Chemistry Commons^™

Interactions Between Temozolomide And Quercetin, Okuma Emile Kasende, Vincent De Paul Nzuwah-Nziko, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Temozolomide and quercetin are both molecules with important pharmaceutical activity, whose effects can mutually enhance one another when clinically applied simultaneously. Quantum chemical calculations are used to examine how the two molecules might interact with one another. The most stabilizing force arises when the aromatic systems of the two molecules are arranged parallel to one another. These stacked configurations are reinforced by H-bonds, but geometries containing only H-bonds, without the aromatic stacking, are much less stable, even if the H-bonds are short and strong. Comparison between B3LYP and B3LYP-D binding energies allows an evaluation of dispersion energy, which is found …

Nx∙∙Y Halogen Bonds. Comparison With Nh∙∙Y H-Bonds And Cx∙∙Y Halogen Bonds, Binod Nepal, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Quantum calculations examine how the NH∙∙Y H-bond compares to the equivalent NX∙∙Y halogen bond, as well as to comparable CH/CX donors. Succinimide and saccharin, and their corresponding halogen-substituted derivatives, are chosen as the prototype NH/NX donors, paired with a wide range of electron donor molecules. The NH∙∙Y H-bond is weakened if the bridging H is replaced by Cl, and strengthened by I; a Br halogen bond is roughly comparable to a H-bond. The lone pairs of the partner molecule are stronger electron donors than are π-systems. Whereas Coulombic forces represent the largest fraction of the attractive force in the H-bonds, …

Nitrogenase Bioelectrocatalysis: Heterogeneous Ammonia And Hydrogen Production By Mofe Protein, Ross D. Milton, Sofiene Abdellaoui, Nimesh Khadka, Dennis R. Dean, Donal Leech, Lance C. Seefeldt, Shelley D. Minteer

Chemistry and Biochemistry Faculty Publications

notrogenase is the only enzyme known to catalyze the reduction of N2 to 2NH3. In vivo, the MoFe protein component of nitrogenase is exclusively reduced by the ATP-hydrolyzing Fe protein in a series of transient association/dissociation steps that are linked to the hyderolysis of two ATP for each electron transeferred. We report MoFe protein immobilized at an electrode surface, where cobaltocene (as an electron mediator that can be observed in real time at a carbon electrode) is used to reduce the MoFe protein (independent of the Fe protein and of ATP hydrolysis) and support the bioelectrocatalytic reduction of protons to …

Segmentation And Additive Approach: A Reliable Technique To Study Noncovalent Interactions Of Large Molecules At The Surface Of Single‐Wall Carbon Nanotubes, Ana M. Torres, Steve Scheiner, Ajit K. Roy, Andrés M. Garay-Tapia, John J. Bustamante, Tapas Kar

Chemistry and Biochemistry Faculty Publications

This investigation explores a new protocol, named Segmentation and Additive approach (SAA), to study exohedral noncovalent functionalization of single-walled carbon nanotubes (SWNTs) with large molecules, such as polymers, bio-molecules etc, by segmenting the entire system into smaller units to reduce computational cost. A key criterion of the segmentation process is the preservation of the molecular structure responsible for stabilization of the entire system in smaller segments. Noncovalent interaction of linoleic acid (LA, C18H32O2), a fatty acid, at the surface of a (10,0) zigzag nanotubeis considered for test purposes. Three smaller segmented models have been created from the full (10,0)-LA system …

Enhancing The Reduction Potential Of Quinones Via Complex Formation, Binod Nepal, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Quantum calculations are used to study the manner in which quinones interact with proton-donating molecules. For neutral donors, a stacked geometry is favored over a H-bond structure. The former is stabilized by charge transfers from the N or O lone pairs to the quinone’s π* orbitals. Following the addition of an electron to the quinone, the radical anion forms strong H-bonded complexes with the various donors. The presence of the donor enhances the electron affinity of the quinone. This enhancement is on the order of 15 kcal/mol for neutral donors, but up to as much as 85 kcal/mol for a …

The Effect Of Pure Infrared Light On The Growth Of Rhodospirrilum Rubrum, Jordan Lee Wilkes

Undergraduate Honors Capstone Projects

Scientists who study aquatic ecosystems quickly notice a diversity of pathways that different microbes and organisms can use to metabolize nutrients found in common ponds or pools. Competition for vital resources, such as light and inorganic minerals, allow only certain organisms to grow in certain niches within these ecosystems. Rhodospirillum rubrum is a gram negative, photosynthetic bacteria that competes for light within aquatic ecosystems in order to survive. R. rubrum is believed to specifically absorb light for photosynthesis at wavelengths in the range of infrared light. It was found that R. rubrum indeed can grow in "dark", anaerobic environments by …

Structural Insights Into The Regulation Of Electron Transfer In Nitrogenase, And Modulating The Reactivity Of The Isolated Iron Molybdenum Cofactor, Andrew J. Rasmussen

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

One of the most important scientific advances in the last century was the Haber-Bosch process, the industrial process of fixing nitrogen from the atmosphere to ammonia. This allowed for the commercial production and sale of nitrogen for important uses such as fertilizer for farming. The Haber-Bosch process is partially credited with the population boom that has been seen in the last century and has greatly increased the standard of living in the developed world today. While this was a great scientific breakthrough, the cost of producing the required ammonia is high, and roughly 2% of worldwide energy is used annually …

Synthesis, Structure-Activity Relationship Study, And Mode Of Action Study Of 1,4-Naphthoquinone Based Anticancer And Antimicrobial Agents, Jaya P. Shrestha

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The first three projects involve the synthesis and the mode of action study of 1,4-naphthoquinone based anticancer agents. These anticancer agents are highly potent against a wide range of cancer cell lines. These compounds showed ~8-fold selectivity towards the lung cancer cell line than the normal cell line. We also studied the mode of action and observed that generation of reactive oxygen species is the primary mode of action.

The final project involves the synthesis of multi-cationic antimicrobial agents. These compounds are active against both bacteria and fungi. These compounds are very easy to synthesize and can be scaled up …

Fluorescent Probes To Investigate Homologous Recombination Dynamics, Eric Parker Davenport

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

As the average cell’s DNA undergoes roughly 1 million molecular lesions per day, learning about one of the repair mechanisms which fixes damaged DNA is a worthwhile endeavor. Such work may provide insights into how to treat or prevent diseases such as cancers and associated genetic disorders. Homologous recombination (HR) is one pathway which is used by cells to repair a specific type of DNA damage, double-strand breaks. While HR is a complex process involving over 25 different proteins, exactly how HR works, including its regulation, is largely unknown. One protein in particular, Rad51, forms a filament on the damaged …

Oxidative Carbon-Carbon Bond Cleavage Reactions Of Metal Flavonolato And Chlorodiketonate Complexes, Sushma L. Saraf

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The research presented in this dissertation focuses on the oxidative cleavage of chemical bonds between two carbon atoms. This type of reactivity is of significant interest due to its potential application toward the development of ways to convert chemical feed stock into useful products such as pharmaceuticals, polymers and fuels in an environmentally benign and cost-efficient manner. Reactions that cleave specific carbon-carbon bonds, are catalyzed by earth-abundant metals, and involve O₂ as the terminal oxidant, are of particular interest.

Our strategy has been to study the oxidative carbon-carbon bond cleavage reactivity of metal complexes containing components similar to structures …

Atp Usage In The Dark-Operative Protochlorophyllide Oxidoreductase, Mark S. Soffe

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Chlorophylls are essential pigment molecules that function in photosynthesis, and serve to aid in utilizing energy from sunlight to power cellular processes in plants, and other organisms. To make chlorophyll, photosynthetic organisms devote an abundance of resources and energy to ensure their appropriate construction. This process of making chlorophylls is highlighted by the penultimate step in the pathway—the conversion of protochlorophyllide (Pchlide) to chlorophyllide a (Chlide).

This conversion can be mediated in two different ways, depending on the type of organism. The first method incorporates the use of a light-activated system called the light-dependent protochlorophyllide oxidoreductase (LPOR). This system, as …

Computational Chemistry Of Non-Covalent Interaction And Its Application In Chemical Catalysis, Vincent De Paul Nzuwah Nziko

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Known to be weaker than conventional covalent bonds, non-covalent bonds, especially hydrogen bond, has shown to be of great importance in molecular structures such as DNA, RNA, proteins and other organic frameworks. In this dissertation, we looked at non-covalent interactions other than the hydrogen bond. Replacement of the bridging hydrogen atom in a typical hydrogen bond by other atoms such a halogen, chalcogen and tetrel lead to the formation of interactions which are comparable in strength to the hydrogen bond. Unlike the hydrogen bond which arises mainly from electrostatics, these unconventional interactions mostly result from induction. Besides studying the fundamentals …

Computational Studies Of Microscopic Superfluidity In 4he Clusters, Angeline R. Wairegi

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The onset of microscopic superfluidity has been reported in ultracold droplets of bosons (⁴He atoms or para-H₂ molecules) containing a variety of molecular dopants. The physics of these droplets involve both Bose-Einstein condensation (BEC) and superfluidity. The two phenomena, while closely related, are not exactly the same. Superfluidity is fundamentally a microscopic effect and thermodynamic limit is necessary; it is still remarkable, though, that the signature of superfluidity has been reported in doped droplets consisting of as few as 4 ⁴He atoms. The studies presented here adopt a molecular vantage point to investigate the quantum mechanics …

Quantum Mechanical Studies Of Charge Assisted Hydrogen And Halogen Bonds, Binod Nepal

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Like cement bridges one brick to another, noncovalent forces also bridge two or more molecules together to form a molecular crystal or molecular cluster. Although weaker than the covalent bond, the existence of noncovalent forces can be seen everywhere from liquid water to construction of complex biomolecules like DNA, RNA, proteins etc. An introduction of suitable charge; positive or negative, on the binding units can increase the strength of noncovalent interaction by several orders of magnitude. The primary aim of this dissertation is to explore some fundamental properties of such charge assisted noncovalent interactions which will be helpful for the …

Heterogeneous And Homogeneous Nickel-Based Electrocatalysts For Oxygen Evolution And Carbon Dioxide Reduction, Meili Sheng

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The growing global energy demand and the increasing concentration of CO₂ in the atmosphere have encouraged the development of renewable energy to replace carbon-based fossil fuels. Electrocatalytic water splitting to form H₂ and O₂ and reduction of CO₂ to CO are appealing processes and we can be directly utilize H₂ and CO as fuels or commodity chemicals in mature industrial processes, which will not alter the current carbon cycle. However, the O₂ evolution reaction of water splitting is a reaction of four-proton and four-electron transfer process, whose kinetics is very sluggish under normal conditions. …

H-Bonding And Stacking Interactions Between Chloroquine And Temozolomide, Okuma Emile Kasende, Vincent De Paul Nzuwah-Nziko, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

The interactions between temozolomide and chloroquine were examined via Dispersion-Corrected Density Functional Theory and MP2 methods. Chloroquine was considered in both its lowest energy structure and in a local minimum where its aromatic system and secondary amine group are free to interact directly with temozolomide. The accessibility of these two components to intermolecular interaction makes the lowest energy dimer of this local monomer minimum competitive in total energy with that involving chloroquine’s most stable monomer geometry. In either case, the most stable heterodimer places the aromatic ring systems of the two molecules parallel and directly above one another in a …

Hydrogen Bonded And Stacked Geometries Of The Temozolomide Dimer, Okuma Emile Kasende, Jules Tshishimbi Muya, Vincent De Paul Nzuwah-Nziko, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Dispersion-corrected Density Functional Theory (DFT) and MP2 quantum chemical methods are used to examine homodimers of temozolomide (TMZ). Of the twelve dimer configurations found to be minima, the antarafacial stacked dimer is the most favored, lower in energy than coplanar dimers which are stabilized by H-bonds. The comparison between B3LYP and B3LYP-D binding energies points to dispersion as a primary factor in stabilizing the stacked geometries. CO(π)→CO(π*)charge transfers between amide groups in the global minimum are identified by NBO, as well as a pair of weak CH∙∙N H-bonds. AIM analysis of the electron density provides an alternative description which includes …

Catalysis Of The Aza-Diels-Alder Reaction By Hydrogen And Halogen Bonds, Vincent De Paul Nzuwah-Nziko, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

The combination of H2C=NH and cis-1,3-butadiene to form a six-membered ring was examined by quantum calculations. The energy barrier for this reaction is substantially lowered by the introduction of an imidazolium catalyst with either a H or halogen (X) atom in the 2-position, which acts via a H or halogen bond to the N atom of the imine, respectively. X=I has the largest effect, and Cl the smallest; Br and H are roughly equivalent. The catalyst retards the formation of the incipient N-C bond from imine to diene while simultaneously accelerating the C-C bond formation. The energy of the π* …

Potential Regulation Of Deadly Water-Borne Shigella Bacteria Pathogenesis Through The Shigella Infection Protein Spa47, Jamie Kingsford

Research on Capitol Hill

• Shigella is a gram-negative, bacterial pathogen typically found in contaminated water sources.
• Each year, Shigella is responsible for over 90 million infections and 100,000 deaths stemming from symptoms of severe dysentery, fever, nausea and vomiting.
• A needle-like apparatus found on the surface of Shigella allows the bacterium to infect host cells.
• Each needle-apparatus has an associated ATPase, a protein that can hydrolyze ATP into ADP and P_i.
• The Shigella needle-apparatus ATPase Spa47 is predicted to provide the energy for infection.
• Spa47 has been shown to be essential for infection – without Spa47, no infection will occur.
• We were …

Building A Better Halide Receptor: Optimum Choice Of Spacer, Binding Unit, And Halosubstitution, Binod Nepal, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Quantum calculations are used to measure the binding of halides to a number of bipodal dicationic receptors, constructed as a pair of binding units separated by a spacer group. A number of variations are studied. A H atom on each binding unit (imidazolium or triazolium) is replaced by Br or I. Benzene, thiophene, carbazole, and dimethylnaphthalene are considered as spacer groups. Each receptor is paired with halides F-, Cl-, Br-, and I-. I-substitution on the binding unit yields a large enhancement of binding, as much as 13 orders of magnitude; a much smaller increase occurs for bromosubstitution. Imidazolium is a …

Comparison Of Π-Hole Tetrel Bonding With Σ-Hole Halogen Bonds In Complexes Of Xcn (X = F, Cl, Br, I) And Nh3, Steve Scheiner, Vincent De Paul Nziko

Chemistry and Biochemistry Faculty Publications

In addition to the standard halogen bond formed when NH₃ approaches XCN (X=F,Cl,Br,I) along its molecular axis, a perpendicular approach is also possible, toward a π-hole that is present above the X-C bond. MP2/aug-cc-pVDZ calculations indicate the latter geometry is favored for X=F, and the σ-hole structure is preferred for the heavier halogens. The π-hole structure is stabilized by charge transfer from the NH₃ lone pair into the π*(CN) antibonding orbital, and is characterized by a bond path from the N of NH₃ to the C atom of XCN, a form of tetrel bond. The most stable …

Electrochemical Oxidation To Construct A Nickel Sulfide/Oxide Heterostructure With Improvement Of Capacitance, Xuan Liu, Bo You, Xin-Yao Yu, Jeffrey Chipman, Yujie Sun

Chemistry and Biochemistry Faculty Publications

Supercapacitors have been widely recognized as a promising device for the storage of renewable energy. Herein, a facile electrochemical oxidation strategy is described to construct a nickel sulfide/oxide heterostructure which enhances the specific areal capacitance of Ni₃S₂ electrode (2035 mF cm^-2 vs. 31 mF cm^-2 at a current density of 8 mA cm^-2), while still maintaining great stability, showing no performance degradation after 5000 charge-discharge cycles. Its exceptional capacitance, advanced rate capability, and superior cycling stability are attributed to the transformed composition and unique nanostructure achieved during electrochemical oxidation, which can provide a …

Microsolvation Of Anions By Molecules Forming Ch∙∙X- Hydrogen Bonds, Steve Scheiner, Binod Nepal

Chemistry and Biochemistry Faculty Publications

Various anions were surrounded by n molecules of CF₃H, which was used as a prototype CH donor solvent, and the structures and energies studied by M06-2X calculations with a 6-31+G∗∗ basis set. Anions considered included the halides F^-, Cl^-, Br^- and I^-, as well as those with multiple proton acceptor sites: CN^-, NO₃ ^-, HCOO^-, CH₃COO^-, HSO₄ ^-, H₂PO₄ ^-, and anions with higher charges SO₄ ^2-, HPO₄ ^2- and PO_{4 …}

Substituent Effects On The Binding Of Halides By Neutral And Dicationic Bis-Triazolium Receptors, Binod Nepal, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

The effects of substituent and overall charge upon the binding of a halide anion by a bis-triazolium receptor are studied by M06-2X DFT calculations, with the aug-cc-pVDZ basis set. Comparison is also made between a receptor that engages in H-bonds, with a halogen-bonding species. Fluoride is clearly most strongly bound, followed by Cl-, Br-, and I- in that order. The dicationic receptor engages in stronger complexes, but not by a very wide margin compared to its neutral counterpart. The binding is enhanced as the substituent on the two triazolium rings becomes progressively more electron-withdrawing. Halogen-substituted receptors, whether neutral or cationic, …

Cobalt-Centred Boron Molecular Drums With The Highest Coordination Number In The Cob16− Cluster, Ivan A. Popov, Tian Jian, Gary V. Lopez, Alexander I. Boldyrev, Lai-Sheng Wang

Chemistry and Biochemistry Faculty Publications

The electron deficiency and strong bonding capacity of boron have led to a vast variety of molecular structures in chemistry and materials science. Here we report the observation of highly symmetric cobalt-centered boron drum-like structures of CoB16⁻, characterized by photoelectron spectroscopy and ab initio calculations. The photoelectron spectra display a relatively simple spectral pattern, suggesting a high symmetry structure. Two nearly degenerate isomers with D8d(I) and C4v (II) symmetries are found computationally to compete for the global minimum. These drum-like structures consist of two B8 rings sandwiching a cobalt atom, which has the highest …

Interactions Between Thiourea And Imines. Prelude To Catalysis, Vincent De Paul Nzuwah-Nziko, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

The interaction between thiourea and a series of imines was examined via high-level ab initio calculations. For each imine, there is a set of stable complexes that represent minima on the potential energy surface. One type is characterized by a pair of symmetric NH···N hydrogen bonds (HBs), with both NH groups of thiourea approaching the imine N from above and below its molecular plane. Another geometry category combines a linear NH···N with a CH···S HB. A third, which is less stable, has the S approaching the imine’s CH2 group, and a stacking arrangement is present in the fourth. Interaction energies …

Dissection Of The Factors Affecting Formation Of A Ch∙∙∙O H-Bond. A Case Study, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Quantum calculations are used to examine how various constituent components of a large molecule contribute to the formation of an internal CH∙∙∙O H-bond. Such a bond is present in the interaction between two amide units, connected together by a series of functional groups. Each group is removed one at a time, so as to monitor the effect of each upon the H-bond, and thereby learn the bare essentials that are necessary for its formation, as well as how its presence affects the overall molecular structure. Also studied is the perturbation caused by change in the length of the aliphatic chain …

Comparison Of Ch∙∙O, Sh∙∙O, Chalcogen, And Tetrel Bonds Formed By Neutral And Cationic Sulfur-Containing Compounds, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

The ability of neutral and charged S-compounds to form different sorts of noncovalent bonds is examined by ab initio calculations. Neutrals are represented by CH3SH and fluoro substituted FSCH3; cations are (CH3)3S+, CH3SH2+, and FHSCH3+. Each is paired with N-methylacetamide (NMA) whose O atom serves as common electron donor. Charged species engage in much stronger noncovalent bonds than do the neutral molecules, by as much as an order of magnitude. The strongest noncovalent bond for any system is a O∙∙SF chalcogen bond wherein the O lies directly opposite a S-F covalent bond, amounting to as much as 39 kcal/mol. Second …

Competitive Halide Binding By Halogen Versus Hydrogen Bonding: Bis-Triazole Pyridinium, Binod Nepal, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

The binding of F-, Cl-, Br-, and I- anions by bis‐triazole‐pyridine (BTP) was examined by quantum chemical calculations. There is one H atom on each of the two triazole rings that chelate the halide via H bonds. These H atoms were replaced by halogens Cl, Br, and I, thus substituting H bonds by halogen bonds. I substitution strongly enhances the binding; Br has a smaller effect, and Cl weakens the interaction. The strength of the interaction is sensitive to the overall charge on the BTP, rising as the binding agent becomes singly and then doubly positively charged. The strongest preference …

A Structurally-Tunable 3-Hydroxyflavone Motif For Visible Light-Induced Carbon Monoxide-Releasing Molecules (Corms), Stacey N. Anderson, Jason M. Richards, Hector J. Esquer, Abby D. Benninghoff, Atta M. Arif, Lisa M. Berreau

Chemistry and Biochemistry Faculty Publications

Molecules that can be used to deliver a controlled amount of carbon monoxide (CO) have the potential to facilitate investigations into the roles of this gaseous molecule in biology and advance therapeutic treatments. This has led to the development of light-induced CO-releasing molecules (photoCORMs). A goal in this field of research is the development of molecules that exhibit a combination of controlled CO release, favorable biological properties (e.g., low toxicity and trackability in cells), and structural tunability to affect CO release. Herein, we report a new biologically-inspired organic photoCORM motif that exhibits several features that are desirable in a next-generation …