I am doing drug-DNA interaction studies theoretically. I have done uv absorption job which is attached herewith. From the output I couldn't get the absorbance value directly. Someone told me by using dipole moment we can derive the absorbance value by using formula and this can be plotted by using gaussview. If you have any idea please guide me.
For optical absorption studies one has to calculate the (0,0}-element of the inverse of the dielectric response matrix for small values of q (small but non-vanishing, theoretically equal to the inverse of the wave-length of the incident light) as a function of frequency (this frequency coincides with the frequency of the incident light, which one varies in experiments); by formally expanding a relevant exponential function for q -> 0, one immediately observes how the matrix elements of the dipole-moment operator are accounted for.
Above, by the (0,0)-element of the response matrix, I mean the element corresponding to K1 = 0 and K2 = 0 of this matrix, the latter being the plane-wave matrix representation of the relevant response operator, where K2 and K2 are reciprocal lattice vectors (I am assuming the system under investigation to be periodic, or otherwise simulated as a periodic system through employing a sufficiently large super cell). For details, see the following work and the relevant references therein (here we consider only the dynamics of the electronic degrees of freedom in the system under consideration; there is also a contribution, which is additive in the adiabatic limit, due to the dynamics of the ionic degrees of freedom, which we do not consider; at relatively high frequencies, this contribution is negligible, as a consequence of the largeness of the ionic mass in comparison with the electronic mass):
http://journals.aps.org/prb/abstract/10.1103/PhysRevB.46.15812
In Fig. 4 (p. 15820) of the above paper we present reflectivity and its logarithmic derivative with respect to frequency. Absorbance is just 1 minus reflectivity.
For completeness, for a non-uniform ground states the (0,0)-element of the inverse of the dielectric response matrix is NOT equal to 1 over the (0,0)-element of the dielectric response matrix, since for non-uniform ground states the former matrix (as well as the latter matrix) is not diagonal; the off-diagonal elements of this matrix are due to the so-called Umklapp processes. Physically, due to Umklapp processes (arising from the fact that in periodic systems wave vectors in scattering processes are conserved only up to a reciprocal-lattice vector) the microscopic electric field E inside a crystal deviates from its macroscopic value, it oscillating around its macroscopic average as function of the spatial coordinate r. For these and other relevant details, see Chapter 27 (beginning on p. 533) of the book Solid State Physics, by Ashcroft & Mermin. Here, amongst others the Clausius-Mossotti relationship is introduced (Eq. (27.35)), which relates the frequency-dependent 'macroscopic' dielectric constant ε (the (0,0)-element of the plane-wave matrix representation of the dielectric operator) and the frequency-dependent 'macroscopic' polarizability α.
Mr./Mrs/Miss Swathi, GaussView is suitable for visualization of theoer IR, Raman and NMR spectra. For UV try with GaussSum: http://gausssum.sourceforge.net/
If you have access to Gaussview, you can plot your UV-vis spectra easily. Open your output file in Gaussview, then go to the results tab and click on the UV-Vis option. If you need to change anything (e.g. FWHM or wavelength/energy), right-click on the plot and select properties.
Mrs/Miss Mohammadi, with with which version of GaussView you operate? Because in my one (Att.) it has not such option (for UV-VIS in results tab.)?
Dear Bodidarka,
You are using Gauss view 3.07 so only you don't have UV-VIS. Just try to upgrade the latest version.
Mr. Swathi, can I kindly asking you to provide a 'look' of results tabs of GaussView5 (latest version) if is possible. On the web-site of the software program (http://www.gaussian.com/g_prod/gv5b.htm) similar to the previouse version/s again it has not available time-limited 'trial' version and again the complete set of options are not shown.
Dear Bojidarka,
Sorry for the late reply ...please take a look at the result tab which is attached herewith.
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