Chimie et sciences biomoléculaires // Chemistry and Biomolecular Sciences

Permanent URI for this collectionhttps://hdl.handle.net/10393/12858

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La chimie générale pour les Gee-Gees
(2025) Roy, Kevin; Zeghal, Mahdi; Thomas, Jessica M.; Focsaneanu, Kathy-Sarah
Ce manuel a été conçu pour les étudiants inscrits au cours CHM1711 Principes de chimie à l'Université d'Ottawa.
General Chemistry for Gee-Gees
(2021) Roy, Kevin; Zeghal, Mahdi; Thomas, Jessica M.; Focsaneanu, Kathy-Sarah
This textbook was designed for students enrolled in CHM1311 Principles of Chemistry at the University of Ottawa.
Photocatalytic Hydrogen Production from Homo- and Hetero-geneous Cobalt (II) Catalysts
(2020) Sharif, Ayni
Various energy sources on which society depends are rapidly depleting in recent years. Alternate fuel sources that are cost efficient, earth abundant, and easily accessible has been urgently sought out by numerous researchers worldwide. Hydrogen represents an excellent target that could meet these pressing needs. This project has identified efficient photocatalytic production of hydrogen from the reduction of water using both homo- and hetero-geneous cobalt (II) complexes. A pincer selenium-nitrogen ligand scaffold, 2,6-bis[(pyrazol-1-yl)methyl]pyridine, was used to support a potential homogeneous catalyst. However, the formation of precipitates during catalytic process raised concerns over certainty of the activity of the homogeneous catalyst. These concerns prompted the investigation of cobalt oxide nanoparticles as potential heterogeneous catalysts. These explorations revealed this system to be a much more efficient catalyst through visible-light photochemistry of reducing water for hydrogen production in the presence of a Ru(bpy)3[2+] photosensitizer and a reductant.
Origin of conformational dynamics in a globular protein
(2019) Damry, Adam M.; Mayer, Marc M.; Broom, Aron; Goto, Natalie K.; Chica, Roberto A.
Protein structures are dynamic, undergoing motions that can play a vital role in function. However, the link between primary sequence and conformational dynamics remains poorly understood. Here, we studied how conformational dynamics can arise in a globular protein by evaluating the impact of individual core-residue substitutions in DANCER-3, a streptococcal protein G domain β1 variant that we previously designed to undergo a specific mode of conformational exchange that has never been observed in the wild-type protein. Using a combination of solution NMR experiments and molecular dynamics simulations, we demonstrate that only two mutations are necessary to create this conformational exchange, and that these mutations work synergistically, with one destabilizing the native structure and the other allowing two new conformational states to be accessed on the energy landscape. Overall, our results show how dynamics can appear in a stable globular fold, a critical step in the molecular evolution of dynamics-linked functions.
Solid-state 1H and 27Al NMR studies of DMSO-kaolinite intercalates
(2017-06-01) Fafard, Jonathan; Terskikh, Victor; Detellier, Christian
Nuclear magnetic resonance (NMR) provides a powerful tool to describe local nuclear environments. In this work, unique structural information on kaolinite and on kaolinite dimethylsulfoxide (DMSO) intercalate were provided by solid-state 1H and 27Al magic-angle spinning (MAS) NMR. The interlayer chemistry of kaolinite (K) was examined by intercalating a select group of highly polar organic molecules or salts into kaolinite as a first step. Once the interlayer space is expanded, the intercalated compounds can be replaced in a second step. Intercalating DMSO into kaolinite to form the DMSO-K intercalate is, thus, a particularly useful first step toward the intercalation of a large variety of molecules, including polymers and ionic liquids. Well developed characterization methods are essential to define the structural modifications of kaolinite, and MAS NMR is a useful complement to other techniques. The use of 1H and 27Al MAS NMR for this purpose has been relatively rare. 1H NMR, nevertheless, can give unique information about kaolinite hydroxyls. Because quadrupolar interactions are sensitive to the local octahedral Al(III) geometry, solid-state 27Al NMR can follow subtle structural modifications in the octahedral sheet. In the present work, the 1H MAS NMR chemical shifts of KGa-1b were unambiguously attributed to the internal surface hydroxyls at 2.7 ppm and to the internal hydroxyls at 1.7 ppm. The 1H MAS NMR chemical shifts of the two methyl groups in DMSO-K are not equivalent and can be attributed to the 2.9 and 4.2 ppm peaks. The 27Al MAS NMR spectra of KGa-1b obtained under different magnetic fields revealed that most of the quadrupolar effects were highly reduced at 21.1 T, whereas the spectra at lower field, 4.7 T, were dominated by quadrupolar effects. The two octahedral Al(III) sites are not equivalent and can be distinguished in the low-field spectral simulation. Increased quadrupolar constants were observed and showed the major perturbations of the local Al symmetry that resulted from DMSO intercalation. Both the 1H and 27Al MAS NMR studies at different magnetic fields afforded important information about the local environments of the kaolinite hydroxyl groups and structural Al(III).
A complete map of the ion chemistry of the naphthalene radical cation? DFT and RRKM modeling of a complex potential energy surface
(2015) Solano, Eduardo A.; Mayer, Paul M.
The fragmentation mechanisms of the naphthalene molecular ion to [M-C4H2](+•), [M-C2H2](+•), [M-H2](+•), and [M-H(•)](+) were obtained at the UB3LYP/6-311+G(3df,2p)//UB3LYP/6-31G(d) level of theory and were subsequently used to calculate the microcanonical rate constants, k(E)'s, for all the steps by the Rice-Ramsperger-Kassel-Marcus formalism. The pre-equilibrium and steady state approximations were applied on different regions of the potential energy profiles to obtain the fragmentation k(E)'s and calculate the relative abundances of the ions as a function of energy. These results reproduce acceptably well the imaging photoelectron-photoion coincidence spectra of naphthalene, in the photon-energy range 14.0-18.8 eV that was previously reported by our group. Prior to dissociation, the molecular ion rapidly equilibrates with a set of isomers that includes the Z- and E-phenylvinylacetylene (PVA) radical cations. The naphthalene ion is the predominant isomer below 10 eV internal energy, with the other isomers remaining at steady state concentrations. Later on, new steady-state intermediates are formed, such as the azulene and 1-phenyl-butatriene radical cations. The naphthalene ion does not eject an H atom directly but eliminates an H2 molecule in a two-step fragmentation. H(•) loss occurs instead from the 1-phenyl-butatriene ion. The PVA ions initiate the ejection of diacetylene (C4H2) to yield the benzene radical cation. Acetylene elimination yields the pentalene cation at low energies (where it can account for 45.9%-100.0% of the rate constant of this channel), in a three-step mechanism starting from the azulene ion. However, above 7.6 eV, the major [M-C2H2](+•) structure is the phenylacetylene cation.
The dehydrogenation of alcohols and hydrocarbons by atomic metal anions
(2015) Mayer, Paul; Halvachizadeh, Jaleh; Mungham, Alex
The reactivity of anionic metal-carbonyl systems toward hydrocarbons, alcohols and a variety of other classes of molecules is well established in the literature. In this study we explored the reactions of atomic metal anions M(-), notably K(-), Cs(-), Co(-), Fe(-), Cu(-) and Ag(-), with alcohols, alkanes, alkenes and alkynes. All of the metal anions deprotonated the alcohols and alkynes. Also observed were the subsequent reactions of the resulting organic anions. Fe(-) and Cu(-) consistently displayed mono- and bis-dehydrogenation of primary and secondary alcohols, and alkanes, alkenes and alkynes to form MH(-) and MH(2)(-). Mechanisms for the dehydrogenation reactions are proposed and substantiated with isotopically-labelled reagents and thermochemical arguments.
Utilizing ion mobility and tandem mass spectrometry to evaluate the structure and behaviour of multimeric cyclodextrin complexes
(2015) Berland, Kevin; Renaud, Justin B.; Mayer, Paul M.
Characterizing noncovalent complexes of molecular dimers and higher complexes using tandem mass spectrometry (MS/MS) can be hindered due to spectral overlap in both the MS and the MS/MS. We investigated the structures and dissociation energetics of multimeric β-cyclodextrin (β-CD) complexes alone or with substrates using combinations of ion mobility spectrometry (IMS), MS/MS, and Rice–Ramsperger–Kassel–Marcus (RRKM) unimolecular rate modelling. The doubly charged β-CD dimers ([(β-CD)2 – 2H+]2−) dissociate to two [β-CD – H+]− ions with the same m/z. IMS was used to separate source generated [(β-CD)2 – 2H+]2− from [β-CD – H+]− and the extent of [(β-CD)2 – 2H+]2− dissociation versus collision energy was determined by modelling changes in the ion’s isotopic profile. The RRKM derived critical energy (E0) for dissociation of [(β-CD)2 – H+]− and [(β-CD)2 – 2H+]2− were 1.85 ± 0.11 eV and 1.79 ± 0.09 eV, respectively, corresponding to a slight decrease in complex stability due to increased charge–charge repulsion in the dianion. This approach was extended to include dimeric complexes complexed to 4,4′-(propane-1,3-diyl) dibenzoic acid (PDDA) and ibuprofen (Ibu).
Electron transfer and multi-atom abstraction reactions betweenatomic metal anions and NO, NO2and SO2J
(2016) Mayer, Paul M; Butson, Jeffery M; Curtis, Sharon
The atomic metal anions Fe¯, Cs¯, Cu¯ and Ag¯ were reacted with NO, NO2 and SO2 to form intact NO¯, NO2¯ and SO2¯ with no fragmentation. Yields for the molecular anions ranged from 4 to 97% and were found to correlate to the exothermicity of the electron transfer process. Sequential oxygen atom extraction was found to take place between the metal anions and NO and NO2. Reactions between NO2 and Fe¯ resulted in FeO¯, FeO2¯ and FeO3¯ while reactions of Cu¯ with NO2 resulted in CuO¯ and CuO2¯. Reactions of Cu¯ and Ag¯ with NO resulted in CuO¯ and AgO¯ respectively.
ClusterMine360: a database of microbial PKS/NRPS biosynthesis
(2012) Conway, Kyle R; Boddy, Christopher N
ClusterMine360 (http://www.clustermine360.ca/) is a database of microbial polyketide and non-ribosomal peptide gene clusters. It takes advantage of crowd-sourcing by allowing members of the community to make contributions while automation is used to help achieve high data consistency and quality. The database currently has >200 gene clusters from >185 compound families. It also features a unique sequence repository containing >10 000 polyketide synthase/non-ribosomal peptide synthetase domains. The sequences are filterable and downloadable as individual or multiple sequence FASTA files. We are confident that this database will be a useful resource for members of the polyketide synthases/non-ribosomal peptide synthetases research community, enabling them to keep up with the growing number of sequenced gene clusters and rapidly mine these clusters for functional information.
Recovery of Red Fluorescent Protein Chromophore Maturation Deficiency through Rational Design
(2012) Moore, Matthew M.; Pandelieva, Antonia T.; Mayo, Stephen L.; Chica, Roberto A.; Oteng-Pabi, Samuel K.
Red fluorescent proteins (RFPs) derived from organisms in the class Anthozoa have found widespread application as imaging tools in biological research. For most imaging experiments, RFPs that mature quickly to the red chromophore and produce little or no green chromophore are most useful. In this study, we used rational design to convert a yellow fluorescent mPlum mutant to a red-emitting RFP without reverting any of the mutations causing the maturation deficiency and without altering the red chromophore’s covalent structure. We also created an optimized mPlum mutant (mPlum-E16P) that matures almost exclusively to the red chromophore. Analysis of the structure/function relationships in these proteins revealed two structural characteristics that are important for efficient red chromophore maturation in DsRed-derived RFPs. The first is the presence of a lysine residue at position 70 that is able to interact directly with the chromophore. The second is an absence of non-bonding interactions limiting the conformational flexibility at the peptide backbone that is oxidized during red chromophore formation. Satisfying or improving these structural features in other maturation-deficient RFPs may result in RFPs with faster and more complete maturation to the red chromophore.
Recovery of Red Fluorescent Protein Chromophore Maturation Deficiency through Rational Design
(2012) Moore, Matthew M.; Oteng-Pabi, Samuel K.; Pandelieva, Antonia T.; Mayo, Stephen L.; Chica, Roberto A.
Red fluorescent proteins (RFPs) derived from organisms in the class Anthozoa have found widespread application as imaging tools in biological research. For most imaging experiments, RFPs that mature quickly to the red chromophore and produce little or no green chromophore are most useful. In this study, we used rational design to convert a yellow fluorescent mPlum mutant to a red-emitting RFP without reverting any of the mutations causing the maturation deficiency and without altering the red chromophore’s covalent structure. We also created an optimized mPlum mutant (mPlum-E16P) that matures almost exclusively to the red chromophore. Analysis of the structure/function relationships in these proteins revealed two structural characteristics that are important for efficient red chromophore maturation in DsRed-derived RFPs. The first is the presence of a lysine residue at position 70 that is able to interact directly with the chromophore. The second is an absence of non-bonding interactions limiting the conformational flexibility at the peptide backbone that is oxidized during red chromophore formation. Satisfying or improving these structural features in other maturation-deficient RFPs may result in RFPs with faster and more complete maturation to the red chromophore.
Solid-State 11B and 13C NMR, IR, and X-ray Crystallographic Characterization of Selected Arylboronic Acids and their Catechol Cyclic Ester
(2012-04-25) Oh, Se-woung; Weiss, Joseph W.E.; Kerneghan, Phillip A.; Korobkov, Ilia; Maly, Kenneth E.; Bryce, David L.
Nine arylboronic acids, seven arylboronic catechol cyclic esters, and two trimeric arylboronic anhydrides (boroxines) are investigated using 11B solid-state NMR spectroscopy at three different magnetic field strengths (9.4, 11.7, and 21.1 T). Through the analysis of spectra of static and magic-angle spinning samples, the 11B electric field gradient and chemical shift tensors are determined. The effects of relaxation anisotropy and nutation field strength on the 11B NMR line shapes are investigated. Infrared spectroscopy was also used to help identify peaks in the NMR spectra as being due to the anhydride form in some of the arylboronic acid samples. Seven new X-ray crystallographic structures are reported. Calculations of the 11B NMR parameters are performed using cluster model and periodic gauge-including projector-augmented wave (GIPAW) density functional theory (DFT) approaches, and the results are compared with the experimental values. Carbon-13 solid-state NMR experiments and spectral simulations are applied to determine the chemical shifts of the ipso carbons of the samples. One bond indirect 13C-11B spin-spin (J) coupling constants are also measured experimentally and compared with calculated values. The 11B/10B isotope effect on the 13C chemical shift of the ipso carbons of arylboronic acids and their catechol esters, as well as residual dipolar coupling, is discussed. Overall, this combined X-ray, NMR, IR, and computational study provides valuable new insights into the relationship between NMR parameters and the structure of boronic acids and esters.
Single Kaolinite Nanometer Layers Prepared by an In Situ Polymerization–Exfoliation Process in the Presence of Ionic Liquids
(2011) Letaief, Sadok; Leclercq, Jérôme; Liu, Yun; Detellier, Christian
A simple chemical route for the exfoliation of kaolinite in the presence of polymerizable ionic liquids and the resulting obtainment of exfoliated nanocomposites is reported. The exfoliation was achieved using three different ionic liquids structurally bearing a vinyl group: 1-methyl-3-(4-vinylbenzyl)imidazolium chloride salt (IL_1), 1-methyl-1-(4-vinylbenzyl)pyrrolidinium chloride (IL_2), and 1-methyl-3-vinyl imidazolium iodide (IL_3) and a urea-kaolinite intercalate as precursor. The reaction was done in one step by an in situ polymerization–exfoliation process. 13C CP/MAS NMR spectra confirmed the spontaneous polymerization of the ionic liquid during the exfoliation process to afford atactic polystyrene derivatives in the case of IL_1 and IL_2. The amount of organic material in the exfoliated nanocomposite was close to 30% as shown by thermal gravimetric analysis. This amount is small in comparison to the amount obtained when the exfoliation was done using sodium polyacrylate (Letaief and Detellier, Langmuir2009, 25, 10975). XRD as well as SEM analysis confirmed a total exfoliation of the kaolinite when the reaction was done using urea kaolinite, whereas a microcomposite, made predominantly of kaolinite platelet aggregates dispersed in the polymeric matrix, was formed when dimethylsulfoxide kaolinite was used as the precursor.
Definitive Solid-State 185/187Re NMR Spectral Evidence for and Analysis of the Origin of High-Order Quadrupole-Induced Effects for I = 5/2
(2011-11-24) Bryce, David L.
Rhenium-185/187 solid-state nuclear magnetic resonance (SSNMR) experiments using NaReO4 and NH4ReO4 powders provide unambiguous evidence for the existence of high-order quadrupole-induced effects (HOQIE) in SSNMR spectra. Fine structure, not predicted by second-order perturbation theory, has been observed in the 185/187Re SSNMR spectrum of NaReO4 at 11.75 T, where the ratio of the Larmor frequency (n0) to the quadrupole frequency (nQ) is B2.6. This is the first experimental observation that under static conditions, HOQIE can directly manifest in SSNMR powder patterns as additional fine structure. Using NMR simulation software which includes the quadrupole interaction (QI) exactly, extremely large 185/187Re nuclear quadrupole coupling constants (CQ) are accurately determined. QI parameters are confirmed independently using solid-state 185/187Re nuclear quadrupole resonance (NQR). We explain the spectral origin of the HOQIE and provide general guidelines that may be used to assess when HOQIE may impact the interpretation of the SSNMR powder pattern of any spin-5/2 nucleus in a large, axially symmetric electric field gradient (EFG). We also quantify the errors incurred when modeling SSNMR spectra for any spin-5/2 nucleus within an axial EFG using second-order perturbation theory. Lastly, we measure rhenium chemical shifts in the solid state for the first time
Calcium binding environments probed by 43Ca NMR spectroscopy
(2010-10-28T19:52:45Z) Bryce, David L.
Calcium is an important component of materials, metalloproteins, minerals, glasses, and small inorganic and organic complexes. However, NMR spectroscopy of the quadrupolar 43Ca nuclide remains difficult primarily due to its low natural abundance and low resonance frequency. In this Perspective, experimental challenges and recent successes in the field are highlighted, with a focus on solid-state 43Ca NMR spectroscopy. Solution 43Ca NMR studies of calcium-binding biomolecules are also presented. The structural insights afforded from quadrupolar and chemical shift parameters are examined. For example: isotropic chemical shifts have been shown to correlate with the mean Ca–O distance and also with calcium coordination number; quadrupolar coupling constants and chemical shift tensor spans have been shown to be useful probes of polymorphism; and, distance measurements involving 43Ca have been recently demonstrated. Lastly, challenges and opportunities for the future are considered.
A solid-state 11B NMR and computational study of boron electric field gradient and chemical shift tensors in boronic acids and boronic esters
(2010-04-20T19:21:03Z) Weiss, Joseph W.E.; Bryce, David L.
The results of a solid-state 11B NMR study of a series of 10 boronic acids and boronic esters with aromatic substituents are reported. Boron-11 electric field gradient (EFG) and chemical shift (CS) tensors obtained from analyses of spectra acquired in magnetic fields of 9.4 and 21.1 T are demonstrated to be useful for gaining insight into the molecular and electronic structure about the boron nucleus. Data collected at 21.1 T clearly show the effects of chemical shift anisotropy (CSA), with tensor spans (Ω) on the order of 10−40 ppm. Signal enhancements of up to 2.95 were achieved with a DFS-modified QCPMG pulse sequence. To understand the relationship between the measured tensors and the local structure better, calculations of the 11B EFG and magnetic shielding tensors for these compounds were conducted. The best agreement was found between experimental results and those obtained from GGA revPBE DFT calculations. A positive correlation was found between Ω and the dihedral angle (CCBO), which describes the orientation of the boronic acid/ester functional group relative to an aromatic system bound to boron. The small boron CSA is discussed in terms of paramagnetic shielding contributions as well as diamagnetic shielding contributions. Although there is a region of overlap, both Ω and the 11B quadrupolar coupling constants tend to be larger for boronic acids than for the esters. We conclude that the span is generally the most characteristic boron NMR parameter of the molecular and electronic environment for boronic acids and esters, and show that the values result from a delicate interplay of several competing factors, including hydrogen bonding, the value of CCBO, and the electron-donating or withdrawing substituents bound to the aromatic ring.

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