^{1,a)}, David C. Clary

^{1}and Anthony J. H. M. Meijer

^{2,b)}

### Abstract

We present quantum dynamical calculations on the conformational changes of glycine in collisions with the He, Ne, and Ar rare-gas atoms. For two conformer interconversion processes ( and ), we find that the probability of interconversion is dependent on several factors, including the energy of the collision, the angle at which the colliding atom approaches the glycine molecule, and the strength of the glycine-atom interaction. Furthermore, we show that attractive interactions between the colliding atom and the glycine molecule catalyze conformer interconversion at low collision energies. In previous infrared spectroscopy studies of glycine trapped in rare-gas matrices and helium clusters, conformer III has been consistently observed, but conformer IV has yet to be conclusively detected. Because of the calculated thermodynamic stability of conformer IV, its elusiveness has been attributed to the conformer interconversion process. However, our calculations present little indication that interconversion occurs more readily than interconversion. Although we cannot determine whether conformer IV interconverts during experimental Ne- and Ar-matrix depositions, our evidence suggests that the conformer should be present in helium droplets. Anharmonic vibrational frequency calculations illustrate that previous efforts to detect conformer IV may have been hindered by the overlap of its IR-absorption bands with those of other conformers. We propose that the redshifted symmetric stretch of conformer IV provides a means for its conclusive experimental detection.

Two of the authors (T.F.M. and D.C.C.) acknowledge fellowships from the National Science Foundation and the Leverhulme Trust, respectively. Another author (A.J.H.M.M.) acknowledges funding from the University of Sheffield. The authors thank Dr. Pierre Çarçabal for his helpful comments.

I. INTRODUCTION

II. THEORY

III. COMPUTATIONAL DETAILS

A. Torsional potential and eigenstates

B. Definition of conformer population

C. Interaction potential

D. Wave-packet calculations

E. Infrared spectrum calculations

IV. RESULTS AND DISCUSSION

A. Scattering calculation results

B. Conformer interconversion mechanisms

C. Detection of conformer IV

V. CONCLUSIONS

### Key Topics

- Infrared spectra
- 19.0
- Absorption spectra
- 8.0
- Vibrational states
- 7.0
- Conformational dynamics
- 6.0
- Fluid drops
- 6.0

## Figures

The conformers of glycine. (a) Conformer populations at determined from neon-matrix infrared spectroscopy (see Ref. 22). (b) Conformer IV not observed experimentally.

The conformers of glycine. (a) Conformer populations at determined from neon-matrix infrared spectroscopy (see Ref. 22). (b) Conformer IV not observed experimentally.

Schematic illustration of conformer interconversion. The upper panel shows a typical experimental setup in which molecules are heated in an oven prior to free-jet expansion and spectroscopic analysis. The lower panel shows the corresponding distribution of conformers. During expansion, the distribution will either experience vertical collapse, preserving the population of high-energy conformers, or it will experience conformer interconversion and exhibit “missing” conformers.

Schematic illustration of conformer interconversion. The upper panel shows a typical experimental setup in which molecules are heated in an oven prior to free-jet expansion and spectroscopic analysis. The lower panel shows the corresponding distribution of conformers. During expansion, the distribution will either experience vertical collapse, preserving the population of high-energy conformers, or it will experience conformer interconversion and exhibit “missing” conformers.

Arrows indicate the two interconversion processes considered in this study. The torsional angles correspond to intramolecular rotation about the C–C bond, C–O single bond, and C–N bond, respectively. Energies determined by single-point calculations at -optimized geometries.

Arrows indicate the two interconversion processes considered in this study. The torsional angles correspond to intramolecular rotation about the C–C bond, C–O single bond, and C–N bond, respectively. Energies determined by single-point calculations at -optimized geometries.

Potential surfaces and vibrational eigenfunctions for the C–C torsion (left panel) and the C–N torsion (right panel). Eigenfunctions plotted in red ( and in the left panel and in the right panel) have nonzero amplitude corresponding to both conformers.

Potential surfaces and vibrational eigenfunctions for the C–C torsion (left panel) and the C–N torsion (right panel). Eigenfunctions plotted in red ( and in the left panel and in the right panel) have nonzero amplitude corresponding to both conformers.

Angle-averaged total interconversion probabilities calculated for the (a) and (b) processes as a function of collision energy. Results shown for collisions involving the He, Ne, and Ar rare-gas atoms. The vertical line indicates the energy of the torsional barrier to interconversion.

Angle-averaged total interconversion probabilities calculated for the (a) and (b) processes as a function of collision energy. Results shown for collisions involving the He, Ne, and Ar rare-gas atoms. The vertical line indicates the energy of the torsional barrier to interconversion.

Angle-averaged direct interconversion probabilities calculated for the (a) and (b) processes as a function of collision energy. Results shown for collisions involving the He, Ne, and Ar rare-gas atoms. The vertical line indicates the energy of the torsional barrier to interconversion.

Angle-averaged direct interconversion probabilities calculated for the (a) and (b) processes as a function of collision energy. Results shown for collisions involving the He, Ne, and Ar rare-gas atoms. The vertical line indicates the energy of the torsional barrier to interconversion.

Angle-dependent total interconversion probabilities for Ne-glycine collisions at energy (a) and (b) . Results for the process are in the left column; results for the process are in the right column. The molecular diagrams illustrate collision angles corresponding to large interconversion probability. Part (c) presents the calculated collision times for the two interconversion processes.

Angle-dependent total interconversion probabilities for Ne-glycine collisions at energy (a) and (b) . Results for the process are in the left column; results for the process are in the right column. The molecular diagrams illustrate collision angles corresponding to large interconversion probability. Part (c) presents the calculated collision times for the two interconversion processes.

Angle-averaged total interconversion probabilities calculated for the process as a function of energy. In (a), the colliding atom mass is set to that of He for all three interaction potentials. In (b), the colliding atom mass is set to that of Ne for all three interaction potentials. The agreement between the two plots indicates that the interconversion probability is more sensitive to the interaction potential than the mass of the colliding atom.

Angle-averaged total interconversion probabilities calculated for the process as a function of energy. In (a), the colliding atom mass is set to that of He for all three interaction potentials. In (b), the colliding atom mass is set to that of Ne for all three interaction potentials. The agreement between the two plots indicates that the interconversion probability is more sensitive to the interaction potential than the mass of the colliding atom.

The sum of the C–C torsional potential and the glycine-Ar interaction potential at various fixed values of the collision distance . The barrier to conformer interconversion lowers as the Ar atom approaches. The collision angle used in this figure is .

The sum of the C–C torsional potential and the glycine-Ar interaction potential at various fixed values of the collision distance . The barrier to conformer interconversion lowers as the Ar atom approaches. The collision angle used in this figure is .

[(a) and (b)] The barrier to interconversion as a function of the collision distance . (c) The barrier to interconversion as a function of the collision distance . The collision angle used for each plot is specified. The Ne and Ar colliding atoms give rise to a substantial barrier-lowering effect; the He colliding atom does not.

[(a) and (b)] The barrier to interconversion as a function of the collision distance . (c) The barrier to interconversion as a function of the collision distance . The collision angle used for each plot is specified. The Ne and Ar colliding atoms give rise to a substantial barrier-lowering effect; the He colliding atom does not.

Infrared-absorption spectra calculated for the distribution of glycine conformers at without interconversion of conformer IV (top) and with interconversion of conformer IV (middle). The bottom curve shows the difference between these two spectra. The conformer IV symmetric stretch at is well separated from other absorptions.

Infrared-absorption spectra calculated for the distribution of glycine conformers at without interconversion of conformer IV (top) and with interconversion of conformer IV (middle). The bottom curve shows the difference between these two spectra. The conformer IV symmetric stretch at is well separated from other absorptions.

## Tables

Comparison of the experimental^{a} and calculated^{b} conformer populations (%) of glycine^{c}.

Comparison of the experimental^{a} and calculated^{b} conformer populations (%) of glycine^{c}.

Fitting parameter for the 1D torsional potentials in Eq. (8).

Fitting parameter for the 1D torsional potentials in Eq. (8).

Parameters used for Ne-glycine and Ar-glycine interaction potentials [Eq. (15)].

Parameters used for Ne-glycine and Ar-glycine interaction potentials [Eq. (15)].

Various parameters for the wave-packet calculations. All values are in a.u. Value is the value for the calculations involving rare-gas atom .

Various parameters for the wave-packet calculations. All values are in a.u. Value is the value for the calculations involving rare-gas atom .

Article metrics loading...

Full text loading...

Commenting has been disabled for this content