Mercury 4.0: from visualization to analysis, design and prediction.

The program Mercury, developed at the Cambridge Crystallographic Data Centre, was originally designed primarily as a crystal structure visualization tool. Over the years the fields and scientific communities of chemical crystallography and crystal engineering have developed to require more advanced structural analysis software. Mercury has evolved alongside these scientific communities and is now a powerful analysis, design and prediction platform which goes a lot further than simple structure visualization.

Core level spectroscopies locate hydrogen in the proton transfer pathway - identifying quasi-symmetrical hydrogen bonds in the solid state.

Short, strong hydrogen bonds (SSHBs) have been a source of interest and considerable speculation over recent years, culminating with those where hydrogen resides around the midpoint between the donor and acceptor atoms, leading to quasi-covalent nature. We demonstrate that X-ray photoelectron spectroscopy (XPS) and near-edge X-ray absorption fine structure (NEXAFS) spectroscopy provide deep insight into the electronic structure of the short OHN hydrogen bond of 3,5-pyridinedicarboxylic acid, revealing for the first time distinctive spectroscopic identifiers for these quasi-symmetrical hydrogen bonds. An intermediate nitrogen (core level) chemical shift occurs for the almost centrally located hydrogen compared to protonated (ionic) and non-ionic analogues, and it reveals the absence of two-site disorder. This type of bonding is also evident through broadening of the nitrogen 1s photoemission and 1s → 1π* peaks in XPS and NEXAFS, respectively, arising from the femtosecond lifetimes of hydrogen in the potential wells slightly offset to either side of the centre. The line-shape of the core level excitations are thus related to the population occupancies, reflecting the temperature-dependent shape of the hydrogen potential energy well. Both XPS and NEXAFS provide a distinctive identifier for these quasi-symmetrical hydrogen bonds, paving the way for detailed studies into their prevalence and potentially unique physical and chemical properties.

In Situ Solid-State Reactions Monitored by X-ray Absorption Spectroscopy: Temperature-Induced Proton Transfer Leads to Chemical Shifts.

The dramatic colour and phase alteration with the solid-state, temperature-dependent reaction between squaric acid and 4,4'-bipyridine has been probed in situ with X-ray absorption spectroscopy. The electronic and chemical sensitivity to the local atomic environment through chemical shifts in the near-edge X-ray absorption fine structure (NEXAFS) revealed proton transfer from the acid to the bipyridine base through the change in nitrogen protonation state in the high-temperature form. Direct detection of proton transfer coupled with structural analysis elucidates the nature of the solid-state process, with intermolecular proton transfer occurring along an acid-base chain followed by a domino effect to the subsequent acid-base chains, leading to the rapid migration along the length of the crystal. NEXAFS thereby conveys the ability to monitor the nature of solid-state chemical reactions in situ, without the need for a priori information or long-range order.

NEXAFS Sensitivity to Bond Lengths in Complex Molecular Materials: A Study of Crystalline Saccharides.

Detailed analysis of the C K near-edge X-ray absorption fine structure (NEXAFS) spectra of a series of saccharides (fructose, xylose, glucose, galactose, maltose monohydrate, α-lactose monohydrate, anhydrous ß-lactose, cellulose) indicates that the precise determination of IPs and σ* shape resonance energies is sensitive enough to distinguish different crystalline saccharides through the variations in their average C-OH bond lengths. Experimental data as well as FEFF8 calculations confirm that bond length variations in the organic solid state of 10(-2) Å can be experimentally detected, opening up the possibility to use NEXAFS for obtaining incisive structural information for molecular materials, including noncrystalline systems without long-range order such as dissolved species in solutions, colloids, melts, and similar amorphous phases. The observed bond length sensitivity is as good as that originally reported for gas-phase and adsorbed molecular species. NEXAFS-derived molecular structure data for the condensed phase may therefore be used to guide molecular modeling as well as to validate computationally derived structure models for such systems. Some results indicate further analytical value in that the σ* shape resonance analysis may distinguish hemiketals from hemiacetals (i.e., derived from ketoses and aldoses) as well as α from ß forms of otherwise identical saccharides.

Intermolecular bonding of hemin in solution and in solid state probed by N K-edge X-ray spectroscopies.

X-ray absorption/emission spectroscopy (XAS/XES) at the N K-edge of iron protoporphyrin IX chloride (FePPIX-Cl, or hemin) has been carried out for dissolved monomers in DMSO, dimers in water and for the solid state. This sequence of samples permits identification of characteristic spectral features associated with the hemin intermolecular bonding. These characteristic features are further analyzed and understood at the molecular orbital (MO) level based on the DFT calculations.

Chemical Speciation and Bond Lengths of Organic Solutes by Core-Level Spectroscopy: pH and Solvent Influence on p-Aminobenzoic Acid.

Through X-ray absorption and emission spectroscopies, the chemical, electronic and structural properties of organic species in solution can be observed. Near-edge X-ray absorption fine structure (NEXAFS) and resonant inelastic X-ray scattering (RIXS) measurements at the nitrogen K-edge of para-aminobenzoic acid reveal both pH- and solvent-dependent variations in the ionisation potential (IP), 1s→π* resonances and HOMO-LUMO gap. These changes unequivocally identify the chemical species (neutral, cationic or anionic) present in solution. It is shown how this incisive chemical state sensitivity is further enhanced by the possibility of quantitative bond length determination, based on the analysis of chemical shifts in IPs and σ* shape resonances in the NEXAFS spectra. This provides experimental access to detecting even minor variations in the molecular structure of solutes in solution, thereby providing an avenue to examining computational predictions of solute properties and solute-solvent interactions.

Incisive probing of intermolecular interactions in molecular crystals: core level spectroscopy combined with density functional theory.

The α-form of crystalline para-aminobenzoic acid (PABA) has been examined as a model system for demonstrating how the core level spectroscopies X-ray photoelectron spectroscopy (XPS) and near-edge X-ray absorption fine-structure (NEXAFS) can be combined with CASTEP density functional theory (DFT) to provide reliable modeling of intermolecular bonding in organic molecular crystals. Through its dependence on unoccupied valence states NEXAFS is an extremely sensitive probe of variations in intermolecular bonding. Prediction of NEXAFS spectra by CASTEP, in combination with core level shifts predicted by WIEN2K, reproduced experimentally observed data very well when all significant intermolecular interactions were correctly taken into account. CASTEP-predicted NEXAFS spectra for the crystalline state were compared with those for an isolated PABA monomer to examine the impact of intermolecular interactions and local environment in the solid state. The effects of the loss of hydrogen-bonding in carboxylic acid dimers and intermolecular hydrogen bonding between amino and carboxylic acid moieties are evident, with energy shifts and intensity variations of NEXAFS features arising from the associated differences in electronic structure and bonding.

Proton transfer and hydrogen bonding in the organic solid state: a combined XRD/XPS/ssNMR study of 17 organic acid-base complexes.

The properties of nitrogen centres acting either as hydrogen-bond or Brønsted acceptors in solid molecular acid-base complexes have been probed by N 1s X-ray photoelectron spectroscopy (XPS) as well as (15)N solid-state nuclear magnetic resonance (ssNMR) spectroscopy and are interpreted with reference to local crystallographic structure information provided by X-ray diffraction (XRD). We have previously shown that the strong chemical shift of the N 1s binding energy associated with the protonation of nitrogen centres unequivocally distinguishes protonated (salt) from hydrogen-bonded (co-crystal) nitrogen species. This result is further supported by significant ssNMR shifts to low frequency, which occur with proton transfer from the acid to the base component. Generally, only minor chemical shifts occur upon co-crystal formation, unless a strong hydrogen bond is formed. CASTEP density functional theory (DFT) calculations of (15)N ssNMR isotropic chemical shifts correlate well with the experimental data, confirming that computational predictions of H-bond strengths and associated ssNMR chemical shifts allow the identification of salt and co-crystal structures (NMR crystallography). The excellent agreement between the conclusions drawn by XPS and the combined CASTEP/ssNMR investigations opens up a reliable avenue for local structure characterization in molecular systems even in the absence of crystal structure information, for example for non-crystalline or amorphous matter. The range of 17 different systems investigated in this study demonstrates the generic nature of this approach, which will be applicable to many other molecular materials in organic, physical, and materials chemistry.

Crystallography aided by atomic core-level binding energies: proton transfer versus hydrogen bonding in organic crystal structures.

Ionic bond or hydrogen bridge? Brønsted proton transfer to nitrogen acceptors in organic crystals causes strong N1s core-level binding energy shifts. A study of 15 organic cocrystal and salt systems shows that standard X-ray photoelectron spectroscopy (XPS) can be used as a complementary method to X-ray crystallography for distinguishing proton transfer from H-bonding in organic condensed matter.

Detection of free base surface enrichment of a pharmaceutical salt by X-ray photoelectron spectroscopy (XPS).

Yellow discoloration was observed at the surface of normally white crystals of a development pharmaceutical fumarate salt, tentatively ascribed to the presence of trace amounts of free base. The impact of impurities on sample properties and behavior can be significant, especially if localized at the surface. No conventional bulk analytical technique could readily provide an explanation for the yellow color, so a surface-sensitive technique, X-ray photoelectron spectroscopy (XPS), was employed to characterize the salt. XPS reveals the presence of free base at the surface through the HN(+)/N ratio. A free radical decarboxylation mechanism is proposed to account for the alterations observed with extended irradiation. The lower intensity carboxyl signal and significantly lower HN(+)/N ratio for the yellow surface samples reveal a higher level of free base at the surface than the white samples. The samples with yellow surfaces could not be successfully milled, which was an important part of the production process for providing material of the required physical quality for product formulation. Identification of residual free base at the surface of the crystalline material, by XPS, was significant for optimization of the crystallization process to yield material of required quality for successful milling at plant scale.

Identification of protonation state by XPS, solid-state NMR, and DFT: characterization of the nature of a new theophylline complex by experimental and computational methods.

Recent studies suggested that X-ray photoelectron spectroscopy (XPS) sensitively determines the protonation state of nitrogen functional groups in the solid state, providing a means for distinguishing between co-crystals and salts of organic compounds. Here we describe how a new theophylline complex with 5-sulfosalicylic acid dihydrate was established as a salt by XPS prior to assignment with conventional methods. The presence of a C=NH(+) (N9) N1s peak in XPS allows assignment as a salt, while this peak is clearly absent for a theophylline co-crystal. The large low frequency shift for N9 observed by (15)N solid-state nuclear magnetic resonance spectroscopy (ssNMR) and corresponding density functional theory (DFT) calculations confirm that protonation has occurred. The crystal structure and further analytical studies confirm the conclusions reached with XPS and ssNMR. This study demonstrates XPS as an alternative technique for determining whether proton transfer has occurred in acid-base complexes.

Salt or co-crystal? Determination of protonation state by X-ray photoelectron spectroscopy (XPS).

Combined (15)N ssNMR and X-ray photoelectron spectroscopy (XPS) investigations for theophylline, a theophylline co-crystal, and a theophyllinium salt demonstrate that XPS allows direct observation of the degree of proton transfer, and thus identification of whether a salt or a co-crystal has been formed. The presence of a strongly binding-energy-shifted N 1s XPS peak with protonation indicates a salt (C==NH(+)), while this peak is unmistakably absent in the co-crystal. XPS should be considered as an alternative and complementary technique to single crystal X-ray diffraction and solid-state nuclear magnetic resonance spectroscopy (ssNMR).