Solid-state DFT Calculations Research Articles

Hydration and Hydrolysis of Boron-Substituted Aluminophosphate BAPO-5 According to Solid-State NMR and DFT Calculations

Hydration and Hydrolysis of Boron-Substituted Aluminophosphate BAPO-5 According to Solid-State NMR and DFT Calculations

Probing the Molecular and Macroscopic Structure of Solid Solutions by Dynamic Nuclear Polarization (DNP) Enhanced 13C and 15N Solid-State NMR Spectroscopy.

Crystallization is a widely used purification technique in the manufacture of active pharmaceutical ingredients (APIs) and precursor molecules. However, when impurities and desired compounds have similar molecular structures, separation by crystallization may become challenging. In such cases, some impurities may form crystalline solid solutions with the desired product during recrystallization. Understanding the molecular structure of these recrystallized solid solutions is crucial to devise methods for effective purification. Unfortunately, there are limited analytical techniques that provide insights into the molecular structure or spatial distribution of impurities that are incorporated within recrystallized products. In this study, we investigated model solid solutions formed by recrystallizing salicylic acid (SA) in the presence of anthranilic acid (AA). These two molecules are known to form crystalline solid solutions due to their similar molecular structures. To overcome challenges associated with the long 1H longitudinal relaxation times (T1(1H)) of SA and AA, we employed dynamic nuclear polarization (DNP) and 15N isotope enrichment to enable solid-state NMR experiments. Results of solid-state NMR experiments and DFT calculations revealed that SA and AA are homogeneously alloyed as a solid solution. Heteronuclear correlation (HETCOR) experiments and plane-wave DFT structural models provide further evidence of the molecular-level interactions between SA and AA. This research provides valuable insights into the molecular structure of recrystallized solid solutions, contributing to the development of effective purification strategies and an understanding of the physicochemical properties of solid solutions.

Repurposing of Antifungal Drug Flucytosine/Flucytosine Cocrystals for Anticancer Activity against Prostate Cancer Targeting Apoptosis and Inflammatory Signaling Pathways.

This study aimed to repurpose the antifungal drug flucytosine (FCN) for anticancer activity together with cocrystals of nutraceutical coformers sinapic acid (SNP) and syringic acid (SYA). The cocrystal screening experiments with SNP resulted in three cocrystal hydrate forms in which two are polymorphs, namely, FCN-SNP F-I and FCN-SNP F-II, and the third one with different stoichiometry in the asymmetric unit (1:2:1 ratio of FCN:SNP:H2O, FCN-SNP F-III). Cocrystallization with SYA resulted in two hydrated cocrystal polymorphs, namely, FCN-SYA F-I and FCN-SYA F-II. All the cocrystal polymorphs were obtained concomitantly during the slow evaporation method, and one of the polymorphs of each system was produced in bulk by the slurry method. The interaction energy and lattice energies of all cocrystal polymorphs were established using solid-state DFT calculations, and the outcomes correlated with the experimental results. Further, the in vitro cytotoxic activity of the cocrystals was determined against DU145 prostate cancer and the results showed that the FCN-based cocrystals (FCN-SNP F-III and FCN-SYA F-I) have excellent growth inhibitory activity at lower concentrations compared with parent FCN molecules. The prepared cocrystals induce apoptosis by generating oxidative stress and causing nuclear damage in prostate cancer cells. The Western blot analysis also depicted that the cocrystals downregulate the inflammatory markers such as NLRP3 and caspase-1 and upregulate the intrinsic apoptosis signaling pathway marker proteins, such as Bax, p53, and caspase-3. These findings suggest that the antifungal drug FCN can be repurposed for anticancer activity.

Polar covalent apex-base bonding in borapyramidanes probed by solid-state NMR and DFT calculations.

Pyramidane molecules have attracted chemists for many decades due to their regular shape, high symmetry and their correspondence in the macroscopic world. Recently, experimental access to a number of examples has been reported, in particular the rarely reported square pyramidal bora[4]pyramidanes. To describe the bonding situation of the nonclassical structure of pyramidanes, we present solid-state Nuclear Magnetic Resonance (NMR) as a versatile tool for deciphering such bonding properties for three now accessible bora[4]pyramidane and dibora[5]pyramidane molecules. 11 B solid-state NMR spectra indicate that the apical boron nuclei in these compounds are strongly shielded (around -50 ppm vs. BF3 -Et2 O complex) and possess quadrupolar coupling constants of less than 0.9 MHz pointing to a rather high local symmetry. 13 C-11 B spin-spin coupling constants have been explored as a measure of the bond covalency in the borapyramidanes. While the carbon-boron bond to the -B(C6 F5 )2 substituents of the base serves as an example for a classical covalent 2-center-2-electron (2c-2e) sp2 -carbon-sp2 -boron σ-bond with 1 J(13 C-11 B) coupling constants in the order of 75 Hz, those of the boron(apical)-carbon(basal) bonds in the pyramid are too small to measure. These results suggest that these bonds have a strongly ionic character, which is also supported by quantum-chemical calculations.

Understanding Cu(i) local environments in MOFs via63/65Cu NMR spectroscopy.

The field of metal-organic frameworks (MOFs) includes a vast number of hybrid organic and inorganic porous materials with wide-ranging applications. In particular, the Cu(i) ion exhibits rich coordination chemistry in MOFs and can exist in two-, three-, and four-coordinate environments, which gives rise to many structural motifs and potential applications. Direct characterization of the structurally and chemically important Cu(i) local environments is essential for understanding the sources of specific MOF properties. For the first time, 63/65Cu solid-state NMR has been used to investigate a variety of Cu(i) sites and local coordination geometries in Cu MOFs. This approach is a sensitive probe of the local Cu environment, particularly when combined with density functional theory calculations. A wide range of structurally-dependent 63/65Cu NMR parameters have been observed, including 65Cu quadrupolar coupling constants ranging from 18.8 to 74.8 MHz. Using the data from this and prior studies, a correlation between Cu quadrupolar coupling constants, Cu coordination number, and local Cu coordination geometry has been established. Links between DFT-calculated and experimental Cu NMR parameters are also presented. Several case studies illustrate the feasibility of 63/65Cu NMR for investigating and resolving inequivalent Cu sites, monitoring MOF phase changes, interrogating the Cu oxidation number, and characterizing the product of a MOF chemical reaction involving Cu(ii) reduction to Cu(i). A convenient avenue to acquire accurate 65Cu NMR spectra and NMR parameters from Cu(i) MOFs at a widely accessible magnetic field of 9.4 T is described, with a demonstrated practical application for tracking Cu(i) coordination evolution during MOF anion exchange. This work showcases the power of 63/65Cu solid-state NMR spectroscopy and DFT calculations for molecular-level characterization of Cu(i) centers in MOFs, along with the potential of this protocol for investigating a wide variety of MOF structural changes and processes important for practical applications. This approach has broad applications for examining Cu(i) centers in other weight-dilute systems.

A focus on applying 63/65Cu solid-state NMR spectroscopy to characterize Cu MOFs.

Metal-organic frameworks (MOFs) are a class of hybrid organic and inorganic porous materials that have shown prospects in applications ranging from gas storage, separation, catalysis, etc. Although they can be studied using various characterization techniques, these methods often do not provide local structural details that help explain their functionality. Zhang et al. (W. Zhang, B. E. G. Lucier, V. V. Terskikh, S. Chen and Y. Huang, Chem. Sci., 2024, https://doi.org/10.1039/D4SC00782D) have recently exploited 63/65Cu solid-state NMR spectroscopy (for the first time) and DFT calculations to elucidate the structures of Cu(i) centers in MOFs. While there are still many challenges in overcoming issues in resolution and sensitivity, this work lays the foundation for further development of solid-state NMR technology in characterizing copper in MOFs or other amorphous solids.

Structural Modeling of O/F Correlated Disorder in TaOF3 and NbOF3-x(OH)x by Coupling Solid-State NMR and DFT Calculations.

The structure of MOF3 (M = Nb, Ta) compounds was precisely modeled by combining powder X-ray diffraction, solid-state NMR spectroscopy, and semiempirical dispersion-corrected DFT calculations. It consists of stacked ∞(MOF3) layers along the c⃗ direction formed by heteroleptic corner-connected MX6 (X = O, F) octahedra. 19F NMR resonance assignments and occupancy rates of the anionic crystallographic sites have been revised. The bridging site is shared equally by the anions, and the terminal site is occupied by F only. An O/F correlated disorder is expected since cis-MO2F4 octahedra are favored, resulting in one-dimensional -F-M-O-M- strings along the <100> and <010> directions. Ten different 2 × 2 × 1 supercells per compound, fulfilling these characteristics, were built. Using DFT calculations and the GIPAW approach, the supercells were relaxed and the 19F isotropic chemical shift values were determined. The agreement between the experimental and calculated 19F spectra is excellent for TaOF3. The 1H and 19F experimental NMR spectra revealed that some of the bridging F atoms are substituted by OH groups, especially in NbOF3. New supercells involving OH groups were generated. Remarkably, the best agreement is obtained for the supercells with the composition closest to that estimated from the 19F NMR spectra, i.e., NbOF2.85(OH)0.15.

Inducing differences in modification degree and binding mode of organophosphonic acid grafted titania by changing pH and hydrocarbon chain length

Organically modified metal oxide surfaces are of interest in many applications since they combine the advantages of metal oxide supports (structural properties, chemical and mechanical stability) and organic functionalities (for specific surface interactions). Although surface modification with organophosphonic acids (PAs) with an alkyl or aminoalkyl functional group on TiO2 has been investigated previously, knowledge of the synthesis-properties correlation (e.g. the binding mode of the PAs) is still lacking, especially for functional group-surface interactions. These are however important as they can influence functional group availability in applications such as (metal) sorption. In this work, the dependence of modification degree and phosphorus chemical environment on pH and chain length (C1 to C6) was investigated with TGA, ICP-OES, nitrogen/argon sorption, XPS, and solid-state 31P NMR and DFT calculations. The TGA and the ICP-OES results showed a clear impact of pH on surface modification degrees, with a different response for modification with alkyl- and aminoalkylphosphonic acids, featuring a more rapid decrease in modification degrees from pH 2 upwards for the alkylphosphonic acids compared to the aminoalkylphosphonic acids. Moreover, a clear correlation can be found between the aminoalkyl chain length and the NH2/NH3+ ratio. In addition, a positive correlation between the modification degree and the protonation degree of the amine group is observed for aminomethylphosphonic acid (AMPA) and 2-aminoethylphosphonic acid (2AEPA) modified samples, while this is absent for longer alkyl chains. This is supported by DFT calculations that indicate that the most stable binding modes of AMPA and 2AEPA grafted on the anatase (101) surface include hydrogen bonds between NH3+ and the surface oxygen atoms, in contrast, the most stable binding modes for 3-aminopropylphosphonic acid (3APPA), 4-aminobutylphosphonic acid (4ABPA), and 6-aminohexylphosphonic acid (6AHPA) grafted on the anatase (101) surface involve a Lewis acid-base interaction between NH2 and a surface Ti site.

Enantioselective catalysts based on metal-organic framework-supported nucleotides

Adenosine triphosphate (ATP) and other nucleotides can be irreversibly bound to the metal-organic framework (MOF) MIL-101(Cr). Analysis of X-ray diffraction data suggests that the location of the adsorbed ATP molecule is in proximity of the Cr3 clusters. Solid-state NMR and DFT calculations indicate that ATP is bound to MIL-101(Cr) through linkages of the terminal phosphate group with Cr(III) of the framework. In the presence of Cu(II) ions, the MOF-supported nucleotides can function as stable and reusable enantioselective heterogeneous catalysts for reactions like Diels-Alder and Michael addition. Compared to the corresponding homogeneous nucleotide-based artificial metalloenzymes (ArMs), the MOF-supported nucleotide-based ArMs exhibit significantly enhanced activity and selectivity in certain cases, demonstrating their potential as a new class of enantioselective heterogeneous catalysts.

SiCO Ceramics as Storage Materials for Alkali Metals/Ions: Insights on Structure Moieties from Solid-State NMR and DFT Calculations.

Polymer-derived silicon oxycarbide ceramics (SiCO) have been considered as potential anode materials for lithium- and sodium-ion batteries. To understand their electrochemical storage behavior, detailed insights into structural sites present in SiCO are required. In this work, the study of local structures in SiCO ceramics containing different amounts of carbon is presented. 13 C and 29 Si solid-state MAS NMR spectroscopy combined with DFT calculations, atomistic modeling, and EPR investigations, suggest significant changes in the local structures of SiCO ceramics even by small changes in the material composition. The provided findings on SiCO structures will contribute to the research field of polymer-derived ceramics, especially to understand electrochemical storage processes of alkali metal/ions such as Na/Na+ inside such networks in the future.

Complexes of NiII, CoII, ZnII, and CuII with Promising Anti-Tuberculosis Drug: Solid-State Structures and DFT Calculations

Four new NiII, CoII, ZnII, and CuII complexes with the promising anti-tuberculosis drug (E/Z)-N′-((5-Hydroxy-3,4-bis(hydroxymethyl)-6-methylpyridin-2-yl)methylene)-isonicotino-hydrazide (LH) were synthesized and characterized by structural methods: single-crystal X-ray diffraction, vibrational spectroscopy, and mass spectrometry. The NiII, CoII, and ZnII metal ions form only amorphous phases with various morphologies according to mass spectrometry and IR spectroscopy. The CuII forms a crystalline 1D coordination polymer with the relative formula {[CuLCl]·0.5H2O}∞1. Even though the LH ligand in the crystalline state includes a mixture of E-/Z-isomers, only the tautomeric iminol E-/Z-form is coordinated by CuII in the crystal. The copper(II) complex crystallizes in the monoclinic P21/n space group with the corresponding cell parameters a = 16.3539(11) Å, b = 12.2647(6) Å, and c = 17.4916(10) Å; α = 90°, β = 108.431(7)°, and γ = 90°. DFT calculations showed that the Z-isomer of the LH ligand in solution has the lowest formation energy due to intramolecular hydrogen bonds. According to the quantum chemical calculations, the coordination environment of the CuII atom during the transfer of the molecule into the solution remains the same as in the crystal, except for the polymeric bond, namely, distorted trigonal bipyramidal. Some of the complexes investigated can be used as effective sensors in biosystems.

Dehydration kinetics and mechanism of the stable isonicotinamide hydrate revealed by terahertz spectroscopy and DFT calculation

The dehydration behavior of pharmaceutical hydrates has a great influence on its physiochemical properties such as stability, dissolution rate and bioavailability. However, how the intermolecular interactions vary during dehydration process remains elusive. In this work, we employed terahertz time-domain spectroscopy (THz-TDS) to probe the low-frequency vibrations and the dehydration process of isonicotinamide hydrate I (INA-H I). Theoretical solid-state DFT calculation was conducted to reveal its mechanism. Vibrational modes which are responsible for the THz absorption peaks were decomposed for better understanding the characters of these low-frequency modes. The result suggests translational motion is the dominant component for water molecules in THz region. Evolution of the THz spectrum of INA-H I during dehydration provides direct evidence of the variations of crystal structure. Based on the THz measurements, a two-step kinetics mode including first-rate reaction and three-dimensional nuclei growth is proposed. And we figure that the low-frequency vibrations of water molecules are the origin of dehydration process of hydrate.

Crystal Structure of Methyl 3-O-α-d-Glucopyranosyl 2-Acetamido-2-Deoxy-α-d-Galactopyranoside Hydrate

Methyl 3-O-α-d-glucopyranosyl 2-acetamido-2-deoxy-α-d-galactopyranoside as a monohydrate, C15H27NO11·H2O, crystallizes in space group P212121, with four molecules in the unit cell. It constitutes the methyl glycoside of the carbohydrate part of the teichoic acid type polysaccharide from Micrococcus sp. A1, in which the disaccharides are joined through phosphodiester linkages. The conformation of the disaccharide is described by the glycosidic torsion angles ϕ = − 31° and ψ = + 1°, and the hydroxymethyl groups of the constituent monosaccharides are present in the gg and gt conformations for the sugar residues having the gluco- and galacto-configuration, respectively. For the N-acetyl group at C2 of the galactosamine residue the torsion angle τH = 147°, i.e., the amide proton has an antiperiplanar relationship to H2 of the sugar ring. The structure shows extensive hydrogen bonding along the a-direction, including the water molecule, and forms sheets with hydrophilic interactions within the sheets as a result of hydrogen bonding between disaccharides as well as hydrophobic interactions between the sheets, in particular, amongst methyl groups of the N-acetyl group of the α-d-GalpNAc residue in the disaccharides.Graphical The structure of the title disaccharide as a monohydrate, C15H27NO11·H2O, which shows extensive hydrogen bonding as well as hydrophobic interactions, was determined from minute crystals using synchrotron radiation and verified by solid state DFT calculations using plane waves.

Porous and Water Stable 2D Hybrid Metal Halide with Broad Light Emission and Selective H2 O Vapor Sorption.

In this work we report a strategy for generating porosity in hybrid metal halide materials using molecular cages that serve as both structure-directing agents and counter-cations. Reaction of the [2.2.2] cryptand (DHS) linker with PbII in acidic media gave rise to the first porous and water-stable 2D metal halide semiconductor (DHS)2 Pb5 Br14 . The corresponding material is stable in water for a year, while gas and vapor-sorption studies revealed that it can selectively and reversibly adsorb H2 O and D2 O at room temperature (RT). Solid-state NMR measurements and DFT calculations verified the incorporation of H2 O and D2 O in the organic linker cavities and shed light on their molecular configuration. In addition to porosity, the material exhibits broad light emission centered at 617 nm with a full width at half-maximum (FWHM) of 284 nm (0.96 eV). The recorded water stability is unparalleled for hybrid metal halide and perovskite materials, while the generation of porosity opens new pathways towards unexplored applications (e.g. solid-state batteries) for this class of hybrid semiconductors.

Experimental identification of the active sites over a plate-like mordenite for the carbonylation of dimethyl ether

<h2>Summary</h2> Mordenite effectively catalyzes the carbonylation of dimethyl ether to methyl acetate, and the activity is ascribed to the amount of the Brønsted acid sites in its 8-member-ring pore. Quantitatively describing the catalytic chemistry over the respective acid sites, however, is experimentally challenging. Here, we report that the specific activity of the T3 site is 4 times greater than that of the T4 site at 473 K, based on selectively populating Al atoms at the T3 and T4 sites over mordenites and precisely discriminating their coordination environments by a combined approach of solid-state NMR experiments and DFT calculations. The exclusive location of Al atom at the T3 site on a plate-like mordenite yields unprecedentedly high activity and elucidates the reaction chemistry for this unique site. Varying the population of Al atoms at the T3 and T4 positions on reference mordenites reveals that the T4 site catalyzes the reaction as well, but to a much lesser extent.

Multi-component crystals containing urea: mechanochemical synthesis and characterization by 35Cl solid-state NMR spectroscopy and DFT calculations

This work discusses the mechanochemical synthesis and characterization of five urea multicomponent crystals by XRD, solid-state NMR, DFT and ab initio molecular dynamics calculations to provide insights into their molecular-level structures.

Exploring the Na+ Locations and Al Distributions in SSZ-39 Zeolite by Solid-State NMR Spectroscopy and DFT Calculations

Exploring the Na+ Locations and Al Distributions in SSZ-39 Zeolite by Solid-State NMR Spectroscopy and DFT Calculations

The Atomic-Level Structure of Mesoporous Hexagonal Boron Nitride Determined by High-Resolution Multinuclear Solid-State NMR Spectroscopy and DFT Calculations

The Atomic-Level Structure of Mesoporous Hexagonal Boron Nitride Determined by High-Resolution Multinuclear Solid-State NMR Spectroscopy and DFT Calculations

Computationally Designed Crystal Structures of the Supertetrahedral Ga4C and Ga4Si Solids.

The structural, mechanical, electrical, and optical properties of new supertetrahedral structures cF-Ga4X (X = C, Si) were studied by using a solid state DFT calculation. The crystal structures of cF-Ga4X are built based on a diamond crystal lattice, in which pairs of adjacent carbon atoms are replaced by Ga4X fragments, where Ga4 is a tetrahedron of gallium atoms. Calculations have shown that new mixed-type supertetrahedral structures are dynamically stable, have densities of 3.49 g/cm3 (X = C) and 2.65 g/cm3 (X = Si), and are narrow band gap semiconductors. From the performed molecular dynamics calculations, it follows that the homogeneous melting temperature of the gallium-carbon structure is in the range from 600 to 700 K and that of the gallium-silicon structure is in the range from 400 to 500 K.

89Y chemical shift anisotropy: a sensitive structural probe of layered yttrium hydroxides revealed by solid-state NMR spectroscopy and DFT calculations

A combination of solid-state NMR (ssNMR) spectroscopy and DFT calculations revealed that the89Y CSA is a sensitive probe to detect the subtle structural changes in layered yttrium hydroxides.