Effect of pH on the Surface Layer of Molecular Crystals at the Solid-Liquid Interface.

Dissolution of solid matter into aqueous solution is one of the most challenging physicochemical aspects related to drug development. While influenced by several parameters, the effect of pH remains the most important one to be fully understood. The dissolution process is essentially controlled by activity at the surface of the molecular crystals, which is difficult to characterize experimentally. To address this, a combination of in situ atomic force microscopy (AFM) with molecular dynamics (MD) simulation is reported. AFM allows for direct visualization of the crystal surface of basic and acidic model compounds (carvedilol and ibuprofen) in contact with an aqueous medium with varying pH. A dramatic increase in surface mobility in the solid-liquid interface could be observed experimentally as a function of pH. The in situ AFM approach opens up for a more detailed understanding of the behavior of particulate matter in solution with importance at different levels, ranging from engineering aspects related to crystallization, and biological considerations related to bioavailability of the final drug product.

Macrocycle ring deformation as the secondary design principle for light-harvesting complexes.

Natural light-harvesting is performed by pigment-protein complexes, which collect and funnel the solar energy at the start of photosynthesis. The identity and arrangement of pigments largely define the absorption spectrum of the antenna complex, which is further regulated by a palette of structural factors. Small alterations are induced by pigment-protein interactions. In light-harvesting systems 2 and 3 from Rhodoblastus acidophilus, the pigments are arranged identically, yet the former has an absorption peak at 850 nm that is blue-shifted to 820 nm in the latter. While the shift has previously been attributed to the removal of hydrogen bonds, which brings changes in the acetyl moiety of the bacteriochlorophyll, recent work has shown that other mechanisms are also present. Using computational and modeling tools on the corresponding crystal structures, we reach a different conclusion: The most critical factor for the shift is the curvature of the macrocycle ring. The bending of the planar part of the pigment is identified as the second-most important design principle for the function of pigment-protein complexes-a finding that can inspire the design of novel artificial systems.

Acute response of biochemical bone turnover markers and the associated ground reaction forces to high-impact exercise in postmenopausal women.

The aim of the study was to examine the acute response of biochemical bone turnover markers (BTM) to high-impact jumping exercise, and to quantify the ground reaction forces (GRF) achieved during each jumping exercise, in postmenopausal women. In a randomized controlled cross-over study over three days, 29 postmenopausal women (age (mean±SD): 60.0±5.6 years) were randomly assigned to 6 x 10 repetitions of three different jumps: countermovement jump (CMJ), drop jump (DJ), diagonal drop jump (DDJ). A fourth day without jumping served as a control (CON). Blood samples were collected before (PRE), after (POST), and 2 hours after (2Hr) exercise. Bone turnover was evaluated by bone formation markers (procollagen type-1 amino-terminal propeptide (P1NP) and osteocalcin (OC)) and the bone resorption marker C-terminal telopeptide of type-1 collagen (CTX). Peak anteroposterior (Fx), mediolateral (Fy), and vertical (Fz) GRF were measured using a force platform. From PRE to POST, P1NP increased (p<0.01) by 7.7±1.8%, 9.4±1.3%, and 10.6±1.6% for CMJ, DJ, and DDJ, which were higher (p<0.01) than CON. OC increased (p<0.05) by 5.5±1.8% for DJ, which was higher (p<0.05) than CON. CTX was not significantly changed at POST. There were no significant differences in BTM Δ-values between the jumps at any time point. For the CMJ, the combined three-axis peak GRF was positively associated with the PRE to POST Δ-change in P1NP (r=0.71, p<0.05). The acute, jumping-induced increase in P1NP and OC without any rise in CTX may indicate increased bone formation. Moreover, the study shows a dose-response relationship between GRF and the acute P1NP response after countermovement jumps.

Quantum Crystallography: Current Developments and Future Perspectives.

Crystallography and quantum mechanics have always been tightly connected because reliable quantum mechanical models are needed to determine crystal structures. Due to this natural synergy, nowadays accurate distributions of electrons in space can be obtained from diffraction and scattering experiments. In the original definition of quantum crystallography (QCr) given by Massa, Karle and Huang, direct extraction of wavefunctions or density matrices from measured intensities of reflections or, conversely, ad hoc quantum mechanical calculations to enhance the accuracy of the crystallographic refinement are implicated. Nevertheless, many other active and emerging research areas involving quantum mechanics and scattering experiments are not covered by the original definition although they enable to observe and explain quantum phenomena as accurately and successfully as the original strategies. Therefore, we give an overview over current research that is related to a broader notion of QCr, and discuss options how QCr can evolve to become a complete and independent domain of natural sciences. The goal of this paper is to initiate discussions around QCr, but not to find a final definition of the field.

Diversity-Oriented Syntheses by Combining CuAAC and Stereoselective INCIC Reactions with Peptides.

Cascade reactions proceeding through peptide-derived N-carbamoyl iminium ions are reported. Two new reactions of N-carbamoyl iminium ions are described, including a stereoselective double cyclization generating N,N'-aminals and an acid-promoted auto-oxidation. Mechanistic investigations revealed that the N,N'-aminal formation is reversible under strongly acidic conditions. Both of these new reactions proved to be completely orthogonal to subsequent CuAAC chemistry. The reactions were performed in solution and on solid support. The robustness and high stereoselectivity of the methodology holds great promise for applications in parallel diversity-oriented synthesis and in combinatorial synthesis for drug screening.

Synthesis and structures of N-alkyl-1,13-dimethoxychromeno- [2,3,4-kl]acridinium salts: the missing azaoxa[4]helicenium.

Helical structures are interesting due to their inherent chirality. Helicenium ions are triarylmethylium structures twisted into configurationally stable helicenes through the introduction of two heteroatom bridges between the three aryl substituents. Of the configurationally stable [4]helicenium ions, derivatives with sulfur, oxygen and nitrogen bridges have already been synthesised. However, one [4]helicenium ion has proven elusive, until now. We present herein the first synthesis of the 1,13-dimethoxychromeno[2,3,4-kl]acridinium (DMCA(+)) [4]helicenium ion. A series of six differently N-substituted DMCA(+) ions as their hexafluorophosphate salts are reported. Their cation stability was evaluated and it was found that DMCA(+) is ideally suited as a phase-transfer catalyst with a pKR+ of 13.0. The selectivity of nucleophilic addition to the central carbon atom of DMCA(+) has been demonstrated with diastereotopic ratios of up to 1:10. The single-crystal structures of several of the DMCA(+) salts were determined, and structural differences between N-aryl- and N-alkyl-substituted cations were observed. The results of a comparative study of the photophysics of the [4]helicenium ions are presented. DMCA(+) is found to be a potent red-emitting dye with a fluorescence quantum yield of 20 % in apolar solvents and a fluorescence lifetime of 12 ns. [4]Helicenium ions, including DMCA(+), all suffer from solvent-induced quenching, which reduces the fluorescence quantum yields significantly (ϕfl < 5 %) in polar solvents. A difference in photophysical properties is observed between N-aryl- and N-alkyl-substituted DMCA(+), which has tentatively been attributed to a difference in molecular conformation.

PhAI: A deep-learning approach to solve the crystallographic phase problem.

X-ray crystallography provides a distinctive view on the three-dimensional structure of crystals. To reconstruct the electron density map, the complex structure factors [Formula: see text] of a sufficiently large number of diffracted reflections must be known. In a conventional experiment, only the amplitudes [Formula: see text] are obtained, and the phases ϕ are lost. This is the crystallographic phase problem. In this work, we show that a neural network, trained on millions of artificial structure data, can solve the phase problem at a resolution of only 2 angstroms, using only 10 to 20% of the data needed for direct methods. The network works in common space groups and for modest unit-cell dimensions and suggests that neural networks could be used to solve the phase problem in the general case for weakly scattering crystals.

Different or the same? exploring the physicochemical properties and molecular mobility of celecoxib amorphous forms.

The influence of different preparation methods on the physicochemical properties of amorphous solid forms have gained considerable attention, especially with recent publications on pharmaceutical polyamorphism. In the present study, we have investigated the possible occurrence of polyamorphism in the drug celecoxib (CEL) by investigating the thermal behavior, morphology, structure, molecular mobility and physical stability of amorphous CEL obtained by quench-cooling (QC), ball milling (BM) and spray drying (SD). Similar glass transition temperatures but different recrystallization behaviors were observed for CEL-QC, CEL-BM and CEL-SD using modulated differential scanning calorimetry analysis. A correlation between the different recrystallization behaviors of the three CEL amorphous forms and the respective distinct powder morphologies, was also found. Molecular dynamics simulations however, reveal that CEL presents similar molecular conformational distributions when subjected to QC and SD. Moreover, the obtained molecular conformational distributions of CEL are different from the ones found in its crystal structure and also from the ones found in the lowest-energy structure obtained by quantum mechanical calculations. The type and strength of CEL hydrogen bond interactions found in CEL-QC and CEL-SD systems are almost identical, though different from the ones presented in the crystal structure. Pair distribution function analyses and isothermal microcalorimetry show similar local structures and structural relaxation times, respectively, for CEL-QC, CEL-BM and CEL-SD. The present work shows that not only similar physicochemical properties (glass transition temperature, and structural relaxation time), but also similar molecular conformational distributions were observed for all prepared CEL amorphous systems. Hence, despite their different recrystallization behaviors, the three amorphous forms of CEL did not show any signs of polyamorphism.

Atomic structures of amyloid cross-beta spines reveal varied steric zippers.

Amyloid fibrils formed from different proteins, each associated with a particular disease, contain a common cross-beta spine. The atomic architecture of a spine, from the fibril-forming segment GNNQQNY of the yeast prion protein Sup35, was recently revealed by X-ray microcrystallography. It is a pair of beta-sheets, with the facing side chains of the two sheets interdigitated in a dry 'steric zipper'. Here we report some 30 other segments from fibril-forming proteins that form amyloid-like fibrils, microcrystals, or usually both. These include segments from the Alzheimer's amyloid-beta and tau proteins, the PrP prion protein, insulin, islet amyloid polypeptide (IAPP), lysozyme, myoglobin, alpha-synuclein and beta(2)-microglobulin, suggesting that common structural features are shared by amyloid diseases at the molecular level. Structures of 13 of these microcrystals all reveal steric zippers, but with variations that expand the range of atomic architectures for amyloid-like fibrils and offer an atomic-level hypothesis for the basis of prion strains.

Unveiling polyamorphism and polyamorphic interconversions in pharmaceuticals: the peculiar case of hydrochlorothiazide.

Polyamorphism has been a controversial and highly debated solid-state phenomenon in both material and pharmaceutical communities. Although some evidence of this fascinating phenomenon has been reported for several inorganic systems, and more recently also for a few organic compounds, the occurrence of polyamorphism is poorly understood and the molecular-level organization of polyamorphic forms is still unknown. Here we have investigated the occurrence of polyamorphism and polyamorphic interconversions in hydrochlorothiazide (HCT), using both experimental and computational methods. Three distinct HCT polyamorphs, presenting distinct physical and thermal stabilities as well as distinct relaxation properties, were systematically prepared using spray-drying (SD), quench-cooling (QC) and ball milling (BM) methods. HCT polyamorph II (obtained by QC) was found to be more physically stable than polyamorphs I and III (obtained by SD and BM, respectively). Furthermore, polyamorphs I and III could be converted into polyamorph II after QC, while polyamorph II did not convert to any other polyamorph after SD or BM. Molecular dynamics simulations show that HCT dihedral angle distributions are significantly different for polyamorphs I and II, which is postulated as a possible explanation for their different physicochemical properties.

Structure of the cross-beta spine of amyloid-like fibrils.

Numerous soluble proteins convert to insoluble amyloid-like fibrils that have common properties. Amyloid fibrils are associated with fatal diseases such as Alzheimer's, and amyloid-like fibrils can be formed in vitro. For the yeast protein Sup35, conversion to amyloid-like fibrils is associated with a transmissible infection akin to that caused by mammalian prions. A seven-residue peptide segment from Sup35 forms amyloid-like fibrils and closely related microcrystals, from which we have determined the atomic structure of the cross-beta spine. It is a double beta-sheet, with each sheet formed from parallel segments stacked in register. Side chains protruding from the two sheets form a dry, tightly self-complementing steric zipper, bonding the sheets. Within each sheet, every segment is bound to its two neighbouring segments through stacks of both backbone and side-chain hydrogen bonds. The structure illuminates the stability of amyloid fibrils, their self-seeding characteristic and their tendency to form polymorphic structures.

Theoretically derived thermodynamic properties can be improved by the refinement of low-frequency modes against X-ray diffraction data.

Herein, a framework for the estimation of the thermodynamic properties of molecular crystals via the refinement of frequencies from density functional theory calculations against X-ray diffraction data is presented. The framework provides an efficient approach to including the contribution of acoustic modes in the thermodynamic properties. The obtained heat capacities for urea, the α- and ß-glycine polymorphs, benzoic acid, and 4'-hydroxyacetophenone are in good agreement with those from adiabatic calorimetry.

Crystal structure and optical properties of a two-sited EuIII compound: an EuIII ion coordinated by two [EuIII(DOTA)]- complexes (DOTA is 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetate).

The structure and solid-state luminescence properties of an EuIII compound with two different lanthanide sites, [Eu(µ-O)5(OH)(H2O)2][Eu(DOTA)(H2O)]2 (DOTA is 1,4,7,10-tetrazacyclododecane-1,4,7,10-tetraacetate, C16H24N4O8), were determined. The compound crystallizes in a laminar structure in the triclinic space group P-1, where the two sites are a free europium(III) ion and an [Eu(DOTA)(H2O)]- complex. The crystal structure was determined using complex data treatment due to nonmerohedral twinning. Experimental data sets were recorded with large redundancy and separated according to scattering domains in order to obtain a reliable structure. In the first site, the [Eu(DOTA)(H2O)]- complex was found to adopt a capped twisted square-antiprismatic (cTSAP) conformation, where a capping water molecule increased the coordination number of the europium(III) site to nine (CN = 9). In the second site, the europium(III) ion was found to be coordinated by two water molecules, one hydroxide group and five oxide groups from neighbouring [Eu(DOTA)(H2O)]- complexes. The coordination geometry of this site was found to be a compressed square antiprism (SAP) and the coordination number of the europium(III) ion was found to be eight (CN = 8). A large increase in the rate constant of luminescence was observed for EuIII in [Eu(DOTA)(H2O)]- in solid-state luminescence spectroscopy measurements compared to in solution, which led to investigations of single crystals in deuterated media to exclude additional effects of quenching. We conclude that the most probable cause of the decrease in the observed luminescence lifetimes is the high asymmetry of the coordination environment of [Eu(DOTA)(D2O)]- in the [Eu(µ-O)5(OD)(D2O)2][Eu(DOTA)(D2O)]2 crystals.

A combined model of electron density and lattice dynamics refined against elastic diffraction data. Thermodynamic properties of crystalline L-alanine.

Thermodynamic stability is an essential property of crystalline materials, and its accurate calculation requires a reliable description of the thermal motion - phonons - in the crystal. Such information can be obtained from periodic density functional theory (DFT) calculations, but these are costly and in some cases insufficiently accurate for molecular crystals. This deficiency is addressed here by refining a lattice-dynamics model, derived from DFT calculations, against accurate high-resolution X-ray diffraction data. For the first time, a normal-mode refinement is combined with the refinement of aspherical atomic form factors, allowing a comprehensive description and physically meaningful deconvolution of thermal motion and static charge density in the crystal. The small and well diffracting L-alanine system was used. Different lattice-dynamics models, with or without phonon dispersion, and derived from different levels of theory, were tested, and models using spherical and aspherical form factors were compared. The refinements indicate that the vibrational information content in the 23 K data is too small to study lattice dynamics, whereas the 123 K data appear to hold information on the acoustic and lowest-frequency optical phonons. These normal-mode models show slightly larger refinement residuals than their counterparts using atomic displacement parameters, and these features are not removed by considering phonon dispersion in the model. The models refined against the 123 K data, regardless of their sophistication, give calculated heat capacities for L-alanine within less than 1 cal mol-1 K-1 of the calorimetric measurements, in the temperature range 10-300 K. The findings show that the normal-mode refinement method can be combined with an elaborate description of the electron density. It appears to be a promising technique for free-energy determination for crystalline materials at the expense of performing a single-crystal elastic X-ray diffraction determination combined with periodic DFT calculations.

Synthesis and characterization of tetrathiafulvalene-substituted di- and tetraethynylethenes with p-nitrophenyl acceptors.

Novel di- and tetraethynylethene (DEE and TEE) compounds functionalized with tetrathiafulvalene (TTF) donor groups and p-nitrophenyl acceptor groups were synthesized by palladium-catalyzed cross-coupling reactions under various conditions. The molecules are strong chromophores and were investigated for their optical properties. Placement of two TTFs and two p-nitrophenyls about a central TEE core provides a molecule with a high third-order optical nonlinearity. The molecules experience reversible oxidations of the TTF units, and the optical properties of the oxidized species were elucidated by spectroelectrochemistry. The degree of quinoid character of the p-nitrophenyl in the molecules was determined by X-ray crystallography.

Heterogeneous nucleation of polymorphs on polymer surfaces: polymer-molecule interactions using a Coulomb and van der Waals model.

The nucleation processes of acetaminophen on poly(methyl methacrylate) and poly(vinyl acetate) have been investigated and the mechanisms of the processes are studied. This is achieved by a combination of theoretical models and computational investigations within the framework of a modified QM/MM method; a Coulomb-van der Waals model. We have combined quantum mechanical computations and electrostatic models at the atomistic level for investigating the stability of different orientations of acetaminophen on the polymer surfaces. Based on the Coulomb-van der Waals model, we have determined the most stable orientation to be a flat orientation, and the strongest interaction is seen between poly(vinyl acetate) and the molecule in a flat orientation in vacuum.

Heterogeneous nucleation of polymorphs on polymer surfaces: polymer-molecule interactions using a heterogeneous dielectric solvation model.

We have investigated the mechanism of the nucleation of acetaminophen on poly(methyl-methacrylate) and poly(vinyl-acetate) utilizing a combination of quantum mechanical computations and electrostatic models. We have used a heterogeneous dielectric solvation model to determine the stability of different orientations of acetaminophen on polymer surfaces. We find that for the nucleation of acetaminophen on the polymer surfaces in vacuum, the most stable orientation is a flat orientation. For the nucleation process in solution where acetaminophen and the polymer surface are surrounded by a solvent, we find that the heterogeneous dielectric solvation model predicts that a sideways orientation is the most stable orientation.

Dynamic quantum crystallography: lattice-dynamical models refined against diffraction data. II. Applications to L-alanine, naphthalene and xylitol.

In the first paper of this series [Hoser & Madsen (2016). Acta Cryst. A72, 206-214], a new approach was introduced which enables the refinement of frequencies of normal modes obtained from ab initio periodic computations against single-crystal diffraction data. In this contribution, the performance of this approach is tested by refinement against data in the temperature range from 23 to 205 K on the molecular crystals of L-alanine, naphthalene and xylitol. The models, which are lattice-dynamical models derived at the Γ point of the Brillouin zone, are able to describe the atomic vibrations of L-alanine and naphthalene to a level where the residual densities are similar to those obtained from the independent atom model. For the more flexible molecule xylitol, larger deviations are found. Hydrogen ADPs (anisotropic displacement parameters) derived from the models are in similar or better agreement with neutron diffraction results than ADPs obtained by other procedures. The heat capacity calculated after normal mode refinement for naphthalene is in reasonable agreement with the heat capacity obtained from calorimetric measurements (to less than 1 cal mol-1 K-1 below 300 K), with deviations at higher temperatures indicating anharmonicity. Standard uncertainties and correlation of the refined parameters have been derived based on a Monte Carlo procedure. The uncertainties are quite small and probably underestimated.

Dynamic quantum crystallography: lattice-dynamical models refined against diffraction data. I. Theory.

This study demonstrates and tests the refinement of a lattice-dynamical model derived from periodic ab initio calculations at the Γ point against elastic diffraction data (X-ray or neutron). Refinement of only a handful of parameters is sufficient to obtain a similar agreement with the data as the conventional crystallographic model using anisotropic displacement parameters. By refinement against X-ray data, H displacement parameters are obtained which compare favourably with those from neutron diffraction experiments. The approach opens the door for evaluating thermodynamic properties, and for refinement against multi-temperature data, against inelastic diffraction data, spectroscopic information and thermal diffuse scattering data.

Superarming of glycosyl donors by combined neighboring and conformational effects.

A novel glycosyl donor that combines the concepts of both conformational and electronic superarming has been synthesized. The reactivity and selectivity of the donor have been tested in competition experiments.