Strategies for teaching NMR spectral interpretation in the undergraduate organic chemistry curriculum are often faculty-centered and can lead to student reliance on rote memorization and “guess and ...check” methods rather than critical-thinking skills for structure determination. This article describes a student-focused methodology for the introduction of NMR spectral interpretation. Guided-inquiry tutorials using NMR prediction tools were developed to enable students to investigate the trends and concepts in 13C and 1H NMR spectral interpretation, with an emphasis on making connections between data and foundational chemical knowledge. A systematic approach to solving unknown structure problems is presented, providing a framework for students to organize spectral data and to build molecules from partial structures. The success of this NMR spectroscopy teaching strategy, which can be adapted for either laboratory or lecture environments, was demonstrated both in positive student survey responses as well as in quantitative data showing a significant improvement in exam question scores.
We report the results of experiments, simulations, and DFT calculations that focus on describing the reaction dynamics observed within the collision-induced dissociation of l-lysine-H+ and its ...side-chain methylated analogues, N ε-methyl-l-lysine-H+ (Me1-lysine-H+), N ε,N ε-dimethyl-l-lysine-H+ (Me2-lysine-H+), and N ε,N ε,N ε-trimethyl-l-lysine-H+ (Me3-lysine-H+). The major pathways observed in the experimental measurements were m/z 130 and 84, with the former dominant at low collision energies and the latter at intermediate to high collision energies. The m/z 130 peak corresponds to loss of N(CH3) n H3–n , while m/z 84 has the additional loss of H2CO2 likely in the form of H2O + CO. Within the time frame of the direct dynamics simulations, m/z 130 and 101 were the most populous peaks, with the latter identified as an intermediate to m/z 84. The simulations allowed for the determination of several reaction pathways that result in these products. A graph theory analysis enabled the elucidation of the significant structures that compose each peak. Methylation results in the preferential loss of the side-chain amide group and a reduction of cyclic structures within the m/z 84 peak population in simulations.
Lithium enolates are widely used nucleophiles with a complicated and only partially understood solution chemistry. Deprotonation of 4-fluoroacetophenone in THF with lithium diisopropylamide occurs ...through direct reaction of the amide dimer to yield a mixed enolate-amide dimer (3), then an enolate homodimer (1-Li)2, and finally an enolate tetramer (1-Li)4, the equilibrium structure. Aldol reactions of both the metastable dimer and the stable tetramer of the enolate were investigated. Each reacted directly with the aldehyde to give a mixed enolate-aldolate aggregate, with the dimer only about 20 times as reactive as the tetramer at −120 °C.
A variety of multinuclear NMR techniques, in combination with X-ray diffraction methods, were used to probe the solution structure of α-aryl lithium enolates of bis(4-fluorobenzyl) ketone (1-H), ...phenyl 4-fluorobenzyl ketone (2-H), and N,N-dimethyl 4-fluorophenylacetamide (3-H) in ethereal solvents and in the presence of cosolvent additives PMDTA, TMTAN, HMPA, and cryptand 2.1.1. All three enolates were dimers in THF solution, and were converted to monomers by the triamine additives, PMDTA and TMTAN. The exchange of the triamine-solvated monomers with their ethereal-solvated dimer counterparts was probed by using dynamic NMR (DNMR). The cosolvent HMPA formed monomers along with minor amounts of lithiate species, (RO)2Li− and (RO)3Li2−, which were also observed when cryptand 2.1.1 was used as a cosolvent, or when mixed lithium−phosphazenium enolate solutions were prepared. Dynamic exchange of lithiate species was investigated by DNMR spectroscopy. The barrier to rotation of the conjugated 4-fluorophenyl ring of these diverse enolate structures was measured and found to be consistent with a resonance picture where lower aggregation states lead to increased delocalization of negative charge. The lithium enolate aggregates identified were compared to the “naked” α-4-fluorophenyl enolates generated with the phosphazene base P4. The barrier to aryl ring rotation was 2.7 kcal/mol higher for the phosphazenium enolate 3-Li·P4H compared to the dimer (3-Li)2. Structural characterization of a phosphazenium enolate through X-ray crystallography was obtained for the first time. Additional aspects of the Schwesinger base P4 were investigated which included characterization of the solution exchange behavior of the protonated and unprotonated forms as well as determination of the solid state structure by X-ray diffraction.
Controlling the self-assembly of thiophene-containing molecules and polymers requires a strong fundamental understanding of the relationship between molecular features and structure-directing forces. ...Here, the effects of ring-substitution position on the two-dimensional self-assembly of monosubstituted thiophenes at the phenyloctane/HOPG interface are studied using scanning tunneling microscopy (STM). The influence of π···π-stacking, hydrogen-bonding, and alkyl-chain interactions are explored computationally. Alteration of the amide attachment point from the 2- to the 3-position induces transformation from head-to-tail packing to head-to-head packing. This may be attributed to canceling of lateral dipoles.
Solution properties of enolates generated using the phosphazene (Schwesinger) base P4- t Bu were investigated by NMR spectroscopy. With a full equivalent of base the benzyl ketones 1a and 1b, the ...acetophenone 2, the arylacetaldehyde 1c, and the methyl arylacetate 1d formed the expected “naked” (P4H+) enolates 3 and 7. However, at a half-equivalent of base the ketones 1a and 1b as well as the aldehyde 1c formed solutions of stable hydrogen-bonded dimeric (enol-enolate) structures (4). The acetophenone 2, on the other hand, forms only traces of the H-bonded dimer 8 during deprotonation of 2. The thermodynamic product was the isomeric self-aldol condensation product 12. The mechanism of this condensation was elucidated by low temperature rapid-injection (RI) NMR spectroscopy. Solutions of 8 stable enough for NMR characterization could be transiently generated by semiprotonation of the enolate 7 with HCl·OEt2 at −130 °C using RINMR. The ester enolate 1d gave no trace of 4d even on a time scale as short as a few seconds at −130 °C either during the semideprotonation of 1d, or during semiprotonation of the enolate 3d. Long-lived solutions of the enols derived from 1a, 1b, 1c, and 2 (but not 1d) could be produced by full protonation of the phosphazene enolates with HCl·OEt2 at low temperature.
Multinuclear NMR spectroscopic studies at low temperature (−110 to −150 °C) revealed that lithium p-fluorophenolate and the lithium enolates of cyclohexanone, cyclopentanone and 4-fluoroacetophenone ...have tetrameric structures in THF/Et2O and THF/Et2O−HMPA by study of the effects of the addition of HMPA. The Z and E isomers of the lithium enolate of 1,3-bis-(4-fluorophenyl)-2-propanone (5F-Li) show divergent behavior. The Z isomer is completely dimeric in pure diethyl ether, and mostly dimeric in 3:2 THF/ether, where monomer could be detected in small amounts. TMTAN and PMDTA convert Z-5F-Li to a monomeric amine complex, and HMPA converts it partially to monomers, and partially to lithiate species (RO)2Li− and (RO)3Li2−. Better characterized solutions of these lithiates were prepared by addition of phosphazenium enolates (using P4-tBu base) to the lithium enolate in 1:1 ratio to form triple ion (RO)2Li− P4H+, or 2:1 ratio to form the higher lithiate (RO)3Li2− (P4H+)2) (quadruple ions). The E isomer of 5F-Li is also dimeric in 3:2 THF/Et2O solution, but is not detectably converted to monomer either by PMDTA or HMPA. In contrast to Z-5F-Li, the E isomer is tetrameric in diethyl ether even in the presence of excess HMPA. Thus for the two isomers of 5F six different enolate structures were characterized: tetramer, dimer, CIP-monomer, SIP-monomer, triple ion, and quadruple ion.
Experimental and computational results are reported on the reaction dynamics taking place within the collision-induced dissociation (CID) of Nɛ, Nɛ, Nɛ-Trimethyl-L-lysine+ (TMe-lysine+) and ...Nɛ-acetyl-L-lysine-H+ (acetyl-lysine-H+). These common post-translational modifications result in a mass difference of only 0.036 Dalton. Resolving these two species directly requires a high-resolution instrument and they share several CID peaks. Nevertheless, the mechanisms observed are strikingly different, particularly at lower internal energies. Reactivity is higher for acetyl-lysine-H+, with decomposition initiated via losses at the N- and C-termini. In contrast, unmodified lysine and TMe-lysine+ exhibit mechanisms that involve an initial loss from the sidechain.
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•TMe-lysine+ and acetyl-lysine-H+ have nearly identical m/z ratios.•Acetyl-lysine-H+ exhibits initial N-/C- terminus collision-induced dissociation.•Acetyl-lysine-H+ show higher decomposition rates than TMe-lysine+.
We present and discuss results from direct dynamics simulations, DFT calculations, and experimental measurements of the collision induced dissociation (CID) of O-phosphorylation of serine-H+ (p-Ser, ...m/z186). Parameters for the interaction potential suitable for use in CID simulations of phosphorylated species were obtained and reported. Within both experiments and simulations, the primary decomposition product is m/z88. This agrees with previous studies, and simulations are consistent with the proposed primary mechanisms suggested in the literature for forming this product. Moreover, the simulations provided insight into an indirect decomposition pathway that forms m/z99 and secondary decomposition pathways observed experimentally at larger collision energies.
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•First direct dynamics study of collision-induced dissociation for a phosphorylated amino acid.•Presents potential energy interaction parameters between argon and phosphorylated amino acids.•Compares phosphorylation vs sulfonation of serine.
We sought to create an undergraduate laboratory experience to introduce the field of proteomics and the associated mass spectrometric (MS) techniques alongside classic protein purification ...methodologies. Students were tasked with the purification and identification of one of the major proteins found in a whey‐based nutritional supplement with the ultimate goal of having students become the drivers of their independent projects. Two major challenges were 1) to complete the experiments in 4‐hour blocks over several weeks in a typical semester and 2) to train sixteen students per lab period on a single mass spectrometer. A six‐week project was developed where students spent four lab periods performing either ion‐exchange or gel filtration chromatography and SDS‐PAGE, and two lab periods gathering bottom‐up and top‐down proteomic data with a matrix‐assisted laser desorption ionization (MALDI) mass spectrometry. The resulting data, peptide mass fingerprints and tandem mass spectra, were analyzed via database searching (i.e. MASCOT) during these weeks or outside the laboratory periods. The abundance of literature on the major whey proteins in terms of the biology, purification, and even proteomic analyses allowed students to determine their mode of protein purification and conditions for MALDI‐MS. This project is fairly low cost and widely applicable to any institution with appropriate facilities.
Support or Funding Information
This work was funded in part by a grant from the Siena College Committee on Teaching and Faculty Development (RSM) and the Siena College School of Science (EEH).
This is from the Experimental Biology 2019 Meeting. There is no full text article associated with this published in The FASEB Journal.
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