Worcester State University

 

Chemistry Abstracts


GREENER SEPARATION OF DYES USING AQUEOUS
BIPHASIC SYSTEMS

Keith Dusoe

Faculty Adviser: Meghna Dilip, Ph.D.

Aqueous Biphasic Systems (ABSs) are a safer and “green” alternative to traditional solvent based extraction methods for environmental remediation since they obviate the need for volatile organic solvents that are often times flammable and carcinogenic. Composed largely of water and non-toxic, non-volatile, and non-flammable components, an ABS allows for rapid extraction of hazardous chemicals without use of auxiliary substances. In this work, the effective partitioning of gentian violet (a known carcinogenic dye) was demonstrated in both a polymer-salt ABS as well as salt-salt ABS. It was shown that the nature of kosmotropic salt, ionic liquid/polyethylene glycol concentration, and pH played a major role in the partitioning of the dyes.

REGIOCHEMISTRY OF RING FORMATION AS A
FUNCTION OF RING SIZE

Hawa Fall and Vivian Nguyen

Faculty Adviser: John Goodchild, Ph.D.

A challenge that often faces the organic chemist is to optimize yields in a reaction where multiple products are possible. In this study, computer modeling is used to help predict the most stable product in such a reaction. The purpose of the study is to investigate ring formation caused by the attack of a nucleophile on a molecule that can cyclize to give products with different sized rings. Gaussian 03 was implemented to calculate the energy of each of the six products formed during the reaction with the use of Hart-Fock (HF) at the 6-31++G (d,p) basis set.

THEORETICAL EXPLANATION OF SELF-CONSISTENT
FIELD APPROXIMATION

Richard Holy

Analyzing molecules and molecular interactions using ab intio methods requires the use of computers because of the complexity of the mathematical algorithms that are the subject of this project. Even the most simple of chemical structures such as a molecule of water takes a large amount of computing power and time to model. With use of “approximations,” we can reduce the amount of computing power and time necessary to use model chemistries at the cost accuracy. The Hartree-Fock Self-Consistent Field method is an approximation that allows one to calculate the properties of a molecule by “averaging” the potential field that an electron may exist in at a point in time.

ATOM ECONOMY ESSAY

Margaret Kerr, Ph.D.

This essay about the green chemistry topic “atom economy” was published by Prentice Hall in the 12th edition of Chemistry for Changing Times, a textbook for non-science majors. Atom economy is a fundamental part of green chemistry and describes how many atoms that are reacted end up in the desired product. Atoms that are not part of the desired product typically are disposed of as waste. To minimize the production of waste, it is important when designing new reactions to consider the atom economics of the reaction. The essay consists of descriptive passages and exercises for students. This popular textbook typically reaches about 100,000 students per year.


FLAVONES IN TEA

Lukasz Kicilinski

Faculty Adviser: John Goodchild, Ph.D.

Flavones are a family of compounds that occur widely in plants. There is evidence that dietary flavones provide health benefits such as protection against cancer. This might be because of the ability of flavones to react with oxidizing agents that damage cells. It has been suggested that green tea protects against cancer in this way and is more effective than black tea. We decided to compare the flavone content of green and black teas using thin layer chromatography.


MODELING THE EFFECT OF RING SIZE ON THE STABILITY OF A METAL-CHELATING NITROGEN LIGAND

Cooper King

Faculty Adviser: Eihab Jaber, Ph.D.

Metal-ligand supramolecular systems have been of interest in new age medicine for removing toxic metals from the body. One important question is how to design the molecules that will selectively bond to heavier, harmful metals. DPA-2 (N,N’-di-2-picolylethylenediamine) and DPA-3 (N,N’-di-2-picolyl-1,3-propanediamine) are polydentate chelating molecules with both ring- and linear-integrated nitrogen donors. Ligand-metal stability with several metals when changing from a 5-membered ring in DPA-2 to 6-membered in DPA-3 was tested. Accuracy was compared among traditional low-level molecular mechanics, scaled to ab-initio Hartree-Fock, and density functional theory B3LYP, and possible partitioning methods were attempted.

RELATIVE STABILITY OF A TRIGONAL BIPYRAMIDAL PHOSPHOROUS VIA ELECTRONEGATIVITY SELECTION

Ryan R. Knihtlla

Faculty Adviser: Eihab Jaber, Ph.D.

Understanding binding affinity and binding stoichiometry between molecules allows for a unique look into ligand binding dynamics by way of selectivity of the molecules. Ligand binding interactions are frequently

coupled to conformational changes in the molecules via electronegativity selection. Computational chemistry allows for a useful method to explore these types of ligand binding interactions and their respective affinities. This work explores these types of ligand binding interactions through the study of Tetrahalide(fluoro) phosphorane molecules by removing the equatorial fluorine atoms and replacing them with less electronegative, using single point energy calculations via ab initio methods with the use of GAUSSIAN 03.

DESIGN OF A CLUSTERED COMPUTING CONFIGURATION FOR QUANTUM CHEMICAL SIMULATIONS

Jason Kost

Faculty Adviser: Eihab Jaber, Ph.D.

High performance computing clusters provide an inexpensive solution for the undergraduate research laboratory to obtain the computational power necessary for the execution of complex quantum chemical simulations. Utilizing readily available commodity computer hardware academically licensable software, these clusters may be assembled with little to no financial investment. In this project, a cluster comprised of 18 single processor desktops with an IBM server acting as the head node was utilized. All systems have installed the open source batch queuing tool Torque, GAMESS quantum chemical computational software, and the Red Hat Enterprise 5 Linux operating system. This setup was then benchmarked in relation to a number of systems in order to quantify any computational gains.

A THEORETICAL INVESTIGATION ON THE FORMATION OF CARBON MONOXIDE POLYMERIC CHAINS

Christina Lovell

Faculty Adviser: Eihab Jaber, Ph.D.

Carbon monoxide molecules have been known to form polymeric-like chains that consist of several molecules in length, with relative stabilities. Understanding the stability of these molecules can help to predict how easily these polymeric forms of carbon monoxide can exist in the atmosphere. As a result, this may provide further information about both the life span and the toxicity of different conformations of these polymeric-like chains of carbon monoxide. With the use of ab initio and density functional theories, we have been able predict the stability of these molecules, by calculating their respective energies and monitoring their energy differences as a function of polyketone length.

COMPUTATIONAL ANALYSIS OF THE CONFIRMATION
OF HEME IN HEMOGLOBIN

Ericca Lucht

Faculty Adviser: Jeffry Nichols, Ph.D.

Hemoglobin is a metalloprotien that transports oxygen in the body. Analysis of the crystalline structure of Hemoglobin through x-ray diffraction shows that the porphryn ring of the Heme group is contorted. In this study the effects of the surrounding amino acids on the geometry of the porphryn ring were compared to the ab initio planar ring. Gaussian 03 was used to calculate single point energies at the DFT-B3LYP levels on both models with a 6-311G(d,p) basis set.

COMPUTATIONAL INVESTIGATION OF CATALYTIC OZONE DESTRUCTION BY HYDROXYL RADICAL

Wyatt G. Merrill and Kevin Sorge

Faculty Adviser: Eihab Jaber, Ph.D.

The hydroxyl radical is known to play a key role in the destruction of ozone in the stratosphere through a cycle that is capable of perpetuating itself. This destructive cycle is carried out in a two step reaction in which the hydroxyl radical catalyzes the creation of diatomic oxygen from ozone and singlet oxygen. Our findings suggest that the enthalpies for this cycle computed at lower levels of ab initio methods and basis sets compare well with experimental findings. We model this cycle via a computational method with the use of GAUSSIAN 03.

ENTHALPIC CONTRIBUTION TO THE STABILIZATION OF
NICKEL ION COMPLEXES

Lucas Miller

Faculty Adviser: Eihab Jaber, Ph.D.

Modern chemists are concerned with the effectiveness of metal ion selection as it is useful in the fields of pharmacology, nanotechnology, and environmental science. For example, the proper selection and retention of a metal ion could allow for more efficient transport to a specific part of the body. Bidentate chelating ligands of a metal ion are known to result in a more stable molecule when compared with monodentate ligands on the same metal ion. In this work, we examine the enthalpic contribution to the stabilization of the metal ion complexes as the molecule becomes more macrocyclic.

SETTING A CHEMICAL TRAP

Taral Naik

Faculty Adviser: John Goodchild, Ph.D.

Organic chemistry is largely about making new molecules, particularly ones that may be useful (such as drugs) or may help us understand nature a little better. Chemists are always seeking new ways to help them construct complex molecules more easily. We are working on a way to set a chemical trap that will be irresistible for some simple molecules. On falling into the trap, they will be converted into molecules that are more complex and more interesting.


THERMODYNAMICS OF THE BIFURCATED HYDROGEN BONDING FORMATIONS OF GUANINE-TETRAMERS, GUANINE-PENTAMERS, AND GUANINE-HEXAMERS

Margaret T. Nguyen

Faculty Adviser: Eihab Jaber, Ph.D.

Telomeres are structures at the ends of chromosomes (endcaps) that are guanine-rich sequences that protect the ends from destruction. These sequences contain domains of G-tetramers in which G-G pairs are held together by intermolecular hydrogen bonding. It is believed that the hydrogen bonding of these G-G pairs occurs by bifurcated interactions in the absence of monovalent cations. Cooperative interactions are thought to play a key role in the stabilization of these G-tetramers. In this work, the enthalpic cooperative contribution to the stabilization of these G-G pairs by bifurcated hydrogen bonding was evaluated by ab initio methods and suggests that they play a pivotal role in the stabilization of these G-tetramers.

COMPUTATIONAL STUDIES OF BIODIESEL USING POTENTIAL ENERGY MAPPING OF METAL CATALYZED ESTERIFICATION

Jessica Sargent and Adham Chebbani

Faculty Adviser: Margaret Kerr, Ph.D.

Usually, biodiesel is produced via a homogenous Brønsted catalyst. However, there are disadvantages that complicate the purification: purity of the reactants, creation of a caustic waste stream, and formation of soap. This process isn’t as efficient with waste oil because of the high free fatty acid content. Hopefully, waste oil can be used to make soap followed by an acid workup to form biodiesel. The free fatty acids in waste vegetable oil can be reacted with a metal halide catalyst to form methyl ester. Computational results using Gaussian 03 were compared with results taken from experimental values to determine the catalyst’s viability.

COMPUTATIONAL STUDIES OF STRATOSPHERIC FORMATION
OF BROMINE NITRATE

Patrick John Sargent

Faculty Adviser: Eihab Jaber, Ph.D.

With the use of computational methods we can provide a unique undergraduate laboratory activity for the study of a complex stratospheric chemistry reaction. The compound of interest for this study is Bromine

Nitrate (BrONO2), which researchers believe to undergo key reactions with ozone during the dark hours of the night. The reactivity of BrONO2 without the need for sunlight allows it to be a key component in ozone destruction. To investigate this reaction, our calculations were conducted at the density functional theory (DFT) at the functional of B3LYP with the 6-311+G(2df) basis in order to calculate the thermodynamic properties of BrONO2 upon reaction with atomic Br.

HOW GREEN ARE “GREEN” CLEANERS?

Bradford Spencer

Faculty Adviser: Meghna Dilip, Ph.D.

Green household cleaners are ubiquitous in the market today, but how green is “green?” Biological Oxygen Demand, Chemical Oxygen Demand, and pH tests were conducted on several readily available household cleaners, in order to validate their relative “green”ness.


 
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