arXiv subjects

Marta Monti

Publications and source records attributed to Marta Monti.

7 recordsLinked to original sources

arXiv2026

Tracking Chirality during Molecular Motor Photoisomerization via Simulated Time-Resolved Circular Dichroism

Ultrafast spectroscopic techniques are widely used to investigate photoinduced processes, yet they remain largely blind to molecular chirality. Here we introduce a framework for simulating time-resolved electronic circular dichroism (TRCD) along an ensemble of nonadiabatic molecular dynamics, and apply it to the photoisomerization of a second-generation molecular motor[1]. While transient absorption captures the overall excited-state dynamics, it cannot distinguish the two photoproduct pathways. The TRCD response, by contrast, resolves the stereochemical branching: trajectories returning to the stable P isomer (right-handed helix) retain a distinct chiroptical band in the visible region, whereas those forming the M isomer (leftl-handed helix) become chiroptically dark as they twist through the conical intersection. This asymmetry constitutes a directly measurable signature of the stereochemical branching, offering a real-time probe of the formation of molecular chirality and concrete predictions for future TRCD experiments.

cond-mat.other↗

arXiv2025

Investigating the Role of pH and Counterions in the Intrinsic Fluorescence of Solid-State L-Lysine

There is currently a growing interest in understanding the origins of intrinsic fluorescence as a way to design non-invasive probes for biophysical processes. In this regard, understanding how pH influences fluorescence in non-aromatic biomolecular assemblies is key to controlling their optical properties in realistic cellular conditions. Here, we combine experiments and theory to investigate the pH-dependent emission of solid-state L-Lysine (Lys). Lys aggregates prepared at different pH values using HCl and H$_2$SO$_4$ exhibit protonation- and counterion-dependent morphology and fluorescence, as shown by microscopy and steady-state measurements. We find an enhancement in the fluorescence moving from acidic to basic conditions. To uncover the molecular origin of these trends, we performed non-adiabatic molecular dynamics simulations on three Lys crystal models representing distinct protonation states. Our simulations indicate that enhanced protonation under acidic conditions facilitates non-radiative decay via proton transfer, whereas basic conditions favor radiative decay. Our combined experimental-theoretical work highlights pH and counterion identity as key factors tuning fluorescence in Lys assemblies, offering insights for designing pH responsive optical materials based on non-aromatic amino acids.

physics.chem-ph↗

arXiv2025

Deconstructing the Origins of Interfacial Catalysis: Why Electric Fields are Inseparable from Solvation

In the last decade, there has been a surge of experiments showing that certain chemical reactions undergo an enormous boost when taken from bulk aqueous conditions to microdroplet environments. The microscopic basis of this phenomenon remains elusive and continues to be widely debated. One of the key driving forces invoked are the specific properties of the air-water interface including the presence of large electric fields and distinct solvation at the surface. Here, using a combination of classical molecular dynamics simulations, the chemical physics of solvation, and unsupervised learning approaches, we place these assumptions under close scrutiny. Using phenol as a model system, we demonstrate that the electric field at the surface of water is not anomalous or unique compared to bulk water conditions. Furthermore, the electric field fluctuations de-correlate on a timescale of ~10 ps implying that their role in activating much slower chemical reactions remains inconclusive. We deploy a recently developed unsupervised learning approach, dubbed information balance, which detects in an agnostic fashion the relationship between the electric field and solvation collective variables. It turns out that the electric field on the hydroxyl group of the phenol is mostly determined by phenol hydration including the proximity and orientation of nearby water molecules. We caution that the growing attention of the role that electric fields have garnered in enhancing chemical reactivity at the air-water interface, may not reflect their actual importance.

physics.chem-ph↗

arXiv2025

Defects at Play: Shaping the Photophysics and Photochemistry of Ice

The mechanisms by which light interacts with ice and the impact of photo-induced reactions are central to our understanding of environmental, atmospheric and astrophysical processes. However, a microscopic description of the photoproducts originating from UV absorption and emission processes has remained elusive. Here we explore the photochemistry of ice using time-dependent hybrid density functional theory on various models of pristine and defective ice Ih. Our investigation of the excited state potential energy surface of the crystal shows that UV absorption can lead to the formation of hydronium ions, hydroxyl radicals and excess electrons. One of the dominant mechanisms of decay from the excited to the ground-state involves the recombination of the electron with the hydroxyl radical yielding hydronium-hydroxide ion-pairs. We find that the details of this charge recombination process sensitively depend on the presence of defects in the lattice, such as vacancies and pre-existing photoproducts. We also observe the formation of Bjerrum defects following UV absorption; we suggest that, together with hydroxide anions, they are likely responsible for prominent features experimentally detected in long UV exposure absorption spectra, remarkably red-shifted relative to short exposure spectra. Our results highlight the key role of defects in determining the onset of absorption and emission processes in ice.

physics.chem-ph↗

arXiv2025

Turning on the Light: Polymorphism-Induced Photoluminescence in Cysteine Crystals

Photoluminescence of non-aromatic supramolecular chemical assemblies has attracted considerable attention in recent years due to its potential for use in molecular sensing and imaging technologies. The underlying structural origins, the mechanisms of light emission in these systems, and the generality of this phenomenon remain elusive. Here, we demonstrate that crystals of L-Cysteine (Cys) formed in heavy water ($\text{D}_2\text{O}$) exhibit distinct packing and hydrogen-bond networks, resulting in significantly enhanced photoluminescence compared to those prepared in $\text{H}_2\text{O}$. Using advanced excited-state simulations, we elucidate the nature of electronic transitions that activate vibrational modes of Cys in $\text{H}_2\text{O}$, particularly those involving thiol (S-H) and amine (C-N) groups, which lead to non-radiative decay. For the crystal formed in $\text{D}_2\text{O}$, these modes appear to be more constrained, and we also observe intersystem crossing from the singlet to the triplet state, indicating a potentially more complex light emission mechanism. Our findings provide new insights into this intriguing phenomenon and introduce innovative design principles for generating emergent fluorophores.

physics.chem-ph↗

arXiv2024

Trajectory Surface Hopping with Tight Binding Density Functional Theory applied to Molecular Motors

Non-adiabatic molecular dynamics (NAMD) has become an essential computational technique for studying the photophysical relaxation of molecular systems after light absorption. These phenomena require approximations that go beyond the Born-Oppenheimer approximation, and the accuracy of the results heavily depends on the electronic structure theory employed. Sophisticated electronic methods, however, make these techniques computationally expensive, even for medium size systems. Consequently, simulations are often performed on simplified models to interpret experimental results. In this context, a variety of techniques have been developed to perform NAMD using approximate methods, particularly Density Functional Tight Binding (DFTB). Despite the use of these techniques on large systems where ab initio methods are computationally prohibitive, a comprehensive validation has been lacking. In this work, we present a new implementation of trajectory surface hopping (TSH) combined with DFTB, utilizing non-adiabatic coupling vectors (NACVs). We selected two different systems for validation, providing an exhaustive comparison with higher-level electronic structure methods. As a case study, we simulated a system from the class of molecular motors, which has been extensively studied experimentally but remains challenging to simulate with ab initio methods due to its inherent complexity. Our approach effectively captures the key photophysical mechanism of dihedral rotation after absorption of light. Additionally, we successfully reproduce the transition from the bright to dark states observed in the time dependent fluorescence experiments, providing valuable insights into this critical part of the photophysical behavior in molecular motors.

physics.chem-ph↗

arXiv2024

Aqueous Solution Chemistry In Silico and the Role of Data Driven Approaches

The use of computer simulations to study the properties of aqueous systems is, today more than ever, an active area of research. In this context, during the last decade there has been a tremendous growth in the use of data-driven approaches to develop more accurate potentials for water as well as to characterize its complexity in chemical and biological contexts. We highlight the progress, giving a historical context, on the path to the development of many-body and reactive potentials to model aqueous chemistry, including the role of machine learning strategies. We focus specifically on conceptual and methodological challenges along the way in performing simulations that seek to tackle problems in modeling the chemistry of aqueous solutions. In conclusion, we summarize our perspectives on the use and integration of advanced data-science techniques to provide chemical insights in physical chemistry and how this will influence computer simulations of aqueous systems in the future.

physics.chem-ph↗