Phase transitions in the crystals of L- and DL-cysteine on cooling: the role of the hydrogen-bond distortions and the side-chain motions. 2. DL-cysteine

Mechanism of Phase Transition in dl-Methionine: Determining Cooperative and Molecule-by-Molecule Transformations

The solid-state phase transition in dl-methionine has been extensively studied because of its atypical behavior. The transition occurs through changes in the molecular conformation and 3D packing of the molecules. Phase transitions in racemic aliphatic amino acid crystals are known to show different behaviors depending on whether conformational changes or packing changes are involved, where the former is thought to proceed through a nucleation-and-growth mechanism in a standard molecule-by-molecule picture, and the latter through a cooperative mechanism. The phase transition of dl-methionine resembles the thermodynamic, kinetic, and structural features of both categories: a conformational change and relative shifts between layers in two directions. The present paper presents molecular dynamics simulations of the phase transition to examine the underlying mechanism from two perspectives: (i) analysis of the scaling behavior of the free energy barriers involved in the phase transition and (ii) a structural inspection of the phase transition. Both methods can help to distinguish between a concerted phase change and a molecule-by-molecule or zip-like mechanism. The free energy predominantly scales with the system size, which suggests a cooperative mechanism. The structural changes draw, however, a slightly more complex picture. The conformational changes appear to occur in a molecule-by-molecule fashion, where the rotational movement is triggered by movement in the same layer. Conformational changes occur on a time scale nearly twice as long as the shifts between layers. Shifts in one direction appear to be less concerted than shifts in the perpendicular direction. We relate this to the edge-free energy involved in these shifts. We believe that the behavior observed in dl-methionine is likely applicable to phase transitions in other layered systems that interact through aliphatic chains as well.

Unravelling the nature of intra-molecular hydrogen bonds in curcumin using in-situ low temperature spectroscopic studies

Curcumin, described as a wonder drug owing to various medicinal, viz. anticancer, antiviral, anti-inflammatory etc., properties, can also be seen as a model molecular system to study strong intra-molecular OH----O hydrogen bonds which govern its physico-chemical properties. The study of these hydrogen bonds is important to understand its binding characteristics. Here, we present systematic in-situ variable temperature studies of curcumin in the range 350-75 K using infrared spectroscopy to analyse the effects of external stresses on molecular structure and hydrogen bonding network. The results have been well supported by Raman spectroscopic studies. Our studies show striking difference in the nature of the two intra-molecular hydrogen bonds, generally considered equivalent, which form at the edges of the molecule. Also, the strongest intra-molecular hydrogen bond involving the enol group, present at the centre of the molecule, depicts a remarkable temperature induced strengthening upon cooling. The studies further indicate that the compound does not show any drastic structural transition in the measured temperature range. However, subtle spectral changes associated with reorientations of the hydrogen bonds are noticed across 210 K. These results will be useful to predict reaction pathways during chemical complexation of curcumin.

A combined approach to characterize ligand-induced solid-solid phase transitions in biomacromolecular crystals

Solid-solid phase transitions (SSPTs) are widespread naturally occurring phenomena. Understanding the molecular mechanisms and kinetics of SSPTs in various crystalline materials, however, has been challenging due to technical limitations. In particular, SSPTs in biomacromolecular crystals, which may involve large-scale changes and particularly complex sets of interactions, are largely unexplored, yet may have important implications for time-resolved crystallography and for developing synthetic biomaterials. The adenine riboswitch (riboA) is an RNA control element that uses ligand-induced conformational changes to regulate gene expression. Crystals of riboA, upon the addition of a ligand, undergo an SSPT from monoclinic to triclinic to orthorhombic. Here, solution atomic force microscopy (AFM) and polarized video microscopy (PVM) are used to characterize the multiple transition states throughout the SSPT in both the forward and the reverse directions. This contribution describes detailed protocols for growing crystals directly on mica or glass surfaces for AFM and PVM characterization, respectively, as well as methods for image processing and phase-transition kinetics analysis.

Effect of Fe (III) on L-asparagine monohydrate investigated under low- and high-temperature conditions

Raman spectra of Fe-doped L-asparagine monohydrate (LAM:Fe) crystal were studied under several temperatures varying from 17 to 490 K. The effect of Fe (III) ion on the stability of the crystal in changing temperature through the vibrational spectra was discussed. The behavior of inter and intra-molecular vibration modes has indicated two phase transitions and an amorphous transformation. These effects were also clarified by X-ray powder diffraction measurements which corroborate very well the Raman data. In addition, we have determinated the lattice parameters of all phases and verified that under low temperature conditions the crystal undergoes a conformational transition whereas under high temperatures its structure transforms from the orthorhombic (P2₁2₁2₁-space group) to the monoclinic (P2₁-space group) symmetry and, after this process, it goes to an amorphous phase due to the start of the decomposition. Finally, differential scanning calorimetry analysis was utilized as complementary technique to investigate the structural stability of LAM:Fe and results are in a good agreement with the Raman and the X-ray diffraction data.

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.

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.

Orientational Adaptations Leading to Plausible Phase Transitions in l-Leucine at Low Temperatures: Revealed by Infrared Spectroscopy

Hydrogen bonding is essential for the stability of amino acids. A change in the geometry and conformation of hydrogen bonds in such molecular systems, for example, under varying thermodynamic conditions of temperature/pressure, may lead to subtle or drastic phase transitions. We demonstrate here the mechanism of temperature-induced phase transitions in the polycrystalline solid sample of l-leucine [(CH₃)₂-C(₄)H-C(₃)H₂-C(₂)H(C(₁)OO^-)(NH₃⁺)], an "essential" amino acid, using in situ Fourier transform infrared spectroscopy in the temperature range 300-4.3 K. Unambiguous spectral signatures of preferred microstructural changes have been reported, which are linked to phase transitions at ∼150 and ∼240 K. The transition at 150 K is found to be associated with a sudden change in reorientation dynamics of the torsional vibrations of the (C₃C₄) group. In contrast, the transition at 240 K is associated with the conformational distortions in the NH₃ group, which causes strengthening of the hydrogen bonds in the ac-plane forming two-dimensional sheets, well separated from each other in the b-direction. These findings pave the way toward settling the long-standing debate on the temperature-induced behavior of l-leucine as well as harnessing its physicochemical properties.

Unusual hydrogen bonding in L-cysteine hydrogen fluoride

L-Cysteine hydrogen fluoride, or bis(L-cysteinium) difluoride-L-cysteine-hydrogen fluoride (1/1/1), 2C3H8NO2S(+)·2F(-)·C3H7NO2S·HF or L-Cys(+)(L-Cys···L-Cys(+))F(-)(F(-)...H-F), provides the first example of a structure with cations of the 'triglycine sulfate' type, i.e. A(+)(A···A(+)) (where A and A(+) are the zwitterionic and cationic states of an amino acid, respectively), without a doubly charged counter-ion. The salt crystallizes in the monoclinic system with the space group P2(1). The dimeric (L-Cys···L-Cys(+)) cation and the dimeric (F(-)···H-F) anion are formed via strong O-H···O or F-H···F hydrogen bonds, respectively, with very short O···O [2.4438 (19) Å] and F···F distances [2.2676 (17) Å]. The F···F distance is significantly shorter than in solid hydrogen fluoride. Additionally, there is another very short hydrogen bond, of O-H···F type, formed by a L-cysteinium cation and a fluoride ion. The corresponding O···F distance of 2.3412 (19) Å seems to be the shortest among O-H···F and F-H···O hydrogen bonds known to date. The single-crystal X-ray diffraction study was complemented by IR spectroscopy. Of special interest was the spectral region of vibrations related to the above-mentioned hydrogen bonds.

Low-temperature polymorphic phase transition in a crystalline tripeptide L-Ala-L-Pro-Gly·H2O revealed by adiabatic calorimetry

We demonstrate application of precise adiabatic vacuum calorimetry to observation of phase transition in the tripeptide L-alanyl-L-prolyl-glycine monohydrate (APG) from 6 to 320 K and report the standard thermodynamic properties of the tripeptide in the entire range. Thus, the heat capacity of APG was measured by adiabatic vacuum calorimetry in the above temperature range. The tripeptide exhibits a reversible first-order solid-to-solid phase transition characterized by strong thermal hysteresis. We report the standard thermodynamic characteristics of this transition and show that differential scanning calorimetry can reliably characterize the observed phase transition with <5 mg of the sample. Additionally, the standard entropy of formation from the elemental substances and the standard entropy of hypothetical reaction of synthesis from the amino acids at 298.15 K were calculated for the studied tripeptide.

Weak hydrogen bonds formed by thiol groups in N-acetyl-(L)-cysteine and their response to the crystal structure distortion on increasing pressure

The effect of hydrostatic pressure on single crystals of N-acetyl-l-cysteine was followed at multiple pressure points from 10(-4) to 6.2 GPa with a pressure step of 0.2-0.3 GPa by Raman spectroscopy and X-ray diffraction. Since in the crystals of N-acetyl-l-cysteine the thiol group is involved in intermolecular hydrogen bonds not as a donor only (bonds S-H···O) but also as an acceptor (bonds N-H···S), increasing the pressure does not result in phase transitions. This makes a contrast with the polymorphs of l- and dl-cysteine, in which multiple phase transitions are observed already at relatively low hydrostatic pressures and are related to the changes in the conformation of the thiol side chains only weakly bound to the neighboring molecules in the structure and thus easily switching over the weak S-H···O and S-H···S hydrogen bonds. No phase transitions occur in N-acetyl-l-cysteine with increasing pressure, and changes in cell parameters and volume vs pressure do not reveal any peculiar features. Nevertheless, a more detailed analysis of the changes in intermolecular distances, in particular, of the geometric parameters of the hydrogen bonds based on X-ray single crystal diffraction analysis, complemented by an equally detailed study of the positions of all the significant bands in Raman spectra, allowed us to study the fine details of subtle changes in the hydrogen bond network. Thus, as pressure increases, a continuous shift of the hydrogen atom of the thiol group from one acceptor (a carboxyl group) to another acceptor (a carbonyl group) is observed. Precise single-crystal X-ray diffraction and polarized Raman spectroscopy structural data reveal the formation of a bifurcated S-H···O hydrogen bond with increasing pressure starting with ∼1.5 GPa. The analysis of the vibrational bands in Raman spectra has shown that different donor and acceptor groups start "feeling" the formation of the bifurcated S-H···O hydrogen bond in different pressure ranges. The results are discussed in relation to some of the previously published data on the effect of high pressure on the polymorphs of l-cysteine, dl-cysteine, and glutathione, that show similarity with the effects reported here for N-acetyl-l-cysteine. The results obtained in this work allow one to suggest new models for the pressure-induced structural rearrangements in the whole family of cysteine-containing crystals.

X-ray diffraction and Raman study of DL-alanine at high pressure: revision of phase transitions

The effect of pressure on DL-alanine has been studied by X-ray powder diffraction (up to 8.3 GPa), single-crystal X-ray diffraction and Raman spectroscopy (up to ∼ 6 GPa). No structural phase transitions have been observed. At ∼ 1.5–2 GPa, cell parameters b and c become accidentally equal to each other, but the space-group symmetry does not change. There is no phase transition between 1.7 and 2.3 GPa, contrary to what has been reported earlier [Belo et al. (2010). Vibr. Spectrosc. 54, 107–111]. The presence of the second phase transition, which was claimed to appear within the pressure range from 6.0 to 7.3 GPa (Belo et al., 2010), is also argued. The changes in the Raman spectra have been shown to be continuous in all the pressure ranges studied.

Low-temperature phase transition in glycine–glutaric acid co-crystals studied by single-crystal X-ray diffraction, Raman spectroscopy and differential scanning calorimetry

The occurrence of a first-order reversible phase transition in glycine–glutaric acid co-crystals at 220–230 K has been confirmed by three different techniques – single-crystal X-ray diffraction, polarized Raman spectroscopy and differential scanning calorimetry. The most interesting feature of this phase transition is that every second glutaric acid molecule changes its conformation, and this fact results in the space-group symmetry change from P21/c to P\bar 1. The topology of the hydrogen-bonded motifs remains almost the same and hydrogen bonds do not switch to other atoms, although the hydrogen bond lengths do change and some of the bonds become inequivalent.

Structure-property relations in crystalline L-leucine obtained from calorimetry, X-rays, neutron and Raman scattering

We have studied the amino acid L-leucine (LEU) using inelastic neutron scattering, X-rays and neutron diffraction, calorimetry and Raman scattering as a function of temperature, focusing on the relationship between the local dynamics of the NH(3), CH(3), CH(2) and CO(2) moieties and the molecular structure of LEU. Calorimetric and diffraction data evidenced two novel phase transitions at about 150 K (T(1)) and 275 K (T(2)). The dynamical susceptibility function, obtained from the inelastic neutron scattering results, shows a re-distribution of the intensity of the vibrational bands that can be directly correlated with the phase transitions observed at T(1) and T(2), as well as with the already reported phase transition at T(3) = 353 K. Through the analysis of the Raman modes, the new structural arrangement observed below T(1) was related to conformational modifications of the CH and CH(3) groups, while the behavior of the N-H stretching vibration, ν(NH(3)), gave insight into the intermolecular N-H…O interactions. The observation of changes in the translational symmetry in the crystalline lattice, as well as anharmonic dynamics, allows for localized motions in LEU.