Water spectra calculations

To elucidate the latter assertion, let us compare the water spectra, calculated in the THz region for our model and for the double-Debye representation (39). We substitute in Eq. (39) the following parameters. 

The water spectra, calculated from Eq. (54), are depicted by dash-dotted lines in Figs. 6a-d for H20 and 6c-h for D20. The principal Debye process (55) is marked in Figs. 6a,d and 6g,h by open circles. Calculation for our mixed model is depicted by thick solid lines. To emphasize the contribution to s of transverse vibrations, we show by dashed lines the permittivity components generated by the a + b + c mechanisms. Therefore, the values of s, marked by dashed curves, do not account for the s L component. 

The approaches based on explicit representations of the environment molecules include full quantum mechanical (QM) and hybrid QM/MM methods. In the former, the supramolecular system that is the object of the calculations cannot be very large for instance, it can be composed of the chromophore and a few solvent molecules ( cluster or microsolvation approach). A full QM calculation can be combined with PCM to take into account the bulk of the medium [5,13], which is also a way to test the accuracy of the PCM and of its parameterization, by comparing PCM only and PCM+microsolvation results. The full QM microsolvation approach is recommended when dealing with chromophore-environment interactions that are not easily modelled in the standard ways, such as those involving Rydberg states. An example is the simulation of the absorption spectrum of liquid water, by calculations on water clusters (all QM), clusters + PCM, and a single molecule + PCM only the cluster approach (with or without PCM) yielded results in agreement with experiment [13] (but we note that this example does not conform to the above requirement for a clear distinction between chromophore and environment). 

Fig. 3. Thioredoxin of E. coli s averaged spectrum calculated using Amber, quasi harmonic analysis. Dashed line- generalized Bom approximation, solid line- MD with explicit water.

We consider a two-fraction (mixed) model comprising the librational (LIB) and vibrational (VIB) states illustrated by Fig. 1. We shall show that consideration of the LIB and VIB states enables the calculation of the water spectrum, as well as that of ice, irrespective of the nature of these states. 

In this section we calculate the water spectrum in the range 0-1000 cm-1. This calculation is based on an analytical theory elaborated in 2005-2006 with the addition of a new criterion (38), related to the 50-cm 1 band in the low-frequency Raman spectrum. The calculation scheme was briefly described in Section II. One of our goals is to compare the spectra of liquid H20 and D20 and the relevant parameters of the model. Particularly, we consider the isotopic shift of the complex permittivity/absorption spectra and the terahertz (THz) spectra of both fluids. Additionally, in Appendix II we take into account the coupling of two modes, pertinent to elastically vibrating HB molecules. 

Figure Bl.4.9. Top rotation-tunnelling hyperfine structure in one of the flipping inodes of (020)3 near 3 THz. The small splittings seen in the Q-branch transitions are induced by the bound-free hydrogen atom tiiimelling by the water monomers. Bottom the low-frequency torsional mode structure of the water duner spectrum, includmg a detailed comparison of theoretical calculations of the dynamics with those observed experimentally [ ]. The symbols next to the arrows depict the parallel (A k= 0) versus perpendicular (A = 1) nature of the selection rules in the pseudorotation manifold.

Fig. 7.12 Experimental and calculated infrared spectra for liquid water. The black dots are the experimental values. The thick curve is the classical profile produced by the molecular dynamics simulation. The thin curve is obtained by applying quantum corrections. (Figure redrawn from Guilbt B 1991. A Molecular Dynamics Study of the Infrared Spectrum of Water. Journal of Chemical Physics 95 1543-1551.)...

On the other hand, a metastable-ion peak at m/e 88.1 (calculated, 88.0) is present in the mass spectrum of 11 (Figure 8) for the formation of m/e 129 from m/e 189, by loss of acetic acid. In the mass spectrum of the D20-exchanged analog, m/e 129 partially shifts to m/e 130 and partially stays at m/e 129. Metastable-ion peaks are also present at m/e 154.8 (calculated, 154.7) and m/e 97.3 (calculated, 97.3) for the loss of water from m/e 189 followed by the loss of ketene, to give an ion at m/e 129. Since m/e 171 from the loss of water remains at m/e 171, the loss of water must involve the hydroxyl hydrogens. Scheme 3 is an attempt to summarize this in terms of structures which are entirely... 

The case of water is particularly convenient because the required high Ka states may be detected in the solar absorption spectrum. However, it is difficult to observe the necessary high vibrational angular momentum states in molecules, which can only be probed by dispersed fluorescence or stimulated emission techniques. On the other hand, it is now possible to perform converged variational calculations on accurate potential energy surfaces, from which one could hope to verify the quantum monodromy and assess the extent to which it is disturbed by perturbations with other modes. Examples of such computed monodromy are seen for H2O in Fig. 2 and LiCN in Fig. 12. 

Applications With the current use of soft ionisation techniques in LC-MS, i.e. ESI and APCI, the application of MS/MS is almost obligatory for confirmatory purposes. However, an alternative mass-spectrometric strategy may be based on the use of oaToF-MS, which enables accurate mass determination at 5 ppm. This allows calculation of the elemental composition of an unknown analyte. In combination with retention time data, UV spectra and the isotope pattern in the mass spectrum, this should permit straightforward identification of unknown analytes. Hogenboom et al. [132] used such an approach for identification and confirmation of analytes by means of on-line SPE-LC-ESI-oaToFMS. Off-line SPE-LC-APCI-MS has been used to determine fluorescence whitening agents (FWAs) in surface waters of a Catalan industrialised area [138]. Similarly, Alonso et al. [139] used off-line SPE-LC-DAD-ISP-MS for the analysis of industrial textile waters. SPE functions here mainly as a preconcentration device. 

Fredin, L., B. Nelander, and G. Ribbegard. 1977. Infrared spectrum of the water dimer in solid nitrogen. I. Assignment and force constant calculations. J. Chem. Phys. 66,4065. 

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