We Are Never Ever Getting (back to) Ideal Symmetry: Structure and Luminescence in a Ten-Coordinated Europium(III) Sulfate Crystal

Our theoretical treatment of electronic structure in coordination complexes often rests on assumptions of symmetry. Experiments rarely provide fully symmetric systems to study. In solution, fluctuation in solvation, variations in conformation, and even changes in constitution occur and complicates the picture. In crystals, lattice distortion, energy transfer, and phonon quenching is in play, but we are able to have distinct symmetries. Yet the question remains: How is the real symmetry in a crystal compared to ideal symmetries? Moreover, at what level of detail do we need to study a system to determine, if the electronic structure behaves as if it has ideal symmetry? Here, we have revisited the Continues Shape Measurement (CShM) approach developed by Ruiz-Martínez and Alvarez to evaluate the structure of ten-coordinated europium(III) ions in a K5Na[Eu2(SO4)6] structure. By comparing the result of the symmetry deviation analysis to luminescence data, we are able to show the effect of small deviations from ideal symmetry. We suggest using a symmetry deviation value, σideal, determined by using our updated approach to Continues Shape Measurements, where we also align the structure via our AlignIt code. AlignIt includes normalization and relative orientation in the symmetry comparison, and by combining the calculated values with the experimentally determined energy level splitting, we were able create the first point on a scale that can show how close to ideal an experimental structure actually is.

Synthesis, Characterization and DFT Calculations of a Novel Pyrazole Derivative 4-(1-Phenyl-5-(p-Tolyl)-2,5-Dihydro-1H-Pyrazol-3-Yl)Benzo[c][1,2,5]Oxadiazole

s Heterocyclic compounds like pyrazoline was synthesized along to the reaction of phenyl hydrazine hydrochloride with 3-(benzo [c][1,2,5] oxadiazol-4-yl)-1-phenylprop-2-en-1-one undergoing in reflux condition. This compound going to begood yields.A thoroughly fresh compound wasindicating by IR, 1H, and 13C elemental analysis. Stimulate the calculated HOMO/LUMO, MEP and mulliken population analysis and NLO was compare to the experimental analysis of this data. The optimized theoretical structure parameters betide collate to the satisfied assent with the experimental structure. Keywords: Pyrazoline, Heterocycles, NLO, HOMO/LUMO, Optimized structure, Mulliken charges. Graphical Abstract

Response-Only Damage Detection Approach of CFRP Gas Tanks Using Clustering and Vibrational Measurements

The advancements in the automotive, aviation, and aerospace industry have led to an increased usage of CFRP high-pressure gas tanks. In order to avoid any fatal accidents, the inspection procedures require accuracy, but also practicality, to be used in the industry. The presented work focuses on response-only metrics from vibrational experimental measurements of the CFRP tank. The power spectral density and transmittance function curves are both compared for the accuracy and ability to be used as metrics for damage detection. Along with the selection of the proper metric, an appropriate clustering algorithm that can accurately group similar states of the structure is of high importance. Two clustering algorithms, agglomerative hierarchical and spectral clustering, are employed and compared for their performance. A small Type V CFRP tank is used as an experimental structure on this benchmark problem. In order to create realistic material damage, the tank is placed on an impact system multiple times where different damage magnitudes are created. After each new state and damage magnitude on the tank, vibrational experimental data are collected. Using the collected data, all the combinations of the mentioned metrics and algorithms are executed and properly compared to evaluate their accuracy.

Structure-Based Understanding of ABCA3 Variants

ABCA3 is a crucial protein of pulmonary surfactant biosynthesis, associated with recessive pulmonary disorders such as neonatal respiratory distress and interstitial lung disease. Mutations are mostly private, and accurate interpretation of variants is mandatory for genetic counseling and patient care. We used 3D structure information to complete the set of available bioinformatics tools dedicated to medical decision. Using the experimental structure of human ABCA4, we modeled at atomic resolution the human ABCA3 3D structure including transmembrane domains (TMDs), nucleotide-binding domains (NBDs), and regulatory domains (RDs) in an ATP-bound conformation. We focused and mapped known pathogenic missense variants on this model. We pinpointed amino-acids within the NBDs, the RDs and within the interfaces between the NBDs and TMDs intracellular helices (IHs), which are predicted to play key roles in the structure and/or the function of the ABCA3 transporter. This theoretical study also highlighted the possible impact of ABCA3 variants in the cytosolic part of the protein, such as the well-known p.Glu292Val and p.Arg288Lys variants.

CONSERVATIONAL ARCHITECTURE EVALUATION AND ENVIRONMENTAL CONTROL SYSTEM BASED ON LONG-TERM ENVIRONMENTAL MONITORING DATA – TAKING GUANGYUAN QIANFOYA CLIFF INSCRIPTIONS CONSERVATIONAL ARCHITECTURE ASSESSMENT AS AN EXAMPLE

The environmental monitoring data of Qianfoya Cliff Inscriptions in Guangyuan, Sichuan Province accumulated since 2014 make it possible to analyze the environmental monitoring data in and out of the Experimental Structure of the Conservational Architecture of Qianfoya Cliff Inscriptions which was built in 2016. By comparing the long long-term environmental pattern and differences between the internal and external part of the section, the results indicate that the Conservational Architecture effectively decrease the frequency of short-term sever winds, strong sunshine and extreme high and low temperatures, reduces the short short-term temperature and humidity variation range, which creates a stable microenvironment conducive to the preservation of statues without changing the long long-term environmental transformation pattern. Moreover, a parameter system for evaluating the conservational architecture, which directly related to environmental damage factors and meets the requirement of measurability and controllability, has been established and control threshold of microenvironment adjustment, which divides abnormal environment state in three levels (caution states, Pre-warning states, Warning states), has been chosen so as to quantitatively evaluate the protection effect of the experimental structure and provide data guidance for daily protection work and environmental control. Based on this parameter system and control thresholds , the total duration of warning states in Qianfoya experimental structure can be reduced by 30% compared with that outside the experimental structure , which further proves that the experimental structure plays a significant role in alleviating the main natural deterioration factors in Qianfoya cliff.

Structure activity relationships and the binding mode of quinolinone-pyrimidine hybrids as reversal agents of multidrug resistance mediated by P-gp

P-gp-associated multidrug resistance is a major impediment to the success of chemotherapy. With the aim of finding non-toxic and effective P-gp inhibitors, we investigated a panel of quinolin-2-one-pyrimidine hybrids. Among the active compounds, two of them significantly increased intracellular doxorubicin and rhodamine 123 accumulation by inhibiting the efflux mediated by P-gp and restored doxorubicin toxicity at nanomolar range. Structure–activity relationships showed that the number of methoxy groups, an optimal length of the molecule in its extended conformation, and at least one flexible methylene group bridging the quinolinone to the moiety bearing the pyrimidine favored the inhibitory potency of P-gp. The best compounds showed a similar binding pattern and interactions to those of doxorubicin and tariquidar, as revealed by MD and hybrid QM/MM simulations performed with the recent experimental structure of P-gp co-crystallized with paclitaxel. Analysis of the molecular interactions stabilizing the different molecular complexes determined by MD and QTAIM showed that binding to key residues from TMH 4–7 and 12 is required for inhibition.

Computational models in the service of X-ray and cryo-EM structure determination

CASP (Critical Assessment of Structure prediction) conducts community experiments to determine the state of the art in computing protein structure from amino acid sequence. The process relies on the experimental community providing information about not yet public or about to be solved structures, for use as targets. For some targets, the experimental structure is not solved in time for use in CASP. Calculated structure accuracy improved dramatically in this round, implying that models should now be much more useful for resolving many sorts of experimental difficulty. To test this, selected models for seven unsolved targets were provided to the experimental groups. These models were from the AlphaFold2 group, who overall submitted the most accurate predictions in CASP14. Four targets were solved with the aid of the models, and, additionally, the structure of an already solved target was improved. An a-posteriori analysis showed that in some cases models from other groups would also be effective. This paper provides accounts of the successful application of models to structure determination, including molecular replacement for X-ray crystallography, backbone tracing and sequence positioning in a Cryo-EM structure, and correction of local features. The results suggest that in future there will be greatly increased synergy between computational and experimental approaches to structure determination.

Reactivities of the Front Pocket N-Cap Cysteines in Human Kinases

Discovery of targeted covalent inhibitors directed at nucleophilic cysteines is attracting enormous interest. The front pocket (FP) N-cap cysteine has been the most popular site of covalent modification in kinases. Curiously, a long-standing hypothesis associates the N-cap position with cysteine hyper-reactivity; however, traditional computational methods suggest that the FP N-cap cysteines in all human kinases are predominantly unreactive at physiological pH. Here we applied a newly developed GPU-accelerated continuous constant pH molecular dynamics (CpHMD) tool to test the N-cap hypothesis and elucidate the cysteine reactivities. Simulations showed that the N-cap cysteines in BTK/BMX/TEC/ITK/TXK, JAK3, and MKK7 sample the reactive thiolate form to varying degrees at physiological pH; however, those in BLK and EGFR/ERBB2/ERBB4 which contain an Asp at the N-cap+3 position adopt the unreactive thiol form. The latter argues in favor of the base-assisted thiol-Michael addition mechanisms as suggested by the quantum mechanical calculations and experimental structure-function studies of EGFR inhibitors. Analysis revealed that the reactive N-cap cysteines are stabilized by hydrogen bond as well as electrostatic interactions, and in their absence a N-cap cysteine is unreactive due to desolvation. To test a corollary of the N-cap hypothesis, we also examined the reactivities of the FP N-cap+2 cysteines in JNK1/JNK2/JNK3 and CASK. Additionally, our simulations predicted the reactive cysteine and lysine locations in all 15 kinases. Our findings offer a systematic understanding of cysteine reactivities in kinases and demonstrate the predictive power and physical insights CpHMD can provide to guide the rational design of targeted covalent inhibitors.

Methodology for rigorous modeling of protein conformational changes by Rosetta using DEER Distance Restraints

We describe an approach for integrating distance restraints from Double Electron-Electron Resonance (DEER) spectroscopy into Rosetta with the purpose of modeling alternative protein conformations from an initial experimental structure. Fundamental to this approach is a multilateration algorithm that harnesses sets of interconnected spin label pairs to identify optimal rotamer ensembles at each residue that fit the DEER decay in the time domain. Benchmarked relative to data analysis packages, the algorithm yields comparable distance distributions with the advantage that fitting the DEER decay and rotamer ensemble optimization are coupled. We demonstrate this approach by modeling the protonation-dependent transition of the multidrug transporter PfMATE to an inward facing conformation with a deviation to the experimental structure of less than 2Å Cα RMSD. By decreasing spin label rotamer entropy, this approach engenders more accurate Rosetta models that are also more closely clustered, thus setting the stage for more robust modeling of protein conformational changes.

Nuclear dynamics of singlet exciton fission in pentacene single crystals

Singlet exciton fission (SEF) is a key process for developing efficient optoelectronic devices. An aspect rarely probed directly, yet with tremendous impact on SEF properties, is the nuclear structure and dynamics involved in this process. Here, we directly observe the nuclear dynamics accompanying the SEF process in single crystal pentacene using femtosecond electron diffraction. The data reveal coherent atomic motions at 1 THz, incoherent motions, and an anisotropic lattice distortion representing the polaronic character of the triplet excitons. Combining molecular dynamics simulations, time-dependent density-functional theory, and experimental structure factor analysis, the coherent motions are identified as collective sliding motions of the pentacene molecules along their long axis. Such motions modify the excitonic coupling between adjacent molecules. Our findings reveal that long-range motions play a decisive part in the electronic decoupling of the electronically correlated triplet pairs and shed light on why SEF occurs on ultrafast time scales.