Computational Spectroscopy in Solution by Integration of Variational and Perturbative Approaches on Top of Clusterized Molecular Dynamics

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.

Molecular Dynamics Simulations Enforcing Nonperiodic Boundary Conditions: New Developments and Application to the Solvent Shifts of Nitroxide Magnetic Parameters

“…All MD simulations were run with a locally modified version of the Gaussian 28 suite of programs using the rotational velocity Verlet (RVV1) integrator 29 with an ϵ = 10 –9 convergence criterion for the calculation of quaternion derivatives, with the exception of CH 3 OH which was treated as a flexible molecule and simulated employing the standard Velocity-Verlet integrator and enforcing holonomic constraints by means of the RATTLE method. 30 The Bussi–Donadio–Parrinello 31 thermostat was used, and a weak coupling scheme was employed in NPT simulations.…”

Fast exploration of potential energy surfaces with a joint venture of quantum chemistry, evolutionary algorithms and unsupervised learning

“…In a forthcoming release of the IM-EA code we will integrate completely the Proxima python API 52 (Pyproxima) to detect topological changes on the fly, but for the present case (Ag + in aqueous solution) the presence of just two different molecular species allowed us to use a fixed topology with distinct fragments. To manipulate fragment coordinates, instead of working with Cartesian coordinates, we adopted a rigid body description based on quaternions 21 for most transformations. Mutation happens then in the following way: first, a fragment is selected; then, with user defined probabilities, one operator is selected among a panel of six choices (note that any move can be excluded by setting its probability to 0):…”

“…In previous contributions [15][16][17] we have proposed and validated the application of one of such algorithms, namely the (λ + µ) Island Model Evolutionary Algorithm (IM-EA hereafter), to the investigation of the conformational landscape of biomolecule building blocks 18 or relatively simple organometallic systems 19 . The present contribu-tion presents a number of relevant improvements to the IM-EA method: (i) in the previous contribution we simply checked the capabilities of the method in exploring PESs of flexible systems with the goal of completeness without an in depth discussion of the importance of various components in the method, which is presented in this manuscript; (ii) we previously limited the exploration to dihedral angles of isolated flexible systems, whereas here we present also a new set of operators based on quaternions 20,21 able to deal with inter-molecular interactions; (iii) we add a number of improvements to the method, with new mutation operators and the Hall of Fame mechanism (see section 2.1) and (iv) introduce effective unsupervised clustering of candidate structures in order to reduce as much as possible the number of expensive quantum chemical (QC) computations; neither the computer code, nor the case studies discussed below were presented before. Once again we carry out an in depth benchmark of several semi empirical (SE) methods [22][23][24][25] in the exploration step and of last-generation methods rooted in the density functional theory (DFT) for the exploitation of the above results to compute accurate structural and spectroscopic parameters.…”

Development, Validation, and Pilot Application of a Generalized Fluctuating Charge Model for Computational Spectroscopy in Solution

“…The RVV1 integrator 26 was used in all simulations, with a convergence criterion ϵ = 10 –9 for the calculation of quaternion derivatives. The “rough walls” 26 boundary condition and the Bussi–Donadio–Parrinello 33 thermostat were used in all the NVT/NPBC simulations. The equilibration of the system involved an initial minimization with the conjugate gradient method and a subsequent simulation for 1000 ps with a small integration step of 0.5 fs and temperature of 298.15 K. The production run was then initiated at 298.15 K and continued for 25 ns with an integration time step of 4.0 fs.…”

“…The TIP3P-FB rigid water molecule was used in all the simulations, whereas the topology and initial GAFF2 parameters of creatinine have been obtained with the PrimaDORAC web interface. The geometries of amine and imine tautomers were optimized at the B3LYP/6-31+G­(d) level taking into account bulk solvent effects by means of the polarizable continuum model (PCM), and point atomic charges were assigned performing a CM5 population analysis of the corresponding Kohn–Sham orbitals, following the protocol adopted with success for the study of several other systems. ,− Molecular structures, atomic labels, and charges for the two tautomers are shown Figure .…”