Bond-stretching vibrations

In an atomic level simulation, the bond stretch vibrations are usually the fastest motions in the molecular dynamics of biomolecules, so the evolution of the stretch vibration is taken as the reference propagator with the smallest time step. The nonbonded interactions, including van der Waals and electrostatic forces, are the slowest varying interactions, and a much larger time-step may be used. The bending, torsion and hydrogen-bonding forces are treated as intermediate time-scale interactions. 

When the above analysis is applied to a diatomic species such as HCl, only k = 0 is present since the only vibration present in such a molecule is the bond stretching vibration, which has a symmetry. Moreover, the rotational functions are spherical harmonics (which can be viewed as D l, m, K (Q,< >,X) functions with K = 0), so the K and K quantum numbers are identically zero. As a result, the product of 3-j symbols... 

A number of hydrocarbon radicals having multiple bonds at the radical centre have also been trapped in inert matrices and studied by IR spectroscopy. Thus, ethynyl radical was obtained by vacuum UV photolysis (9) of matrix-isolated acetylene (Shepherd and Graham, 1987) as well as when acetylene and argon atoms excited in a microwave discharge were codeposited at 12 K (Jacox and Olson, 1987). An appearance of diacetylene bands was observed when the matrices were warmed up, while the absorptions of the radical C2H disappeared. Detailed isotopic studies of D-and C-labelled ethynyl radicals showed a surprisingly low frequency of the C=C bond stretching vibration at 1846 cm instead of c.2100cm for a true C=C triple bond (the band at 2104 cm was attributed to the... 

The driving force for the temperature-dependent spin crossover (SCO) is the entropy difference between the HS and the LS isomers which arises mainly from a shift of the vibrational frequencies when passing from the HS to the LS state [97-99]. This frequency shift has been studied by IR- and Raman-spectroscopy and recently also by NIS [23, 39, 87]. The NIS method is isotope ( Fe) selective and, therefore, its focus is on iron-ligand bond-stretching vibrations which exhibit the most prominent contribution to the frequency shift upon SCO [87]. 

The analysis of relations between intensities in the region of double bond stretching vibrations >c=n in the Raman spectra, allows one to arrive at a conclusion about s-cis- or s-trans -conformation of multiple bonds. The ratio between intensities of the high-frequency band to the low-frequency one for s-trans -conformers appears usually to be more than 0.5, whereas for s-cis -conformers it is less than 0.25 (393, 394). 

The enzymatic reaction was performed at 30 °C for 2 hours in a volume of 1 ml of 250 mM phosphate buffer (pH 6.5) containing 50 mM of KOH, 32 U/ml of the enzyme, and [1- C]-substrate. The product was isolated as the methyl ester. When the (S)-enantiomer was employed as the substrate, C remained completely in the product, as confirmed by C NMR and HRMS. In addition, spin-spin coupling between and was observed in the product, and the frequency of the C-O bond-stretching vibration was down-shifted to 1690 cm" (cf. 1740 cm for C-O). On the contrary, reaction of the (R)-enantiomer resulted in the formation of (R)-monoacid containing C only within natural abundance. These results clearly indicate that the pro-R carboxyl group of malonic acid is ehminated to form (R)-phenylpropionate with inversion of configuration [28]. This is in sharp contrast to the known decarboxylation reaction by malonyl CoA decarboxylase [1] and serine hydroxymethyl transferase [2], which proceeds with retention of configuration. 

Fig. 4. Relationship between the sulfur-sulfur bond stretching vibration Vjs (in cm ) of a certain bond in homocyclic sulfur rings and the corresponding bond length djg (in pm). For equivalent bonds within a molecule (equal d j values) the V55 values were averaged to eliminate the splitting by vibrational coupling. The data were taken from the compounds indicated in the Figure...

Actually, however, at least for an isolated XH Y system, the change in length of the H-bonds occurs rhythmically with the frequency of the v(XH Y) vibration. In effect the vKK vibration is frequency modulated by the v(XB. Y) vibration. From a consideration of this more precise classical picture Batuev [29, 30] has shown that the broad band should actually consist of a series of sub-bands of frequencies rXH (XH Y). This is the frequency modulation theory of the origin of the broad vXH bands. This explanation also implies that the band should become narrow at low temperatures when the amplitude of the H-bond stretching vibration is small. 

We found that rc of the O H- - -Cl- hydrogen-bond length increases from 14 2 ps at 25 °C, to 24 5 ps at 65 °C, to 30 6 ps at 85 °C. This increase of rc can be explained within the framework of the Brownian oscillator model. The time constant rc is related to the frequency cchb of the hydrogen-bond stretch vibration via rc = t/o hr [11], with 7 the damping of the hydrogen-bond stretch vibration. An increase in temperature leads to a decrease of wI1B, and thus to an increase of rc. 

H. Hamaguchi I would like to comment on the stilbene photoisomerization in solution. We recently found an interesting linear relationship between the dephasing time of the central double-bond stretch vibration of Si franj-stilbene, which was measured by time-resolved Raman spectroscopy, and the rate of isomerization in various solutions. Although the linear relationship has not been established in an extensive range of the isomerization rate, I can point out that the vibrational dephasing time measured by Raman spectroscopy is an important source of information on the solvent-induced vibrational dynamics relevant to the reaction dynamics in solution. 

Alkynes and allenes. Absorptions arising from multiple bond stretching vibrations are important features in the i.r. spectra of both these types of compounds. 

Heat capacities of polyatomic molecules can be explained by the same arguments. As discussed in Chapter 3, bond-stretching vibrational frequencies can be over 100 THz. At room temperature k T heat capacity (which explains why most diatomics give cv % 5R/2, the heat capacity from translation and rotation alone). Polyatomic molecules typically have some very low-frequency vibrations, which do contribute to the heat capacity at room temperature, and some high-frequency vibrations which do not. 

Fig. 7.22. Difference IR spectrum (a) that characterizes the transformation (=Si-0)2 Si = 0 + N20- -(=Si-0)2Si<02N2 on the surface of reactive silica, and absorption bands of the first overtone of the Si = O bond stretching vibration in the (=Si-0)2Si = O group (b) with different isotopic compositions (=Si-0) 8Si = 160 (sample I), and (=Si-0) 8 Si = 160 + (=Si-0) 8Si = lsO (sample II).

Conjugated Systems The alkene bond stretching vibrations in conjugated dienes without a center of symmetry interact to produce two C=C stretching bands. The spectrum of an unsymmetrical conjugated diene, such as 1,3-pentadiene, shows absorption near... 

The VCD of helical, single and double stranded ribonucleic add (RNA) polymers was first reported by Keiderling s group in vibrations associated with double bond stretching vibrations of the bases in RNA [53]. The optical activity was found to be due to the coupling of the virtually achiral stretching vibrations which are arranged in a... 

P=0 Thomas and Chittenden (5,38 441 have carried out a thorough series of studies on the identification of organophosphorus compounds. The group frequency tables in these studies enable interpretation of many of the characteristic features in the spectra of nerve agents and related chemicals. Several structure-spectrum relationships give specific information on the molecule. One very valuable relation discovered by Thomas is the dependence of the position of the P=0 bond stretching vibration, vp=0, on the substituents on the phosphorus, represented by n constants ... 

Tertiary amines Tertiary amines do not have a NH bond, so there is no evidence for the amine group in the 3400-3250 cm-1 region. Because the CN bond-stretching vibration is difficult to assign in the fingerprint region, tertiary amines are not readily identified from their IR spectra. Chemical tests are helpful in such cases. 

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