Abstract
Multiscale QM/MM approaches have become the most suitable and effective methods for the investigation of spectroscopic properties of medium- or large-size chromophores in condensed phases. On these grounds, we are developing a novel workflow aimed at improving the generality, reliability, and ease of use of the available tools. In the present paper, we report the latest developments of such an approach with specific reference to a general workplan starting with the addition of acetonitrile to the panel of solvents already available in the General Liquid Optimized Boundary (GLOB) model enforcing nonperiodic boundary conditions (NPBC). Next, the solvatochromic shifts induced by acetonitrile on both rigid (uracil and thymine) and flexible (thyrosine) chromophores have been studied introducing in our software a number of new features ranging from rigid-geometry NPBC molecular dynamics based on the quaternion formalism to a full integration of variational (ONIOM) and perturbative (perturbed matrix method (PMM)) approaches for describing different solute–solvent topologies and local fluctuations, respectively. Finally, thymine and uracil have been studied also in methanol to point out the generality of the computational strategy. While further developments are surely needed, the strengths of our integrated approach even in its present version are demonstrated by the accuracy of the results obtained by an unsupervised approach and coupled to a computational cost strongly reduced with respect to that of conventional QM/MM models without any appreciable accuracy deterioration.
Highlights
Prediction of the spectra of medium-size semirigid chromophores in the gas phase is a nontrivial problem, needing a careful balance between feasibility and accuracy.[1]
The general robustness of the quaternion-based approach for propagating the equations of motion has been extensively tested in previous studies for TIP4P water[48−50] systems under periodic boundary conditions (PBC); our purpose here is to fully assess the integrator stability under different conditions
The results are quite similar to those obtained by Rozmanov et al for TIP4P water: less than six iterations are needed for time steps of 0.5 or 1.0 fs, and about eight iterations for larger time steps, the higher error obtained for δt = 1.0 fs with respect to 2.0 and 4.0 fs being related to the reduced number of iterations performed
Summary
Prediction of the spectra of medium-size semirigid chromophores in the gas phase is a nontrivial problem, needing a careful balance between feasibility and accuracy.[1]. Only well-devised and purposely tailored strategies can provide a satisfactory modeling, since each step of the overall procedure requires a fine tuning of the accuracy/cost ratio, which must be balanced with that of the other steps and with the final sought accuracy In this framework, the main aim of this contribution is to present some of the latest developments we have implemented into a general workflow for the study of the spectroscopic features of medium-to-large-size chromophores in condensed phases. The main aim of this contribution is to present some of the latest developments we have implemented into a general workflow for the study of the spectroscopic features of medium-to-large-size chromophores in condensed phases This effort is based on our opinion that computational spectroscopy will not become a routine companion of experimental studies in the analysis of challenging systems until general and user-friendly tools have been developed and validated.[11] Broadly speaking, a general QM/MM tool includes three main ingredients: (i) classical sampling of the complete system; (ii) selection of a representative number of system configurations for performing
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