Phase Transitions in the Crystals of l- and dl-Cysteine on Cooling: Intermolecular Hydrogen Bonds Distortions and the Side-Chain Motions of Thiol-Groups. 1. l-Cysteine

THz spectroscopy on the amino acids L-serine and L-cysteine

We present a detailed study on the temperature-dependent THz spectra of the polycrystalline amino acids, L-serine and L-cysteine, for wavenumbers from 20 to 120 cm-1 and temperatures from 4 to 300 K. Even though the structure of these two amino acids is very similar, with a sulfur atom in the side chain of cysteine instead of an oxygen atom in serine, the excitation spectra are drastically different. Obviously, the vibrational dynamics strongly depend on the ability of cysteine to form sulfur-hydrogen bonds. In addition, cysteine undergoes an order-disorder type phase transition close to 80 K, documented by additional specific heat experiments, with accompanying anomalies in the THz results. On increasing temperatures, well-defined vibrational excitations exhibit significant shifts in the eigenfrequencies with concomitant line-broadening yielding partly overlapping modes. Interestingly, several modes completely lose all their dipolar strength and are unobservable under ambient conditions. Comparing the recent results to the published work utilizing THz, Raman, and neutron-scattering techniques, as well as with ab initio simulations, we aim at a consistent analysis of the results ascribing certain eigenfrequencies to distinct collective lattice modes. We document that THz spectra can be used to fine-tune the parameters of model calculations and as fingerprint properties of certain amino acids. In addition, we analyzed the low-temperature heat capacity of both the compounds and detected strong excess contributions compared to the canonical Debye behavior of crystalline solids, indicating soft excitations and a strongly enhanced phonon-density of states at low frequencies.

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 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.

Exploring the Stability and Disorder in the Polymorphs of L-Cysteine through Density Functional Theory and Vibrational Spectroscopy

Static and dynamic density functional calculations are reported for the four known polymorphs of l-cysteine. Static calculations are used to explore the relative free energies (within the harmonic approximation) of the polymorphs as a function of pressure. An important feature of the structural differences between the polymorphs is shown to be the dihedral angle of the C-C-S-H bond. It is shown that, by varying this angle, it is possible to move between hydrogen bonding motifs S-H···S and S-H···O in all four polymorphs. The energetics for dihedral angle rotation are explored, and the barriers for rotation between the hydrogen bonding motifs have been calculated for each polymorph. Two possible models for the experimental disorder observed in Form I at room temperature are explored using both static and dynamic methods; a domain disorder model, where the disorder is localized, and a dispersed disorder model, where the disorder is randomly distributed throughout the crystal. Molecular dynamics calculations show transitions between the two hydrogen bonding motifs occurring in the dispersed disorder model at 300 and 350 K. In addition, molecular dynamics calculations of Form IV also showed the onset of hydrogen bond disorder at 300 K. Calculations of the predicted infrared and terahertz absorption are performed for both the static and dynamic simulations, and the results are compared with experimental results to understand the influence of disorder on the observed spectra.

High Level Electronic Structure Calculation of Molecular Solid-State NMR Shielding Constants

In this work, we present a quantum mechanics/molecular mechanics (QM/MM) approach for the computation of solid-state nuclear magnetic resonance (SS-NMR) shielding constants (SCs) for molecular crystals. Besides applying standard-DFT functionals like GGAs (PBE), meta-GGAs (TPSS), and hybrids (B3LYP), we apply a double-hybrid (DSD-PBEP86) functional as well as MP2, using the domain-based local pair natural orbital (DLPNO) formalism, to calculate the NMR SCs of six amino acid crystals. All the electronic structure methods used exhibit good correlation of the NMR shieldings with respect to experimental chemical shifts for both ¹H and ¹³C. We also find that local electronic structure is much more important than the long-range electrostatic effects for these systems, implying that cluster approaches using all-electron/Gaussian basis set methods might offer great potential for predictive computations of solid-state NMR parameters for organic solids.

Synthesis and properties of helical polystyrene derivatives with amino acid side groups

A series of polystyrene derivatives with chiral amide groups with a controlled molecular weight and narrow molecular weight distribution were synthesized by reversible addition–fragmentation chain transfer (RAFT) radical polymerization.

Raman spectroscopy of captopril crystals under low-temperature conditions

The polymorphism is a characteristic of several active principles, and can affect the bioavailability of a drug. Among the drugs used in the treatment of heart diseases, captopril is one of the most widely used in the world. Despite the knowledge of vibrational properties of captopril under high temperature and under high pressure, a lack of information impedes the understanding of the substance in the crystal form at low temperatures. In this research, we investigated the vibrational properties of captopril crystals under cryogenic conditions in the 300-8 K interval using Raman spectroscopy. By observing the behavior of the inter- and intra-molecular vibrations it was possible to infer that the captopril molecules suffered a rearranging into the unit cell due slight orientational changes mainly involving CH⋯O hydrogen bonds. The phenomenon occurs in a large temperature range. However, the observed changes do not suggest the occurrence of a structural phase transition and the Raman spectra indicate that the trans conformation is recorded down to the lowest temperature available in the experiments.

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.

Towards Accurate Predictions of Proton NMR Spectroscopic Parameters in Molecular Solids

The factors contributing to the accuracy of quantum-chemical calculations for the prediction of proton NMR chemical shifts in molecular solids are systematically investigated. Proton chemical shifts of six solid amino acids with hydrogen atoms in various bonding environments (CH, CH₂ , CH₃ , OH, SH and NH₃ ) were determined experimentally using ultra-fast magic-angle spinning and proton-detected 2D NMR experiments. The standard DFT method commonly used for the calculations of NMR parameters of solids is shown to provide chemical shifts that deviate from experiment by up to 1.5 ppm. The effects of the computational level (hybrid DFT functional, coupled-cluster calculation, inclusion of relativistic spin-orbit coupling) are thoroughly discussed. The effect of molecular dynamics and nuclear quantum effects are investigated using path-integral molecular dynamics (PIMD) simulations. It is demonstrated that the accuracy of the calculated proton chemical shifts is significantly better when these effects are included in the calculations.

High-pressure studies on l,l-dileucine crystals by Raman spectroscopy and synchrotron X-ray diffraction combined with DFT calculations

The vibrational properties of the dipeptide l-leucyl-l-leucine hydrate were investigated through Raman and infrared spectroscopy. With the aid of first principle calculations using the density functional theory, the assignment of the vibrational modes from the material was furnished. In addition, the behavior of the crystal under high pressure was investigated using Raman spectroscopy (~8 GPa) and synchrotron X-ray diffraction (~26 GPa). The results show significant changes in both the X-ray diffractogram and the Raman spectra, suggesting that l-leucyl-l-leucine hydrate undergoes a phase transition between 2.3 and 2.9 GPa. Finally, for pressures above 16 GPa the broadening of X-ray peaks suggests a disorder in the crystal lattice induced by high-pressure effects.

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.

Phase transformation in the C form of myristic-acid crystals and DFT calculations

In this study, the vibrational frequencies of myristic acid (CH₃(CH₂)₁₂COOH) were obtained using density functional theory calculations, and the results were compared with experimental Raman and infrared data. Additionally, Raman spectra of crystalline myristic acid were recorded in the 300-20 K range. Raman spectroscopy gives important insights into the effect of low temperatures on its monoclinic phase. X-ray diffraction was performed from 298 to 133 K to provide additional information about the cryogenic behavior of the crystals. These undergo a phase transformation, which was confirmed by differential scanning calorimetry through an enthalpy anomaly observed at low temperatures. Raman spectra and X-ray diffraction refinement of the cell parameters in combination with differential scanning calorimetry at low temperatures revealed slight modifications, confirming a conformational change in the myristic acid molecules involving rearrangement of dimers within the unit cell.

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.

Conformational change in the C form of palmitic acid investigated by Raman spectroscopy and X-ray diffraction

Fatty acids are substances found in most living beings in nature. Here we report the effect of the low temperature in the vibrational and structural properties of the C form of palmitic acid, a fatty acid with 16 carbon atoms. The Raman spectra were obtained in the temperature interval from 300 to 18K in the spectral range between 30 and 3100 cm(-1). The assignment of the duly observed bands was done based on the density functional theory. On cooling, the main changes observed in the lattice mode region of the Raman spectra were interpreted as a conformational modification undergone by the palmitic acid molecules in the unit cell. The X-ray diffraction measurements were obtained from 290 to 80K showing a slight modification in the lattice parameters at about 210K. Differential scanning calorimetry (DSC) measurements were recorded between 150 and 300K and no enthalpic anomaly in the DSC thermogram was observed. These techniques provided strong evidence of the conformational change in the molecules of palmitic acid at low temperatures.

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.

Unusual specific heat of almost dry L-cysteine and L-cystine amino acids

A detailed quantitative analysis of the specific heat in the 0.5- to 200-K temperature range for almost dry L-cysteine and its dimer, L-cystine, amino acids is presented. We report the occurrence of a sharp first-order transition at ∼76 K for L-cysteine associated with the thiol group ordering which was successfully modeled with the two-dimensional Ising model. We demonstrated that quantum rotors, two-level systems (TLS), Einstein oscillators, and acoustic phonons (the Debye model) are essential ingredients to correctly describe the overall experimental data. Our analysis pointed out the absence of the TLS contribution to the low temperature specific heat of L-cysteine. This result was similar to that found in other noncrystalline amorphous materials, e.g., amorphous silicon, low density amorphous water, and ultrastable glasses. L-cystine presented an unusual nonlinear acoustic dispersion relation ω(q)=vq0.95 and a Maxwell-Boltzmann-type distribution of tunneling barriers. The presence of Einstein oscillators with ΘE∼70 K was common in both systems and adequately modeled the boson peak contributions.

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.

Silanization of solid surfaces via mercaptopropylsilatrane: a new approach of constructing gold colloid monolayers

Mercaptopropylsilatrane (MPS) was investigated as a novel self-assembled film on silica surfaces and also as a novel adhesive layer for the construction of a gold colloid monolayer on silica surfaces.

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.

Anharmonic transitions in nearly dry L-cysteine I

Two special dynamical transitions of universal character have recently been observed in macromolecules (lysozyme, myoglobin, bacteriorhodopsin, DNA and RNA) at T* ~100-150 K and T(D) ~180-220 K. The underlying mechanisms governing these transitions have been the subject of debate. In the present work, a survey is reported on the temperature dependence of structural, vibrational and thermodynamical properties of a nearly anhydrous amino acid (orthorhombic polymorph of the amino acid l-cysteine at a hydration level of 3.5%). The temperature dependence of x-ray powder diffraction patterns, Raman spectra and specific heat revealed these two transitions at T* = 70 K and T(D) = 230 K for this sample. The data were analyzed considering amino acid-amino acid, amino acid-water, water-water phonon-phonon interactions and molecular rotor activation. Our results indicated that the two referred temperatures define the triggering of very simple and particular events that govern all the interactions of the biomolecular: activation of CH(2) rigid rotors (T < T* ), phonon-phonon interactions between specific amino acid and water dimer vibrational modes (T* < T < T(D)), and water rotational barriers surpassing (T > T(D)).

Photodetachment-photoelectron spectroscopy of HS- x H2S and DS- x D2S: the transition states of the SH + H2S and SD + D2S reactions

The transition state region for neutral hydrogen transfer reactions can be accessed by photodetachment of a stable negative ion with a geometry similar to that of the neutral transition state. In this work the SH + H(2)S and SD + D(2)S reactions are investigated by photodetachment-photoelectron spectroscopy of HS(-) x H(2)S and DS(-) x D(2)S. The spectra exhibit vibrational structure which is attributed to the antisymmetric stretching mode (H-atom motion) of the neutral transitions state for H-atom transfer. The spectra are compared to one-dimensional simulations performed using a wave packet propagation scheme. Electronic structure calculations of the anionic, neutral and transition-state geometries and calculations of the vertical detachment energy at different levels of theory are used to support the analysis of the spectra. A vertical detachment energy VDE of 3.06 eV has been determined.

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

Structural strain and a first-order phase transition in the crystalline DL-cysteine on cooling and on reverse heating were followed by Raman spectroscopy and X-ray diffraction. The transition is reversible and has a large hysteresis (over 100 K). The temperature at which the transition is observed depends strongly on the cooling/heating rate. The phase transition is accompanied by crystal fragmentation. The low-temperature phase could be obtained not only as a result of the solid-state transformation in situ as a polycrystalline sample (with strong preferred orientation, or without it, depending on the preparative technique), but also (using an original crystallization technique) as a single crystal of the quality suitable for structural analysis. For the first time, the crystal structure of the low-temperature phase was solved independently by powder and by single-crystal diffraction techniques. The spectral changes were correlated with the precise diffraction data on the intramolecular conformations and the intermolecular hydrogen bonding before and after the phase transition. The role of the distortion of the intermolecular hydrogen bonds and of the motions of the -CH(2)SH side chains in the phase transition is discussed in a comparison with the low-temperature phase transition in L-cysteine, which is of a different type and preserves the single crystals intact (Kolesov et al. J. Phys. Chem. B, 2008, 112 (40), 12827-12839).

Monoclinic modification of N-[(1,1-dimethyl-ethoxy)carbon-yl]-3-[(R)-prop-2-en-1-ylsulfin-yl]-(R)-alanine ethyl ester at 200 (1) K

In the monoclinic polymorph of the title compound, C₁₃H₂₃NO₅S, inter­molecular N—H⋯O hydrogen bonds link mol­ecules into one-dimensional chains along [100]. The atoms of the terminal propenyl group are disordered over two sets of sites with refined occupancies of 0.69 (2) and 0.31 (2).