Positions Of Hydrogen Atoms Research Articles

“Seeing Is Believing”: How Neutron Crystallography Informs Enzyme Mechanisms by Visualizing Unique Water Species

Hydrogen is the lightest atom and composes approximately half of the atomic content in macromolecules, yet their location can only be inferred or predicted in most macromolecular structures. This is because hydrogen can rarely be directly observed by the most common structure determination techniques (such as X-ray crystallography and electron cryomicroscopy). However, knowledge of hydrogen atom positions, especially for enzymes, can reveal protonation states of titratable active site residues, hydrogen bonding patterns, and the orientation of water molecules. Though we know they are present, this vital layer of information, which can inform a myriad of biological processes, is frustratingly invisible to us. The good news is that, even at modest resolution, neutron crystallography (NC) can reveal this layer and has emerged this century as a powerful tool to elucidate enzyme catalytic mechanisms. Due to its strong and coherent scattering of neutrons, incorporation of deuterium into the protein crystal amplifies the power of NC. This is especially true when solvation and the specific participation of key water molecules are crucial for catalysis. Neutron data allow the modeling of all three atoms in water molecules and have even revealed previously unobserved and unique species such as hydronium (D3O+) and deuteroxide (OD−) ions as well as lone deuterons (D+). Herein, we briefly review why neutrons are ideal probes for identifying catalytically important water molecules and these unique water-like species, limitations in interpretation, and four vignettes of enzyme success stories from disparate research groups. One of these groups was that of Dr. Chris G. Dealwis, who died unexpectedly in 2022. As a memorial appreciation of his scientific career, we will also highlight his interest and contributions to the neutron crystallography field. As both the authors were mentored by Chris, we feel we have a unique perspective on his love of molecular structure and admiration for neutrons as a tool to query those structures.

The Hydrogen-Bond Continuum in the Salt/Cocrystal Systems of Quinoline and Chloro-Nitrobenzoic Acids.

This study investigates the hydrogen-bond geometry in six two-component solid systems composed of quinoline and chloro-nitrobenzoic acids. New X-ray diffraction studies were conducted using both the conventional independent-atom model and the more recent Hirshfeld atom-refinement method, with the latter providing precise hydrogen-atom positions. The systems can be divided into salts (the hydrogen atom transferred to the quinoline nitrogen), cocrystals (the hydrogen atom retained by the acid), and intermediate structures. Solid-state NMR experiments corroborated the X-ray diffraction-derived H-N distances. DFT calculations, using five functionals including hybrid B3LYP and PBE0, showed varying energy profiles for the hydrogen bonds, with notable differences across functionals. These calculations revealed different preferences for salt or cocrystal structures, depending on the functional used. Path-integral molecular dynamics simulations incorporating nuclear quantum effects demonstrated significant hydrogen-atom delocalization, forming a hydrogen-bond continuum, and provided average N-H distances in excellent agreement with experimental results. This comprehensive experimental and theoretical approach highlights the complexity of multicomponent solids. The study emphasizes that the classification into salts or cocrystals is frequently inadequate, as the hydrogen atom is often significantly delocalized in the hydrogen bond. This insight is crucial for understanding and predicting the behavior of such systems in pharmaceutical applications.

Probing Short-Range Interactions in Isostructural Hydrate and Perhydrate of Dabrafenib by Magic-Angle Spinning Solid-State NMR.

Dabrafenib (DBF), an anticancer drug, exhibits isostructural properties in its hydrate (DBF⊃H2O) and perhydrate (DBF⊃H2O2) forms, as revealed by single-crystal X-ray diffraction. Despite the H2O and H2O2 solvent molecules occupying identical locations, the two polymorphs have different thermal behaviors. In general, determination of stoichiometry of H2O in the perhydrate crystals is difficult due to the presence of both H2O and H2O2 in the same crystal voids. This study utilizes magic-angle spinning (MAS) solid-state NMR (SSNMR) combined with gauge-included projector augmented wave calculations to characterize the influence of solvent molecules on the local environment in pseudopolymorphs. SSNMR experiments were employed to assign 1H, 13C, and 15N peaks and identify spectral differences in the isostructural pseudopolymorphs. Proton spectroscopy at fast MAS was used to identify and quantify H2O2/H2O in DBF⊃H2O2 (mixed hydrate/perhydrate). 1H-1H dipolar-coupling-based experiments were recruited to confirm the 3D molecular packing of solvent molecules in DBF⊃H2O and DBF⊃H2O2. Homonuclear (1H-1H) and heteronuclear (1H-14N) distance measurements, in conjunction with diffraction structures and optimized hydrogen atom positions by density functional theory, helped decipher local interactions of H2O2 with DBF and their geometry in DBF⊃H2O2. This integrated X-ray structure, quantum chemical calculations, and NMR study of pseudopolymorphs offer a practical approach to scrutinizing crystallized solvent interactions in the crystal lattice even without high-resolution crystal structures or artificial sample enrichment.

Regular relations of the composition, structure and properties of crystals of hydrogen-containing compounds

Research subject. Crystals of hydrogen-containing compounds belonging to the superprotonic family. Aim. To obtain knowledge about regular relations between composition, atomic structure, real structure and physical properties of materials, with the purpose of elucidating processes occurring in condensed state and forming the basis for modification of known or obtaining new compounds. Materials and methods. Experimental data were obtained using a set of complementary physical methods, including structural analysis using X-rays, synchrotron radiation and neutrons, optical microscopy, and atomic force microscopy. Results. Experimental data on the atomic structure, real structure, and physical properties of superprotonic crystals, including systems of hydrogen bonds and their changes, were obtained. Conclusions. The physical properties of superprotonic crystals are significantly affected by hydrogen bonding systems and their changes, primarily by the formation of dynamically disordered hydrogen bonds with energetically equivalent positions of hydrogen atoms. When carrying out diagnostics of crystalline samples, account should be taken of their real structure, including the structure of surface layers and the presence of crystallization water. These factors may affect the measured physical parameters, the boundaries of existence of phases, the formation of a multiphase state under variations in temperature.

Dynamical refinement with multipolar electron scattering factors.

Dynamical refinement is a well established method for refining crystal structures against 3D electron diffraction (ED) data and its benefits have been discussed in the literature [Palatinus, Petříček & Corrêa, (2015). Acta Cryst. A71, 235-244; Palatinus, Corrêa et al. (2015). Acta Cryst. B71, 740-751]. However, until now, dynamical refinements have only been conducted using the independent atom model (IAM). Recent research has shown that a more accurate description can be achieved by applying the transferable aspherical atom model (TAAM), but this has been limited only to kinematical refinements [Gruza et al. (2020). Acta Cryst. A76, 92-109; Jha et al. (2021). J. Appl. Cryst. 54, 1234-1243]. In this study, we combine dynamical refinement with TAAM for the crystal structure of 1-methyluracil, using data from precession ED. Our results show that this approach improves the residual Fourier electrostatic potential and refinement figures of merit. Furthermore, it leads to systematic changes in the atomic displacement parameters of all atoms and the positions of hydrogen atoms. We found that the refinement results are sensitive to the parameters used in the TAAM modelling process. Though our results show that TAAM offers superior performance compared with IAM in all cases, they also show that TAAM parameters obtained by periodic DFT calculations on the refined structure are superior to the TAAM parameters from the UBDB/MATTS database. It appears that multipolar parameters transferred from the database may not be sufficiently accurate to provide a satisfactory description of all details of the electrostatic potential probed by the 3D ED experiment.

Modeling defect formation in nano-ZrO2 under He and H+ irradiation

In the given work, compliance with the distribution law of defect vacancies formed in ZrO2 crystal irradiated with 2[Formula: see text]MeV energy H[Formula: see text] ions at room temperature was studied (The fluxes density for the H[Formula: see text] ion was chosen to be 1017 ions/cm2). The effect of H[Formula: see text] ions with fluxes density at different temperatures (500∘C, 600∘C, 700∘C, 800∘C and 900∘C) on W and S parameters was determined. The mechanism of formation of nanoclusters in the ZrO2 crystal structure under the influence of H[Formula: see text] radiation, the vacancy cluster formed by 2Zr vacancies and 4O vacancies, and its location in triple spaces with hydrogen atoms were determined. 2Zr and 4 vacancies were determined by the [Formula: see text] values of the vacancy clusters growing under the influence of radiation and the positions of hydrogen atoms in the 1VZr, 1VO, di-VZrO triple-VZrO2 vacancy groups.

Crystal Engineering of Hydrogen Bonding for Direct Air Capture of CO2: A Quantum Crystallography Perspective

Rising atmospheric CO2 levels demand efficient and sustainable carbon capture solutions. Direct air capture (DAC) via crystallizing hydrogen-bonded frameworks such as carbonate salts has emerged as a promising approach. This review explores the potential of crystal engineering, in tandem with advanced quantum crystallography techniques and computational modeling, to unlock the full potential of DAC materials. We examine the critical role of hydrogen bonding and other noncovalent interactions within a family of bis-guanidines that governs the formation of carbonate salts with high CO2 capture capacity and low regeneration energies for utilization. Quantum crystallography and charge density analysis prove instrumental in elucidating these interactions. A case study of a highly insoluble carbonate salt of a 2,6-pyridine-bis-(iminoguanidine) exemplifies the effectiveness of these approaches. However, challenges remain in the systematic and precise determination of hydrogen atom positions and atomic displacement parameters within DAC materials using quantum crystallography, and limitations persist in the accuracy of current energy estimation models for hydrogen bonding interactions. Future directions lie in exploring diverse functional groups, designing advanced hydrogen-bonded frameworks, and seamlessly integrating experimental and computational modeling with machine learning. This synergistic approach promises to propel the design and optimization of DAC materials, paving the way for a more sustainable future.

Tuning the polarity of charge carriers in N-heterocyclic carbene-based single-molecule junctions via atomic manipulation.

Tuning the polarity of charge carriers at a single-molecular level is essential for designing complementary logic circuits in the field of molecular electronics. Herein, the transport properties of N-heterocyclic carbene (NHC)-linked single-molecule junctions are investigated using the ab initio quantum transport approach. The results reveal that the hydrogen atoms in NHCs function as a switch for regulating the polarity of charge carriers. Dehydrogenation changes the chemical nature of NHC anchors, thereby rendering holes as the major charge carriers rather than electrons. Essentially, dehydrogenation changes the anchoring group from electron-rich to electron-deficient. The electrons transferred to molecules from the electrodes raise the molecular level closer to the Fermi level, thus resulting in charge carrier polarity conversion. This conversion is influenced by the position and number of hydrogen atoms in the NHC anchors. To efficiently and decisively alter charge carrier polarity via atomic manipulation, a methyl substitution approach is developed and verified. These results confirm that atomic manipulation is a significant method for modulating the polarity of charge carriers in NHC-based single-molecule devices.

The refinement of the parameters of β-turns using neutron diffraction data

Beta-bends are a difficult to interpret type of polypeptide chain backbone structure of globular proteins. Beta-bends are usually classified according to the dihedral angles φ and ψ of amino acid residues i + 1 and i + 2. Ramachandran map analysis of amino acid residues i + 1 and i + 2 indicates the resulting conformational stresses in bending. The mechanism of stabilization of their energetically disadvantageous conformations is still unclear. This kind of conformation stresses can only be compensated by additional interactions, such as additional hydrogen bonds, whose geometry and energy compensates for the beta-bending stress. Neutronography is the only available direct method for determining the position of hydrogen atoms in the structures of chemical compounds, including proteins. In this work, beta-bends from 176 protein structures from PDB established by neutronography are studied. In these structures, 3733 beta-bends were found using the i → i + 3 hydrogen bonding criterion. Using clustering by the magnitude of conformational angles, eight types of bends were newly identified. The magnitudes of conformational angles for each type of bend were determined. The hypothesis of additional hydrogen bonding to stabilize the bend was not confirmed, suggesting that the bending stress is compensated by other factors.

Enhancing hydrogen positions in X-ray structures of transition metal hydride complexes with dynamic quantum crystallography.

Hirshfeld atom refinement (HAR) is a method which enables the user to obtain more accurate positions of hydrogen atoms bonded to light chemical elements using X-ray data. When data quality permits, this method can be extended to hydrogen-bonded transition metals (TMs), as in hydride complexes. However, addressing hydrogen thermal motions with HAR, particularly in TM hydrides, presents a challenge. At the same time, proper description of thermal vibrations can be vital for determining hydrogen positions correctly. In this study, we employ tools such as SHADE3 and Normal Mode Refinement (NoMoRe) to estimate anisotropic displacement parameters (ADPs) for hydrogen atoms during HAR and IAM refinements performed for seven structures of TM (Fe, Ni, Cr, Nb, Rh and Os) and metalloid (Sb) hydride complexes for which both the neutron and the X-ray structures have been determined. A direct comparison between neutron and HAR/SHADE3/NoMoRe ADPs reveals that the similarity between neutron hydrogen ADPs and those estimated with NoMoRe or SHADE3 is significantly higher than when hydrogen ADPs are refined with HAR. Regarding TM-H bond lengths, traditional HAR exhibits a slight advantage over the other methods. However, combining NoMoRe/SHADE3 with HAR results in a minor decrease in agreement with neutron TM-H bond lengths. For the Cr complex, for which high-resolution X-ray data were collected, an investigation of resolution-related effects was possible.

Locating Hydrogen Positions for COF-300 by Cryo-3D Electron Diffraction.

Covalent organic frameworks (COFs) have wide-ranging applications, and their host-guest interactions play an essential role in the achievement of COF functions. To investigate these host-guest interactions, it is necessary to locate all atoms, especially hydrogen atoms. However, it is difficult to determine the hydrogen atomic positions in COFs because of the complexities in synthesizing high-quality large single crystals. Three-dimensional electron diffraction (3D ED) has unique advantages for the structural determination of nanocrystals and identification of light atoms. In this study, it was demonstrated for the first time that the hydrogen atoms of a COF, not only on the framework but also on the guest molecule, can be located by 3D ED using continuous precession electron diffraction tomography (cPEDT) under cryogenic conditions. The host-guest interactions were clarified with the location of the hydrogen atoms. These findings provide novel insights into the investigation of COFs.

Determination of hydrogen atom position in Stryker's reagent through the application of quantum crystallographic methods on MicroED data

Determination of hydrogen atom position in Stryker's reagent through the application of quantum crystallographic methods on MicroED data

Locating Hydrogen Positions for COF‐300 by Cryo‐3D Electron Diffraction

Locating Hydrogen Positions for COF‐300 by Cryo‐3D Electron Diffraction

Quantum crystallographic method improves the accuracy of screening of inhibitors: A set of Alzheimer’s disease responsible protein‐ligand complexes

AbstractBackgroundIn drug design and development, identification of lead structure is a crucial step to predict the ligand binding affinity and functional potency with any of target enzyme/protein. The recently developed quantum crystallographic method (fragment‐based approach) has been used as a substitutional way to calculate the interaction energies. This quantum mechanical level information gives a deeper understanding of structural facts with the position of hydrogen atoms and valence electron distributions. It is very much essential to understanding the electronic properties of drug‐receptor interactions. Therefore, the quantum crystallographic based interaction energy calculation is a better alternative method to docking score‐based modelling.MethodA set of AD responsible protein‐ligand complexes were selected for the quantitative analysis. Molecular docking of selected compounds with four different enzymes (AChE/BChE/BACE1/GSK3β) was carried out and then, all the selected complexes have been subjected to MD simulation. Later, the 3D coordinates of ligand with active site residues (around 4Å from the ligand) were used for quantum crystallographic studies.ResultThe screened molecules are forming strong hydrogen bonding and hydrophobic interactions with active site residues of all four enzymes; particularly, π‐π stacking, π‐cationic, π‐alkyl and π‐σ types of interactions, which are highly stable during dynamic behavior. After the quantum crystallographic studies, the interaction energies of selected compounds with different active site residues of all four enzymes were analyzed; it is ranged from ‐20.83 to ‐3.92 kcal/mol and the total interaction energies of each complex are higher than binding energy gained from MD simulation. And, the RMSD of each molecule was compared with the corresponding geometry of solid‐state and dynamic state; it is found to be significantly low (>0.5Å) and similar. Interestingly, the correlation between experimental IC50 and averaged interaction energies of selected compounds exhibits good agreement.ConclusionThe in‐silico results revealed conformational flexibility, high stability and compactness, binding affinity and orientation of the target molecules in the active site residues of all enzymes in the physiological nature (water‐medium). Quantum crystallographic method is a novel approach that opens new window to delineate the different type of interactions at electronic level. And, it may allow us to design new drug against target disease.

Insight into Intergranular Corrosion of the Aluminum Alloy 2024-T3: Effect of Pre-Charged Hydrogen

2024-T3 aluminum alloy has been widely applied in aviation fields, whilst the accumulation of hydrogen at grain boundaries deteriorates the mechanical properties and corrosion resistance. The intergranular corrosion of 2024-T3 related to hydrogen permeation was investigated. Atom probe tomography was used to observe the precise position of hydrogen atoms in relation to grain boundaries. The ionic current density of the H pre-charged surface was studied by in situ scanning vibrating electrode technique. Results show that the distribution of H is highly related to the S-phase at grain boundaries and the H pre-charging significantly improves the charge transfer efficiency at the initial period of intergranular corrosion process while the enhancement effect is then gradually weakened. The study provided new insight into hydrogen distribution at grain boundaries and its impact on the intergranular corrosion of 2024-T3 aluminum alloy, which can be informative and instructive for the research of corrosion in aluminum alloy.

A crystal structure refinement of uralolite, Ca2Be4(PO4)3(OH)3∙5H2O, from Weinebene, Austria

The crystal structure of uralolite, Ca2Be4(PO4)3(OH)3·5H2O, from the spodumene deposit of Weinebene, Carinthia, Austria, has been refined with X-ray single crystal data gathered on a CCD diffractometer. Uralolite is monoclinic, space group P21/n, a = 6.553(1), b = 16.005(3), c = 15.979(3) Å, β = 101.63(1)°, V = 1641.5(5) Å3. While previously only isotropic displacement parameters and no hydrogen atom positions were reported for uralolite, now anisotropic displacement parameters were used for non-hydrogen atoms and hydrogen atoms were located and refined yielding R1 = 0.038 for 3909 observed reflections. Uralolite is built up from corrugated layers [Be4(PO4)3(OH)3]4- parallel to (010), which contain Z-shaped groups of four BeO4 tetrahedra sharing corners via three OH groups and are further crosslinked by PO4 tetrahedra. Two Ca atoms in Ca(Ophosphate)5(H2O)2 coordination and an interstitial water molecule link these layers along [010]. The OH groups and the Ca-bonded H2O molecules are all involved in hydrogen bonds with O···O distances of 2.780(2) − 3.063(2) Å and O-H···O angles of 150(1) − 179(1)° excluding a bifurcated bond. The interstitial water molecule displays a distorted tetrahedral environment of O atoms and accepts and donates each two hydrogen bonds. The crystal structure exhibits a C2/c pseudosymmetry for the [Be4(PO4)3(OH)3]4- layers and the Ca atoms. However, the disposition of the water molecules and an asymmetric hydrogen bond pattern involving OH groups as well as H2O molecules are decisive for the lowering of the symmetry of the structure to the true space group P21/n.

First Observation of Quantum Diffusion in Non-Cubic Metal: Deuterium Diffusion in In

Diffusion of deuterium in indium is studied herein. In the temperature range 200–350 K, mass transfer is controlled predominantly by the mechanism of overbarrier atomic jumps; at temperatures from 80 to 120 K, by tunneling; whereas in the range from 120 to 200 K, there takes place a gradual transition from one migration mechanism to the other. These results are of fundamental significance since it is shown for the first time that quantum diffusion can be observed in a metal with a crystal lattice other than the body centered cubic one. Conditions are specified that are necessary for the observation of quantum diffusion of hydrogen: low values of Debye temperature, density of atomic packing in the lattice, and distance between the nearest equilibrium positions of hydrogen atoms. Moreover, data on the influence of point defects on hydrogen tunneling in solids are gained for the first time as well. The quantum diffusion coefficient is twice as high in the sample with enhanced vacancy concentration.

Hybridization of Wide-Angle X-ray and Neutron Diffraction Techniques in the Crystal Structure Analyses of Synthetic Polymers

The development in the crystal structure analysis of synthetic polymers using the hybridized combination of wide-angle X-ray and neutron diffraction (WAXD and WAND, respectively) techniques has been reviewed with many case studies performed by the authors. At first, the technical development was reviewed, in which the usage of high-energy synchrotron X-ray source was emphasized for increasing the total number of the observable diffraction peaks, and several examples were introduced. Secondly, the usage of the WAND method was introduced, in which the successful extraction of hydrogen atomic positions was described. The third example is to show the importance for the hybrid combination of these two diffraction methods. The quantitative WAXD data analysis gave the crystal structures of at-poly(vinyl alcohol) (at-PVA) and at-PVA-iodine complex. However, the thus-proposed structure models were found not to reproduce the observed WAND data very much. The reason came from the remarkable difference in the atomic scattering powers of the constituting atomic species between WAXD and WAND phenomena. The introduction of statistical disorder solved this serious problem, which reproduced both of the observed WAXD and WAND data consistently. The more systematic combination of WAXD and WAND methods, or the so-called X-N method, was applied also to the quantitative evaluation of the bonded electron density distribution along the skeletal chains, where the results about polydiacetylene single crystals were presented as the first successful study. Finally, the application of WAND technique in the trace of structural changes induced under the application of external stress or temperature was described. The future perspective is described for the development of structural science of synthetic polymers on the basis of the combined WAXD/WAND techniques.

Locating the hydrogen atoms in endohedral clusterfullerenes by density functional theory.

There is a unique type of endohedral clusterfullerene containing a hydrogen atom inside the carbon cage (hydrogen-containing clusterfullerenes, HCFs). Unfortunately, the precise positions of the H atoms cannot be determined by powerful single-crystal X-ray diffraction, and thus, the reported internal cluster structures of HCFs are ambiguous. In this study, HCFs were investigated using density functional theory calculations. Various internal cluster structures were obtained for Sc4CNH@Ih(7)-C80 and then carefully inspected to summarize all the favorable H locations in the HCFs. Encouragingly, following these structural characteristics, a new Sc4C2H@Ih(7)-C80 isomer with a μ3-H coordination to three Sc atoms was found to be 12.6 kcal mol-1 more stable than a previously reported isomer. It also holds a much larger SOMO-LUMO gap energy (3.57 vs. 2.36 eV). Its increased stability was further understood by the formation of multicenter bonds (three-center one-electron, three-center two-electron, and even four-center two-electron bonds) and electron density topology analyses. The changed H position may lead to rather different electronic structures, bonding states, and relative stability, indicating its critical role in HCFs. The simulated infrared and Raman spectra based on the new structure also agree fairly well with the experimental observations. Our work not only successfully locates the unpredictable H atom inside HCFs but also demonstrates a practical strategy to quickly determine the internal cluster configurations for more complex clusterfullerenes.

A combined solid-state NMR and quantum chemical calculation study of hydrogen bonding in two forms of α-d-glucose

Hydrogen bonding plays an important role in the structure and function of a wide range of materials. Solid-state 1H nuclear magnetic resonance (NMR) spectroscopy provides a very sensitive tool to investigate the local structure of hydrogen atoms involved in hydrogen bonding. While there is extensive 1H solid-state NMR data on O–H - - O hydrogen bonding in solid carboxylic acids, there has been no systematic 1H solid-state NMR studies of hydroxyl groups in carbohydrates (and hydroxyl groups in general). With a view to studying the hydrogen bonding in more complex materials such as cellulose polymorphs, we carried out a detailed solid-state 1H NMR investigation of the model compounds α-d-glucose and α-d-glucose monohydrate. Through a combination of fast magic-angle spinning (MAS), combined rotation and multiple pulse spectroscopy (CRAMPS), and two-dimensional (2D) correlation experiments carried out at ultrahigh magnetic fields, it was possible to assign all of the aliphatic (CH), hydroxyl (OH), and water (H2O) 1H chemical shifts in both forms of α-d-glucose. Plane-wave DFT calculations were employed to improve the hydrogen atom positions for α-d-glucose monohydrate and to calculate 1H chemical shifts, providing additional support for the experimentally determined peak assignments. Finally, the relationship between the hydroxyl 1H chemical shifts and their hydrogen bonding geometry was investigated and compared to the well-established relationship for carboxylic acid protons.