Crystal structures of amino acids: from bond lengths in glycine to metal complexes and high-pressure polymorphs

Amino Acid Polymerization on Silica Surfaces

The polymerization of unactivated amino acids (AAs) is an important topic because of its applications in various fields including industrial medicinal chemistry and prebiotic chemistry. Silica as a promoter for this reaction, is of great interest owing to its large abundance and low cost. The amide/peptide bond synthesis on silica has been largely demonstrated but suffers from a lack of knowledge regarding its reaction mechanism, the key parameters, and surface features that influence AA adsorption and reactivity, the selectivity of the reaction product, the role of water in the reaction, etc. The present review addresses these problems by summarizing experimental and modeling results from the literature and attempts to rationalize some apparent divergences in published results. After briefly presenting the main types of silica surface sites and other relevant macroscopic features, we discuss the different deposition procedures of AAs, whose importance is often neglected. We address the possible AA adsorption mechanisms including covalent grafting and H-bonding and show that they are highly dependent on silanol types and density. We then consider how the adsorption mechanisms determine the occurrence and outcome of AA condensation (formation of cyclic dimers or of long linear chains), and outline some recent results that suggest significant polymerization selectivity in systems containing several AAs, as well as the formation of specific elements of secondary structure in the growing polypeptide chains.

In situ Raman spectroscopy and synchrotron X-ray diffraction studies on maleic acid under high pressure conditions

Maleic acid was studied by Raman spectroscopy and powder synchrotron X-ray diffraction (XRD) under high pressure conditions by using a diamond anvil cell. The Raman spectroscopy measurements were performed from ambient pressure up to 9.2 GPa in the 100-3200 cm-1 spectral range. While the XRD measurements were performed up to 10.1 GPa. Here we present the pressure-dependence behavior from both the Raman modes and cell parameters. Maleic acid lattice parameters decrease anisotropically as a function of pressure and a reduction of 27% in the volume of the unit cell was observed. Modifications in the material's compressibility were observed at around 2 and 6 GPa.

Manipulating the Piezoelectric Response of Amino Acid-Based Assemblies by Supramolecular Engineering

Variation in the molecular architecture significantly affects the electronic and supramolecular structure of biomolecular assemblies, leading to dramatically altered piezoelectric response. However, relationship between molecular building block chemistry, crystal packing and quantitative electromechanical response is still not fully understood. Herein, we systematically explored the possibility to amplify the piezoelectricity of amino acid-based assemblies by supramolecular engineering. We show that a simple change of side-chain in acetylated amino acids leads to increased polarization of the supramolecular arrangements, resulting in significant enhancement of their piezoelectric response. Moreover, compared to most of the natural amino acid assemblies, chemical modification of acetylation increased the maximum piezoelectric tensors. The predicted maximal piezoelectric strain tensor and voltage constant of acetylated tryptophan (L-AcW) assemblies reach 47 pm V^-1 and 1719 mV m/N, respectively, comparable to commonly used inorganic materials such as bismuth triborate crystals. We further fabricated an L-AcW crystal-based piezoelectric power nanogenerator that produces a high and stable open-circuit voltage of over 1.4 V under mechanical pressure. For the first time, the illumination of a light-emitting diode (LED) is demonstrated by the power output of an amino acid-based piezoelectric nanogenerator. This work presents the supramolecular engineering toward the systematic modulation of piezoelectric response in amino acid-based assemblies, facilitating the development of high-performance functional biomaterials from simple, readily available, and easily tailored building blocks.

Homocysteine fibrillar assemblies display cross-talk with Alzheimer's disease β-amyloid polypeptide

High levels of homocysteine are reported as a risk factor for Alzheimer's disease (AD). Correspondingly, inborn hyperhomocysteinemia is associated with an increased predisposition to the development of dementia in later stages of life. Yet, the mechanistic link between homocysteine accumulation and the pathological neurodegenerative processes is still elusive. Furthermore, despite the clear association between protein aggregation and AD, attempts to develop therapy that specifically targets this process have not been successful. It is envisioned that the failure in the development of efficacious therapeutic intervention may lie in the metabolomic state of affected individuals. We recently demonstrated the ability of metabolites to self-assemble and cross-seed the aggregation of pathological proteins, suggesting a role for metabolite structures in the initiation of neurodegenerative diseases. Here, we provide a report of homocysteine crystal structure and self-assembly into amyloid-like toxic fibrils, their inhibition by polyphenols, and their ability to seed the aggregation of the AD-associated β-amyloid polypeptide. A yeast model of hyperhomocysteinemia indicates a toxic effect, correlated with increased intracellular amyloid staining that could be rescued by polyphenol treatment. Analysis of AD mouse model brain sections indicates the presence of homocysteine assemblies and the interplay between β-amyloid and homocysteine. This work implies a molecular basis for the association between homocysteine accumulation and AD pathology, potentially leading to a paradigm shift in the understanding of AD initial pathological processes.

Amino acid hydrogen oxalate quasiracemates – hydrocarbon side chains

Amino acid hydrogen oxalate quasiracemates form robust crystal structure motifs that are assessed for conformational similarity and degree of inversion symmetry.

Amino acid hydrogen oxalate quasiracemates – sulfur containing side chains

A new family of quasiracemic materials constructed from sulfur-containing amino acid hydrogen oxalates form supramolecular assemblies that divert significantly from near centrosymmetric alignment.

A Proline-Based Tectons and Supramolecular Synthons for Drug Design 2.0: A Case Study of ACEI

Proline is a unique, endogenous amino acid, prevalent in proteins and essential for living organisms. It is appreciated as a tecton for the rational design of new bio-active substances. Herein, we present a short overview of the subject. We analyzed 2366 proline-derived structures deposited in the Cambridge Structure Database, with emphasis on the angiotensin-converting enzyme inhibitors. The latter are the first-line antihypertensive and cardiological drugs. Their side effects prompt a search for improved pharmaceuticals. Characterization of tectons (molecular building blocks) and the resulting supramolecular synthons (patterns of intermolecular interactions) involving proline derivatives, as presented in this study, may be useful for in silico molecular docking and macromolecular modeling studies. The DFT, Hirshfeld surface and energy framework methods gave considerable insight into the nature of close inter-contacts and supramolecular topology. Substituents of proline entity are important for the formation and cooperation of synthons. Tectonic subunits contain proline moieties characterized by diverse ionization states: -N and -COOH(-COO-), -N+ and -COOH(-COO-), -NH and -COOH(-COO-), -NH+ and -COOH(-COO-), and -NH2+ and -COOH(-COO-). Furthermore, pharmacological profiles of ACE inhibitors and their impurities were determined via an in silico approach. The above data were used to develop comprehensive classification, which may be useful in further drug design studies.

Effect of Chirality on the Compression of 2-(2-Oxo-1-pyrrolidinyl)butyramide: A Tale of Two Crystals

Understanding polymorphism in chiral systems for drug manufacturing is essential to avoid undesired therapeutic effects. Generally, polymorphism is studied through changes in temperature and solution concentration. A less common approach is the application of pressure. The goal of this work is to investigate the effect of pressure on levetiracetam (pure enantiomer) and etiracetam (racemic compound). Anisotropic compressions of levetiracetam and etiracetam are observed to 5.26 and 6.29 GPa, respectively. The most compressible direction for both was identified to be perpendicular to the layers of the structure. Raman spectroscopy and an analysis of intermolecular interactions suggest subtle phase transitions in levetiracetam (∼2 GPa) and etiracetam (∼1.5 GPa). The stability of etiracetam increases with respect to levetiracetam on compression; hence, the chiral resolution of this system is unfavorable using pressure. This work contributes to the ongoing efforts in understanding the stability of chiral systems.

Phenylalanine dimer assembly structure as the basic building block of an amyloid like photoluminescent nanofibril network

A phenylalanine dimer assembly (Phe-DA) is reported as a basic constituent of a light emitting β-amyloid type nanofibril network. The size and composition of the Phe-DA structure were characterized using various theoretical and experimental techniques. Further, the mechanism involved in the phenylalanine self-assembly process from Phe-DA to the nanofibril network was studied using optical spectroscopy and small angle X-ray scattering (SAXS). The discovery of Phe-DA and its unique optical properties may pave the way for design and development of novel theranostics against metabolite based pathalogical disorders. Further, the role of the Phe-DA structure as the elementary unit in the formation of a long range assembly structure may provide vital understanding for the development of functional materials using simple organic molecules.

A Short Review of Current Computational Concepts for High-Pressure Phase Transition Studies in Molecular Crystals

High-pressure chemistry of organic compounds is a hot topic of modern chemistry. In this work, basic computational concepts for high-pressure phase transition studies in molecular crystals are described, showing their advantages and disadvantages. The interconnection of experimental and computational methods is highlighted, showing the importance of energy calculations in this field. Based on our deep understanding of methods’ limitations, we suggested the most convenient scheme for the computational study of high-pressure crystal structure changes. Finally, challenges and possible ways for progress in high-pressure phase transitions research of organic compounds are briefly discussed.

Heteromolecular compounds in binary systems of amino acids with opposite and same chiralities

Equimolar and non-equimolar heterocompounds of amino acids are examined with a common approach considering their molecular dimers, side chain structures and conformations.

The Effect of Pressure on Halogen Bonding in 4-Iodobenzonitrile

The crystal structure of 4-iodobenzonitrile, which is monoclinic (space group I2/a) under ambient conditions, contains chains of molecules linked through C≡N···I halogen-bonds. The chains interact through CH···I, CH···N and π-stacking contacts. The crystal structure remains in the same phase up to 5.0 GPa, the b axis compressing by 3.3%, and the a and c axes by 12.3 and 10.9 %. Since the chains are exactly aligned with the crystallographic b axis these data characterise the compressibility of the I···N interaction relative to the inter-chain interactions, and indicate that the halogen bond is the most robust intermolecular interaction in the structure, shortening from 3.168(4) at ambient pressure to 2.840(1) Å at 5.0 GPa. The π∙∙∙π contacts are most sensitive to pressure, and in one case the perpendicular stacking distance shortens from 3.6420(8) to 3.139(4) Å. Packing energy calculations (PIXEL) indicate that the π∙∙∙π interactions have been distorted into a destabilising region of their potentials at 5.0 GPa. The structure undergoes a transition to a triclinic ( P 1 ¯ ) phase at 5.5 GPa. Over the course of the transition, the initially colourless and transparent crystal darkens on account of formation of microscopic cracks. The resistance drops by 10% and the optical transmittance drops by almost two orders of magnitude. The I···N bond increases in length to 2.928(10) Å and become less linear [<C-I∙∙∙N = 166.2(5)°]; the energy stabilises by 2.5 kJ mol^-1 and the mixed C-I/I..N stretching frequency observed by Raman spectroscopy increases from 249 to 252 cm^-1. The driving force of the transition is shown to be relief of strain built-up in the π∙∙∙π interactions rather than minimisation of the molar volume. The triclinic phase persists up to 8.1 GPa.

A large anisotropic plasticity of L-leucinium hydrogen maleate preserved at cryogenic temperatures

L-Leucinium hydrogen maleate crystals are very plastic at ambient conditions. Here it is shown that this plasticity is preserved at least down to 77 K. The structural changes in the temperature range 293-100 K were followed in order to rationalize the large anisotropic plasticity in this compound. To the best of our knowledge, this is the first reported example of an organic compound remaining so plastic at cryogenic conditions.

Effect of pressure on slit channels in guanine sodium salt hydrate: a link to nucleobase intermolecular interactions

The crystal structure of a hydrate of the sodium salt of guanine (2Na⁺·C₅H₃N₅O²⁻·7H₂O) was studied at high pressure by single-crystal X-ray diffraction and Raman spectroscopy.

Structural investigation and compression of a co-crystal of indomethacin and saccharin

Indomethacin : saccharin cocrystal has been studied under high pressure conditions and the amide interactions compared with previous high pressure studies.

High-pressure polymorphism in l-threonine between ambient pressure and 22 GPa

The amino acid l-threonine undergoes three phase transitions between ambient pressure and 22.3 GPa which modify both hydrogen bonding and the molecular conformation.

Organization of Amino Acids into Layered Supramolecular Secondary Structures

The unique physiochemical properties and multiscale organization of layered materials draw the attention of researchers across a wide range of scientific disciplines. Layered structures are commonly found in diverse biological systems where they fulfill various functions. A prominent example of layered biological materials is the organization of proteins and polypeptides into the archetypal aggregated amyloidal structures. While the organization of proteins into amyloid structures was initially associated with various degenerative disorders, it was later revealed that proteins not related to any disease could also form identical layered assemblies. Thus, it appears that the ability of peptides and proteins to produce amyloid-like aggregates represents a generic property of polyamides to assemble into higher order fibrillar structures. In the aggregated state, the peptide backbone forms β-sheet structures which are further organized into layered arrangements. We have recently extended the identified amyloidogenic building blocks to include not only peptides or proteins, but also single amino acids and other metabolites. High resolution spectroscopy and crystallography analyses confirm the clear potential of amino acids and other metabolites to form layered amyloid-like aggregates showing biophysical and biochemical properties similar to protein amyloids. Therefore, the generic propensity of peptides and proteins backbones to assemble into layered organizations may emanate from their basic building block, the amino acid. In this Account, we aim to introduce the concept of supramolecular β-sheet organization of single amino acids and to present an analysis of their layered-structure organization based on single crystal structures. We demonstrate that, despite the different side-chains that considerably vary in their chemical properties, all coded amino acids display a layer-like assembly stabilized by α-amine to α-carboxyl H-bonds, resembling supramolecular β-sheet structures, while the side-chains determine the higher order organization of the layers. Our work presents the first analysis of the β-sheet propensity of single amino acids in their unbound form, indicating an evolutionary predisposition. We classify the amino acids β-sheet propensity on the basis of the interlayer separation distance in the crystal packing, which correlates well with previously reported classifications based on various criteria, such as hydrophobicity, steric bulkiness, and folding. In addition, we demonstrate that the relative direction of α-amine to α-carboxyl H-bonding pattern provides critical insights regarding the stabilization of parallel versus antiparallel β-sheet structures by the various amino acids. Taken together, our analysis of amino acid crystals provides substantial information regarding protein folding and dynamics and could serve as basic rules set for the design of potential building blocks for molecular self-assembly to produce functional materials of tunable properties, an important objective of bottom-up nanotechnology.

Redetermination of the solvent-free crystal structure of l-proline

The title compound, (S)-pyrrolidine-2-carb-oxy-lic acid (C5H9NO2), commonly known as l-proline, crystallized without the inclusion of any solvent or water mol-ecules through the slow diffusion of diethyl ether into a saturated solution of l-proline in ethanol. l-Proline crystallized in its zwitterionic form and the mol-ecules are linked via N-H⋯O hydrogen bonds, resulting in a two-dimensional network. In comparison to the only other publication of a single-crystal structure of l-proline without inclusions [Kayushina & Vainshtein (1965 ▸). Kristallografiya, 10, 833-844], the R1 value is significantly improved (0.039 versus 0.169) and thus, our data provides higher precision structural information.

Behavior of intermolecular interactions in α-glycine under high pressure

Pressure-response on the crystal structure of deuterated α-glycine was investigated at room temperature, using powder and single-crystal X-ray diffraction, and powder neutron diffraction measurements under high pressure. No phase change was observed up to 8.7 GPa, although anisotropy of the lattice compressibility was found. No significant changes in the compressibility and the intramolecular distance between non-deuterated α-glycine and deuterated α-glycine were observed. Neutron diffraction measurements indicated the distance of the intermolecular D⋯O bond along with the c-axis increased with compression up to 6.4 GPa. The distance of another D⋯O bond along with the a-axis decreased with increasing pressure and became the shortest intermolecular hydrogen bond above 3 GPa. In contrast, the lengths of the bifurcated N-D⋯O and C-D⋯O hydrogen bonds, which are formed between the layers of the α-glycine molecules along the b-axis, decreased significantly with increasing pressure. The decrease of the intermolecular distances resulted in the largest compressibility of the b-axis, compared to the other two axes. The Hirshfeld analysis suggested that the reduction of the void region size, rather than shrinkage of the strong N-D⋯O hydrogen bonds, occurred with compression.

Magnetically textured powders—an alternative to single-crystal and powder X-ray diffraction methods

Structure determination of materials in their crystalline phase aids in the understanding and design of their functions.

Reactions of Antitumor Active Dirhodium(II) Tetraacetate Rh2(CH3COO)4 with Cysteine and Its Derivatives

We have combined results from several spectroscopic techniques to investigate the aerobic reactions of Rh2(AcO)4 (AcO- = CH3COO-) with l-cysteine (H2Cys) and its derivatives d-penicillamine (3,3'-dimethylcysteine, H2Pen), with steric hindrance at the thiol group, and N-acetyl-l-cysteine (H2NAC), with its amino group blocked. Previous investigations have shown that antitumor active dirhodium(II) carboxylates may irreversibly inhibit enzymes containing a thiol group at or near their active sites. Also, cysteine, the only thiol-containing proteinogenic amino acid, interacts in vivo with this class of antitumor compounds, but structural information on the products of such reactions is lacking. In the present study, the reactions of Rh2(AcO)4 and H2L were carried out in aqueous solutions at the pH of mixing (acidic) and at physiological pH, using the different mole ratios 1:2, 1:4, and 1:6, which resulted in the same products in increasing yields. Electrospray ionization mass spectrometry (ESI-MS) indicates formation of dimeric [RhIII 2Pen4]2- or oligomeric {RhIII 2L4} n (L = Cys, NAC) complexes with bridging thiolate groups. Analyses of Rh K edge extended X-ray absorption fine structure (EXAFS) data reveal 3-4 Rh-S and 2-3 Rh-(N/O) bonds around six-coordinated Rh(III) ions at mean distances of 2.33 ± 0.02 and 2.09 ± 0.02 Å, respectively. In the N-acetyl-l-cysteine compound, the RhIII···RhIII distance 3.10 ± 0.02 Å obtained from the EXAFS spectrum supports trithiolate bridges between the Rh(III) ions, as was also found when using glutathione as ligand. In the cysteine and penicillamine complexes, double thiolate bridges join the Rh(III) ions, with the nonbridging Cys2- and Pen2- ligands in tridentate chelating (S,N,O) mode, which is consistent with the ΔδC = 7.3-8.4 ppm shift of the COO- signal in their carbon-13 cross polarization magic angle spinning (CPMAS) NMR spectra. For the penicillamine complex, the 2475.6 eV peak in its S K edge X-ray absorption near edge structure (XANES) spectrum shows partial oxidation, probably caused by peroxide generated from reduction of dissolved O2, of thiolato to sulfenato (S=O) groups, which were also identified by ESI-MS for all three {RhIII 2L4} n compounds.

Accurate Bond Lengths to Hydrogen Atoms from Single-Crystal X-ray Diffraction by Including Estimated Hydrogen ADPs and Comparison to Neutron and QM/MM Benchmarks

Amino acid structures are an ideal test set for method-development studies in crystallography. High-resolution X-ray diffraction data for eight previously studied genetically encoding amino acids are provided, complemented by a non-standard amino acid. Structures were re-investigated to study a widely applicable treatment that permits accurate X-H bond lengths to hydrogen atoms to be obtained: this treatment combines refinement of positional hydrogen-atom parameters with aspherical scattering factors with constrained "TLS+INV" estimated hydrogen anisotropic displacement parameters (H-ADPs). Tabulated invariom scattering factors allow rapid modeling without further computations, and unconstrained Hirshfeld atom refinement provides a computationally demanding alternative when database entries are missing. Both should incorporate estimated H-ADPs, as free refinement frequently leads to over-parameterization and non-positive definite H-ADPs irrespective of the aspherical scattering model used. Using estimated H-ADPs, both methods yield accurate and precise X-H distances in best quantitative agreement with neutron diffraction data (available for five of the test-set molecules). This work thus solves the last remaining problem to obtain such results more frequently. Density functional theoretical QM/MM computations are able to play the role of an alternative benchmark to neutron diffraction.

Accurate hydrogen parameters for the amino acid L-leucine

The structure of the primary amino acid L-leucine has been determined for the first time by neutron diffraction. This was made possible by the use of modern neutron Laue diffraction to overcome the previously prohibitive effects of crystal size and quality. The packing of the structure into hydrophobic and hydrophilic layers is explained by the intermolecular interaction energies calculated using the PIXEL method. Variable-temperature data collections confirmed the absence of phase transitions between 120 and 300 K in the single-crystal form.

Charge-regulation phase transition on surface lattices of titratable sites adjacent to electrolyte solutions: An analog of the Ising antiferromagnet in a magnetic field

We report a charge-patterning phase transition on two-dimensional square lattices of titratable sites, here regarded as protonation sites, placed in a low-dielectric medium just below the planar interface between this medium and a salt solution. We calculate the work-of-charging matrix of the lattice with use of a linear Debye-Hückel model, as input to a grand-canonical partition function for the distribution of occupancy patterns. For a large range of parameter values, this model exhibits an approximate inverse cubic power-law decrease of the voltage produced by an individual charge, as a function of its in-lattice separation from neighboring titratable sites. Thus, the charge coupling voltage biases the local probabilities of proton binding as a function of the occupancy of sites for many neighbors beyond the nearest ones. We find that even in the presence of these longer-range interactions, the site couplings give rise to a phase transition in which the site occupancies exhibit an alternating, checkerboard pattern that is an analog of antiferromagnetic ordering. The overall strength W of this canonical charge coupling voltage, per unit charge, is a function of the Debye length, the charge depth, the Bjerrum length, and the dielectric coefficients of the medium and the solvent. The alternating occupancy transition occurs above a curve of thermodynamic critical points in the (pH-pK,W) plane, the curve representing a charge-regulation analog of variation of the Néel temperature of an Ising antiferromagnet as a function of an applied, uniform magnetic field. The analog of a uniform magnetic field in the antiferromagnet problem is a combination of pH-pK and W, and 1/W is the analog of the temperature in the antiferromagnet problem. We use Monte Carlo simulations to study the occupancy patterns of the titratable sites, including interactions out to the 37th nearest-neighbor category (a distance of √74 lattice constants), first validating simulations through comparison with exact and approximate results for the nearest-neighbor case. We then use the simulations to map the charge-patterning phase boundary in the (pH-pK,W) plane. The physical parameters that determine W provide a framework for identifying and designing real surfaces that could exhibit charge-patterning phase transitions.

Twin displacive phase transitions in amino acid quasiracemates

Three quasiracemates, L-norleucine:D-methionine, L-norvaline:D-norleucine, and L-norvaline:D-methionine, were crystallized to see how they differ from regular racemates in terms of crystal structure (studied by single-crystal X-ray diffraction) and of thermally induced phase transitions (studied by differential scanning calorimetry). Two types of transitions are detected between 100 and 450 K and structurally characterized: (1) displacive transitions of the molecular bilayers that form the crystal and (2) continuous or discontinuous disordering transitions in the amino acid side chains. Uniquely for the quasiracemates, the displacive transition proceeds in two close steps as only one surface of each molecular bilayer slides at first, upon forming an intermediate phase, while the other surface follows at a slightly higher temperature. Altogether, 18 new single-crystal structure-refinement data sets are reported for these three quasiracemates.

Are gamma amino acids promising tools of crystal engineering? – Multicomponent crystals of baclofen

The crystal structure, thermal analysis and powder X-ray analysis of the multicomponent crystals formed between baclofen and selected monocarboxylic acids, dicarboxylic acids and p-toluene sulfonic acid are presented.