Digital Tool for the Analysis of UV–Vis Spectra of Olive Oils and Educational Activities with High School and Undergraduate Students

UV–vis absorption spectroscopy is one of the most accessible spectroscopic techniques at the high school educational level, and it is usually introduced in analytical chemistry courses due to its high versatility and to the wide range of applications in many fields of chemistry. Within this framework, we have developed an easy-to-use “simulation tool” to identify and quantify the main pigments in a relatively complex food matrix, such as olive oil and seeds’ oils. This digital software, freely available, can be used by high school students and first-year undergraduate students to analyze the UV–vis absorption spectrum of olive oils recorded in the bulk without any chemical treatment. In this paper, we are reporting the basic principles of the spectroscopic method and the way to use the “simulation tool” with several examples and explanations that are useful for students and teachers. In the second part of the paper, several examples of activities about the chemistry of olive oil, realized with the fifth classes’ students of a high school technical institute (K–12 level) and undergraduate students of an introductory course in spectroscopy in the second year of the Chemistry Degree Course, are reported. These activities were performed partially face-to-face and partially in distance learning mode during the COVID-19 pandemic. The main learning outcomes, methodological issues, and students’ feedback resulting from these experiences are reported and commented on, showing the potential of the simulation tool for educational purposes

Multiscale approaches to describe multichromophoric systems in complex environments

The modeling of supramolecular aggregates is an interesting challenge in the field of computational chemistry. In this work we applied multiscale approaches by combining quantum-mechanical and classical methods for the study of multichromophoric systems embedded in complex environments. Different multichromophoric systems have been investigated by applying an excitonic strategy and a particular attention has been devoted to the reproduction of excitonic optical spectra. An interesting class of multichromophoric systems is constituted by pigment-protein light harvesting complex specialized in the sunlight energy absorption in photosynthetic organisms. A novel approach based on the integration of classical molecular dynamics with fully polarizable QM/classical methods has been presented and applied to two different light-harvesting systems

Coloranti tannici e fibre di lana: studio integrato computazionale e spettroscopico dei complessi ferro-gallici con matrice proteica

In molti arazzi e tessili storici le fibre di lana colorate in nero con tannini naturali e mordente a base di ferro mostrano un avanzato stato di degradazione. In questo elaborato presentiamo uno studio computazionale, integrato con analisi spettroscopiche, volto alla caratterizzazione delle interazioni chimico-fisiche presenti all'interno del sistema colorante-mordente-fibra proteica

Achieving Linear Scaling in Computational Cost for a Fully Polarizable MM/Continuum Embedding

In this paper, we present a new, efficient implementation of a fully polarizable QM/MM/continuum model based on an induced-dipoles polarizable force field and on the Conductor-like Screening Model as a polarizable continuum in combination with a self-consistent field QM method. The paper focuses on the implementation of the MM/continuum embedding, where the two polarizable methods are fully coupled to take into account their mutual polarization. With respect to previous implementations, we achieve for the first time a linear scaling with respect to both the computational cost and the memory requirements without limitations on the molecular cavity shape. This is achieved thanks to the use of the recently developed ddCOSMO model for the continuum and the Fast Multipole Method for the force field, together with an efficient iterative procedure. Therefore, it becomes possible to include in the classical layer as much as several tens of thousands of atoms with a limited computational effort

Introduction to Light Properties and Basic Principles of Spectroscopy at the High-School Level: A Pilot Study

Spectroscopy is the basis of many applications in chemistry; however, the basic principles of light, light–matter interaction, and the operation of spectrophotometers are rarely present in chemistry curricula at the high-school level, or they are only briefly introduced to students before focusing on analytical chemistry applications. In this work, we report the results of a study conducted over several years, aimed to design, optimise, and put into practice a didactic sequence on light phenomena such as reflection, refraction, interference, diffraction, and light dispersion, as well as the basic principles of ultraviolet–visible spectroscopy and spectroscopic instruments. Difficult concepts of light phenomena and related topics were deeply investigated, focusing on the best ways to teach them to high-school students in the framework of the content-specific components identified in the topic-specific pedagogical content knowledge theoretical model. Inquiry-based learning and interactive STEM laboratory activities were combined with a historical epistemological teaching method. Short introductory videos were also recorded to help students during the remote lessons in the COVID-19 pandemic period. In this paper, we report and discuss the research strategy used in order to design and implement the sequence of educational activities, leading to a final optimised didactic sequence that was tested in a pilot study. The main results were obtained from the experimentation with several classes in two high-school technical institutes with a chemistry and material sciences curriculum, along with a group of undergraduate students during the first part of an introductory course on molecular spectroscopy

Towards an ab initio description of the optical spectra of light-harvesting antennae: application to the CP29 complex of photosystem II.

Only going beyond the static crystal picture through molecular dynamics simulations can a realistic excitonic picture of the light-harvesting complex CP29 be obtained using a multiscale polarizable QM/MM approach

Geometry Optimization in Polarizable QM/MM Models: The Induced Dipole Formulation

We present the mathematical derivation and the computational implementation of the analytical geometry derivatives for a polarizable QM/MM model (QM/MMPol). In the adopted QM/MMPol model, the focused part is treated at QM level of theory, while the remaining part (the environment) is described classically as a set of fixed charges and induced dipoles. The implementation is performed within the ONIOM procedure, resulting in a polarizable embedding scheme, which can be applied to solvated and embedded systems and combined with different polarizable force fields available in the literature. Two test cases characterized by strong hydrogen-bond and dipole-dipole interactions, respectively, are used to validate the method with respect to the nonpolarizable one. Finally, an application to geometry optimization of the chromophore of Rhodopsin is presented to investigate the impact of including mutual polarization between the QM and the classical parts in conjugated systems

The role of charge-transfer states in the spectral tuning of antenna complexes of purple bacteria

The LH2 antenna complexes of purple bacteria occur, depending on light conditions, in various different spectroscopic forms, with a similar structure but different absorption spectra. The differences are related to point changes in the primary amino acid sequence, but the molecular-level relationship between these changes and the resulting spectrum is still not well understood. We undertook a systematic quantum chemical analysis of all the main factors that contribute to the exciton structure, looking at how the environment modulates site energies and couplings in the B800-850 and B800-820 spectroscopic forms of LH2. A multiscale approach combining quantum chemistry and an atomistic classical embedding has been used where mutual polarization effects between the two parts are taken into account. We find that the loss of hydrogen bonds following amino acid changes can only explain a part of the observed blue-shift in the B850 band. The coupling of excitonic states to charge-transfer states, which is different in the two forms, contributes with a similar amount to the overall blue-shift

The Fenna-Matthews-Olson Protein Revisited: A Fully Polarizable (TD)DFT/MM Description

We report a combined molecular dynamics and quantum mechanics (QM)/molecular mechanics (MM) analysis of the excitonic properties of the Fenna-Matthews-Olson (FMO) protein by using a polarizable MM model combined with a time-dependent density functional theory description. Overall, our results indicate that structural fluctuations, electrostatic interactions, and short-range quantum effects can significantly modulate the model Hamiltonian parameters (site energies and couplings). We find that the specific interactions with the axial ligand and the hydrogen-bonded residues are responsible for the energy ladder, with their effects being mainly due to electrostatic interactions, but with short-range quantum contributions that are not negligible. In addition, a striking modulation of the screening effects experienced by the BChl pairs, due to the heterogeneous polarizability of the FMO and solvent environment, is observed. Finally, we find that the exciton model gives a reliable description of the delocalized excited states in the complex. Teaching an old protein new tricks: A critical investigation into the role of both structural and electrostatic effects of the environment in determining the excitonic states of the Fenna-Matthews-Olson protein is carried out by using a polarizable quantum mechanics/molecular mechanics model (see figure)

Limits and potentials of quantum chemical methods in modelling photosynthetic antennae

Advances in electronic spectroscopies with femtosecond time resolution have provided new information on the excitonic processes taking place during the energy conversion in natural photosynthetic antennae. This has promoted the development of new theoretical protocols aiming at accurately describing the properties and mechanisms of exciton formation and relaxation. In this perspective, we provide an overview of the quantum chemical based approaches, trying to underline both the potentials of the methods and their weaknesses. In particular three main aspects will be analysed, the quantum mechanical description of excitonic parameters (site energies and couplings), the incorporation of environmental effects on these parameters through hybrid quantum/classical approaches, and the modelling of the dynamical coupling among such parameters and the vibrations of the pigment-protein complex