Nanoscale Chemical Imaging of Nanoparticles under Real-World Wastewater Treatment Conditions
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99 GENERAL AND MISCELLANEOUS↗
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Alkyl Chain Regiochemistry of Benzotriazole‐Based Donor Polymers Influencing Morphology and Performances of Non‐Fullerene Organic Solar Cells
Abstract The effects of alkyl chain regiochemistry on the properties of donor polymers and performances of non‐fullerene organic solar cells are investigated. Two donor polymers (PfBTAZ and PfBTAZS) are compared that have nearly identical chemical structures except for the regiochemistry of alkyl chains. The optical properties and crystallinity of two polymers are nearly identical yet the PfBTAZ:O‐IDTBR blend exhibits nearly double domain size compared to the blend based on PfBTAZS:O‐IDTBR. To reveal the origins of the very different domain size of two blends, the morphology of neat polymer films is characterized, and it is found that PfBTAZ tends to aggregate into much larger polymer fibers without the presence of O‐IDTBR. This indicates that it is not the polymer:O‐IDTBR interactions but the intrinsic aggregation properties of two polymers that determine the morphology features of neat and blend films. The stronger aggregation tendency of PfBTAZ could be explained by its more co‐planar geometry of the polymer backbone arising from the different alkyl chain regiochemistry. Combined with the similar trend observed in another set of donor polymers (PTFB‐P and PTFB‐PS), the results provide an important understanding of the structure–property relationships that could guide the development of donor polymers for non‐fullerene organic solar cells.
Chen, Shangshang↗
Regulation of Side‐Chain Symmetry for Delaying Triplet Formation and Suppressing Non‐Radiative Loss in Organic Solar Cells
Abstract The structural revolutions of non‐fullerene acceptors (NFAs) have driven continuous efficiency breakthroughs in organic solar cells (OSCs). Rational regulation of NFA structures toward efficient exciton dissociation and mitigated non‐radiative recombination is pivotal for OSCs. The incorporation of asymmetric side chains on NFAs can often achieve these goals by inducing a desirable aggregate state. However, it lacks the studies to directly correlate the side‐chain symmetry of NFAs with the exciton delocalization and triplet dynamics in OSCs. Herein, The influence of structural symmetry on the aggregate properties is systematically investigated and exciton/charge dynamics based on two developed biaxial‐conjugated NFAs with varied side‐chain symmetry. The symmetric NFA having diverse molecular packing orientations can form multiple charge transfer channels in its blend with polymer donor, which cannot be found in that comprising the asymmetric ones. Moreover, a slower rate and lower ratio of the spin‐triplet state are formed in the blend of symmetric NFA, resulting in a much lower non‐radiative voltage loss in corresponding OSCs. This study reveals the distinct advantages of symmetric NFAs in both aggregate properties and exciton/charge dynamics over those of asymmetric ones, paving the way for developing high‐performance OSCs using easier‐to‐prepare, low‐cost symmetric materials.
Chemistry↗
Stimulation of synaptoneurosome glutamate release by monomeric and fibrillated α-synuclein
The α-synuclein protein exists in vivo in a variety of covalently modified and aggregated forms associated with Parkinson's disease (PD) pathology. However, the specific proteoform structures involved with neuropathological disease mechanisms are not clearly defined. Since α-synuclein plays a role in presynaptic neurotransmitter release, an in vitro enzyme-based assay was developed to measure glutamate release from mouse forebrain synaptoneurosomes (SNs) enriched in synaptic endings. Glutamate measurements utilizing SNs from various mouse genotypes (WT, over-expressers, knock-outs) suggested a concentration dependence of α-synuclein on calcium/depolarization-dependent presynaptic glutamate release from forebrain terminals. In vitro reconstitution experiments with recombinant human α-synuclein proteoforms including monomers and aggregated forms (fibrils, oligomers) produced further evidence of this functional impact. Notably, brief exogenous applications of fibrillated forms of α-synuclein enhanced SN glutamate release but monomeric forms did not, suggesting preferential membrane penetration and toxicity by the aggregated forms. However, when applied to brain tissue sections just prior to homogenization, both monomeric and fibrillated forms stimulated glutamate release. Immuno-gold and transmission electron microscopy (TEM) detected exogenous fibrillated α-synuclein associated with numerous SN membranous structures including synaptic terminals. Western blots and immuno-gold TEM were consistent with SN internalization of α-synuclein. Additional studies revealed no evidence of gross disruption of SN membrane integrity or glutamate transporter function by exogenous α-synuclein. Finally, overall excitotoxicity, due to enhanced glutamate release in the face of either overexpressed monomeric α-synuclein or extrasynaptic exposure to fibrillated α-synuclein, should be considered as a potential neuropathological pathway during the progression of PD and other synucleinopathies.
59 BASIC BIOLOGICAL SCIENCES↗
Three-repeat and four-repeat tau isoforms form different oligomers
Different tauopathies are characterized by the isoform-specific composition of the aggregates found in the brain and by structurally distinct tau strains. Although tau oligomers have been implicated as important neurotoxic species, little is known about how the primary structures of the six human tau isoforms affect tau oligomerization because the oligomers are metastable and difficult to analyze. To address this knowledge gap, here, we analyzed the initial oligomers formed by the six tau isoforms in the absence of posttranslational modifications or other manipulations using dot blots probed by an oligomer-specific antibody, native-PAGE/western blots, photo-induced cross-linking of unmodified proteins, mass-spectrometry, and ion-mobility spectroscopy. We found that under these conditions, three-repeat (3R) isoforms are more prone than four-repeat (4R) isoforms to form oligomers. In this study, we also tested whether known inhibitors of tau aggregation affect its oligomerization using three small molecules representing different classes of tau aggregation inhibitors, Methylene Blue (MB), the molecular tweezer CLR01, and the all-D peptide TLKIVW, for their ability to inhibit or modulate the oligomerization of the six tau isoforms. Unlike their reported inhibitory effect on tau fibrillation, the inhibitors had little or no effect on the initial oligomerization. Our study provides novel insight into the primary–quaternary structure relationship of human tau and suggests that 3R-tau oligomers may be an important target for future development of compounds targeting pathological tau assemblies.
59 BASIC BIOLOGICAL SCIENCES↗
Using AI Simulations to Dynamically Model Multi-agent Multi-team Energy Systems
The complexity of energy systems is well known as they are complex and intricate systems. As a result, many extant studies have used many simplifications or generalizations that do not accurately reflect the nature of this complex system. In particular, most HVAC systems are modeled as a single unit, or several large units, rather than as a hierarchical composite (e.g., as a floor rather than as a collection of disparate rooms). The net result of this is that the simulations are too generic to perform meaningful analysis, machine learning, or integrated simulation. We propose using a multi-agent multi-team strategic simulations framework called SiMAMT to better define, model, simulate, and learn the HVAC environment. SiMAMT allows us to create distinct models for each type of room, hierarchically aggregate them into units (like floors, or sections), and then into larger sets (like buildings or a campus), and then perform a simulation that interacts with each sub-element individually, the teams of sub-elements collectively, and the entire set in aggregation. Further, and most importantly, we additionally model another ‘team’ within the simulation framework - the users of the systems. Again, each individual is modeled distinctly, aggregated into sub-sets, then collected into large sets. Each user, or agent, is performing on their own but with respect to the larger team goals. This provides a simulation that has a much higher model fidelity and more applicable results that match the real-world.
Franklin, D. Michael↗
A mutant (‘lab strain’) of the hyperthermophilic archaeon Pyrococcus furiosus , lacking flagella, has unusual growth physiology
In this paper, a mutant (‘lab strain’) of the hyperthermophilic archaeon Pyrococcus furiosus DSM3638 exhibited an extended exponential phase and atypical cell aggregation behavior. Genomic DNA from the mutant culture was sequenced and compared to wild-type (WT) DSM3638, revealing 145 genes with one or more insertions, deletions, or substitutions (12 silent, 33 amino acid substitutions, and 100 frame shifts). Approximately, half of the mutated genes were transposases or hypothetical proteins. The WT transcriptome revealed numerous changes in amino acid and pyrimidine biosynthesis pathways coincidental with growth phase transitions, unlike the mutant whose transcriptome reflected the observed prolonged exponential phase. Targeted gene deletions, based on frame-shifted ORFs in the mutant genome, in a genetically tractable strain of P. furiosus (COM1) could not generate the extended exponential phase behavior observed for the mutant. For example, a putative radical SAM family protein (PF2064) was the most highly up-regulated ORF (>25-fold) in the WT between exponential and stationary phase, although this ORF was unresponsive in the mutant; deletion of this gene in P. furiosus COM1 resulted in no apparent phenotype. On the other hand, frame-shifting mutations in the mutant genome negatively impacted transcription of a flagellar biosynthesis operon (PF0329-PF0338).Consequently, cells in the mutant culture lacked flagella and, unlike the WT, showed minimal evidence of exopolysaccharide-based cell aggregation in post-exponential phase. Finally, electron microscopy of PF0331-PF0337 deletions in P. furiosus COM1 showed that absence of flagella impacted normal cell aggregation behavior and, furthermore, indicated that flagella play a key role, beyond motility, in the growth physiology of P. furiosus.
59 BASIC BIOLOGICAL SCIENCES↗
Litter quantity, litter chemistry, and soil texture control changes in soil organic carbon fractions under bioenergy cropping systems of the North Central U.S.
Soil organic carbon (SOC) storage is a critical component of the overall sustainability of bioenergy cropping systems. Predicting the influence of cropping systems on SOC under diverse scenarios requires a mechanistic understanding of the underlying processes driving SOC accumulation and loss. We used a density fractionation technique to isolate three SOC fractions that are conceptualized to vary in SOC protection from decomposition. The free light fraction (FLF) is particulate SOC that is present in the inter-aggregate soil matrix, the occluded light fraction (OLF) is contained within aggregates, and the heavy fraction (HF) is associated with minerals. We evaluated surface (0 to 10 cm depth) SOC fraction changes from baseline conditions 5 years after biofuel cropping system establishment at two temperate sites with contrasting soil textures. The biofuel cropping systems included no-till maize, switchgrass, prairie, and hybrid poplar. The FLF concentration (g fraction C g bulk soil-1) did not change significantly from baseline levels under any of the cropping systems at either site after 5 years. Except for poplar, OLF concentrations were reduced in all systems at the site with coarse-textured soils and maintained at the site with fine-textured soils. In poplar systems, OLF concentrations were maintained on coarse-textured soils and increased on fine-textured soils. The HF concentrations also increased under poplar on the coarse-textured soil. A structural equation model indicated that OLF concentrations increased with lower litter C:N, and HF concentrations increased with greater litter quantity and lower litter C:N mass ratios. C:N increased over time within all SOC fractions, suggesting that all pools are sensitive to land-use change on sub-decadal timescales. In agreement with modern SOC theory, our empirical results indicate that increasing litter input quantity and promoting plant species with low C:N litter may improve SOC storage in aggregate and mineral-associated soil fractions.
09 BIOMASS FUELS↗
Development of energetic and enzymatic limitations on microbial carbon cycling in soils
Soil organic carbon (SOC) constitutes an important reservoir in the global carbon cycle that is vulnerable to transformation and loss from land use and climate change. Anoxic conditions protect SOC from microbial degradation through limiting the energetics of respiration and inhibiting extracellular oxidative enzymes. Given growing evidence of prevalent anaerobic microsites in upland soils, we designed an experiment testing the development of dissolved organic carbon (DOC) signatures of energetic and enzymatic limitations on microbial carbon utilization across simulated soil aggregates or peds. Reactors comprised a soil column “aggregate” underlying an advective “macropore” channel. Soils received downward diffusive inputs of aerated porewater media with added nitrate, sulfate, or no amendment—where native ferrihydrite served as dominant anaerobic terminal electron acceptor (TEA). After 40 days, added nitrate resulted in highest bulk respiration and DOC production while sulfate did not differ from the control. Nominal oxidation state of carbon (NOSC) was higher (more favorable) with added TEAs at soil surfaces and decreased with depth, while NOSC in the non-amended soil remained lower and constant with depth. DOC generally increased with depth, which along with decreasing NOSC values indicates joint electron-donor and acceptor control over respiration energetics. Of all organic compound classes, only the relative abundance of phenolics increased between 0 and 0.5 cm depth, which aligns with the oxic-anoxic transition and suggests oxidative enzyme inhibition. Furthermore, our results suggest that oxygen limitation within upland soil aggregates may preserve SOC via both energetic and enzymatic C protection mechanisms, which are vulnerable upon exposure to oxygen.
54 ENVIRONMENTAL SCIENCES↗
Environmental controls on the kinetics of iron-sulfur cluster nucleation and nanoparticle formation
Anoxic, sulfidic conditions have been prevalent since the early Proterozoic and favor aqueous iron-sulfur (FeS aq ) clusters as a major fraction of the soluble, reduced iron and sulfur pool. FeS aq cluster formation and nucleation is driven by the high affinity between ferrous iron (Fe(II)) and sulfide (HS − ), ultimately yielding particles that precipitate as iron sulfide minerals. FeS aq clusters were recently shown to be bioavailable sources of iron and sulfur for a variety of anaerobes, yet little is known of the factors that influence the kinetics of their formation and nucleation. Here we apply computational and spectroscopic approaches to investigate the dynamics of FeS aq nucleation, cluster growth, precipitation, and redissolution as a function of Fe(II)/HS − concentration, temperature, and pH. Experiments were conducted under excess HS − to mimic euxinic conditions common to contemporary anaerobic aquatic ecosystems and those of the Proterozoic. Density functional theory calculations reveal the key role of water oxygen-iron interactions in stabilizing small FeS aq clusters and promoting solubility. Dynamic light scattering revealed a concentration-dependent increase in the kinetics of FeS aq nucleation and cluster aggregation. Increasing temperature promoted FeS aq cluster nucleation and aggregation while also enhancing dissolution. Alkaline pH also promoted FeS aq nucleation and cluster aggregation. At 25 °C, pH 7.0, and at reactant concentrations of 30 µM, FeS aq clusters < 10 nm in diameter remained in solution for > 2 h. These results underscore the importance of temperature, pH, and reactant concentration in the kinetics of FeS aq nucleation and cluster growth that, in turn, influence their bioavailability in anaerobic ecosystems.
Aquatic ecosystems↗
Substrate-induced luminescence response of terbium-containing polymeric vesicles doped with the tetra- and bis-1,3-diketone derivatives of calix[4]arenes bearing nonyl substituents at the lower rims
Polymeric aggregates (~100 nm) based on polydiacetylenic acid doped with the luminescent Tb{sup III} complexes with the tetra- and bis-1,3-diketonate derivatives of calix[4]arenes with nonyl substituents at the lower rims are considered as potential nanosensors. The obtained colloidally stable mixed aggregates can generate a substrate-induced luminescent response in aqueous solutions of 2,2´,6´,2´´-terpyridine in the micromolar concentration range due to the coordination of the latter by Tb{sup III} ions on the aggregate surface.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Carbon Monoxide Poisoning Resistance and Structural Stability of Single Atom Alloys
Platinum group metals (PGMs) serve as highly active catalysts in a variety of heterogeneous chemical processes. Unfortunately, their high activity is accompanied by a high affinity for CO and thus, PGMs are susceptible to poisoning. Alloying PGMs with metals exhibiting lower affinity to CO could be an effective strategy toward preventing such poisoning. In this work, we use density functional theory to demonstrate this strategy, focusing on highly dilute alloys of PGMs (Pd, Pt, Rh, Ir and Ni) with poison resistant coinage metal hosts (Cu, Ag, Au), such that individual PGM atoms are dispersed at the atomic limit forming single atom alloys (SAAs). We show that compared to the pure metals, CO exhibits lower binding strength on the majority of SAAs studied, and we use kinetic Monte Carlo simulation to obtain relevant temperature programed desorption spectra, which are found to be in good agreement with experiments. Additionally, we consider the effects of CO adsorption on the structure of SAAs. We calculate segregation energies which are indicative of the stability of dopant atoms in the bulk compared to the surface layer, as well as aggregation energies to determine the stability of isolated surface dopant atoms compared to dimer and trimer configurations. Our calculations reveal that CO adsorption induces dopant atom segregation into the surface layer for all SAAs considered here, whereas aggregation and island formation may be promoted or inhibited depending on alloy constitution and CO coverage. Furthermore, this observation suggests the possibility of controlling ensemble effects in novel catalyst architectures through CO-induced aggregation and kinetic trapping.
36 MATERIALS SCIENCE↗
Inhibiting and Remodeling Toxic Amyloid-Beta Oligomer Formation Using a Computationally Designed Drug Molecule That Targets Alzheimer’s Disease
Alzheimer’s disease (AD) is rapidly reaching epidemic status among a burgeoning aging population. Much evidence suggests the toxicity of this amyloid disease is most influenced by the formation of soluble oligomeric forms of amyloid β-protein, particularly the 42-residue alloform (Aβ42). Developing potential therapeutics in a directed, streamlined approach to treating this disease is necessary. Here we utilize the joint pharmacophore space (JPS) model to design a new molecule [AC0107] incorporating structural characteristics of known Aβ inhibitors, blood-brain barrier permeability, and limited toxicity. To test the molecule’s efficacy experimentally, we employed ion mobility mass spectrometry (IM-MS) to discover [AC0107] inhibits the formation of the toxic Aβ42 dodecamer at both high (1:10) and equimolar concentrations of inhibitor. Atomic force microscopy (AFM) experiments reveal that [AC0107] prevents further aggregation of Aβ42, destabilizes preformed fibrils, and reverses Aβ42 aggregation. This trend continues for long-term interaction times of 2 days until only small aggregates remain with virtually no fibrils or higher order oligomers surviving. Pairing JPS with IM-MS and AFM presents a powerful and effective first step for AD drug development. .
62 RADIOLOGY AND NUCLEAR MEDICINE↗
A phase model approach for thermostatically controlled load demand response
A significant portion of electricity consumed worldwide is used to power thermostatically controlled loads (TCLs) such as air conditioners, refrigerators, and water heaters. Because the short-term timing of operation of such systems is inconsequential as long as their long-run average power consumption is maintained, they are increasingly used in demand response (DR) programs to balance supply and demand on the power grid. Here, we present an ab initio phase model for general TCLs, and use the concept to develop a continuous oscillator model of a TCL and compute its phase response to changes in temperature and applied power. This yields a simple control system model that can be used to evaluate control policies for modulating the power consumption of aggregated loads with parameter heterogeneity and stochastic drift. We demonstrate this concept by comparing simulations of ensembles of heterogeneous loads using the continuous state model and an established hybrid state model. The developed phase model approach is a novel means of evaluating DR provision using TCLs, and is instrumental in estimating the capacity of ancillary services or DR on different time scales. We further propose a novel phase response based open-loop control policy that effectively modulates the aggregate power of a heterogeneous TCL population while maintaining load diversity and minimizing power overshoots. This is demonstrated by low-error tracking of a regulation signal by filtering it into frequency bands and using TCL sub-ensembles with duty cycles in corresponding ranges. As a result, control policies that can maintain a uniform distribution of power consumption by aggregated heterogeneous loads will enable distribution system management (DSM) approaches that maintain stability as well as power quality, and further allow more integration of renewable energy sources.
24 POWER TRANSMISSION AND DISTRIBUTION↗
How close are urban scale building simulations to measured data? Examining bias derived from building metadata in urban building energy modeling
Residential and commercial buildings in the United States accounted for 40% of total energy in 2020. Building energy modeling (BEM) is a useful tool that allows individuals, researchers, companies, or utilities to save energy by optimizing buildings through estimation of building technology savings and performance projection of building energy under various environmental conditions. Urban building energy modeling (UBEM) expands the scope beyond individual buildings to the buildings in a neighborhood, city, utility and more. Yet there is a knowledge gap in the literature as to how these models compare to measured data on an individual and aggregated basis. As UBEM data and methods continue to develop, it is important to consider the accuracy, bias, and limitations of the models. Here, nation-scale data and UBEM software suite named Automatic Building Energy Modeling (AutoBEM) was used to model 50,843 buildings in Chattanooga, Tennessee. The uncalibrated simulation results were compared to aggregated 15-minute electricity data for the year 2019 with visualizations highlighting sources of bias in building data and the AutoBEM framework while considering how they relate to other UBEM methods. Estimation of building type and year of constructions are found to be the major sources of bias. Accounting for the amount of conditioned area per building significantly improves the overall fit of the simulated energy use intensity. it was found that inherent variation in building energy use contributes to R 2 values between 0.008 and 0.095 across building types but slope values near 1 for the total number of buildings. This indicates the need for building aggregation for representative building energy modeling with data sources available at an urban scale while illustrating the need for additional individual building data and model improvement beyond the originally produced UBEM models for individual building analysis.
32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
First-Principles study of interface capture of Ni during high-temperature oxidation of NiCr alloys
The formation of precipitated phases of less reactive metals within an oxide scale during alloy oxidation can disrupt its structural integrity, significantly compromising the protective function of the oxide. To better understand this phenomenon, it is crucial to investigate the atomic-level diffusion mechanisms that drive precipitate formation. In this study, we employ first-principles calculations to examine the diffusion and aggregation of Ni atoms across the NiCr/Cr 2 O 3 interface during the high-temperature oxidation of NiCr alloys. Our results reveal that, in the absence of Cr vacancies, Ni atoms predominantly remain within the NiCr substrate, with minimal migration toward the Cr 2 O 3 layer. However, when Cr vacancies are present at both the NiCr/Cr 2 O 3 interface and within the Cr 2 O 3 bulk, Ni atoms exhibit a strong propensity to migrate from the NiCr substrate into the Cr 2 O 3 bulk, where they aggregate into Ni-rich regions with a corundum structure. This study provides valuable atomic-level insights into the diffusion and aggregation of less-reactive metals at the alloy/oxide interface, enhancing our understanding of solute capture and its contribution to the degradation of oxidation resistance in alloys.
Chen, Jianmin [Xiangtan University (China)] (ORCID↗
The N-terminal strand modulates immunoglobulin light chain fibrillogenesis
Highlights: •We evaluated the impact of mutations in the N-terminal strand of 6aJL2 protein. •Mutations destabilized the protein in a position-dependent manner. •Destabilizing mutations accelerated the fibrillogenesis by shortening the lag time. •The effect on the kinetic of fibril elongation by seeding was of different nature. •The N-terminal strand is buried in the fibrillar state of 6aJL2 protein. -- Abstract: It has been suggested that the N-terminal strand of the light chain variable domain (V{sub L}) protects the molecule from aggregation by hindering spurious intermolecular contacts. We evaluated the impact of mutations in the N-terminal strand on the thermodynamic stability and kinetic of fibrillogenesis of the V{sub L} protein 6aJL2. Mutations in this strand destabilized the protein in a position-dependent manner, accelerating the fibrillogenesis by shortening the lag time; an effect that correlated with the extent of destabilization. In contrast, the effect on the kinetics of fibril elongation, as assessed in seeding experiments was of different nature, as it was not directly dependant on the degree of destabilization. This finding suggests different factors drive the nucleation-dependent and elongation phases of light chain fibrillogenesis. Finally, taking advantage of the dependence of the Trp fluorescence upon environment, four single Trp substitutions were made in the N-terminal strand, and changes in solvent exposure during aggregation were evaluated by acrylamide-quenching. The results suggest that the N-terminal strand is buried in the fibrillar state of 6aJL2 protein. This finding suggest a possible explanation for the modulating effect exerted by the mutations in this strand on the aggregation behavior of 6aJL2 protein.
60 APPLIED LIFE SCIENCES↗
At least 10% shorter C–H bonds in cryogenic protein crystal structures than in current AMBER forcefields
High resolution protein crystal structures resolved with X-ray diffraction data at cryogenic temperature are commonly used as experimental data to refine forcefields and evaluate protein folding simulations. However, it has been unclear hitherto whether the C–H bond lengths in cryogenic protein structures are significantly different from those defined in forcefields to affect protein folding simulations. This article reports the finding that the C–H bonds in high resolution cryogenic protein structures are 10–14% shorter than those defined in current AMBER forcefields, according to 3709 C–H bonds in the cryogenic protein structures with resolutions of 0.62–0.79 Å. Also, 20 all-atom, isothermal–isobaric, 0.5-μs molecular dynamics simulations showed that chignolin folded from a fully-extended backbone formation to the native β-hairpin conformation in the simulations using AMBER forcefield FF12SB at 300 K with an aggregated native state population including standard error of 10 ± 4%. However, the aggregated native state population with standard error reduced to 3 ± 2% in the same simulations except that C–H bonds were shortened by 10–14%. Furthermore, the aggregated native state populations with standard errors increased to 35 ± 3% and 26 ± 3% when using FF12MC, which is based on AMBER forcefield FF99, with and without the shortened C–H bonds, respectively. These results show that the 10–14% bond length differences can significantly affect protein folding simulations and suggest that re-parameterization of C–H bonds according to the cryogenic structures could improve the ability of a forcefield to fold proteins in molecular dynamics simulations. - Highlights: • Cryogenic crystal structures are commonly used in computational studies of proteins. • C–H bonds in the cryogenic structures are shorter than those defined in forcefields. • A survey of 3709 C–H bonds shows that the cryogenic bonds are 10–14% shorter. • The 10–14% differences affect molecular dynamics simulations of protein folding. • Shortening C–H bonds by 10–14% can improve protein folding simulations.
60 APPLIED LIFE SCIENCES↗