R. J. Lavrich

Experimental studies of peptide bonds: Identification of the C7eq conformation of the alanine dipeptide analog N-acetyl-alanine N′-methylamide from torsion-rotation interactions

Rotational spectra of the biomimetic molecule, alanine dipeptide and the double 15N(15N2) isotopomer have been observed using a pulsed-molecular-beam Fourier transform microwave spectrometer. The spectra reveal tunneling splittings from the torsional mode structure of two of its three methyl rotors. The torsional states assigned include one AA-state and two AE-states (i.e., AE and EA) for each isotopomer. The AA-states are well-fit to A-reduction asymmetricrotor Hamiltonians. The “infinite-barrier-limit” rotational constants of the 14N2 isotopomer are A=1710.97(8)u2009MHz, B=991.89(9)u2009MHz, and C=716.12(6)u2009MHz. The AE-states are analyzed independently using “high-barrier” torsion-rotation Hamiltonians, yielding observedminus-calculated standard deviations of 100-fold for the 15N2 isotopomer) when analyzed in a ρ-axis frame where ρb=ρc=0. The best-fit torsion-rotation parameters provide accurate V3 barriers and C3 rotor axis angles for both methyl groups. The observed ...

Conformational analysis of the jet-cooled peptide mimetic ethylacetamidoacetate from torsion-rotation spectra

Rotational spectra of two conformers of the peptide mimetic, ethyl-acetamidoacetate, were measured in a molecular beam using a Fourier-transform microwave spectrometer. In each conformer, internal rotation of the acetyl methyl group gives rise to observable splittings in the spectrum. From analysis of the torsion-rotation interactions, the methyl group’s orientation has been determined in the principal axis frame of each conformer and is shown to unambiguously identify its conformational form. One conformer exists in the all-trans configuration and belongs to CS point group and the second, higher-energy conformer has C1 symmetry. Two separate theoretical fitting procedures are applied to assess the reliability of the structural information and are shown to be essentially equivalent. For example, methyl torsional barriers are 63.7(1) cm−1 versus 67.1(1) cm−1 and 64.8(1) cm−1 versus 67.5(1) cm−1 for the CS and C1 conformers, respectively, and principal axis orientations of the methyl groups agree to ±0.1°. ...

The microwave spectrum of a two-top peptide mimetic: The N-acetyl alanine methyl ester molecule

The rotational spectrum of N-acetyl alanine methyl ester, a derivative of the biomimetic, N-acetyl alanine N-methyl amide or alanine dipeptide, has been measured using a mini Fourier transform spectrometer between 9 and 25 GHz as part of a project undertaken to determine the conformational structures of various peptide mimetics from the torsion-rotation parameters of low-barrier methyl tops. Torsion-rotation splittings from two of the three methyl tops capping the acetyl end of the -NH-C(=O)- and the methoxy end of -C(=O)-O- groups account for most of the observed lines. In addition to the AA state, two E states have been assigned and include an AE state having a torsional barrier of 396.45(7) cm(-1) (methoxy rotor) and an EA state having a barrier of 64.96(4) cm(-1) (acetyl rotor). The observed torsional barriers and rotational constants of alanine dipeptide and its methyl ester are compared with predictions from Möller-Plesset second-order perturbation theory (MP2) and density functional theory (DFT) in an effort to explore systematic errors at the two levels of theory. After accounting for zero-point energy differences, the torsional barriers at the MP2/cc-pVTZ level are in excellent agreement with experiment for the acetyl and methoxy groups while DFT predictions range from 8% to 80% too high or low. DFT is found to consistently overestimate the overall molecular size while MP2 methods give structures that are undersized. Structural discrepancies of similar magnitude are evident in previous DFT results of crystalline peptides.

High Resolution Spectroscopic Studies of 1-(1-naphthyl)ethylamine in S0 and S1: Exploring the Dependence of Circular Dichroism on Conformational Structure

Abstract Rotationally resolved spectra of gas-phase samples of 1-(1-naphthyl)-ethylamine (NEA) and amine deuterated forms have been obtained in the microwave and ultraviolet regions, with the isotopomers initially prepared in their zero-point vibrational levels by cooling in pulsed jet and molecular beam supersonic expansions. A single parameter set that includes inertial parameters and 14 N nuclear quadrupole constants has accounted for nearly all transitions observed in the Fourier-transform microwave spectrum at 2 K and indicates the presence of only one geometrical isomer in the jet-cooled expansion. The rotational constants, dipole moment orientation, and the amine hydrogen atom positions have been used to identify the conformation of the attached chiral group from among nine possible isomeric forms. The S 1 rotational constants and electronic transition moment orientation have been obtained from high resolution molecular beam data of the band origin at 31771.56(2) cm −1 . Excited state “gas phase” predictions from ab initio theory at the CIS/6-31G(d,p) and CIS/6-311xa0+xa0G(d) levels are compared with the observed S 1 results and with circular dichroism (CD) data obtained for solution phase samples of ( S )-NEA in cyclohexane. Distinguishing spectral features are found in the calculated CD spectra of the three lowest energy conformers arising from rotation about the C–CH(NH 2 )CH 3 bond, all of which are thermally populated at room temperature. While the predictions at both levels are in fair agreement with the observed gas phase results, CIS/6-31G(d,p) theory is found to be inadequate to model the condensed phase CD spectrum. In constrast, the calculated spectrum of the equilibrium mixture of conformers at the CIS/6-311xa0+xa0G(d) level is in good qualitative agreement with the observed CD results and indicates the importance of diffuse functions for the accurate prediction of chiroptical properties of NEA. The most noteworthy exception is the predicted rotatory strength of the S 1 origin, which is overestimated by more than 10-fold. Possible reasons for this discrepancy with experiment include a reversal of S 1 (L b ) and S 2 (L a ) states from the absence of electron correlation and/or the neglect of room-temperature solvent effects. These results provide for rigorous benchmark tests of theoretical models and further elucidate the importance of the conformational structure for determinations of absolute stereochemistry from CD spectra.

Continuous-Wave Terahertz Spectroscopy of Plasmas and Biomolecules

Continuous-wave linear-absorption spectroscopy based on THz radiation generated by solid-state photomixers has been applied to the investigation of the dynamics of biomolecules in polyethylene matrices and to line shape studies of HF for diagnostics of semiconductor etching plasmas. The THz spectra of biotin and myoglobin have been obtained using a variable-temperature, cryogenic sampling system. The spectrum of biotin displays a small number of discrete absorptions over the temperature range from 4.2 K to room temperature while the spectrum of myoglobin has no obvious resonance structure at the >10% fractional absorption level. Spectral predictions from the lowest energy ab initio conformations of biotin are in poor agreement with experiment, suggesting the need to include condensed-phase environmental interactions for qualitative predictions of the THz spectrum. Vibrational anharmonicity is used to model the line shapes that result from drastic changes in vibrational sequence level populations of biotin over this temperature range. Anharmonicity factors (χeωe/ωe) at the levels of 0.1% to 0.8% are obtained from non-linear least squares fits of the observed resonances and illustrate their important for refining model predictions. Application of the photomixer system to line shape studies in etching plasmas has been used to study the formation efficiency and translational temperature of HF at 1.2 THz under different operating conditions. These results will aid in understanding the chemistry of industry-standard fluorocarbon and oxygenated fluorocarbon etching plasmas.