Chemistry Commons^™

Visible Light-Triggered Carbon Monoxide-Releasing Molecules, Marina Popova

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Carbon monoxide (CO) is now well established as one of the signaling molecules in higher organisms, including humans. Due to its physiological roles, CO is now accepted as a potential therapeutic agent. The use of CO gas has been studied in multiple clinical trials. Vasodilation, anti-inflammatory, anti-apoptotic, anti-proliferative and cytoprotective effects are just a few of the pharmacological actions attributed to CO gas in various models of diseases. Use of inhaled CO gas as a therapeutic has many limitations which necessitate the development of a new approach for CO delivery. In order to handle CO safely, compounds that release CO …

Influence Of Monomer Deformation On The Competition Between Two Types Of Σ-Holes In Tetrel Bonds, Rafal Wysokiński, Mariusz Michalczyk, Wiktor Zierkiewicz, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

One of several tetrel (T) atoms was covalently attached to three F atoms and a substituted phenyl ring. A NH3 base can form a tetrel bond with TF3C6H2R3(T = Si, Ge, Sn, Pb; R = H, F, CH3) in a position opposite either an F atom or the ring. The σ-hole opposite the highly electron-withdrawing F (T-F) is more intense than that opposite the ring (T-C). However, when the Lewis base deforms from a tetrahedral to a trigonal bipyramidal shape so as to accommodate the base, it is the T-C σ-hole that is more intense. Accordingly, it is the T-C …

Multiple Local Σ-Aromaticity Of Nonagermanide Clusters, Nikolay V. Tkachenko, Alexander I. Boldyrev

Chemistry and Biochemistry Faculty Publications

Nonagermanide clusters are widely used in inorganic synthesis and are actively studied by experimentalists and theoreticians. However, chemical bonding of such versatile species is still not completely understood. In our work we deciphered a bonding pattern for various experimentally obtained nonagermanide species. We localized the electron density via the AdNDP algorithm for the model structures ([Ge₉]⁴⁻, [Ge₉{P(NH₂)₂}₃]⁻, Cu[Ge₉{P(NH₂)₂}₃] and Cu(NHC)[Ge₉{P(NH₂)₂}₃]) and obtained a simple and chemically intuitive bonding pattern which …

Interactions Of (My) 6 (M = Zn, Cd; Y = O, S, Se) Quantum Dots With N-Bases, Mariusz Michalczyk, Wiktor Zierkiewicz, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

(MY)₆ clusters, with M = Zn and Cd and Y = O, S, Se, form double-layer drum-like structures containing M–Y covalent bonds. The positive regions near the M atoms attract the N atom of both NH₃ and NMe₃ so as to form a noncovalent M···N bond. This bond is quite strong, with interaction energies exceeding 35 kcal/mol. The bond strength diminishes with reduced electronegativity of the Y atom (O > S > Se) and is stronger for M = Zn than for Cd. Trimethylation of the base enhances the bond strength. The interaction is dominated by the electrostatic component …

The Nifz Accessory Protein Has An Equivalent Function In Maturation Of Both Nitrogenase Mofe Protein P-Clusters, Emilio Jimenez-Vicente, Zhi-Yong Yang, Julia S. Martin Del Campo, Valarie L. Cash, Lance C. Seefeldt, Dennis R. Dean

Chemistry and Biochemistry Faculty Publications

The Mo-dependent nitrogenase comprises two interacting components called the Fe protein and the MoFe protein. The MoFe protein is an α₂β₂ heterotetramer that harbors two types of complex metalloclusters, both of which are necessary for N₂reduction. One type is a 7Fe-9S-Mo-C-homocitrate species designated FeMo-cofactor, which provides the N₂-binding catalytic site, and the other is an 8Fe-7S species designated the P-cluster, involved in mediating intercomponent electron transfer to FeMo-cofactor. The MoFe protein's catalytic partner, Fe protein, is also required for both FeMo-cofactor formation and the conversion of an immature form of P-clusters to the …

Hydrated Sulfate Clusters So42–(H2o)N (N = 1–40): Charge Distribution Through Solvation Shells And Stabilization, Maksim Kulichenko, Nikita Fedik, Konstantin V. Bozhenko, Alexander I. Boldyrev

Chemistry and Biochemistry Faculty Publications

Investigations of inorganic anion SO₄^2– interactions with water are crucial for understanding the chemistry of its aqueous solutions. It is known that the isolated SO₄^2– dianion is unstable, and three H₂O molecules are required for its stabilization. In the current work, we report our computational study of hydrated sulfate clusters SO₄^2–(H₂O)_n (n = 1–40) in order to understand the nature of stabilization of this important anion by water molecules. We showed that the most significant charge transfer from dianion SO₄^2– to H₂O takes …

On The Capability Of Metal-Halogen Groups To Participate In Halogen Bonds, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

A number of halogen (X) atoms were covalently attached to a metal (M) and the ability of the X atom to act as electron acceptor in a halogen bond to nucleophile NCH was assessed. Both Cl and Br were considered as halogen atom, with NH3 and CO as other ligands attached to the metal. Metals tested were Ti, Mn, and Zn in various combinations of oxidation state, coordination, and overall charge. In the majority of cases, the strong electron-releasing power of the metal imbues the halogen atom with a high negative partial charge and minimizes the development of a σ-hole. …

3-Hydroxyflavones And 3-Hydroxy-4-Oxoquinolines As Carbon Monoxide-Releasing Molecules, Tatiana Soboleva, Lisa M. Berreau

Chemistry and Biochemistry Faculty Publications

Carbon monoxide-releasing molecules (CORMs) that enable the delivery of controlled amounts of CO are of strong current interest for applications in biological systems. In this review, we examine the various conditions under which CO is released from 3-hydroxyflavones and 3-hydroxy-4-oxoquinolines to advance the understanding of how these molecules, or derivatives thereof, may be developed as CORMs. Enzymatic pathways from quercetin dioxygenases and 3-hydroxy-4-oxoquinoline dioxygenases leading to CO release are examined, along with model systems for these enzymes. Base-catalyzed and non-redox-metal promoted CO release, as well as UV and visible light-driven CO release from 3-hydroxyflavones and 3-hydroxy-4-oxoquinolines, are summarized. The visible …

Optical Stability Of 1,1′-Binaphthyl Derivatives, Nikolay V. Tkachenko, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

The racemization process of various 1,1′-binaphthyl derivatives is studied by quantum calculations. The preferred racemization pathway passes through a transition state belonging to the C_i symmetry group. The energy barrier for this process is independent of solvation, the electron-withdrawing/releasing power of substituents, or their ability to engage in H-bonds within the molecule. The primary factor is instead the substituent size. The barrier is thus reduced when the −OH groups of 1,1′-bi-2-naphthol are replaced by H. There is a drop in the barrier also when the substituents are moved from the 2,2′ positions to 6,6′, where they will not come …

Hexacoordinated Tetrel-Bonded Complexes Between Tf4 (T = Si, Ge, Sn, Pb) And Nch. Competition Between Σ- And Π-Holes, Mariusz Michalczyk, Wiktor Zierkiewicz, Rafal Wysokiński, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

In order to accommodate the approach of two NCH bases, a tetrahedral TF4 molecule (T=Si,Ge,Sn,Pb) distorts into an octahedral structure in which the two bases can be situated either cis or trans to one another. The square planar geometry of TF4, associated with the trans arrangement of the bases, is higher in energy than its see-saw structure which corresponds to the cis trimer. On the other hand, the square geometry offers an unobstructed path of the bases to the π-holes above and below the tetrel atom so enjoys a higher interaction energy than is the case for the σ-holes approached …

Molecular Rotation In 3 Dimensions At An Air/Water Interface Using Femtosecond Time Resolved Sum Frequency Generation, Yi Rao, Yuqin Qian, Gang-Hua Deng, Ashlie Kinross, Nicholas J. Turro, Kenneth B. Eisenthal

Chemistry and Biochemistry Faculty Publications

This paper presents the first study of the rotations of rigid molecules in 3 dimensions at the air/water interface, using the femtosecond time resolved sum frequency generation (SFG) technique. For the purpose of this research, the aromatic dye molecule C153 was chosen as an example of a molecule having two functional groups that are SFG active, one being the hydrophilic −−C==O group and the other the hydrophobic −−CF₃ group. From polarized SFG measurements, the orientations of the two chromophores with respect to the surface normal were obtained. On combining these results with the known relative orientation of the two …

Transition State Interactions In A Promiscuous Enzyme: Sulfate And Phosphate Monoester Hydrolysis By Pseudomonas Aeruginosa Arylsulfatase, Bert Van Loo, Ryan Berry, Usa Boonyuen, Mark F. Mohamed, Marko Golicnik, Alvan C. Hengge, Florian Hollfelder

Chemistry and Biochemistry Faculty Publications

Pseudomonas aeruginosa arylsulfatase (PAS) hydrolyses sulfate and, promiscuously, phosphate monoesters. Enzyme-catalyzed sulfate transfer is crucial to a wide variety of biological processes, but detailed studies of the mechanistic contributions to its catalysis are lacking. We present linear free energy relationships (LFERs) and kinetic isotope effects (KIEs) of PAS and active site mutants that suggest a key role for leaving group (LG) stabilization. In LFERs PAS^_WT has a much less negative Brønsted coefficient (ß_{leaving group} ^obs-Enz=-0.33) than the uncatalyzed reaction (ß_{leaving group} ^obs=-1.81). This situation is diminished when cationic active site groups are exchanged for alanine. …

Structural And Functional Characterization Of Sulfonium Carbon-Oxygen Hydrogen Bonding In The Deoxyamino Sugar Methyltransferase Tyim1, Robert J. Fick, Scott Horowitz, Brandon G. Mcdole, Mary C. Clay, Ryan A. Mehl, Hashim M. Al-Hashimi, Steve Scheiner, Raymond C. Trievel

Chemistry and Biochemistry Faculty Publications

The N-methyltransferase TylM1 from Streptomyces fradiae catalyzes the final step in the biosynthesis of the deoxyamino sugar mycaminose, a substituent of the antibiotic tylosin. The high-resolution crystal structure of TylM1 bound to the methyl donor S-adenosylmethionine (AdoMet) illustrates a network of carbon-oxygen (CH•••O) hydrogen bonds between the substrate’s sulfonium cation and residues within the active site. These interactions include hydrogen bonds between the methyl and methylene groups of the AdoMet sulfonium cation and the hydroxyl groups of Tyr14 and Ser120 in the enzyme. To examine the functions of these interactions, we generated Tyr14 to phenylalanine (Y14F) and Ser120 to alanine …

Comparison Of Σ-Hole And Π-Hole Tetrel Bonds In Complexes Of Borazine With Th3f And F2to/H2to (T=C,Si,Ge), Jingru Zhang, Qingze Hu, Qing-Zhong Li, Steve Scheiner, Shufeng Liu

Chemistry and Biochemistry Faculty Publications

The complexes between borazine and TH3F/F2TO/H2TO (T=C, Si, Ge) are investigated with high-level quantum chemical calculations. Borazine has three sites of negative electrostatic potential: the N atom, the ring center, and the H atom of the B-H bond, while TH3F and F2TO/H2TO provide the σ-hole and π-hole, respectively, for the tetrel bond. The N atom of borazine is the favored site for both the σ and π-hole tetrel bonds. Less stable dimers include a σ-tetrel bond to the borazine ring center and to the BH proton. The π-hole tetrel-bonded complexes are more strongly bound than aretheirσ-hole counterparts. Due to the …

Switchable Aromaticity In An Isostructural Mn Phthalocyanine Series Isolated In Five Separate Redox States, Camden Hunt, Madeline Peterson, Cassidy Anderson, Tieyan Chang, Guang Wu, Steve Scheiner, Gabriel Ménard

Chemistry and Biochemistry Faculty Publications

The synthesis and characterization of a new phthalocyanine(Pc) Mn-nitride complex, (OEtPc)MnN (2; OEtPc= 1,4,8,11,15,18,22,25-octaethoxy-Pc), as well as its stable, readily accessible oxidized (2+ and 22+) and reduced (2-, 22-) congeners is reported. This unique isostructural series displays switchable aromatic character spanning the aromatic (2), non-aromatic (22+), and antiaromatic (22-) triad, in addition to the open-shell radical states (2+, 2-). All complexes were structurally characterized and displayed significant structural distortions at the redox extrema (22+, 22-) consistent with proposed [16 or 18]annulene π ring circuit models. Spectroscopic and computational studies further support these models. This isolated, fully characterized, isostructural series spanning …

Catalytic Mechanism For The Conversion Of Salicylate Into Catechol By The Flavin-Dependent Monooxygenase Salicylate Hydroxylase, Débora M. A. Costa, Stefanya V. Gómez, Simara S. De Araújo, Mozart S. Pereira, Rosemeire B. Alves, Denize C. Favaro, Alvan C. Hengge, Ronaldo A. P. Nagem, Tiago A. S. Brandão

Chemistry and Biochemistry Faculty Publications

Salicylate hydroxylase (NahG) is a flavin-dependent monooxygenase that catalyzes the decarboxylative hydroxylation of salicylate into catechol in the naphthalene degradation pathway in Pseudomonas putida G7. We explored the mechanism of action of this enzyme in detail using a combination of structural and biophysical methods. NahG shares many structural and mechanistic features with other versatile flavin-dependent monooxygenases, with potential biocatalytic applications. The crystal structure at 2.0 Å resolution for the apo form of NahG adds a new snapshot preceding the FAD binding in flavin-dependent monooxygenases. The k_cat/K_m for the salicylate reaction catalyzed by the holo form is …

Dual Geometry Schemes In Tetrel Bonds: Complexes Between Tf4(T = Si, Ge, Sn) And Pyridine Derivatives, Wiktor Zierkiewicz, Mariusz Michalczyk, Rafał Wysokiński, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

When an N-base approaches the tetrel atom of TF4(T = Si, Ge, Sn) the latter moleculedeforms from a tetrahedral structure in the monomer to a trigonal bipyramid. The base can situateitself at either an axial or equatorial position, leading to two different equilibrium geometries.The interaction energies are considerably larger for the equatorial structures, up around 50 kcal/mol,which also have a shorter R(T··N) separation. On the other hand, the energy needed to deform thetetrahedral monomer into the equatorial structure is much higher than the equivalent deformationenergy in the axial dimer. When these two opposite trends are combined, it is the axial …

Development Of Ultrafast Broadband Electronic Sum Frequency Generation For Charge Dynamics At Surfaces And Interfaces, Gang-Hua Deng, Yuqin Qian, Yi Rao

Chemistry and Biochemistry Faculty Publications

Understandings of population and relaxation of charges at surfaces and interfaces are essential to improve charge collection efficiency for energy conversion, catalysis, and photosynthesis. Existing time-resolved surface and interface tools are limited to either under ultrahigh vacuum or in a narrow wavelength region with the loss of spectral information. There lacks an efficient time-resolved surface/interface-specific electronic spectroscopy under ambient conditions for the ultra fast surface/interface dynamics. Here we developed a novel technique for surface/interface-specific broadband electronic sum frequency generation (ESFG). The broadband ESFG was based on a stable two-stage BiB₃O₆ crystal-based optical parametric amplifier, which generates a …

Differential Binding Of Tetrel-Bonding Bipodal Receptors To Monatomic And Polyatomic Anions, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Previous work has demonstrated that a bidentate receptor containing a pair of Sn atoms can engage in very strong interactions with halide ions via tetrel bonds. The question that is addressed here concerns the possibility that a receptor of this type might be designed that would preferentially bind a polyatomic over a monatomic anion since the former might better span the distance between the two Sn atoms. The binding of Cl⁻ was thus compared to that of HCOO⁻, HSO₄⁻, and H₂PO₄⁻ with a wide variety of bidentate receptors. A pair …

Carbene Triel Bonds Between Trr3 (Tr=B, Al) And N-Heterocyclic Carbenes, Zongqing Chi, Wenbo Dong, Qingzhong Li, Xin Yang, Steve Scheiner, Shufeng Liu

Chemistry and Biochemistry Faculty Publications

The carbene triel bond is predicted and characterized by theoretical calculations. The C lone pair of N‐heterocyclic carbenes (NHCs) is allowed to interact with the central triel atom of TrR₃ (Tr = B and Al; R = H, F, Cl, and Br). The ensuing bond is very strong, with an interaction energy of nearly 90 kcal/mol. Replacement of the C lone pair by that of either N or Si weakens the binding. The bond is strengthened by electron‐withdrawing substituents on the triel atom, and the reverse occurs with substitution on the NHC. However, these effects do not strictly follow …

Chemical Analysis Of Aerosol Particle Surfaces, Hillary Woolf

Fall Student Research Symposium 2018

Aerosol particles are thought to impact climate properties. The ability to probe aerosols to understand their chemical properties has been difficult due to a lack of appropriate analytical techniques. Here we present interface-specific SHS techniques to allow for in situ analysis of aerosol particles. Transportation of aerosols from their collection site to the laboratory disturbs their chemical and physical properties thus making it difficult to take accurate measurements of aerosol particles. We show that using a CCD detector is a more effective option for producing more sensitive results and can greatly reduce sampling time and could possibly detect measurements from …

Quantum Mechanical Studies Of N-H···N Hydrogen Bonding In Acetamide Derivatives And Amino Acids, Sandra J. Lundell

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Proteins are made of vast chains of amino acids that twist and fold into intricate designs. These structures are held in place by networks of noncovalent interactions. One of these, the hydrogen bond, forms bridges between adjacent pieces of the protein chain and is one of the most important contributors to the shape and stability of proteins. Hydrogen bonds come in all shapes and sizes and a full understanding of these not only aids in our understanding of proteins in general but can bridge the gap to finding cures to many protein-related diseases, such as sickle-cell anemia. The primary aim …

Inorganic Electrocatalysts For Innovative Water Splitting And Organic Upgrading, Nan Jiang

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The booming worldwide demand for energy and the increasing concerns about global warming due to fossil fuel consumption have urged the development of techniques for storing and converting renewable and clean energy resources. Electrocatlytic or photoelectrocatalytic water splitting to generate green energy carrier H₂ with sustainable energy input, like solar, has been regarded as an attractive strategy for carbon-neutral energy needs. However, the sluggish kinetics for both half reactions (HER and OER), high overpotentials and thermodynamic requirements, and H₂ and O₂ gas crossover have been regarded as the major challenges, which limit its widespread application.

On account …

Carbon Monoxide On Demand: Light-Induced Co Release Of Flavonols, Stacey N. Anderson

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Carbon monoxide (CO) is an extremely useful molecule with applications in industrial manufacturing, synthetic procedures as a C1 building block, and as a potential pharmaceutical to produce anti-inflammatory effects and vasodilation. However, the toxicity associated with CO has prevented its full utilization. In order to safely handle CO, compounds and molecules have been developed that act as storage materials for the gas. Ideal storage platforms only release CO upon stimulation via a trigger. Light activation is the most desirable trigger as it can be regulated in terms of the intensity and the wavelength of light used. The majority of light-induced …

Crystallographic And Computational Characterization Of Methyl Tetrel Bonding In S-Adenosylmethionine-Dependent Methyltransferases, Raymond C. Trievel, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Tetrel bonds represent a category of non-bonding interaction wherein an electronegative atom donates a lone pair of electrons into the sigma antibonding orbital of an atom in the carbon group of the periodic table. Prior computational studies have implicated tetrel bonding in the stabilization of a preliminary state that precedes the transition state in S_N2 reactions, including methyl transfer. Notably, the angles between the tetrel bond donor and acceptor atoms coincide with the prerequisite geometry for the S_N2 reaction. Prompted by these findings, we surveyed crystal structures of methyltransferases in the Protein Data Bank and discovered …

Kinetic Characterization Of The Shigella Type Three Secretion System Atpase Spa47 Using Α-32p Atp, Heather B. Case, Nicholas E. Dickenson

Chemistry and Biochemistry Faculty Publications

ATPases represent a diverse class of enzymes that utilize ATP hydrolysis to support critical biological functions such as driving ion pumps, providing mechanical work, unfolding/folding proteins, and supporting otherwise thermodynamically unfavorable chemical reactions. We have recently shown that the Shigella protein Spa47 is an ATPase that supports protein secretion through its specialized type three secretion apparatus (T3SA), supporting infection of human host cells. Characterizing ATPases, such as Spa47, requires a means to accurately determine enzyme activity (ATP hydrolysis) as a function of time, reaction conditions, and potential cofactors, regulators, inhibitors, etc. Here, we describe a detailed protocol for characterizing …

Interfacing Nickel Nitride And Nickel Boosts Both Electrocatalytic Hydrogen Evolution And Oxidation Reactions, Fuzhan Song, Wei Li, Jiaqi Yang, Guanqun Han, Peilin Liao, Yujie Sun

Chemistry and Biochemistry Faculty Publications

Electrocatalysts of the hydrogen evolution and oxidation reactions (HER and HOR) are of critical importance for the realization of future hydrogen economy. In order to make electrocatalysts economically competitive for large-scale applications, increasing attention has been devoted to developing noble metal-free HER and HOR electrocatalysts especially for alkaline electrolytes due to the promise of emerging hydroxide exchange membrane fuel cells. Herein, we report that interface engineering of Ni₃N and Ni results in a unique Ni₃N/Ni electrocatalyst which exhibits exceptional HER/HOR activities in aqueous electrolytes. A systematic electrochemical study was carried out to investigate the superior hydrogen …

Dependence Of Nmr Chemical Shifts Upon Ch Bond Lengths Of A Methyl Group Involved In A Tetrel Bond, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Four different Lewis acids that might participate in a tetrel bond with a nucleophile (SEt₂Me⁺, NMe₄⁺, SMe₂, NMe₃) are examined. The NMR chemical shifts of the methyl C and H atoms are calculated as the CH bond lengths are systematically stretched and contracted, in the absence of a base. The C shielding diminishes by roughly 2 ppm for a stretch of 0.01 Å, while that of H drops by only 0.3 ppm. The deshieldings caused purely by the bond length changes are far too small to account for the …

An Updated Description Of The Hydrogen Bond And Related Noncovalent Bonds, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

The hydrogen bond is typically introduced briefly in General Chemistry as a simple electrostatic phenomenon involving a small and select group of atoms, a definition which is typically unchanged through higher levels in the curriculum. But this definition has undergone dramatic modernization of which students should be made aware. The original formulation in terms of only F, O, and N atoms has broadened very considerably, encompassing C as well as atoms from lower rows in the periodic table. The influence of hybridization, substituents, and overall charge cannot be overlooked. In addition to the Coulombic attraction, there are other “covalent” contributors …

Triel-Bonded Complexes Between Trr3 (Tr = B, Al, Ga; R = H, F, Cl, Br, Ch3) And Pyrazine, Mariusz Michalczyk, Wiktor Zierkiewicz, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Complexes between TrR3 (Tr = B, Al, Ga; R= H, F, Cl, Br, CH3)molecules and pyrazine have been characterized at the MP2 and CCSD(T) levels of theory. The adducts can be grouped according to the type of molecular arrangement. The first situation places the Tr atom in the plane of the pyrazine ring and contains a triel bond to the N lone pair. For the boron complexes the orbital interaction energy is almost equal to the electrostatic component, while the former is only half the latter for Tr= Al and Ga. The two monomers are stacked above one another in …