Physical Sciences and Mathematics Commons^™

Development Of Fertilizer Coatings From Polyglyoxylate-Polyester Blends Responsive To Root-Driven Ph Change., Spencer M Heuchan, Bo Fan, Jessica J Kowalski, Elizabeth R Gillies, Hugh A L Henry

Chemistry Publications

Many current controlled-release fertilizers (CRFs) are coated with nonbiodegradable polymers that can contribute to microplastic pollution. Here, coatings of self-immolative poly(ethyl glyoxylate) (PEtG) capped with a carbamate and blended with polycaprolactone (PCL) or poly(l-lactic acid) (PLA) were evaluated. They were designed to depolymerize and release fertilizers in the vicinity of plant roots, where the pH is lower than that in the surrounding environment. PEtG/PCL coatings exhibited significant temperature and pH effects, requiring 18 days at pH 5 and 30 °C, compared to 77 days at pH 7 and 22 °C, to reach 15% mass loss. Plant roots were also effective …

Charging And Supercharging Of Proteins For Mass Spectrometry: Recent Insights Into The Mechanisms Of Electrospray Ionization., Lars Konermann, Haidy Metwally, Quentin Duez, Insa Peters

Chemistry Publications

Electrospray ionization (ESI) is an essential technique for transferring proteins from solution into the gas phase for mass spectrometry and ion mobility spectrometry. The mechanisms whereby [M + zH]^z+ protein ions are released from charged nanodroplets during ESI have been controversial for many years. Here we discuss recent computational and experimental studies that have shed light on many of the mysteries in this area. Four types of protein ESI experiments can be distinguished, each of which appears to be associated with a specific mechanism. (i) Native ESI proceeds according to the charged residue model (CRM) that entails droplet evaporation …

Altering The Optoelectronic Properties Of Boron Difluoride Formazanate Dyes Via Conjugation With Platinum(Ii)-Acetylides, Jasveer S. Dhindsa, Adyn Melenbacher, Stephanie M. Barbon, Martin J. Stillman, Joe Gilroy

Chemistry Publications

The combination of π-conjugated organic compounds and Pt(II)-acetylides is a powerful strategy for the production of functional optoelectronic materials. The presence of the heavy element, Pt, in these compounds enhances electronic delocalization generally resulting in low-energy absorption and emission maxima and often leads to intersystem crossing, resulting in phosphorescence. When boron complexes of N-donor ligands, such as boron dipyrromethenes (BODIPYs), are involved the molecular and polymeric materials produced have properties that are advantageous for their use as oxygen-sensors, in triplet–triplet annihilation, and as the functional components of photovoltaics. Based on these exciting results, we endeavored to thoroughly examine the effect …

In Search Of The Hot Spot., Danielle M Mcrae, François Lagugné-Labarthet

Chemistry Publications

Tip-enhanced spectroscopy and its Raman variant, tip-enhanced Raman spectroscopy (TERS), provide the possibility to spatially resolve the vibrations of a single molecule when combined with ultra-high vacuum technology, but this technique suffers from poor time resolution2,3. On the other hand, surface-enhanced Raman spectroscopy (SERS) is a more common technique, and is used for many imaging and bioanalytical applications, still with single molecule sensitivity but, unlike TERS, without spatially resolved molecular imaging capabilities4. In SERS, the roughness and geometric characteristics of metallic surfaces (in general Al, Ag or Au) are exploited to enable high spatial …

Carving Plasmon Modes In Silver Sierpiński Fractals, Isobel C. Bicket, Edson P. Bellido, Danielle M. Mcrae, Francois Lagugne-Labarthet, Gianluigi A. Botton

Chemistry Publications

The surface plasmon resonance (SPR) modes of the first three generations of a Sierpiński fractal triangle are investigated using electron energy loss spectroscopy (EELS) complemented with finite difference time domain simulations. The Sierpiński fractal geometry is created in a subtractive manner, by carving triangular apertures into the triangular prism of the previous fractal generation. The ability of the fractal antenna to efficiently utilize space in coupling to long wavelength excitations is confirmed on the single nanostructure level via redshifting of the primary dipole mode as the fractal generation is increased. Through application of the Babinet principle, it is demonstrated that …

Synthesis Of Functionalized Tetrahydropyridines By Sncl4-Mediated [4+2] Cycloaddition Between Donor–Acceptor Cyclobutanes And Nitriles, David Tong, Jackie Wu, Nathan Bazinski, Donghyun Koo, Naresh Vemula, Brian Pagenkopf

Chemistry Publications

Cycloadditions of strained carbocycles promoted by Lewis acids are powerful methods to construct heterocyclic frameworks. In fact, the formal [3+2] cycloadditions of donor-acceptor (DA) cyclopropanes with nitriles has seen particular success in synthesis. In this work, we report on the first [4+2] cycloaddition of nitriles with DA cyclobutanes via Lewis acid activation. Tetrahydropyridine derivatives were obtained in up to 91% yield from various aryl activated cyclobutane diesters and aliphatic or aromatic nitriles.

Synthesis Of Unsymmetrical Bis(Phosphine) Oxides And Their Phosphines Via Secondary Phosphine Oxide Precursors, James R. Pedroarena, Bryan P. Nell, Lev N. Zakharov, David R. Tyler

Chemistry Publications

The unsymmetrical bidentate phosphine ligands (Me)₂PCH₂CH₂CH₂P(Et)₂ (14), (Me)₂PCH₂CH₂CH₂P(iPr)₂ (15), (Me)₂PCH₂CH₂CH₂P(Cy)₂ (16), and (Me)₂PCH₂CH₂CH₂P(Ph)₂ (17) were synthesized using air–stable phosphine oxide intermediates. In the first step, sodium phosphinites formed by deprotonation of (Me)₂P(O)H, (Et)₂P(O)H, and (iPr)₂P(O)H were alkylated by 1-bromo-3-chloropropane. The different substitution rates of the chloride and bromide groups allowed the isolation of the intermediates (Me)₂P(O)CH …

Testing The Robustness Of Solution Force Fields For Md Simulations On Gaseous Protein Ions., Justin H Lee, Katja Pollert, Lars Konermann

Chemistry Publications

It is believed that electrosprayed proteins and protein complexes can retain solution-like conformations in the gas phase. However, the lack of high-resolution structure determination methods for gaseous protein ions implies that their properties remain poorly understood. Many practitioners tackle this difficulty by complementing mass spectrometry-based experiments with molecular dynamics (MD) simulations. It is a potential problem that the standard MD force fields used for this purpose (such as OPLS-AA/L and CHARMM) were optimized for solution conditions. The question whether these force fields produce meaningful gas-phase data has received surprisingly little attention. Standard force fields are overpolarized to account for an …

What Is The Accuracy Limit Of Adiabatic Linear-Response Tddft Using Exact Exchange–Correlation Potentials And Approximate Kernels?, Jaspreet Kaur, Egor Ospadov, Viktor N. Staroverov

Chemistry Publications

Calculation of vertical excitation energies by the adiabatic linear-response time-dependent density-functional theory (TDDFT) requires static Kohn–Sham potentials and exchange–correlation kernels. When these quantities are derived from standard density-functional approximations (DFA), mean absolute errors (MAE) of the method are known to range from 0.2 eV to over 1 eV, depending on the functional and type of excitation. We investigate how the performance of TDDFT varies when increasingly accurate exchange–correlation potentials derived from Hartree–Fock (HF) and post-HF wavefunctions are combined with different approximate kernels. The lowest MAEs obtained in this manner for valence excitations are about 0.15–0.2 eV, which appears to be …

Probing Mid-Infrared Plasmon Resonances In Extended Radial Fractal Structures., Gregory Q Wallace, Danielle M Mcrae, François Lagugné-Labarthet

Chemistry Publications

Infrared (IR) antennas made of metallic nanostructures are widely tunable from the near- to the far-IR range. They can be utilized for a variety of applications such as light harvesting and photonic filters, and their structural linear or circular anisotropy can be exploited to further enhance the sensitivity of spectroscopic measurements. Here gold dendritic fractal structures that were optimized to exhibit multiple resonances in the mid-IR range were characterized using a scattering-type scanning near-field optical IR microscope. The spatially resolved IR maps associated with the individual modes serve as a basis to understand the mode evolution between each fractal generation.

Acid-Mediated N-Iodosuccinimide-Based Thioglycoside Activation For The Automated Solution-Phase Synthesis Of Α-1,2-Linked-Rhamnopyranosides, Victoria R. Kohout, Alyssa L. Pirinelli, Nicola L.B. Pohl

Chemistry Publications

Carbohydrate structures are often complex. Unfortunately, synthesis of the range of sugar combinations precludes the use of a single coupling protocol or set of reagents. Adapting known, reliable bench-chemistry reactions to work via automation will help forward the goal of synthesizing a broad range of glycans. Herein, the preparation of di- and tri-saccharides of alpha 1→2 rhamnan fragments is demonstrated using thioglycoside donors with the development for a solution-phase-based automation platform of commonly used activation conditions using N-iodosuccinimide (NIS) with trimethylsilyl triflate. Byproducts of the glycosylation reaction are shown to be compatible with hydrazine-based deprotection conditions, lending broader functionality …

Organic Chemistry With A Biographical Emphasis: Solutions To In-Chapter Exercises, Timothy Soderberg

Chemistry Publications

The solutions to the in-chapter exercises of Organic Chemistry with a Biological Emphasis volume 1 and 2.

Organic Chemistry With A Biological Emphasis: Solutions To Selected End-Of-Chapter Problems, Timothy Soderberg

Chemistry Publications

The solutions to the in-chapter exercises of Organic Chemistry with a Biological Emphasis volume 1 and 2.

Organic Chemistry With A Biological Emphasis Volume Ii, Timothy Soderberg

Chemistry Publications

The traditional approach to teaching Organic Chemistry, taken by most of the textbooks that are currently available, is to focus primarily on the reactions of laboratory synthesis, with much less discussion - in the central chapters, at least - of biological molecules and reactions. This is despite the fact that, in many classrooms, a majority of students are majoring in Biology or Health Sciences rather than in Chemistry, and are presumably taking the course in order to learn about the chemistry that takes place in living things.

In an effort to address this disconnect, I have developed a textbook for …

Organic Chemistry With A Biological Emphasis Volume I, Timothy Soderberg

Chemistry Publications

The traditional approach to teaching Organic Chemistry, taken by most of the textbooks that are currently available, is to focus primarily on the reactions of laboratory synthesis, with much less discussion - in the central chapters, at least - of biological molecules and reactions. This is despite the fact that, in many classrooms, a majority of students are majoring in Biology or Health Sciences rather than in Chemistry, and are presumably taking the course in order to learn about the chemistry that takes place in living things.

In an effort to address this disconnect, I have developed a textbook for …

Poly(Ester Amide) Particles For Controlled Delivery Of Celecoxib., Ian J Villamagna, Trent N Gordon, Mark B Hurtig, Frank Beier, Elizabeth R Gillies

Chemistry Publications

Many potential pharmacological treatments for osteoarthritis can result in undesirable side effects due to the systemic administration of drugs, making the direct delivery of drugs to joints an attractive alternative. Poly(ester amide)s (PEAs) have been shown to exhibit promising properties for the development of particle-based intra-articular delivery vehicles. However, a limited range of PEA structures has been investigated. In this study, we prepared and characterized the properties of two different PEA particles composed of l-phenylalanine, sebacic acid, and either 1,4-butanediol or 1,8-octanediol (PBSe and POSe, respectively). The anti-inflammatory drug celecoxib (CXB) was encapsulated into the particles. Despite minor structural differences, …

Oxoborane Formation Turns On Formazanate-Based Photoluminescence, Ryan R. Maar, Nicholas A. Hoffman, Viktor N. Staroverov, Joe Gilroy

Chemistry Publications

The synthesis of compounds containing multiple bonds to boron has challenged main-group chemists for decades. Despite significant progress, the possibility that the formation of such bonds can turn on photoluminescence has received minimal attention. We report an oxoborane (B=O) complex that is electronically stabilized by a formazanate ligand in the absence of significant steric bulk and, unlike the common BX₂ (X = F, Cl) formazanate adducts, exhibits intense photoluminescence. The latter property was rationalized through density-functional calculations which indicated that the B=O bond enhances photoluminescence by drastically reducing differences between the ligand's geometries in the ground and excited states. …

Mechanism Of Electrospray Supercharging For Unfolded Proteins: Solvent-Mediated Stabilization Of Protonated Sites During Chain Ejection., Insa Peters, Haidy Metwally, Lars Konermann

Chemistry Publications

Proteins that are unfolded in solution produce higher charge states during electrospray ionization (ESI) than their natively folded counterparts. Protein charge states can be further increased by the addition of supercharging agents (SCAs) such as sulfolane. The mechanism whereby these supercharged [M + zH] ^z+ ions are formed under unfolded conditions remains unclear. Here we employed a combination of mass spectrometry (MS), ion mobility spectrometry (IMS), and molecular dynamics (MD) simulations for probing the ESI mechanism under denatured supercharging conditions. ESI of acid-unfolded apo-myoglobin (aMb) in the presence of sulfolane produced charge states around 27+, all the way to fully …

Optoelectronic, Aggregation, And Redox Properties Of Double-Rotor Boron Difluoride Hydrazone Dyes, Daniela Cappello, Denis A.B. Therien, Viktor N. Staroverov, Francois Lagugne-Labarthet, Joe Gilroy

Chemistry Publications

We develop the chemistry of boron difluoride hydrazone dyes (BODIHYs) bearing two aryl substituents and explore their properties. The low-energy absorption bands (λ_max = 427–464 nm) of these dyes depend on the nature of the N-aryl groups appended to the BODIHY framework. Electron-donating and extended p-conjugated groups cause a red shift, whereas electron-withdrawing groups result in a blue shift. The title compounds were weakly photoluminescent in solution and strongly photoluminescent as thin films (λ_PL = 525–578 nm) with quantum yields of up to 18% and lifetimes of 1.1–1.7 ns, consistent with the dominant radiative decay through fluorescence. …

Protein Ions Generated By Native Electrospray Ionization: Comparison Of Gas Phase, Solution, And Crystal Structures., Maryam Bakhtiari, Lars Konermann

Chemistry Publications

Experiments and molecular dynamics (MD) simulations in the literature indicate that gaseous proteins generated by electrospray ionization (ESI) can retain native-like structures. However, the exact properties of these ions remain to be explored. Focusing on ubiquitin and lysozyme, we examined several pertinent questions. (1) We applied solvent MD runs to test whether the X-ray structures of both proteins are affected by crystal packing. Main and side-chain orientations were retained in solution, providing a justification for the hitherto unscrutinized approach of relying on crystal data for "solution" versus gas-phase comparisons. (2) Most earlier gas-phase protein MD investigations employed short (ns) simulation …

Effect Of Drug Loading On The Properties Of Temperature-Responsive Polyester-Poly(Ethylene Glycol)-Polyester Hydrogels, D. Andrew Prince, Ian J. Villamagna, Cameron C. Hopkins, John R. De Bruyn, Elizabeth R. Gillies

Chemistry Publications

Hydrogels that can undergo gelation upon injection in vivo are promising systems for the site-specific delivery of drugs. In particular, some thermo-responsive gels require no chemical additives but simply gel in response to a change from a lower temperature to physiological temperature (37 °C). The gelation mechanism does not involve covalent bonds, and it is possible that incorporation of drugs into the hydrogel could disrupt gelation. We investigated the incorporation of drugs into thermo-responsive hydrogels based on poly(ϵ-caprolactone-co-lactide)-block-poly(ethylene glycol)-block-poly(ϵ-caprolactone-co-lactide) (PCLA–PEG–PCLA). Significant differences in properties and in the response …

One-Step Femtosecond Laser Ablation Synthesis Of Sub-3 Nm Gold Nanoparticles Stabilized By Silica, Mallory G. John, Katharine M. Tibbetts

Chemistry Publications

No abstract provided.

Conserved Vibrational Coherence In The Ultrafast Rearrangement Of 2-Nitrotoluene Radical Cation, Derrick Ampadu Boateng, Mi'kayla D. Word, Lavrenty Gutsev, Puru Jena, Katharine M. Tibbetts

Chemistry Publications

2-Nitrotoluene (2-NT) is a good model for both photolabile protecting groups for organic synthesis and the military explosive 2,4,6-trinitrotoluene (TNT). In addition to the direct C−NO2 bond-cleavage reaction that initiates detonation in TNT, 2-NT undergoes an H atom attack reaction common to the photolabile 2-nitrobenzyl group, which forms the aci-nitro tautomer. In this work, femtosecond pump−probe measure- ments with mass spectrometric detection and density functional theory (DFT) calculations demonstrate that the initially prepared vibrational coherence in the 2-NT radical cation (2- NT+) is preserved following H atom attack. Strong-field adiabatic ionization is used to prepare 2-NT+, which can overcome a …

Probing Coherent Vibrations Of Organic Phosphonate Radical Cations With Femtosecond Time-Resolved Mass Spectrometry, Derrick Ampadu Boateng, Mi'kayla D. Word, Katharine M. Tibbetts

Chemistry Publications

Organic phosphates and phosphonates are present in a number of cellular components that can be damaged by exposure to ionizing radiation. This work reports femtosecond time-resolved mass spectrometry (FTRMS) studies of three organic phosphonate radical cations that model the DNA sugar-phosphate backbone: dimethyl methylphosphonate (DMMP), diethyl methylphosphonate (DEMP), and diisopropyl methylphosphonate (DIMP). Upon ionization, each molecular radical cation exhibits unique oscillatory dynamics in its ion yields resulting from coherent vibrational excitation. DMMP has particularly well-resolved 45 fs (732 ± 28 cm−1) oscillations with a weak feature at 610–650 cm−1, while DIMP exhibits bimodal oscillations with a period of ∼55 fs …

Single-Step Fret-Based Detection Of Femtomoles Dna, Kumar Sapkota, Anisa Kaur, Caleb Donkoh-Moore, Soma Dhakal

Chemistry Publications

Sensitive detection of nucleic acids and identification of single nucleotide polymorphism (SNP) is crucial in diagnosis of genetic diseases. Many strategies have been developed for detection and analysis of DNA, including fluorescence, electrical, optical, and mechanical methods. Recent advances in fluorescence resonance energy transfer (FRET)-based sensing have provided a new avenue for sensitive and quantitative detection of various types of biomolecules in simple, rapid, and recyclable platforms. Here, we report single-step FRET-based DNA sensors designed to work via a toehold-mediated strand displacement (TMSD) process, leading to a distinct change in the FRET efficiency upon target binding. Using single-molecule FRET (smFRET), …

Multifaceted Water Dynamics In Spherical Nanocages, M. Von Domaros, D. Bratko, B. Kirchner, G. Hummer, A. Luzar

Chemistry Publications

We present a new method to study position- dependent, anisotropic diffusion tensors inside spherically confined systems—a geometry that is common to many chemical nanoreactors. We use this method to elucidate the surprisingly rich solvent dynamics of confined water. The spatial variation of the strongly anisotropic diffusion predicted by the model agrees with the results of explicit molecular dynamics simulations. The same approach can be directly transferred to the transport of solutes to and from reaction sites located at nanoreactor interfaces. We com- plement our study by a detailed analysis of wa- ter hydrogen bond kinetics, which is intimately coupled to …

Anisotropic Structure And Dynamics Of Water Under Static Electric Fields, M. Shafiei, M. Von Domaros, D. Bratko, A. Luzar

Chemistry Publications

We study the structure and dynamics of water subject to a range of static external electric fields, using molecular dynamics simulations. In particular, we monitor the changes in hydrogen bond kinetics, reorientation dynamics, and translational motions of water molecules. We find that water molecules translate and rotate slower in elec- tric fields, because the tendency to reinstate the aligned orientation reduces the prob- ability of finding a new hydrogen bond partner and hence increases the probability of reforming already ruptured bonds. Furthermore, dipolar alignment of water mole- cules with the field results in structural and dynamic anisotropies even though the …

Thermo-Responsive And Covalently Cross-Linkable Hydrogels For Intra-Articular Drug Delivery, Andy Prince, Ian J. Villamagna, Aneta Borecki, Frank Beier, John R. De Bruyn, Mark Hurtig, Elizabeth Gillies

Chemistry Publications

The local delivery of drugs to joints is a recognized strategy in the treatment of osteoarthritis. Hydrogels, particularly those that can be injected as liquids but undergo gelation in the joint, are promising platforms for intra-articular drug delivery. However, their properties must be carefully designed and tuned to achieve sustained drug release, which has been a challenge with previous hydrogels. We describe here the use of a combination of non-covalent thermal gelation and covalent cross-linking with poly(caprolactone-co-lactide)(PCLA)-poly(ethylene glycol)(PEG)-PCLA triblock copolymers to achieve hydrogels with sustained drug release in joints. The hybrid cross-linking approach afforded higher viscoelastic and compression …

Coherent Vibrational And Dissociation Dynamics Of Polyatomic Radical Cations, Katharine M. Tibbetts

Chemistry Publications

The ultrafast dynamics of polyatomic radical cat- ions contribute to important processes including energy transfer in photovoltaics, electron transfer in photocataly- sis, radiation-induced DNA damage, and chemical reac- tions in the upper atmosphere and space. Probing these dynamics in the gas phase is challenging due to the rapid dissociation of polyatomic radical cations following elec- tron removal, which arises from excess electronic excita- tion of the molecule during the ionization process. This Concept article introduces the reader to how the pump- probe technique of femtosecond time-resolved mass spectrometry (FTRMS) can overcome this challenge to capture coherent vibrational dynamics on the …

Single-Molecule Analysis Of I-Motif Within Self-Assembled Dna Duplexes And Nanocircles, Anoja Megalathan, Bobby D. Cox, Peter D. Wilkerson, Anisa Kaur, Kumar Sapkota, Joseph E. Reiner, Soma Dhakal

Chemistry Publications

The cytosine (C)-rich sequences that can fold into tetraplex structures known as i-motif are prevalent in genomic DNA. Recent studies of i-motif–forming sequences have shown increasing evidence of their roles in gene regulation. However, most of these studies have been performed in short single-stranded oligonucleotides, far from the intracellular environment. In cells, i-motif–forming sequences are flanked by DNA duplexes and packed in the genome. Therefore, exploring the conformational dynamics and kinetics of i-motif under such topologically constrained environments is highly relevant in predicting their biological roles. Using single-molecule fluorescence analysis of self-assembled DNA duplexes and nanocircles, we show that the …