Low frequency modes in molecular crystals. XIX. Methyl torsions and barriers to internal rotation of some three top molecules with <i>C</i>3 symmetry

Durig, J. R.; Craven, S. M.; Mulligan, J. H.; Hawley, C. W.; Bragin, J.

doi:10.1063/1.1679360

Cited by 28 publications

(7 citation statements)

References 25 publications

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“…A number of infrared and Raman studies on monosubstituted amides in both liquid and solid state suggested the presence of in-phase and outof phase CCH 3 and NCH 3 methyl torsions in the 6900-9000 GHz frequency range. [58][59][60][61] Fig. 4 VDOS profiles at room temperature obtained from NS experiments (black diamonds) and MD simulations (pink line) on dry NALMA.…”

Section: Resultsmentioning

confidence: 99%

Painting biological low-frequency vibrational modes from small peptides to proteins

Perticaroli

Russo

Paolantoni

et al. 2015

Phys. Chem. Chem. Phys.

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Protein low-frequency vibrational modes are an important portion of a proteins' dynamical repertoire. Yet, it is notoriously difficult to isolate specific vibrational features in the spectra of proteins. Given an appropriately chosen model peptide, and using different experimental conditions, we can simplify the system and gain useful insights into the protein vibrational properties. Combining neutron scattering, depolarized light scattering, and molecular dynamics simulations, we analyse the low frequency vibrations of biological molecules, comparing the results from a small globular protein, lysozyme, and an amphiphilic peptide, NALMA, both in solution and in powder states. Lysozyme and NALMA present similar spectral features in the frequency range between 1 and 10 THz. With the aid of MD simulations, we assign the spectral features to methyl groups' librations (1-5 THz) and hindered torsions (5-10 THz) in NALMA. Our data also show that, while proteins display boson peak vibrations in both powder and solution forms, NALMA exhibits boson peak vibrations in powder form only. This provides insight into the nature of this feature, suggesting a connection of BP collective motions to a characteristic length scale of heterogeneities present in the system. These results provide context for the use of model peptide systems to study protein dynamics; demonstrating both their utility, and the great care that has to be used in extrapolating results observed in powder to solutions.

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Section: Resultsmentioning

confidence: 99%

Painting biological low-frequency vibrational modes from small peptides to proteins

Perticaroli

Russo

Paolantoni

et al. 2015

Phys. Chem. Chem. Phys.

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“…Correspondingly, the C02 that forms inside the crystal has been observed to escape preferentially from the (102) face. In the loss of HC1 by p-aminosalicylic acid hydrochloride,82 the escape of HC1 was also found to be dependent on the crystal habit of the sample, and in the reaction between gaseous Cl2 and solid 2-methylphenol,83 6or 4-chlorinated derivatives were obtained depending on how the crystal samples had been cut.…”

Section: Some Examplesmentioning

confidence: 97%

Crystal chemistry in organic solids

Gavezzotti¹,

Simonetta²

1982

Chem. Rev.

166

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“…Calculations of rotation barrier about the central C-O bond in C3COC (Figure 1) yields a 3-fold symmetrical potential where the maxima occur when a methyl group eclipses one of the three -CH 3 groups on the quaternary C atom at a barrier of 2.9 kcal/mol. Durig et al 40 reported the barrier of 3.57 kcal/mol from the analysis of far-infrared spectra in the gas phase. This 0.7 kcal/mol difference for the barrier results in an error of 0.3 and 0.03 cal/(mol K) at 298 K for the entropy and heat capacity contribution from internal rotation, respectively.…”

Section: Entropies (S°(t)'s) and Heat Capacities (C P (T)'s) (50 E T/...mentioning

confidence: 99%

Structures, Intramolecular Rotation Barriers, and Thermochemical Properties of Methyl Ethyl, Methyl Isopropyl, and Methyl tert-Butyl Ethers and the Corresponding Radicals

Chen

Bozzelli

2003

J. Phys. Chem. A

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Structures and thermochemical properties, ∆H°f 298 , S°(T), and C p (T) (50 e T/K e 5000) of three ethers and the corresponding radicals were determined by ab initio and density functional calculations. Molecular structures and vibration frequencies were determined at the B3LYP/6-31G(d,p) and MP2/6-31G(d,p) levels, with single point calculations for the energy at the B3LYP/6-311+G(3df,2p) and MP2/6-311+G(2df,2p) levels, respectively, and with composite methods CBSQ and G3(MP2) with B3LYP/6-31G(d,p) and MP2/6-31G(d,p) optimized geometries. Enthalpies of formation (∆H°f 298 ) were determined at each calculation level using the group balance isodesmic reactions. Standard entropy, S°(T), and heat capacity, C p (T), from vibrational, translational, and external rotational contributions were calculated using the rigid-rotor-harmonic-oscillator approximation based on the vibration frequencies and structures obtained from the density functional study. Potential barriers for internal rotation were calculated at the B3LYP/6-31G(d) level, and hindered internal rotational contributions to entropy and heat capacity were calculated by summation over the energy levels obtained by direct diagonalization of the Hamiltonian matrix of hindered internal rotations. Evaluations of data from the isodesmic reactions at each calculation level results in the enthalpy of formation being -52.22 ( 0.84, -60.13 ( 0.94, and -67.78 ( 1.44 kcal/mol for methyl ethyl ether (CCOC), methyl isopropyl ether (C2COC), and methyl tert-butyl ether (C3COC), respectively. Standard enthalpies are -1.67 ( 0.98, -9.31 ( 2.18, and -7.93 ( 1.81 kcal/mol for methyl ethyl ether radicals, C • H 2 CH 2 OCH 3 (C • COC), CH 3 C • HOCH 3 (CC • OC), and CH 3 CH 2 OC • H 2 (CCOC • ), respectively. Standard enthalpies are -10.06 ( 0.85, -17.33 ( 2.38, and -16.75 ( 1.71 kcal/mol for methyl isopropyl ether radicals, C •, and (CH 3 ) 2 CHOC • H 2 (C2COC • ), respectively. Methyl tert-butyl ether radicals have enthalpies of -17.74 ( 1.13 and -24.54 ( 1.97 kcal/mol for C • H 2 (CH 3 ) 2 COCH 3 (C3 • COC) and (CH 3 ) 3 COC • H 2 (C3COC • ), respectively. Bond strengths on the ethers are in order C-H bond > C-C bond > central C-O bond > terminal C-O bond, with one exception of C-C bond energy for C2COC being slightly lower than that of the C-O bond (C2C-OC) by 0.5 kcal/mol. Thermodynamic properties of the O/C2 group and the ether gauche interaction term were determined for group additivity application. The hydrogen bond increment group values for ROCJ, RJCOC, and RCJOC were also derived.

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Low frequency modes in molecular crystals. XIX. Methyl torsions and barriers to internal rotation of some three top molecules with C3 symmetry

Cited by 28 publications

References 25 publications

Painting biological low-frequency vibrational modes from small peptides to proteins

Painting biological low-frequency vibrational modes from small peptides to proteins

Crystal chemistry in organic solids

Structures, Intramolecular Rotation Barriers, and Thermochemical Properties of Methyl Ethyl, Methyl Isopropyl, and Methyl tert-Butyl Ethers and the Corresponding Radicals

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