Vibrational Spectroscopy Through Time Averaged Fourier Transform of Autocorrelated Molecular Dynamics Data: Introducing the Free SEMISOFT Web-Platform.

Vibrational spectroscopy calculations based on classical molecular dynamics simulations are widely employed in a variety of popular fields, for instance, computational biochemistry and materials science. These calculations commonly rely on the Fourier transform of the velocity autocorrelation function. One major drawback of the method is that calculated spectra are difficult to interpret due to the large number of closely spaced signals. In this paper, we show how theory can help to overcome this issue by means of a time-average technique, and we introduce free software to perform such calculations for anyone who may take advantage of it. The studies presented here involve the classical vibrational spectra of aniline microsolvated by a water molecule and gas-phase deoxyguanosine. The software is made available in the form of a free web-platform, named SEMISOFT (http://semisoft.unimi.it/), whereby, upon upload of the classical trajectory, the user gets the corresponding time-averaged spectrum. Furthermore, since the evaluation of response functions through autocorrelated data is quite a general approach, the web-platform can be directly employed in many other research fields besides chemistry.