Liposomal Copermeation Assay Reveals Unexpected Membrane Interactions of Commonly Prescribed Drugs.

The permeation of small molecules across biological membranes is a crucial process that lies at the heart of life. Permeation is involved not only in the maintenance of homeostasis at the cell level but also in the absorption and biodistribution of pharmacologically active substances throughout the human body. Membranes are formed by phospholipid bilayers that represent an energy barrier for permeating molecules. Crossing this energy barrier is assumed to be a singular event, and permeation has traditionally been described as a first-order kinetic process, proportional only to the concentration gradient of the permeating substance. For a given membrane composition, permeability was believed to be a unique property dependent only on the permeating molecule itself. We provide experimental evidence that this long-held view might not be entirely correct. Liposomes were used in copermeation experiments with a fluorescent probe, where simultaneous permeation of two substances occurred over a single phospholipid bilayer. Using an assay of six commonly prescribed drugs, we have found that the presence of a copermeant can either enhance or suppress the permeation rate of the probe molecule, often more than 2-fold in each direction. This can have significant consequences for the pharmacokinetics and bioavailability of commonly prescribed drugs when used in combination and provide new insight into so-far unexplained drug-drug interactions as well as changing the perspective on how new drug candidates are evaluated and tested.

Lewis Acidic Aluminosilicates: Synthesis, 27Al MQ/MAS NMR, and DFT-Calculated 27Al NMR Parameters.

Porous aluminosilicates are functional materials of paramount importance as Lewis acid catalysts in the synthetic industry, yet the participating aluminum species remain poorly studied. Herein, a series of model aluminosilicate networks containing [L-AlO3] (L = THF, Et3N, pyridine, triethylphosphine oxide (TEPO)) and [AlO4]- centers were prepared through nonhydrolytic sol-gel condensation reactions of the spherosilicate building block (Me3Sn)8Si8O20 with L-AlX3 (X = Cl, Me, Et) and [Me4N] [AlCl4] compounds in THF or toluene. The substoichiometric dosage of the Al precursors ensured complete condensation and uniform incorporation, with the bulky spherosilicate forcing a separation between neighboring aluminum centers. The materials were characterized by 1H, 13C, 27Al, 29Si, and 31P MAS NMR and FTIR spectroscopies, ICP-OES, gravimetry, and N2 adsorption porosimetry. The resulting aluminum centers were resolved by 27Al TQ/MAS NMR techniques and assigned based on their spectroscopic parameters obtained by peak fitting (δiso, CQ, η) and their correspondence to the values calculated on model structures by DFT methods. A clear correlation between the decrease in the symmetry of the Al centers and the increase of the observed CQ was established with values spanning from 4.4 MHz for distorted [AlO4]- to 15.1 MHz for [THF-AlO3]. Products containing exclusively [TEPO-AlO3] or [AlO4]- centers could be obtained (single-site materials). For L = THF, Et3N, and pyridine, the [AlO4]- centers were formed together with the expected [L-AlO3] species, and a viable mechanism for the unexpected emergence of [AlO4]- was proposed.

Reliable Dimerization Energies for Modeling of Supramolecular Junctions.

Accurate estimates of intermolecular interaction energy, ΔE, are crucial for modeling the properties of organic electronic materials and many other systems. For a diverse set of 50 dimers comprising up to 50 atoms (Set50-50, with 7 of its members being models of single-stacking junctions), benchmark ΔE data were compiled. They were obtained by the focal-point strategy, which involves computations using the canonical variant of the coupled cluster theory with singles, doubles, and perturbative triples [CCSD(T)] performed while applying a large basis set, along with extrapolations of the respective energy components to the complete basis set (CBS) limit. The resulting ΔE data were used to gauge the performance for the Set50-50 of several density-functional theory (DFT)-based approaches, and of one of the localized variants of the CCSD(T) method. This evaluation revealed that (1) the proposed "silver standard" approach, which employs the localized CCSD(T) method and CBS extrapolations, can be expected to provide accuracy better than two kJ/mol for absolute values of ΔE, and (2) from among the DFT techniques, computationally by far the cheapest approach (termed "ωB97X-3c/vDZP" by its authors) performed remarkably well. These findings are directly applicable in cost-effective yet reliable searches of the potential energy surfaces of noncovalent complexes.

Simple Route to [PSH][B9H14] and a Contemporary Study of Its Solid-State Dynamic Behavior.

The 1,8-bis(dimethylamino)naphthalenium ([PSH]+) decaborane salt, [PSH][B10H13], has been found to react in ethanol to form [PSH][B9H14] (1), affording a simple route to the synthesis of the arachno-nonaborate anion. This new polyhedral salt is characterized by NMR spectroscopy and X-ray diffraction. The measurement of diffusion coefficients by NMR methods demonstrates that the [PSH]+ cation and the [B9H14]- anion form ion pairs in a non-coordinating solvent such as CH2Cl2, whereas in CD3CN the formation of ion pairs was not observed. Insights into the long-known low-energy dynamic behavior, which involves the bridging and endo-terminal hydrogen atoms, are elucidated using DFT calculations. Salts [PSH][B9H14] (1) and [PSH][B9H14]·0.5CHCl3 (solvated, 1·0.5CHCl3) have also been studied by X-ray diffraction analysis. A solid-state NMR study has demonstrated that K[B9H14] and [PSH][B9H14] (1) undergo significantly different motion regimes, being a low-energy, weakly temperature-dependent process for 1, which may be ascribed to some type of low-amplitude reorientation of the whole boron cages. This process may be the mechanism for the low- to-room-temperature order-disorder hidden transition found by X-ray analysis.

On the Intermolecular Interactions in Thiophene-Cored Single-Stacking Junctions.

There have been attempts, both experimental and based on density-functional theory (DFT) modeling, at understanding the factors that govern the electronic conductance behavior of single-stacking junctions formed by pi-conjugated materials in nanogaps. Here, a reliable description of relevant stacked configurations of some thiophene-cored systems is provided by means of high-level quantum chemical approaches. The minimal structures of these configurations, which are found using the dispersion-corrected DFT approach, are employed in calculations that apply the coupled cluster method with singles, doubles and perturbative triples [CCSD(T)] and extrapolations to the complete basis set (CBS) limit in order to reliably quantify the strength of intermolecular binding, while their physical origin is investigated using the DFT-based symmetry-adapted perturbation theory (SAPT) of intermolecular interactions. In particular, for symmetrized S-Tn dimers (where "S" and "T" denote a thiomethyl-containing anchor group and a thiophene segment comprising "n" units, respectively), the CCSD(T)/CBS interaction energies are found to increase linearly with n ≤ 6, and significant conformational differences between the flanking 2-thiophene group in S-T1 and S-T2 are described by the CCSD(T)/CBS and SAPT/CBS computations. These results are put into the context of previous work on charge transport properties of S-Tn and other types of supramolecular junctions.

Quantifying the Intrinsic Strength of C-H⋯O Intermolecular Interactions.

It has been recognized that the C-H⋯O structural motif can be present in destabilizing as well as highly stabilizing intermolecular environments. Thus, it should be of interest to describe the strength of the C-H⋯O hydrogen bond for constant structural factors so that this intrinsic strength can be quantified and compared to other types of interactions. This description is provided here for C2h-symmetric dimers of acrylic acid by means of the calculations that employ the coupled-cluster theory with singles, doubles, and perturbative triples [CCSD(T)] together with an extrapolation to the complete basis set (CBS) limit. Dimers featuring the C-H⋯O and O-H⋯O hydrogens bonds are carefully investigated in a wide range of intermolecular separations by the CCSD(T)/CBS approach, and also by the symmetry-adapted perturbation theory (SAPT) method, which is based on the density-functional theory (DFT) treatment of monomers. While the nature of these two types of hydrogen bonding is very similar according to the SAPT-DFT/CBS calculations and on the basis of a comparison of the intermolecular potential curves, the intrinsic strength of the C-H⋯O interaction is found to be about a quarter of its O-H⋯O counterpart that is less than one might anticipate.

Anisotropy, segmental dynamics and polymorphism of crystalline biogenic carboxylic acids.

Carboxylic acids of the Krebs cycle possess invaluable biochemical significance. Still, there are severe gaps in the availability of thermodynamic and crystallographic data, as well as ambiguities prevailing in the literature on the thermodynamic characterization and polymorph ranking. Providing an unambiguous description of the structure, thermodynamics and polymorphism of their neat crystalline phases requires a complex multidisciplinary approach. This work presents results of an extensive investigation of the structural anisotropy of the thermal expansion and local dynamics within these crystals, obtained from a beneficial cooperation of NMR crystallography and ab initio calculations of non-covalent interactions. The observed structural anisotropy and spin-lattice relaxation times are traced to large spatial variations in the strength of molecular interactions in the crystal lattice, especially in the orientation of the hydrogen bonds. A completely resolved crystal structure for oxaloacetic acid is reported for the first time. Thanks to multi-instrumental calorimetric effort, this work clarifies phase behavior, determines third-law entropies of the crystals, and states definitive polymorph ranking for succinic and fumaric acids. These thermodynamic observations are then interpreted in terms of first-principles quasi-harmonic calculations of cohesive properties. A sophisticated model capturing electronic, thermal, and configurational-entropic effects on the crystal structure approaches captures the subtle Gibbs energy differences governing polymorph ranking for succinic and fumaric acids, representing another success story of computational chemistry.

A computational inspection of the dissociation energy of mid-sized organic dimers.

The gas-phase value of the dissociation energy (D0) is a key parameter employed in both experimental and theoretical descriptions of noncovalent complexes. The D0 data were obtained for a set of mid-sized organic dimers in their global minima which was located using geometry optimizations that applied ample basis sets together with either the conventional second-order Møller-Plesset (MP2) method or several dispersion-corrected density-functional theory (DFT-D) schemes. The harmonic vibrational zero-point (VZP) and deformation energies from the MP2 calculations were combined with electronic energies from the coupled cluster theory with singles, doubles, and iterative triples [CCSD(T)] extrapolated to the complete basis set (CBS) limit to estimate D0 with the aim of inspecting values that were most recently measured, and an analogous comparison was performed using the DFT-D data. In at least one case (namely, for the aniline⋯methane cluster), the D0 estimate that employed the CCSD(T)/CBS energies differed from experiment in the way that could not be explained by a possible deficiency in the VZP contribution. Curiously, one of the DFT-D schemes (namely, the B3LYP-D3/def2-QZVPPD) was able to reproduce all measured D0 values to within 1.0 kJ/mol from experimental error bars. These findings show the need for further measurements and computations of some of the complexes. In order to facilitate such studies, the physical nature of intermolecular interactions in the investigated dimers was analyzed by means of the DFT-based symmetry-adapted perturbation theory.

Formation and local structure of framework Al Lewis sites in beta zeolites.

Framework AlFR Lewis sites represent a substantial portion of active sites in H-BEA zeolite catalysts activated at low temperatures. We studied their nature by 27Al WURST-QCPMG nuclear magnetic resonance (NMR) and proposed a plausible mechanism of their formation based on periodic density functional theory calculations constrained by 1H MAS, 27Al WURST-QCPMG, and 29Si MAS NMR experiments and FTIR measurements. Our results show that the electron-pair acceptor of AlFR Lewis sites corresponds to an AlTRI atom tricoordinated to the zeolite framework, which adsorbs a water molecule. This AlTRI-OH2 complex is reflected in 27Al NMR resonance with δiso = 70 ± 5 ppm and CQ = 13 ± 2 MHz. In addition, the AlTRI atom with adsorbed acetonitrile-d3 (the probe of AlFR Lewis sites in FTIR spectroscopy) exhibits a similar 27Al NMR resonance. We suggest that these AlFR Lewis sites are formed from Al-OH-Si-O-Si-O-Si-OH-Al sequences located in 12-rings (i.e., close unpaired Al atoms).

A Cost Effective Scheme for the Highly Accurate Description of Intermolecular Binding in Large Complexes.

There has been a growing interest in quantitative predictions of the intermolecular binding energy of large complexes. One of the most important quantum chemical techniques capable of such predictions is the domain-based local pair natural orbital (DLPNO) scheme for the coupled cluster theory with singles, doubles, and iterative triples [CCSD(T)], whose results are extrapolated to the complete basis set (CBS) limit. Here, the DLPNO-based focal-point method is devised with the aim of obtaining CBS-extrapolated values that are very close to their canonical CCSD(T)/CBS counterparts, and thus may serve for routinely checking a performance of less expensive computational methods, for example, those based on the density-functional theory (DFT). The efficacy of this method is demonstrated for several sets of noncovalent complexes with varying amounts of the electrostatics, induction, and dispersion contributions to binding (as revealed by accurate DFT-based symmetry-adapted perturbation theory (SAPT) calculations). It is shown that when applied to dimeric models of poly(3-hydroxybutyrate) chains in its two polymorphic forms, the DLPNO-CCSD(T) and DFT-SAPT computational schemes agree to within about 2 kJ/mol of an absolute value of the interaction energy. These computational schemes thus should be useful for a reliable description of factors leading to the enthalpic stabilization of extended systems.

Enantiotropy of Simvastatin as a Result of Weakened Interactions in the Crystal Lattice: Entropy-Driven Double Transitions and the Transient Modulated Phase as Seen by Solid-State NMR Spectroscopy.

In crystalline molecular solids, in the absence of strong intermolecular interactions, entropy-driven processes play a key role in the formation of dynamically modulated transient phases. Specifically, in crystalline simvastatin, the observed fully reversible enantiotropic behavior is associated with multiple order-disorder transitions: upon cooling, the dynamically disordered high-temperature polymorphic Form I is transformed to the completely ordered low-temperature polymorphic Form III via the intermediate (transient) modulated phase II. This behavior is associated with a significant reduction in the kinetic energy of the rotating and flipping ester substituents, as well as a decrease in structural ordering into two distinct positions. In transient phase II, the conventional three-dimensional structure is modulated by periodic distortions caused by cooperative conformation exchange of the ester substituent between the two states, which is enabled by weakened hydrogen bonding. Based on solid-state NMR data analysis, the mechanism of the enantiotropic phase transition and the presence of the transient modulated phase are documented.

Microporous Hyper-Cross-Linked Polymers with High and Tuneable Content of Pyridine Units: Synthesis and Application for Reversible Sorption of Water and Carbon Dioxide.

New hyper-cross-linked porous organic polymers (POPs) with a high content of pyridine segments (7.86 mmol pyridine g-1 ), and a micro/mesoporous texture are reported. The networks are achieved by the chain-growth homopolymerization of 2,6- and 3,5-diethynylpyridines. The pyridine segments form links interconnecting the polyacetylene main chains in these networks. The content of pyridine segments in the networks can be tuned by copolymerizing diethynylpyridines with 1,3-diethynylbenzene. The pyridine rings in the networks serve as base and hydrophilic centers for the sorption of CO2 and water. The homopolymer pyridine networks are highly efficient in the low-pressure adsorption/desorption of CO2 . This sorption mode is promising for the postcombustion removal of CO2 from the fuel gas. The poly(3,5-diethynylpyridine) network exhibits high efficiency in capturing and releasing water vapor (determined capacity 376 mg g-1 at 298 K and relative humidity (RH) = 90% is one of the highest values reported for POPs) and is a promising material for the cyclic water harvesting from air. The reported networks are characterized by 13 C cross-polarization magic angle spinning NMR, thermogravimetric analysis, and N2 adsorption/desorption and their efficiency in CO2 and H2 O capturing is discussed in relation to the content and type of incorporated pyridine segments.

A Volumetric Analysis of the 1H NMR Chemical Shielding in Supramolecular Systems.

The liquid state NMR chemical shift of protons is a parameter frequently used to characterize host-guest complexes. Its theoretical counterpart, that is, the 1H NMR chemical shielding affected by the solvent (1H CS), may provide important insights into spatial arrangements of supramolecular systems, and it can also be reliably obtained for challenging cases of an aggregation of aromatic and antiaromatic molecules in solution. This computational analysis is performed for the complex of coronene and an antiaromatic model compound in acetonitrile by employing the GIAO-B3LYP-PCM approach combined with a saturated basis set. Predicted 1H CS values are used to generate volumetric data, whose properties are thoroughly investigated. The 1H CS isosurface, corresponding to a value of the proton chemical shift taken from a previous experimental study, is described. The presence of the 1H CS isosurface should be taken into account in deriving structural information about supramolecular hosts and their encapsulation of small molecules.

On the Many-Body Expansion of an Interaction Energy of Some Supramolecular Halogen-Containing Capsules.

A tetramer model was investigated of a remarkably stable iodine-containing supramolecular capsule that was most recently characterized by other authors, who described emergent features of the capsule's formation. In an attempt to address the surprising fact that no strong pair-wise interactions between any of the respective components were experimentally detected in condensed phases, the DFT (density-functional theory) computational model was used to decompose the total stabilization energy as a sum of two-, three- and four-body contributions. This model considers complexes formed between either iodine or bromine and the crucial D4d-symmetric form of octaaryl macrocyclic compound cyclo[8](1,3-(4,6-dimethyl)benzene that is surrounded by arenes of a suitable size, namely, either corannulene or coronene. A significant enthalpic gain associated with the formation of investigated tetramers was revealed. Furthermore, it is shown that the total stabilization of these complexes is dominated by binary interactions. Based on these findings, comments are made regarding the experimentally observed behavior of related multicomponent mixtures.

Reconstructing Reliable Powder Patterns from Spikelets (Q)CPMG NMR Spectra: Simplification of UWNMR Crystallography Analysis.

Spikelets NMR spectra are very popular as they enable the shortening of experimental time and give the possibility to obtain required NMR parameters for nuclei with ultrawide NMR patterns. Unfortunately, these resulted ssNMR spectra cannot be fitted directly in common software. For this reason, we developed UWNMRSpectralShape (USS) software which transforms spikelets NMR patterns into single continuous lines. Subsequently, these reconstructed spectral envelopes of the (Q)CPMG spikelets patterns can be loaded into common NMR software and automatically fitted, independently of experimental settings. This allows the quadrupole and chemical shift parameters to be accurately determined. Moreover, it makes fitting of spikelets NMR spectra exact, fast and straightforward.

Gallium Species Incorporated into MOF Structure: Insight into the Formation of a 3D Polycrystalline Gallium-Imidazole Framework.

The formation of a polycrystalline 3D gallium-imidazole framework (MOF) was closely studied in three steps using ssNMR, XRPD, and TGA. In all steps, the reaction products show relatively high temperature stability up to 500 °C. The final product was examined by structural analysis using NMR crystallography combined with TG and BET analyses, which enabled a detailed characterization of the polycrystalline MOF system on the atomic-resolution level. 71Ga ssNMR spectra provided valuable structural information on the coexistence of several distinct gallium species, including a tunable liquid phase. Moreover, using an NMR crystallography approach, two structurally asymmetric units of Ga(Im6)6- incorporated into the thermally stable polycrystalline 3D matrix were identified. Prepared polycrystalline MOF material with polymorphic gallium species is promising for use in catalytic processes.

Polymorphic Forms of Valinomycin Investigated by NMR Crystallography.

A dodecadepsipeptide valinomycin (VLM) has been most recently reported to be a potential anti-coronavirus drug that could be efficiently produced on a large scale. It is thus of importance to study solid-phase forms of VLM in order to be able to ensure its polymorphic purity in drug formulations. The previously available solid-state NMR (SSNMR) data are combined with the plane-wave DFT computations in the NMR crystallography framework. Structural/spectroscopical predictions (the PBE functional/GIPAW method) are obtained to characterize four polymorphs of VLM. Interactions which confer a conformational stability to VLM molecules in these crystalline forms are described in detail. The way how various structural factors affect the values of SSNMR parameters is thoroughly analyzed, and several SSNMR markers of the respective VLM polymorphs are identified. The markers are connected to hydrogen bonding effects upon the corresponding (13C/15N/1H) isotropic chemical shifts of (CO, Namid, Hamid, Hα) VLM backbone nuclei. These results are expected to be crucial for polymorph control of VLM and in probing its interactions in dosage forms.

Parametrizing the Spatial Dependence of 1H NMR Chemical Shifts in π-Stacked Molecular Fragments.

Most recently a renewed interest in several areas has arisen in factors governing the 1H NMR chemical shift (1H CS) of protons in aromatic systems. Therefore, it is important to describe how 1H CS values are affected by π-stacking intermolecular interactions. The parametrization of radial and angular dependences of the 1H CS is proposed, which is based on conventional gauge-independent atomic orbital (GIAO) calculations of explicit molecular fragments. Such a parametrization is exemplified for a benzene dimer with intermonomer vertical and horizontal distances which are in the range of values often found in crystals of organic compounds. Results obtained by the GIAO calculations combined with B3LYP and MP2 methods were compared, and revealed qualitatively the same trends in the 1H CS data. The parametrization was found to be quantitatively correct for the T-shaped benzene dimers, and its limitations were discussed. Parametrized 1H CS surfaces should become useful for providing additional restraints in the search of site-specific information through an analysis of structurally induced 1H CS changes.

Monitoring the Site-Specific Solid-State NMR Data in Oligopeptides.

Reliable values of the solid-state NMR (SSNMR) parameters together with precise structural data specific for a given amino acid site in an oligopeptide are needed for the proper interpretation of measurements aiming at an understanding of oligopeptides' function. The periodic density functional theory (DFT)-based computations of geometries and SSNMR chemical shielding tensors (CSTs) of solids are shown to be accurate enough to support the SSNMR investigations of suitably chosen models of oriented samples of oligopeptides. This finding is based on a thorough comparison between the DFT and experimental data for a set of tripeptides with both 13Cα and 15Namid CSTs available from the single-crystal SSNMR measurements and covering the three most common secondary structural elements of polypeptides. Thus, the ground is laid for a quantitative description of local spectral parameters of crystalline oligopeptides, as demonstrated for the backbone 15Namid nuclei of samarosporin I, which is a pentadecapeptide (composed of five classical and ten nonproteinogenic amino acids) featuring a strong antimicrobial activity.

Effect of Alkali-Free Synthesis and Post-Synthetic Treatment on Acid Sites in Beta Zeolites.

Beta zeolites with Si/Al around 14 were prepared using three new alkali-free synthesis methods based on the application of amorphous aluminosilicate precursor and calcined in ammonia or air. All samples exhibit structural and textural properties of standard beta zeolite. Comprehensive study by 27Al and 29Si MAS NMR, together with FTIR adsorption of d3-acetonitrile and pyridine were used to characterize the influence of both the synthesis and calcination procedure on the framework Al atoms and related Brønsted and Lewis acid sites. While calcination in ammonia preserves all framework Al atoms, calcination in air results in 15% release of framework Al, but without restrictions of the accessibility of the beta zeolite channel system for bulky pyridine molecules. Terminal (SiO)3AlOH groups present in the hydrated zeolites were suggested as a precursor of framework Al-Lewis sites. Surprisingly, the mild dealumination of the air-calcined zeolites result in an increase of the concentration of Brønsted acid sites and a decrease of the total concentration of Lewis sites with the formation of the extra-framework ones.