics and treatment of cancer and other diseases. This has been …
Multiscale Molecular Modeling Studies Of The Dynamics And Catalytic Mechanisms Of Iron(Ii)- And Zinc(Ii)-Dependent Metalloenzymes, Sodiq O. Waheed
Multiscale Molecular Modeling Studies Of The Dynamics And Catalytic Mechanisms Of Iron(Ii)- And Zinc(Ii)-Dependent Metalloenzymes, Sodiq O. Waheed
Dissertations, Master's Theses and Master's Reports
Enzymes are biological systems that aid in specific biochemical reactions. They lower the reaction barrier, thus speeding up the reaction rate. A detailed knowledge of enzymes will not be achievable without computational modeling as it offers insight into atomistic details and catalytic species, which are crucial to designing enzyme-specific inhibitors and impossible to gain experimentally. This dissertation employs advanced multiscale computational approaches to study the dynamics and reaction mechanisms of non-heme Fe(II) and 2-oxoglutarate (2OG) dependent oxygenases, including AlkB, AlkBH2, TET2, and KDM4E, involved in DNA and histone demethylation. It also focuses on Zn(II) dependent matrix metalloproteinase-1 (MMP-1), which helps …
Multilevel Computational Investigation Into The Catalytic Mechanisms Of Matrix Metalloproteinase-1 And Fat Mass And Obesity-Associated Enzyme, Ann Varghese
Dissertations, Master's Theses and Master's Reports
Enzymes are biological macromolecules, typically proteins, that efficiently accelerate the rate of chemical reactions. Their remarkable catalytic power plays a vital role in essential processes across all kingdoms of life. Nowadays, computational chemistry methods provide valuable insights into enzymatic functions aiding our understanding of biological processes and providing advancements in fields such as biomedical sciences, biomimetic catalysis, drug design and biotechnology. This dissertation employs multilevel computational chemistry methods to investigate the structure-function relationships and the catalytic mechanisms of two metalloenzymes -Zn(II)-dependent matrix metalloproteinase-1 (MMP-1) and non-heme Fe(II)/2-oxoglutarate (2OG) dependent fat-mass and obesity-associated (FTO) enzyme. Chapter 2 explores the role of …
Molecular Dynamics Modeling Of Polymers For Aerospace Composites, Swapnil Sambhaji Bamane
Molecular Dynamics Modeling Of Polymers For Aerospace Composites, Swapnil Sambhaji Bamane
Dissertations, Master's Theses and Master's Reports
Polymer matrix composite materials are widely used as structural materials in aerospace and aeronautical vehicles. Resin/reinforcement wetting and the effect of polymerization on the thermo-mechanical properties of the resin are key parameters in the manufacturing of aerospace composite materials. Determining the contact angle between combinations of liquid resin and reinforcement surfaces is a common method for quantifying wettability. It is challenging to determine contact angle values experimentally of high-performance resins on CNT materials such as CNT, graphene, bundles or yarns, and BNNT surfaces. It is also experimentally difficult to determine the effect of polymerization reaction on material properties of a …
Predicting The Reactivities And Reaction Mechanisms Of Photochemically Produced Reactive Intermediates, Benjamin Barrios Cerda
Predicting The Reactivities And Reaction Mechanisms Of Photochemically Produced Reactive Intermediates, Benjamin Barrios Cerda
Dissertations, Master's Theses and Master's Reports
Photochemically produced reactive intermediates (PPRIs) such as the hydroxyl radical, carbonate radical (CO3•-) singlet oxygen (1O2) and triplet state of chromophoric dissolved organic matter (3CDOM*) are formed in sunlit natural waters upon photoexcitation of chromophoric dissolved organic matter (CDOM). PPRIs react with the organic compounds involved in key environmental processes, resulting in transformation products of smaller molecular weight than their parent compounds. Photochemical transformation of these key water constituents due to their reactions with PPRIs may pose potential effects on human and aquatic ecosystems. Consequently, there is a need …
Theoretical Investigation On Optical Properties Of 2d Materials And Mechanical Properties Of Polymer Composites At Molecular Level, Geeta Sachdeva
Theoretical Investigation On Optical Properties Of 2d Materials And Mechanical Properties Of Polymer Composites At Molecular Level, Geeta Sachdeva
Dissertations, Master's Theses and Master's Reports
The field of two-dimensional (2D) layered materials provides a new platform for studying diverse physical phenomena that are scientifically interesting and relevant for technological applications. Theoretical predictions from atomically resolved computational simulations of 2D materials play a pivotal role in designing and advancing these developments. The focus of this thesis is 2D materials especially graphene and BN studied using density functional theory (DFT) and molecular dynamics (MD) simulations. In the first half of the thesis, the electronic structure and optical properties are discussed for graphene, antimonene, and borophene. It is found that the absorbance in (atomically flat) multilayer antimonene (group …
Multilevel Computational Investigation Into The Dynamics And Reaction Mechanisms Of Non-Heme Iron And 2-Oxoglutarate Dependent Enzymes, Shobhit Sanjeev Chaturvedi
Multilevel Computational Investigation Into The Dynamics And Reaction Mechanisms Of Non-Heme Iron And 2-Oxoglutarate Dependent Enzymes, Shobhit Sanjeev Chaturvedi
Dissertations, Master's Theses and Master's Reports
Computational chemistry methods have been extensively applied to investigate biological systems. This dissertation utilizes a multilevel computational approach to explore the dynamics and reaction mechanisms of two groups of enzymes belonging to non-heme Fe(II) and 2-oxoglutarate (2OG) dependent superfamily – histone lysine demethylases from class 7 and ethylene forming enzyme (EFE). Chapter 2 uncovers the role of conformational dynamics in the substrate selectivity of histone lysine demethylases 7A and 7B. The molecular dynamics (MD) simulations of the two enzymes revealed the importance of linker flexibility and dynamics in relative orientations of the reader (PHD) and the catalytic (JmjC) domains. Chapter …