Chemistry Commons^™

Comparison Of Various Means Of Evaluating Molecular Electrostatic Potentials For Noncovalent Interactions, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

The various heterodimers formed by a series of Lewis acids with NH3 as Lewis base are identified. Lewis acids include those that can form chalcogen (HSF and HSBr), pnicogen (H2PF and H2PBr), and tetrel (H3SiF and H3SiBr) bonds, as well as H‐bonds and halogen bonds. The molecular electrostatic potential (MEP) of each Lewis acid is considered in a number of ways. Pictorial versions show broad regions of positive and negative MEP, on surfaces that vary with respect to either the value of the chosen isopotential, or their distance from the nuclei. Specific points are identified where the MEP reaches a …

Can Hcch/Hbnh Break B=N/C=C Bonds Of Single-Wall Bn/Carbon Nanotubes At Their Surface?, Tapas Kar, Peter Grüninger, Steve Scheiner, Holger F. Bettinger, Ajit K. Roy

Chemistry and Biochemistry Faculty Publications

The iminoborane (HBNH) molecule, which prefers cycloaddition reactions, selectively breaks a B=N bond of smaller diameter single-wall BNNTs and expands a ring at their surface, either at the edges or at the middle of the tube. Density functional theory (DFT) is used to test whether its organic counterpart HCCH can do the same with BNNTs. HCCH-BNNT complexes are identified and transition states located for these combination reactions. Also explored are possible reactions of HBNH with SWNTs and HCCH with SWNTs. Data suggest that B=N (C=C) bond breaking, followed by ring expansion at the surface may be possible. Although [2+2] cycloaddition …

Halogen Bonds Formed Between Substituted Imidazoliums And N Bases Of Varying N-Hybridization, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Heterodimers are constructed containing imidazolium and its halogen-substituted derivatives as Lewis acid. N in its sp³, sp² and sp hybridizations is taken as the electron-donating base. The halogen bond is strengthened in the Cl < Br < I order, with the H-bond generally similar in magnitude to the Br-bond. Methyl substitution on the N electron donor enhances the binding energy. Very little perturbation arises if the imidazolium is attached to a phenyl ring. The energetics are not sensitive to the hybridization of the N atom. More regular patterns appear in the individual phenomena. Charge transfer diminishes uniformly on going from amine to imine to nitrile, a pattern that is echoed by the elongation of the C-Z (Z=H, Cl, Br, I) bond in the Lewis acid. These trends are also evident in the Atoms in Molecules topography of the electron density. Molecular electrostatic potentials are not entirely consistent with energetics. Although I of the Lewis acid engages in a stronger bond than does H, it is the potential of the latter which is much more positive. The minimum on the potential of the base is most negative for the nitrile even though acetonitrile does not form the strongest bonds. Placing the systems in dichloromethane solvent reduces the binding energies but leaves intact most of the trends observed in vacuo; the same can be said of ∆G in solution.

Special Issue: Intramolecular Hydrogen Bonding 2017, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Even after more than a century of study [1–6], scrutiny, and detailed examination, the H-bond continues [7–12] to evoke a level of fascination that surpasses many other phenomena. Perhaps it is the ability of the simple H atom, with but a single electron, to act as a glue that maintains contact between much more complicated species. Or it might be its geometry, which prefers to hold the bridging proton on a direct line between the two heavy atoms. Not to be ignored are the spectral features of the H-bond: the large red shift of the stretching frequency of the covalent …

Universal Surface Engineering Of Transition Metals For Superior Electrocatalytic Hydrogen Evolution In Neutral Water, Bo You, Xuan Liu, Guoxiang Hu, Sheraz Gul, Junko Yano, De-En Jiang, Yujie Sun

Chemistry and Biochemistry Faculty Publications

The development of low-cost hybrid water splitting-biosynthetic systems that mimic natural photosynthesis to achieve solar-to-chemical conversion is of great promise for future energy demands, but often limited by the kinetically sluggish hydrogen evolution reaction (HER) on the surface of nonprecious transition metal catalysts in neutral media. It is thus highly desirable to rationally tailor the reaction interface to boost the neutral HER catalytic kinetics. Herein, we report a general surface nitrogen modification of diverse transition metals (e.g. iron, cobalt, nickel, copper, and nickel-cobalt alloy), accomplished by a facile low-temperature ammonium carbonate treatment, for significantly improved hydrogen generation from neutral water. …

Deciphering Delocalized Bonding In Excited States, Solvated Species And Novel 0-, 1-, 2-, And 3-Dimensional Chemical Systems, Alexander Boldyrev

Funded Research Records

No abstract provided.

Chemical Tools For Delivery Of Carbon Monoxide, Lisa Berreau

Funded Research Records

No abstract provided.

New Strategies For Investigating Oxidative Aliphatic Carbon-Carbon Bond Cleavage Reactions, Lisa Berreau

Funded Research Records

No abstract provided.

Systematic Elucidation Of Factors That Influence The Strength Of Tetrel Bonds, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Quantum calculations are used to examine the properties of heterodimers formed by a series of tetrel-containing molecules with NH₃ as universal Lewis base. TH₄ was taken as a starting point, with T= C, Si, Ge, and Sn. The H atoms were replaced by various numbers of F atoms: TH₃F, TF₃H, and TF₄ so as to monitor the effects of adding electron-withdrawing substituents. Unsubstituted TH₄ molecules form the weakest tetrel bonds, only up to about 2 kcal/mol. The bond is strengthened when the H opposite NH₃ is replaced by F, rising up …

Collaborative Research: Refining And Testing Methods For Identifying And Quantifying Gaseous Oxidized Mercury In Air, Seth Lyman

Funded Research Records

No abstract provided.

Chemical Bonding In Novel 0-, 1-, 2-, And 3-Dimensional Chemical Species, Ivan A. Popov

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

While the trial and error approach is still being a dominant pathway for synthesis of various compounds in chemistry, computation-driven approaches have recently been shown to be a very efficient way towards the rational design of new materials with tailored properties. In principle, theoretical design of materials may not only significantly reduce the costs associated with the experiment, but may also result in the prediction of novel compounds possessing completely unexpected geometries. These compounds can serve as long-lived catalysts, powerful batteries, efficient solar cells, or reliable energy storage materials. Since geometric structure of any system is related to its electronic …

Caffeine And Acetaminophen Concentration And Other Water Quality Parameters Along The Middle To Lower Bear River, Autumn Slade

Undergraduate Honors Capstone Projects

Various water quality parameters were measured at seven sites along the Middle to Lower Bear River and compared across the sites, to past data and to set standards in Utah and Idaho. Much of the data was comparable to past data with most state standards being met. However, nitrate was above indicator level for half of the sites, and turbidity is a problem at the last two sites. Also, chloride and unionized ammonia are at high levels by the last site. Overall, the river tended to decrease in water quality as it moved downstream, with dams like at Cutler Reservoir …

Role Of Atp Hydrolysis And Mechanism Of Substrate Reduction In Nitrogenase, Sudipta Shaw

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Nitrogen is essential for life on earth as it is a major constituent of amino acids and nucleic acids. Nitrogen gas (N₂) is the most abundant form of nitrogen in the atmosphere but the strong N≡N bond makes it unavailable for most organisms. Certain prokaryotes known as diazotrophs possess the unique ability to convert N₂ to ammonia (NH₃) which can be utilized by other organisms as a source of nitrogen. The diazotrophs perform this difficult reaction with the help of a complex metalloenzyme, nitrogenase. This enzyme is a major contributor of the fixed source of …

Conservative Tryptophan Mutations In Protein Tyrosine Phosphatase Ptp1b And Its Effect On Catalytic Rate And Chemical Reaction, Teisha Richan

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Protein-tyrosine phosphatases (PTPs) catalyze the hydrolysis of phosphorylated tyrosines by a 2-step mechanism involving nucleophilic attack by cysteine and general acid catalysis by aspartic acid. In most PTPs the aspartic acid resides on a flexible protein loop, consisting of about a dozen residues, called the WPD loop. PTP catalysis rates span several orders of magnitude, and differences in WPD loop dynamics have recently been show to correlate with the rate of enzymatic catalysis. The rate of WPD loop motion could possibly be related to a widely conserved tryptophan residue on the WPD loop. Therefore, point mutants were made in PTP1B …

First-Row Transition Metal Sulfides And Phosphides As Competent Electrocatalysts For Water Splitting, Nan Jiang

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Solar energy is a carbon-neutral and renewable energy resource. Its nature of intermittence and unequal distribution requires efficient solar energy capture, conversion, and storage. Solar-driven water splitting to produce hydrogen and oxygen is widely considered as an appealing approach to meet this goal, in which hydrogen acts as a green energy carrier. Water splitting consists of two redox half reactions: hydrogen evolution reaction (HER) and oxygen evolution reaction (OER). Both reactions involve the transfer of multiple electrons and protons and possess high energy barriers to proceed at appreciable rates, hence catalysts are needed.

A large number of HER and OER …

Assembly Of Effective Halide Receptors From Components. Comparing Hydrogen, Halogen, Tetrel Bonds, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Receptors for halide anions are constructed based on the imidazolium unit, and then replacing the H-bonding C-H group firstby halogen-bonding C-I and then by tetrel-bonding C-SnH3 and C-SiF3.Attaching a phenyl ring to any of these species has little effect on its ability to bind a halide, but incorporation of a second imidazolium to the benzene connector, forming a bidentate dicationic receptor, greatly enhances the binding. Addition of electron-withdrawing F atoms to each imidazolium adds a further increment. F- consistently binds more strongly to the various receptor models than does Cl-. Whereas replacement of the H atom on the imidazolium groups …

Solvation Enhances The Distinction Between Carboxylated Armchair And Zigzag Single-Wall Carbon Nanotubes (Swnt-Cooh), Tapas Kar, Upendra Adhikari, Steve Scheiner, Ajit K. Roy, Renato L. T. Parreira, Pedro A. De S. Bergamo, Giovanni F. Caramori, Felipe S. S. Schneider

Chemistry and Biochemistry Faculty Publications

The effect of various solvents on the structures and properties of carboxylated SWNTs has been explored using the Same Level Different Basis Set approach (SLDB), where B3LYP functional of density functional theory (DFT) was applied. Armchair (4,4) and zigzag (8,0) and (9,0) tubes were considered as the test bed. In order to simulate varying concentration of –COOH groups, one to five acids groups were placed at one end of these tubes. These samples were placed in different solvents (namely, CS2, THF and water) with varying polarity and results were compared with gas-phase properties. Similar to the gas-phase, zigzag tubes also …

Comparison Of Halide Receptors Based On H, Halogen, Chalogen, Pnicogen, And Tetrel Bonds, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

A series of halide receptors are constructed and the geometries and energetics of their binding to F-, Cl-, and Br- assessed by quantum calculations. The dicationic receptors are based on a pair of imidazolium units, connected via a benzene spacer. The imidazoliums each donate a proton to a halide in a pair of H-bonds. Replacement of the two bonding protons by Br leads to binding via a pair of halogen bonds. Likewise, chalcogen, pnicogen, and tetrel bonds occur when the protons are replaced, respectively, by Se, As, and Ge. Regardless of the binding group considered, F- is bound much more …

Comparison Of Tetrel Bonds In Neutral And Protonated Complexes Of Pyridinetf3 And Furantf3 (T = C, Si, And Ge) With Nh3, Mingxiu Liu, Qing-Zhong Li, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Ab initio calculations have been performed for the complexes H+–PyTX3⋯NH3 and H+–furanTF3⋯NH3 (T = C, Si, and Ge; X = F and Cl) with focus on geometries, energies, orbital interactions, and electron densities to study the influence of protonation on the strength of tetrel bonding. The primary interaction mode between α/β-furanCF3/p-PyCF3 and NH3 changes from an F⋯H hydrogen bond to a C⋯N tetrel bond as a result of protonation. Importantly, the protonation has a prominent enhancing effect on the strength of tetrel bonding with an increase in binding energy from 14 to 30 kcal mol−1. The tetrel bonding becomes stronger …

Flipped Learning In Synchronously-Delivered, Geographically-Dispersed General Chemistry Classrooms, Michael A. Christiansen, Louis Nadelson, Lianna K. Etchberger, Marilyn M. Cuch, Trish A. Kingsford, Leslie O. Woodward

Chemistry and Biochemistry Faculty Publications

In synchronously-delivered, multi-site classrooms, the physical separation between distance students and instructors may create a perceived divide that negatively affects learning. Building on prior experience in flipping organic chemistry in single-site face-to-face (F2F) classes, we decided to extend our approach to multi-site, synchronously-delivered general chemistry courses. Our thought was to narrow the perceived instructor-student divide in distance teaching by using the flexible in-class time that flipping affords to increase the number of positive teacher/distance-student interactions. In this effort, we gradually developed a technique called “bridging questions,” through which the instructor becomes more familiar with student interests and then connects those …

Electrocatalytic Valorization Of Biomass Intermediates Via 1st-Row Transition Metal Electrocatalysts, Yujie Sun

Funded Research Records

No abstract provided.

In-Class Versus At-Home Quizzes: Which Is Better? A Flipped Learning Study In A Two-Site Synchronously-Broadcast Organic Chemistry Course, Michael A. Christensen, Alyssia M. Lambert, Louis S. Nadelson, Kami M. Dupree, Trish A. Kingsford

Chemistry and Biochemistry Faculty Publications

We recently shared our design of a two-semester flipped organic chemistry course, in which we gave students in-class quizzes to incentivize attendance and watching the lecture videos in advance. With a second iteration, we planned to make the video-watching experience more engaging. We accordingly hypothesized that if students completed short at-home quizzes while watching the videos, then attentiveness, engagement, and learning would increase. We tested this with a later section of the course, dividing the material into 13 units. For units 1-6, we gave in-class quizzes; for 7-13, quizzes were at home. Although units 1-6 and 7-13 covered different material, …

Assessment Of The Presence And Strength Of H-Bonds By Means Of Corrected Nmr, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

The downfield shift of the NMR signal of the bridging proton in a H-bond (HB) is composed of two elements. The formation of the HB causes charge transfer and polarization that lead to a deshielding. A second factor is the mere presence of the proton-accepting group, whose electron density and response to an external magnetic field induce effects at the position of the bridging proton, exclusive of any H-bonding phenomenon. This second positional shielding must be subtracted from the full observed shift in order to assess the deshielding of the proton caused purely by HB formation. This concept is applied …

Infrared Spectroscopy Of The Nitrogenase Mofe Protein Under Electrochemical Control: Potential-Triggered Co Binding, P. Paengnakorn, Philip A. Ash, Sudipta K. Shaw, Karamatullah Danyal, T. Chen, Dennis R. Dean, Lance C. Seefeldt, Kylie A. Vincent

Chemistry and Biochemistry Faculty Publications

We demonstrate electrochemical control of the nitrogenase MoFe protein, in the absence of Fe protein or ATP, using europium(III/II) polyaminocarboxylate complexes as electron transfer mediators. This allows the potential dependence of proton reduction and inhibitor (CO) binding to the active site FeMo-cofactor to be established. Reduction of protons to H2 is catalyzed by the wild type MoFe protein and Β-98^Tyr→His and Β-^99Phe→His variants of the MoFe protein at potentials more negative than -800 mV (vs. SHE), with greater electrocatalytic proton reduction rates observed for the variants compared to the wild type protein. Electrocatalytic proton reduction is strongly …

Highly Selective Halide Receptors Based Upon Chalcogen, Pnicogen, And Tetrel Bonds, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

The interactions of halides with a number of bipodal receptors are examined via quantum chemical methods. The receptors are based upon a dithieno thiophene framework in which two S atoms can engage in a pair of chalcogen bonds with a halide. These two S atoms are replaced by P and As atoms to compare chalcogen with pnicogen bonding, and by Ge which engages in tetrel bonds with the receptor. Zero, one, and two O atoms are added to the thiophene S atom which is not directly involved in the interaction with the halides. Fluoride is bound the most strongly, followed …

Interactions Between Temozolomide And Guanine And Its S And Se‐Substituted Analogues, Okuma Emile Kasende, Aristote Matondo, Jules Tshishimbi Muya, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Temozolomide was paired with guanine, 6-selenoguanine, and 6-thioguanine, as well as the SH tautomer of the latter. The potential energy surface of each heterodimer was searched for all minima, using Dispersion-Corrected Density Functional Theory and MP2 methods. Among the dozens of minima, three categories were observed. Stacked geometries place the aromatic systems of the two molecules parallel to one another, while the two systems are roughly perpendicular to one another in a second category. Also found are coplanar structures held together by H-bonds. Dispersion proves to be a dominating attractive force for the stacked structures, less so for perpendicular, and …

Interactions Of Nucleic Acid Bases With Temozolomide. Stacked, Perpendicular, And Coplanar Heterodimers, Okuma Emile Kasende, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Temozolomide (TMZ) was paired with each of the five nucleic acid bases, and the potential energy surface searched for all minima, in the context of dispersion-corrected density functional theory and MP2 methods. Three types of arrangements were observed, with competitive stabilities. Coplanar H-bonding structures, reminiscent of Watson–Crick base pairs were typically the lowest in energy, albeit by a small amount. Also very stable were perpendicular arrangements that included one or more H-bonds. The two monomers were stacked approximately parallel to one another in the third category, some of which contained weak and distorted H-bonds. Dispersion was found to be a …

Monitoring The Charge Distribution During Proton And Sodium Ion Conduction Along Chains Of Water Molecules And Protein Residues, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Quantum calculations are used to determine the level of delocalization of the charge of a cation as it translates along a chain of water molecules or glycine residues. Charge dispersal is monitored via the molecular electrostatic potential and the dipole moment of the entire system. The positive charge is largely localized on the water molecule on which the proton is situated, but becomes more intense and extended as the proton moves along the chain. The positive charge is more delocalized in protonated polyglycine, where it extends over at least an entire residue. Displacement of the proton along the chain intensifies …

Effects Of Angular Deformation On The Energetics Of The Sn2 Reaction, Vincent De Paul Nzuwah-Nziko, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Quantum calculations are applied to a number of model SN2 reactions. The halides F-, Cl-, and Br- were allowed to attack the central C atom of a set of CH2RI molecules, with R= H, CH3, CH=CH2, C≡CH, and C≡N. For each system the X∙∙C∙∙I angle was distorted in set increments from the optimized value, and the activation energy computed for each angle. The energy of the transition state rose in conjunction with this deformation. However, the distortion energy of the initial X-∙∙CH2RI reaction complex was similar in magnitude. As a result, the activation energy of the reaction was quite insensitive …

Interpretation Of Spectroscopic Markers Of Hydrogen Bonds, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Quantum calculations are used to examine whether a AH∙∙D H-bond is unambiguously verified by a downfield shift of the bridging proton’s NMR signal or a red (or blue) shift of the AH stretching frequency in the IR spectrum. It is found that such IR band shifts will occur even if the two groups experience weak or no attractive force, or if they are drawn in so close together that their interaction is heavily repulsive. The mere presence of a proton-acceptor molecule can affect the chemical shielding of a position occupied by a proton-donor by virtue of its electron density, even …