Searcharxiv⌕ Search

arXiv subjects

Ali Hassanali

Publications and source records attributed to Ali Hassanali.

At least 19 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↗
arXiv2026

Glassy Signatures in Water's Second Liquid

The origin of water's anomalous behavior remains a central open problem in the physical sciences and is often attributed to a liquid-liquid transition (LLT) between high- and low-density liquid states deep in the supercooled regime. Experimental access to this region has been challenging due to rapid crystallization, leaving atomistic simulations as a major source of supporting evidence. Using extensive machine-learning-accelerated first-principles simulations in direct comparison with spectroscopic, structural, and dynamical experimental measurements, we show that features commonly interpreted as signatures of two-liquid behavior coincide with the onset of dramatic dynamical slowing down characteristic of an emerging non-ergodic glassy state. Specifically, we find that two-state fluctuations associated with an LLT, are also consistent with a transformation from a high-density liquid to a kinetically constrained low-density glassy-like state. By mapping equilibrium dynamics across pressure and temperature, our results call for a closer examination of water's metastable landscape, in which two-state behavior may reflect a relatively high glass-transition temperature of low-density water, 189~$\pm$~8 K---curiously close to the temperature commonly associated with the proposed LLT.

cond-mat.soft↗
arXiv2026

Hydrogen-Bond Donor-Acceptor Imbalance in Low-Frequency Terahertz Water Spectra

The low-frequency dielectric response of liquid water is commonly described by a dominant Debye relaxation together with additional faster contributions whose microscopic origin remains debated. Here we show that the dielectric function of water between 0.14 and 1.21 THz can be represented by a collective Debye relaxation plus a Drude-Smith term constrained to the zero-dc-conductivity limit. The Drude-Smith spectral weight increases upon heating pure H2O from 20 C to 50 C and decreases upon isotopic substitution (D2O at 20 C vs. H2O at 20 C). Molecular dynamics simulations including nuclear quantum effects show correlated changes in the population of water molecules with unequal numbers of donated and accepted hydrogen-bonds. Ab-initio-based spectra calculations further indicate that the ~0.1-1 THz response contains both nuclear-motion and explicit electronic-polarisation/charge-redistribution contributions. We therefore interpret the excess low-frequency THz response as a localised, mixed nuclear-electronic dielectric response correlated with transient donor-acceptor imbalance in the hydrogen-bond network.

physics.chem-ph↗
arXiv2026

Investigating causality between principal components in protein dynamics

Principal component analysis (PCA) is widely used to characterize collective protein motions from molecular dynamics (MD) simulations. While PCA identifies the dominant modes of structural fluctuation, it does not reveal whether different principal components (PCs) causally influence each other. Here, we investigate this question using a recently introduced causal-discovery framework [Del Tatto et al, PNAS 2024], which allows to infer putative causal asymmetries between high-dimensional time series. We apply this approach to long-timescale MD trajectories of two proteins. By analyzing relationships among PCs, we construct directed networks describing how PCs influence one another across time scales. These directional relationships, whose existence is a necessary condition for the presence of a causal link, are not captured by conventional covariance-based analyses and provide information that is complementary to PCA and Time-lagged Independent Component Analysis (TICA). Our results suggest that our causal inference approach can uncover previously hidden aspects of the dynamical organization of protein motions and offer a new perspective on this very popular class of collective variables.

physics.chem-ph↗
arXiv2026

Quantum nuclear and band-dispersion effects recover near-UV absorption in short-hydrogen-bonded organic crystals

Near-UV optical absorption is increasingly reported in hydrogen-bonded organic and biomolecular materials lacking aromatic or extended pi-conjugated chromophores, yet its microscopic origin remains unresolved and electronic-structure calculations often overestimate experimental absorption onsets. Here, we combine machine-learned interatomic potentials for large-scale classical and quantum nuclear sampling with periodic excited-state calculations to address this discrepancy in L-pyroglutamine ammonium, an experimentally established glutamine-derived crystal containing a well-resolved short hydrogen bond and exhibiting non-aromatic near-UV optical response. Using controlled in silico ion substitutions that vary the surrounding hydrogen-bond environment while preserving this scaffold, we compute optical spectra from configurations sampled along classical and quantum nuclear trajectories using hybrid-functional time-dependent density functional theory. We show that nuclear quantum effects stabilise proton-sharing configurations that are strongly suppressed classically, redshifting the lowest bright excitations by 0.5-0.8 eV and raising the fraction of configurations with bright excitations below 6 eV from approximately 3% to approximately 30%. Explicit Brillouin-zone sampling provides a further, mechanistically distinct redshift of 0.5-1.1 eV, reflecting modest but significant indirect electronic character. Only when both effects are incorporated does the calculated onset recover the experimental 3.8-4.5 eV range. These results establish quantum proton fluctuations and reciprocal-space convergence as cooperative but physically distinct ingredients required for predictive optical spectroscopy of strongly hydrogen-bonded molecular materials.

physics.chem-ph↗
arXiv2026

Transferable machine learning of excited-state dynamics with extremal pooling

Photochemical processes govern phenomena ranging from solar energy conversion and atmospheric chemistry to vision and photosynthesis. Accurate simulation of these processes requires modeling excited-state potential energy surfaces, often involving chemical reactions, tasks that remain computationally prohibitive for extended systems and long timescales using traditional \textit{ab initio} methods. Machine learning interatomic potentials have revolutionized ground-state simulations, but their extension to excited states faces fundamental challenges: standard architectures assume energy extensivity, an assumption that fails for excited states. Here, we present a size-intensive machine-learning framework for excited-state dynamics based on \textit{extremal pooling} of predicted atomic HOMO and LUMO contributions. Trained exclusively on excitations energies and forces, the architecture learns interpretable atomic-level contributions that encode physical information on the extent of electron localization. We demonstrate this framework on the photoexcited solvated electron in liquid water, a paradigmatic problem in radiation chemistry leading to competing pathways involving both hydrogen-atom dissociation and proton-coupled electron transfer. The model not only reproduces the relevant chain of reactions and product species that form during excitation, but also allows one to explicitly study the dynamics of the solvated electron in quantitative agreement with previously reported Restricted Open-Shell Kohn-Sham calculations, while enabling excited-state simulations of periodic systems at length and time scales inaccessible to the reference electronic-structure method. This work establishes a general strategy for machine learning-driven excited-state dynamics applicable to diverse photochemical systems, from molecular chromophores in solution to extended condensed-phase systems.

physics.chem-ph↗
arXiv2026

Machine learning the non-radiative decay modes in photochemical processes

Non-radiative decay in photoexcited molecular systems is driven by nuclear motion toward conical intersections (CIs), where electronic states become degenerate and nonadiabatic transitions occur. Identifying the nuclear degrees of freedom responsible for CI access from nonadiabatic molecular dynamics (NAD) simulations remains challenging because the underlying motions are high-dimensional and collective. Here, we introduce an unsupervised, information-theoretic framework based on Differentiable Information Imbalance (DII) to identify the nuclear coordinates governing CI access directly from trajectory surface hopping (TSH) simulations. By quantifying correlations between structural descriptors and electronic observables, including energy gaps and oscillator strengths, the method ranks nuclear degrees of freedom by predictive relevance. A multi-step protocol then extracts low-dimensional, physically interpretable modes associated with non-radiative decay. We apply the framework to the methaniminium cation, furan, L-glutamine, L-pyroglutamine-ammonium, and a photoactive molecular motor. Across all systems, the method recovers known mechanistic coordinates while revealing the relative importance of competing modes when multiple structural distortions contribute to CI access. The analysis also reveals a systematic distinction between observables: energy gaps are typically governed by a small number of localized coordinates, whereas oscillator strengths depend on more collective and distributed structural rearrangements. Overall, the DII-based framework combines predictive power with direct interpretability, providing a general and scalable route for extracting mechanistic insight from high-dimensional NAD data and constructing reduced-dimensional models of excited-state dynamics.

physics.chem-ph↗
arXiv2026

Beyond the Virial Expansion: Microscopic Origins of Partial Molar Volumes in LiCl Solutions

Although electrolyte density measurements have been reported for over a century, employing them to obtain accurate partial molar volume (PMV) profiles as a function of salt concentration has remained elusive. Obtaining such curves requires precise density measurements combined with a proper treatment of the associated virial expansion. In this work, we obtain PMV profiles for aqueous LiCl solutions. The resulting data enable the development of highly accurate force fields for Li$^+$ and Cl$^-$ ions, revealing a clear progression from isolated ions to ion pairs and ultimately to higher-order chain and ring structures. Because ion clustering emerges from complex, nonlocal interactions, it cannot be easily mapped onto specific virial terms. Instead, a direct structural and volumetric interpretation can be achieved by partitioning molecular dynamic (MD) simulation snapshots into three-dimensional polyhedral regions associated with individual salt ions and water molecules. The corresponding ionic and water volumes from this treatment quantitatively reproduce the experimental PMV curve. The results demonstrate that the PMV for salt increases (while that of water decreases) up to 6.7 M. Above this concentration, the direction reverses as three- and four-body interactions become prominent. Complementary multivariate curve resolution (MCR) Raman spectroscopy and density functional theory (DFT) calculations elucidate the molecular-level details of water electrostriction, which also persists up to 6.7 M. Significantly, the PMV data can be correlated with key thermodynamic properties, including the osmotic coefficient and the eutectic point. The procedures established here provide a general framework for modeling electrolyte solutions and enable the development of a new generation of accurate force fields for aqueous ions.

physics.chem-ph↗
arXiv2026

Interfacial Electric Fields in Water Nanodroplets are Weakly Dependent on Curvature and pH

The origin of enhanced reactivity in aqueous microdroplets remains debated, with interfacial electric fields (IEFs) often invoked as catalytic drivers. Here, we provide a quantum-mechanical, spatially resolved characterization of the electric field at air-water interfaces by combining deep-learning molecular dynamics with \emph{ab initio} re-sampling. Across planar interfaces and nanodroplets of varying curvature and charge state, we find an outward-oriented field of $\sim 1.0$--$1.2$ V/Å along the intrinsic surface normal. Crucially, its magnitude scales linearly with the average number of hydrogen bonds per interfacial molecule, directly tying the field to the local hydrogen-bond network. Despite its large magnitude and contrary to common expectations, we find that curvature and pH exert only a minor influence on the IEF, becoming negligible at experimentally relevant droplet sizes and pH. Consequently, the reactivity differences observed in $μ$m-sized droplets cannot be ascribed to variations in the IEF, which changes by a factor of only $\sim10^{-5}$ between $3$ and $40μ$m-sized droplets. Moreover, the IEF is localized inside the interfacial region and rapidly vanishes within a few Å. This strong spatial confinement renders the IEF strongly tied to the local electronic structure, identifying it as a local property of the air-water boundary rather than an independent physical driver of ``on-water'' catalysis.

physics.chem-ph↗
arXiv2026

Collective Electronic Polarization Drives Charge Asymmetry at Oil-Water Interfaces

Why kinetically stable oil droplets in water spontaneously acquire a negative charge remains one of the most vigorously debated questions in interfacial science. Here, we combine neural-network based deep potential molecular dynamics with a data-driven and information theory approach to probe the real-space electron density at an extended decane-water interface. While decane-water clusters show nearly symmetric forward and backward charge transfer (CT) and thus negligible net CT, the extended interface displays a systematic electronic asymmetry, yielding a net CT from water to the hydrocarbon phase producing an average surface charge density of $\sim0.006~e^{-}\,\mathrm{nm}^{-2}$ on the oil phase. This imbalance is accompanied by much larger intra-phase self-polarization, particularly within the hydrocarbon phase, demonstrating that collective many-body polarization dominates the interfacial electronic response. Structural analysis reveals an asymmetry between forward C--H$\cdots$O and backward O--H$\cdots$C motifs, providing a microscopic origin for a net CT from one phase to the other. Curiously, both the water O--H and decane C--H covalent bonds incur subtle contractions which originate from a response to the charge-separation layers at the interface. These features are fully consistent with the weak improper hydrogen-bonds forming at the oil-water interface that results in blue-shifts of the C-H modes.

physics.chem-ph↗
arXiv2026

The Photochemical Birth of the Hydrated Electron in Liquid Water

The photophysics and photochemistry associated with irradiating UV light in liquid water is central to numerous physical, chemical and biological processes. One of the key events involved in this process is the generation of the hydrated electron. Despite long study from both experimental and theoretical fronts, a unified understanding of the underlying mechanisms associated with the generation of the solvated electron have remained elusive. Here, using excited-state molecular dynamics simulations of condensed phase photoexcited liquid water, we unravel the key sequence of chemical events leading to the creation of the hydrated electron on the excited state. The process begins through the excitation localized mostly on specific topological defects in the hydrogen-bond network of water which is subsequently followed by two main reaction pathways. The first, leads to the creation of a hydrogen atom culminating in non-radiative decay back to the ground-state within 100 femtoseconds. The second involves a proton coupled electron transfer, giving rise to the formation of the hydronium ion, hydroxyl radical and the hydrated excess electron on the excited-state. This process is facilitated by ultrafast coupled rotational and translational motions of water molecules leading to the formation of water mediated ion-radical pairs in the network. These species can survive on the picosecond timescale and ultimately modulate the emission of visible photons. All in all, our findings provide fresh perspectives into the interpretation of several independent time-dependent spectroscopies measured over the last decades, paving the way for new directions on both theoretical and experimental fronts.

physics.chem-ph↗
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

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

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

Dynamical Heterogeneity in Supercooled Water and its Spectroscopic Fingerprints

A growing body of theoretical and experimental evidence strongly supports the existence of a second liquid-liquid critical point (LLCP) in deeply supercooled water leading to the co-existence of two phases: a high-and low-density liquid (HDL and LDL). While the thermodynamics associated with this putative LLCP has been well characterised through numerical simulations, the dynamical properties of these two phases close to the critical point remain much less understood. In this work, we investigate their dynamical and spectroscopic features using machine-learning interatomic potentials (MLIPs). Dynamical analyses using the van-Hove correlation function, reveal that LDL exhibits very sluggish and heterogeneous molecular mobility, in contrast to the faster and more homogeneous dynamics of HDL. Infrared absorption (IR) spectra further show clear vibrational distinctions between LDL and HDL, in particular in the far IR region between 400 - 1000 cm-1. Together, these findings provide new dynamical fingerprints that clarify the microscopic behavior of supercooled water and offer valuable guidance for experimental efforts aimed at detecting the long-sought liquid-liquid transition.

cond-mat.soft↗
arXiv2025

Acid Base Chemistry of Short Hydrogen Bonds: A Tale of Schrödinger's Cat in Glutamine-Derived Crystals

Short hydrogen bonds (SHBs), defined by donor-acceptor distances below 2.5 Angstrom, represent a distinct regime in acid-base chemistry where conventional models of hydrogen bonding break down. In an organic crystal formed via a temperature-induced chemical transformation of L-glutamine, we previously identified an SHB that is permissive to proton transfer, leading to a characteristic double-well potential implying an activated process. Herein, using path-integral ab initio molecular dynamics (PI-AIMD), we show that nuclear quantum effects (NQEs) completely eliminate the classical barrier, leading to a symmetrization of the proton along the hydrogen bond. While in the classical case the proton transfer is strongly coupled to the rocking modes of the ammonium ion in the crystal, NQEs significantly reduce these correlations. Examining the electronic structure through Wannier centers (WCs) further reveals a quantum-driven redistribution of bonding electrons, blurring the distinction between hydrogen bonding and covalency. Taken together, our findings indicate that NQEs in this organic crystal lead to a situation where both the donor and acceptor can simultaneously act as both an acid and a base.

physics.chem-ph↗
arXiv2025

Opportunities and Challenges in Unsupervised Learning: The Case of Aqueous Electrolyte Solutions

Machine learning has emerged as a powerful tool in atomistic simulations, enabling the identification of complex patterns in molecular systems limiting human intervention and bias. However, the practical implementation of these methods presents significant technical challenges, particularly in the selection of hyperparameters and in the physical interpretability of machine-learned descriptors. In this work, we systematically investigate these challenges by applying an unsupervised learning protocol to a fundamental problem in physical chemistry namely, how ions perturb the local structure of water. Using the Smooth Overlap of Atomic Positions(SOAP) descriptors, we demonstrate how the intrinsic dimension (ID) serves as a guide for selecting hyperparameters and interpreting structural complexity. Furthermore, we construct a high-dimensional free energy landscape encompassing all water environments surrounding different ions. This analysis reveals how the physical properties of ions are intricately reflected in their hydration shells, shaping the landscape through specific connections between different minima. Our findings highlight the difficulty in balancing algorithmic automation with the need of employing both physical and chemical intuition, particularly for the construction of meaningful descriptors and for the interpretation of final results. By critically assessing the methodological hurdles associated with unsupervised learning, we provide a road map for researchers looking to harness these techniques for studying electrolyte and aqueous solutions in general.

physics.chem-ph↗
arXiv2025

Towards a robust approach to infer causality in molecular systems satisfying detailed balance

The ability to distinguish between correlation and causation of variables in molecular systems remains an interesting and open area of investigation. In this work, we probe causality in a molecular system using two independent computational methods that infer the causal direction through the language of information transfer. Specifically, we demonstrate that a molecular dynamics simulation involving a single Tryptophan in liquid water displays asymmetric information transfer between specific collective variables, such as solute and solvent coordinates. Analyzing a discrete Markov-state and Langevin dynamics on a 2D free energy surface, we show that the same kind of asymmetries can emerge even in extremely simple systems, undergoing equilibrium and time-reversible dynamics. We use these model systems to rationalize the unidirectional information transfer in the molecular system in terms of asymmetries in the underlying free energy landscape and/or relaxation dynamics of the relevant coordinates. Finally, we propose a computational experiment that allows one to decide if an asymmetric information transfer between two variables corresponds to a genuine causal link.

physics.chem-ph↗