Extensive structural rearrangement of intraflagellar transport trains underpins bidirectional cargo transport.

Bidirectional transport in cilia is carried out by polymers of the IFTA and IFTB protein complexes, called anterograde and retrograde intraflagellar transport (IFT) trains. Anterograde trains deliver cargoes from the cell to the cilium tip, then convert into retrograde trains for cargo export. We set out to understand how the IFT complexes can perform these two directly opposing roles before and after conversion. We use cryoelectron tomography and in situ cross-linking mass spectrometry to determine the structure of retrograde IFT trains and compare it with the known structure of anterograde trains. The retrograde train is a 2-fold symmetric polymer organized around a central thread of IFTA complexes. We conclude that anterograde-to-retrograde remodeling involves global rearrangements of the IFTA/B complexes and requires complete disassembly of the anterograde train. Finally, we describe how conformational changes to cargo-binding sites facilitate unidirectional cargo transport in a bidirectional system.

Potent Henipavirus Neutralization by Antibodies Recognizing Diverse Sites on Hendra and Nipah Virus Receptor Binding Protein.

Hendra (HeV) and Nipah (NiV) viruses are emerging zoonotic pathogens in the Henipavirus genus causing outbreaks of disease with very high case fatality rates. Here, we report the first naturally occurring human monoclonal antibodies (mAbs) against HeV receptor binding protein (RBP). All isolated mAbs neutralized HeV, and some also neutralized NiV. Epitope binning experiments identified five major antigenic sites on HeV-RBP. Animal studies demonstrated that the most potent cross-reactive neutralizing mAbs, HENV-26 and HENV-32, protected ferrets in lethal models of infection with NiV Bangladesh 3 days after exposure. We solved the crystal structures of mAb HENV-26 in complex with both HeV-RBP and NiV-RBP and of mAb HENV-32 in complex with HeV-RBP. The studies reveal diverse sites of vulnerability on RBP recognized by potent human mAbs that inhibit virus by multiple mechanisms. These studies identify promising prophylactic antibodies and define protective epitopes that can be used in rational vaccine design.

Structural Titration of Slo2.2, a Na+-Dependent K+ Channel.

The stable structural conformations that occur along the complete reaction coordinate for ion channel opening have never been observed. In this study, we describe the equilibrium ensemble of structures of Slo2.2, a neuronal Na+-activated K+ channel, as a function of the Na+ concentration. We find that Slo2.2 exists in multiple closed conformations whose relative occupancies are independent of Na+ concentration. An open conformation emerges from an ensemble of closed conformations in a highly Na+-dependent manner, without evidence of Na+-dependent intermediates. In other words, channel opening is a highly concerted, switch-like process. The midpoint of the structural titration matches that of the functional titration. A maximum open conformation probability approaching 1.0 and maximum functional open probability approaching 0.7 imply that, within the class of open channels, there is a subclass that is not permeable to ions.

Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration.

Water is known to play an important role in collagen self-assembly, but it is still largely unclear how water-collagen interactions influence the assembly process and determine the fibril network properties. Here, we use the H[Formula: see text]O/D[Formula: see text]O isotope effect on the hydrogen-bond strength in water to investigate the role of hydration in collagen self-assembly. We dissolve collagen in H[Formula: see text]O and D[Formula: see text]O and compare the growth kinetics and the structure of the collagen assemblies formed in these water isotopomers. Surprisingly, collagen assembly occurs ten times faster in D[Formula: see text]O than in H[Formula: see text]O, and collagen in D[Formula: see text]O self-assembles into much thinner fibrils, that form a more inhomogeneous and softer network, with a fourfold reduction in elastic modulus when compared to H[Formula: see text]O. Combining spectroscopic measurements with atomistic simulations, we show that collagen in D[Formula: see text]O is less hydrated than in H[Formula: see text]O. This partial dehydration lowers the enthalpic penalty for water removal and reorganization at the collagen-water interface, increasing the self-assembly rate and the number of nucleation centers, leading to thinner fibrils and a softer network. Coarse-grained simulations show that the acceleration in the initial nucleation rate can be reproduced by the enhancement of electrostatic interactions. These results show that water acts as a mediator between collagen monomers, by modulating their interactions so as to optimize the assembly process and, thus, the final network properties. We believe that isotopically modulating the hydration of proteins can be a valuable method to investigate the role of water in protein structural dynamics and protein self-assembly.

MS-BACL: enhancing metabolic stability prediction through bond graph augmentation and contrastive learning.

MOTIVATION: Accurately predicting molecular metabolic stability is of great significance to drug research and development, ensuring drug safety and effectiveness. Existing deep learning methods, especially graph neural networks, can reveal the molecular structure of drugs and thus efficiently predict the metabolic stability of molecules. However, most of these methods focus on the message passing between adjacent atoms in the molecular graph, ignoring the relationship between bonds. This makes it difficult for these methods to estimate accurate molecular representations, thereby being limited in molecular metabolic stability prediction tasks. RESULTS: We propose the MS-BACL model based on bond graph augmentation technology and contrastive learning strategy, which can efficiently and reliably predict the metabolic stability of molecules. To our knowledge, this is the first time that bond-to-bond relationships in molecular graph structures have been considered in the task of metabolic stability prediction. We build a bond graph based on 'atom-bond-atom', and the model can simultaneously capture the information of atoms and bonds during the message propagation process. This enhances the model's ability to reveal the internal structure of the molecule, thereby improving the structural representation of the molecule. Furthermore, we perform contrastive learning training based on the molecular graph and its bond graph to learn the final molecular representation. Multiple sets of experimental results on public datasets show that the proposed MS-BACL model outperforms the state-of-the-art model. AVAILABILITY AND IMPLEMENTATION: The code and data are publicly available at https://github.com/taowang11/MS.

Art and Science of the Cellular Mesoscale.

Experimental information from microscopy, structural biology, and bioinformatics may be integrated to build structural models of entire cells with molecular detail. This integrative modeling is challenging in several ways: the intrinsic complexity of biology results in models with many closely packed and heterogeneous components; the wealth of available experimental data is scattered among multiple resources and must be gathered, reconciled, and curated; and computational infrastructure is only now gaining the capability of modeling and visualizing systems of this complexity. We present recent efforts to address these challenges, both with artistic approaches to depicting the cellular mesoscale, and development and application of methods to build quantitative models.

Molecular Structure Engineering of Isomeric Additives for Long Lifetime Zn Anodes.

Modulating the solvation structure of hydrated zinc ions using organic additives stands as a pragmatic approach to suppress dendrite formation and corrosion on zinc metal anodes (ZMAs), thereby enhancing the rechargeability of aqueous Zn-ion batteries. However, fundamental screening principles for organic additives with diverse molecular structures remain elusive, especially for isomers with the same molecular formula. This study delves into the impact of three isomeric hexagonal alcohols (mannitol, sorbitol, and galactitol) as additives in adjusting Zn2+ solvation structural behaviors within ZnSO4 baseline electrolytes. Electrical measurements and molecular simulations reveal the specific molecular structure of mannitol, which features interweaving electron clouds between adjacent hydroxyl groups, achieving a high local electron cloud density. This phenomenon significantly enhances desolvation abilities, thus establishing a more stable anode/electrolyte interface chemistry. Even at 5 mA cm-2 for 2.5 mAh cm-2 capacity, Zn||Zn symmetric cells with mannitol-regulated electrolyte display an impressive 1170 h lifespan, far exceeding those with other isomer additives and is nearly tenfold longer than that with a pure ZnSO4 electrolyte (120 h). Rather than strictly adhering to focusing on chemical composition, this study with emphasis on optimizing molecular structure offers a promising untapped dimension to screen more efficient additives to enhance the reversibility of ZMAs.

Exploring the complexity of amyloid-beta fibrils: structural polymorphisms and molecular interactions.

The aggregation of amyloid-beta (Aß) peptides into cross-ß structures forms a variety of distinct fibril conformations, potentially correlating with variations in neurodegenerative disease progression. Recent advances in techniques such as X-ray crystallography, solid-state NMR, and cryo-electron microscopy have enabled the development of high-resolution molecular structures of these polymorphic amyloid fibrils, which are either grown in vitro or isolated from human and transgenic mouse brain tissues. This article reviews our current understanding of the structural polymorphisms in amyloid fibrils formed by Aß40 and Aß42, as well as disease-associated mutants of Aß peptides. The aim is to enhance our understanding of various molecular interactions, including hydrophobic and ionic interactions, within and among cross-ß structures.

Grouping approaches based on structure alone are insufficient to conclude about toxicological properties-the example of monoamine-based chelates.

Aminocarboxylic acid (monoamine-based) chelating agents such as GLDA, MGDA, NTA, and EDG are widely used in a variety of products and processes. In the European Union, based on the Green Deal and the Chemicals Strategy for Sustainability (CSS), there is an increasing tendency to speed up chemical hazard evaluation and to regulate chemicals by grouping substances based on molecular structure similarity. Recently, it was proposed to group polycarboxylic acid monoamines, hydroxy derivatives and their salts with monovalent cations, and to consider all group members as potential carcinogens based on the official CLP classification of one group member, viz. NTA, which is classified as suspected carcinogen Cat. 2. In this review, we show that a grouping approach for harmonized classification and labeling based on molecular structure alone, disregarding existing animal test data as well as current scientific and regulatory knowledge, would result in incorrect classification. Using such a simplistic, although considered pragmatic approach, classification of all group members upfront would not improve protection of human health. Instead, it could not only lead to unnecessary additional vertebrate animal testing but also to onerous and disproportionate restrictions being placed on the use of these valuable substances; some of these even being considered as green chemicals.

Modeling the Structure of Ketoprofen-Poly(vinylpyrrolidone) Amorphous Solid Dispersions with Empirical Potential Structure Refinements of X-ray Scattering Data.

The metastability of amorphous formulations poses barriers to their safe and widespread commercialization. The propensity of amorphous solid dispersions (ASDs) to crystallize is directly linked to their molecular structure. Amorphous structures are inherently complex and thus difficult to fully characterize by experiments, which makes structural simulations an attractive route for investigating which structural characteristics correlate with ASD stability. In this study, we use empirical potential structure refinement (EPSR) to create molecular models of ketoprofen-poly(vinylpyrrolidone) (KTP/PVP) ASDs with 0-75 wt % drug loading. The EPSR technique uses X-ray total scattering measurements as constraints, yielding models that are consistent with the X-ray data. We perform several simulations to assess the sensitivity of the EPSR approach to input parameters such as intramolecular bond rotations, PVP molecule length, and PVP tacticity. Even at low drug loading (25 wt %), ∼40% of KTP molecules participate in KTP-KTP hydrogen bonding. The extent of KTP-PVP hydrogen bonding does not decrease significantly at higher drug loadings. However, the models' relative uncertainties are too large to conclude whether ASDs' lower stabilities at high drug loadings are due to changes in drug-excipient hydrogen bonding or a decrease in steric hindrance of KTP molecules. This study illustrates how EPSR, combined with total scattering measurements, can be a powerful tool for investigating structural characteristics in amorphous formulations and developing ASDs with improved stability.

Hydrochar and Its Dissolved Organic Matter Aged in a 30-Month Rice-Wheat Rotation System: Do Primary Aging Factors Alter at Different Stages?

Hydrochar, recognized as a green and sustainable soil amendment, has garnered significant attention. However, information on the aging process in soil and the temporal variability of hydrochar remains limited. This study delves deeper into the interaction between hydrochar and soil, focusing on primary factors influencing hydrochar aging during a 30-month rice-wheat rotation system. The results showed that the initial aging of hydrochar (0-16 months) is accompanied by the development of specific surface area and leaching of hydrochar-derived dissolved organic matter (HDOM), resulting in a smaller particle size and reduced carbon content. The initial aging also features a mineral shield, while the later aging (16 to 30 months) involves surface oxidation. These processes collectively alter the surface charge, hydrophilicity, and composition of aged hydrochar. Furthermore, this study reveals a dynamic interaction between the HDOM and DOM derived from soil, plants, and microbes at different aging stages. Initially, there is a preference for decomposing labile carbon, whereas later stages involve the formation of components with higher aromaticity and molecular weight. These insights are crucial for understanding the soil aging effects on hydrochar and HDOM as well as evaluating the interfacial behavior of hydrochar as a sustainable soil amendment.

Advanced tools for molecular characterization of bio-based and biodegradable polymers.

Bio-based and biodegradable materials play a vital role in a sustainable and green economy. These materials must exhibit properties that are similar to or better than the properties of oil- or coal-based materials and require sophisticated synthesis technologies and detailed knowledge of structure-property correlations. For comprehensive molecular structure elucidation, advanced analytical methods, including coupled and hyphenated techniques that combine advanced fractionation and information-rich spectroscopic detectors, are an indispensable tool. One important tool for fractionating complex polymers regarding molecular size is size exclusion chromatography. For fractionating polymers with regard to chemical composition, solvent (or temperature) gradient HPLC has been developed. The combination of different liquid chromatography methods in comprehensive two-dimensional HPLC setups is another important tool. Today, a toolbox of HPLC methods is in place that enables the fractionation of complex bio-based and biodegradable polymers according to the most important molecular parameters including molecular size, composition, functionality, and branching. Here, an overview of the different techniques and some major applications is presented. Some representative developments in the field are discussed, and different techniques, experimental protocols, and applications are highlighted.

Conformational Sampling in Computational Studies of Natural Products: Why Is It Important?

Conformational sampling is a vital component of a reliable computational chemistry investigation. With the aim of illustrating the importance of conformational sampling, and building awareness among new practitioners, we present a series of case studies that show how the quality and reliability of computational studies depend on undertaking a thorough conformer search. The examples are drawn from the most common types of research questions in natural products chemistry, but the fundamental principles apply more generally to computational studies of molecular structure and behavior in any field of chemistry.

Discovery of internal rotation and conformers of 1,2-dichloroethane: the dawn of the concept of conformation.

In 1932, Mizushima and Higasi reported the dependence of the dipole moments of 1,2-dichloroethane on both temperature and solvent in the Proceedings of the Imperial Academy, Japan. This report was followed by their first proposal of the existence of conformers that exchanged by internal rotation about a C-C single bond based on experimental data. Their monumental work marked the beginning of the essential concept of conformation in modern stereochemistry. Their proposal was later confirmed by the direct observation of the anti and gauche conformers of 1,2-dichloroethane by Raman spectroscopy, and further supported by other experimental and theoretical methods. The relative stabilities of the anti and gauche conformers of 1,2-dichloroethane and other 1,2-disubstituted ethanes were discussed in terms of steric, electrostatic, and stereoelectronic effects based on analysis of calculated data. Those studies influenced the development of subsequent research in organic chemistry, such as the conformational analysis of cyclohexane derivatives and the isolation of chiral gauche conformers.

Evolution characteristics and molecular constraints of microbial communities during coal biogasification.

This study investigates the production of biomethane, and variation in microbial community and coal molecular structures using gas chromatography, 16S rRNA high-throughput sequencing and Fourier transform infrared spectroscopy. Additionally, the factors influencing microbial community structure at a molecular level are discussed. The results demonstrate that bituminous coal exhibits a higher biomethane yield than anthracite coal. In bituminous coal samples, Escherichia and Proteiniphilum are the predominant bacteria at day 0, while Macellibacteroides dominates from days 5 to 35. Methanofollis is the dominated archaea during days 0 to 15, followed by Methanosarcina on day 35. In anthracite coal samples, Soehngenia is the dominant bacterial genus at day 0; however, it transitions to mainly Soehngenia and Aminobacterium within days 5-15 before evolving into Acetomicrobium on day 35. Methanocorpusculum is predominantly found in archaeal communities during days 0-15 but shifts to Methanosarcina on day 35. Alpha diversity analysis reveals that bacterial communities have higher species abundance and diversity compared to archaeal communities. Redundancy analysis indicates a significant correlation between coal molecular structure and bacterial community composition (P value < 0.05), whereas no correlation exists with archaeal community composition (P value > 0.05). The research findings provide theoretical support for revealing the biological gasification mechanisms of coal.

Molecular Structure of Salicylic Acid and Its Hydrates: A Rotational Spectroscopy Study.

We present a study of salicylic acid and its hydrates, with up to four water molecules, done by employing chirped-pulse Fourier transform microwave spectroscopy. We employed the spectral data set of the parent, 13C, and 2H isotopologues to determine the molecular structure and characterize the intra- and intermolecular interactions of salicylic acid and its monohydrate. Complementary theoretical calculations were done to support the analysis of the experimental results. For the monomer, we analyzed structural properties, such as the angular-group-induced bond alternation (AGIBA) effect. In the microsolvates, we analyzed their main structural features dominated by the interaction of water with the carboxylic acid group. This work contributes to seeding information on how water molecules accumulate around this group. Moreover, we discussed the role of cooperative effects further stabilizing the observed inter- and intramolecular hydrogen bond interactions.

Calculation of Some Low-Lying Electronic Excitations of Barium Monofluoride Using the Equation of Motion (EOM)-CC3 Method with an Effective Core Potential Approach.

Barium monofluoride (BaF) is a polar molecule of interest in measurements of the electron electric dipole moment. For this purpose, efforts are underway to investigate this molecule embedded within cryogenic matrices, e.g., in solid Ne. For a theoretical understanding of the electronic structure of such an embedded molecule, the need arises for efficient methods which are accurate but also able to handle a number of atoms which surround the molecule. The calculation for gas-phase BaF can be reduced to involve only outer electrons by representing the inner core of Ba with a pseudopotential, while carrying out a non-relativistic calculation with an appropriate basis set. Thus, the method is effectively at a scalar-relativistic level. In this work, we demonstrate to which extent this can be achieved using coupled-cluster methods to deal with electron correlation. As a test case, the SrF(X2Σ+→B2Σ+) transition is investigated, and excellent accuracy is obtained with the EOM-CC3 method. For the BaF(X2Σ+→A'2Δ, X2Σ+→A2Π, X2Σ+→B2Σ+) transitions, various coupled-cluster approaches are compared with very good agreement for EOM-CC3 with experimentally derived spectroscopic parameters, at the level of tens of cm-1. An exception is the excitation to the A'2Δ state, for which the energy is overestimated by 230cm-1. The poor convergence behavior for this particular state is demonstrated by providing results from calculations with basis sets of n = 3, 4, 5)-zeta quality. The calculated excitation energy for the B2Σ+ state agrees better with a deperturbation analysis than with the effective spectroscopic value, with a difference of 120cm-1.

Caffeine-Legal Natural Stimulant with Open Research Perspective: Spectroscopic and Theoretical Characterization.

Caffeine is an alkaloid with a purine structure and has been well known for centuries due to its presence in popular drinks-tea and coffee. However, the structural and spectroscopic parameters of this compound, as well as its chemical and biological activities, are still not fully known. In this study, for the first time, we report on the measured oxygen-17 NMR spectra of this stimulant. To support the assignment of our experimental NMR data, extensive quantum chemical calculations of NMR parameters, including nuclear magnetic shielding constants and indirect spin-spin coupling constants, were performed. In a theoretical study, using nine efficient density functionals (B3LYP, BLYP, BP86, CAM-B3LYP, LC-BLYP, M06, PBE0, TPSSh, wB97x), and in combination with a large and flexible correlation-consistent aug-cc-pVTZ basis set, the structure and NMR parameters were predicted for a free molecule of caffeine and in chloroform, DMSO and water. A polarized continuum model (PCM) was used to include a solvent effect. As a result, an optimal methodology was developed for predicting reliable NMR data, suitable for studies of known, as well as newly discovered, purines and similar alkaloids. The results of the current work could be used in future basic and applied studies, including NMR identification and intermolecular interactions of caffeine in various raw materials, like plants and food, as well as in the structural and spectroscopic characterization of new compounds with similar structures.

Molecular Simulation Analysis of Polyurethane Molecular Structure under External Electric Field.

Polyurethane (PU) materials are extensively utilized in power equipment. This paper introduces a comprehensive evaluation method that combines electromagnetics and computational chemistry based on the Density Functional Theory (DFT) to elucidate the impact of external electric fields on the molecular structure of PU during electrical contact. The study focuses on the microstructural and molecular energy changes in the hard (HS) and soft (SS) segments of PU under the influence of an electric field of uniform intensity. Findings indicate that the total energy of HS molecules decreases markedly as the electric field intensity increases, accompanied by a significant rise in both the dipole moment and polarizability. Conversely, the total energy and polarizability of the SS molecules decrease, while the dipole moment experiences a slight increase. Under the influence of a strong electric field, HS molecules tend to stretch towards the extremities of the main chain, leading to structural instability and the cleavage of hydroxyl O-H bonds. Meanwhile, the carbon chain of the SS molecules twists towards the center under the electric field, with no chemical bond rupture observed. At an electric field intensity of 8.227 V/nm, the HOMO-LUMO gap of the HS molecule narrows sharply, signifying a rapid decline in the molecular structure stability, corroborated by infrared spectroscopy analysis. These findings offer theoretical insights and guidance for the modification of PU materials in power equipment applications.

Intermolecular Interactions between Aldehydes and Alcohols: Conformational Equilibrium and Rotational Spectra of Acrolein-Methanol Complex.

The rotational spectra of the 1:1 complex formed by acrolein and methanol and its deuterated isotopologues have been analyzed. Two stable conformations in which two hydrogen bonds between the two moieties are formed were detected. The rotational lines show a hyperfine structure due to the methyl group internal rotation in the complex and the V3 barriers hindering the motion were determined as 2.629(5) kJ mol-1 and 2.722(5) kJ mol-1 for the two conformations, respectively. Quantum mechanical calculations at the MP2/aug-cc-pVTZ level and comprehensive analysis of the intermolecular interactions, utilizing NCI and SAPT approaches, highlight the driving forces of the interactions and allow the determination of the binding energies of complex formation.