an-inexpensive-adaptation-commercial-microwave-reactor-for-solid

An Inexpensive Adaptation of a Commercial Microwave Reactor for Solid Phase Peptide Synthesis

A home-built apparatus to perform solid phase peptide synthesis (SPPS), assisted by microwave irradiation and heating, is presented. In contrast to ...

Fairfield University

(19)F NMR spectra of two neutral, organic-soluble helical peptide octamers, each labeled at its N terminus with either 4-fluorobenzamide or 4-trifluoromethylbenzamide, in solvents with widely varying dielectric constants have been observed. The peptides are oligomers of alpha-aminoisobutyric acid (Aib), which is a residue known to form stable 3(10) helices in organic solution. In relation to the (19)F NMR spectra of a control molecule, the peptide terminating in 4-fluorobenzamide shows a solvent-dependent downfield chemical shift of between approximately 1.5 and approximately 4 ppm, whilst the peptide terminating in 4-trifluoromethylbenzamide shows only an approximately 0.2 ppm chemical shift dependence on the solvent dielectric constant. The experimental observations were compared to calculated values of the electric field generated by the correlation of dipolar amide units through the peptide's helical conformation. We find the chemical-shift response of the 4-fluorobenzamide group to the peptide's calculated electric field is consistent with the magnitude of (19)F chemical shift dispersion observed in proteins.

19F NMR chemical shifts induced by a helical peptide.

Isotope-edited FT-IR spectroscopy is a combined synthetic and spectroscopic method used to characterize local (e.g., residue-level) vibrational environments of biomolecules. We have prepared the 3(10) helical peptide Z-Aib6-OtBu and seven (13)C-enriched analogues that vary only in the number and position(s) of (13)C═O isotopic enrichment. FT-IR spectra of these eight peptides solvated in the nonpolar aprotic solvent dichloromethane have been collected and compared to frequency, intensity, and normal mode results of DFT calculations. Single (13)C enrichment of amide functional groups tends to localize amide I vibrational eigenmodes, providing residue-specific information regarding the local environment (e.g., hydrogen bonding or solvent exposure) of the peptide bond. Double (13)C enrichment of Z-Aib6-OtBu allows for examination of interamide coupling between two labeled amide functional groups, providing experimental evidence of interamide coupling in the context of 3(10) helical structure. Although the calculated and observed interamide couplings of Z-Aib6-OtBu are a few cm(-1) and less, the eight peptides exhibit distinct infrared spectra, revealing details of interamide coupling and residue level vibrational environments.

FT-IR spectroscopy and density functional theory calculations of 13C isotopologues of the helical peptide Z-Aib6-OtBu.

The conformational preferences of a series of capped peptides containing the helicogenic amino acid aminoisobutyric acid (Aib) (Z-Aib-OH, Z-(Aib)-OMe, and Z-(Aib)-OMe) are studied in the gas phase under expansion-cooled conditions. Aib oligomers are known to form 3-helical secondary structures in solution and in the solid phase. However, in the gas phase, accumulation of a macrodipole as the helix grows could inhibit helix stabilization. Implementing single-conformation IR spectroscopy in the NH stretch region, Z-Aib-OH and Z-(Aib)-OMe are both observed to have minor conformations that exhibit dihedral angles consistent with the 3-helical portion of the Ramachandran map (ϕ, ψ = -57°, -30°), even though they lack sufficient backbone length to form 10-membered rings which are a hallmark of the developed 3-helix. For Z-(Aib)-OMe three conformers are observed in the gas phase. Single-conformation infrared spectroscopy in both the NH stretch (Amide A) and C[double bond, length as m-dash]O stretch (Amide I) regions identifies the main conformer as an incipient 3-helix, having two free NH groups and two C10 H-bonded NH groups, labeled an F-F-10-10 structure, with a calculated dipole moment of 13.7 D. A second minor conformer has an infrared spectrum characteristic of an F-F-10-7 structure in which the third and fourth Aib residues have ϕ, ψ = 75°, -74° and -52°, 143°, Ramachandran angles which fall outside of the typical range for 3-helices, and a dipole moment that shrinks to 5.4 D. These results show Aib to be a 3-helix former in the gas phase at the earliest stages of oligomer growth.

Conformation-specific spectroscopy of capped, gas-phase Aib oligomers: tests of the Aib residue as a 3-helix former.

Aminoisobutyric acid (Aib) oligomers are known to form racemic mixtures of enantiomeric left- and right-handed structures. The introduction of a chiral cap converts the enantiomeric structures into diastereomers that, in principle, afford spectroscopic differentiation. Here, we screen different C-terminal caps based on a model Aib dipeptide using double resonance laser spectroscopy in the gas phase to record IR and UV spectra of individual conformations present in the supersonic expansion: NH-benzyl (NHBn) as a reference structure because of its common use as a fluorophore in similar studies, NH- p-fluorobenzyl (NHBn-F), and α-methylbenzylamine (AMBA). For both the NHBn and NHBn-F caps, a single conformer is observed, with infrared spectra assignable to an enantiomeric pair of type II/II' β-turns in these molecules lacking a chiral center. The higher oscillator strength of the NHBn-F cap enabled UV-UV hole burning, not readily accomplished with the NHBn cap. The AMBA-capped structure, with its chiral center, produced two unique conformers, one of which was a nearly identical left-handed type II β-turn, while the minor conformer is assigned to a C7-C7 sequential double ring, which is an emergent form of a 2-ribbon. Although not observed, the type II' β-turn diastereomer, with opposite handedness, is calculated to be 11 kJ/mol higher in energy, a surprisingly large difference. This destabilization is attributed primarily to steric interference between the C-terminal acyl oxygen of the peptide and the chirality-inducing methyl of the AMBA group. Last, computational evidence indicates that the use of an N-terminal aromatic cap hinders the formation of a 3-helix in Ac-Aib dipeptides.

Single-Conformation Spectroscopy of Capped Aminoisobutyric Acid Dipeptides: The Effect of C-Terminal Cap Chromophores on Conformation.

We present a detailed study of the time-dependent photophysics and photochemistry of a known conformation of the two protonated pentapeptides Leu-enkephalin (Tyrosine-Glycine-Glycine-Phenylalanine-Leucine, YGGFL) and its chromophore-swapped analogue FGGYL, carried out under cryo-cooled conditions in the gas phase. Using ultraviolet-infrared (UV-IR) double resonance, we record excited state IR spectra as a function of time delay between UV and IR pulses. We identify unique Tyr OH stretch transitions due to the S state and the vibrationally excited triplet state(s) formed by intersystem crossing, T(v). Photofragment mass spectra are recorded out of the S origin and following UV-IR double resonance. Several competing site-specific fragmentation pathways are discovered involving peptide backbone cleavage, Tyr side chain loss, and N-terminal NH loss mediated by electron transfer. In YGGFL, IR excitation in the S state promotes electron transfer (ET) from the aromatic ring to the N-terminal R-NH group leading to loss of neutral NH. This product channel is missing in FGGYL due to the larger distance for ET from Y(4) to NH. Selective loss of the Tyr side chain occurs out of an excited state process following UV excitation and is further enhanced by IR excitation in S and T(v) states of both YGGFL and FGGYL. Finally, IR excitation in the S or T(v) states fragments the peptide backbone exclusively at amide(4), producing the b cation. We postulate that this selective fragmentation results from intersystem crossing to produce vibrationally excited triplets with enough energy to launch the proton along a proton conduit present in the known starting structure.

Article	Year
19F NMR chemical shifts induced by a helical peptide. Chembiochem : a European journal of chemical biology\| PubMed ID: 16755623	2006
FT-IR spectroscopy and density functional theory calculations of 13C isotopologues of the helical peptide Z-Aib6-OtBu. The journal of physical chemistry. B\| PubMed ID: 24328243	2014
Conformation-specific spectroscopy of capped, gas-phase Aib oligomers: tests of the Aib residue as a 3-helix former. Physical chemistry chemical physics : PCCP\| PubMed ID: 27711552	2016
Single-Conformation Spectroscopy of Capped Aminoisobutyric Acid Dipeptides: The Effect of C-Terminal Cap Chromophores on Conformation. The journal of physical chemistry. A\| PubMed ID: 30973730	2019
Site-Specific Photochemistry along a Protonated Peptide Scaffold. Journal of the American Chemical Society\| PubMed ID: 38687970	2024

Matthew A. Kubasik

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