Effect of solvation on the ionization of guanine nucleotide: A hybrid QM/EFP study

Abstract

Ionization of nucleobases is affected by their biological environment, which includes both the effect of adjacent nucleotides as well as the presence of water around it. Guanine and its nucleotide have the lowest ionization potentials among the various DNA bases. Therefore, the threshold of ionization is dependent on that of guanine and its characterization is crucial to the prediction of interaction of light with DNA. We investigate the effect of solvation on the vertical ionization energies (VIEs) of guanine and its nucleotide. In this work, we have used hybrid quantum mechanics/molecular mechanics (QM/MM) approach with effective fragment potential as the MM method of choice and equation-of-motion coupled-cluster for ionization potential with singles and doubles (EOM-IP-CCSD) as the QM method. The performance of the hybrid scheme with respect to the full QM method shows an accuracy of ≤ 0.02-0.04 eV. The lowest few ionizations of the nucleotide are found to be from different parts of the moiety, that is, the nucleic acid base, phosphate, or sugar, and these ionization energies are very closely spaced giving rise to a very complicated spectrum. Furthermore, microsolvation has large effects on these ionizations and can lead to red or blue shift depending on the position of the water molecule. Even a single water molecule can change the order of ionized states in the nucleotide. The VIEs of the bulk solvated chromophores are predicted and compared to existing experimental spectra. The predominant role of polarization in the solvatochromic shift is noticed. © 2017 Wiley Periodicals, Inc.

Ask Not How Many, But Where They Are: Substituents Control Energetic Ordering of Frontier Orbitals/Electronic Structures in Isomeric Methoxy-Substituted Dibenzochrysenes

“…28,29 Accordingly, in this manuscript, we performed electronic structure calculations of neutral DBCs and their cation radicals using B1LYP-40/6-31G(d) level of theory. Due to the important role of the solvation in stabilization of charged molecules and the effect on the nature of the excited states, 21,30,31 we also performed (vide inf ra) a comparative analysis of the electronic structure of DBC cation radicals in solvents with varied polarity using polarizable continuum model (PCM) .…”

Efficient treatment of molecular excitations in the liquid phase environment via stochastic many-body theory

“…Phenol in water is a ubiquitous motif in biological chromophores, and hence this system has attracted interest in the past. 6,35 Thymine and phenylalanine are studied in the context of DNA molecules 2,34,39,78,79 and amino acids. 40,41,[80][81][82] While phenol is the simplest and represents a "rigid" system (only a hydroxyl group is attached to the benzene ring), thymine has a methyl group attached to the ring, which can freely rotate.…”

“…Embedding of the density functional theory (DFT) [26][27][28][29][30] is computationally inexpensive and yields eigenvalues corresponding to valence states, but these levels fundamentally do not correspond to QP energies and also contain no information about excited-state lifetimes. 31 The state-of-the-art quantum chemistry approaches, e.g., CCSD(T) 32,33 and EOM-CC [34][35][36][37][38][39][40][41] provide accurate predictions for IP and EA. However, they do a) Electronic mail: vlcek@ucsb.edu not capture QP lifetimes either and suffer from a high computational cost.…”

Appraisal of dispersion damping functions for the effective fragment potential method

“…The effective fragment potential (EFP) method is a widely used polarizable force field that is obtained by automated parameterization of a physicallymotivated functional form, based on ab initio quantum chemistry. [1][2][3][4] It has been used in hybrid quantum mechanics/molecular mechanics (QM/MM) calculations, both in the ground state [5][6][7][8][9][10][11] and for vertical excitation spectra. [12][13][14][15][16] Motivated by the success of empirical dispersion potentials in density functional theory (DFT), 17,18 another potential application of EFP is to use its dispersion component as a parameter-free correction for DFT or even Hartree-Fock (HF) theory.…”