This Is AuburnElectronic Theses and Dissertations

Computational screening strategies for rational biocatalyst and electrocatalyst design and development




Ali, Ashraf

Type of Degree

PhD Dissertation


Chemical Engineering

Restriction Status


Restriction Type


Date Available



In most of the important aspects of modern civilization such as food production, energy usage, or biomedical and biochemical advances, catalysis plays a crucial role in supporting these efforts. For a greener and sustainable future, catalysis research has been increased many-fold, and one of the first steps toward this end is to understand the fundamental structure-property relationships underlying catalysis for crucial systems. Another critical step to advancing the field of catalysis is to look into the microscopic details of the underlying reaction pathways and key intermediates. In order to probe these steps and gain new insights, computational modeling employing computational chemistry and chemical engineering principles from the atomistic to macroscopic levels is a potent tool. In the dissertation presented, the catalytic phenomena of enzyme and electrolysis is elucidated with computational chemistry tools. In the study of biocatalysis, the activity of one of the most commonly used industrial biocatalysts, serine protease, has been explored to provide new insights. The reaction pathway analysis of serine protease is investigate using quantum mechanical cluster (QM-cluster) calculations with density functional theory (DFT). A new pathway has been proposed to resolve the long standing debate surround the His-flip mechanism established in literature. The Gibbs free energy of activation, rate coefficient, and the Gibbs free energy of reaction are used compare the both pathways. With these critical thermochemical and kinetic parameters, detailed reaction path analysis has been performed on a peptide bond cleavage by the active site of a serine protease, and hitherto results of this study indicate the viability of the proposed pathway. In the study of electrocatalysis, first, a systematic study of various non-hybrid and hybrid molybdenum dichalcogenides/graphene (MoCh2/Gr; Ch = S, Se, Te) nanocomposite for the hydrogen evolution reaction (HER) has been performed using periodic plane-wave DFT calculations. The electronic structure, adsorption energetics, and adsorption site specificity for hydrogen adsorption for several different catalytic sites on the nanocomposite have been investigated. Combining the computational results with experimental descriptors provided by a collaborative group, screening of MoCh2/Gr materials for HER electrocatalyst is carried out, MoSTe/Gr is found to be the best cathodic material for HER. In the second project of electrocatalysis, a rational strategy has been developed to design a better cathodic material for HER. The material for this catalyst is based on the result of previous project: molybdenum sulfotelluride/graphene (MoSxTey/Gr) nanocomposite. Molecular modeling studies have been performed with periodic plane-wave DFT, and hydrogen binding energetics for various MoSxTey/Gr is carried out with multiple ratio of Mo, S, and Te. These studies show that the nanocomposites consisting of slightly more Te than S atom and higher amount of Mo than the stoichiometric ratio should demonstrate enhancement in catalytic performance. An independent experimental study performed by a collaborative group supported these computational findings.