Vibrational analysis beyond the harmonicity from Ab initio molecular dynamics: Case of cytosine in its anhydrous and aqueous forms

Abstract

This study provides the set of theoretical anharmonic fundamental transitions for cytosine in its anhydrous and hydrated forms from a vibrational analysis issuing from a time-dependent approach. This evaluation is compared to the time-independent VPT2 approach and to the experimental data available in the literature for the two forms. To investigate the vibrational property of a solute in a polar protic solvent, that is, the aqueous form of cytosine in this particular case, a practicable computational strategy to properly take into account the solvent effect is proposed. This is done by considering a combination of polarizable continuum model and of discrete solvent molecules model. The number of solvent molecules was chosen in such a way that the solute-solvent complex presents only one dominant stable conformer at 298 K. The quality of this combined solvent model is illustrated by comparing the structural and anharmonic vibrational properties achieved with those obtained from a purely implicit and purely explicit solvent model. Structural optimizations, harmonic frequencies, and anharmonic frequencies issuing from the VPT2 evaluation [33] were performed with the Gaussian09 program [34]. Electronic structure calculations were performed at the DFT level using CARBONNIERE ET AL.

The water molecule arrangement over the side chain of some aliphatic amino acids: A quantum chemical and bottom‐up investigation

“…The presently used computational methodologies based on clusters of water molecules to study the structure and properties of aqueous solutions of biomolecules is a fairly consolidated procedure …”

Vibrational Fingerprints of Low-Lying PtnP2n (n = 1–5) Cluster Structures from Global Optimization Based on Density Functional Theory Potential Energy Surfaces

“…The GSAM code has been applied successfully for the structural investigation of binary clusters such as gallium arsenide (Ga n As m , 5 < n + m < 8) 42 , tin telluride (Sn n Te n , n = 2−8) 43 and aluminum-based clusters 44,45 (Si n−1 Al, n = 3−10 and Al n L n with L = H or Cl and n = 4−7) and for the investigation of the vibrational fingerprints of molecular clusters such as microhydrated cytosine (C,nH 2 O, n = 1−5) 46 and microhydrated sodium nitrate ((NaNO 3 ,nH 2 O) x , n = 1-3, x = 1-3) 47 .…”

Vibrational mode assignment of finite temperature infrared spectra using the AMOEBA polarizable force field

“…Most of the time, detailed interpretation of such experiments involves theoretical calculations. [16][17][18][19][20][21][22] We have recently proposed the extension of the polarizable AMOEBA force field [23][24][25] to infrared spectroscopy of gas phase peptide models. The main drawback of this approach is the use of scaling factors to compensate for anharmonicity and the fact that calculations are restricted to 0 K, even though temperature effects are known to be significant.…”