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Cryptochromes are proteins that are highly conserved across species and in many instances bind the flavin adenine dinucleotide (FAD) cofactor within their photolyase-homology region (PHR) domain. The FAD cofactor has multiple redox states that help catalyze reactions, and absorbs photons at about 450 nm, a feature linked to the light-related functions of cryptochrome proteins. Reactive oxygen species (ROS) are produced from redox reactions involving molecular oxygen and are involved in a myriad of biological processes. Superoxide O2•–is an exemplary ROS that may be formed through electron transfer from FAD to O2, generating an electron radical pair. Although the formation of a superoxide–FAD radical pair has been speculated, it is still unclear if the required process steps could be realized in cryptochrome. Here, we present results from molecular dynamics (MD) simulations of oxygen interacting with the PHR domain of Arabidopsis thalianacryptochrome 1 (AtCRY1). Using MD simulation trajectories, oxygen binding locations are characterized through both the O2–FAD intermolecular distance and the local protein environment. Oxygen unbinding times are characterized through replica simulations of the bound oxygen. Simulations reveal that oxygen molecules can localize at certain sites within the cryptochrome protein for tens of nanoseconds, and superoxide molecules can localize for significantly longer. This relatively long-duration molecule binding suggests the possibility of an electron-transfer reaction leading to superoxide formation. Estimates of electron-transfer rates using the Marcus theory are performed for the identified potential binding sites. Molecular oxygen binding results are compared with recent results demonstrating long-time oxygen binding within the electron-transfer flavoprotein (ETF), another FAD binding protein.

Elevated fluoride concentrations in drinking water cause dental and skeletal disease and pose a major human health challenge in many parts of the world. Precipitation of fluoride in mineral matrices is an attractive method of remediation due to its low cost and ease of use. Here we demonstrate that fluoride can be effectively removed from groundwater by adding a mixture of hydroxyapatite and calcite and cycling the pH. Below 20 ppm fluoride, fluoride precipitates as fluoroapatite on the hydroxyapatite surface; at higher fluoride concentrations, fluoride precipitates as fluorite. The efficiency of fluoride removal can be controlled by changing the hydroxyapatite : calcite ratio. Experiments with simulated groundwater from areas with high geogenic fluoride show that common groundwater ions have minimal effect on fluoride sorption or precipitation. This technique thus has widespread applicability to remediation of fluoride-contaminated groundwater around the world as well as ancillary waste streams where fluoride is a byproduct of industrial processes.

Reactive oxygen species (ROS) exert a wide range of biological effects from beneficial regulatory function to deleterious oxidative stress. The electron transfer flavoprotein (ETF) is ubiquitous to life and is associated with aerobic metabolism and ROS production due to its location in the mitochondria. Quantifying oxygen localization within the ETF complex is critical for understanding the potential for electron transfer and radical pair formation between flavin adenine dinucleotide (FAD) cofactor and superoxide during ROS formation. Our study employed all-atom molecular dynamics simulations and identified several novel, long-lived oxygen binding sites within the ETF complex that appear near the FAD cofactor. Site locations, the local electrostatic environment, and characteristic oxygen binding times for each site were evaluated to establish factors that may lead to possible charge transfer reactions and superoxide formation within the ETF complex. The study revealed that some oxygen binding sites are naturally linked to protein domain features, suggesting opportunities to engineer and control ROS production and subsequent dynamics.

Polymer synthesis routes result in macromolecules with molecular weight dispersity ĐMthat depends on the polymerization mechanism. The lowest dispersity polymers are those made by anionic and atom-transfer radical polymerization, which exhibit narrow distributions ĐM= Mw/Mn∼ 1.02–1.04. Even for small dispersity, the chain length can vary by a factor of two from the average. The impact of chain length dispersity on the viscoelastic response remains an open question. Here, the effects of dispersity on stress relaxation and shear viscosity of entangled polyethylene melts are studied using molecular dynamics simulations. Melts with chain length dispersity, which follow a Schulz–Zimm (SZ) distribution with ĐM= 1.0–1.16, are studied for times up to 800 μs, longer than the terminal time. These systems are compared to those with binary and ternary distributions. The stress relaxation functions are extracted from the Green–Kubo relation and from stress relaxation following a uniaxial extension. At short and intermediate time scales, both the mean squared displacement and the stress relaxation function G(t) are independent of ĐM. At longer times, the terminal relaxation time decreases with increasing ĐM. In this time range, the faster motion of the shorter chains results in constraint release for the longer chains.

Photoresponsive molecules can be integrated into glassy materials to probe the local environment and invoke responsive changes in polymer behavior. For example, recent experiments and simulations have studied increased stability in vapor-deposited glasses by examining the photoisomerization rate of a probe molecule. At the theoretical level, past work relied on coarse-grained simulations to explain the role of photoisomerization on glass behavior. In order to effectively exploit these molecular probes, an ability to quantify how the local environment influences the photoisomerization rate is needed. In this work, we present all-atom molecular-dynamics (MD) simulations of molecular glasses of photoresponsive azobenzene (AB) molecules. The stability of these in-silico samples is probed using photoisomerization, where AB molecules can undergo trans → cis transition upon light exposure. Vapor-deposited and bulk-cooled glasses of AB are simulated using a classical dihedral-switching potential developed by Böckmann et al. (J. Phys. Chem. A2010,114,745–754) to model the photoisomerization process. The MD simulations include thousands of molecules and run for tens of nanoseconds. These size and time scales allow us to explore the broad distribution of photoisomerization wait times, which yields two results. First, the wait-time distributions for both physical vapor deposition and bulk-cooled glasses depend strongly on sample and local density, showing that density or local packing is a primary factor in glass stability against photoisomerization and the experimentally measured photoresponse. Second, the distribution follows a power-law with exponent b≈ 1.25–1.3 that extends to longer times with increasing density. The power-law distribution suggests a connection with previous experiments that related barriers to photoisomerization with an effective photoisomerization temperature.

Pressure-driven assembly of ligand-grafted gold nanoparticle superlattices is a promising approach for fabricating gold nanostructures, such as nanowires and nanosheets. Optimizing this fabrication method will require extending our understanding of superlattice mechanics to regimes of high pressures. We use molecular dynamics simulations to characterize the response of alkanethiol-grafted gold nanoparticle superlattices to applied hydrostatic pressures up to 15 GPa. At low applied pressures, intrinsic voids govern the mechanics of compaction. As applied pressures increase, the void collapse and ligand compression depend significantly on the ligand length. These microstructural observations correlate directly with trends in bulk modulus and elastic constants. For short ligands, core–core contact between gold nanoparticles is observed at high pressures, which augurs irreversible response and eventual sintering. This presintering behavior was unexpected under hydrostatic loading and is observed only for the shortest ligands.

Coarse-grained (CG) polymer simulations can access longer times and larger lengths than all-atom (AA) molecular dynamics simulations; however, not all CG models correctly reproduce polymer properties on all length scales. Here we coarse-grain atomistic position data from polyethylene (PE) and polytetrafluoroethylene (PTFE) melt simulations by combining λ backbone carbon atoms in a single CG bead. Resulting CG variables have correlations along the chain backbone that depend on the coarse-graining scale λ and are generally not reproduced by independent bond-length, bond-angle and torsion-angle distributions. By constructing distributions of CG variables equivalent to those from simulated CG potentials we are able to evaluate the bond-orientation correlation for different CG models at reduced computational cost. CG models and potentials that include only nonbonded, bond-length, and bond-angle interactions computed by Boltzmann inversion correctly reproduce the CG variable distributions but do not necessarily reproduce the chain stiffness, overestimating the persistence length Lpand end-to-end distance ⟨R2⟩1/2with increasing λ. While CG models that include an independent torsion angle match the bond-orientation correlation and ⟨R2⟩1/2better, only approximate models that include correlations between bond and torsion angles match the true bond-orientation correlation.

The distinctive viscoelastic behavior of polymers results from a coupled interplay of motion on multiple length and time scales. Capturing the broad time and length scales of polymer motion remains a challenge. Using polyethylene (PE) as a model macromolecule, we construct coarse-grained (CG) models of PE with three to six methyl groups per CG bead and probe two critical aspects of the technique: pressure corrections required after iterative Boltzmann inversion (IBI) to generate CG potentials that match the pressure of reference fully atomistic melt simulations and the transferability of CG potentials across temperatures. While IBI produces nonbonded pair potentials that give excellent agreement between the atomistic and CG pair correlation functions, the resulting pressure for the CG models is large compared with the pressure of the atomistic system. We find that correcting the potential to match the reference pressure leads to nonbonded interactions with much deeper minima and slightly smaller effective bead diameter. However, simulations with potentials generated by IBI and pressure-corrected IBI result in similar mean-square displacements (MSDs) and stress autocorrelation functions G(t) for PE melts. While the time rescaling factor required to match CG and atomistic models is the same for pressure- and non-pressure-corrected CG models, it strongly depends on temperature. Transferability was investigated by comparing the MSDs and stress autocorrelation functions for potentials developed at different temperatures.