Accurate Structure Determination Research Articles

Time‐domain spectra of ultrasonic wave transmitted through granite and gypsum samples containing artificial defects

AbstractThe internal defects in rock masses can significantly impact the quality and safety of geotechnical projects. Mechanical waves, as a common nondestructive testing (NDT) method, can reflect the external and internal structures of rock or rock masses. Analyses on the reflected and transmitted waves enable nondestructive identification and assessment of potential defects within rocks. Previous studies mainly focused on the variation of single or limited wave features like main frequency, amplitude and energy between the intact and non‐intact samples. In fact, most information contained in the waveforms is neglected. Techniques of data mining can provide a powerful tool to reveal this information and therefore a more accurate determination of the internal structures. In this study, 995,412 NDT data from 14 types of granite and gypsum samples with different cross‐section shapes and different types of defects are recorded by an ultrasonic wave generation and collection system. This dataset can be used not only as the training data for defect classification in NDT but also as a good reference for conventional NDT analyses. Besides, time‐series data analysis is an opportunity and challenging issue, this dataset holds great potential for broader application in general time‐series classification analysis.

Integrating 19F Distance Restraints for Accurate Protein Structure Determination by Magic Angle Spinning NMR Spectroscopy.

Traditional protein structure determination by magic angle spinning (MAS) solid-state NMR spectroscopy primarily relies on interatomic distances up to 8 Å, extracted from 13C-, 15N-, and 1H-based dipolar-based correlation experiments. Here, we show that 19F fast (60 kHz) MAS NMR spectroscopy can supply additional, longer distances. Using 4F-Trp,U-13C,15N crystalline Oscillatoria agardhii agglutinin (OAA), we demonstrate that judiciously designed 2D and 3D 19F-based dipolar correlation experiments such as (H)CF, (H)CHF, and FF can yield interatomic distances in the 8-16 Å range. Incorporation of fluorine-based restraints into structure calculation improved the precision of Trp side chain conformations as well as regions in the protein around the fluorine containing residues, with notable improvements observed for residues in proximity to the Trp pairs (W10/W17 and W77/W84) in the carbohydrate-binding loops, which lacked sufficient long-range 13C-13C distance restraints. Our work highlights the use of fluorine and 19F fast MAS NMR spectroscopy as a powerful structural biology tool.

Phase Prediction via Crystal Structure Similarity in the Periodic Number Representation.

The periodic number (PN) representation of the chemical systems, introduced by Dmitri Mendeleev, uncovers the fundamental principle of chemical similarity in a straightforward way. In this framework, the rows correspond to the principal quantum numbers of the elements' electronic configurations when considered isolated atoms. This systematic arrangement allows for a deeper understanding of the relationships and patterns among the elements. In this study, we propose a novel strategy for structure type (prototype) prediction by utilizing the PN concept to identify possible modifications and phase stability of unexplored chemical systems. Our PN-based crystal structure prediction (PNcsp) program, which evaluates similarity through PN neighboring in the phase map, provides the most probable prototypes for unknown and unreported modifications of given phases in binary and higher order chemical systems. We applied PNcsp to 59 distinct chemical systems whose equimolar phases are indicated in the respective phase diagrams but lack accurate experimental structure determination. Our methodology identified 93 prototypes for these 59 equiatomic phases, of which 47 exhibit mechanical and dynamic stability. Notably, this approach discovered 19 entirely novel, fully stable polymorphic phases, thereby expanding the known landscape of potential materials. Furthermore, we demonstrated that this method is also effective for nonequimolar and higher order systems.

Enhancing solution structural analysis of large molecular proteins through optimal stereo array isotope labeling of aromatic amino acids

The observation of side-chain peaks of aromatic amino acids is the prerequisite for a high-resolution three-dimensional structure determination of proteins by NMR. However, it becomes difficult with increasing molecular size due to an increased transverse relaxation and the control of the relaxation pathway is needed to achieve the observation. We demonstrated that even for the large molecular size of 82 kDa Malate synthase G (MSG), the aromatic 13C-1H (CH) peaks of Tryptophan (Trp) and Phenylalanine (Phe) residues can be observed with high quality using a systematic stable isotope labeling scheme, Stereo-Array Isotope Labeling (SAIL) method. However, the sequence specific assignments of these peaks relied on the use of amino acid substitutions, employing an inefficient method that required many isotopes labeled samples. In this study, we developed novel SAIL amino acids that allow for the observation of the aromatic ring δ,ζ and the aliphatic β position peak of Phe residues. The application of TROSY-based experiment to the isolated CH moieties resulted in the successful observation of discernible and resolved CH peaks in Phe residues in MSG. In MSG, the sequence-specific assignments of the backbone and Cβ positions have already been confirmed. Therefore, using this labeling method, the δ and β position peaks of Phe residues can be clearly assigned in a sequence-specific and stereospecific manner through experiments based on intra-residue NOE. Furthermore, the NOESY experiment also allows for the acquisition of information pertaining to the conformation of Phe residues, such as the χ1 dihedral angle, providing valuable insights for the determination of accurate protein structures and in dynamic analysis. This new SAIL amino acids open an avenue to achieve a variety of NMR analysis of large molecular proteins, including a high-resolution structure determination and dynamics and interaction analysis.

Structural Elucidation of Ubiquitin via Gas-Phase Ion/Ion Cross-Linking Reactions Using Sodium-Cationized Reagents Coupled with Infrared Multiphoton Dissociation.

Accurate structural determination of proteins is critical to understanding their biological functions and the impact of structural disruption on disease progression. Gas-phase cross-linking mass spectrometry (XL-MS) via ion/ion reactions between multiply charged protein cations and singly charged cross-linker anions has previously been developed to obtain low-resolution structural information on proteins. This method significantly shortens experimental time relative to conventional solution-phase XL-MS but has several technical limitations: (1) the singly deprotonated N-hydroxysulfosuccinimide (sulfo-NHS)-based cross-linker anions are restricted to attachment at neutral amine groups of basic amino acid residues and (2) analyzing terminal cross-linked fragment ions is insufficient to unambiguously localize sites of linker attachment. Herein, we demonstrate enhanced structural information for alcohol-denatured A-state ubiquitin obtained from an alternative gas-phase XL-MS approach. Briefly, singly sodiated ethylene glycol bis(sulfosuccinimidyl succinate) (sulfo-EGS) cross-linker anions enable covalent cross-linking at both ammonium and amine groups. Additionally, covalently modified internal fragment ions, along with terminal b-/y-type counterparts, improve the determination of linker attachment sites. Molecular dynamics simulations validate experimentally obtained gas-phase conformations of denatured ubiquitin. This method has identified four cross-linking sites across 8+ ubiquitin, including two new sites in the N-terminal region of the protein that were originally inaccessible in prior gas-phase XL approaches. The two N-terminal cross-linking sites suggest that the N-terminal half of ubiquitin is more compact in gas-phase conformations. By comparison, the two C-terminal linker sites indicate the signature transformation of this region of the protein from a native to a denatured conformation. Overall, the results suggest that the solution-phase secondary structures of the A-state ubiquitin are conserved in the gas phase. This method also provides sufficient sensitivity to differentiate between two gas-phase conformers of the same charge state with subtle structural variations.

Broadening environmental research in the era of accurate protein structure determination and predictions

Broadening environmental research in the era of accurate protein structure determination and predictions

High Temperature Electron Diffraction on Organic Crystals: In Situ Crystal Structure Determination of Pigment Orange 34.

Small molecule structures and their applications rely on good knowledge of their atomic arrangements. However, the crystal structures of these compounds and materials, which are often composed of fine crystalline domains, cannot be determined with single-crystal X-ray diffraction. Three-dimensional electron diffraction (3D ED) is already becoming a reliable method for the structure analysis of submicrometer-sized organic materials. The reduction of electron beam damage is essential for successful structure determination and often prevents the analysis of organic materials at room temperature, not to mention high temperature studies. In this work, we apply advanced 3D ED methods at different temperatures enabling the accurate structure determination of two phases of Pigment Orange 34 (C34H28N8O2Cl2), a biphenyl pyrazolone pigment that has been industrially produced for more than 80 years and used for plastics application. The crystal structure of the high-temperature phase, which can be formed during plastic coloration, was determined at 220 °C. For the first time, we were able to observe a reversible phase transition in an industrial organic pigment in the solid state, even with atomic resolution, despite crystallites being submicrometer in size. By localizing hydrogen atoms, we were even able to detect the tautomeric state of the molecules at different temperatures. This demonstrates that precise, fast, and low-dose 3D ED measurements enable high-temperature studies the door for general in situ studies of nanocrystalline materials at the atomic level.

Phase Identification and Discovery of an Elusive Polymorph of Drug‐Polymer Inclusion Complex Using Automated 3D Electron Diffraction

Abstract3D electron diffraction (3D ED) has shown great potential in crystal structure determination in materials, small organic molecules, and macromolecules. In this work, an automated, low‐dose and low‐bias 3D ED protocol has been implemented to identify six phases from a multiple‐phase melt‐crystallisation product of an active pharmaceutical ingredient, griseofulvin (GSF). Batch data collection under low‐dose conditions using a widely available commercial software was combined with automated data analysis to collect and process over 230 datasets in three days. Accurate unit cell parameters obtained from 3D ED data allowed direct phase identification of GSF Forms III, I and the known GSF inclusion complex (IC) with polyethylene glycol (PEG) (GSF‐PEG IC‐I), as well as three minor phases, namely GSF Forms II, V and an elusive new phase, GSF‐PEG IC‐II. Their structures were then directly determined by 3D ED. Furthermore, we reveal how the stabilities of the two GSF‐PEG IC polymorphs are closely related to their crystal structures. These results demonstrate the power of automated 3D ED for accurate phase identification and direct structure determination of complex, beam‐sensitive crystallisation products, which is significant for drug development where solid form screening is crucial for the overall efficacy of the drug product.

Phase Identification and Discovery of an Elusive Polymorph of Drug-Polymer Inclusion Complex Using Automated 3D Electron Diffraction.

3D electron diffraction (3D ED) has shown great potential in crystal structure determination in materials, small organic molecules, and macromolecules. In this work, an automated, low-dose and low-bias 3D ED protocol has been implemented to identify six phases from a multiple-phase melt-crystallisation product of an active pharmaceutical ingredient, griseofulvin (GSF). Batch data collection under low-dose conditions using a widely available commercial software was combined with automated data analysis to collect and process over 230 datasets in three days. Accurate unit cell parameters obtained from 3D ED data allowed direct phase identification of GSF Forms III, I and the known GSF inclusion complex (IC) with polyethylene glycol (PEG) (GSF-PEG IC-I), as well as three minor phases, namely GSF Forms II, V and an elusive new phase, GSF-PEG IC-II. Their structures were then directly determined by 3D ED. Furthermore, we reveal how the stabilities of the two GSF-PEG IC polymorphs are closely related to their crystal structures. These results demonstrate the power of automated 3D ED for accurate phase identification and direct structure determination of complex, beam-sensitive crystallisation products, which is significant for drug development where solid form screening is crucial for the overall efficacy of the drug product.

Molecular Gas-Phase Conformational Ensembles.

Accurately determining the global minima of a molecular structure is important in diverse scientific fields, including drug design, materials science, and chemical synthesis. Conformational search engines serve as valuable tools for exploring the extensive conformational space of molecules and for identifying energetically favorable conformations. In this study, we present a comparison of Auto3D, CREST, Balloon, and ETKDG (from RDKit), which are freely available conformational search engines, to evaluate their effectiveness in locating global minima. These engines employ distinct methodologies, including machine learning (ML) potential-based, semiempirical, and force field-based approaches. To validate these methods, we propose the use of collisional cross-section (CCS) values obtained from ion mobility-mass spectrometry studies. We hypothesize that experimental gas-phase CCS values can provide experimental evidence that we likely have the global minimum for a given molecule. To facilitate this effort, we used our gas-phase conformation library (GPCL) which currently consists of the full ensembles of 20 small molecules and can be used by the community to validate any conformational search engine. Further members of the GPCL can be readily created for any molecule of interest using our standard workflow used to compute CCS values, expanding the ability of the GPCL in validation exercises. These innovative validation techniques enhance our understanding of the conformational landscape and provide valuable insights into the performance of conformational generation engines. Our findings shed light on the strengths and limitations of each search engine, enabling informed decisions for their utilization in various scientific fields, where accurate molecular structure determination is crucial for understanding biological activity and designing targeted interventions. By facilitating the identification of reliable conformations, this study significantly contributes to enhancing the efficiency and accuracy of molecular structure determination, with particular focus on metabolite structure elucidation. The findings of this research also provide valuable insights for developing effective workflows for predicting the structures of unknown compounds with high precision.

Computational Biology and Chemistry with AI and ML

Deep learning, a transformative force in computational biology, has reshaped biological data analysis and interpretation terrain. This review delves into the multifaceted role of deep knowledge in this field, exploring its historical roots, inherent advantages, and persistent challenges. It investigates explicitly its application in two pivotal domains: DNA sequence classification, where it has been used to identify disease-causing mutations, and protein structure prediction from sequence data, where it has enabled the accurate determination of protein tertiary structures. Moreover, it offers a glimpse into the future trajectory of this dynamic field, sparking intrigue and excitement about the potential of deep learning.

DiffraGAN: a conditional generative adversarial network for phasing single molecule diffraction data to atomic resolution.

Proteins that adopt multiple conformations pose significant challenges in structural biology research and pharmaceutical development, as structure determination via single particle cryo-electron microscopy (cryo-EM) is often impeded by data heterogeneity. In this context, the enhanced signal-to-noise ratio of single molecule cryo-electron diffraction (simED) offers a promising alternative. However, a significant challenge in diffraction methods is the loss of phase information, which is crucial for accurate structure determination. Here, we present DiffraGAN, a conditional generative adversarial network (cGAN) that estimates the missing phases at high resolution from a combination of single particle high-resolution diffraction data and low-resolution image data. For simulated datasets, DiffraGAN allows effectively determining protein structures at atomic resolution from diffraction patterns and noisy low-resolution images. Our findings suggest that combining single particle cryo-electron diffraction with advanced generative modeling, as in DiffraGAN, could revolutionize the way protein structures are determined, offering an alternative and complementary approach to existing methods.

Pressure-Assisted Synthesis of Highly Crystalline 1T''-Lix MoS2.

Lix MoS2 is not only a lithium battery material, but is also an important precursor for the synthesis of MoS2 nanomaterials. Current syntheses of MoS2 , such as in n-butyllithium/LiBH4 or electrochemically, are not satisfying in terms of defined stoichiometry and crystallinity, so an accurate experimental crystal structure determination of this important and widely used material has been long awaited. A high-pressure/high-temperature synthesis yielded highly crystalline 1T''-Lix MoS2 (x=1, 1.333). 1T''-LiMoS2 crystallizes in the space group P with a=6.2482(3) Å, b=6.6336(3) Å, c=6.7480(3) Å, α=119.321(2)°, β=90.010(2)° and γ=90.077(2)°. The arrangement of Mo atoms within the b-c-plane confirmed a predicted Peierls distortion. A similar atom distribution pattern to that of Mo is also observed for the lithium atoms. Calculation of bond valence site energies gave an activation barrier of 1.244 eV for 2D lithium-ion migration. For x=1.333, a phase-pure synthesis was achieved.

Phase-Dependence of Molecular Structures Arising from Weak London Dispersion Interactions.

ConspectusThe structures of molecules can be different in different phases. Intermolecular forces, even those of weak noncovalent interactions (WNCIs), can lead to a preference for quite different conformations in the solid, the gas, and the liquid phases. WNCIs can cause variations in bond lengths, angles, and torsional angles. Since structure is a fundamental concept in chemistry, the knowledge of structural changes with phase is important to understand the source and effects of distorting contributions from WNCIs but also as a predictive tool for the design and stabilization of new bonding situations.X-ray crystallography is ubiquitous and now mostly straightforward to perform, but facilities for the determination of accurate gas-phase structure determination are rare, and gas-phase work is laborious and time-consuming. There are currently about 1.25 million crystal structures and more than 12 500 experimental gas-phase structures, but the intersection of the two data sets that can tell us about the structural differences of the same molecule in different phases is surprisingly small.In this Account, we describe several cases of WNCI-dominated systems for which accurate experimental structure determinations exist for both the gas phase and the solid state and, in one case, also for solution. The examples include aryl-aryl, aryl-alkyl, and alkyl-alkyl interactions; systems with chalcogen and halogen bonding; and fluorine-based interactions in arylboranes. We work out the role of WNCIs in stabilizing large, strained, or sterically overloaded molecules. We will show how flexible molecules will fold under the action of WNCIs when isolated in the gas and how they fold or unfold when they are embedded in an environment of neighbors in crystals. We will show how they can vary in strength when the substitution patterns in aryl groups are changed by different halogens and how intramolecular WNCIs, such as those forming rings, change when such systems experience additional intermolecular WNCIs.Overall, we hope that this Account will give the reader an idea of the type and magnitude of structural changes that can be expected from a free molecule in the gas phase or a single molecule calculated by quantum chemistry compared with one embedded in a crystal. This should define the limits of comparability and provide some predictive concepts of the distortions and variations to be expected.

SARS-CoV-2 proteins structural studies using synchrotron radiation.

In the process of the development of structural biology, both the size and the complexity of the determined macromolecular structures have grown significantly. As a result, the range of application areas for the results of structural studies of biological macromolecules has expanded. Significant progress in the development of structural biology methods has been largely achieved through the use of synchrotron radiation. Modern sources of synchrotron radiation allow to conduct high-performance structural studies with high temporal and spatial resolution. Thus, modern techniques make it possible to obtain not only static structures, but also to study dynamic processes, which play a key role in understanding biological mechanisms. One of the key directions in the development of structural research is the drug design based on the structures of biomolecules. Synchrotron radiation offers insights into the three-dimensional time-resolved structure of individual viral proteins and their complexes at atomic resolution. The rapid and accurate determination of protein structures is crucial for understanding viral pathogenicity and designing targeted therapeutics. Through the application of experimental techniques, including X-ray crystallography and small-angle X-ray scattering (SAXS), it is possible to elucidate the structural details of SARS-CoV-2 virion containing 4 structural, 16 nonstructural proteins (nsp), and several accessory proteins. The most studied potential targets for vaccines and drugs are the structural spike (S) protein, which is responsible for entering the host cell, as well as nonstructural proteins essential for replication and transcription, such as main protease (Mpro), papain-like protease (PLpro), and RNA-dependent RNA polymerase (RdRp). This article provides a brief overview of structural analysis techniques, with focus on synchrotron radiation-based methods applied to the analysis of SARS-CoV-2 proteins.

Quantum crystallography for accurate structure determination and chemical bonding analysis

Quantum crystallography for accurate structure determination and chemical bonding analysis

Analysis of Cell Glycogen with Quantitation and Determination of Branching Using Liquid Chromatography-Mass Spectrometry.

Glycogen is a highly branched biomacromolecule that functions as a glucose buffer. It is involved in multiple diseases such as glycogen storage disorders, diabetes, and even liver cancer, where the imbalance between biosynthetic and catabolic enzymes results in structural alterations and abnormal accumulation of glycogen that can be toxic to cells. Accurate and sensitive glycogen quantification and structural determination are prerequisites for understanding the phenotypes and biological functions of glycogen under these conditions. In this research, we furthered cell glycogen characterization by presenting a highly sensitive method to measure the glycogen content and degree of branching. The method employed a novel fructose density gradient as an alternative to the traditional sucrose gradient to fractionate glycogen from cell mixtures using ultracentrifugation. Fructose was used to avoid the large glucose background, allowing the method to be highly quantitative. The glycogen content was determined by quantifying 1-phenyl-3-methyl-5-pyrazolone (PMP)-derivatized glucose residues obtained from acid-hydrolyzed glycogen using ultra-high-performance liquid chromatography/triple quadrupole mass spectrometry (UHPLC/QqQ-MS). The degree of branching was determined through linkage analysis where the glycogen underwent permethylation, hydrolysis, PMP derivatization, and UHPLC/QqQ-MS analysis. The new approach was used to study the effect of insulin on the glycogen phenotypes of human hepatocellular carcinoma (Hep G2) cells. We observed that cells produced greater amounts of glycogen with less branching under increasing insulin levels before reaching the cell's insulin-resistant state, where the trend reversed and the cells produced less but higher-branched glycogen. The advantage of this method lies in its high sensitivity in characterizing both the glycogen level and the structure of biological samples.

Ab initio structural study of 2-imino-4-thiazolidinone derivatives and their anti-proliferative activity against A549 and H460 human lung carcinoma cells

This theoretical work focuses on the determination of structural properties of a series of 2-iminothiazolidin-4-one derivatives and of their anti-proliferative activity against A549 and H460 human lung carcinoma cells. First, we performed benchmarks on the 2-iminothiazolidin-4-one subunit in gas phase and in aqueous solvent using first principle approaches. These benchmarks validated the use of B3LYP/6–311++G(d,p) method for the accurate determination of the equilibrium structures, vibrational spectroscopy and properties of 2-iminothiazolidin-4-one derivatives. We applied this method to investigate these derivatives of interest. We also deduced their reactivity descriptors. Afterward, we used some of these descriptors to establish quantitative structure activity relationships models for such activity in aqueous phase. These models were obtained by multiple regression analysis procedures. The predictivity of our models was estimated using the leave-one-out method. In sum, our work should be useful to predict the inhibitory activity of this class of molecules and to fight against lung cancer.

Laboratory rotational spectroscopy and astronomical search for 2-ethylacrolein

The rotational spectrum of 2-ethylacrolein was investigated by pulsed jet Fourier transform microwave spectroscopy complementary with quantum chemical calculations. The rotational spectra of both conformers cis and gauche and their all mono-substituted 13C and 18O isotopologues were measured and assigned in natural abundance, allowing the accurate structural determinations on their heavy-atom skeletons. The relative population ratio of cis to gauche in pulsed jets was estimated to be ≈ 3:1. With the accurate rotational transition frequencies, radio astronomical searches toward the massive star-forming region Sgr B2(N) were carried out by using the Shanghai Tianma 65 m radio telescope. No transition lines belonging to 2-ethylacrolein were detected, the upper limits of column densities for cis and gauche were derived to be 7.52 × 1013 cm−2 and 1.29 × 1015 cm−2, respectively.

Adaptive Encapsulation of 1,ω‐Amino‐Acids within the “Pyrene Box”

AbstractPyrene boxes, self‐assembled from 1,3,5,8‐pyrene‐tetrasulfonate anions, PTS4− and Guanidinium G+, amino‐guanidinium AG+ and hydrated alkali counter cations have been used for the encapsulation of 1,ω‐amino‐acids of variable lengths. The NMR spectroscopy illustrates that these systems are stable in aqueous solution and encapsulation process involves dynamic or fixed guest molecules within Pyrene box, depending of the nature of the counter‐cations. The amide bond coupling between the amino‐guanidinium AG+ and encapsulated 1,ω‐amino‐acid guests occur in water in the absence of coupling catalysts. The variable co‐encapsulation of the guests via multivalent stabilizing interactions shed light that chemical selection can be obtained from mixtures of 1,ω‐amino‐acids. Our study involving a comprehensive screening of 18 co‐crystal structures help to understand the in‐situ fixation of 1,ω‐amino‐acid guests and their accurate determination of unconventional structures under confinement.