A comparative study of the anisotropy of lattice strain induced in the crystals of L-serine by cooling down to 100 K or by increasing pressure up to 4.4 GPa

Structural and vibrational analysis of glycyl-L-phenylalanine and phase transition under high-pressure

The structural and vibrational properties of the glycyl-L-phenylalanine dipeptide were investigated using vibrational spectroscopy (Raman and infrared) and first-principle calculations. Raman spectroscopy measurements were performed between 100 and 3200 cm-1 and infrared spectroscopy from 100 and 3200 cm-1 under ambient conditions. The conformational analysis of the zwitterionic form of the dipeptide was performed using the B3LYP functional, the 6-311++ base set and the Polarizable Continuum Model of solvation, determining the lowest energy conformation and assigning the vibrational modes. The effect of pressure on the glycyl-1-phenylalanine crystal was investigated using the Raman spectroscopy between 0.0 and -7.1 GPa in the spectral region of 100 - 3200 cm-1. As a result, conformational changes around 1.0 GPa were observed in the lattice modes and in some internal modes, showing a reorganization of the molecule in the crystal. In the decompression process, it was observed that the conformational change is reversible and the original Raman spectrum is recoverd.

Rapid chiral purity identification of mandelic acid by Raman spectra in the O-H stretching region

Chiral molecules play a very important role in biological systems, and more and more chiral drugs are used in the treatment of diseases. Mandelic acid (MA) is an important chiral starting substance or the key intermediate of some chiral drugs, and the rapid detection of its chiral purity is very important in the synthesis, separation and detection of drugs. In this study, we developed a method for rapid determination of chiral purity of MA by Raman spectroscopy, and measured a series of Raman spectra of different chiral MA. Through the analysis, it is found that the OH stretching vibration peak can be used to identify the components of chiral molecules, and the enantiomeric excess (ee value) obtained is in good agreement with the real value, and the error is about 5%. The experimental detection speed is fast and the efficiency is high. Our work firstly provides a new idea for the purity detection of chiral molecules by the original Raman spectrum.

N-Iodosaccharin-pyridine co-crystal system under pressure: experimental evidence of reversible twinning

This work presents a single-crystal X-ray diffraction study of an organic co-crystal composed of N-iodosaccharin and pyridine (NISac·py) under hydrostatic pressure ranging from 0.00 (5) GPa to 4.5 (2) GPa. NISac·py crystallizes in the monoclinic system (space group B2₁/e). The unconventional setting of the space group is adopted (the conventional setting is P2₁/c, No. 14) to emphasise the strongly pseudo-orthorhombic symmetry of the lattice, with a β angle very close to 90°. The crystal structure contains one molecule each of N-iodosaccharin (NISac) and pyridine (py) in the asymmetric unit (Z' = 1), linked via an N_sac...I...N'_py halogen-bonding motif. A gradual modification of this motif is observed under pressure as a result of changes in the crystalline environment. Mechanical twinning is observed under compression and the sample splits into two domains, spanning an unequal volume that is mapped by a twofold rotation about the [100] direction of the B2₁/e unit cell. The twinning is particularly significant at high pressure, being reversible when the pressure is released. The structure of the twinned sample reveals the continuity of a substantial substructure across the composition plane. The presence of this common substructure in the two orientations of the twinned individuals can be interpreted as a structural reason for the formation of the twin and is the first observed example in a molecular crystal. These results indicate that the anisotropy of intermolecular interactions in the crystal structure results in an anisotropic strain generated upon the action of hydrostatic compression. Periodic density functional theory calculations were carried out by considering an isotropic external pressure, the results showing good agreement with the experimental findings. The bulk modulus of the crystal was obtained from the equations of state, being 7 (1) GPa for experimental data and 6.8 (5) GPa for theoretical data.

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.

Spectroscopic studies of temperature induced phase transitions in metal-organic complex trans-PtCl2(PEt3)2

Tuning of molecular and electronic properties of Pt(II)-organic complexes have a profound effect on their applications in the fields of technology, pharmaceuticals and crystal engineering. Here, we present combined infrared and Raman spectroscopic investigations on trans-PtCl₂(PEt₃)₂ systematically carried out at various temperatures from 300 to 4.2 K in a wide spectral range. The studies suggest drastic orientational changes of different moieties around 180 K and 130 K in the ligand groups attached to the central Pt atom. This is accompanied by a systematic strengthening of C-H⋯Cl hydrogen bonds in the 180-130 K temperature range. A discontinuous change in intensity, peak variations of modes and emergence of new modes across 180 K and 130 K in the lattice region are suggestive of a possible structural phase transition. It is interesting to note that the spectral signatures of the low temperature phase are different from those reported recently for the high pressure phase in this compound. These studies will be useful in better understanding the physico-chemical properties of metal-organic complexes in order to exploit their applications in various bio-chemical and technological fields.

Perceptible isotopic effect in 3D-framework of α-glycine at low temperatures

Glycine, the most fundamental amino acid, albeit studied for many decades, has kept researchers captivated with interesting structural variations relevant to important biological, astrophysical and technological applications. We report here a noticeable effect of deuteration on the three dimensional hydrogen bonding network of α-glycine using low temperature infrared absorption studies in a wide spectral range, corroborated with Raman scattering studies. These systematic studies in the range 300-4.2 K have demonstrated a relatively compact assembly of glycine molecules in the three dimensional bilayered structure of hydrogenated glycine (gly-h) at low temperatures. This is inferred from a remarkable temperature effect in the weak intra-bilayer hydrogen bond ~ along the b-axis, which strengthens upon cooling. A pronounced increase in the intensity of NH₃ torsional and NH stretching modes has been observed. This is accompanied with a large rate of stiffening and softening respectively of these modes upon cooling and a change in slope across 210 K and 80 K. In contrast, the D---O hydrogen bond lengths in fully deuterated isotope (gly-d), as estimated using empirical correlation, show that the weak intra-bilayer hydrogen bond is not strengthened upon cooling down to 180 K, whereas the stronger intra-layer hydrogen bonds in the ac-plane become further strong. The ND₃ torsional vibrations show no temperature effect. This implies a relatively stable two dimensional layered structure formed by strongly hydrogen bonded glycine sheets in the ac-plane. Below 180 K, similar qualitative trends have been obtained for the hydrogen bond lengths in the two isotopes. In addition, temperature induced variation of the characteristic "indicator" band of zwitterionic gly-h and gly-d has also been reported.

Experimental and DFT dimer modeling studies of the H-bond induced-vibration modes of l-β-Homoserine

The vibrational spectra for l-β-Homoserine have been measured (IR absorption: 4000-400cm^-1/Raman spectra: 4000-200cm^-1). Characteristic vibrational modes of ammonium (-NH₃⁺), carboxylate (-CO₂^-) and hydroxyl (-OH) groups across the 3700-1400cm^-1 are all identified to have originated in inter-molecular hydrogen bonding involving these functional groups. DFT calculations at B3LYP/6-311++G(d, p) level have yielded a single neutral monomer in the gas phase. Since as a member of the amino acids which are known to possess zwitterionic structure in condensed phase, the neutral monomer of l-β-Homoserine is optimized to a zwitterionic structure in a water medium. Consideration of two dimer structures, one dimer with -NH‧‧‧O bond and another -OH‧‧‧O bond, has given rise to vibrational modes that satisfactorily fit to all the observed absorption and Raman bands. It is found that the dimer with -OH‧‧‧O bond (binding energy, 8.896kcal/mol) is more tightly bound than the dimer with -NH‧‧‧O bond (8.363kcal/mol).

High-pressure crystallography of periodic and aperiodic crystals

More than five decades have passed since the first single-crystal X-ray diffraction experiments at high pressure were performed. These studies were applied historically to geochemical processes occurring in the Earth and other planets, but high-pressure crystallography has spread across different fields of science including chemistry, physics, biology, materials science and pharmacy. With each passing year, high-pressure studies have become more precise and comprehensive because of the development of instrumentation and software, and the systems investigated have also become more complicated. Starting with crystals of simple minerals and inorganic compounds, the interests of researchers have shifted to complicated metal-organic frameworks, aperiodic crystals and quasicrystals, molecular crystals, and even proteins and viruses. Inspired by contributions to the microsymposium 'High-Pressure Crystallography of Periodic and Aperiodic Crystals' presented at the 23rd IUCr Congress and General Assembly, the authors have tried to summarize certain recent results of single-crystal studies of molecular and aperiodic structures under high pressure. While the selected contributions do not cover the whole spectrum of high-pressure research, they demonstrate the broad diversity of novel and fascinating results and may awaken the reader's interest in this topic.

Sarcosine and betaine crystals upon cooling: structural motifs unstable at high pressure become stable at low temperatures

The crystal structures of N-methyl derivatives of the simplest amino acid glycine, namely sarcosine (C3H7NO2) and betaine (C5H11NO2), were studied upon cooling by single-crystal X-ray diffraction and single-crystal polarized Raman spectroscopy. The effects of decreasing temperature and increasing hydrostatic pressure on the crystal structures were compared. In particular, we have studied the behavior upon cooling of those structural motifs in the crystals, which are involved in structural rearrangement during pressure-induced phase transitions. In contrast to their high sensitivity to hydrostatic compression, the crystals of both sarcosine and betaine are stable to cooling down to 5 K. Similarly to most α-amino acids, the crystal structures of the two compounds are most rigid upon cooling in the direction of the main structural motif, namely head-to-tail chains (linked via the strongest N-H···O hydrogen bonds and dipole-dipole interactions in the case of sarcosine, or exclusively by dipole-dipole interactions in the case of betaine). The anisotropy of linear strain in betaine does not differ much upon cooling and on hydrostatic compression, whereas this is not the case for sarcosine. Although the interactions between certain structural motifs in sarcosine and betaine weaken as a result of phase transitions induced by pressure, the same interactions strengthen when volume reduction results from cooling.

Can the thermal expansion be controlled by varying the hydrogen bond dimensionality in polymorphs?

A higher dimensional (1-D) hydrogen bonded form shows smaller thermal expansion than a lower dimensional (0-D) hydrogen bonded form of 2-butynoic acid.

Effect of pressure on methylated glycine derivatives: relative roles of hydrogen bonds and steric repulsion of methyl groups

Infinite head-to-tail chains of zwitterions present in the crystals of all amino acids are known to be preserved even after structural phase transitions. In order to understand the role of the N-H...O hydrogen bonds linking zwitterions in these chains in structural rearrangements, the crystal structures of the N-methyl derivatives of glycine (N-methylglycine, or sarcosine, with two donors for hydrogen bonding; two polymorphs of N,N-dimethylglycine, DMG-I and DMG-II, with one donor for hydrogen bond; and N,N,N-trimethylglycine, or betaine, with no hydrogen bonds) were studied at different pressures. Methylation has not only excluded the formation of selected hydrogen bonds, but also introduced bulky mobile fragments into the structure. The effects of pressure on the systems of the series were compared with respect to distorting and switching over hydrogen bonds and inducing reorientation of the methylated fragments. Phase transitions with fragmentation of the single crystals into fine powder were observed for partially methylated N-methyl- and N,N-dimethylglycine, whereas the structural changes in betaine were continuous with some peculiar features in the 1.4-2.9 GPa pressure range and accompanied by splitting of the crystals into several large fragments. Structural rearrangements in sarcosine and betaine were strongly dependent on the rate of pressure variation: the higher the rate of increasing pressure, the lower the pressure at which the phase transition occurred.

A high-pressure single-crystal to single-crystal phase transition in DL-alaninium semi-oxalate monohydrate with switching-over hydrogen bonds

A single-crystal to single-crystal transition in DL-alaninium semi-oxalate monohydrate at a pressure between 1.5 and 2.4 GPa was studied by single-crystal X-ray diffraction and Raman spectroscopy. This is the first example of a single-crystal diffraction study of a high-pressure phase transition in a crystalline amino acid salt hydrate. Selected hydrogen bonds switch over and become bifurcated, whereas the others are compressed continuously. The transition is accompanied by pronounced discontinuities in the cell parameters and volume versus pressure, although no radical changes in the molecular packing are induced. Although, in contrast to DL-alanine, in the crystal structure of the salt there are short O-H···O hydrogen bonds, the structure of the salt is more compressible. At the same time, the structure of DL-alanine does not undergo pressure-induced phase transitions, whereas the structure of DL-alaninium semi-oxalate monohydrate does, and at a relatively low pressure. The anisotropy of lattice strain for the low-pressure phase differs from that on cooling at ambient pressure; interestingly, the anisotropy of the pressure-induced compression of the high-pressure phase is quite similar to the lattice strain of the low-pressure phase on cooling.

Effect of pressure on crystalline L- and DL-serine: revisited by a combined single-crystal X-ray diffraction at a laboratory source and polarized Raman spectroscopy study

Information on the effect of pressure on hydrogen bonds, which could be derived from single-crystal X-ray diffraction at a laboratory source and polarized Raman spectroscopy, has been compared. L-Serine and DL-serine were selected for this case study. The role of hydrogen bonds in pressure-induced phase transitions in the first system and in the structural stability of the second one are discussed. Non-monotonic distortion of selected hydrogen bonds in the pressure range below ∼ 1–2 GPa, a change in the compression mechanism at ∼ 2–3 GPa, and the evidence of formation of bifurcated N—H...O hydrogen bonds in DL-serine at ∼ 3–4 GPa are considered.

Proton-driven spin diffusion in rotating solids via reversible and irreversible quantum dynamics

Proton-driven spin diffusion (PDSD) experiments in rotating solids have received a great deal of attention as a potential source of distance constraints in large biomolecules. However, the quantitative relationship between the molecular structure and observed spin diffusion has remained obscure due to the lack of an accurate theoretical description of the spin dynamics in these experiments. We start with presenting a detailed relaxation theory of PDSD in rotating solids that provides such a description. The theory applies to both conventional and radio-frequency-assisted PDSD experiments and extends to the non-Markovian regime to include such phenomena as rotational resonance (R(2)). The basic kinetic equation of the theory in the non-Markovian regime has the form of a memory function equation, with the role of the memory function played by the correlation function. The key assumption used in the derivation of this equation expresses the intuitive notion of the irreversible dissipation of coherences in macroscopic systems. Accurate expressions for the correlation functions and for the spin diffusion constants are given. The theory predicts that the spin diffusion constants governing the multi-site PDSD can be approximated by the constants observed in the two-site diffusion. Direct numerical simulations of PDSD dynamics via reversible Liouville-von Neumann equation are presented to support and compliment the theory. Remarkably, an exponential decay of the difference magnetization can be observed in such simulations in systems consisting of only 12 spins. This is a unique example of a real physical system whose typically macroscopic and apparently irreversible behavior can be traced via reversible microscopic dynamics. An accurate value for the spin diffusion constant can be usually obtained through direct simulations of PDSD in systems consisting of two (13)C nuclei and about ten (1)H nuclei from their nearest environment. Spin diffusion constants computed by this method are in excellent agreement with the spin diffusion constants obtained through equations given by the relaxation theory of PDSD. The constants resulting from these two approaches were also in excellent agreement with the results of 2D rotary resonance recoupling proton-driven spin diffusion (R(3)-PDSD) experiments performed in three model compounds, where magnetization exchange occurred over distances up to 4.9 Å. With the methodology presented, highly accurate internuclear distances can be extracted from such data. Relayed transfer of magnetization between distant nuclei appears to be the main (and apparently resolvable) source of uncertainty in such measurements. The non-Markovian kinetic equation was applied to the analysis of the R(2) spin dynamics. The conventional semi-phenomenological treatment of relxation in R(2) has been shown to be equivalent to the assumption of the Lorentzian spectral density function in the relaxatoin theory of PDSD. As this assumption is a poor approximation in real physical systems, the conventional R(2) treatment is likely to carry a significant model error that has not been recognized previously. The relaxation theory of PDSD appears to provide an accurate, parameter-free alternative. Predictions of this theory agreed well with the full quantum mechanical simulations of the R(2) dynamics in the few simple model systems we considered.

Direct observation of transient Ostwald crystallization ordering from racemic serine solutions

The Ostwald rule of stages describes the conjectured transitioning through metastable polymorphic crystal structures during crystallization. Direct observation of the Ostwald rule of stages using was performed using solutions of simple amino acids by second-order nonlinear optical imaging of chiral crystals (SONICC). SONICC, which is based on second-harmonic generation (SHG) imaging, enabled detection of homochiral microcrystals that survived only a few seconds before being converted to the more stable SHG-inactive polymorphic forms.

Effect of hydrostatic pressure on the γ-polymorph of glycine. 1. A polymorphic transition into a new δ-form

The results of a high-resolution powder diffraction study of the effect of high hydrostatic pressure up to 8 GPa on the pure γ-polymorph of glycine (P31) are discussed. A phase transition with a jumpwise change of cell volume and cell parameters was observed. The transition starts at about 2.73 GPa and is still not complete even at 7.85 GPa. The crystal structure of the previously unknown high-pressure polymorph of glycine (δ-polymorph) could be solved and refined in the space group Pn. In this structure, glycine zwitter-ions are linked via NH…O hydrogen bonds into layers, which form double-layered bands via additional NH…O hydrogen bonds. The structure of the individual layers in the high-pressure polymorph is similar to that in the previously known α- (P21/n) and β- (P21) forms, but the packing of the layers is essentially different. The pressure-induced polymorphic transformation in the γ-glycine can be compared with a change in the secondary structure of a peptide, when a helix is transformed into a sheet.

Variable temperature (100—295 K) single-crystal X-ray diffraction study of the α-polymorph of glycylglycine and a glycylglycine hydrate

The crystal structures of theα-polymorph of glycylglycine (glygly) and of its hydrate (glygly × 1.5 H2O) were refined by single-crystal X-ray diffraction at 100, 150, 220, and 295 K (glygly) and at 100, 200, 295 K (glygly × 1.5 H2O). The values of the volume thermal expansions of glygly and its hydrate were shown to be larger than for the three polymorphs of glycine. The anisotropy of strain on cooling was analyzed. Despite a smaller bulk thermal expansion measured for glygly, linear strain (both compression and expansion) along the axes of the strain ellipsoids was larger for the structure of glygly, than for the structure of glygly × 1.5 H2O. The contributions of the distortion of the intermolecular hydrogen bonds and of the conformational changes of the zwitter-ions to the lattice strain are considered.

A comparative study of the anisotropy of lattice strain induced in the crystals of DL-serine by cooling down to 100 K, or by increasing pressure up to 8.6 GPa. A comparison with L-serine

The anisotropy of lattice strain in the crystals of DL-serine (P21/n) on cooling down to 100 K and with increasing hydrostatic pressure up to 8.6 GPa was studied by single-crystal X-ray diffraction. In contrast to L-serine undergoing pressure-induced phase transitions at about 5 and 8 GPa, no phase transitions were observed in DL-serine at least up to 8.6 GPa (the highest pressure reached in the experiment). The anisotropy of strain in DL-serine on cooling was shown to be radically different from that with increasing pressure. The response of the crystal structure of DL-serine to cooling and to increasing pressure was considerably different from that of L-serine.

High-pressure diffraction studies of molecular organic solids. A personal view

This paper discusses the trends in the experimental studies of molecular organic solids at high pressures by diffraction techniques. Crystallization of liquids, crystallization from solutions and solid-state transformations are considered. Special attention is paid to the high-pressure studies of pharmaceuticals and of biomimetics.