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Issue 42, 2010
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Study of the optical and magnetic properties of pyrimidine in water combining PCM and QM/MM methodologies

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Abstract

The solvent effects on the low-lying absorption spectrum and on the 15N chemical shielding of pyrimidine in water are calculated using the combined and sequential Monte Carlo simulation and quantum mechanical calculations. Special attention is devoted to the solute polarization. This is included by an iterative procedure previously developed where the solute is electrostatically equilibrated with the solvent. In addition, we verify the simple yet unexplored alternative of combining the polarizable continuum model (PCM) and the hybrid QM/MM method. We use PCM to obtain the average solute polarization and include this in the MM part of the sequential QM/MM methodology, PCM-MM/QM. These procedures are compared and further used in the discrete and the explicit solvent models. The use of the PCM polarization implemented in the MM part seems to generate a very good description of the average solute polarization leading to very good results for the n–π* excitation energy and the 15N nuclear chemical shield of pyrimidine in aqueous environment. The best results obtained here using the solute pyrimidine surrounded by 28 explicit water molecules embedded in the electrostatic field of the remaining 472 molecules give the statistically converged values for the low lying n–π* absorption transition in water of 36 900 ± 100 (PCM polarization) and 36 950 ± 100 cm−1 (iterative polarization), in excellent agreement among one another and with the experimental value observed with a band maximum at 36 900 cm−1. For the nuclear shielding 15N the corresponding gas–water chemical shift obtained using the solute pyrimidine surrounded by 9 explicit water molecules embedded in the electrostatic field of the remaining 491 molecules give the statistically converged values of 24.4 ± 0.8 and 28.5 ± 0.8 ppm, compared with the inferred experimental value of 19 ± 2 ppm. Considering the simplicity of the PCM over the iterative polarization this is an important aspect and the computational savings point to the possibility of dealing with larger solute molecules. This PCM-MM/QM approach reconciles the simplicity of the PCM model with the reliability of the combined QM/MM approaches.

Graphical abstract: Study of the optical and magnetic properties of pyrimidine in water combining PCM and QM/MM methodologies

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Publication details

The article was received on 04 Apr 2010, accepted on 17 Aug 2010 and first published on 20 Sep 2010


Article type: Paper
DOI: 10.1039/C0CP00122H
Citation: Phys. Chem. Chem. Phys., 2010,12, 14023-14033

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    Study of the optical and magnetic properties of pyrimidine in water combining PCM and QM/MM methodologies

    V. Manzoni, M. L. Lyra, R. M. Gester, K. Coutinho and S. Canuto, Phys. Chem. Chem. Phys., 2010, 12, 14023
    DOI: 10.1039/C0CP00122H

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