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Hydrogen bonds between coordinated water molecules: A crystallographic and density functional study
Published: 18 September 2024 by MDPI in The 4th International Online Conference on Crystals session Crystal Engineering

Hydrogen bond is the most abundant noncovalent interaction of water molecules. Previous studies have shown that the strength of the water–water hydrogen bond (-5.0 kcal/mol) increases if one of the water molecules coordinates to transition metal (-9.7 kcal/mol). One of the indicators of this strengthening is the shortening of H∙∙∙O hydrogen bond distances in the crystal structures deposited in the Cambridge Structural Database (CSD).

To study how the coordination of both water molecules influences their hydrogen bonds, we used the ConQuest program to screen high-quality crystal structures deposited in the CSD. The contacts between two aqua ligands in these crystal structures were accepted as hydrogen bonds if the O∙∙∙O distance was shorter than 4.0 Å and the O-H∙∙∙O angle was bigger than 110°. The energies of hydrogen bonds were calculated using the B97D/def2-TZVP level of theory.

The majority of the obtained hydrogen bonds have H∙∙∙O distances between 1.8 Å and 2.0 Å, which is longer than hydrogen bonds between coordinated and free water (1.6 – 1.8 Å). Although this might point towards the weakening of hydrogen bonds by the coordination of both water molecules, the DFT calculations show that the energy of a single hydrogen bond between aqua ligands reaches -11.0 kcal/mol, most likely due to increased dispersion effects. We found that the observed increase in the lengths of hydrogen bonds between aqua ligands is induced by the size of aqua complexes and their tendency to form multiple simultaneous hydrogen bonds. Our DFT calculations show that the supramolecular structures with multiple hydrogen bonds between aqua ligands reach an interaction energy of ‑70.0 kcal/mol.

This study implies that the coordination of both water molecules further increases the strength of their hydrogen bonds and shows that hydrogen bonds between aqua ligands are significant contributors to the stability of supramolecular systems of metal complexes.

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C-H/O interactions of aromatic ligands in organometallic compounds—crystallographic and density functional study
Published: 18 September 2024 by MDPI in The 4th International Online Conference on Crystals session Crystal Engineering

C-H/O interactions are among the most abundant weak hydrogen bonds due to the omnipresence of C-H groups and oxygen atoms. Previous studies have shown that coordination with metals can cause the strengthening of noncovalent interactions, such as hydrogen bonds, stacking interactions, cation–π, and anion–π interactions. In this work, we studied the influence of transition metal coordination on C-H/O interactions of aromatic ligands in organometallic complexes.

Crystal structures of high quality, deposited in the Cambridge Structural Database (CSD, version 5.43, November 2022), were studied using the ConQuest program (version 2022.3.0) to find C-H/O interactions between the η6-coordinated benzene and the oxygen atom of a Z1-O-Z2 fragment, where Z1 or Z2 could be any atom. The contact was accepted as a C-H/O interaction if the O∙∙∙H distance was shorter than 2.9 Å and the C-H∙∙∙O angle was bigger than 110°. The density functional theory was employed to calculate the energies of C-H/O interactions.

Our CSD search resulted in 152 C-H/O interactions of coordinated benzene, mostly in organometallic half-sandwich compounds. The analysis of geometrical parameters shows that preferred O∙∙∙H distances in these interactions are between 2.3 Å and 2.5 Å. These O∙∙∙H distances are shorter for coordinated than uncoordinated aromatic rings, indicating that coordinated aromatic rings form stronger C-H/O hydrogen bonds than uncoordinated ones. These findings are confirmed by our preliminary B3LYP-D3/aug-cc-pVDZ calculations, which showed that in the organometallic half-sandwich model system Cr(C6H6)(CO)3∙∙∙H2O the C-H/O interaction reaches the energy of -3.88 kcal/mol, which is considerably stronger than the C-H/O interaction between (uncoordinated) benzene and water (-1.64 kcal/mol).

Our joint crystallographic and computational study points towards the enhanced ability of coordinated aromatic rings to form substantial C-H/O interactions. This study provides further insights into the strengthening of noncovalent interactions via transition metal coordination.

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Study of synthesized molecular chiral lactam structures for volatile compound profile enrichment using gas chromatography–mass spectrometry (GC-MS) technique

In a study of the chiral enantiomer structure of cyclic trilactams possessing C3 symmetry, the dimer structure was established through the formation of three NH···O type complementary H-bonds at three amides which were applied as agents for volatile compound profile extraction in a sample via the liquid phase extraction technique.

The extraction efficiency of cyclic trilactam materials for analytes found in perfume samples was assessed using HS-SPME-GC-MS. The experimental arrangement of perfume solution was combined with the materials in EtOH solvent in an open vial, while the perfume in EtOH (without the materials) served as the control. Following overnight evaporation at room temperature, the remaining liquid was collected for HS-SPME-GC-MS analysis. Extraction took place overnight to explore the materials' extraction efficiency and facilitate re-crystallization. The materials underwent re-crystallization, with the collected crystals revealing a similar shape to the observed dimers. This suggests a robust hydrogen bonding interaction within the dimer and the volatile compounds interacting. A list of identified compounds during extraction was compiled for each material and the control. The enrichment peak areas in the chromatogram results were determined as the analyte peak area in the sample containing the materials to the area of the same analyte in the control. This indicated the extraction performance of volatile analytes in the sample containing the materials compared with the control sample, such as Linalylformate (5.1±0.015)×107, Citronellol (5.1±4.2)×106, Carvone (4.2±3.5)×105, Linalylacetate (2.5±2.2)×107 and α-Terpinylacetate (2.3±1.7)×105 of the main potential compounds. Higher enrichment signifies stronger interactions between the analytes and these materials.

The solubility between the compounds in less polar solvents can be attributed to their structural features and the nature of the solvent. Specifically, the solubility of each compound is influenced by factors such as polarity, hydrogen bonding capability, and the molecular size and shape of the compounds can influence their interactions with the solvent molecules, further impacting solubility differences between compounds in less polar solvents.

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Sorbents and catalysts based on mesostructured silica for pollutant removal and Carbon Capture and Utilization technologies
, , , , , , , ,

In recent years, concerns about heavy metal pollution and rising CO2 levels contributing to global warming have intensified. This study focuses on synthesizing and functionalizing mesostructured silicas (MCM-41, MCM-48) to develop amine–silica sorbents for potential applications in removing Cd2+ from aqueous solutions and in Carbon Capture and Utilization (CCU) technologies. Due to their ordered mesoporous structure, nitrogen's lone pairs donating to Cd2+, and the high affinity of amines for CO2, amine–silica sorbents are suitable for these applications. Additionally, mesostructured silica-based composites were developed by impregnating MCM-41 with copper, zinc, and zirconium oxidic phases (CZZ) for potential use in the catalytic hydrogenation of CO2 to methanol.
Mesostructured silica was synthesized using the sol–gel technique with a templating agent, a siliceous alkoxide precursor, and two distinct solvent systems—water (MCM-41) and water/ethanol (MCM-48). Amine–silica sorbents were obtained through post-synthesis grafting with aminopropyltriethoxysilane, and were tested for Cd2+ removal and CO2 capture. To reduce the environmental impact of the grafting process, an eco-friendly solvent (butanol instead of toluene) was used. The CZZ@MCM-41 composites were prepared through auto-combustion. For developing Cd2+-removal sorbents and CZZ catalysts, mesostructured silica was also synthesized from industrial waste (hexafluorosilicic acid, FSA). All sorbents were characterized using XRD, TEM-EDX, TEM, N2-physisorption, thermogravimetric analysis, and ATR-FTIR.
MCM-48 was obtained by adding ethanol as a co-solvent, maintaining other experimental conditions equal to MCM-41 synthesis. MCM-41 from both FSA and TEOS exhibited similar textural properties. The amino groups' concentration was similar (~2 mmol/g) for MCM-41 functionalized with either toluene or butanol; however, the use butanol instead of toluene resulted in a lower CO2 adsorption performance (968 μmol CO2/g sorbent vs. 480 μmol CO2/g sorbent). Amine–silica sorbents showed a Cd2+ removal efficiency of 98-99% and an adsorbed cadmium amount (qe) of ~40-45 mgCd(II)/g sorbent for MCM-41 from both TEOS and FSA.

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Influence of the seed-layer material on the direct growth of zinc-tin oxide (ZTO) nanostructures

Recently, metal oxide nanostructures have seen significant advancements in synthesis and device integration. Considering the sustainability of materials and processes, as well as multifunctionality, zinc-tin oxide nanostructures are among the most promising oxide nanostructures being researched. Their ternary oxide nature allows for impressive multifunctionality, with applications including catalysis, electronics, sensors, and energy harvesting. To synthesize these materials, the use of seed layers can be beneficial since it can influence the growth of nanostructures and is advantageous for applications where nanostructures on film are desired, such as photocatalysis and sensors.

In this work, several seed layers (namely Cu, stainless steel, Cr, Ni, etc.) were tested for the synthesis of ZTO nanostructures. It was generally observed that the structures grown on the seed layers differed from those obtained with the seed-layer-free hydrothermal method (under similar synthesis conditions [1-3]), demonstrating the effectiveness of seed layers in influencing growth. Various types of structures were obtained, such as ZnSnO3 nanowires and Zn2SnO4 nanoparticles, octahedrons, and nanowires. The results suggest a correlation between the phase of the employed seed layer and the resultant phase of the nanostructures. Furthermore, it was generally seen that while shorter times favored the production of nanostructures, longer times resulted in thin films with a nanostructured surface when employing the seed layers [4]. This emphasizes the influence of seed layers on nanostructure growth, not only by inducing the phase but also by accelerating the growth process.

References:

  1. Rovisco, A. et al., ACS Appl. Nano Mater. 2018, 1, 3986–3997.
  2. Rovisco, A. et al., Nanomaterials 2019, 9, 1002.
  3. Rovisco, A. et al., In Novel Nanomaterials; IntechOpen, 2021.
  4. Rovisco, A., PhD Thesis, Universidade NOVA de Lisboa, 2019.
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Sodium polymolybdates grown by low-thermal-gradient Czochralski technique for scintillating applications
, ,

Presented work is dedicated to the search of new perspective scintillating materials for rare events physics, particularly neutrinoless double beta-decay projects. Such implementations imposes strict requirements on scintillator quality and radioactive background. Most bivalent cations have radioactive isotopes, thus, light alkali cations are better fitted for this purpose. Moreover, due to their small ionic radii Li and Na are less substituted by U and Th.

Another issue with obtaining crystals for scintillation purposes is the minimal working size of the element – 40*40 mm3 while maintaining uniformity in entire bulk volume. We propose the low-thermal-gradient Czochralski technique (LTG Cz) developed at NIIC SB RAS as a unique technology for obtaining bulk oxide crystals of high optical quality. Temperature gradients in LTG Cz compared to the conventional Czochralski technique are two orders of magnitude lower, ​​less than 1 deg/cm.

In literature several versions of Na2O-MoO3 phase diagrams are presented, stating stable compounds Na2MoO4, Na2Mo2O7, Na2Mo4O13 (impossible for obtaining because of polymorphic phase transition) and in different works Na4Mo9O29, Na6Mo10O33, Na6Mo11O36. Space group of the compound Na6Mo11O36 was determined on powder samples as triclinic. In presented work, NaxMoyOz crystals were grown by LTG Cz technique. Space group of Na6Mo11O36 crystal sample was determined as monoclinic.

Acknowledgements

This work was supported by the Russian Science Foundation № 23-23-10068 and Novosibirsk Region Grant № p-49 (https://rscf.ru/project/23-23-10068).

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Crystal structure determination and Hirshfeld surface analysis of C17H11N3O azo compound.
, , ,

Introduction

Azo compounds are one of the most frequently used compounds in organic chemistry, mainly because of their relatively simple preparation methods. They were, therefore, widely used, especially as dyes for textiles, printing inks, printing cosmetics, and food additives. In addition to their use as dyes, they have attracted much attention from chemists as their potential applications are important.

Methods

The X-ray diffraction of our structure established by Bruker APEXII diffractometer achieves not only the size of the mesh but also the nature of chemical bonds and form molecules. All this information is of fundamental importance for the study of material properties that depend either on their atomic structure or defects of this structure.

Results

The crystal structure shows a dimer that crystallizes in space group P-1 of triclinic system. There are two molecules (A and B) in the asymmetric unit. The crystal structure features three types of intermolecular N-H···O, C-H···O, and C-H···N hydrogen bonds. The C-H..A bind molecules in the crystal and form ribbons along [110]. These ribbons are linked via π-stacking interactions involving the benzene and naphthalene rings of inversion-related A and inversion-related B molecules, thus forming a three-dimensional structure.

The contributions to crystal stacking were studied using Hirshfeld surface analysis.

Conclusion

In this work, we have demonstrated not only the structure of (E)-1-[2-(2-Cyanophenyl)diazen-2-ium-1-yl]naphthalen-2-olate but also the Hirshfeld surface analysis; the azo dyes herein synthesized are good candidates for further study.

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Chemical Equitable Partitions of Inorganic Lattices

Introduction. Graph-theoretical approaches in the study of materials can shed new light on their structure--property relationships. Here, a novel concept termed Chemical Equitable Partition (CEP) [1,2] was used as a means to look at crystal symmetries and classify atoms accordingly.
Methods. The study focused on inorganic perovskites and oxides, without partial or mixed occupancies. Atom pairs were marked as adjacent when the sum of the atoms’ radii exceeded the pair distance, respecting unit-cell periodicity. Atom radii proposed by Alvarez [3] were used (occasionally rescaled to reproduce coordination numbers). The atoms’ connectivity profiles were processed as described by Michos and Raptis [1] to derive Chemical Equitable Partitions. Electrostatic lattice site potentials were calculated using VESTA’s [4] built-in functionality. CEP cells were compared to the atom groups defined by Wyckoff positions, on the one hand, and site potentials, on the other.
Results. Highly symmetric cells featured identical partitions, according to CEP, Wyckoff positions, and Madelung potentials, whereas CEP in systems with lower symmetry was a refinement of the partitions with respect to electrostatic potentials and Wyckoff positions.
Conclusions. CEP provides an alternative perspective on crystal structure and symmetry. Forthcoming research will specify how CEP seamlessly incorporates organic moieties, as found in hybrid organic/inorganic crystals, within a unifying framework.

References
1. I. Michos, V. Raptis. Graph Partitions in Chemistry. Entropy 2023, 25 (11), 1504.
2. V. Raptis, A. Kaltzoglou. Graph Theoretical Analysis as an Aid in the Elucidation of Structure-Property Relations of Perovskite Materials. AIP Conf Proc 2024, 3030 (1), 110005.
3. S. Alvarez. A cartography of the van der Waals territories. Dalton Trans 2013, 42, 8617–8635.
4. K. Momma, F. Izumi. VESTA 3 for three-dimensional visualization of crystal, volumetric and morphology data. J Appl Crystallogr 2011, 44, 1272-1276.

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Exploring the Impact of Edge and Surface Sites on Functionalized Graphene-based Membrane in H2S Adsorption: A Computational Study

In our modern world, environmental concerns have become paramount, with a particular focus on mitigating the release of harmful gases into the atmosphere. One such gas of significant concern is hydrogen sulfide (H2S), known for its noxious odor and detrimental effects on both human health and the environment. This study delves into the crucial importance of removing H2S from effluent gases before their release into the environment. We bridge existing knowledge gaps by investigating the adsorption of hydrogen sulfide on graphene sheets, utilizing advanced computational tools. Through detailed simulations, we explore various adsorption sites on the graphene surface, including top (T), bridge (B), and hollow (H) sites, to determine the most effective removal mechanisms. Most importantly, we carefully explore the impact of the adsorption sites present at the edge and center regions of the graphene surface. Our study reveals that there are significant differences in the adsorption strength of hydrogen sulfide across the sites present at the edge and surface regions of the graphene sheets, confirming that edge sites are more effective for hydrogen sulfide adsorption. The findings derived from our study not only contribute to a deeper understanding of hydrogen sulfide adsorption but also highlight the promising role of carboxylate-function-decorated graphene (via its edge and surface sites and functional group assessment) in environmentally friendly gas removal technologies.

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As V AND AsIII REMOVAL FROM WATER BY DIFFERENT IRON OXYHYDROXIDES NANOSORBENTS
, , , , , ,

Introduction

Arsenic pollution in surface water and groundwater is a worldwide problem originated by dissolution of arsenic from soil, mainly due to anthropogenic activities. Due to the possibility to form inner-sphere complexes, the high surface-to-volume ratio and, therefore, the high density of active sites (-OH groups), nanopowders of iron oxides and oxyhydroxides show a high affinity for arsenate and arsenite species in wide pH ranges and pollutant concentrations.

Methods

Akaganeite (β-FeOOH), ferrihydrite (Fe5HO8·4H2O), and feroxyhyte (δ-FeOOH) were synthesized by simple precipitation methods and tested for the removal of arsenic from water by changing different parameters (initial concentration, contact time, ionic strength, presence of competing ions and solid to liquid ratio). The same experimental conditions for the batch tests allowed a direct comparison between the adsorbents. All sorbents were characterized by XRD, TEM and HRTEM, N2-physisorption, ELS, TGA,ATR-FTIR.

Results

Thanks to its high and positive surface charge, akaganeite is found to be the most promising sorbent in the whole pH range for As(V) (adsorption capacity equal to 99% for CAs = 100 mg/L); it also shows good adsorption capacity for As(III) (81% and 83% for pH 3 and pH 8 respectively at 100 mg/L,). The best sorbent for As(III) is, however, ferrihydrite (98% at 100 mg/L for both pH 3 and pH 8), due to its high surface area. Preliminary results on feroxyhyte prove its suitability as a sorbent for As(V) (92% at 100 mg/L for pH 3).

Conclusions

Akaganeite is the most promising sorbent in the whole pH range for As(V), while ferrihydrite is the best sorbent for As(III). Results on feroxyhyte proved its suitability as a sorbent for As(V) as a promising alternative to akageneite, due to its straightforward and quick synthesis process.

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