Quantum-Classical Calculation of Vibronic Spectra along a Reaction Path: The Case of the ECD of Easily Interconvertible Conformers with Opposite Chiral Responses

Photophysics of a nucleic acid-protein crosslinking model strongly depends on solvation dynamics: an experimental and theoretical study

We present a combined experimental and theoretical study of the photophysics of 5-benzyluracil (5BU) in methanol, which is a model system for interactions between nucleic acids and proteins. A molecular dynamics study of 5BU in solution through efficient DFT-based hybrid ab initio potentials revealed a remarkable conformational flexibility - allowing the population of two main conformers - as well as specific solute-solvent interactions, which both appear as relevant factors for the observed 5BU optical absorption properties. The simulated absorption spectrum, calculated on such an ensemble, enabled a molecular interpretation of the experimental UV-Vis lowest energy band, which is also involved in the induced photo-reactivity upon irradiation. In particular, the first two excited states (mainly involving the uracil moiety) both contribute to the 5BU lowest energy absorption. Moreover, as a key finding, the nature and brightness of such electronic transitions are strongly influenced by 5BU conformation and the microsolvation of its heteroatoms.

FCclasses3: Vibrationally-resolved spectra simulated at the edge of the harmonic approximation

We introduce FCclasses3, a code to carry out vibronic simulations of electronic spectra and nonradiative rates, based on the harmonic approximation. Key new features are: implementation of the full family of vertical and adiabatic harmonic models, vibrational analysis in curvilinear coordinates, extension to several electronic spectroscopies and implementation of time-dependent approaches. The use of curvilinear valence internal coordinates allows the adoption of quadratic model potential energy surfaces (PES) of the initial and final states expanded at arbitrary configurations. Moreover, the implementation of suitable projectors provides a robust framework for defining reduced-dimensionality models by sorting flexible coordinates out of the harmonic subset, so that they can then be treated at anharmonic level, or with mixed quantum classical approaches. A set of tools to facilitate input preparation and output analysis is also provided. We show the program at work in the simulation of different spectra (one and two-photon absorption, emission and resonance Raman) and internal conversion rate of a typical rigid molecule, anthracene. Then, we focus on absorption and emission spectra of a series of flexible polyphenyl molecules, highlighting the relevance of some of the newly implemented features. The code is freely available at http://www.iccom.cnr.it/en/fcclasses/.

Computational Model for Electrochemical Surface-Enhanced Raman Scattering: Key Role of the Surface Charges and Synergy between Electromagnetic and Charge-Transfer Enhancement Mechanisms

We present a computational model for electrochemical surface-enhanced Raman scattering (EC-SERS). The surface excess of charge induced by the electrode potential (V_el) was introduced by applying an external electric field to a set of clusters [Ag_n]^q with (n, q) of (19, ±1) or (20, 0) on which a molecule adsorbs. Using DFT/TD-DFT calculations, these metal-molecule complexes were classified by the adsorbate partial charge, and the main V_el-dependent properties were simultaneously studied with the aid of vibronic resonance Raman computations, namely, changes on the vibrational wavenumbers, relative intensities, and enhancement factors (EFs) for all SERS mechanisms: chemical or nonresonant, and resonance Raman with bright states of the adsorbate, charge-transfer (CT) states, and plasmon-like excitations on the metal cluster. We selected two molecules to test our model, pyridine, for which V_el has a remarkable effect, and 9,10-bis((E)-2-(pyridin-4-yl)vinyl)anthracene, which is almost insensitive to the applied bias. The results nicely reproduced most of the experimental observations, while the limitations of our approach were critically evaluated. We detected that accounting explicitly for the surface charges is key for EC-SERS models and that the highest calculated EFs, up to 10⁷ to 10⁸, are obtained by interstate coupling of bright local excitations of the metal cluster and CT states. These results highlight the importance of nonadiabatic effects in SERS and the capabilities of EC-SERS as a technique with potential to study excited-state coupling by tuning the CT and plasmon-like states by manipulating V_el.

Theory and algorithms for chiroptical properties and spectroscopies of aqueous systems

Chiroptical properties and spectroscopies are valuable tools to study chiral molecules and assign absolute configurations. The spectra that result from chiroptical measurements may be very rich and complex, and hide much of their information content. For this reason, the interplay between experiments and calculations is especially useful, provided that all relevant physico-chemical interactions that are present in the experimental sample are accurately modelled. The inherent difficulty associated to the calculation of chiral signals of systems in aqueous solutions requires the development of specific tools, able to account for the peculiarities of water-solute interactions, and especially its ability to form hydrogen bonds. In this perspective we discuss a multiscale approach, which we have developed and challenged to model the most used chiroptical techniques.

Ab-initio molecular dynamics and hybrid explicit-implicit solvation model for aqueous and nonaqueous solvents: GFP chromophore in water and methanol solution as case study

Solute-solvent interactions are proxies for understanding how the electronic density of a chromophore interacts with the environment in a more exhaustive way. The subtle balance between polarization, electrostatic, and non-bonded interactions need to be accurately described to obtain good agreement between simulations and experiments. First principles approaches providing accurate configurational sampling through molecular dynamics may be a suitable choice to describe solvent effects on solute chemical-physical properties and spectroscopic features, such as optical absorption of dyes. In this context, accurate energy potentials, obtained by hybrid implicit/explicit solvation methods along with employing nonperiodic boundary conditions, are required to represent bulk solvent around a large solute-solvent cluster. In this work, a novel strategy to simulate methanol solutions is proposed combining ab initio molecular dynamics, a hybrid implicit/explicit flexible solvent model, nonperiodic boundary conditions, and time dependent density functional theory. As case study, the robustness of the proposed protocol has been gauged by investigating the microsolvation and electronic absorption of the anionic green fluorescent protein chromophore in methanol and aqueous solution. Satisfactory results are obtained, reproducing the microsolvation layout of the chromophore and, as a consequence, the experimental trends shown by the optical absorption in different solvents.

CPL Spectra of Camphor Derivatives in Solution by an Integrated QM/MD Approach

We extend a recently proposed computational strategy for the simulation of absorption spectra of semi-rigid molecular systems in condensed phases to the emission spectra of flexible chromophores. As a case study, we have chosen the CPL spectrum of camphor in methanol solution, which shows a well-defined bisignate shape. The first step of our approach is the quantum mechanical computation of reference spectra including vibrational averaging effects and taking bulk solvent effects into account by means of the polarizable continuum model. In the present case, the large amplitude inversion mode is explicitly treated by a numerical approach, whereas the other small-amplitude vibrational modes are taken into account within the harmonic approximation. Next, the snapshots of classical molecular dynamics computations are clusterized and one representative configuration from each cluster is used to compute a reference spectrum. In the present case, different clusters correspond to the two stable conformers of camphor in the S1 excited electronic state and, for each of them, to different numbers of strong solute-solvent hydrogen bonds. Finally, local fluctuation effects within each cluster are taken into account by means of the perturbed matrix model. The overall procedure leads to good agreement with experiment for absorption and emission spectra together with their chiral counterparts, thus allowing to analyze the role of different effects (stereo-electronic, vibrational, environmental) in tuning the overall experimental spectra.

The role of chlorine position in the electronic circular dichroism of chlorophenyl-ethanol investigated by vibronic calculations

(R)-1-phenyl-ethanol (PhEtOH) and the different isomers of (R)-1-(chlorophenyl)ethanol (ClPhEtOH) exhibit very interesting electronic circular dichroism (ECD) in methanol. In all cases, the spectrum shows clear vibronic features, but it is monosignated and negative for PhEtOH and meta-ClPhEtOH, positive for the ortho isomer and bisignated for the para isomer. We used computational chemistry to rationalise this behaviour adopting CAM-B3LYP/def2-TZVP, describing the bulk solvent effects with polarizable continuum models and solute-solvent specific interactions with clusters comprising the solute and two solvent molecules. We adopted harmonic vibronic models to compute the ECD spectral shapes of all stable conformers, and we obtained the room-temperature spectra by Boltzmann average. Simulated spectra are in very good agreement with experiment and allow us to rationalise their difference in terms of the relevance of Franck-Condon (FC) and Herzberg-Teller (HT) intensity-borrowing contributions, modulated by the substituent effect. The bisignated shape of the spectrum of para-ClPhEtOH arises from the competition of opposite-sign FC and HT bands, promoted by different vibrational modes. Due to the challenges we document in computing its ECD spectrum, para-ClPhEtOH represents a good test case to help the development of novel methodologies for an improved description of weak vibronic ECD spectra of flexible systems in explicit solvents.

Adiabatic-Molecular Dynamics Generalized Vertical Hessian Approach: A Mixed Quantum Classical Method To Compute Electronic Spectra of Flexible Molecules in the Condensed Phase

We present a general mixed quantum classical method that couples classical molecular dynamics (MD) and vibronic models to compute the shape of electronic spectra of flexible molecules in the condensed phase without, in principle, any phenomenological broadening. It is based on a partition of the nuclear motions of the solute + solvent system in "soft" and "stiff" vibrational modes and an adiabatic hypothesis that assumes that stiff modes are much faster than soft ones. In this framework, the spectrum is rigorously expressed as a conformational integral of quantum vibronic spectra along the stiff coordinates only. Soft modes enter at the classical level through the conformational distribution that is sampled with classical MD runs. In each configuration, reduced-dimensionality quadratic Hamiltonians are built in the space of the stiff coordinates only, thanks to a generalization of the Vertical Hessian harmonic model and an iterative application of projectors in internal coordinates to remove soft modes. Quantum vibronic spectra, specific for each sampled configuration of the soft coordinates, are then computed at the desired temperature with efficient time-dependent techniques, and the global spectrum simply arises from their average. For consistency of the whole procedure, classical MD runs are performed with quantum-mechanically derived force fields, parameterized at the same level of theory selected for generating the quadratic Hamiltonians along the stiff coordinates. Application to N-methyl-6-oxyquinolinium betaine in water, dithiophene in ethanol, and cyanidine in water is presented to show the performance of the method.

Time-Dependent Formulation of Resonance Raman Optical Activity Spectroscopy

In this work, we extend the theoretical framework recently developed for the simulation of resonance Raman (RR) spectra of medium-to-large sized systems to its chiral counterpart, namely, resonance Raman optical activity (RROA). The theory is based on a time-dependent (TD) formulation, with the transition tensors obtained as half-Fourier transforms of the appropriate cross-correlation functions. The implementation has been kept as general as possible, supporting adiabatic and vertical models for the PES representation, both in Cartesian and internal coordinates, with the possible inclusion of Herzberg-Teller (HT) effects. Thanks to the integration of this TD-RROA procedure within a general-purpose quantum-chemistry program, both solvation and leading anharmonicity effects can be included in an effective way. The implementation is validated on one of the smallest chiral molecule (methyloxirane). Practical applications are illustrated with three medium-size organic molecules (naproxen-OCD₃, quinidine and 2-Br-hexahelicene), whose simulated spectra are compared to the corresponding experimental data.

A computational study of the vibrationally-resolved electronic circular dichroism spectra of single-chain transoid and cisoid oligothiophenes in chiral conformations

We simulate the vibronic profile of the electronic circular dichroism (ECD) spectra of oligothiophenes in cisoid and transoid chiral arrangements. We consider oligomers of different lengths, from two to fifteen units, and investigate extensively how the ECD spectral shapes depend on the inter-ring torsions. In general, the molecular structures we consider are not stationary points of the ground state potential energy surface. Therefore, in order to perform vibronic calculations, we present a new computational protocol able to define reduced-dimensionality models where the effect of the off-equilibrium modes is removed. This is done adopting a description of the vibrational motions in curvilinear internal coordinates, and vertical harmonic models coupled with an iterative application of projectors to define energy Hessians, and therefore effective normal modes, in the space complementary to the one of the off-equilibrium coordinates. Although we consider both Franck-Condon and Herzberg-Teller contributions, the results show that transoid twisted ribbons always give rise to monosignated ECD spectra, while bi-signated and multi-signated spectra are expected for cisoid helices. These findings are explained on the basis of the different transition strengths of the lowest electronic states imparted by the different spatial arrangement, that is almost linear for transoid structures and more globular for cisoid ones. We predicted the chiroptical response of a large number of possible molecular arrangements. These data are employed to critically discuss the experimental ECD of polythiophenes in different experimental conditions, forming either aggregates or host-guest complexes. The method here proposed to perform vibronic calculations in reduced-dimensionality models is of general applicability and its potential interest goes beyond the practical application presented here.

Unraveling electronic absorption spectra using nuclear quantum effects: Photoactive yellow protein and green fluorescent protein chromophores in water

Many physical phenomena must be accounted for to accurately model solution-phase optical spectral line shapes, from the sampling of chromophore-solvent configurations to the electronic-vibrational transitions leading to vibronic fine structure. Here we thoroughly explore the role of nuclear quantum effects, direct and indirect solvent effects, and vibronic effects in the computation of the optical spectrum of the aqueously solvated anionic chromophores of green fluorescent protein and photoactive yellow protein. By analyzing the chromophore and solvent configurations, the distributions of vertical excitation energies, the absorption spectra computed within the ensemble approach, and the absorption spectra computed within the ensemble plus zero-temperature Franck-Condon approach, we show how solvent, nuclear quantum effects, and vibronic transitions alter the optical absorption spectra. We find that including nuclear quantum effects in the sampling of chromophore-solvent configurations using ab initio path integral molecular dynamics simulations leads to improved spectral shapes through three mechanisms. The three mechanisms that lead to line shape broadening and a better description of the high-energy tail are softening of heavy atom bonds in the chromophore that couple to the optically bright state, widening the distribution of vertical excitation energies from more diverse solvation environments, and redistributing spectral weight from the 0-0 vibronic transition to higher energy vibronic transitions when computing the Franck-Condon spectrum in a frozen solvent pocket. The absorption spectra computed using the combined ensemble plus zero-temperature Franck-Condon approach yield significant improvements in spectral shape and width compared to the spectra computed with the ensemble approach. Using the combined approach with configurations sampled from path integral molecular dynamics trajectories presents a significant step forward in accurately modeling the absorption spectra of aqueously solvated chromophores.

Steady-State Linear and Non-linear Optical Spectroscopy of Organic Chromophores and Bio-macromolecules

Bio-macromolecules as DNA, lipid membranes and (poly)peptides are essential compounds at the core of biological systems. The development of techniques and methodologies for their characterization is therefore necessary and of utmost interest, even though difficulties can be experienced due to their intrinsic complex nature. Among these methods, spectroscopies, relying on optical properties are especially important to determine their macromolecular structures and behaviors, as well as the possible interactions and reactivity with external dyes—often drugs or pollutants—that can (photo)sensitize the bio-macromolecule leading to eventual chemical modifications, thus damages. In this review, we will focus on the theoretical simulation of electronic spectroscopies of bio-macromolecules, considering their secondary structure and including their interaction with different kind of (photo)sensitizers. Namely, absorption, emission and electronic circular dichroism (CD) spectra are calculated and compared with the available experimental data. Non-linear properties will be also taken into account by two-photon absorption, a highly promising technique (i) to enhance absorption in the red and infra-red windows and (ii) to enhance spatial resolution. Methodologically, the implications of using implicit and explicit solvent, coupled to quantum and thermal samplings of the phase space, will be addressed. Especially, hybrid quantum mechanics/molecular mechanics (QM/MM) methods are explored for a comparison with solely QM methods, in order to address the necessity to consider an accurate description of environmental effects on spectroscopic properties of biological systems.

Simulation of Vibronic Spectra of Flexible Systems: Hybrid DVR-Harmonic Approaches

Our general framework for the simulation of vibrational signatures in electronic spectra has been extended to treat one large-amplitude motion (LAM) at the anharmonic level, coupled to the other small-amplitude motions (SAM) treated as harmonic. The coupling between LAM and SAM is minimized thanks to the use of delocalized internal coordinates, which are built automatically from the molecular topology. General LAMs can be employed, ranging from intrinsic reaction coordinates to rigid or flexible paths based on the distinguished coordinate approach. The anharmonic model is based on a fully numerical method based on the discrete variable representation (DVR) theory, supporting different types of boundary conditions. The inclusion of this model in a general-purpose electronic structure code makes available to the user a large panel of quantum chemistry models, for both isolated and condensed phases. The flexibility and reliability of the new framework are illustrated by some case studies, covering various types of LAMs, ranging from a small test case, the photoelectron spectrum of ammonia, to larger systems, such as phenylanthracene and cyclobutanone.

The shape of the electronic circular dichroism spectrum of (2,6-dimethylphenyl)(phenyl)methanol: interplay between conformational equilibria and vibronic effects

Analysis of the interplay between conformational equilibria, solvent effects and vibronic contributions in the ECD spectra.