Conformational Distribution Research Articles

Graphene oxide as a potential carrier or remover for flotation collectors: A molecular dynamics study

In order to explore graphene oxide (GO) as a potential carrier or remover for flotation collectors in complex environments, the study investigated the individual and competitive adsorption processes of flotation collectors on GO using molecular dynamics (MD) simulations through 2-Methylpropoxymethanedithioate (CS), a xanthate-based collector, and Diethylthiophosphate (PS), an aerofloat-based collector. The distribution of molecular conformations, center-of-mass distance calculations, radial distribution function analysis, hydrogen bonding analysis and interaction force calculations were used to conclude that when CS and PS were under competing adsorption systems, both molecules adsorb more strongly on the GO surface than under individual adsorption systems, and CS molecules could promote the adsorption of PS. Coulomb interactions between the two organic molecules were the driving force for them to show a more dispersive effect under competitive adsorption conditions, and van der Waals forces were the main reason why both molecules can adsorb on the GO surface. This work provided some theoretical implications for improving the flotation environment as well as industrial wastewater treatment.

Chirality-Controlled Mercapto-β-cyclodextrin Covalent Organic Frameworks for Selective Adsorption and Chromatographic Enantioseparation.

Chiral covalent organic frameworks (CCOFs) benefit from superior stability, abundant chiral environment, and homogeneous pore configuration. In its constructive tactics, only the post-modification method allows for the integration of supramolecular chiral selectors into achiral COFs. Here, the finding utilizes 6-deoxy-6-mercapto-β-cyclodextrin (SH-β-CD) as chiral subunits and 2,5-dihydroxy-1,4-benzenedicarboxaldehyde (DVA) as the platform molecule to synthesize chiral functional monomers through thiol-ene click reactions and directly establish ternary "pendant-type" SH-β-CD COFs. The chiral site density on SH-β-CD COFs was regulated by changing the proportion of chiral monomers to obtain an optimal construction strategy and remarkably improve the ability of chiral separation. SH-β-CD COFs were coated on the inner wall of the capillary in a covalently bound manner. The prepared open tubular capillary was achieved for the separation of six chiral drugs. By combining the outcomes of selective adsorption and chromatographic separation, we observed the higher density of chiral sites in the CCOFs, and poorer results were achieved. From the perspective of spatial conformational distribution, we interpret the variation in the performance of these chirality-controlled CCOFs for selective adsorption and chiral separation.

Dissecting the Effect of ALS Mutation G335D on the Early Aggregation of the TDP-43 Amyloidogenic Core Peptide: Helix-to-β-Sheet Transition and Conformational Shift.

The aggregation of TAR DNA-binding protein of 43 kDa (TDP-43) into fibrillary deposits is associated with amyotrophic lateral sclerosis (ALS). The 311-360 fragment of TDP-43 (TDP-43311-360), the amyloidogenic core region, can spontaneously aggregate into fibrils, and the ALS-associated mutation G335D has an enhanced effect on TDP-43311-360 fibrillization. However, the molecular mechanism underlying G335D-enhanced aggregation at atomic level remains largely unknown. By utilizing all-atom molecular dynamics (MD) and replica exchange with solute tempering 2 (REST2) simulations, we investigated influences of G335D on the dimerization (the first step of aggregation) and conformational ensemble of the TDP-43311-360 peptide. Our simulations show that G335D mutation increases inter-peptide interactions, especially inter-peptide hydrogen-bonding interactions in which the mutant site has a relatively large contribution, and enhances the dimerization of TDP-43311-360 peptides. The α-helix regions in the NMR-resolved conformation of the TDP-43311-360 monomer (321-330 and 335-343) play an essential role in the formation of the dimer. G335D mutation induces helix unfolding and promotes α-to-β conversion. G335D mutation alters the conformational distribution of TDP-43311-360 dimers and causes population shift from helix-rich to β-sheet-rich conformations, which facilitates the fibrillization of the TDP-43311-360 peptide. Our MD and REST2 simulation results suggest that the 321-330 region is of paramount importance to α-to-β transition and could be the initiation site for TDP-43311-360 fibrillization. Our work reveals the mechanism underlying the enhanced aggregation propensity of the G335D TDP-43311-360 peptide, which provides atomistic insights into the G335D mutation-caused pathogenicity of TDP-43 protein.

Early events in amyloid-β self-assembly probed by time-resolved solid state NMR and light scattering

Self-assembly of amyloid-β peptides leads to oligomers, protofibrils, and fibrils that are likely instigators of neurodegeneration in Alzheimer’s disease. We report results of time-resolved solid state nuclear magnetic resonance (ssNMR) and light scattering experiments on 40-residue amyloid-β (Aβ40) that provide structural information for oligomers that form on time scales from 0.7 ms to 1.0 h after initiation of self-assembly by a rapid pH drop. Low-temperature ssNMR spectra of freeze-trapped intermediates indicate that β-strand conformations within and contacts between the two main hydrophobic segments of Aβ40 develop within 1 ms, while light scattering data imply a primarily monomeric state up to 5 ms. Intermolecular contacts involving residues 18 and 33 develop within 0.5 s, at which time Aβ40 is approximately octameric. These contacts argue against β-sheet organizations resembling those found previously in protofibrils and fibrils. Only minor changes in the Aβ40 conformational distribution are detected as larger assemblies develop.

Conformational Distributions of Phenyl β-D-Glucopyranoside and Gastrodin in Solution by Vibrational Optical Activity and Theoretical Calculations.

The conformational landscapes of two highly flexible monosaccharide derivatives, namely phenyl β-D-glucopyranoside (ph-β-glu) and 4-(hydroxymethyl)phenyl β-D-glucopyranoside, also commonly known as gastrodin, were explored using a combined experimental and theoretical approach. For the infrared, Raman, and the associated vibrational optical activity (VOA), i.e., vibrational circular dichroism and Raman optical activity, experiments of these two compounds in DMSO and in water were carried out. Extensive and systematic conformational searches were performed using a recently developed conformational searching tool called CREST (conformer-rotamer ensemble sampling tool) in the two solvents. Fourteen and twenty-four low-energy conformers were identified at the DFT level for ph-β-glu and gastrodin, respectively. The spectral simulations of individual conformers were done at the B3LYP-D3BJ/def2-TZVPD level with the polarizable continuum model of the solvents. The VOA spectral features exhibit much higher specificity to conformational differences than their parent infrared and Raman. The excellent agreements achieved between the experimental and simulated VOA spectra allow for the extraction of experimental conformational distributions of these two carbohydrates in solution directly. The experimental percentage abundances based on the hydroxymethyl (at the pyranose ring) conformations G+, G-, and T for ph-β-glu were obtained to be 15%, 75%, and 10% in DMSO and 53%, 40%, and 7% in water, respectively, in comparison to the previously reported gas phase values of 68%, 25%, and 7%, highlighting the important role of solvents in conformational preferences. The corresponding experimental distributions for gastrodin are 56%, 22%, and 22% in DMSO and 70%, 21%, and 9% in water.

Confining donor conformation distributions for efficient thermally activated delayed fluorescence with fast spin-flipping

Fast spin-flipping is the key to exploit the triplet excitons in thermally activated delayed fluorescence based organic light-emitting diodes toward high efficiency, low efficiency roll-off and long operating lifetime. In common donor-acceptor type thermally activated delayed fluorescence molecules, the distribution of dihedral angles in the film state would have significant influence on the photo-physical properties, which are usually neglected by researches. Herein, we find that the excited state lifetimes of thermally activated delayed fluorescence emitters are subjected to conformation distributions in the host-guest system. Acridine-type flexible donors have a broad conformation distribution or bimodal distribution, in which some conformers feature large singlet-triplet energy gap, leading to long excited state lifetime. Utilization of rigid donors with steric hindrance can restrict the conformation distributions in the film to achieve degenerate singlet and triplet states, which is beneficial to efficient reverse intersystem crossing. Based on this principle, three prototype thermally activated delayed fluorescence emitters with confined conformation distributions are developed, achieving high reverse intersystem crossing rate constants greater than 106 s−1, which enable highly efficient solution-processed organic light-emitting diodes with suppressed efficiency roll-off.

Direct Visualization of the Dynamic Process of Epsilon Toxin on Hemolysis.

Hemolysis is the process of rupturing erythrocytes (red blood cells) by forming nanopores on their membranes using hemolysins, which then impede membrane permeability. However, the self-assembly process before the state of transmembrane pores and underlying mechanisms of conformational change are not fully understood. In this work, theoretical and experimental evidence of the pre-pore morphology of Clostridium perfringens epsilon toxin (ETX), a typical hemolysin, is provided using in situ atomic force microscopy (AFM) complemented by molecular dynamics (MD) simulations to detect the conformational distribution of different states in Mica. The AFM suggests that the ETX pore is formed in two stages: ETX monomers first attach to the membrane and form a pre-pore in no special conditions required, which then undergo a conformational change to form a transmembrane pore at temperatures above the critical point in the presence of receptors. The authors' MD simulations reveal that initial nucleation occurs when specific amino acids adsorb to negatively charged mica cavities. This work fills the knowledge gap in understanding the early stage of hemolysis and the oligomerization of hemolysins. Moreover, the newly identified pre-pore of ETX holds promise as a candidate for nanopore applications.

Intermediate-aided allostery mechanism for α-glucosidase by Xanthene-11v as an inhibitor using residue interaction network analysis

Exploring allosteric inhibition and the discovery of new inhibitor binding sites are important studies in protein regulation mechanisms and drug discovery. Structural and network-based analyses of trajectories resulting from molecular dynamics (MD) simulations have been developed to discover protein dynamics, landscape, functions, and allosteric regions. Here, an experimentally suggested non-competitive inhibitor, xanthene-11v, was considered to explore its allosteric inhibition mechanism in α-glucosidase MAL12. Comparative structural and network analyses were applied to eight 250 ns independent MD simulations, four of which were performed in the free state and four of which were performed in ligand-bound forms. Projected two-dimensional free energy landscapes (FEL) were constructed from the probabilistic distribution of conformations along the first two principal components. The post-simulation analyses of the coordinates, side-chain torsion angles, non-covalent interaction networks, network communities, and their centralities were performed on α-glucosidase conformations and the intermediate sub-states. Important communities of residues have been found that connect the allosteric site to the active site. Some of these residues like Thr307, Arg312, TYR344, ILE345, Phe357, Asp406, Val407, Asp408, and Leu436 are the key messengers in the transition pathway between allosteric and active sites. Evaluating the probability distribution of distances between gate residues including Val407 in one community and Phe158, and Pro65 in another community depicted the closure of this gate due to the inhibitor binding. Six macro states of protein were deduced from the topology of FEL and analysis of conformational preference of free and ligand-bound systems to these macro states shows a combination of lock-and-key, conformational selection, and induced fit mechanisms are effective in ligand binding. All these results reveal structural states, allosteric mechanisms, and key players in the inhibition pathway of α-glucosidase by xanthene-11v.

Rational Design of Meso-Diaminopimelate Dehydrogenase with Enhanced Reductive Amination Activity for Efficient Production of d-p-Hydroxyphenylglycine.

d-p-hydroxyphenylglycine (d-HPG) is an important intermediate in the pharmaceutical industry. In this study, a tri-enzyme cascade for the production of d-HPG from l-HPG was designed. However, the amination activity of Prevotella timonensis meso-diaminopimelate dehydrogenase (PtDAPDH) toward 4-hydroxyphenylglyoxylate (HPGA) was identified as the rate-limiting step. To overcome this issue, the crystal structure of PtDAPDH was solved, and a "binding pocket and conformation remodeling" strategy was developed to improve the catalytic activity toward HPGA. The best variant obtained, PtDAPDHM4, exhibited a catalytic efficiency (kcat/Km) that was 26.75-fold higher than that of the wild type. This improvement was due to the enlarged substrate-binding pocket and enhanced hydrogen bond networks around the active center; meanwhile, the increased number of interdomain residue interactions drove the conformation distribution toward the closed state. Under optimal transformation conditions, PtDAPDHM4 produced 19.8 g/L d-HPG from 40 g/L racemate DL-HPG in a 3 L fermenter within 10 h, with 49.5% conversion and >99% enantiomeric excess. Our study provides an efficient three-enzyme cascade pathway for the industrial production of d-HPG from racemate DL-HPG. IMPORTANCE d-p-hydroxyphenylglycine (d-HPG) is an important intermediate in the synthesis of antimicrobial compounds. d-HPG is mainly produced via chemical and enzymatic approaches, and enzymatic asymmetric amination employing diaminopimelate dehydrogenase (DAPDH) is considered an attractive method. However, the low catalytic activity of DAPDH toward bulky 2-keto acids limits its applications. In this study, we identified a DAPDH from Prevotella timonensis and created a mutant, PtDAPDHM4, which exhibited a catalytic efficiency (kcat/Km) toward 4-hydroxyphenylglyoxylate that was 26.75-fold higher than that of the wild type. The novel strategy developed in this study has practical value for the production of d-HPG from inexpensive racemate DL-HPG.

Patient-Specific Pre-Treatment VMAT Plan Verification Using Gamma Passing Rates

Continuous gantry motion, continuous beam modulation, and variable dose rate are used in volumetric modulated arc therapy (VMAT) to obtain highly conformal radiation therapy dose distributions. Several errors during daily radiation therapy treatment can be sources of uncertainties in dose delivery. These errors include monitor unit calculation errors and other human mistakes. Due to the uncertainties in the excessively modulated VMAT plan, the intended dose distribution is not delivered perfectly, leading to a mismatch between the measured and planned dose distributions. This necessitates an extensive and effective quality assurance (QA) program for both machine and patient. In this study, VMAT QA plan verification of 62 head and neck (HN) and 19 prostate cases was done using Octavius 4D setup with its associating VeriSoft gamma analysis software. The plans showed a maximum 3D gamma passing rate with 4 mm/3 % gamma acceptance criteria, i.e., 99.7 % for the HN cancer cases and 99.5 % for the prostate cancer cases. Local gamma analysis was also performed for both regions. Furthermore, 2D and volumetric gamma analyses were also carried out. Gamma analysis with respect to different axis was also carried out. It was known that the transversal axis showed the highest gamma passing rate in both HN and prostate cases, i.e., 99.17 % and 98.3 %, respectively. The transverse axis came to be a better fit for the planned dose distribution.

Mutational and Environmental Effects on the Dynamic Conformational Distributions of Lys48-Linked Ubiquitin Chains.

In multidomain proteins, individual domains connected by flexible linkers are dynamically rearranged upon ligand binding and sensing changes in environmental factors, such as pH and temperature. Here, we characterize dynamic domain rearrangements of Lys48-linked ubiquitin (Ub) chains as models of multidomain proteins in which molecular surfaces mediating intermolecular interactions are involved in intramolecular domain-domain interactions. Using NMR and other biophysical techniques, we characterized dynamic conformational interconversions of diUb between open and closed states regarding solvent exposure of the hydrophobic surfaces of each Ub unit, which serve as binding sites for various Ub-interacting proteins. We found that the hydrophobic Ub-Ub interaction in diUb was reinforced by cysteine substitution of Lys48 of the distal Ub unit because of interaction between the cysteinyl thiol group and the C-terminal segment of the proximal Ub unit. In contrast, the replacement of the isopeptide linker with an artificial ethylenamine linker minimally affected the conformational distributions. Furthermore, we demonstrated that the mutational modification allosterically impacted the exposure of the most distal Ub unit in triUb. Thus, the conformational interconversion of Ub chains offers a unique design framework in Ub-based protein engineering not only for developing biosensing probes but also for allowing new opportunities for the allosteric regulation of multidomain proteins.

Applying the column generation method to the intensity modulated high dose rate brachytherapy inverse planning problem

Objective. Intensity modulated high dose rate brachytherapy (IMBT) is a rapidly developing application of brachytherapy where anisotropic dose distributions can be produced at each source dwell position. This technique is made possible by placing rotating metallic shields inside brachytherapy needles or catheters. By dynamically directing the radiation towards the tumours and away from the healthy tissues, a more conformal dose distribution can be obtained. The resulting treatment planning involves optimizing dwell position and shield angle (DPSA). The aim of this study was to investigate the column generation method for IMBT treatment plan optimization. Approach. A column generation optimization algorithm was developed to optimize the dwell times and shield angles. A retrospective study was performed on 10 prostate cases using RapidBrachyMCTPS. At every iteration, the plan was optimized with the chosen DPSA which would best improve the cost function that was added to the plan. The optimization process was stopped when the remaining DPSAs would not add value to the plan to limit the plan complexity. Main results. The average number of DPSAs and voxels were 2270 and 7997, respectively. The column generation approach yielded near-optimal treatment plans by using only 11% of available DPSAs on average in ten prostate cases. The coverage and organs at risk constraints passed in all ten cases. Significance. The column generation method produced high-quality deliverable prostate IMBT plans. The treatment plan quality reached a plateau, where adding more DPSAs had a minimal effect on dose volume histogram parameters. The iterative nature of the column generation method allows early termination of the treatment plan creation process as soon as the dosimetric indices from dose volume histogram satisfy the clinical requirements or if their values stabilize.

ALS-Linked A315T and A315E Mutations Enhance β-Barrel Formation of the TDP-43307-319 Hexamer: A REST2 Simulation Study.

Pathogenic mutations of transactivation response element DNA-binding protein 43 (TDP-43) are closely linked with amyotrophic lateral sclerosis (ALS). It was recently reported that two ALS-linked familial mutants A315T and A315E of TDP-43307-319 peptides can self-assemble into oligomers including tetramers, hexamers, and octamers, among which hexamers were suggested to form the β-barrel structure. However, due to the transient nature of oligomers, their conformational properties and the atomic mechanisms underlying the β-barrel formation remain largely elusive. Herein, we investigated the hexameric conformational distributions of the wild-type (WT) TDP-43307-319 fragment and its A315T and A315E mutants by performing all-atom explicit-solvent replica exchange with solute tempering 2 simulations. Our simulations reveal that each peptide can self-assemble into diverse conformations including ordered β-barrels, bilayer β-sheets and/or monolayer β-sheets, and disordered complexes. A315T and A315E mutants display higher propensity to form β-barrel structures than the WT, which provides atomic explanation for their enhanced neurotoxicity reported previously. Detailed interaction analysis shows that A315T and A315E mutations increase inter-molecular interactions. Also, the β-barrel structures formed by the three different peptides are stabilized by distinct inter-peptide side-chain hydrogen bonding, hydrophobic, and aromatic stacking interactions. This study demonstrates the enhanced β-barrel formation of the TDP-43307-319 hexamer by the pathogenic A315T and A315E mutations and reveals the underlying molecular determinants, which may be helpful for in-depth understanding of the ALS-mutation-induced neurotoxicity of TDP-43 protein.

Designer molecules of the synaptic organizer MDGA1 reveal 3D conformational control of biological function

MDGAs (MAM domain-containing glycosylphosphatidylinositol anchors) are synaptic cell surface molecules that regulate the formation of trans-synaptic bridges between neurexins (NRXNs) and neuroligins (NLGNs), which promote synaptic development. Mutations in MDGAs are implicated in various neuropsychiatric diseases. MDGAs bind NLGNs in cis on the postsynaptic membrane and physically block NLGNs from binding to NRXNs. In crystal structures, the six immunoglobulin (Ig) and single fibronectin III domains of MDGA1 reveal a striking compact, triangular shape, both alone and in complex with NLGNs. Whether this unusual domain arrangement is required for biological function or other arrangements occur with different functional outcomes is unknown. Here, we show that WT MDGA1 can adopt both compact and extended 3D conformations that bind NLGN2. Designer mutants targeting strategic molecular elbows in MDGA1 alter the distribution of 3D conformations while leaving the binding affinity between soluble ectodomains of MDGA1 and NLGN2 intact. In contrast, in a cellular context, these mutants result in unique combinations of functional consequences, including altered binding to NLGN2, decreased capacity to conceal NLGN2 from NRXN1β, and/or suppressed NLGN2-mediated inhibitory presynaptic differentiation, despite the mutations being located far from the MDGA1-NLGN2 interaction site. Thus, the 3D conformation of the entire MDGA1 ectodomain appears critical for its function, and its NLGN-binding site on Ig1-Ig2 is not independent of the rest of the molecule. As a result, global 3D conformational changes to the MDGA1 ectodomain via strategic elbows may form a molecular mechanism to regulate MDGA1 action within the synaptic cleft.

Intrafraction tumor motion monitoring and dose reconstruction for liver pencil beam scanning proton therapy

Pencil beam scanning (PBS) proton therapy can provide highly conformal target dose distributions and healthy tissue sparing. However, proton therapy of hepatocellular carcinoma (HCC) is prone to dosimetrical uncertainties induced by respiratory motion. This study aims to develop intra-treatment tumor motion monitoring during respiratory gated proton therapy and combine it with motion-including dose reconstruction to estimate the delivered tumor doses for individual HCC treatment fractions. Three HCC-patients were planned to receive 58 GyRBE (n=2) or 67.5 GyRBE (n=1) of exhale respiratory gated PBS proton therapy in 15 fractions. The treatment planning was based on the exhale phase of a 4-dimensional CT scan. Daily setup was based on cone-beam CT (CBCT) imaging of three implanted fiducial markers. An external marker block (RPM) on the patient's abdomen was used for exhale gating in free breathing. This study was based on 5 fractions (patient 1), 1 fraction (patient 2) and 6 fractions (patient 3) where a post-treatment control CBCT was available. After treatment, segmented 2D marker positions in the post-treatment CBCT projections provided the estimated 3D motion trajectory during the CBCT by a probability-based method. An external-internal correlation model (ECM) that estimated the tumor motion from the RPM motion was built from the synchronized RPM signal and marker motion in the CBCT. The ECM was then used to estimate intra-treatment tumor motion. Finally, the motion-including CTV dose was estimated using a dose reconstruction method that emulates tumor motion in beam's eye view as lateral spot shifts and in-depth motion as changes in the proton beam energy. The CTV homogeneity index (HI) The CTV homogeneity index (HI) was calculated as . The tumor position during spot delivery had a root-mean-square error of 1.3mm in left-right, 2.8mm in cranio-caudal and 1.7mm in anterior-posterior directions compared to the planned position. On average, the CTV HI was larger than planned by 3.7%-points (range: 1.0-6.6%-points) for individual fractions and by 0.7%-points (range: 0.3-1.1%-points) for the average dose of 5 or 6 fractions. A method to estimate internal tumor motion and reconstruct the motion-including fraction dose for PBS proton therapy of HCC was developed and demonstrated successfully clinically.

Conformational multiplicity of bacterial ferric binding protein revealed by small angle x-ray scattering and molecular dynamics calculations.

This study combines molecular dynamics (MD) simulations with small angle x-ray scattering (SAXS) measurements to investigate the range of conformations that can be adopted by a pH/ionic strength (IS) sensitive protein and to quantify its distinct populations in solution. To explore how the conformational distribution of proteins may be modified in the environmental niches of biological media, we focus on the periplasmic ferric binding protein A (FbpA) from Haemophilus influenzae involved in the mechanism by which bacteria capture iron from higher organisms. We examine iron-binding/release mechanisms of FbpA in varying conditions simulating its biological environment. While we show that these changes fall within the detectable range for SAXS as evidenced by differences observed in the theoretical scattering patterns calculated from the crystal structure models of apo and holo forms, detection of conformational changes due to the point mutation D52A and changes in ionic strength (IS) from SAXS scattering profiles have been challenging. Here, to reach conclusions, statistical analyses with SAXS profiles and results from different techniques were combined in a complementary fashion. The SAXS data complemented by size exclusion chromatography point to multiple and/or alternative conformations at physiological IS, whereas they are well-explained by single crystallographic structures in low IS buffers. By fitting the SAXS data with unique conformations sampled by a series of MD simulations under conditions mimicking the buffers, we quantify the populations of the occupied substates. We also find that the D52A mutant that we predicted by coarse-grained computational modeling to allosterically control the iron binding site in FbpA, responds to the environmental changes in our experiments with conformational selection scenarios that differ from those of the wild type.

Thermodynamics and Kinetics of a Partial Peptide of K+ Channels: DFT Transition State Calculations Coupled with Temperature-Controlled Gas Phase Laser Spectroscopy

Abstract K+ channels selectively conduct K+ at a high conduction rate, but not smaller Na+ and Li+. To provide an insight into the conduction mechanism previously, we experimentally observed the temperature dependence of the conformer distributions of a model peptide in K+ channels (Ac-Tyr-NHMe) complexed with alkali metal ions (Li+, Na+, K+, Rb+, and Cs+) by gas phase laser spectroscopy. The K+ and Rb+ complexes showed a more significant temperature dependence than the Li+ complexes, whose conformer distributions barely varied. This different behavior with temperature can be interpreted either thermodynamically (entropy vs. enthalpy) or kinetically (barrier height). Due to the lack of temperature dependence of the Li+ complex, we could not determine which factor, an enthalpy-driven structure or a high energy barrier, governs the Li+ complex’s behavior. To resolve this issue, we carried out DFT transition state calculations and time-dependent simulation of the metal complexes’ conformer distributions based on the theoretical barrier heights. By comparing the experimental and computational data, the origin of the variation in the temperature dependence among different ion complexes was determined to be thermodynamic.

Electronic Structure of Exciplexes and the Role of Local Triplet States on Efficiency of Thermally Activated Delayed Fluorescence

In this work, we present an investigation of the electronic states in a series of thermally activated delayed fluorescence (TADF) exciplexes formed with the popular electron-transport compound TpBpTa and hole-transporting TCTA, TAPC, TPD10, TPD, and NPB. We rationalize the photophysical behavior of exciplexes by using computational methods and demonstrate that the reason for the commonly observed temporal red shift in the time-resolved spectra is related to the distribution of molecular conformations, thus CT energy, in film. We also use spectrally resolved thermoluminescence (SRTL) measurements to give insight into the trapping phenomena in exciplex blends. The results demonstrate that trapped charge carriers in the majority of studied exciplexes recombine through the luminescent intermolecular CT state. In addition, we report OLED devices using the said exciplexes in the emissive layer. The best performance is obtained with the TCTA:TpBpTa and TAPC:TpBpTa exciplexes showing maximum external quantum efficiencies (EQEs) of 8.8% and 7.2%, respectively.

Modeling and Simulation of Bacterial Outer Membranes with Lipopolysaccharides and Capsular Polysaccharides.

Capsule is one of the common virulence factors in Gram-negative bacteria protecting pathogens from host defenses and consists of long-chain capsular polysaccharides (CPS) anchored in the outer membrane (OM). Elucidating structural properties of CPS is important to understand its biological functions as well as the OM properties. However, the outer leaflet of the OM in current simulation studies is represented exclusively by LPS due to the complexity and diversity of CPS. In this work, representative Escherichia coli CPS, KLPS (a lipid A-linked form) and KPG (a phosphatidylglycerol-linked form), are modeled and incorporated into various symmetric bilayers with co-existing LPS in different ratios. All-atom molecular dynamics simulations of these systems have been conducted to characterize various bilayer properties. Incorporation of KLPS makes the acyl chains of LPS more rigid and ordered, while incorporation of KPG makes them less ordered and flexible. These results are consistent with the calculated area per lipid (APL) of LPS, in which the APL of LPS becomes smaller when KLPS is incorporated, whereas it gets larger when KPG is included. Torsional analysis reveals that the influence of the CPS presence on the conformational distributions of the glycosidic linkages of LPS is small, and minor differences are also detected for the inner and outer regions of the CPS. Combined with previously modeled enterobacterial common antigens (ECAs) in the form of mixed bilayers, this work provides more realistic OM models as well as the basis for characterization of interactions between the OM and OM proteins.

Loading the tumor with 31P, 63Cu and 89Y provides an in vivo prompt gamma-based range verification for therapeutic protons

Introduction: The main rationale for using protons in cancer treatment is based on the highly conformal dose distribution and normal tissue spearing compared to conventional radiotherapy. The main limit of proton therapy is the particle range uncertainty due to patient setup, dose calculation and imaging. To account for this, a safety margin is added to the tumor to ensure the prescribed dose to the target. Reducing range uncertainties would result in the reduction of irradiation volume and would allow full exploitation of the proton therapy benefits. In this work, we presented a feasibility study for a strategy to achieve in vivo proton range verification based on prompt gammas (PG). This approach relies on the detection of signature prompt gammas, generated by the interaction of primary protons with a non-radioactive element, that is selectively loaded into a tumor with a drug carrier. The number of characteristic gammas is directly related to the proton range, and its measurement provides an estimate of the position at which the primary beam stops with respect to the tumor location.Method: We identified the criteria for selecting potential candidate materials and combined them with TALYS predictions to make the selection. We carried out an experimental campaign to characterize the PG spectra generated by the chosen materials when irradiated with therapeutic protons and compared them with TOPAS Monte Carlo toolkit predictions.Results: We identified 31-Phosphorous, 63-Copper and 89-Yttrium as potential candidates for this application based on TALYS calculations. The experimental data confirmed that all candidates emit signature prompt gammas different from water (here used as a proxy for normal tissue), and that the gamma yield is directly proportional to the element concentration in the solution. Four specific gamma lines were detected for both 31P (1.14, 1.26, 1.78, and 2.23 MeV) and 63Cu (0.96, 1.17, 1.24, 1.326 MeV), while only one for 89Y (1.06 MeV). The simulations indicate that the count of characteristic gammas is directly proportional to the proton range, reaching in some cases a saturation value around the tumor’s far edge. The results also indicate that to achieve a range accuracy below the current value of 2–3 mm, the uncertainty on the prompt gammas count has to be below 5% for 31-Phosphorous and 63-Copper, or 10% for 89-Yttrium.Discussion: We demonstrated that loading the tumor with a label element prior to proton treatment generates signature gammas that can be used to verify the beam range in vivo, reaching a potential range accuracy below the current limitations. This approach can be either used stand-alone or combined with other existing methodologies to further improve range resolution.