Effects of molecular dynamics and solvation on the electronic structure of molecular probes

Evaluation of All-Atom and Martini 3 Coarse-Grained Force Fields from the Structural Investigation of Nitroxide Spin Probes and Their Confinement in Beta-Cyclodextrin

Nitroxide radicals have found wide applications as spin labels or probes, and their guest-host interactions with cyclodextrins exhibit enhanced applications in electron spin resonance (ESR) spectroscopy and imaging due to improved biostability toward reducing agents. Although the computational prediction of the guest-host binding has become increasingly common for small ligands, molecular simulations regarding the conformational preferences of hosted spin probes have not been conducted. Here we present molecular dynamics simulations at an atomistic level for a set of four TEMPO (2,2,6,6-tetramethylpiperidine 1-oxyl) spin probes and thereafter develop coarse-grained models compatible with the recent version of the Martini force field (v 3.0) to tackle their encapsulation in the cavity of β-cyclodextrin (βCD) for which experimental ESR data are available. The results indicate that the atomistic descriptions perform well in relation to the structural parameters derived from X-ray diffraction as well as hydrogen bonding and hydrogen patterns and predict that the guest-host complexation is hydrophobically driven by the presence of a methyl group pair of the spin probe at the cavity center of βCD. The spin probe mobility at the binding site reveals the nitroxide group orientation toward the secondary rim of the cyclodextrin and the alternating presence of the two methyl group pairs inside the cavity, features in agreement with the experimental behavior of the ESR parameters. The coarse-grained parameterizations of TEMPO probes and βCD rely on optimizing the bonded and nonbonded parameters with references to the atomistic simulation results, and they are capable of recovering the orientation and location of the spin probe inside the cyclodextrin cavity predicted by the atomistic guest-host complexes. The results suggest the cyclodextrin host-guest system as a powerful validation suite to evaluate new coarse-grained parameterizations of small ligands and future extensions to functionalized cyclodextrins in inclusion complexes.

Second-Order Mass-Weighting Scheme for Atom-Centered Density Matrix Propagation Molecular Dynamics

The atom-centered density matrix propagation (ADMP) method is an extended Lagrangian approach to ab initio molecular dynamics, which includes the density matrix in an orthonormalized atom-centered Gaussian basis as additional, fictitious, electronic degrees of freedom, classically propagated along with the nuclear ones. A high adiabaticity between the nuclear and electronic subsystems is mandatory in order to keep the trajectory close to the Born-Oppenheimer (BO) surface. In this regard, the fictitious electronic mass μ, being a symmetric, nondiagonal matrix in its most general form, represents a free parameter, exploitable to optimize the propagation of the electronic density. Although mass-weighting schemes in ADMP exist, a systematic procedure to define an optimal value of the fictitious masses is not available yet. In this work, in order to rationally evaluate the electronic mass, fictitious electronic normal modes are defined through the diagonalization of the Hessian of the electronic density matrix. If the same frequency is imposed on all such modes (compatible with the chosen integration time step), then the corresponding μ matrix can be calculated and then employed for the following propagation. Analysis of several ADMP test simulations reveals that such Hessian-based mass-weighting approach is able to ensure, together with a 0.1/0.2 fs time steps, a high separation between the (real) nuclear and the (fictitious) electronic frequencies, which determines a high adiabaticity. This high, unprecedented, accuracy in the propagation leads, in turn, to low errors in the estimated nuclear vibrational frequencies, making the ADMP method totally comparable to a fully converged BO molecular dynamics simulation but more computationally efficient. This work, therefore, contributes to a further development of the ADMP ab initio molecular dynamics method, aimed at improving its accuracy through a more rational evaluation of the fictitious electronic mass parameter.

Towards reliable references for electron paramagnetic resonance parameters based on quantum chemistry: the case of verdazyl radicals

We present an efficient and accurate computational procedure to calculate properties measurable by EPR spectroscopy. We simulate a molecular dynamics (MD) trajectory by employing the quantum mechanically derived force field (QMDFF) [S. Grimme, J. Chem. Theory Comput., 2014, 10, 4497] and sample the trajectory at different time steps. For each snapshot EPR properties are calculated with a hybrid density functional theory (DFT) method. EPR spectra are simulated based on the averaged results. We applied the strategy to a number of previously published and novel verdazyl radicals, for which we recorded EPR spectra. The resulting simulated spectra are compatible with experiment already before employing an additional fitting step, in contrast to those from single point electronic-structure calculations. After the refinement, the experimental data are excellently reproduced, and the fitted EPR parameters do not deviate much from the calculated ones. This provides confidence in ascribing a direct physical meaning to the refined data in terms of experimental EPR parameters rather than merely considering them as mathematical fit parameters. We also find that couplings to hydrogen nuclei have a significant influence on the spectra of verdazyl radicals.

Electronic delocalization, charge transfer and hypochromism in the UV absorption spectrum of polyadenine unravelled by multiscale computations and quantitative wavefunction analysis

The characterization of the electronically excited states of DNA strands populated upon solar UV light absorption is essential to unveil light-induced DNA damage and repair processes. We report a comprehensive analysis of the electronic properties of the UV spectrum of single-stranded polyadenine based on theoretical calculations that include excitations over eight nucleobases of the DNA strand and environmental effects by a multiscale quantum mechanics/molecular mechanics scheme, conformational sampling by molecular dynamics, and a meaningful interpretation of the electronic structure by quantitative wavefunction analysis. We show that electronic excitations are extended mainly over two nucleobases with additional important contributions of monomer-like excitations and excitons delocalized over three monomers. Half of the spectral intensity derives from locally excited and Frenkel exciton states, while states with partial charge-transfer character account for the other half and pure charge-transfer states represent only a minor contribution. The hypochromism observed when going from the isolated monomer to the strand occurs independently from delocalization and charge transfer and is instead explained by long-range environmental perturbations of the monomer states.

Absorption and Emission Spectra of a Flexible Dye in Solution: a Computational Time-Dependent Approach

The spectroscopic properties of the organic chromophore 4-naphthoyloxy-1-methoxy-2,2,6,6-tetramethylpiperidine (NfO-TEMPO-Me) in toluene solution are explored through an integrated computational strategy combining a classical dynamic sampling with a quantum mechanical description within the framework of the time-dependent density functional theory (TDDFT) approach. The atomistic simulations are based on an accurately parametrized force field, specifically designed to represent the conformational behavior of the molecule in its ground and bright excited states, whereas TDDFT calculations are performed through a selected combination of hybrid functionals and basis sets to obtain optical spectra closely matching the experimental findings. Solvent effects, crucial to obtain good accuracy, are taken into account through explicit molecules and polarizable continuum descriptions. Although, in the case of toluene, specific solvation is not fundamental, the detailed conformational sampling in solution has confirmed the importance of a dynamic description of the molecular geometry for a reliable description of the photophysical properties of the dye. The agreement between theoretical and experimental data is established and a robust protocol for the prediction of the optical behaviour of flexible fluorophores in solution is set.