A comprehensive classification and nomenclature of carboxyl-carboxyl(ate) supramolecular motifs and related catemers: implications for biomolecular systems

1H/17O Chemical Shift Waves in Carboxyl-Bridged Hydrogen Bond Networks in Organic Solids

We report solid-state 1H and 17O NMR results for four 17O-labeled organic compounds each containing an extensive carboxyl-bridged hydrogen bond (CBHB) network in the crystal lattice: tetrabutylammonium hydrogen di-[17O2]salicylate (1), [17O4]quinolinic acid (2), [17O4]dinicotinic acid (3), and [17O2]Gly/[17O2]Gly·HCl cocrystal (4). The 1H isotropic chemical shifts found for protons involved in different CBHB networks are between 8.2 and 20.5 ppm, which reflect very different hydrogen-bonding environments. Similarly, the 17O isotropic chemical shifts found for the carboxylate oxygen atoms in CBHB networks, spanning a large range between 166 and 341 ppm, are also remarkably sensitive to the hydrogen-bonding environments. We introduced a simple graphical representation in which 1H and 17O chemical shifts are displayed along the H and O atomic chains that form the CBHB network. In such a depiction, because wavy patterns are often observed, we refer to these wavy patterns as 1H/17O chemical shift waves. Typical patterns of 1H/17O chemical shift waves in CBHB networks are discussed. The reported 1H and 17O NMR parameters for the CBHB network models examined in this study can serve as benchmarks to aid in spectral interpretation for CBHB networks in proteins.

Computational Design of Photosensitive Polymer Templates To Drive Molecular Nanofabrication

Molecular electronics promises the ultimate level of miniaturization of computers and other machines as organic molecules are the smallest known physical objects with nontrivial structure and function. But despite the plethora of molecular switches, memories, and motors developed during the almost 50-years long history of molecular electronics, mass production of molecular computers is still an elusive goal. This is mostly due to the lack of scalable nanofabrication methods capable of rapidly producing complex structures (similar to silicon chips or living cells) with atomic precision and a small number of defects. Living nature solves this problem by using linear polymer templates encoding large volumes of structural information into sequence of hydrogen bonded end groups which can be efficiently replicated and which can drive assembly of other molecular components into complex supramolecular structures. In this paper, we propose a nanofabrication method based on a class of photosensitive polymers inspired by these natural principles, which can operate in concert with UV photolithography used for fabrication of current microelectronic processors. We believe that such a method will enable a smooth transition from silicon toward molecular nanoelectronics and photonics. To demonstrate its feasibility, we performed a computational screening of candidate molecules that can selectively bind and therefore allow the deterministic assembly of molecular components. In the process, we unearthed trends and design principles applicable beyond the immediate scope of our proposed nanofabrication method, e.g., to biologically relevant DNA analogues and molecular recognition within hydrogen-bonded systems.

Synthesis, solid state characterization, theoretical and experimental spectroscopic studies of the new lanthanide complexes

Three new complexes Na[Ln(pic)₄]ּ⋅2.5H₂O (Ln = Tb, Eu or Gd; pic = picolinate) were synthesized and characterized by infrared spectroscopy, powder X-ray diffraction and thermogravimetric analyses. The molecular structures of the complexes have been determined by single-crystal X-ray diffraction. The three isostructural lanthanide complexes crystalize in the hexagonal system with space group P6₁22 to Eu complex and Gd complex and space group P6₅22 to Tb complex. In each of the complexes, the picolinate ligands are bonded to Ln³⁺ and Na⁺ ions by different coordination modes promoting polymeric structures. The photoluminescent properties of complexes were studied and combined with theoretical studies using the density functional theory (DFT: B3LYP, PBE1PBE) and the semiempirical method AM1/Sparkle from the single crystal X-ray diffraction structures to assign a suitable model for describing the system. The B3LYP DFT functional was considered the most adequate for providing structural properties of the compounds and for describing luminescence properties. The excited triplet states (T₁) and excited singlet states (S₁) of the ligand were determined theoretically using Time-dependent DFT calculations (TD-DFT: B3LYP, CAM-B3LYP and LC-wPBE) and INDO/S-CIS, with the best agreement with experimental values obtained from the LC-wPBE DFT functional. The photoluminescent spectra of the complexes and their lifetime measurements were determined indicating that the Eu complex and Tb complex display different intramolecular energy transfer mechanisms with higher efficiency to ligand-to-terbium energy transfer. In addition, the experimental and theorical Judd-Ofelt intensity parameters and quantum yields of the complexes were also determined and discussed besides to a proposed 9-state diagram to describe the luminescence properties of the Eu complex. The low value of emission quantum efficiency of ⁵D₀ emitting level of Eu(III) ion was explained by the presence of the ligand-to-metal charge transfer state (LMCT) evidenced experimentally and theoretically. A good agreement was obtained between the proposed kinetic model and experimental results showing the consistency of the set of rate equations assumed and the intramolecular pathways proposed.

Combined NMR Spectroscopy and Quantum-Chemical Calculations in Fluorescent 1,2,3-Triazole-4-carboxylic Acids Fine Structures Analysis

The peculiarities of the optical properties of 2-aryl-1,2,3-triazole acids and their sodium salts were investigated in different solvents (1,4-dioxane, dimethyl sulfoxide DMSO, methanol MeOH) and in mixtures with water. The results were discussed in terms of the molecular structure formed by inter- and intramolecular noncovalent interactions (NCIs) and their ability to ionize in anions. Theoretical calculations using the Time-Dependent Density Functional Theory (TDDFT) were carried out in different solvents to support the results. In polar and nonpolar solvents (DMSO, 1,4-dioxane), fluorescence was provided by strong neutral associates. Protic MeOH can weaken the acid molecules' association, forming other fluorescent species. The fluorescent species in water exhibited similar optical characteristics to those of triazole salts; therefore, their anionic character can be assumed. Experimental 1H and 13C-NMR spectra were compared to their corresponding calculated spectra using the Gauge-Independent Atomic Orbital (GIAO) method and several relationships were established. All these findings showed that the obtained photophysical properties of the 2-aryl-1,2,3-triazole acids noticeably depend on the environment and, therefore, are good candidates as sensors for the identification of analytes with labile protons.

Crystal Structure of an Archaeal Tyrosyl-tRNA Synthetase Bound to Photocaged L-Tyrosine and Its Potential Application to Time-Resolved X-ray Crystallography

Genetically encoded caged amino acids can be used to control the dynamics of protein activities and cellular localization in response to external cues. In the present study, we revealed the structural basis for the recognition of O-(2-nitrobenzyl)-L-tyrosine (oNBTyr) by its specific variant of Methanocaldococcus jannaschii tyrosyl-tRNA synthetase (oNBTyrRS), and then demonstrated its potential availability for time-resolved X-ray crystallography. The substrate-bound crystal structure of oNBTyrRS at a 2.79 Å resolution indicated that the replacement of tyrosine and leucine at positions 32 and 65 by glycine (Tyr32Gly and Leu65Gly, respectively) and Asp158Ser created sufficient space for entry of the bulky substitute into the amino acid binding pocket, while Glu in place of Leu162 formed a hydrogen bond with the nitro moiety of oNBTyr. We also produced an oNBTyr-containing lysozyme through a cell-free protein synthesis system derived from the Escherichia coli B95. ΔA strain with the UAG codon reassigned to the nonnatural amino acid. Another crystallographic study of the caged protein showed that the site-specifically incorporated oNBTyr was degraded to tyrosine by light irradiation of the crystals. Thus, cell-free protein synthesis of caged proteins with oNBTyr could facilitate time-resolved structural analysis of proteins, including medically important membrane proteins.

Effect of substituents in novel bioactive tavaborole derivatives on the intermolecular interaction hierarchy

Tavaborole, a molecule based on the benzoxaborole scaffold, is an effective antifungal drug marketed under the Kerydin® trademark.

Bis(pyrazol-1-yl)methane-4,4′-dicarboxylic Acid

The molecular structure of bis(pyrazol-1-yl)methane-4,4′-dicarboxylic acid (H2bpmdc) was determined by single crystal X-Ray diffraction analysis. The compound crystallizes in a monoclinic crystal system; the unit cell contains four formula units. The molecules of H2bpmdc are linked into zig-zag chains by intermolecular carboxyl–carboxyl hydrogen bonds. Other types of supramolecular interactions, namely, CH···N and CH···O short contacts, CH–π interactions and carbonyl–carbonyl interactions were detected in the crystal structure.

Two Unexpected Temperature-Induced Supermolecular Isomers from Multi-Topic Carboxylic Acid: Hydrogen Bonding Layer or Helix Tube

Under ambient conditions or 160 °C, two supramolecular isomers, namely [(H4PTTA)(H2O)2(DMF)] and [(H4PTTA)(H2O)3]··Guest (1-L and 1-H, H4PTTA = N-phenyl-N'-phenyl bicyclo[2.2.2]oct-7-ene-2,3,5,6-tetracarboxdiimide tetra-carboxylic acid, Guest = DMF and H2O), were obtained through the reaction of H4PTTA in a mixture of H2O and dimethylformamide. The single crystal structures reveal the temperature-dependent supramolecular isomerism derived from the torsion of semi-rigid of H4PTTA. The 1-L prepared at room temperature is a hydrogen bond based achiral layer, while the hydrothermal synthesized 1-H is isomer resulted in an H-bond-based chiral tubes-packed supramolecular framework.

Salts of purine alkaloids caffeine and theobromine with 2,6-dihydroxybenzoic acid as coformer: structural, theoretical, thermal and spectroscopic studies

The study of various forms of pharmaceutical substances with specific physicochemical properties suitable for putting them on the market is one of the elements of research in the pharmaceutical industry. A large proportion of active pharmaceutical ingredients (APIs) occur in the salt form. The use of an acidic coformer with a given structure and a suitable pK_a value towards purine alkaloids containing a basic imidazole N atom can lead to salt formation. In this work, 2,6-dihydroxybenzoic acid (26DHBA) was used for cocrystallization of theobromine (TBR) and caffeine (CAF). Two novel salts, namely, theobrominium 2,6-dihydroxybenzoate, C₇H₉N₄O₂⁺·C₇H₅O₄^- (I), and caffeinium 2,6-dihydroxybenzoate, C₈H₁₁N₄O₂⁺·C₇H₅O₄^- (II), were synthesized. Both salts were obtained independently by slow evaporation from solution, by neat grinding and also by microwave-assisted slurry cocrystallization. Powder X-ray diffraction measurements proved the formation of the new substances. Single-crystal X-ray diffraction studies confirmed proton transfer between the given alkaloid and 26DHBA, and the formation of N-H...O hydrogen bonds in both I and II. Unlike the caffeine cations in II, the theobromine cations in I are paired by noncovalent N-H...O=C interactions and a cyclic array is observed. As expected, the two hydroxy groups in the 26DHBA anion in both salts are involved in two intramolecular O-H...O hydrogen bonds. C-H...O and π-π interactions further stabilize the crystal structures of both compounds. Steady-state UV-Vis spectroscopy showed changes in the water solubility of xanthines after ionizable complex formation. The obtained salts I and II were also characterized by theoretical calculations, Fourier-transform IR spectroscopy (FT-IR), thermogravimetric analysis (TGA), differential scanning calorimetry (DSC) and elemental analysis.

Stereoelectronic power of oxygen in control of chemical reactivity: the anomeric effect is not alone

Although carbon is the central element of organic chemistry, oxygen is the central element of stereoelectronic control in organic chemistry. Generally, a molecule with a C-O bond has both a strong donor (a lone pair) and a strong acceptor (e.g., a σ*_C-O orbital), a combination that provides opportunities to influence chemical transformations at both ends of the electron demand spectrum. Oxygen is a stereoelectronic chameleon that adapts to the varying situations in radical, cationic, anionic, and metal-mediated transformations. Arguably, the most historically important stereoelectronic effect is the anomeric effect (AE), i.e., the axial preference of acceptor groups at the anomeric position of sugars. Although AE is generally attributed to hyperconjugative interactions of σ-acceptors with a lone pair at oxygen (negative hyperconjugation), recent literature reports suggested alternative explanations. In this context, it is timely to evaluate the fundamental connections between the AE and a broad variety of O-functional groups. Such connections illustrate the general role of hyperconjugation with oxygen lone pairs in reactivity. Lessons from the AE can be used as the conceptual framework for organizing disjointed observations into a logical body of knowledge. In contrast, neglect of hyperconjugation can be deeply misleading as it removes the stereoelectronic cornerstone on which, as we show in this review, the chemistry of organic oxygen functionalities is largely based. As negative hyperconjugation releases the "underutilized" stereoelectronic power of unshared electrons (the lone pairs) for the stabilization of a developing positive charge, the role of orbital interactions increases when the electronic demand is high and molecules distort from their equilibrium geometries. From this perspective, hyperconjugative anomeric interactions play a unique role in guiding reaction design. In this manuscript, we discuss the reactivity of organic O-functionalities, outline variations in the possible hyperconjugative patterns, and showcase the vast implications of AE for the structure and reactivity. On our journey through a variety of O-containing organic functional groups, from textbook to exotic, we will illustrate how this knowledge can predict chemical reactivity and unlock new useful synthetic transformations.

Elucidation of the molecular interactions that enable stable assembly and structural diversity in multicomponent immune receptors

Multicomponent immune receptors are essential complexes in which distinct ligand-recognition and signaling subunits are held together by interactions between acidic and basic residues of their transmembrane helices. A 2:1 acidic-to-basic motif in the transmembrane domains of the subunits is necessary and sufficient to assemble these receptor complexes. Here, we study a prototype for these receptors, a DAP12-NKG2C 2:1 heterotrimeric complex, in which the two DAP12 subunits each contribute a single transmembrane Asp residue, and the NKG2C subunit contributes a Lys to form the complex. DAP12 can also associate with 20 other subunits using a similar motif. Here, we use molecular-dynamics simulations to understand the basis for the high affinity and diversity of interactions in this group of receptors. Simulations of the transmembrane helices with differing protonation states of the Asp-Asp-Lys triad identified a structurally stable interaction in which a singly-protonated Asp-Asp pair forms a hydrogen-bonded carboxyl-carboxylate clamp that clasps onto a charged Lys side chain. This polar motif was also supported by density functional theory and a Protein Data Bank-wide search. In contrast, the helices are dynamic at sites distal to the stable carboxyl-carboxylate clamp motif. Such a locally stable but globally dynamic structure is well suited to accommodate the sequence and structural variations in the transmembrane helices of multicomponent receptors, which mix and match subunits to create combinatorial functional diversity from a limited number of subunits. It also supports a signaling mechanism based on multisubunit clustering rather than propagation of rigid conformational changes through the membrane.

Hydrogen-bond directionality and symmetry in [C(O)NH](N)2P(O)-based structures: a comparison between X-ray crystallography data and neutron-normalized values, and evaluation of reliability

For [C(O)NH](N)₂P(O)-based structures, the magnitude of the differences in the N-H...O, H...O=P and H...O=C angles has been evaluated when the N-H bond lengths, determined by X-ray diffraction, were compared to the neutron normalized values and the maximum percentage difference was obtained, i.e. about 3% for the angle even if the N-H bond lengths have a difference of about 30% (0.7 Å for the X-ray and 1.03 Å for the neutron-normalized value). The symmetries of the crystals are discussed with respect to the symmetry of the molecules, as well as to the symmetry of hydrogen-bonded motifs, and the role of the most directional hydrogen bond in raising the probability of obtaining centrosymmetric crystal structures is investigated. The work was performed by considering nine new X-ray crystal structures and 204 analogous structures retrieved from the Cambridge Structural Database.

Strong intramolecular hydrogen bonding in confined amino acids

Intramolecular hydrogen bonding is evaluated in three different amino acids encapsulated in C₆₀ fullerene in the context of electron density analysis. While conventional intramolecular hydrogen bonding in isolated amino acids are dominated by electrostatic character, it is shown that strong intramolecular hydrogen bonding can be formed in confined amino acids so that in two cases covalent intramolecular hydrogen bonding is appeared in the confined species. Also, results show that zwitterionic amino acids are stable in confined state, where no implicit or explicit solvation is applied. Covalent character for intramolecular hydrogen bonding in amino acids have not yet been reported.

Structural characterization and theoretical calculations of the monohydrate of the 1:2 cocrystal salt formed from acriflavine and 3,5-dinitrobenzoic acid

The synthesis and structural characterization of the monohydrated 1:2 cocrystal salt of acriflavine with 3,5-dinitrobenzoic acid [systematic name: 3,6-diamino-10-methylacridin-10-ium 3,5-dinitrobenzoate-3,5-dinitrobenzoic acid-water (1/1/1), C₁₄H₁₄N₃⁺·C₇H₃N₂O₆^-·C₇H₄N₂O₆·H₂O] are reported. Single-crystal X-ray diffraction measurements show that the title solvated monohydrate salt crystalizes in the monoclinic space group P2₁ with one acriflavine cation, a 3,5-dinitrobenzoate anion, a 3,5-dinitrobenzoic acid molecule and a water molecule in the asymmetric unit. The neutral and anionic forms of 3,5-dinitrobenzoic acid are linked via O-H...O hydrogen bonds to form a monoanionic dimer. Neighbouring monoanionic dimers of 3,5-dinitrobenzoic acid are linked by nitro-nitro N-O...N and nitro-acid N-O...π intermolecular interactions to produce a porous organic framework. The acriflavine cations are linked with carboxylic acid molecules directly via amine-carboxy N-H...O, amine-nitro N-H...O and acriflavine-carboxy C-H...O hydrogen bonds, and carboxy-acriflavine C-O...π, nitro-acriflavine N-O...π and acriflavine-nitro π-π interactions, or through the water molecule by amino-water N-H...O and water-carboxy O-H...O hydrogen bonds, and are located in the voids of the porous organic framework. The intermolecular interactions were studied using the CrystalExplorer program to provide information about the interaction energies and the dispersion, electrostatic, polarization and repulsion contributions to the lattice energy.

Novel Purine Alkaloid Cocrystals with Trimesic and Hemimellitic Acids as Coformers: Synthetic Approach and Supramolecular Analysis

In this work, benzene-1,3,5-tricarboxylic (trimesic acid, TMSA) and benzene-1,2,3-tricarboxylic acid (hemimellitic acid, HMLA) were used as coformers for cocrystal synthesis with chosen purine alkaloids. Theobromine (TBR) forms cocrystals TBR·TMSA and TBR·HMLA with these acids. Theophylline (TPH) forms cocrystals TPH·TMSA and TPH·HMLA, the cocrystal hydrate TPH·TMSA·2H₂O and the salt hydrate (TPH)⁺·(HMLA)^-·2H₂O. Caffeine (CAF) forms the cocrystal CAF·TMSA and the cocrystal hydrate CAF·HMLA·H₂O. The purine alkaloid derivatives were obtained by solution crystallization and by neat or liquid-assisted grinding. The powder X-ray diffraction method was used to confirm the synthesis of the novel substances. All of these solids were structurally characterized, and all synthons formed by purine alkaloids and carboxylic acids were recognized using a single-crystal X-ray diffraction method. The Cambridge Structural Database was used to determine the frequency of occurrence of analyzed supramolecular synthons, which is essential at the crystal structure design stage. Determining the influence of structural causes on the various synthon formations and molecular arrangements in the crystal lattice was possible using structurally similar purine alkaloids and two isomers of benzenetricarboxylic acid. Additionally, UV-vis measurements were made to determine the effect of cocrystallization on purine alkaloid solubility.

Reducing crystal structure overprediction of ibuprofen with large scale molecular dynamics simulations

Reduction of a large dataset of computationally predicted structures of ibuprofen by employing molecular dynamics and biased simulations at finite temperature and pressure.

Unveiling the structural features of the host–guest complexes of carboxylated pillar[5]arene with viologen derivatives

Here we describe inclusion and self-assembly behavior of carboxylated pillar[5]arene with four viologen derivatives.

Incorporation of carboxylated pillar[5]arene and strontium(ii) into supramolecular coordination complexes of different nuclearities

The nuclearity of the coordination complexes of carboxylated pillar[5]arene and strontium(ii) can be varied with the aid of phenanthroline as a coligand.

Diabat method for polymorph free energies: Extension to molecular crystals

Lattice-switch Monte Carlo and the related diabat methods have emerged as efficient and accurate ways to compute free energy differences between polymorphs. In this work, we introduce a one-to-one mapping from the reference positions and displacements in one molecular crystal to the positions and displacements in another. Two features of the mapping facilitate lattice-switch Monte Carlo and related diabat methods for computing polymorph free energy differences. First, the mapping is unitary so that its Jacobian does not complicate the free energy calculations. Second, the mapping is easily implemented for molecular crystals of arbitrary complexity. We demonstrate the mapping by computing free energy differences between polymorphs of benzene and carbamazepine. Free energy calculations for thermodynamic cycles, each involving three independently computed polymorph free energy differences, all return to the starting free energy with a high degree of precision. The calculations thus provide a force field independent validation of the method and allow us to estimate the precision of the individual free energy differences.

Structural Elucidation of Enantiopure and Racemic 2-Bromo-3-Methylbutyric Acid

Halogenated carboxylic acids have been important compounds in chemical synthesis and indispensable research tools in biochemical studies for decades. Nevertheless, the number of structurally characterized simple α-brominated monocarboxylic acids is still limited. We herein report the crystallization and structural elucidation of (R)- and rac-2-bromo-3-methylbutyric acid (2-bromo-3-methylbutanoic acid, 1) to shed light on intermolecular interactions, in particular hydrogen bonding motifs, packing modes and preferred conformations in the solid-state. The crystal structures of (R)- and rac-1 are revealed by X-ray crystallography. Both compounds crystallize in the triclinic crystal system with Z = 2; (R)-1 exhibits two crystallographically distinct molecules. In the crystal, (R)-1 forms homochiral O–H···O hydrogen-bonded carboxylic acid dimers with approximate non-crystallographic C2 symmetry. In contrast, rac-1 features centrosymmetric heterochiral dimers with the same carboxy syn···syn homosynthon. The crystal packing of centrosymmetric rac-1 is denser than that of its enantiopure counterpart (R)-1. The molecules in both crystal structures adopt a virtually identical staggered conformation, despite different crystal environments, which indicates a preferred molecular structure of 1. Intermolecular interactions apart from classical O–H···O hydrogen bonds do not appear to have a crucial bearing on the solid-state structures of (R)- and rac-1.

Effect of intramolecular hydrogen-bond formation on the molecular conformation of amino acids

The molecular conformation of the carboxyl group can be crucial for its chemical properties and intermolecular interactions, especially in complex molecular environments such as polypeptides. Here, we study the conformational behaviour of the model amino acid N-acetylproline in solution at room temperature with two-dimensional infrared spectroscopy. We find that the carboxyl group of N-acetylproline adopts two distinct conformations, syn- and anti-. In the syn-conformer the O-H group is oriented at  ~60^∘ with respect to the C=O and in the anti-conformer the O-H is anti-parallel to the C=O. In hydrogen-bond accepting solvents such as dimethyl sulfoxide or water, we observe that, similar to simple carboxylic acids, around 20% of the -COOH groups adopt an anti-conformation. However, when N-acetylproline is dissolved in a weakly hydrogen-bond accepting solvent (acetonitrile), we observe the formation of a strong intramolecular hydrogen bond between the carboxyl group in the anti-conformation and the amide group, which stabilizes the anti-conformer, increasing its relative abundance to ~60%.

Peptide Side-COOH Groups Have Two Distinct Conformations under Biorelevant Conditions

The carboxyl (COOH) side chain groups of amino acids, such as aspartic acid, play an important role in biochemical processes, including enzymatic proton transport. In many theoretical studies, it was found that the (bio)chemical reactivity of the carboxyl group strongly depends on the conformation of this group. Interestingly, up to now there has been no experimental investigation of the geometry and the stability of different COOH conformers under biorelevant conditions. Here, we investigate the conformational isomerism of the side chain COOH group of N-acetyl aspartic acid amide using polarization-resolved two-dimensional infrared spectroscopy. We find that the carboxyl group shows two distinct near-planar conformers (syn and anti) when dissolved in water at room temperature. Both conformers are significantly populated in aqueous solution (75 ± 10% and 25 ± 10% for syn and anti, respectively). Molecular dynamics simulations show that the anti conformer interacts more strongly with water molecules than the syn conformer, explaining why this conformer is significantly present in aqueous solution.

Optical Resolution of Dimethyl α-Hydroxy-Arylmethylphosphonates via Diastereomer Complex Formation Using Calcium Hydrogen O,O′-Dibenzoyl-(2R,3R)-Tartrate; X-Ray Analysis of the Complexes and Products

Two dimethyl α-hydroxy-arylmethylphosphonates (aryl = Ph and 2-MeOPh) were subjected to optical resolution via diastereomer complex formation applying the acidic calcium salt of O,O′-dibenzoyl-(2R,3R)-tartaric acid as the resolving agent. The dominating diastereomer complexes, whose structure was determined by single crystal X-ray measurements, were obtained in 96% and 68% diastereomer excess values, respectively. After decomposing the diastereomer formations by extraction, and after recrystallizations, the major enantiomer (S and R, respectively) of the α-hydroxyphosphonates were prepared in enantiomeric excess values of 96% and 68%, respectively. The stereostructure of the two α-hydroxy-arylmethylphosphonates was again established by X-ray measurements. Detailed study on the X-ray data allowed valuable conclusions on the nature of the coordination in the complexes (intermolecular interactions), and on the H-bonding.

Molecular imaging of extracellular matrix proteins with targeted probes using magnetic resonance imaging

The extracellular matrix (ECM) consists of proteins and carbohydrates that supports different biological structures and processes such as tissue development, elasticity, and preservation of organ structure. Diseases involving inflammation, fibrosis, tumor invasion, and injury are all attributed to the transition of the ECM from homeostasis to remodeling, which can significantly change the biochemical and biomechanical features of ECM components. While contrast agents have played an indispensable role in facilitating clinical diagnosis of diseases using magnetic resonance imaging (MRI), there is a strong need to develop novel biomarker-targeted imaging probes for in vivo visualization of biological processes and pathological alterations at a cellular and molecular level, for both early diagnosis and monitoring drug treatment. Herein, we will first review the pathological accumulation and characterization of ECM proteins recognized as important molecular features of diseases. Developments in MRI probes targeting ECM proteins such as collagen, fibronectin, and elastin via conjugation of existing contrast agents to targeting moieties and their applications to various diseases, are also reviewed. We have also reviewed our progress in the development of collagen-targeted protein MRI contrast agent with significant improvement in relaxivity and metal binding specificity, and their applications in early detection of fibrosis and metastatic cancer. This article is categorized under: Diagnostic Tools > in vivo Nanodiagnostics and Imaging Biology-Inspired Nanomaterials > Peptide-Based Structures Biology-Inspired Nanomaterials > Protein and Virus-Based Structures.

The Structural Details of Aspirin Molecules and Crystals

We revisit, in the key of structural chemistry, one of the most known and important drugs: the aspirin. Although apparently simple, the factors determining the molecular structure and supramolecular association in crystals are not trivial. We addressed the problem from experimental and theoretical sides, considering issues from X-ray measurements and results of first-principle reconstruction of molecule and lattices by ab initio calculations. Some puzzling problems can give headaches to specialists and intrigue the general public. Thus, the reported polymorphism of aspirin is disputed, a so-called form II being alleged as a result of misinterpretation. At the same time, were presented evidences that the structure of common form I can be disrupted by domains where the regular packing is changed to the pattern of form II. The problems appear even at the level of independent molecule: the most stable conformation computed by various techniques of electronic structure differs from those encountered in crystals. Because the energy difference between the related conformational isomers (computed as most stable vs. the experimental structure) is small, about 1 kcal/mol, comprised in the error bars of used methods, the unresting question is whether the modelling is imprecise, or the supramolecular factors are mutating the conformational preferences. By a detective following of the issue, the intermolecular effects were made responsible for the conformation of the molecule in crystal. The presented problems were gathered from literature results, debates, glued with modelling and analysis redone by ourselves, in order to secure the unitary view of the considered prototypic topic.

Crystal structures and Hirshfeld surface analyses of a des-A-B-aromatic steroidal compound, and two of its derivatives, having a trans-2,3,4,5-tetrahydro-3a-methyl-7-methoxybenz[e]indane skeleton – structural comparisons with reported tetrahydrobenz[e]indene derivatives

The crystal structures and Hirshfeld surface analyses of the des-A-B-aromatic steroid derivative, (3a,9b)-1,2,3a,4,5,9b-hexahydro-7-methoxy-3a-methyl-3H-benz[e]-inden-3-one (or 5-methoxy-des-A-estra-5,7,9-triene-17-one) 1, its acetohydrazide derivative, 2, and its hydrazone derivative, 3, are reported. All three compounds crystallize in chiral space groups: compounds 1 and 2 in the orthorhombic space group P212121 each with one molecule in the asymmetric unit, and compound 3 in the monoclinic space group P21 with two similar but independent molecules, Mol A and Mol B, in the asymmetric unit. Both the five-membered and six-membered non-aromatic rings in all three compounds have envelope or near envelope shapes. In compounds 2 and 3 the N=N units have (E)-arrangements. The intermolecular interactions in crystals of compound 1 are C–H · · · O hydrogen bonds and C–H · · · π interactions, in compound 2 N–H · · · O and C–H · · · O hydrogen bonds and C–H · · · π interactions are present, while in compound 3 there are just C–H · · · π interactions. An important substructure in 1 is a sheet of molecules, composed of R 6 6 ( 44 ) ${\rm{R}}_6^6(44)$ rings, formed from C–H · · · O(methoxy) and C–H · · · O(carbonyl) hydrogen bonds, the molecules of which form columns linked via the B and D rings, i.e. in a head-to-tail fashion. Compound 2 is an acylhydrazonyl compound, in which the two independent molecules are linked into asymmetric dimers via strong classical N–H · · · O hydrogen bonds, with the formation of R 2 2 ( 8 ) ${\rm{R}}_2^2(8)$ rings. In both 1 and 2, further intermolecular interactions result in 3-dimensional structures, while compound 3 has a 1-dimensional structure arising from C–H · · · O interactions generating spiral chains. The results have been compared with existing data.

N-Tosyl-L-proline benzene hemisolvate: a rare example of a hydrogen-bonded carboxylic acid dimer with symmetrically disordered H atoms

The carboxylic acid group is an example of a functional group which possess a good hydrogen-bond donor (-OH) and acceptor (C=O). For this reason, carboxylic acids have a tendency to self-assembly by the formation of hydrogen bonds between the donor and acceptor sites. We present here the crystal structure of N-tosyl-L-proline (TPOH) benzene hemisolvate {systematic name: (2S)-1-[(4-methylbenzene)sulfonyl]pyrrolidine-2-carboxylic acid benzene hemisolvate}, C₁₂H₁₅NO₄S·0.5C₆H₆, (I), in which a cyclic R₂²(8) hydrogen-bonded carboxylic acid dimer with a strong O-(1/2H)...(1/2H)-O hydrogen bond is observed. The compound was characterized by single-crystal X-ray diffraction and NMR spectroscopy, and crystallizes in the space group I2 with half a benzene molecule and one TPOH molecule in the asymmetric unit. The H atom of the carboxyl OH group is disordered over a twofold axis. An analysis of the intermolecular interactions using the noncovalent interaction (NCI) index showed that the TPOH molecules form dimers due to the strong O-(1/2H)...(1/2H)-O hydrogen bond, while the packing of the benzene solvent molecules is governed by weak dispersive interactions. A search of the Cambridge Structural Database revealed that the disordered dimeric motif observed in (I) was found previously only in six crystal structures.

A Million Crystal Structures: The Whole Is Greater than the Sum of Its Parts

The founding in 1965 of what is now called the Cambridge Structural Database (CSD) has reaped dividends in numerous and diverse areas of chemical research. Each of the million or so crystal structures in the database was solved for its own particular reason, but collected together, the structures can be reused to address a multitude of new problems. In this Review, which is focused mainly on the last 10 years, we chronicle the contribution of the CSD to research into molecular geometries, molecular interactions, and molecular assemblies and demonstrate its value in the design of biologically active molecules and the solid forms in which they are delivered. Its potential in other commercially relevant areas is described, including gas storage and delivery, thin films, and (opto)electronics. The CSD also aids the solution of new crystal structures. Because no scientific instrument is without shortcomings, the limitations of CSD research are assessed. We emphasize the importance of maintaining database quality: notwithstanding the arrival of big data and machine learning, it remains perilous to ignore the principle of garbage in, garbage out. Finally, we explain why the CSD must evolve with the world around it to ensure it remains fit for purpose in the years ahead.

Assessing the Conformational Equilibrium of Carboxylic Acid via Quantum Mechanical and Molecular Dynamics Studies on Acetic Acid

Accurate hydrogen placement in molecular modeling is crucial for studying the interactions and dynamics of biomolecular systems. The carboxyl functional group is a prototypical example of a functional group that requires protonation during structure preparation. To our knowledge, when in their neutral form, carboxylic acids are typically protonated in the syn conformation by default in classical molecular modeling packages, with no consideration of alternative conformations, though we are not aware of any careful examination of this topic. Here, we investigate the general belief that carboxylic acids should always be protonated in the syn conformation. We calculate and compare the relative energetic stabilities of syn and anti acetic acid using ab initio quantum mechanical calculations and atomistic molecular dynamics simulations. We focus on the carboxyl torsional potential and configurations of microhydrated acetic acid from molecular dynamics simulations, probing the effects of solvent, force field (GAFF vs GAFF2), and partial charge assignment of acetic acid. We show that while the syn conformation is the preferred state, the anti state may in some cases also be present under normal NPT conditions in solution.

Geometric H/D isotope effect in a series of organic salts involving short O–H⋯O hydrogen bonds between carboxyl and carboxylate groups

Noticeable elongations of donor–acceptor distances upon deuteration are confirmed in short O–H⋯O hydrogen bonds between carboxyl and carboxylate groups.

Combining two distinctive intermolecular forces in designing ternary co-crystals and molecular salts of 1,3,5-trinitrobenzene, 9-anthracenecarboxylic acid and ten substituted pyridines

Coloured three component complexes are made using both charge transfer and hydrogen bonding intermolecular interactions.

Crystal structures and Hirshfeld surface analyses of seven 7-aryl-4,7-dioxoheptanoic acids: differing carboxylic acid interactions leading to dimers, chains and three-dimensional arrays

Crystal structures and Hirshfeld surface analysis are reported of seven aryl-CO–CH2CH2COCH2CH2CO2H derivatives, namely aryl=4-ClC6H4, 1: 2-HOC6H4, 2: (2,4-(MeO)2C6H3, 3: 3,5-Me2-4-MeOC6H2, 4: 4-MeC6H4, 5: C6H5, 6: 2,4-(HO)2C6H3, 7. There are significant differences in their molecular conformations and their crystal packing. Within the group of compounds, three different types of carboxylic acid intermolecular interactions are exhibited, all involving O–H···O hydrogen bonds. These three types are (i) symmetric R2 2(8) dimers formed from pairs of O–H···O hydrogen bonds in compounds 1–5, (ii) infinite 1D homo-assemblies of carboxylic groups (homo-AA,A catemers), and (iii), a 3-D array, in which there are no direct carboxylic acid–carboxylic acid interactions, generated from O–H···O interactions of each carboxylic acid group with the hydroxyl and carbonyl groups of other molecules in 7. Each of the carboxylic acid groups in the catemer exhibit anti arrangements with all the carboxylic acid oxygen atoms lying in a plane. Disorder is exhibited in the carboxylic acid groups in 2 and 6. With the variety of oxygen substituents present in 1–7, a large number of O–H···O and C–H···O hydrogen bonds are exhibited, resulting in all cases in three dimension assemblies. In 1–5, interlayer contacts between the carboxylic acid R2 2(8) dimers in rows, with differing sets of weaker C–H···O and/or C–H···π interactions, result in the formation of two-molecular wide columns and/or infinite sheets. While column and sheet sub structures can also be designated in compound 6, on linking the carboxylic acid groups with other substituents via C–H···O, C–H···π and C=O···π interactions, these differ from those in 1–5 due to the different arrangements of the CO2H groups.

Geometric isotope effect of deuteration in a hydrogen-bonded host-guest crystal

Deuteration of a hydrogen bond by replacing protium (H) with deuterium (D) can cause geometric changes in the hydrogen bond, known as the geometric H/D isotope effect (GIE). Understanding the GIEs on global structures and bulk properties is of great importance to study structure–property relationships of hydrogen-bonded systems. Here, we report a hydrogen-bonded host–guest crystal, imidazolium hydrogen terephthalate, that exemplifies striking GIEs on its hydrogen bonds, phases, and bulk dielectric transition property. Upon deuteration, the donor–acceptor distance in the O–H···O hydrogen bonds in the host structure is found to increase, which results in a change in the global hydrogen-bonded supramolecular structure and the emergence of a new phase (i.e., isotopic polymorphism). Consequently, the dynamics of the confined guest, which depend on the internal pressure exerted by the host framework, are substantially altered, showing a downward shift of the dielectric switching temperature.

Deuterating a hydrogen bond can change the bond’s geometry, a phenomenon known as the geometric isotope effect (GIE). Here, the authors find that a hydrogen-bonded host–guest crystal, imidazolium hydrogen terephthalate, exhibits significant GIE on its hydrogen bonds, changing its crystal phases and bulk dielectric properties.

Impact of chirality on peculiar ibuprofen molecular dynamics: hydrogen bonding organization and syn vs. anti carboxylic group conformations

Impact of chirality (R and S enantiomers) on syn vs. anti carboxylic group conformations, hydrogen bond dimers and peculiar ibuprofen molecular dynamics.

Z-effect reversal in carboxylic acid associates

The conformational preferences of carboxylic acids (Z-effect) can be reversed by H-bonding to anions due to the supramolecular stereoelectronic effect.

Solvent and anion facilitated conformational changes in benzylamine substituted thiazolamine

Solvent and anion guided conformational adjustments in the syn–anti–syn form of N,N′-(1,4-phenylene-bis(methylene))-bis(5-methylthiazol-2-amine) and the utility of nitrate ions in stabilizing the anti–anti–anti form are established.