214. Structure of benzene. Part IV. Infra-red absorption spectra of benzene and hexadeuterobenzene both as vapour and as liquid

In this paper we present the first investigations on an isolated linear depsipetide CyCO-Gly-Lac-NH-PhOMe (cyclohexylcarbonyl-glycine-lactate-2-anisidine abbreviated as MOC) in a molecular beam experiment. Depsipeptides are a special subclass of peptides which contain at least one ester bond replacing a peptide bond. This leads to a different folding behavior and a different biological activity compared to a "normal" peptide. In order to analyze the folding of an isolated depsipeptide on a molecular level a variety of combined IR/UV methods including IR/IR/UV experiments are applied to MOC. Three different isomers are identified in combination with DFT calculations using the hybrid functional B3LYP-D3 with a TZVP basis set. The most stable structure shows a tweezer-like arrangement between the aromatic chromophore and the aliphatic cyclohexyl ring. A characteristic feature of this structure is that it is stabilized by dispersion interactions resulting from CH/π interactions. If dispersion is not taken into account this structural arrangement is no longer a minimum on the potential energy surface indicating the importance of dispersion interactions.

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“…see ref. 75-78, spectroscopically observed bands above 1800 cm À1 have already been discussed. For benzene a band at 1808 cm À1 was obtained.…”

Section: Resultsmentioning

confidence: 90%

“…For benzene a band at 1808 cm À1 was obtained. 75 Further experiments with different ortho-substituted benzene derivatives revealed vibrations in the region of 1810 to 1870 cm À1 . 77 All these bands were assigned to combination bands arising from the out-of-plane CH deformation fundamentals (of the aromatic ring).…”

Section: Resultsmentioning

confidence: 98%

Structural investigations on a linear isolated depsipeptide: the importance of dispersion interactions

Stamm

Bernhard

Gerhards

2016

Phys. Chem. Chem. Phys.

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“…This is neither found with Voronoi dipole moments nor is there a corresponding peak in the experimental data. 68,69 The reason for that is the symmetry breaking by the Wannier functions. The localization produces alternating single and double bonds in the ring (see Fig.…”

Section: Resultsmentioning

confidence: 99%

Voronoi dipole moments for the simulation of bulk phase vibrational spectra

Thomas

Brehm

Kirchner

2015

Phys. Chem. Chem. Phys.

110

174

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We present the Voronoi tessellation of electron density data to obtain molecular dipole moments in bulk phase ab initio molecular dynamics simulations for the calculation of vibrational spectra. Opposed to the established scheme of maximally localized Wannier functions, this approach does not rely on computationally demanding localization procedures. Nevertheless, we show at the examples of methanol, benzene, and phenol that it provides infrared and Raman spectra of similar quality and is even superior in specific cases like the Raman spectra of benzene and phenol. We have also applied the Voronoi method to a mixture of the ionic liquid 1-ethyl-3-methylimidazolium acetate with water, and show that it is advantageous in systems with significant charge transfer.

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“…This result is consistent with the prediction of Herzfeld et althat the frequency difference between the two ν 14 modes of C 6 H 6 and C 6 D 6 should be small, because they both arise from the stretching vibration of benzene's skeleton carbons 34 . In fact, a weak sharp band was observed at 1393 cm −1 in the IR spectrum of liquid C 6 D 6 as early as 1936 by Bailey et al 61 ., and a sharp band with medium intensity at 1390 cm −1 was also observed in Miller's experimental IR spectrum of liquid C 6 D 6 62 . Miller, however, attempted to assign this band to one of the two combination bands ν 6 + ν 18 and ν 4 + ν 17 .…”

Section: Experimental Infrared Spectrum Reassignment Of Crystalline Bmentioning

confidence: 95%

Intrinsic molecular vibration and rigorous vibrational assignment of benzene by first-principles molecular dynamics

Wang

2020

Sci Rep

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Vibrational assignment, which establishes the correspondence between vibrational modes and spectral frequencies, is a key step in any spectroscopic study. Due to the lack of experimental technique to directly observe the thermal vibration of atoms, the assignment is usually done by empirical trial-and-error method with considerable uncertainty. Here we demonstrate a successful study of intrinsic molecular vibration property based on first-principles molecular dynamics trajectory. A unified approach for calculating and assigning vibrational frequencies is developed and applied to solve some historical issues of benzene vibration. As a major achievement, the experimental frequencies of benzene a2g and b2u vibrations are reassigned, which breaks a deadlock in contemporary spectroscopic science and removes a cloud over the application of density-functional theory in organic chemistry. This work paves the way for the comprehensive realization of the first-principles spectroscopic research, and provides crucial clues to solve the century-old problems of Kekule resonance, π-deformation, and aromaticity.

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214. Structure of benzene. Part IV. Infra-red absorption spectra of benzene and hexadeuterobenzene both as vapour and as liquid

Cited by 23 publications

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Structural investigations on a linear isolated depsipeptide: the importance of dispersion interactions

Structural investigations on a linear isolated depsipeptide: the importance of dispersion interactions

Voronoi dipole moments for the simulation of bulk phase vibrational spectra

Intrinsic molecular vibration and rigorous vibrational assignment of benzene by first-principles molecular dynamics

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