Observations of low-lying dark states in several photosynthetic complexes challenge our understanding of the mechanisms behind their efficient energy transfer processes. Computational models are... Show moreObservations of low-lying dark states in several photosynthetic complexes challenge our understanding of the mechanisms behind their efficient energy transfer processes. Computational models are necessary for providing novel insights into the nature and function of dark states, especially since these are not directly accessible in spectroscopy experiments. Here, we will focus on signatures of dark-type states in chlorosomes, a light-harvesting complex from green sulfur bacteria well-known for uniting a broad absorption band with very efficient energy transfer. In agreement with experiments, our simulations of two-dimensional electronic spectra capture the ultrafast exciton transfer occurring in 100s of femtoseconds within a single chlorosome cylinder. The sub-100 fs process corresponds to relaxation within the single-excitation manifold in a single chlorosome tube, where all initially created populations in the bright exciton states are quickly transferred to dark-type exciton states. Structural inhomogeneities on the local scale cause a redistribution of the oscillator strength, leading to the emergence of these dark-type exciton states, which dominate ultrafast energy transfer. The presence of the dark-type exciton states suppresses energy loss from an isolated chlorosome via fluorescence quenching, as observed experimentally. Our results further question whether relaxation to dark-exciton states is a leading process or merely competes with transfer to the baseplate within the photosynthetic apparatus of green sulfur bacteria. Show less
Pol, R.W.I. van der; Brinkmann, B.W.; Sevink, G.J.A. 2024
A fundamental understanding of proton transport through graphene nanopores, defects, and vacancies is essential for advancing two-dimensional proton exchange membranes (PEMs). This study employs... Show moreA fundamental understanding of proton transport through graphene nanopores, defects, and vacancies is essential for advancing two-dimensional proton exchange membranes (PEMs). This study employs ReaxFF molecular dynamics, metadynamics, and density functional theory to investigate the enhanced proton transport through a graphene nanopore. Covalently functionalizing the nanopore with a benzenesulfonic group yields consistent improvements in proton permeability, with a lower activation barrier (≈0.15 eV) and increased proton selectivity over sodium cations. The benzenesulfonic functionality acts as a dynamic proton shuttle, establishing a favorable hydrogen-bonding network and an efficient proton transport channel. The model reveals an optimal balance between proton permeability and selectivity, which is essential for effective proton exchange membranes. Notably, the benzenesulfonic-functionalized graphene nanopore system achieves a theoretically estimated proton diffusion coefficient comparable to or higher than the current state-of-the-art PEM, Nafion. Ergo, the benzenesulfonic functionalization of graphene nanopores, firmly holds promise for future graphene-based membrane development in energy conversion devices. Show less
Milano, G.; Sevink, G.J.A.; Lu, Z.Y.; Zhao, Y.; De Nicola, A.; Munaò, G.; Kawakatsu, T. 2024
The antenna complex of green sulfur bacteria, the chlorosome, is one of the most efficient supramolecular systems for efficient long-range exciton transfer in nature. Femtosecond transient... Show moreThe antenna complex of green sulfur bacteria, the chlorosome, is one of the most efficient supramolecular systems for efficient long-range exciton transfer in nature. Femtosecond transient absorption experiments provide new insight into how vibrationally induced quantum overlap between exciton states supports highly efficient long-range exciton transfer in the chlorosome of Chlorobium tepidum. Our work shows that excitation energy is delocalized over the chlorosome in <1 ps at room temperature. The following exciton transfer to the baseplate occurs in ∼3 to 5 ps, in line with earlier work also performed at room temperature, but significantly faster than at the cryogenic temperatures used in previous studies. This difference can be attributed to the increased vibrational motion at room temperature. We observe a so far unknown impact of the excitation photon energy on the efficiency of this process. This dependency can be assigned to distinct optical domains due to structural disorder, combined with an exciton trapping channel competing with exciton transfer toward the baseplate. An oscillatory transient signal damped in <1 ps has the highest intensity in the case of the most efficient exciton transfer to the baseplate. These results agree well with an earlier computational finding of exciton transfer driven by low-frequency rotational motion of molecules in the chlorosome. Such an exciton transfer process belongs to the quantum coherent regime, for which the Förster theory for intermolecular exciton transfer does not apply. Our work hence strongly indicates that structural flexibility is important for efficient long-range exciton transfer in chlorosomes. Show less
Ingested nanomaterials are exposed to many metabolites that are produced, modified, or regulated by members of the enteric microbiota. The adsorption of these metabolites potentially affects the... Show moreIngested nanomaterials are exposed to many metabolites that are produced, modified, or regulated by members of the enteric microbiota. The adsorption of these metabolites potentially affects the identity, fate, and biodistribution of nanomaterials passing the gastrointestinal tract. Here, we explore these interactions using in silico methods, focusing on a concise overview of 170 unique enteric microbial metabolites which we compiled from the literature. First, we construct quantitative structure–activity relationship (QSAR) models to predict their adsorption affinity to 13 metal nanomaterials, 5 carbon nanotubes, and 1 fullerene. The models could be applied to predict log k values for 60 metabolites and were particularly applicable to ‘phenolic, benzoyl and phenyl derivatives’, ‘tryptophan precursors and metabolites’, ‘short-chain fatty acids’, and ‘choline metabolites’. The correlations of these predictions to biological surface adsorption index descriptors indicated that hydrophobicity-driven interactions contribute most to the overall adsorption affinity, while hydrogen-bond interactions and polarity/polarizability-driven interactions differentiate the affinity to metal and carbon nanomaterials. Next, we use molecular dynamics (MD) simulations to obtain direct molecular information for a selection of vitamins that could not be assessed quantitatively using QSAR models. This showed how large and flexible metabolites can gain stability on the nanomaterial surface via conformational changes. Additionally, unconstrained MD simulations provided excellent support for the main interaction types identified by QSAR analysis. Combined, these results enable assessing the adsorption affinity for many enteric microbial metabolites quantitatively and support the qualitative assessment of an even larger set of complex and biologically relevant microbial metabolites to carbon and metal nanomaterials. Show less
The most efficient light-harvesting antennae found in nature, chlorosomes, are molecular tubular aggregates (TMAs) assembled by pigments without protein scaffolds. Here, we discuss a classification... Show moreThe most efficient light-harvesting antennae found in nature, chlorosomes, are molecular tubular aggregates (TMAs) assembled by pigments without protein scaffolds. Here, we discuss a classification of chlorosomes as a unique tubular plastic crystal and we attribute the robust energy transfer in chlorosomes to this unique nature. To systematically study the role of supramolecular tube chirality by molecular simulation, a role that has remained unresolved, we share a protocol for generating realistic tubes at atomic resolution. We find that both the optical and the mechanical behavior are strongly dependent on chirality. The optical-chirality relation enables a direct interpretation of experimental spectra in terms of overall tube chirality. The mechanical response shows that the overall chirality regulates the hardness of the tube and provides a new characteristic for relating chlorosomes to distinct chirality. Our protocol also applies to other TMA systems and will inspire other systematic studies beyond lattice models. Show less
Understanding the uptake of nanoparticles (NPs) by different types of cellular membranes plays a pivotal role in the design of NPs for medical applications and in avoiding adverse effects that... Show moreUnderstanding the uptake of nanoparticles (NPs) by different types of cellular membranes plays a pivotal role in the design of NPs for medical applications and in avoiding adverse effects that result in nanotoxicity. Yet, the role of key design parameters, such as the bare NP material, NP size and surface reactivity, and the nature of NP coatings, in membrane remodelling and uptake mechanisms is still very poorly understood, particularly towards the lower range of NP dimensions that are beyond the experimental imaging resolution. The same can be said about the role of a particular membrane composition. Here, we systematically employ biased and unbiased molecular dynamics simulations to calculate the binding energy for three bare materials (Ag/SiO2/TiO2) and three NP sizes (1/3/5 nm diameter) with a representative lung surfactant membrane, and to study their binding kinetics. The calculated binding energies show that irrespective of size, Ag nanoparticles bind very strongly to the bilayer, while the NPs made of SiO2 or TiO2 experience very low to no binding. The unbiased simulations provide insight into how the NPs and membrane affect each other in terms of the solvent-accessible surface area (SASA) of the NPs and the defect types and fluidity of the membrane. Using these systematic fine-grained results in coarsening procedures will pave the way for simulations considering NP sizes that are well beyond the membrane thickness, i.e. closer to experimental dimensions, for which different binding characteristics and more significant membrane remodelling are expected. Show less
Chlorosomes stand out for their highly efficient excitation energy transfer (EET) in extreme low light conditions. Yet, little is known about the EET when a chlorosome is excited to a pure state... Show moreChlorosomes stand out for their highly efficient excitation energy transfer (EET) in extreme low light conditions. Yet, little is known about the EET when a chlorosome is excited to a pure state that is an eigenstate of the exciton Hamiltonian. In this work, we consider the dynamic disorder in the intermolecular electronic coupling explicitly by calculating the electronic coupling terms in the Hamiltonian using nuclear coordinates that are taken from molecular dynamics simulation trajectories. We show that this dynamic disorder is capable of driving the evolution of the exciton, being a stationary state of the initial Hamiltonian. In particular, long-distance excitation energy transfer between domains of high exciton population and oscillatory behavior of the population in the site basis are observed, in line with two-dimensional electronic spectroscopy studies. We also found that in the high exciton population domains, their population variation is correlated with their overall coupling strength. Analysis in a reference state basis shows that such dynamic disorder, originating from thermal energy, creates a fluctuating landscape for the exciton and promotes the EET process. We propose such dynamic disorder as an important microscopic origin for the high efficient EET widely observed in different types of chlorosomes, bioinspired tubular aggregates, or other light-harvesting complexes. Show less
Liu, X.; He, M.; Calvani, D.; Qi, H.; Sai Sankar Gupta, K.B.; Groot, H.J.M. de; ... ; Schneider, G.F. 2020
Lipid A is one of the three components of bacterial lipopolysaccharides constituting the outer membrane of Gram-negative bacteria, and is recognized to have an important biological role in the... Show moreLipid A is one of the three components of bacterial lipopolysaccharides constituting the outer membrane of Gram-negative bacteria, and is recognized to have an important biological role in the inflammatory response of mammalians. Its biological activity is modulated by the number of acyl-chains that are present in the lipid and by the dielectric medium, i.e., the type of counter-ions, through electrostatic interactions. In this paper, we report on a coarse-grained model of chemical variants of Lipid A based on the hybrid particle-field/molecular dynamics approach (hPF-MD). In particular, we investigate the stability of Lipid A bilayers for two different hexa- and tetra-acylated structures. Comparing particle density profiles along bilayer cross-sections, we find good agreement between the hPF-MD model and reference all-atom simulation for both chemical variants of Lipid A. hPF-MD models of constituted bilayers composed by hexa-acylated Lipid A in water are stable within the simulation time. We further validate our model by verifying that the phase behavior of Lipid A/counterion/water mixtures is correctly reproduced. In particular, hPF-MD simulations predict the correct self-assembly of different lamellar and micellar phases from an initially random distribution of Lipid A molecules with counterions in water. Finally, it is possible to observe the spontaneous formation and stability of Lipid A vesicles by fusion of micellar aggregates. Show less
Nicola, A. de; Munao, G.; Grizzuti, N.; Auriemma, F.; Rosa, C. de; Sevink, G.J.A.; Milano, G. 2020
The tacticity of vinyl polymer chains strongly affects the physical properties of polymeric materials, as example the chain conformations and stiffness. In the present work we tested how the hybrid... Show moreThe tacticity of vinyl polymer chains strongly affects the physical properties of polymeric materials, as example the chain conformations and stiffness. In the present work we tested how the hybrid Particle-Field Molecular Dynamics (PF-MD) technique is capable to describe conformational differences of polymer chains as function of the tacticity. In particular, we focus on tacticity effect of atactic, isotactic, and syndiotactic polypropylene (PP) homopolymer melts. We found that PF-MD simulations exhibit dependence of Flory's Characteristic Ratio from the fraction of racemo diads along the PP chains in qualitative agreement with Small Angle Neutron Scattering (SANS) experiments and theoretical previsions. Finally, we calculated and compared the packing length parameter on very high stereoregular syndiotactic PP systems with rheological measurements. A qualitative agreement between the calculated and experimental packing length is found. Show less
