A multiscale approach to model hydrogen bonding: The case of polyamide

Comprehending the Efficacy of Whitlock's Caffeine-Pincered Molecular Tweezer on β-Amyloid Aggregation

Alzheimer's disease (AD) stands as one of the most prevalent neurodegenerative conditions, leading to cognitive impairment, with no cure and preventive measures. Misfolding and aberrant aggregation of amyloid-β (Aβ) peptides are believed to be the underlying cause of AD. These amyloid aggregates culminate in the development of toxic Aβ oligomers and subsequent accumulation of β-amyloid plaques amidst neuronal cells in the brain, marking the hallmarks of AD. Drug development for the potentially curative treatment of Alzheimer's is, therefore, a tremendous challenge for the scientific community. In this study, we investigate the potency of Whitlock's caffeine-armed molecular tweezer in combating the deleterious effects of Aβ aggregation, with special emphasis on the seven residue Aβ16-22 fragment. Extensive all-atom molecular dynamics simulations are conducted to probe the various structural and conformational transitions of the peptides in an aqueous medium in both the presence and absence of tweezers. To explore the specifics of peptide-tweezer interactions, radial distribution functions, contact number calculations, binding free energies, and 2-D kernel density plots depicting the variation of distance-angle between the aromatic planes of the peptide-tweezer pair are computed. The central hydrophobic core, particularly the aromatic Phe residues, is crucial in the development of harmful amyloid oligomers. Notably, all analyses indicate reduced interpeptide interactions in the presence of the tweezer, which is attributed to the tweezer-Phe aromatic interaction. Upon increasing the tweezer concentration, the residues of the peptide are further encased in a hydrophobic environment created by the self-aggregating tweezer cluster, leading to the segregation of the peptide residues. This is further aided by the weakening of interstrand hydrogen bonding between the peptides, thereby impeding their self-aggregation and preventing the formation of neurotoxic β-amyloid. Furthermore, the study also highlights the efficacy of the molecular tweezer in destabilizing preformed amyloid fibrils as well as hindering the aggregation of the full-length Aβ1-42 peptide.

Exploring the Role of Hydroxy- and Phosphate-Terminated cis-1,4-Polyisoprene Chains in the Formation of Physical Junction Points in Natural Rubber: Insights from Molecular Dynamics Simulations

This study elucidates the pivotal role of terminal structures in cis-1,4-polyisoprene (PI) chains, contributing to the exceptional mechanical properties of Hevea natural rubber (NR). NR's unique networking structure, crucial for crack resistance, elasticity, and strain-induced crystallization, involves two terminal groups, ω and α. The proposed ω terminal structure is dimethyl allyl-(trans-1,4-isoprene)2, and α terminals exist in various forms, including hydroxy, ester, and phosphate groups. Among others, we investigated three types of cis-1,4-PI with different terminal combinations: HPIH (pure PI with H terminal), ωPIα6 (PI with ω and α6 terminals), and ωPIPO4 (PI with ω and PO4 terminals) and revealed significant dynamics variations. Hydrogen bonds between α6 and α6 and PO4 and PO4 residues in ωPIα6 and ωPIPO4 systems induce slower dynamics of hydroxy- and phosphate-terminated PI chains. Associations between α6 and α6 and PO4 and PO4 terminals are markedly stronger than ω and ω, and hydrogen terminals in HPIH and ω PIα6,PO4 systems. Phosphate terminals exhibit a stronger mutual association than hydroxy terminals. Potentials of mean force analysis and cluster-formation-fraction computations reveal stable clusters in ωPIα6 and ωPIPO4 , supporting the formation of polar aggregates (physical junction points). Notably, phosphate terminal groups facilitate large and highly stable phosphate polar aggregates, crucial for the natural networking structure responsible for NR's outstanding mechanical properties compared to synthetic PI rubber. This comprehensive investigation provides valuable insights into the role of terminal groups in cis-1,4-PI melt systems and their profound impact on the mechanical properties of NR.

Nontrivial effects of geometric and charge defects on one-dimensional confined water

Water confined within nanochannels with specific functionalities serves as the foundation for a variety of emerging nanofluidic applications. However, the structure and dynamics of the confined liquid are susceptibly influenced by practically hard-to-avoid defects, yet knowledge of this fact remains largely unexplored. Here, using extensive molecular dynamics simulations, we elucidate the significant influence of geometric and charge defects on one-dimensional confined water. We show that the two types of defects can both reshape the water density distribution by constraining the translocation of water molecules along the circumferential direction. In addition to structural alterations, collective translocation and rotation of water slabs arise during transportation under external pressure. Below the temperature threshold marking the initiation of liquid-solid transition, the geometric defect retards water diffusion through a pinning effect, while the charge defect induces an anti-freezing effect. The latter is attributed to the electrostatic interaction between the charge defect and water molecules that hinders the formation of a stable hydrogen bond network by disrupting molecular dipole orientation. Consequently, this behavior results in a reduction in the number and lifetime of hydrogen bonds within the phase transition interval. The distinct roles of the two types of defects could be utilized to control the structure and dynamics of confined liquids that may result in distinct functionalities for nanofluidic applications.

Hydrogen bonding heterogeneity correlates with protein folding transition state passage time as revealed by data sonification

Protein-protein and protein-water hydrogen bonding interactions play essential roles in the way a protein passes through the transition state during folding or unfolding, but the large number of these interactions in molecular dynamics (MD) simulations makes them difficult to analyze. Here, we introduce a state space representation and associated "rarity" measure to identify and quantify transition state passage (transit) events. Applying this representation to a long MD simulation trajectory that captured multiple folding and unfolding events of the GTT WW domain, a small protein often used as a model for the folding process, we identified three transition categories: Highway (faster), Meander (slower), and Ambiguous (intermediate). We developed data sonification and visualization tools to analyze hydrogen bond dynamics before, during, and after these transition events. By means of these tools, we were able to identify characteristic hydrogen bonding patterns associated with "Highway" versus "Meander" versus "Ambiguous" transitions and to design algorithms that can identify these same folding pathways and critical protein-water interactions directly from the data. Highly cooperative hydrogen bonding can either slow down or speed up transit. Furthermore, an analysis of protein-water hydrogen bond dynamics at the surface of WW domain shows an increase in hydrogen bond lifetime from folded to unfolded conformations with Ambiguous transitions as an outlier. In summary, hydrogen bond dynamics provide a direct window into the heterogeneity of transits, which can vary widely in duration (by a factor of 10) due to a complex energy landscape.

Second inflection point of supercooled water surface tension induced by hydrogen bonds: A molecular-dynamics study

Surface tension of supercooled water is a fundamental property in various scientific processes. In this study, we perform molecular dynamics simulations with the TIP4P-2005 model to investigate the surface tension of supercooled water down to 220 K. Our results show a second inflection point (SIP) in the surface tension at temperature TSIP ≈ 267.5 ± 2.3 K. Using an extended IAPWS-E functional fit for the water surface tension, we calculate the surface excess internal-energy and entropy terms of the excess Helmholtz free energy. Similar to prior studies [Wang et al., Phys. Chem. Chem. Phys. 21, 3360 (2019); Gorfer et al., J. Chem. Phys. 158, 054503 (2023)], our results show that the surface tension is governed by two driving forces: a surface excess entropy change above the SIP and a surface excess internal-energy change below it. We study hydrogen-bonding near the SIP because it is the main cause of water's anomalous properties. With decreasing temperature, our results show that the entropy contribution to the surface tension reaches a maximum slightly below the SIP and then decreases. This is because the number of hydrogen bonds increases more slowly below the SIP. Moreover, the strengths and lifetimes of the hydrogen bonds also rise dramatically below the SIP, causing the internal-energy term to dominate the excess surface free energy. Thus, the SIP in the surface tension of supercooled TIP4P-2005 water is associated with an increase in the strengths and lifetimes of hydrogen bonds, along with a decrease in the formation rate (#/K) of new hydrogen bonds.

Force matching and iterative Boltzmann inversion coarse grained force fields for ZIF-8

Despite the intense activity at electronic and atomistic resolutions, coarse grained (CG) modeling of metal-organic frameworks remains largely unexplored. One of the main reasons for this is the lack of adequate CG force fields. In this work, we present iterative Boltzmann inversion and force matching (FM) force fields for modeling ZIF-8 at three different coarse grained resolutions. Their ability to reproduce structure, elastic tensor, and thermal expansion is evaluated and compared with that of MARTINI force fields considered in previous work [Alvares et al., J. Chem. Phys. 158, 194107 (2023)]. Moreover, MARTINI and FM are evaluated for their ability to depict the swing effect, a subtle phase transition ZIF-8 undergoes when loaded with guest molecules. Overall, we found that all our force fields reproduce structure reasonably well. Elastic constants and volume expansion results are analyzed, and the technical and conceptual challenges of reproducing them are explained. Force matching exhibits promising results for capturing the swing effect. This is the first time these CG methods, widely applied in polymer and biomolecule communities, are deployed to model porous solids. We highlight the challenges of fitting CG force fields for these materials.

Tertiary Plasticity Drives the Efficiency of Enterocin 7B Interactions with Lipid Membranes

The ability of antimicrobial peptides to efficiently kill their bacterial targets depends on the efficiency of their binding to the microbial membrane. In the case of enterocins, there is a three-part interaction: initial binding, unpacking of helices on the membrane surface, and permeation of the lipid bilayer. Helical unpacking is driven by disruption of the peptide hydrophobic core when in contact with membranes. Enterocin 7B is a leaderless enterocin antimicrobial peptide produced from Enterococcus faecalis that functions alone, or with its cognate partner enterocin 7A, to efficiently kill a wide variety of Gram-stain positive bacteria. To better characterize the role that tertiary structural plasticity plays in the ability of enterocin 7B to interact with the membranes, a series of arginine single-site mutants were constructed that destabilize the hydrophobic core to varying degrees. A series of experimental measures of structure, stability, and function, including CD spectra, far UV CD melting profiles, minimal inhibitory concentrations analysis, and release kinetics of calcein, show that decreased stabilization of the hydrophobic core is correlated with increased efficiency of a peptide to permeate membranes and in killing bacteria. Finally, using the computational technique of adaptive steered molecular dynamics, we found that the atomistic/energetic landscape of peptide mechanical unfolding leads to free energy differences between the wild type and its mutants, whose trends correlate well with our experiment.

How do Antimicrobial Peptides Interact with the Outer Membrane of Gram-Negative Bacteria? Role of Lipopolysaccharides in Peptide Binding, Anchoring, and Penetration

Gram-negative bacteria possess a complex structural cell envelope that constitutes a barrier for antimicrobial peptides that neutralize the microbes by disrupting their cell membranes. Computational and experimental approaches were used to study a model outer membrane interaction with an antimicrobial peptide, melittin. The investigated membrane included di[3-deoxy-d-manno-octulosonyl]-lipid A (KLA) in the outer leaflet and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE) in the inner leaflet. Molecular dynamics simulations revealed that the positively charged helical C-terminus of melittin anchors rapidly into the hydrophilic headgroup region of KLA, while the flexible N-terminus makes contacts with the phosphate groups of KLA, supporting melittin penetration into the boundary between the hydrophilic and hydrophobic regions of the lipids. Electrochemical techniques confirmed the binding of melittin to the model membrane. To probe the peptide conformation and orientation during interaction with the membrane, polarization modulation infrared reflection absorption spectroscopy was used. The measurements revealed conformational changes in the peptide, accompanied by reorientation and translocation of the peptide at the membrane surface. The study suggests that melittin insertion into the outer membrane affects its permeability and capacitance but does not disturb the membrane's bilayer structure, indicating a distinct mechanism of the peptide action on the outer membrane of Gram-negative bacteria.

Properties of aqueous electrolyte solutions at carbon electrodes: effects of concentration and surface charge on solution structure, ion clustering and thermodynamics in the electric double layer

Surfaces are able to control physical-chemical processes in multi-component solution systems and, as such, find application in a wide range of technological devices. Understanding the structure, dynamics and thermodynamics of non-ideal solutions at surfaces, however, is particularly challenging. Here, we use Constant Chemical Potential Molecular Dynamics (CμMD) simulations to gain insight into aqueous NaCl solutions in contact with graphite surfaces at high concentrations and under the effect of applied surface charges: conditions where mean-field theories describing interfaces cannot (typically) be reliably applied. We discover an asymmetric effect of surface charge on the electric double layer structure and resulting thermodynamic properties, which can be explained by considering the affinity of the surface for cations and anions and the cooperative adsorption of ions that occurs at higher concentrations. We characterise how the sign of the surface charge affects ion densities and water structure in the double layer and how the capacitance of the interface-a function of the electric potential drop across the double layer-is largely insensitive to the bulk solution concentration. Notably, we find that negatively charged graphite surfaces induce an increase in the size and concentration of extended liquid-like ion clusters confined to the double layer. Finally, we discuss how concentration and surface charge affect the activity coefficients of ions and water at the interface, demonstrating how electric fields in this region should be explicitly considered when characterising the thermodynamics of both solute and solvent at the solid/liquid interface.

Fine Tuning Water States in Hydrogels for High Voltage Aqueous Batteries

Hydrogels are widely used as quasi-solid-state electrolytes in aqueous batteries. However, they are not applicable in high-voltage batteries because the hydrogen evolution reaction cannot be effectively suppressed even when water is incorporated into the polymer network. Herein, by profoundly investigating the states of water molecules in hydrogels, we designed supramolecular hydrogel electrolytes featuring much more nonfreezable bound water and much less free water than that found in conventional hydrogels. Specifically, two strategies are developed to achieve this goal. One strategy is adopting monomers with a variety of hydrophilic groups to enhance the hydrophilicity of polymer chains. The other strategy is incorporating zwitterionic polymers or polymers with counterions as superhydrophilic units. In particular, the nonfreezable bound water content increased from 0.129 in the conventional hydrogel to >0.4 mg mg-1 in the fabricated hydrogels, while the free water content decreased from 1.232 to ∼0.15 mg mg-1. As a result, a wide electrochemical stability window of up to 3.25 V was obtained with the fabricated hydrogels with low concentrations of incorporated salts and enhanced hydrophilic groups or superhydrophilic groups. The ionic conductivities achieved with our developed hydrogel electrolytes were much higher than those in the conventional highly concentrated salt electrolytes, and their cost is also much lower. The designed supramolecular hydrogel electrolytes endowed an aqueous K-ion battery (AKIB) system with a high voltage plateau of 1.9 V and contributed to steady cycling of the AKIB for over 3000 cycles. The developed supramolecular hydrogel electrolytes are also applicable to other batteries, such as aqueous lithium-ion batteries, hybrid sodium-ion batteries, and multivalent-ion aqueous batteries, and can achieve high voltage output.

Liquid-Liquid Phase Separation of the Intrinsically Disordered Domain of the Fused in Sarcoma Protein Results in Substantial Slowing of Hydration Dynamics

Formation of liquid condensates plays a critical role in biology via localization of different components or via altered hydrodynamic transport, yet the hydrogen-bonding environment within condensates, pivotal for solvation, has remained elusive. We explore the hydrogen-bond dynamics within condensates formed by the low-complexity domain of the fused in sarcoma protein. Probing the hydrogen-bond dynamics sensed by condensate proteins using two-dimensional infrared spectroscopy of the protein amide I vibrations, we find that frequency-frequency correlations of the amide I vibration decay on a picosecond time scale. Interestingly, these dynamics are markedly slower for proteins in the condensate than in a homogeneous protein solution, indicative of different hydration dynamics. All-atom molecular dynamics simulations confirm that lifetimes of hydrogen-bonds between water and the protein are longer in the condensates than in the protein in solution. Altered hydrogen-bonding dynamics may contribute to unique solvation and reaction dynamics in such condensates.

Molecular-Scale Exploration of Mechanical Properties and Interactions of Poly(lactic acid) with Cellulose and Chitin

Poly(lactic acid) (PLA), one of the pillars of the current overarching displacement trend switching from fossil- to natural-based polymers, is often used in association with polysaccharides to increase its mechanical properties. However, the use of PLA/polysaccharide composites is greatly hampered by their poor miscibility, whose underlying nature is still vastly unexplored. This work aims to shed light on the interactions of PLA and two representative polysaccharide molecules (cellulose and chitin) and reveal structure-property relationships from a fundamental perspective using atomistic molecular dynamics. Our computational strategy was able to reproduce key experimental mechanical properties of pure and/or composite materials, reveal a decrease in immiscibility in PLA/chitin compared to PLA/cellulose associations, assert PLA-oriented polysaccharide reorientations, and explore how less effective PLA-polysaccharide hydrogen bonds are related to the poor PLA/polysaccharide miscibility. The connection between the detailed chemical interactions and the composite behavior found in this work is beneficial to the discovery of new biodegradable and natural polymer composite mixtures that can provide needed performance characteristics.

Unravel the Tangle: Atomistic Insight into Ultrahigh Curcumin-Loaded Polymer Micelles

Amphiphilic ABA-triblock copolymers, comprised of poly(2-oxazoline) and poly(2-oxazine), can solubilize poorly water-soluble molecules in a structure-dependent manner forming micelles with exceptionally high drug loading. All-atom molecular dynamics simulations are conducted on previously experimentally characterized, curcumin-loaded micelles to dissect the structure-property relationships. Polymer-drug interactions for different levels of drug loading and variation in polymer structures of both the inner hydrophobic core and outer hydrophilic shell are investigated. In silico, the system with the highest experimental loading capacity shows the highest number of drug molecules encapsulated by the core. Furthermore, in systems with lower loading capacity outer A blocks show a greater extent of entanglement with the inner B blocks. Hydrogen bond analyses corroborate previous hypotheses: poly(2-butyl-2-oxazoline) B blocks, found experimentally to have reduced loading capacity for curcumin compared to poly(2-propyl-2-oxazine), establish fewer but longer-lasting hydrogen bonds. This possibly results from different sidechain conformations around the hydrophobic cargo, which is investigated by unsupervised machine learning to cluster monomers in smaller model systems mimicking different micelle compartments. Exchanging poly(2-methyl-2-oxazoline) with poly(2-ethyl-2-oxazoline) leads to increased drug interactions and reduced corona hydration; this suggests an impairment of micelle solubility or colloidal stability. These observations can help driving forward a more rational a priori nanoformulation design.

Role of Terminal Groups of cis-1,4-Polyisoprene Chains in the Formation of Physical Junction Points in Natural Rubber

The terminal structures of cis-1,4-polyisoprene (PI) chains play a vital role in the excellent comprehensive performance of Hevea natural rubber (NR) with properties such as high toughness, tear-resistance, and wet skid resistance. The cis-1,4-polyisoprene chain constituting NR exhibits a distinct composition of terminal groups comprising two distinct types, namely, the ω and α terminal groups. The structures of the ω terminal [dimethyl allyl (DMA)-(trans-1,4-isoprene)2] and six kinds of α end groups of the polymer chain of NR have been explored by utilizing a newly developed 2D NMR method. In the present work, we examine different kinds of PI melt systems, and we choose various combinations of terminal groups: Hydrogen, one DMA unit with two trans isoprene units as ω end groups and ester-terminated isopentene (α1), hydroxy-terminated isopentene (α2), ester-terminated isobutane (α3), hydroxy-terminated isobutane (α4), ester-terminated 1,4-cis-isoprene (α5), and hydroxy-terminated 1,4-cis-isoprene (α6), i.e., HPIH (PI0)-pure PI (Hydrogen terminal), ωPIα1 (PII), ωPIα2 (PIII), ωPIα3 (PIIII), ωPIα4 (PIIV), ωPIα5 (PIV), and ωPIα6 (PIVI). We evaluated dynamic and static properties of PI chains such as the end-to-end vector autocorrelation function (C(t)), its average relaxation time (τ), end-to-end distance (Ree), and radius of gyration (Rg). We also estimated the diffusion coefficients of polyisoprene chains and pair correlation functions [radial distribution functions (RDFs)], potentials of mean force (PMFs) in between end residues, and survival probability (P(τ)) of end groups around the end group by analyzing the equilibrated trajectories of full-atom MD simulations. As per the examination of C(t), rotational relaxation time τ, and RDFs, we discovered that the existence of a strong hydrogen bond in α2-α2, α4-α4, and α6-α6 residues makes the dynamics of hydroxy-terminated polyisoprene chains in ωPIα2,α4,α6 melt systems slower. From the analyses of RDFs and PMFs (W(r)), the association between [α2]-[α2], [α4]-[α4], and [α6]-[α6] terminals in ωPIα2,α4,α6 melt systems is significantly stronger than in [ISO]-[ISO] [Hydrogen terminated 1,4-cis-isoprene:(ISO)] in HPIH and ω-ω, [α1]-[α1], [α3]-[α3], and [α5]-[α5] in ωPIα1,α3,α5 systems. We quantified the fraction of cluster formation of terminal groups of a given size in the seven PI melt systems by employing the criteria of PMFs. It is revealed that no stable cluster exists in the HPIH, ωPIα1, ωPIα3, and ωPIα5 melt systems. Conversely, in the ωPIα2, ωPIα4, and ωPIα6 systems, we perceived stable clusters of [(α2)p] [(α4)p] and [(α6)p] end groups where p (2 ≤ x ≤ 6). These stable clusters validate the presence of physical junction points in between hydroxy-terminated polyisoprene chains through their α2, α4, and α6 terminals. These physical junction points might be crucial for superior properties of NR such as high toughness, crack growth resistance, and strain-induced crystallization.

Investigating the Hydrogen Bond-Induced Self-Assembly of Polysulfamides Using Molecular Simulations and Experiments

In this paper, we present a synergistic, experimental, and computational study of the self-assembly of N,N'-disubstituted polysulfamides driven by hydrogen bonds (H-bonds) between the H-bonding donor and acceptor groups present in repeating sulfamides as a function of the structural design of the polysulfamide backbone. We developed a coarse-grained (CG) polysulfamide model that captures the directionality of H-bonds between the sulfamide groups and used this model in molecular dynamics (MD) simulations to study the self-assembly of these polymers in implicit solvent. The CGMD approach was validated by reproducing experimentally observed trends in the extent of crystallinity for three polysulfamides synthesized with aliphatic and/or aromatic repeating units. After validation of our CGMD approach, we computationally predicted the effect of repeat unit bulkiness, length, and uniformity of segment lengths in the polymers on the extent of orientational and positional order among the self-assembled polysulfamide chains, providing key design principles for tuning the extent of crystallinity in polysulfamides in experiments. Those computational predictions were then experimentally tested through the synthesis and characterization of polysulfamide architectures.

Sampling the Bulk Viscosity of Water with Molecular Dynamics Simulation in the Canonical Ensemble

The bulk viscosity, a transport coefficient in the Navier-Stokes equation, is often neglected in the continuum mechanics of Newtonian fluids. Recently, however, the role of the bulk viscosity is highlighted in the area of surface and interface-related phenomena, in systematic model up-scaling and as an important quantity for the interpretation of acoustic sensor data. The prediction of the bulk viscosity usually employs molecular dynamics and the Green-Kubo linear response theory, which is used to sample transport properties in general from molecular trajectories. Since simulations are usually carried out at specified state points in concert with the evaluation of other thermodynamic properties, the role of thermostats in molecular dynamics needs to be explored systematically. In this work, we carefully investigate the role of thermostatting schemes and numerical implementations of the Green-Kubo formalism, in particular in the canonical ensemble, using two popular water force field models. It turns out that the sampling of the bulk and shear viscosities is a delicate challenge since details of thermostatting and numerical subtleties may have an influence on the results beyond statistical uncertainties. Based on the present findings, we conclude with hints on how to construct robust sampling in the canonical ensemble for the bulk viscosity.

Stable amorphous solid dispersion of flubendazole with high loading via electrospinning

In this work, an important step is taken towards the bioavailability improvement of poorly water-soluble drugs, such as flubendazole (Flu), posing a challenge in the current development of many novel oral-administrable therapeutics. Solvent electrospinning of a solution of the drug and poly (2-ethyl-2-oxazoline) (PEtOx) is demonstrated to be a viable strategy to produce stable nanofibrous amorphous solid dispersions (ASDs) with ultrahigh drug-loadings (up to 55 wt% Flu) and long-term stability (at least one year). Importantly, at such high drug loadings, the concentration of the polymer in the electrospinning solution has to be lowered below the concentration where it can be spun in absence of the drug as the interactions between the polymer and the drug result in increased solution viscosity. A combination of experimental analysis and molecular dynamics simulations revealed that this formulation strategy provides strong, dominant and highly stable hydrogen bonds between the polymer and the drug, which is crucial to obtain the high drug-loadings and to preserve the long-term amorphous character of the ASDs upon storage. In vitro drug release studies confirm the remarkable potential of this electrospinning formulation strategy by significantly increased drug solubility values and dissolution rates (respectively tripled and quadrupled compared to the crystalline drug), even after storing the formulation for one year.

Threonine Cavities Are Targetable Motifs That Control Alpha-Synuclein Fibril Growth

Recent high-resolution structures of alpha-synuclein (aSyn) fibrils offer promise for rational approaches to drug discovery for Parkinson's disease and Lewy body dementia. Harnessing the first such structures, we previously used molecular dynamics and free energy calculations to suggest that threonines 72 and 75─which line water-filled cavities within the fibril stacks─may be of central importance in stabilizing fibrils. Here, we used experimental mutagenesis of both wild-type and A53T aSyn to show that both threonine residues play important but surprisingly disparate roles in fibril nucleation and elongation. The T72A mutant, but not T75A, resulted in a large increase in the extent of fibrillization during primary nucleation, leading us to posit that T72 acts as a "brake" on run-away aggregation. An expanded set of simulations of five recent high-resolution fibril structures suggests that confinement of cavity waters around T72 correlates with this finding. In contrast, the T75A mutation led to a modest decrease in the extent of fibrillization. Furthermore, both T72A and T75A completely blocked the initial fibril elongation in seeded fibrillization. To test whether these threonine-lined cavities are druggable targets, we used computational docking to identify potential small-molecule binders. We show that the top-scoring hit, aprepitant, strongly promotes fibril growth while specifically interacting with aSyn fibrils and not monomer, and we offer speculation as to how such compounds could be used therapeutically.

All-Atom Molecular Dynamics of Pure Water-Methane Gas Hydrate Systems under Pre-Nucleation Conditions: A Direct Comparison between Experiments and Simulations of Transport Properties for the Tip4p/Ice Water Model

(1) Background: New technologies involving gas hydrates under pre-nucleation conditions such as gas separations and storage have become more prominent. This has necessitated the characterization and modeling of the transport properties of such systems. (2) Methodology: This work explored methane hydrate systems under pre-nucleation conditions. All-atom molecular dynamics simulations were used to quantify the performance of the TIP4P/2005 and TIP4P/Ice water models to predict the viscosity, diffusivity, and thermal conductivity using various formulations. (3) Results: Molecular simulation equilibrium was robustly demonstrated using various measures. The Green–Kubo estimation of viscosity outperformed other formulations when combined with TIP4P/Ice, and the same combination outperformed all TIP4P/2005 formulations. The Green–Kubo TIP4P/Ice estimation of viscosity overestimates (by 84% on average) the viscosity of methane hydrate systems under pre-nucleation conditions across all pressures considered (0–5 MPag). The presence of methane was found to increase the average number of hydrogen bonds over time (6.7–7.8%). TIP4P/Ice methane systems were also found to have 16–19% longer hydrogen bond lifetimes over pure water systems. (4) Conclusion: An inherent limitation in the current water force field for its application in the context of transport properties estimations for methane gas hydrate systems. A re-parametrization of the current force field is suggested as a starting point. Until then, this work may serve as a characterization of the deviance in viscosity prediction.

Implementation of Telescoping Boxes in Adaptive Steered Molecular Dynamics

Long-time dynamical processes, such as those involving protein unfolding and ligand interactions, can be accelerated and realized through steered molecular dynamics (SMD). The challenge has been the extraction of information from such simulations that generalize for complex nonequilibrium processes. The use of Jarzynski's equality opened the possibility of determining the free energy along the steered coordinate, but sampling over the nonequilibrium trajectories is slow to converge. Adaptive steered molecular dynamics (ASMD) and other related techniques have been introduced to overcome this challenge through the use of stages. Here, we take advantage of these stages to address the numerical cost that arises from the required use of very large solvent boxes. We introduce telescoping box schemes within adaptive steered molecular dynamics (ASMD) in which we adjust the solvent box between stages and thereby vary (and optimize) the required number of solvent molecules. We have benchmarked the method on a relatively long α-helical peptide, Ala₃₀, with respect to the potential of mean force and hydrogen bonds. We show that the use of telescoping boxes introduces little numerical error while significantly reducing the computational cost.

Revealing the Anticorrelation Behavior Mechanism between the Grotthuss and Vehicular Diffusions for Proton Transport in Concentrated Acid Solutions

In this study, we performed reactive molecular dynamics simulations to characterize proton solvation and transport in concentrated hydrochloric acid solutions. The correlation contribution to the total proton mean square displacement is found to be negative for all acid concentrations, indicating the anticorrelation between the Grotthuss and vehicular diffusions. For the vehicular diffusion, the hydronium ions tend to move freely toward the lone pair side independent of acid concentrations, whereas for the Grotthuss diffusion, the proton hopping direction is limited to one of the hydrogen-bonded water molecules on the opposite side of the lone pair region, which are specifically oriented with respect to the neighboring hydronium ion at higher acid concentrations. This result is justified by our findings of the higher fraction of proton rattling with the single hopping event and longer hydrogen bond lifetimes at higher acid concentrations. However, the angular distribution for both the vehicular and Grotthuss diffusions is found to be rather broad and comparable for all acid concentrations, and thus, the anticorrelation shows a minimal dependence on the acid concentration. Our results reveal that the anticorrelation behavior between the vehicle and Grotthuss diffusions is attributed to the amphiphilic nature of hydronium ions and thus is independent of the acid concentrations in solutions.

Supramolecular Proton Conductors Self-Assembled by Organic Cages

Proton conduction is vital for living systems to execute various physiological activities. The understanding of its mechanism is also essential for the development of state-of-the-art applications, including fuel-cell technology. We herein present a bottom-up strategy, that is, the self-assembly of Cage-1 and -2 with an identical chemical composition but distinct structural features to provide two different supramolecular conductors that are ideal for the mechanistic study. Cage-1 with a larger cavity size and more H-bonding anchors self-assembled into a crystalline phase with more proton hopping pathways formed by H-bonding networks, where the proton conduction proceeded via the Grotthuss mechanism. Small cavity-sized Cage-2 with less H-bonding anchors formed the crystalline phase with loose channels filled with discrete H-bonding clusters, therefore allowing for the translational diffusion of protons, that is, vehicle mechanism. As a result, the former exhibited a proton conductivity of 1.59 × 10^-4 S/cm at 303 K under a relative humidity of 48%, approximately 200-fold higher compared to that of the latter. Ab initio molecular dynamics simulations revealed distinct H-bonding dynamics in Cage-1 and -2, which provided further insights into potential proton diffusion mechanisms. This work therefore provides valuable guidelines for the rational design and search of novel proton-conducting materials.

How sodium chloride extends lifetime of bulk nanobubbles in water

We present a molecular dynamics simulation study on the effects of sodium chloride addition on stability of a nitrogen bulk nanobubble in water. We find that the lifetime of the bulk nanobubble is extended in the presence of NaCl and reveal the underlying mechanisms. We do not observe spontaneous accumulation or specific arrangement of ions/charges around the nanobubble. Importantly, we quantitatively show that the N₂ molecule selectively diffuses through water molecules rather than pass by any ions after it leaves the nanobubble due to the much weaker water-water interactions than ion-water interactions. The strong ion-water interactions cause hydration effects and disrupt hydrogen bond networks in water, which leave fewer favorable paths for the diffusion of N₂ molecules, and by that reduce the degree of freedom in the dissolution of the nanobubble and prolong its lifetime. These results demonstrate that the hydration of ions plays an important role in stability of the bulk nanobubble by affecting the dynamics of hydrogen bonds and the diffusion properties of the system, which further confirm and interpret the selective diffusion path of N₂ molecules and the extension of lifetime of the nanobubble. The new atomistic insights obtained from the present research could potentially benefit the practical application of bulk nanobubbles.

Effects of Salt Concentration on the Water and Ion Self-Diffusion Coefficients of a Model Aqueous Sodium-Ion Battery Electrolyte

The aqueous sodium-ion battery is a promising alternative to the well-known lithium-ion battery owing to the large abundance of sodium ion resources. Although it is safer than the lithium-ion battery, the voltage window of the sodium-ion battery is narrower than that of the lithium-ion battery, thus limiting its practical implementation. Therefore, a highly concentrated electrolyte is required to address this issue. In the present work, the effect of the salt concentration on the transport properties of water molecules is investigated via theoretical analyses at the quantum mechanical level. A molecular dynamics simulation at the quantum mechanical level revealed that as the salt concentration increases, the ion-water interactions became stronger, leading to a lower diffusivity and a lower electronic band gap. These imply that the superconcentrated aqueous-based electrolytes have high potentials for the sodium-ion battery applications.

Development of hybrid coarse-grained atomistic models for rapid assessment of local structuring of polymeric semiconductors

Decades of work in the field of computational study of semiconducting polymers using atomistic models illustrate the challenges of generating equilibrated models for this class of materials. While adopting a coarse-grained model can be helpful, the process of developing a suitable model is particularly non-trivial and time-consuming for semiconducting polymers due to a large number of different interactions with some having an anisotropic nature. This work introduces a procedure for the rapid generation of a hybrid model for semiconducting polymers where atoms of secondary importance (those in the alkyl side chains) are transformed into coarse-grained beads to reduce the computational cost of generating an equilibrated structure. The parameters are determined from easy-to-equilibrate simulations of very short oligomers and the model is constructed to enable a very simple back-mapping procedure to reconstruct geometries with atomistic resolution. The model is illustrated for three related polymers containing DPP (diketopyrrolopyrrole) to evaluate the transferability of the potential across different families of polymers. The accuracy of the model, determined by comparison with the results of fully equilibrated simulations of the same material before and after back-mapping, is fully satisfactory for two out of the three cases considered. We noticed that accuracy can be determined very early in the workflow so that it is easy to assess when the deployment of this method is advantageous. The hybrid representation can be used to evaluate directly the electronic properties of structures sampled by the simulations.

Hydrogen Coupling on Platinum Using Artificial Neural Network Potentials and DFT

To date, the understanding of reactions at solid-liquid interfaces has proven challenging, mainly because of the inaccessible nature of such systems to current experimental techniques with atomic resolution. This has meant that many important features, including free energy barriers and the atomistic structure of intermediates, remain unknown. To tackle these issues, we construct and utilize a high-dimensional neural network (HDNN) potential for the simulation of hydrogen evolution at the HCl(aq)/Pt(111) interface, taking into consideration the influence of adsorbate-adsorbate, adsorbate-solvent interactions, and ion solvation explicitly. Long time scale MD simulations reveal coadsorbed H_ad/H₂O_ad on the surface. The free energy profiles for the Tafel and Heyrovsky type hydrogen coupling are extracted using umbrella sampling. It is found that the preferential mechanism can change depending on the surface coverage, highlighting the dual mechanistic nature for HER on Pt(111). Our work demonstrates the importance of controlling the solvent-substrate interactions in developing catalysts beyond Pt.

Surface functionalization of boron nitride nanosheet with folic acid: Toward an enhancement in Doxorubicin anticancer drug loading performance

Loading of the Doxorubicin (DOX) as an anticancer drug molecule on boron nitride (BN) nanosheets with different sizes, in the presence and absence of Folic Acid (FA) functional groups, are investigated using molecular dynamic simulations. The obtained results from these investigations revealed that the drug molecules are spontaneously adsorbed the carriers and form stable complexes. It is also shown that an increase the nanosheet leads to an enhancement in its capacity to adsorb the drugs. Furthermore, the conjugation of BN with the FA group not only improves the BN efficiency for the drug adsorption but also helps the drug-carrier complex to target the cancerous cells. Evaluation of interaction energies reveals that L-J interaction plays an essential role in the adsorption of the drug molecules on the BN. The radial distribution function (RDF) shows that the highest drug position probability is around 0.6 nm away from the BN surface. Atomic RDF analysis is in line with the interaction energy analysis and proved that π-π stacking contributes the most to this process. Hydrogen bond (HB) analysis also shows that, although limited, the columbic interaction can be helpful in the adsorption process. Moreover, the free energy (FE) surface is explored for a system containing a BN nanosheet, an FA group, and a DOX molecule through metadynamics simulations. The obtained results reveal that the lowest FE point located in coordinations d1 = 0.70 nm and d2 = 0.84 nm, and energetically reached -280.42 kJ/mol. It can be concluded from the FE calculations that while the FA is stuck on the substrate, DOX faces difficulty in the way it be adsorbed. In return, it will be hard for the molecule to be released from the BN surface through desorption processes in neutral pH because it faces an energy barrier with a height of ∼100 kJ/mol at 1.6 nm.

The important role of non-covalent interactions for the vibrational circular dichroism of lactic acid in aqueous solution

We present a computational study of vibrational circular dichroism (VCD) in solutions of (S)-lactic acid, relying on ab initio molecular dynamics (AIMD) and full solvation with bulk water. We discuss the effect of the hydrogen bond network on the aggregation behaviour of the acid: while aggregates of the solute represent conditions encountered in a weakly interacting solvent, the presence of water drastically interferes with the clusters - more strongly than originally anticipated. For both scenarios we computed the VCD spectra by means of nuclear velocity perturbation theory (NVPT). The comparison with experimental data allows us to establish a VCD-structure relationship that includes the solvent network around the chiral solute. We suggest that fundamental modes with strong polarisation such as the carbonyl stretching vibration can borrow VCD from the chirally restructured solvent cage, which extends the common explanatory models of VCD generation in aqueous solution.

From System Modeling to System Analysis: The Impact of Resolution Level and Resolution Distribution in the Computer-Aided Investigation of Biomolecules

The ever increasing computer power, together with the improved accuracy of atomistic force fields, enables researchers to investigate biological systems at the molecular level with remarkable detail. However, the relevant length and time scales of many processes of interest are still hardly within reach even for state-of-the-art hardware, thus leaving important questions often unanswered. The computer-aided investigation of many biological physics problems thus largely benefits from the usage of coarse-grained models, that is, simplified representations of a molecule at a level of resolution that is lower than atomistic. A plethora of coarse-grained models have been developed, which differ most notably in their granularity; this latter aspect determines one of the crucial open issues in the field, i.e. the identification of an optimal degree of coarsening, which enables the greatest simplification at the expenses of the smallest information loss. In this review, we present the problem of coarse-grained modeling in biophysics from the viewpoint of system representation and information content. In particular, we discuss two distinct yet complementary aspects of protein modeling: on the one hand, the relationship between the resolution of a model and its capacity of accurately reproducing the properties of interest; on the other hand, the possibility of employing a lower resolution description of a detailed model to extract simple, useful, and intelligible information from the latter.

Relevance of hydrogen bonded associates to the transport properties and nanoscale dynamics of liquid and supercooled 2-propanol

2-Propanol was investigated, in both the liquid and supercooled states, as a model system to study how hydrogen bonds affect the structural relaxation and the dynamics of mesoscale structures, of approximately several Ångstroms, employing static and quasi-elastic neutron scattering and molecular dynamics simulation. Dynamic neutron scattering measurements were performed over an exchanged wave-vector range encompassing the pre-peak, indicative of the presence of H-bonding associates, and the main peak. The dynamics observed at the pre-peak is associated with the formation and disaggregation of the H-bonded associates and is measured to be at least one order of magnitude slower than the dynamics at the main peak, which is identified as the structural relaxation. The measurements indicate that the macroscopic shear viscosity has a similar temperature dependence as the dynamics of the H-bonded associates, which highlights the important role played by these structures, together with the structural relaxation, in defining the macroscopic rheological properties of the system. Importantly, the characteristic relaxation time at the pre-peak follows an Arrhenius temperature dependence whereas at the main peak it exhibits a non-Arrhenius behavior on approaching the supercooled state. The origin of this differing behavior is attributed to an increased structuring of the hydrophobic domains of 2-propanol accommodating a more and more encompassing H-bond network, and a consequent set in of dynamic cooperativity.

Development of Coarse-Grained Models for Poly(4-vinylphenol) and Poly(2-vinylpyridine): Polymer Chemistries with Hydrogen Bonding

In this paper, we identify the modifications needed in a recently developed generic coarse-grained (CG) model that captured directional interactions in polymers to specifically represent two exemplary hydrogen bonding polymer chemistries-poly(4-vinylphenol) and poly(2-vinylpyridine). We use atomistically observed monomer-level structures (e.g., bond, angle and torsion distribution) and chain structures (e.g., end-to-end distance distribution and persistence length) of poly(4-vinylphenol) and poly(2-vinylpyridine) in an explicitly represented good solvent (tetrahydrofuran) to identify the appropriate modifications in the generic CG model in implicit solvent. For both chemistries, the modified CG model is developed based on atomistic simulations of a single 24-mer chain. This modified CG model is then used to simulate longer (36-mer) and shorter (18-mer and 12-mer) chain lengths and compared against the corresponding atomistic simulation results. We find that with one to two simple modifications (e.g., incorporating intra-chain attraction, torsional constraint) to the generic CG model, we are able to reproduce atomistically observed bond, angle and torsion distributions, persistence length, and end-to-end distance distribution for chain lengths ranging from 12 to 36 monomers. We also show that this modified CG model, meant to reproduce atomistic structure, does not reproduce atomistically observed chain relaxation and hydrogen bond dynamics, as expected. Simulations with the modified CG model have significantly faster chain relaxation than atomistic simulations and slower decorrelation of formed hydrogen bonds than in atomistic simulations, with no apparent dependence on chain length.

Dynamical Accuracy of Water Models on Supercooling

Molecular dynamics (MD) simulations are commonly used to explore the structural and dynamical properties of supercooled bulk water in the so-called "no man's land" (NML) (150-227 K), where crystallization occurs almost instantaneously. This approach has provided significant insight into experimentally inaccessible phenomena. In this paper, we compare the dynamics of simulations using one-, three-, and four-body water models to experimentally measured quasielastic neutron scattering spectra. We show that the agreement between simulated and experimental data becomes substantially worse with a decrease in temperature toward the deeply supercooled regime. It was found that it is mainly the nature of the local dynamics that is poorly reproduced, as opposed to the macroscopic properties such as the diffusion coefficient. This strongly implies that the molecular mechanism describing the water dynamics is poorly captured in the MD models, and simulated structural and dynamical properties of supercooled water in NML must be interpreted with care.

Ligand-protein interactions in lysozyme investigated through a dual-resolution model

A fully atomistic (AT) modeling of biological macromolecules at relevant length- and time-scales is often cumbersome or not even desirable, both in terms of computational effort required and a posteriori analysis. This difficulty can be overcome with the use of multiresolution models, in which different regions of the same system are concurrently described at different levels of detail. In enzymes, computationally expensive AT detail is crucial in the modeling of the active site in order to capture, for example, the chemically subtle process of ligand binding. In contrast, important yet more collective properties of the remainder of the protein can be reproduced with a coarser description. In the present work, we demonstrate the effectiveness of this approach through the calculation of the binding free energy of hen egg white lysozyme with the inhibitor di-N-acetylchitotriose. Particular attention is payed to the impact of the mapping, that is, the selection of AT and coarse-grained residues, on the binding free energy. It is shown that, in spite of small variations of the binding free energy with respect to the active site resolution, the separate contributions coming from different energetic terms (such as electrostatic and van der Waals interactions) manifest a stronger dependence on the mapping, thus pointing to the existence of an optimal level of intermediate resolution.

100th Anniversary of Macromolecular Science Viewpoint: Modeling and Simulation of Macromolecules with Hydrogen Bonds: Challenges, Successes, and Opportunities

Macromolecular materials with directional interactions such as hydrogen bonds exhibit numerous attractive features in terms of structure, thermodynamics, and dynamics. Besides enabling precise tuning of desirable geometries in the assembled state (e.g., programmable coordination numbers depending on the valency of the directional interaction), mixing in a blend/composite through stabilization via hydrogen bonds between the various components, hydrogen bonds can also impart responsiveness to external stimuli (e.g., temperature, pH). In biomacromolecules (e.g., proteins, DNA, polysaccharides), hydrogen bonds play a key role in stabilizing secondary and tertiary structures, which in turn define the function of these macromolecules. In this Viewpoint, I present the challenges, successes, and opportunities for molecular modeling and simulations to conduct fundamental and application-focused research on macromolecular materials with hydrogen bonding interactions. The past successes and limitations of atomistic simulations are discussed first, followed by highlights from recent developments in coarse-grained modeling and their use in studies of (synthetic and biologically relevant) macromolecular materials. Model development focused on polynucleotides (e.g., DNA, RNA, etc.), polypeptides, polysaccharides, and synthetic polymers at experimentally relevant conditions are highlighted. This viewpoint ends with potential future directions for macromolecular modeling and simulations with other types of directional interactions beyond hydrogen bonding.

The effect of temperature on water desalination through two-dimensional nanopores

Two-dimensional (2D) materials such as graphene, molybdenum sulfide, and hexagonal boron nitride are widely studied for separation applications such as water desalination. Desalination across such 2D nanoporous membranes is largely influenced by the bulk transport properties of water, which are, in turn, sensitive to the operating temperature. However, there have been no studies on the effect of temperature on desalination through 2D nanopores. We investigated water desalination through hydrogen functionalized graphene nanopores of varying pore areas at temperatures 275.0 K, 300.0 K, 325.0 K, and 350.0 K. The water flux showed a direct relation with the diffusion coefficient and an inverse relation with the hydrogen-bond lifetime. As a direct consequence, the water flux was found to be related to the temperature as per the Arrhenius equation, similar to an activated process. The results from the present study improve the understanding on water and ion permeation across nanoporous 2D materials at different temperatures. Furthermore, the present investigation suggests a kinetic model, which can predict the water and ion permeation based on the characteristics of the nanopore.

Insight into Cellulose Dissolution with the Tetrabutylphosphonium Chloride-Water Mixture using Molecular Dynamics Simulations

All-atom molecular dynamics simulations are utilized to determine the properties and mechanisms of cellulose dissolution using the ionic liquid tetrabutylphosphonium chloride (TBPCl)–water mixture, from 63.1 to 100 mol % water. The hydrogen bonding between small and large cellulose bundles with 18 and 88 strands, respectively, is compared for all concentrations. The Cl, TBP, and water enable cellulose dissolution by working together to form a cooperative mechanism capable of separating the cellulose strands from the bundle. The chloride anions initiate the cellulose breakup, and water assists in delaying the cellulose strand reformation; the TBP cation then more permanently separates the cellulose strands from the bundle. The chloride anion provides a net negative pairwise energy, offsetting the net positive pairwise energy of the peeling cellulose strand. The TBP–peeling cellulose strand has a uniquely favorable and potentially net negative pairwise energy contribution in the TBPCl–water solution, which may partially explain why it is capable of dissolving cellulose at moderate temperatures and high water concentrations. The cellulose dissolution declines rapidly with increasing water concentration as hydrogen bond lifetimes of the chloride–cellulose hydroxyl hydrogens fall below the cellulose’s largest intra-strand hydrogen bonding lifetime.

Solvation of cholesterol in different solvents: a molecular dynamics simulation study

To the best of our knowledge, molecular dynamics simulations of an isolated cholesterol immersed in four different solvents of varying polarity, such as water, methanol, dimethyl sulfoxide and benzene, were reported for the first time to gain insights into the structural and dynamical properties. The study was mainly focused on the evaluation of solvation of cholesterol with respect to its hydrophilic and hydrophobic structural components in the form of respective functional groups interacting with the solvents. Structural evaluations suggested that both hydrophilic and hydrophobic groups of cholesterol were interacting with the solvents, in particular methanol and dimethyl sulfoxide, which presented both types of interactions that are polar and non-polar. On the other hand, the highly polar water and non-polar benzene demonstrated extreme solvation behavior, since water was involved only in hydrogen bonding to the solute hydroxyl group and non-polar benzene formed strong van der Waals interactions only. Furthermore, the hydrophobic effect of cholesterol was also analyzed mainly in polar solvents, as the effect was more pronounced in the polar environment thereby preventing the solvent mobility in the solvation layer(s). The dynamical properties in terms of lateral diffusion and hydrogen bond dynamics as well as free energies of solvation also corroborated the findings based on the structural data and the hydrophobic character of cholesterol was later quantified by the computation of the averaged solvent accessible surface area. The polarity effect of the solvents on the aggregation property of cholesterol was further investigated, which is of big concern from the clinical point of view due to its major role in cardiovascular ailments. It was another major finding of the present study that aggregation was shown to be facilitated by highly polar solvents like water.

Molecular Dynamics Study of the Effect of l-Alanine Chiral Dopants on Diluted Chromonic Solutions

Atomistic molecular dynamics simulations have been performed for disodium cromoglycate (DSCG) chromonic solutions mixed with l-alanine chiral dopants. We study the fundamental molecular mechanisms induced by low concentrations of l-alanine on diluted DSCG solutions, including their effect on the chromonic aggregates, the solvent, and sodium counterions. Simulations reveal that l-alanine molecules primarily interact with DSCG stacks establishing salt bridges between their respective ammonium and carboxylate groups. Our results demonstrate that l-alanine and sodium counterions jointly establish an intricate network of noncovalent interactions around DSCG aggregates that decreases the global electrostatic repulsion of the chromonic system. Two possible structural effects in DSCG aggregates arise from this electronic stabilization: the increment of the total number of consecutively stacked aromatic planes per DSCG aggregate (intracolumnar effect) or the partial separation reduction between neighboring DSCG columnar sections due to the simultaneous bridging of intercolumnar DSCG carboxylate sites by sodium counterions, forming sodium bridges (intercolumnar effect). Sodium bridges may be responsible for the formation of stacking faults in DSCG aggregates in the form of lateral overlap junctions. This mechanism would explain the difference between lower X-ray correlation lengths with the expected persistence length in chromonics.

From quantum to subcellular scales: multi-scale simulation approaches and the SIRAH force field

Modern molecular and cellular biology profits from astonishing resolution structural methods, currently even reaching the whole cell level. This is encompassed by the development of computational methods providing a deep view into the structure and dynamics of molecular processes happening at very different scales in time and space. Linking such scales is of paramount importance when aiming at far-reaching biological questions. Computational methods at the interface between classical and coarse-grained resolutions are gaining momentum with several research groups dedicating important efforts to their development and tuning. An overview of such methods is addressed herein, with special emphasis on the SIRAH force field for coarse-grained and multi-scale simulations. Moreover, we provide proof of concept calculations on the implementation of a multi-scale simulation scheme including quantum calculations on a classical fine-grained/coarse-grained representation of double-stranded DNA. This opens the possibility to include the effect of large conformational fluctuations in chromatin segments on, for instance, the reactivity of particular base pairs within the same simulation framework.