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Chemistry, Volume 3, Issue 2 (June 2021) – 15 articles

Cover Story (view full-size image): Are there any easy ways of predicting how molecules will aggregate in the solid state? To address this question, four methods were ranked for their ability to forecast which hydrogen bonds are most likely to appear in an organic crystalline solid. Protocols based on molecular electrostatic potentials (MEPs), hydrogen-bond energies (HBEs), hydrogen-bond propensity (HBP), and hydrogen-bond coordination (HBC) were applied to crystal structures of pyrazole-based molecules. HBE correctly predicted all observed primary hydrogen bonds, followed by HBP (87.5%), and HBC = MEPs (62.5%). These models, which only need a 2-D chemical structure as input, offer a starting point for crystal-structure prediction and constitute a valuable risk assessment of potential challenges in the manufacture of organic chemicals. View this paper.
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Article
Preparation and Antimicrobial Properties of Alginate and Serum Albumin/Glutaraldehyde Hydrogels Impregnated with Silver(I) Ions
Chemistry 2021, 3(2), 672-686; https://0-doi-org.brum.beds.ac.uk/10.3390/chemistry3020047 - 14 Jun 2021
Viewed by 795
Abstract
Calcium alginate (CaALG) hydrogel beads and two sets of composite beads, formed from a combination of calcium alginate/propylene glycol alginate/human serum albumin (CaALG/PGA/HSA) and from calcium alginate with the quaternary ammonium salt, (3-(trimethoxysilyl)propyl)-octadecyldimethylammonium chloride (QA), (CaALG/QA), were prepared. Bovine serum albumin (BSA) was [...] Read more.
Calcium alginate (CaALG) hydrogel beads and two sets of composite beads, formed from a combination of calcium alginate/propylene glycol alginate/human serum albumin (CaALG/PGA/HSA) and from calcium alginate with the quaternary ammonium salt, (3-(trimethoxysilyl)propyl)-octadecyldimethylammonium chloride (QA), (CaALG/QA), were prepared. Bovine serum albumin (BSA) was condensed with glutaraldehyde (GLA) to form a BSA/GLA hydrogel. The corresponding Ag+-containing gels of all of the above hydrogels were also formed, and slow leaching of the biocidal transition metal ion from the gels bestowed broad spectrum antimicrobial activity. In the absence of added Ag+, CaALG/QA was the only material to deliver marginal to moderate antibacterial and antifungal effects. The Ag+ impregnated hydrogel systems have the potential to maintain the antimicrobial properties of silver, minimising the risk of toxicity, and act as reservoirs to afford ongoing sterility. Full article
(This article belongs to the Special Issue Recent Advances in Antimicrobial Materials)
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Article
Study of the Performance of Particles Based on Modified Starches Containing Potassium Sorbate and Incorporated into Biodegradable Films: Physicochemical Characterization and Antimicrobial Action
Chemistry 2021, 3(2), 658-671; https://0-doi-org.brum.beds.ac.uk/10.3390/chemistry3020046 - 27 May 2021
Viewed by 1065
Abstract
Ultrasound technique was used to produce native and acetylated cassava starch particles containing potassium sorbate (KS). In order to obtain an active packaging, films with addition of native starch particles containing KS (NKSPF) or added with acetylated starch particles containing KS (AKSPF) were [...] Read more.
Ultrasound technique was used to produce native and acetylated cassava starch particles containing potassium sorbate (KS). In order to obtain an active packaging, films with addition of native starch particles containing KS (NKSPF) or added with acetylated starch particles containing KS (AKSPF) were formulated. As control systems, films without KS (CF) or added with KS that was not retained in particles (KSF), were produced. The NKSPF and AKSPF microstructure was consistent with composite materials. Tensile test revealed that CF and KSF were ductile and extensible (stress at break (σb) 2.8–2.5 MPa and strain at break (εb) 284–206%), while NKSPF and AKSPF were more resistant films with higher Young’s Modulus (148–477 MPa) and σb (3.6–17 MPa) but lower εb (40–11%). Moreover, NKSPF and AKSPF developed lower Yellowness Index (6.6–6.5) but higher opacity (19–23%) and solubility in water (31–35%) than KSF (9, 10.8% and 9%, respectively). It was observed that KSF and NKSPF moderately reduced the Zygosaccharomyces bailii growth while AKSPF showed the highest yeast inhibition, three Log-cycles, compared to CF. Additionally, FTIR spectroscopy revealed intensified interactions between KS and modified starch. It was concluded that starch sonication and acetylation were useful modifications to produce particles carrier of KS that improved the physical and antimicrobial performance of active films. Full article
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Article
Two Types of PPARγ Ligands Identified in the Extract of Artemisia campestris
Chemistry 2021, 3(2), 647-657; https://0-doi-org.brum.beds.ac.uk/10.3390/chemistry3020045 - 23 May 2021
Viewed by 735
Abstract
The 70% ethanol extract of Artemisia campestris was screened to find PPARγ ligands using the PPARγ ligand-responsive chimera luciferase reporter system. Capillartemisin B was identified as a PPARγ ligand that stimulated lipid accumulation in 3T3-L1 cells. By further purification of PPARγ ligands from [...] Read more.
The 70% ethanol extract of Artemisia campestris was screened to find PPARγ ligands using the PPARγ ligand-responsive chimera luciferase reporter system. Capillartemisin B was identified as a PPARγ ligand that stimulated lipid accumulation in 3T3-L1 cells. By further purification of PPARγ ligands from a large-scale preparation of the methanol extract of Artemisia campestris, we isolated and identified eupatilin and santaflavone as PPARγ ligands. Weak PPARγ ligand activity of eupatilin or santaflavone in reporter assay was enhanced by a PPARγ antagonist, GW9662, suggesting that santaflavone or eupatilin and GW9662 bound simultaneously to the multiple sub-pockets of the PPARγ ligand-binding domain (LBD) and cooperatively activated PPARγ. Docking simulation suggested that eupatilin binds to the Ω-pocket but not to the AF-2 pocket of Y-shaped PPARγ LBD where artepillin C that differs from capillartemisin B at the C-5′ position without hydroxy group binds. Eupatilin or santaflavone with or without GW9662 did not stimulate lipid accumulation in differentiated 3T3-L1 cells, suggesting that binding of each compound alone or with GW9662 to the Ω-pocket which stimulated the PPARγ-responsive reporter expression was not enough to stimulate lipid accumulation. The PPARγ ligands found in this study have a potential to design the fragment-based drug design of a novel PPARγ ligand that cover the Y-shaped PPARγ LBD. Full article
(This article belongs to the Section Biological and Natural Products)
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Review
Catalytic Converters for Vehicle Exhaust: Fundamental Aspects and Technology Overview for Newcomers to the Field
Chemistry 2021, 3(2), 630-646; https://0-doi-org.brum.beds.ac.uk/10.3390/chemistry3020044 - 20 May 2021
Viewed by 1055
Abstract
This works aims to provide an understanding on basic chemical kinetics pertaining to three-way catalytic (TWC) converters from an educational perspective, aimed at those novel readers in this field. Rate of reactions and its factors are explained, showcasing that the chosen catalyst is [...] Read more.
This works aims to provide an understanding on basic chemical kinetics pertaining to three-way catalytic (TWC) converters from an educational perspective, aimed at those novel readers in this field. Rate of reactions and its factors are explained, showcasing that the chosen catalyst is the main factor affecting the overall rate of reaction. Furthermore, this overview revisit insights of the catalytic converter structure and the environmental issues that come along with it. Lastly, the chemical and physical properties of the reactants and products-pollutant and less-toxic gases—are discussed, in order to gather a better understanding of the reactants and products that enters a catalytic converter. Full article
(This article belongs to the Special Issue 2021 Profile Papers by Chemistry' Editorial Board Members)
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Article
Assessment of Computational Tools for Predicting Supramolecular Synthons
Chemistry 2021, 3(2), 612-629; https://0-doi-org.brum.beds.ac.uk/10.3390/chemistry3020043 - 03 May 2021
Cited by 1 | Viewed by 827
Abstract
The ability to predict the most likely supramolecular synthons in a crystalline solid is a valuable starting point for subsequently predicting the full crystal structure of a molecule with multiple competing molecular recognition sites. Energy and informatics-based prediction models based on molecular electrostatic [...] Read more.
The ability to predict the most likely supramolecular synthons in a crystalline solid is a valuable starting point for subsequently predicting the full crystal structure of a molecule with multiple competing molecular recognition sites. Energy and informatics-based prediction models based on molecular electrostatic potentials (MEPs), hydrogen-bond energies (HBE), hydrogen-bond propensity (HBP), and hydrogen-bond coordination (HBC) were applied to the crystal structures of twelve pyrazole-based molecules. HBE, the most successful method, correctly predicted 100% of the experimentally observed primary intermolecular-interactions, followed by HBP (87.5%), and HBC = MEPs (62.5%). A further HBC analysis suggested a risk of synthon crossover and synthon polymorphism in molecules with multiple binding sites. These easy-to-use models (based on just 2-D chemical structure) can offer a valuable risk assessment of potential formulation challenges. Full article
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Article
Erdmann’s Anion—An Inexpensive and Useful Species for the Crystallization of Illicit Drugs after Street Confiscations
Chemistry 2021, 3(2), 598-611; https://0-doi-org.brum.beds.ac.uk/10.3390/chemistry3020042 - 30 Apr 2021
Cited by 1 | Viewed by 796
Abstract
Erdmann’s anion [1,6-diammino tetranitrocobaltate(III)] is useful in the isolation and crystallization of recently confiscated street drugs needing to be identified and catalogued. The protonated form of such drugs forms excellent crystals with that anion; moreover, Erdmann’s salts are considerably less expensive than the [...] Read more.
Erdmann’s anion [1,6-diammino tetranitrocobaltate(III)] is useful in the isolation and crystallization of recently confiscated street drugs needing to be identified and catalogued. The protonated form of such drugs forms excellent crystals with that anion; moreover, Erdmann’s salts are considerably less expensive than the classically used AuCl4 anion to isolate them, while preparation of high-quality crystals is equally easy in both cases. We describe the preparation and structures of the K+CoH6N6O8 and NH4+CoH6N7O8, salts of Erdmann’s. In addition, herein are described the preparations of this anion’s salts with cocaine (C17H28CoN7O12), with methamphetamine (C10H22CoN7O8), and with methylone (C22H34CoN8O14), whose preparation and stereochemistry had been characterized by the old AuCl4 salts methodology. For all species in this report, the space groups and cell constants were determined at 296 and 100 K, looking for possible thermally induced polymorphism—none was found. Since the structures were essentially identical at the two temperatures studied, we discuss only the 100 K results. Complete spheres of data accessible to a Bruker ApexII diffractometer with Cu–Kα radiation, λ = 1.54178 Å, were recorded and used in the refinements. Using the refined single crystal structural data for the street drugs, we computed their X-ray powder diffraction patterns, which are beneficial as quick identification standards in law enforcement work. Full article
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Article
Solid Phase Nitrosylation of Enantiomeric Cobalt(II) Complexes
Chemistry 2021, 3(2), 585-597; https://0-doi-org.brum.beds.ac.uk/10.3390/chemistry3020041 - 28 Apr 2021
Cited by 1 | Viewed by 876
Abstract
Accompanied by a change in color from red to black, the enantiomorphic phases of the cobalt complexes of a chiral salen ligand (L2−, Co(L)·CS2, and Co(L) (L = LS,S or LR,R)) chemisorb NO (g) at atmospheric [...] Read more.
Accompanied by a change in color from red to black, the enantiomorphic phases of the cobalt complexes of a chiral salen ligand (L2−, Co(L)·CS2, and Co(L) (L = LS,S or LR,R)) chemisorb NO (g) at atmospheric pressure and rt over hours for the CS2 solvated phase, and within seconds for the desolvated phase. NO is installed as an axial nitrosyl ligand. Aligned but unconnected voids in the CS2 desorbed Co(LR,R)·CS2 structure indicate conduits for the directional desorption of CS2 and reversible sorption of NO, which occur without loss of crystallinity. Vibrational circular dichroism (VCD) spectra have been recorded for both hands of LH2, Zn(L), Co(L)·CS2, Co(L), Co(NO)(L), and Co(NO)(L)·CS2, revealing significant differences between the solution-state and solid-state spectra. Chiral induction enables the detection of the νNO band in both condensed states, and surprisingly also the achiral lattice solvent (CS2CS at 1514 cm−1)) in the solid-state VCD. Solution-state spectra of the paramagnetic Co(II) complex shows a nearly 10-fold enhancement and more extensive inversion of polarity of the vibrations of dominant VCD bands compared to the spectra of the diamagnetic compounds. This enhancement is less pronounced when there are fewer polarity inversions in the solid state VCD spectra. Full article
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Article
Absolute Configuration of In Situ Crystallized (+)-γ-Decalactone
Chemistry 2021, 3(2), 578-584; https://0-doi-org.brum.beds.ac.uk/10.3390/chemistry3020040 - 21 Apr 2021
Cited by 1 | Viewed by 860
Abstract
Knowledge about the absolute configuration of small bioactive organic molecules is essential in pharmaceutical research because enantiomers can exhibit considerably different effects on living organisms. X-ray crystallography enables chemists to determine the absolute configuration of an enantiopure compound due to anomalous dispersion. Here, [...] Read more.
Knowledge about the absolute configuration of small bioactive organic molecules is essential in pharmaceutical research because enantiomers can exhibit considerably different effects on living organisms. X-ray crystallography enables chemists to determine the absolute configuration of an enantiopure compound due to anomalous dispersion. Here, we present the determination of the absolute configuration of the flavoring agent (+)-γ-decalactone, which is liquid under ambient conditions. Single crystals were grown from the liquid in a glass capillary by in situ cryo-crystallization. Diffraction data collection was performed using Cu-Kα radiation. The absolute configuration was confirmed. The molecule consists of a linear aliphatic non-polar backbone and a polar lactone head. In the solid state, layers of polar and non-polar sections of the molecule alternating along the c-axis of the unit cell are observed. In favorable cases, this method of absolute configuration determination of pure liquid (bioactive) agents or liquid products from asymmetric catalysis is a convenient alternative to conventional methods of absolute structure determination, such as optical rotatory dispersion, vibrational circular dichroism, ultraviolet-visible spectroscopy, use of chiral shift reagents in proton NMR and Coulomb explosion imaging. Full article
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Perspective
Carbohydrate-Based Azacrown Ethers in Asymmetric Syntheses
Chemistry 2021, 3(2), 550-577; https://0-doi-org.brum.beds.ac.uk/10.3390/chemistry3020039 - 15 Apr 2021
Cited by 1 | Viewed by 800
Abstract
Carbohydrate-based crown ethers represent a special group of chiral phase transfer catalysts. Several derivatives of these macrocycles have been synthesized in our research group. Among these compounds, monoaza-15-crown-5 lariat ethers proved to be effective phase transfer and enantioselective catalysts in certain reactions. Those [...] Read more.
Carbohydrate-based crown ethers represent a special group of chiral phase transfer catalysts. Several derivatives of these macrocycles have been synthesized in our research group. Among these compounds, monoaza-15-crown-5 lariat ethers proved to be effective phase transfer and enantioselective catalysts in certain reactions. Those chiral azacrown ethers incorporating various carbohydrate moieties in the macrocyclic structure are reviewed, which generated asymmetric induction in reactions, such as Michael addition, epoxidation of enones, Darzens condensation and Michael-initiated ring-closure (MIRC) reaction. Effects on the catalytic activity of the structural changes are the focus. Full article
(This article belongs to the Special Issue Organic Chemistry Research in Hungary)
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Article
Exploitation of Baird Aromaticity and Clar’s Rule for Tuning the Triplet Energies of Polycyclic Aromatic Hydrocarbons
Chemistry 2021, 3(2), 532-549; https://0-doi-org.brum.beds.ac.uk/10.3390/chemistry3020038 - 14 Apr 2021
Cited by 2 | Viewed by 1136
Abstract
Polycyclic aromatic hydrocarbons (PAH) are a prominent substance class with a variety of applications in molecular materials science. Their electronic properties crucially depend on the bond topology in ways that are often highly non-intuitive. Here, we study, using density functional theory, the triplet [...] Read more.
Polycyclic aromatic hydrocarbons (PAH) are a prominent substance class with a variety of applications in molecular materials science. Their electronic properties crucially depend on the bond topology in ways that are often highly non-intuitive. Here, we study, using density functional theory, the triplet states of four biphenylene-derived PAHs finding dramatically different triplet excitation energies for closely related isomeric structures. These differences are rationalised using a qualitative description of Clar sextets and Baird quartets, quantified in terms of nucleus independent chemical shifts, and represented graphically through a recently developed method for visualising chemical shielding tensors (VIST). The results are further interpreted in terms of a 2D rigid rotor model of aromaticity and through an analysis of the natural transition orbitals involved in the triplet excited states showing good consistency between the different viewpoints. We believe that this work constitutes an important step in consolidating these varying viewpoints of electronically excited states. Full article
(This article belongs to the Special Issue A Special Issue in Honor of Professor Josef Michl)
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Article
The Impact of Structural Defects on Iodine Adsorption in UiO-66
Chemistry 2021, 3(2), 525-531; https://0-doi-org.brum.beds.ac.uk/10.3390/chemistry3020037 - 12 Apr 2021
Cited by 1 | Viewed by 892
Abstract
Radioactive I2 (iodine) produced as a by-product of nuclear fission poses a risk to public health if released into the environment, and it is thus vital to develop materials that can capture I2 vapour. Materials designed for the capture and storage [...] Read more.
Radioactive I2 (iodine) produced as a by-product of nuclear fission poses a risk to public health if released into the environment, and it is thus vital to develop materials that can capture I2 vapour. Materials designed for the capture and storage of I2 must have a high uptake capacity and be stable for long-term storage due the long half-life of 129I. UiO-66 is a highly stable and readily tuneable metal-organic framework (MOF) into which defect sites can be introduced. Here, a defective form of UiO-66 (UiO-66-FA) was synthesised and the presence of missing cluster moieties confirmed using confocal fluorescence microscopy and gas sorption measurements. The uptake of I2 vapour in UiO-66-FA was measured using thermal gravimetric analysis coupled mass spectrometry (TGA-MS) to be 2.25 g g−1, almost twice that (1.17 g g−1) of the pristine UiO-66. This study will inspire the design of new efficient I2 stores based upon MOFs incorporating structural defects. Full article
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Article
Molecular Docking and Molecular Dynamics Simulation Studies of Quinoline-3-Carboxamide Derivatives with DDR Kinases–Selectivity Studies towards ATM Kinase
Chemistry 2021, 3(2), 511-524; https://0-doi-org.brum.beds.ac.uk/10.3390/chemistry3020036 - 11 Apr 2021
Viewed by 866
Abstract
Quinoline-3-carboxamides are an essential class of drug-like small molecules that are known to inhibit the phosphatidylinositol 3-kinase-related kinases (PIKK) family kinases. The quinoline nitrogen is shown to bind to the hinge region of the kinases, making them competitive inhibitors of adenosine triphosphate (ATP). [...] Read more.
Quinoline-3-carboxamides are an essential class of drug-like small molecules that are known to inhibit the phosphatidylinositol 3-kinase-related kinases (PIKK) family kinases. The quinoline nitrogen is shown to bind to the hinge region of the kinases, making them competitive inhibitors of adenosine triphosphate (ATP). We have previously designed and synthesized quinoline-3-carboxamides as potential ataxia telangiectasia mutated (ATM) kinase inhibitors to function as an adjuvant treatment with DNA damaging agents. This article discusses the molecular docking studies performed with these derivatives with the DNA damage and response (DDR) kinases-ATM, ataxia telangiectasia and rad3 related (ATR), and DNA dependent protein kinase catalytic subunit (DNA-PKcs) and highlights their selectivity towards ATM kinase. Docking studies were also performed with mTOR and PI3Kγ, which are close homologs of the DDR kinases. Molecular dynamics simulations were performed for one of the inhibitors against all the enzymes to establish the stability of the interactions involved. Finally, the absorption, distribution, metabolism, and excretion (ADME) properties of the inhibitors were predicted using the QikProp manual in Maestro. In conclusion, the molecules synthesized showed high selectivity towards the ATM kinase in comparison with the other kinases, though the sequence similarity between them was relatively high. Full article
(This article belongs to the Special Issue Molecular Docking in Drug Discovery)
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Editorial
Supramolecular Chemistry in the 3rd Millennium
Chemistry 2021, 3(2), 509-510; https://0-doi-org.brum.beds.ac.uk/10.3390/chemistry3020035 - 08 Apr 2021
Viewed by 700
Abstract
The description of supramolecular chemistry as “chemistry beyond the molecule” (Jean-Marie Lehn, 1987 Nobel Lecture and Gautam R [...] Full article
(This article belongs to the Special Issue Supramolecular Chemistry in the 3rd Millennium)
Review
Polyprotic Acids and Beyond—An Algebraic Approach
Chemistry 2021, 3(2), 454-508; https://0-doi-org.brum.beds.ac.uk/10.3390/chemistry3020034 - 07 Apr 2021
Viewed by 809
Abstract
For an N-protic acid–base system, the set of nonlinear equations (i.e., mass action and balance laws) provides a simple analytical solution/formula for any integer N ≥ 1. The approach is applicable for the general case of zwitterionic acids HNA+Z (e.g., [...] Read more.
For an N-protic acid–base system, the set of nonlinear equations (i.e., mass action and balance laws) provides a simple analytical solution/formula for any integer N ≥ 1. The approach is applicable for the general case of zwitterionic acids HNA+Z (e.g., amino acids, NTA, and EDTA), which includes (i) the “ordinary acids” as a special case (Z = 0) and (ii) surface complexation. Examples are presented for N = 1 to 6. The high-N perspective allows the classification of equivalence points (including isoionic and isoelectric points). Principally, there are two main approaches to N-protic acids: one from hydrochemistry and one “outside inorganic hydrochemistry”. They differ in many ways: the choice of the reference state (either HNA or A−N), the reaction type (dissociation or association), the type/nature of the acidity constants, and the structure of the formulas. Once the (nonlinear) conversion between the two approaches is established, we obtain a systematics of acidity constants (macroscopic, microscopic, cumulative, and Simms). Finally, from the viewpoint of statistical mechanics (canonical isothermal–isobaric ensemble), buffer capacities, buffer intensities, and higher pH derivatives are actually fluctuations in the form of variance, skewness, and kurtosis. Full article
(This article belongs to the Section Theoretical Chemistry)
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Article
Chloropentaphenyldisiloxane—Model Study on Intermolecular Interactions in the Crystal Structure of a Monofunctionalized Disiloxane
Chemistry 2021, 3(2), 444-453; https://0-doi-org.brum.beds.ac.uk/10.3390/chemistry3020033 - 29 Mar 2021
Cited by 4 | Viewed by 869
Abstract
Small functional siloxane units have gained great interest as molecular model systems for mimicking more complex silicate structures both in nature and in materials chemistry. The crystal structure of chloropentaphenyldisiloxane, which was synthesized for the first time, was elucidated by single-crystal X-ray diffraction [...] Read more.
Small functional siloxane units have gained great interest as molecular model systems for mimicking more complex silicate structures both in nature and in materials chemistry. The crystal structure of chloropentaphenyldisiloxane, which was synthesized for the first time, was elucidated by single-crystal X-ray diffraction analysis. The molecular crystal packing was studied in detail using state-of-the-art Hirshfeld surface analysis together with a two-dimensional fingerprint mapping of the intermolecular interactions. It was found that the phenyl C–H bonds act as donors for both weak C–H···π and C–H···Cl hydrogen bond interactions. The influence of intramolecular Si–O–Si bond parameters on the acceptor capability of functional groups in intermolecular hydrogen bond interactions is discussed. Full article
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