Chemistry Commons^™

Regioselectivity Of The Interaction Of Temozolomide With Borane And Boron Trifluoride, Okuma Emile Kasende, Jules Tshishimbi Muya, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

MP2 and B3LYP calculations are used to predict the most favorable site of temozolomide toward BH3 and BF3 which are classical Lewis acids. Binding energies, charge transfers, and bond length perturbations of the temozolomide in various complexes indicate that the N12 atom is the preferred attack site for BH3, while BF3 prefers the O17 atom. The interactions are quite strong, as much as 100 kJ/mol for BH3 and more than 60 kJ/mol for BF3. The molecular electrostatic potential surrounding temozolomide is most negative around the O atoms, which is unable to explain the energetic order of binding of the Lewis …

Relative Toxicity Of Select Dehydropyrrolizidine Alkaloids And Evaluation Of A Heterozygous P53 Knockout Mouse Model For Dehydropyrrolizidine Alkaloid Induced Carcinogenesis, Ammon W. Brown

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Dehydropyrrolizidine alkaloids (DHPAs) are toxins produced by approximately 3% of the world’s flowering plants that can be present naturally or as contaminants in animal feed and the human food supply. Many of these compounds have been determined to cause cancer in animals and probably also cause cancer in humans. Due to the difficulty in obtaining sufficient amounts of pure DHPAs most toxicity research has been done via injection of a small amount into the abdomen of a rodent, although natural exposure is exclusively oral. For the same reason, cancer research is limited to a handful of the hundreds of known …

Computational Prediction And Rational Design Of Novel Clusters, Nanoparticles, And Solid State Materials, Alexander S. Ivanov

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The prediction of structure at the atomic level is one of the most fundamental challenges in materials science. Indeed, the structure is arguably the most important piece of information about a material, as it determines pretty much all properties of a material. Knowing the structure, one can analyze a large number of properties of a material, even before it is synthesized – the crucial importance of structure prediction for computational molecular design. This dissertation describes the technique of reliable theoretical predictions and presents the results on the successfully predicted unusual clusters, nanoparticles and solid state materials. The major part of …

Synthesis Of Fluorogenic Probes For Studying Biomass Degradation And Synthesis Of New Antifungal Aminoglycosides, Qian Zhang

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

For the first project, a library of fifteen commercially purchased and synthetic fluorogenic probes were employed for the investigation of biomass degradation using extract of white-rot fungi. These discoveries prove that it is possible to employ fungi for selective degradation or release of hemicelluloses from biomass. This work is supported by Sun Grant Western Regional Center/DOT "Bioprospecting for Enzymes to Break Lignin-Hemicellulose Bond" ($300,000,09/01/2011-08/31/2013)

The second project is focused on synthesizing new aminoglycoside analogs and exploring the potential to revive traditional antibacterial kanamycin as new type of antifungal agents. Although aminoglycosides antibiotics are mainly used as antibacterial agents, this project …

The Infrared Spectrum Of The He-C2d2 Complex, N. Moazzen-Ahmadi, A. R. W. Mckellar, Berta Fernandez, David Farrelly

Chemistry and Biochemistry Faculty Publications

Spectra of the helium-acetylene complex are elusive because this weakly bound system lies close to the free rotor limit. Previously, limited assignments of He–C2D2 transitions in the R(0) region of the ν3 fundamental band (≈2440 cm⁻¹) were published. Here, new He–C2D2 infrared spectra of this band are obtained using a tunable optical parametric oscillator laser source to probe a pulsed supersonic slit jet expansion from a cooled nozzle, and the analysis is extended to the weaker and more difficult P(1) and R(1) regions. A term value approach is used to obtain a consistent set of “experimental” energy levels. …

Intramolecular S···O Chalcogen Bond As Stabilizing Factor In Geometry Of Substituted Phenyl-Sf3 Molecules, Vincent De Paul Nziko, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Density functional methods are used to examine the geometries and energetics of molecules containing a phenyl ring joined to the trigonal bipyramidal SF3 framework. The phenyl ring has a strong preference for an equatorial position. This preference remains when one or two ether -CH2OCH3 groups are added to the phenyl ring, ortho to SF3, wherein an apical structure lies nearly 30 kcal/mol higher in energy. Whether equatorial or apical, the molecule is stabilized by a S···O chalcogen bond, sometimes augmented by CH···F or CH···O H-bonds. The strength of the intramolecular S···O bond is estimated to lie in the range between …

Synthesis And Characterization Of Polymer (Sulfonated Poly-Ether-Ether-Ketone) Based Nanocomposite (H-Boron Nitride) Membrane For Hydrogen Storage, R. Muthu Nareth, S. Rajashabla, Ramaiyan Navaneetha Kannan

All Physics Faculty Publications

The development of light weight and compact hydrogen storage materials is still prerequisite to fuel-cell technology to be fully competitive. The present experimental study reports the hydrogen storage capability of sulfonated poly-ether-ether-ketone (SPEEK)-hexagonal boron nitride (h-BN) (SPEEK-h-BN) nanocomposite membranes. The nanocomposite membranes are prepared by considering various amount of h-BN (0, 1, 3 and 5 wt. %) by phase inversion technique. The degree of sulfonation of the PEEK (SPEEK) is found to be 65% by Proton Nuclear Magnetic Resonance (¹H NMR) spectroscopy. Hydrogen adsorption studies have been carried out using a Seiverts-like hydrogenation setup. The membranes are characterized …

Homologous Recombination, Regulation, And Breast Cancer Emergence, Elliot Corless

Research on Capitol Hill

No abstract provided.

Tetrel, Chalcogen, And Ch⋅⋅O Hydrogen Bonds In Complexes Pairing Carbonyl-Containing Molecules With 1, 2, And 3 Molecules Of Co2, L. M. Azofra, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

The complexes formed by H2CO, CH3CHO, and (CH3)2CO with 1, 2, and 3 molecules of CO2 are studied by ab initio calculations. Three different types of heterodimers are observed, most containing a tetrel bond to the C atom of CO2, and some supplemented by a CH⋅⋅O H-bond. One type of heterodimer is stabilized by an anti-parallel arrangement of the C=O bonds of the two molecules. The binding energies are enhanced by methyl substitution on the carbonyl, and vary between 2.4 and 3.5 kcal/mol. Natural bond orbital analysis identifies a prime source of interaction as charge transfer into the π*(CO) antibonding …

Impact Of Detergent On The Biophysical Properties And Immune Response Of The Ipadb Fusion Protein, A Candidate Subunit Vaccine Against Shigella Spp., X. Chen, S. P. Choudhari, F. J. Martinez-Becerra, J. H. Kim, N. E. Dickenson, R. T. Toth, S. B. Joshi, J. C. Greenwood, J. D. Clements, W. D. Picking, C. R. Middaugh, W. L. Picking

Chemistry and Biochemistry Faculty Publications

Shigella spp. are causative agents of bacillary dysentery, a human illness with high global morbidity levels, particularly among elderly and infant populations. Shigella infects via the fecal-oral route, and its virulence is dependent upon a type III secretion system (T3SS). Two components of the exposed needle tip complex of the Shigella T3SS, invasion plasmid antigen D (IpaD) and IpaB, have been identified as broadly protective antigens in the mouse lethal pneumonia model. A recombinant fusion protein (DB fusion) was created by joining the coding sequences of IpaD and IpaB. The DB fusion is coexpressed with IpaB's cognate chaperone, IpgC, for …

Electrodeposited Cobalt-Phosphorous-Derived Films As Competent Bifunctional Catalysts For Overall Water Splitting, Nan Jiang, Bo You, Meili Sheng, Yujie Sun

Chemistry and Biochemistry Faculty Publications

One of the challenges to realize large-scale water splitting is the lack of active and low-cost electrocatalysts for its two half reactions: H2 and O2 evolution reactions (HER and OER). Herein, we report that cobalt-phosphorous-derived films (Co-P) can act as bifunctional catalysts for overall water splitting. The as-prepared Co-P films exhibited remarkable catalytic performance for both HER and OER in alkaline media, with a current density of 10 mAcm¢2 at overpotentials of ¢94 mV for HER and 345 mV for OER and Tafel slopes of 42 and 47 mV/dec, respectively. They can be employed as catalysts on both anode and …

Fe Protein-Independent Substrate Reduction By Nitrogenase Mofe Protein Variants, Karamatullah Danyal, Andrew J. Rasmussen, Stephen M. Keable, Boyd S. Inglet, Studipta Shaw, Oleg A. Zadvornyy, Simon Duval, Dennis R. Dean, Simone Raugei, John W. Peters, Lance C. Seefeldt

Chemistry and Biochemistry Faculty Publications

The reduction of substrates catalyzed by nitrogenase normally requires nucleotide-dependent Fe protein delivery of electrons to the MoFe protein, which contains the active site FeMo cofactor. Here, it is reported that independent substitution of three amino acids (β- 98Tyr→His, α-64Tyr→His, and β-99Phe→His) located between the P cluster and FeMo cofactor within the MoFe protein endows it with the ability to reduce protons to H2, azide to ammonia, and hydrazine to ammonia without the need for Fe protein or ATP. Instead, electrons can be provided by the low-potential reductant polyaminocarboxylate-ligated Eu(II) (Em values of −1.1 to −0.84 V vs the normal …

Chalcogen Bonds In Complexes Of Soxy (X, Y = F, Cl) With Nitrogen Bases, Luis Miguel Azofra, Ibon Alkorta, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

SOF2, SOFCl, and SOCl2 were each paired with a series of N bases. The potential energy surface of the binary complexes were characterized by MP2 calculations with double and triple-ξ basis sets, extrapolated to complete sets. The most stable configurations contained a S···N chalcogen bond with interaction energies as high as 6.8 kcal/mol. These structures are stabilized by a Nlp→σ*(S−Z) electron transfer (Z = O, F, Cl), complemented by Coulombicattraction of N to theσ-hole opposite the Z atom. N···S−F and N···S−Cl chalcogen bonds are stronger than N···S = O interactions.Formation of each chalcogen bond elongates all of the internalcovalent bonds …

Synthesis And Characterization Of Polymer (Sulfonated Poly-Ether-Ether-Ketone) Based Nanocomposite (H-Boron Nitride) Membrane For Hydrogen Storage, Naresh Muthu, S. Rajashabala, R. Kannan

Chemistry and Biochemistry Faculty Publications

The development of light weight and compact hydrogen storage materials is still prerequisite to fuel-cell technology to be fully competitive. The present experimental study reports the hydrogen storage capability of sulfonated poly-ether-ether-ketone (SPEEK)-hexagonal boron nitride (h-BN) (SPEEK-h-BN) nanocomposite membranes. The nanocomposite membranes are prepared by considering various amount of h-BN (0, 1, 3 and 5 wt. %) by phase inversion technique. The degree of sulfonation of the PEEK (SPEEK) is found to be 65% by Proton Nuclear Magnetic Resonance (¹H NMR) spectroscopy. Hydrogen adsorption studies have been carried out using a Seiverts-like hydrogenation setup. The membranes are characterized …

Antifungal Amphiphilic Aminoglycoside K20: Bioactivities And Mechanism Of Action, Sanjib K. Shrestha, Cheng-Wei Tom Chang, Nicole Meissner, John Oblad, Jaya P. Shrestha, Kevin N. Sorensen, Michelle M. Grilley, Jon Y. Takemoto

Chemistry and Biochemistry Faculty Publications

K20 is a novel amphiphilic antifungal aminoglycoside that is synthetically derived from the antibiotic kanamycin A. Reported here are investigations of K20′s antimicrobial activities, cytotoxicity, and fungicidal mechanism of action. In vitro growth inhibitory activities against a variety of human and plant pathogenic yeasts, filamentous fungi, and bacteria were determined using microbroth dilution assays and time-kill curve analyses, and hemolytic and animal cell cytotoxic activities were determined. Effects on Cryptococcus neoformans H-99 infectivity were determined with a preventive murine lung infection model. The antifungal mechanism of action was studied using intact fungal cells, yeast lipid mutants, and small unilamellar lipid …

Designed Supramolecular Filamentous Peptides: Balance Of Nanostructure, Cytotoxicity And Antimicrobial Activity, Dawei Xu, Linhai Jiang, Anju Singh, Derek Dustin, Miao Yang, Ling Liu, Reidar Lund, Timothy J. Sellati, He Dong

Chemistry and Biochemistry Faculty Publications

This work demonstrates a design strategy to optimize antimicrobial peptides with an ideal balance of minimal cytotoxicity, enhanced stability, potent cell penetration and effective antimicrobial activity, which hold great promise for the treatment of intracellular microbial infections and potentially systemic anti-infective therapy.

The Interplay Between Charge Transfer, Rehybridization, And Atomic Charges In The Internal Geometry Of Subunits In Noncovalent Interactions, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

When a noncovalent bond is formed, there is frequently some charge transfer from one subunit to the other. The interaction also causes changes in the atomic charges and hybridization patterns of bonding orbitals. The manner in which these various effects combine to cause elongations or contractions of bonds within the individual subunits is examined. In both the cases of CH···O H-bonds and P···N pnicogen bonds, the bond length changes are consistent with the guiding principles generally known as Bent’s rules.

Structure And Multi-Center Bonding: From Atomic Clusters To Solid Phase Materials, Timur R. Galeev

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The work presented in this dissertation has been focused on structure, stability, and chemical bonding of atomic clusters and solid-state compounds. The common thread was development of theoretical models and methods capable of interpreting bonding and hence, structures of these species. A major part of this work presents joint experimental and theoretical studies of a large series of doped boron clusters. The dissertation introduces a new theoretical tool for interpretation of bonding of solid phase materials in chemically intuitive terms of localized and multi-center bonds. Understanding how interactions between atoms in sub-nano clusters and solid-state compounds determine their structures, physical …

Detailed Analysis Of The Domains Of Mtr4 And How They Regulate Helicase Activity, Lacy Leigh Taylor

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The central dogma states that DNA is transcribed into RNA, which is then translated into protein. This concept conveys a minimal view of the role of RNA, portraying it simply as an intermediary between DNA and protein. However, it is now known that the role of RNA in the cell is critical in regulating protein expression both directly and indirectly. RNA in the cell typically goes through modifications to become active (on) and inactive (off) to eventually become targeted for degradation and start the cycle all over again. The protein complex that regulates the proper maturation and degradation of RNA …

Advancement Of Petroleum Diesel Alternatives Utilizing A Multifaceted And Interdepartmental Approach, Michael Morgan

UCUR

The advancement of biologically derived alternatives to petroleum diesel fuel requires a multifaceted approach. At Utah State University we use an interdisciplinary team including the Colleges of Engineering, Agriculture & Applied Sciences, and Science in conjunction with industry partners to drive innovation in improving the science behind petroleum diesel alternatives. With increasing petroleum use, depleting reserves, increasing emissions standards, and other factors, there is need for petroleum diesel alternatives that are cost effective, offer improvement, and perform similarly to petroleum diesel. Our team has focused on the use of oleaginous microbes utilizing low value effluent and waste sources including sugars …

Less Cookbook And More Research! Synthetic Efforts Toward Jbir-94 And Jbir-125: A Student-Designed Research Project In A Sophomore Organic Chemistry Lab, Mike A. Christiansen, C. L. Crawford, C. D. Mangum

Chemistry and Biochemistry Faculty Publications

In light of the meaningful learning gains that can be obtained through a genuine research experience, chemistry educators have had a longstanding interest in making teaching labs less “cookbook-like” and more research-driven [1]. With this mindset, we recently restructured our two-semester sophomore organic chemistry lab course to include a synthesis project that was chosen, designed, and carried out by students. This led to progress toward the syntheses of JBIR-94 and JBIR-125, two antioxidative/anticancer natural products that have yet to be assembled through organic chemistry. The major drawback of our course redesign is that it requires close supervision by an instructor …

A Column Free Protein Purification Procedure Using E. Coli Single ‐ Stranded Dna Binding Protein (Ssb) As An Affinity Tag, Mark Soffe

Research on the Hill (Salt Lake City)

SSBs are DNA binding proteins that are essential components of cells and play key roles in DNA replication, repair, and recombination. Here we utilize two biochemical properties associated with the E. coli SSB protein to develop a novel procedure to purify proteins using a resin-free strategy to combat the largest bottleneck in biochemical research— obtaining uncontaminated, single proteins from the total cellular contents.

1. E. coli SSB binds to single stranded DNA (ssDNA) with extremely high affinity.

2. It is also a unique protein with respect to its purification—it is possible to obtain greater than 95% pure SSB from the …

Facile Preparation Of 1st-­‐Row Transition Metal Chalcogenides As Hydrogen Evolution Catalysts In Water, Lia Bogoev

Research on the Hill (Salt Lake City)

Hydrogen, when generated directly from water with renewal energy input, is a promising chemical fuel for sustainable energy applications. As such, the development of synthetic catalysts of hydrogen evolution reaction (HER) that functionally mimic the elegant water reduction chemistry of hydrogenase enzymes have attracted broad interest, but creating molecular systems that utilize earth-abundant elements and achieve high activity, low overpotential, and long-term stability in green aqueous media remains a significant challenge. Solid-state inorganic compounds offer an alternative strategy to meet this goal. Our group is developing 1st-row transition metal chalcogenides via facile potential dynamic deposition as competent HER catalysts in …

Effects Of Charge And Substituent On The S∙∙∙N Chalcogen Bond, U. Adhikari, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Neutral complexes containing a S···N chalcogen bond are compared with similar systems in which a positive charge has been added to the S-containing electron acceptor, using high-level ab initio calculations. The effects on both XS···N and XS+···N bonds are evaluated for a range of different substituents X = CH3, CF3, NH2, NO2, OH, Cl, and F, using NH3 as the common electron donor. The binding energy of XMeS···NH3 varies between 2.3 and 4.3 kcal/mol, with the strongest interaction occurring for X = F. The binding is strengthened by a factor of 2–10 in charged XH2S+···NH3 complexes, reaching a maximum of …

Competition Between Lone Pair-Π, Halogen Bond, And Hydrogen Bond In Adducts Of Water With Perhalogenated Alkenes C2clnf4-N (N = 0-4), U. Adhikari, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

A thorough search of the potential energy surface is carried out for heterodimers of water with C2ClnF4−n. Three different types of interactions are observed. Structures dominated by a lone pair–π interaction have the highest binding energies, and are stabilized by charge transfer from O lone pairs of H2O to the Csingle bondC π* antibonding orbital of the alkene. Halogen-bonded O⋯Cl complexes are slightly less strongly bound, followed by OH⋯X hydrogen bonds. The replacements of Cl by F atoms have only small effects upon binding energies. Inclusion of vibrational and entropic effects removes the clear energetic superiority of lp–π binding energies. …

Complexation Of N So2 Molecules (N=1,2,3) With Formaldehyde And Thioformaldehyde, L. M. Azofra, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Ab initio and density functional theory calculations are used to examine complexes formed between H2CO and H2CS with 1, 2, and 3 molecules of SO2. The nature of the interactions is probed by a variety of means, including electrostatic potentials, natural bond orbital, atoms in molecules, energy decomposition, and electron density redistribution maps. The dimers are relatively strongly bound, with interaction energies exceeding 5 kcal/mol. The structures are cyclic, containing both a O/S⋯S chalcogen bond and a CH⋯O H-bond. Addition of a second SO2 molecule leads to a variety of heterotrimer structures, most of which resemble the original dimer, where …

Complexes Containing Co2 And So2. Mixed Dimers, Trimers And Tetramers, L. M. Azofra, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Mixed dimers, trimers and tetramers composed of SO2 and CO2 molecules are examined by ab initio calculations to identify all minimum energy structures. While AIM formalism leads to the idea of a pair of C···O bonds in the most stable heterodimer, bound by some 2 kcal mol(-1), NBO analysis describes the bonding in terms of charge transfer from O lone pairs of SO2 to the CO π* antibonding orbitals. The second minimum on the surface, just slightly less stable, is described by AIM as containing a single O···O chalcogen bond. The NBO picture is that of two transfers in opposite …

Interaction Between Temozolomide And Water: Preferred Binding Sites, O. E. Kasende, A. Matondo, M. Muzomwe, J. T. Muya, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Computational methods are used to predict the most favorable site of temozolomide towards attack by a water molecule. The energetics of the various complexes are presented as well as their geometries, including perturbations of each subunit caused by the presence of the other. Molecular electrostatic potential and Natural Bond Orbital (NBO) data are used to understand the interactions which conclude the terminal amide group is the preferred attack site where water can act as simultaneous proton donor and acceptor. Other potential proton acceptor N atoms within the aromatic ring structure represent weaker binding sites. Some of the less strongly bound …

Substituent Effects In The Noncovalent Bonding Of So2 To Molecules Containing A Carbonyl Group. The Dominating Role Of The Chalcogen Bond, L. M. Azofra, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

The SO2 molecule is paired with a number of carbonyl-containing molecules, and the properties of the resulting complexes are calculated by high-level ab initio theory. The global minimum of each pair is held together primarily by a S···O chalcogen bond wherein the lone pairs of the carbonyl O transfer charge to the π* antibonding SO orbital, supplemented by smaller contributions from weak CH···O H-bonds. The binding energies vary between 4.2 and 8.6 kcal/mol, competitive with even some of the stronger noncovalent forces such as H-bonds and halogen bonds. The geometrical arrangement places the carbonyl O atom above the plane of …

An Exploration Of The Ozone Dimer Potential Energy Surface, L. M. Azofra, I. Alkorta, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

The (O3)2 dimer potential energy surface is thoroughly explored at the ab initio CCSD(T) computational level. Five minima are characterized with binding energies between 0.35 and 2.24 kcal/mol. The most stable may be characterized as slipped parallel, with the two O3 monomers situated in parallel planes. Partitioning of the interaction energy points to dispersion and exchange as the prime contributors to the stability, with varying contributions from electrostatic energy, which is repulsive in one case. Atoms in Molecules analysis of the wavefunction presents specific O⋯O bonding interactions, whose number is related to the overall stability of each dimer. All internal …