The Resonance Raman Spectrum of Cytosine in Water: Analysis of the Effect of Specific Solute–Solvent Interactions and Non-Adiabatic Couplings
, Javier Cerezo 3,4, Roberto Improta 5,* and Fabrizio Santoro 3,*
Round 1
Reviewer 1 Report
The work under review is devoted to a computer study of vibrational resonance spectra of Raman scattering in a wide range of excitation frequencies for cytosine in water. The calculations are based on potential energy surfaces obtained using time-dependent density functional theory (TD-DFT). The Gaussian16 software package with two different functionals CAM-B3LYP and PBE0 was used in combination with the 6-311G+(d,p) basis set. Vibronic computations neglecting inter-state couplings and exploiting analytical time-correlation functions were performed by the original FCclasses 3.0 code. The topic of studying the interactions of excited states is relevant for the quantum chemistry of molecules and may be of interest to a limited circle of readers. The article can be published in the journal Molecule, but requires minor revision.
1. When describing the methodology, the authors refer to their works [23, 25, 27]. However, a few words about the CAM-B3LYP functionality should be mentioned and referenced. This is important because a comparative conclusion is made about the results of applying the functionals. The symbol K in formula (5), (8) has a different meaning. It is necessary to explain.
2. In fig. 1 has (a) and (b), but no explanation.
3. In the text or Supporting Information, it was possible to provide information about the geometric parameters of the molecular structures used. The symmetry group of these structures is not given, and the irreducible representations are present in Table 1.
4. The conclusion is too cumbersome. Part of the material can be moved to the discussion section.
5. The expediency of drawing figures 7, 8 is not obvious. They are referenced in Section 3.3, but they are not discussed themselves.
Author Response
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Author Response File: 
Author Response.pdf
Reviewer 2 Report
The paper "The Resonance Raman Spectrum of Cytosine in Water: Analysis of the Effect of Specific Solute-Solvent Interactions and Nonadiabatic Couplings" is devoted to the computational study of the vibrational resonance Raman spectra of cytosine in water, which used PBE0 and CAM-B3LYP methods. In addition, solvent effect was considered implicitly using PCM and explicitly adding six water molecules to cytosine. Several excited states were identified and took under consideration to investigate their coupling and interference effects. Interference and nonadiabatic effects are reported to have relatively small effect, while the resonance with the first bright state contributes mainly into vibrational resonance Raman bands at excitation wavelength for the range of 244 to 290 nm (save for 244 nm, where another bright state also contributes). Authors were able to describe the experimental Raman spectra by the theoretical ones with a good fitting quality, which improved additionally in the case of explicit account of solvent molecules. The paper sheds new light on the behavior of one of the nucleotides in aqueous solution and provides a lot of novel information about its vibrational spectra. The results of the contribution can be further used by spectroscopists to study oligonucleotides and DNA molecules in aqueous solution.
The only unclear moment for me in this manuscript is the initial configuration of solvate complex with six water molecules. As it was shown in papers (10.1007/s11426-010-0065-4, 10.1021/ja062842p), even simples H-bonded complex of glycine with one water molecules produes dozens of conformers differing by geometry and energy (and spectra as well). Had Authors performed such an analysis for their complex of cytosine with 6 water molecules? What was the base to prefer the chosen complex over all other possibilities?
The similarity between experimental spectrum (purple curve) and the calculated one (6 water molecules, orange curve) on Fig. 2, top, seem startling as real solution contains far more molecules of water than a model. Does not it matter at all?
Summarizing, this is an excellent manuscrpt, which I gladly recommend to publish.
Author Response
please check attached file
Author Response File: Author Response.pdf
