QM/MM calculation of solvent effects on absorption spectra of guanine

Abstract

Electronic spectra of guanine in the gas phase and in water were studied by quantum mechanical/molecular mechanical (QM/MM) methods. Geometries for the excited-state calculations were extracted from ground-state molecular dynamics (MD) simulations using the self-consistent-charge density functional tight binding (SCC-DFTB) method for the QM region and the TIP3P force field for the water environment. Theoretical absorption spectra were generated from excitation energies and oscillator strengths calculated for 50 to 500 MD snapshots of guanine in the gas phase (QM) and in solution (QM/MM). The excited-state calculations used time-dependent density functional theory (TDDFT) and the DFT-based multireference configuration interaction (DFT/MRCI) method of Grimme and Waletzke, in combination with two basis sets. Our investigation covered keto-N7H and keto-N9H guanine, with particular focus on solvent effects in the low-energy spectrum of the keto-N9H tautomer. When compared with the vertical excitation energies of gas-phase guanine at the optimized DFT (B3LYP/TZVP) geometry, the maxima in the computed solution spectra are shifted by several tenths of an eV. Three effects contribute: the use of SCC-DFTB-based rather than B3LYP-based geometries in the MD snapshots (red shift of ca. 0.1 eV), explicit inclusion of nuclear motion through the MD snapshots (red shift of ca. 0.1 eV), and intrinsic solvent effects (differences in the absorption maxima in the computed gas-phase and solution spectra, typically ca. 0.1-0.3 eV). A detailed analysis of the results indicates that the intrinsic solvent effects arise both from solvent-induced structural changes and from electrostatic solute-solvent interactions, the latter being dominant.

Time-resolved photoelectron imaging of the isolated deprotonated nucleotides

“…65 In the solution phase, Gua itself is rarely studied as it has poor solubility, although dGMP -has been studied in a number of experiments with transient absorption 1,16,66 and fluorescence upconversion. 14, 16, 19, 67 14, 16, 19, 64 As for gas phase Gua excited at around 4.7 eV, solvated dGMP -is observed to relax through biexponential kinetics.…”

“…16 Computational studies show that solvation dramatically blueshifts the first 1 nπ* state, to the extent where it is considered to be unlikely to have any substantial influence on the dynamics. 65 68 The dynamics then proceed purely through CIs between the 1 L a and S 0 states, although there are indications that the presence of the solvent influences which path -and ultimately which CI -is accessed to relax back to the ground electronic state. The combination of ESI and photoelectron imaging allows us, for the first time, the record the time resolved photoelectron spectrum of a Gua moiety in the gas phase (albeit in its nucleotide).…”

Assessment of a composite CC2/DFT procedure for calculating 0–0 excitation energies of organic molecules

“…In a similar vein, the use of reference data from experimental spectra measured in solution calls for a treatment of solvent effects, which makes it less straightforward to directly assess the intrinsic quality of the quantum chemical description of an excited state. In this regard, gas-phase data are preferable for benchmarking purposes, despite the many methodological possibilities [8][9][10] to model solvatochromic shifts [11][12][13][14].…”

The behavior of active diffusiophoretic suspensions: An accelerated Laplacian dynamics study

“…There are many related topics that we could have covered, but did not. As just a few examples, we mention density matrix functional theory, 402,403 solvatochromic shifts, [404][405][406][407][408] efficient ways to treat core orbitals, [409][410][411][412][413] and many-body WFT methods that use the KS-DFT reference determinant as a reference wave function. [148][149][150][151]183,[261][262][263][264][414][415][416][417] We also de-emphasized applications and validations for specific systems, for which other reviews are available.…”