An exceptional series of phase transitions in hydrophobic amino acids with linear side chains

NMR crystallography of amino acids

The development of NMR crystallography methods requires a reliable database of chemical shifts measured for systems with known crystal structure. We measured and assigned carbon and hydrogen chemical shifts of twenty solid natural amino acids of known polymorphic structure, meticulously determined using powder X-ray diffraction. We then correlated the experimental data with DFT-calculated isotropic shieldings. The small size of the unit cell of most amino acids allowed for advanced computations using various families of DFT functionals, including generalized gradient approximation (GGA), meta-GGA and hybrid DFT functionals. We tested several combinations of functionals for geometry optimizations and NMR calculations. For carbon shieldings, the widely used GGA functional PBE performed very well, although an improvement could be achieved by adding shielding corrections calculated for isolated molecules using a hybrid functional. For hydrogen nuclei, we observed the best performance for NMR calculations carried out with structures optimized at the hybrid DFT level. The high fidelity of the calculations made it possible to assign additional signals that could not be assigned based on experiments alone, for example signals of two non-equivalent molecules in the unit cell of some of the amino acids.

Mechanism for Stabilizing an Amorphous Drug Using Amino Acids within Co-Amorphous Blends

Designing co-amorphous formulations is now recognized as a relevant strategy for improving the bioavailability of low-molecular-weight drugs. In order to determine the most suitable low-molecular-weight excipients for stabilizing the drug in the amorphous state, screening methods were developed mostly using amino acids as co-formers. The present study focused on the analysis of the thermal stability of co-amorphous blends prepared by cryo-milling indomethacin with several amino acids in order to understand the stabilization mechanism of the drug in the amorphous state. Combining low- and mid-frequency Raman investigations has provided information on the relation between the physical properties of the blends and those of the H-bond network of the amorphous drug. This study revealed the surprising capabilities of L-arginine to stiffen the H-bond network in amorphous indomethacin and to drastically improve the stability of its amorphous state. As a consequence, this study suggests that amino acids can be considered as stiffeners of the H-bond network of indomethacin, thereby improving the stability of the amorphous state.

Heat Capacities of L-Cysteine, L-Serine, L-Threonine, L-Lysine, and L-Methionine

In an effort to establish reliable thermodynamic data for amino acids, heat capacity and phase behavior are reported for L-cysteine (CAS RN: 52-90-4), L-serine (CAS RN: 56-45-1), L-threonine (CAS RN: 72-19-5), L-lysine (CAS RN: 56-87-1), and L-methionine (CAS RN: 63-68-3). Prior to heat capacity measurements, initial crystal structures were identified by X-ray powder diffraction, followed by a thorough investigation of the polymorphic behavior using differential scanning calorimetry in the temperature range from 183 K to the decomposition temperature determined by thermogravimetric analysis. Crystal heat capacities of all five amino acids were measured by Tian-Calvet calorimetry in the temperature interval (262-358) K and by power compensation DSC in the temperature interval from 215 K to over 420 K. Experimental values of this work were compared and combined with the literature data obtained with adiabatic calorimetry. Low-temperature heat capacities of L-threonine and L-lysine, for which no or limited literature data was available, were measured using the relaxation (heat pulse) calorimetry. As a result, reference heat capacities and thermodynamic functions for the crystalline phase from near 0 K to over 420 K were developed.

Identification of incommensurability in L-Leucine ; are lattice instabilities can be considered as general phenomena in hydrophobic amino acids?

L-Leucine is an essential amino acid which focuses lot of investigations on its phase transition sequence for more than fifty years. Combining Raman spectroscopy and X-ray diffraction experiments provides a...

Thermal neutron cross sections of amino acids from average contributions of functional groups

The experimental thermal neutron cross sections of the 20 proteinogenic amino acids have been measured over the incident-neutron energy range spanning from 1 meV to 10 keV and data have been interpreted using the multi-phonon expansion based on first-principles calculations. The scattering cross section, dominated by the incoherent inelastic contribution from the hydrogen atoms, can be rationalised in terms of the average contributions of different functional groups, thus neglecting their correlation. These results can be used for modelling the total neutron cross sections of complex organic systems like proteins, muscles, or human tissues from a limited number of starting input functions. This simplification is of crucial importance for fine-tuning of transport simulations used in medical applications, including boron neutron capture therapy as well as secondary neutrons-emission induced during proton therapy. Moreover, the parametrized neutron cross sections allow a better treatment of neutron scattering experiments, providing detailed sample self-attenuation corrections for a variety of biological and soft-matter systems.

Structure and spectroscopy of methionyl-methionine for aquaculture

The amino acid L-methionine is an essential amino acid and is commonly used as a feed supplement in terrestrial animals. It is less suitable for marine organisms because it is readily excreted. It is also highly water soluble and this results in loss of the feed and eutrophication of the water. To address these problems, the dipeptide DL-methionyl-DL-methionine (trade name: AQUAVI Met-Met) has been developed as a dedicated methionine source for aquaculture. The commercial product is a mixture of a racemic crystal form of D-methionyl-D-methionine/L-methionyl-L-methionine and a racemic crystal form of D-methionyl-L-methionine/L-methionyl-D-methionine. In this work, we have computationally, structurally, spectroscopically and by electron microscopy characterised these materials. The microscopy and spectroscopy demonstrate that there is no interaction between the DD-LL and DL-LD racemates on any length scale from the macroscopic to the nanoscale.

One-carbon metabolism, folate, zinc and translation

The translation process, central to life, is tightly connected to the one-carbon (1-C) metabolism via a plethora of macromolecule modifications and specific effectors. Using manual genome annotations and putting together a variety of experimental studies, we explore here the possible reasons of this critical interaction, likely to have originated during the earliest steps of the birth of the first cells. Methionine, S-adenosylmethionine and tetrahydrofolate dominate this interaction. Yet, 1-C metabolism is unlikely to be a simple frozen accident of primaeval conditions. Reactive 1-C species (ROCS) are buffered by the translation machinery in a way tightly associated with the metabolism of iron-sulfur clusters, zinc and potassium availability, possibly coupling carbon metabolism to nitrogen metabolism. In this process, the highly modified position 34 of tRNA molecules plays a critical role. Overall, this metabolic integration may serve both as a protection against the deleterious formation of excess carbon under various growth transitions or environmental unbalanced conditions and as a regulator of zinc homeostasis, while regulating input of prosthetic groups into nascent proteins. This knowledge should be taken into account in metabolic engineering.

Volatility Study of Amino Acids by Knudsen Effusion with QCM Mass Loss Detection

This work presents a new Knudsen effusion apparatus employing continuous monitoring of sample deposition using a quartz-crystal microbalance sensor with internal calibration by gravimetric determination of the sample mass loss. The apparatus was tested with anthracene and 1,3,5-triphenylbenzene and subsequently used for the study of sublimation behavior of several proteinogenic amino acids. Their low volatility and thermal instability strongly limit possibilities of studying their sublimation behavior and available literature data. The results presented in this work are unique in their temperature range and low uncertainty required for benchmarking theoretical studies of sublimation behavior of molecular crystals. The possibility of dimerization in the gas phase that would invalidate the effusion experiments is addressed and disproved by theoretical calculations. The enthalpy of sublimation of each amino acid is analyzed based on the contributions in two hypothetical sublimation paths involving the proton transfer in the solid and in the gas phase.

On the mechanism of solid-state phase transitions in molecular crystals - the role of cooperative motion in (quasi)racemic linear amino acids

During single-crystal-to-single-crystal (SCSC) phase transitions, a polymorph of a compound can transform to a more stable form while remaining in the solid state. By understanding the mechanism of these transitions, strategies can be developed to control this phenomenon. This is particularly important in the pharmaceutical industry, but also relevant for other industries such as the food and agrochemical industries. Although extensive literature exists on SCSC phase transitions in inorganic crystals, it is unclear whether their classications and mechanisms translate to molecular crystals, with weaker interactions and more steric hindrance. A comparitive study of SCSC phase transitions in aliphatic linear-chain amino acid crystals, both racemates and quasi-racemates, is presented. A total of 34 transitions are considered and most are classified according to their structural change during the transition. Transitions without torsional changes show very different characteristics, such as transition temperature, enthalpy and free energy, compared with transitions that involve torsional changes. These differences can be rationalized using classical nucleation theory and in terms of a difference in mechanism; torsional changes occur in a molecule-by-molecule fashion, whereas transitions without torsional changes involve cooperative motion with multiple molecules at the same time.

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.

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.

The Rich Solid-State Phase Behavior of l-Phenylalanine: Disappearing Polymorphs and High Temperature Forms

After years of controversy over the solid state structure of the essential amino acid l-phenylalanine, four different polymorphic forms were published recently. The common form I has symmetry P21 with four molecules in the asymmetric unit (Z' = 4), similar to form III, but with a different arrangement of molecular bilayers. Form II, obtained from the hydrate at very low humidity, is unrelated to forms I and III, as is the high-density form IV. The present investigation demonstrates that this prototype aromatic amino acid has two additional high-temperature phases Ih and IIIh obtained from form I and form III above 458 and 440 K, respectively, when flipping between two alternative side-chain conformations becomes dynamic and causes pairs of molecules, initially crystallographically independent, to become equivalent above a sharp transition temperature. These abrupt and reversible phase changes occur with a reduction of Z' from 4 (low T) to 2 (high T) and modified crystal symmetry. We furthermore experienced an example of disappearing polymorph for form I which after growing form III in one of our laboratories could no longer be crystallized at room temperature. In contrast, form III crystals may be irreversibly converted to form I crystals as a result of sliding of molecular bilayers in the crystal at elevated temperature. No conversions between the high-temperature forms Ih and IIIh were found. The remarkable crystallographic results are here corroborated by Molecular Dynamics and metadynamics simulations of the form I - form III system.

Triethylphosphine as a molecular gear - phase transitions in ferrocenyl-acetylide-gold(I)

A sequence of two discontinuous phase transitions, occurring just above 125 K and 148 K, has been observed for a ferrocenyl-acetylide-gold(I) complex with triethylphosphine, structure (1), by means of a multi-temperature single-crystal X-ray diffraction technique. Three distinct phases have been identified. The high-temperature α and low-temperature γ phases share the same space group Pbca, whereas the intermediate β phase is in the Pb2₁a subgroup of Pbca. In all phases molecules of (1) form well defined double layers, with PEt₃ groups interlocking in planes perpendicular to c. On the molecular level, both phase transitions involve almost uniquely a conformational change of triethylphosphine: a gear-like rotation around the P-Au axis and concerted flips of the ethyl moieties. The mechanism of these transitions may be imagined as initiated by a rotation of a single PEt₃ group in a double layer (a single gear movement), followed by adjacent phosphines adjusting their conformations as a result of steric strain. The structural changes underlying phase transitions are sequential, occurring layer-wise, the γ→β transition involving approximately every other layer in the crystal lattice, the β→α yielding a total conformation change. The sequence of phase transitions results in a noticeable contraction of the crystal cell volume.

Amino Acid Chiral Selection Via Weak Interactions in Stellar Environments: Implications for the Origin of Life

Magnetochiral phenomena may be responsible for the selection of chiral states of biomolecules in meteoric environments. For example, the Supernova Amino Acid Processing (SNAAP) Model was proposed previously as a possible mode of magnetochiral selection of amino acids by way of the weak interaction in strong magnetic fields. In earlier work, this model was shown to produce an enantiomeric excess (ee) as high as 0.014% for alanine. In this paper we present the results of molecular quantum chemistry calculations from which ees are determined for the α-amino acids plus isovaline and norvaline, which were found to have positive ees in meteorites. Calculations are performed for both isolated and aqueous states. In some cases, the aqueous state was found to produce larger ees reaching values as high as a few percent under plausible conditions.

Structural aspects of displacive transformations: what can optical microscopy contribute? Dehydration of Sm2(C2O4)3·10H2O as a case study

For martensitic transformations the macroscopic crystal strain is directly related to the corresponding structural rearrangement at the microscopic level. In situ optical microscopy observations of the interface migration and the change in crystal shape during a displacive single crystal to single crystal transformation can contribute significantly to understanding the mechanism of the process at the atomic scale. This is illustrated for the dehydration of samarium oxalate decahydrate in a study combining optical microscopy and single-crystal X-ray diffraction.

Polymorphism of the quasiracemate d-2-aminobutyric acid:l-norvaline

A new polymorphic quasiracemate d-2-aminobutyric acid:l-norvaline has been discovered and its reversible single-crystal-to-single-crystal phase transition has been studied using XRD, DSC and thermal microscopy. The low temperature form I is fully ordered, while form II shows two conformations for l-norvaline with a 50/50 occupancy.