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We introduce a fragment orbital-based fewest switches surface hopping method, FOB-SH, designed to efficiently simulate charge carrier transport in strongly fluctuating condensed phase systems such as organic semiconductors and biomolecules. The charge carrier wavefunction is expanded and the electronic Hamiltonian constructed in a set of singly occupied molecular orbitals of the molecular sites that mediate the charge transfer. Diagonal elements of the electronic Hamiltonian (site energies) are obtained from a force field, whereas the off-diagonal or electronic coupling matrix elements are obtained using our recently developed analytic overlap method. We derive a general expression for the exact forces on the adiabatic ground and excited electronic state surfaces from the nuclear gradients of the charge localized electronic states. Applications to electron hole transfer in a model ethylene dimer and through a chain of ten model ethylenes validate our implementation and demonstrate its computational efficiency. On the larger system, we calculate the qualitative behaviour of charge mobility with change in temperature T for different regimes of the intermolecular electronic coupling. For small couplings, FOB-SH predicts a crossover from a thermally activated regime at low temperatures to a band-like transport regime at higher temperatures. For higher electronic couplings, the thermally activated regime disappears and the mobility decreases according to a power law. This is interpreted by a gradual loss in probability for resonance between the sites as the temperature increases. The polaron hopping model solved for the same system gives a qualitatively different result and underestimates the mobility decay at higher temperatures. Taken together, the FOB-SH methodology introduced here shows promise for a realistic investigation of charge carrier transport in complex organic, aqueous, and biological systems. [ABSTRACT FROM AUTHOR]

Thermoelectric materials convert a temperature gradient into a voltage. This phenomenon is relatively well understood for inorganic materials but much less so for organic semiconductors (OSs). These materials present a challenge because the strong thermal fluctuations of electronic coupling between the molecules result in partially delocalized charge carriers that cannot be treated with traditional theories for thermoelectricity. Here, we develop a quantum dynamical simulation approach revealing in atomistic detail how the charge carrier wave function moves along a temperature gradient in an organic molecular crystal. We find that the wave function propagates from hot to cold in agreement with the experiment, and we obtain a Seebeck coefficient in good agreement with experimental measurements that are also reported in this work. Detailed analysis reveals that gradients in thermal electronic disorder play an important role in determining the magnitude of the Seebeck coefficient, opening unexplored avenues for the design of OSs with improved Seebeck coefficients.

The protonation state of molecules and surfaces is pivotal in various disciplines, including (electro-)catalysis, geochemistry, biochemistry, and pharmaceutics. Accurately and efficiently determining acidity constants is critical yet challenging, particularly when explicitly considering the electronic structure, thermal fluctuations, anharmonic vibrations, and solvation effects. In this research, we employ thermodynamic integration accelerated by committee Neural Network potentials, training a single machine learning model that accurately describes the relevant protonated, deprotonated, and intermediate states. We investigate two deprotonation reactions at the BiVO 4 (010)-water interface, a promising candidate for efficient photocatalytic water splitting. Our results illustrate the convergence of the required ensemble averages over simulation time and of the final acidity constant as a function of the Kirkwood coupling parameter. We demonstrate that simulation times on the order of nanoseconds are required for statistical convergence. This time scale is currently unachievable with explicit ab-initio molecular dynamics simulations at the hybrid DFT level of theory. In contrast, our machine learning workflow only requires a few hundred DFT single point calculations for training and testing. Exploiting the extended time scales accessible, we furthermore asses the effect of commonly applied bias potentials. Thus, our study significantly advances calculating free energy differences with ab-initio accuracy., (© 2024 Wiley-VCH GmbH.)

The interaction of condensed phase systems with external electric fields is of major importance in a myriad of processes in nature and technology, ranging from the field-directed motion of cells (galvanotaxis), to geochemistry and the formation of ice phases on planets, to field-directed chemical catalysis and energy storage and conversion systems including supercapacitors, batteries and solar cells. Molecular simulation in the presence of electric fields would give important atomistic insight into these processes but applications of the most accurate methods such as ab-initio molecular dynamics (AIMD) are limited in scope by their computational expense. Here we introduce Perturbed Neural Network Potential Molecular Dynamics (PNNP MD) to push back the accessible time and length scales of such simulations. We demonstrate that important dielectric properties of liquid water including the field-induced relaxation dynamics, the dielectric constant and the field-dependent IR spectrum can be machine learned up to surprisingly high field strengths of about 0.2 V Å -1 without loss in accuracy when compared to ab-initio molecular dynamics. This is remarkable because, in contrast to most previous approaches, the two neural networks on which PNNP MD is based are exclusively trained on molecular configurations sampled from zero-field MD simulations, demonstrating that the networks not only interpolate but also reliably extrapolate the field response. PNNP MD is based on rigorous theory yet it is simple, general, modular, and systematically improvable allowing us to obtain atomistic insight into the interaction of a wide range of condensed phase systems with external electric fields., (© 2024. The Author(s).)

Theory, computation, and experiment have given strong evidence that charge carriers in organic molecular crystals form partially delocalized quantum objects that diffuse very efficiently via a mechanism termed transient delocalization. It is currently unclear how prevalent this mechanism is for exciton transport. Here we carry out simulation of singlet Frenkel excitons (FE) in a molecular organic semiconductor that belongs to the class of nonfullerene acceptors, O-IDTBR, using the recently introduced FE surface hopping nonadiabatic molecular dynamics method. We find that FE are, on average, localized on a single molecule in the crystal due to sizable reorganization energy and moderate excitonic couplings. Yet, our simulations suggest that the diffusion mechanism is more complex than simple local hopping; in addition to hopping, we observe frequent transient delocalization events where the exciton wave function expands over 10 or more molecules for a short period of time in response to thermal excitations within the excitonic band, followed by de-excitation and contraction onto a single molecule. The transient delocalization events lead to an increase in the diffusion constant by a factor of 3-4, depending on the crystallographic direction as compared to the situation where only local hopping events are considered. Intriguingly, O-IDTBR appears to be a moderately anisotropic 3D "conductor" for excitons but a highly anisotropic 2D conductor for electrons. Taken together with previous simulation results, two trends seem to emerge for molecular organic crystals: excitons tend to be more localized and slower than charge carriers due to higher internal reorganization energy, while exciton transport tends to be more isotropic than charge transport due to the weaker distance dependence of excitonic versus electronic coupling.

Multiheme cytochromes (MHCs) are the building blocks of highly conductive micrometre-long supramolecular wires found in so-called electrical bacteria. Recent studies have revealed that these proteins possess a long supramolecular array of closely packed heme cofactors along the main molecular axis alternating between perpendicular and stacking configurations (TST = T-shaped, stacked, T-shaped). While TST arrays have been identified as the likely electron conduit, the mechanisms of outstanding long-range charge transport observed in these structures remain unknown. Here we study charge transport on individual small tetraheme cytochromes (STCs) containing a single TST heme array. Individual STCs are trapped in a controllable nanoscale tunnelling gap. By modulating the tunnelling gap separation, we are able to selectively probe four different electron pathways involving 1, 2, 3 and 4 heme cofactors, respectively, leading to the determination of the electron tunnelling decay constant along the TST heme motif. Conductance calculations of selected single-STC junctions are in excellent agreement with experiments and suggest a mechanism of electron tunnelling with shallow length decay constant through an individual STC. These results demonstrate that an individual TST motif supporting electron tunnelling might contribute to a tunnelling-assisted charge transport diffusion mechanism in larger TST associations., Competing Interests: The authors declare no competing financial interest., (This journal is © The Royal Society of Chemistry.)

The physiological problem of chronic inflammation and its associated pathologies attract ongoing attention with regard to methods for their control. Current systemic pharmacological treatments present problematic side effects. Thus, the possibility of new anti-inflammatory compounds with differing mechanisms of action or biophysical properties is enticing. Cationic polymers, with their ability to act as carriers for other molecules or to form bio-compatible materials, present one such possibility. Although not well described, several polycations such as chitosan and polyarginine, have displayed anti-inflammatory properties. The present work shows the ubiquitous laboratory transfection reagent, polyethylenimine (PEI) and more specifically low molecular weight branched PEI (B-PEI) as also possessing such properties. Using a RAW264.7 murine cell line macrophage as an inflammation model, it is found the B-PEI 700 Da as being capable of reducing the production of several pro-inflammatory molecules induced by the endotoxin lipopolysaccharide. Although further studies are required for elucidation of its mechanisms, the revelation that such a common lab reagent may present these effects has wide-ranging implications, as well as an abundance of possibilities., (© 2024 The Authors. Macromolecular Bioscience published by Wiley‐VCH GmbH.)

Coupled trajectory mixed quantum-classical (CTMQC) dynamics is a rigorous approach to trajectory-based non-adiabatic dynamics, which has recently seen an improvement to energy conservation via the introduction of the CTMQC-E algorithm. Despite this, the method's two key quantities distinguishing it from Ehrenfest dynamics, the modified Born-Oppenheimer momentum and the quantum momentum, require regularization procedures in certain circumstances. Such procedures in the latter can cause instabilities, leading to undesirable effects, such as energy drift and spurious population transfer, which is expected to become increasingly prevalent when the system gets larger as such events would happen more frequently. We propose a further modification to CTMQC-E, which includes a redefinition of the quantum momentum, CTMQC-EDI (double intercept), such that it has no formal divergences. We then show for Tully models I-III and the double arch model that the algorithm has greatly improved total energy conservation and negligible spurious population transfer at all times, in particular in regions of strong non-adiabatic coupling. CTMQC-EDI, therefore, shows promise as a numerically robust non-adiabatic dynamics technique that accounts for decoherence from first principles and that is scalable to large molecular systems and materials., (© 2023 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).)

Evidence shows that charge carriers in organic semiconductors self-localize because of dynamic disorder. Nevertheless, some organic semiconductors feature reduced mobility at increasing temperature, a hallmark for delocalized band transport. Here we present the temperature-dependent mobility in two record-mobility organic semiconductors: dinaphtho[2,3-b:2',3'-f]thieno[3,2-b]-thiophene (DNTT) and its alkylated derivative, C8-DNTT-C8. By combining terahertz photoconductivity measurements with atomistic non-adiabatic molecular dynamics simulations, we show that while both crystals display a power-law decrease of the mobility (μ) with temperature (T) following μ ∝ T -n , the exponent n differs substantially. Modelling reveals that the differences between the two chemically similar semiconductors can be traced to the delocalization of the different states that are thermally accessible by charge carriers, which in turn depends on their specific electronic band structure. The emerging picture is that of holes surfing on a dynamic manifold of vibrationally dressed extended states with a temperature-dependent mobility that provides a sensitive fingerprint for the underlying density of states., (© 2023. The Author(s), under exclusive licence to Springer Nature Limited.)