Amyloids are proteins of a cross-β structure found as deposits in several diseases and also in normal tissues (nails, spider net, silk). Aromatic amino acids are frequently found in amyloid deposits. ...Although they are not indispensable, aromatic amino acids, phenylalanine, tyrosine and tryptophan, enhance significantly the kinetics of formation and thermodynamic stability, while tape or ribbon-like morphology is represented in systems with experimentally detected π-π interactions between aromatic rings. Analysis of geometries and energies of the amyloid PDB structures indicate the prevalence of aromatic-nonaromatic interactions and confirm that aromatic-aromatic interactions are not crucial for the amyloid formation.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
A study of crystal structures from the Cambridge Structural Database (CSD) and DFT calculations reveals that parallel pyridine–pyridine and benzene–pyridine interactions at large horizontal ...displacements (offsets) can be important, similar to parallel benzene–benzene interactions. In the crystal structures from the CSD preferred parallel pyridine–pyridine interactions were observed at a large horizontal displacement (4.0–6.0 Å) and not at an offset of 1.5 Å with the lowest calculated energy. The calculated interaction energies for pyridine–pyridine and benzene–pyridine dimers at a large offset (4.5 Å) are about 2.2 and 2.1 kcal mol−1, respectively. Substantial attraction at large offset values is a consequence of the balance between repulsion and dispersion. That is, dispersion at large offsets is reduced, however, repulsion is also reduced at large offsets, resulting in attractive interactions.
This way or that: In crystal structures from the Cambridge Structural Database preferred parallel pyridine–pyridine interactions are observed at large horizontal displacements (4.0–6.0 Å, see picture) and not at an offset of 1.5 Å, which had the lowest calculated energy.
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Water molecules from crystal structures archived in the CSD show a relatively large range both in the bond angle and bond lengths. High level
ab initio
calculations at the CCSD(T)/CBS level predicted ...a possibility for energetically low-cost (±1 kcal mol
−1
) changes of the bond angle and bond lengths in a wide range, from 96.4° to 112.8° and from 0.930 Å to 0.989 Å, respectively.
High level
ab initio
calculations predicted a possibility for energetically low-cost (±1 kcal mol
−1
) change of the bond angle and bond lengths in wide range,from 96.4° to 112.8° and from 0.930 Å to 0.989 Å, respectively.
Quantum chemical calculations were performed on model systems of stacking interactions between the acac type chelate rings of nickel, palladium, and platinum. CCSD(T)/CBS calculations showed that ...chelate-chelate stacking interactions are significantly stronger than chelate-aryl and aryl-aryl stacking interactions. Interaction energy surfaces were calculated at the LC-ωPBE-D3BJ/aug-cc-pVDZ level, which gives energies in good agreement with CCSD(T)/CBS. The stacking of chelates in an antiparallel orientation is stronger than the stacking in a parallel orientation, which is in agreement with the larger number of antiparallel stacked chelates in crystal structures from the Cambridge Structural Database. The strongest antiparallel chelate-chelate stacking interaction is formed between two platinum chelates, with a CCSD(T)/CBS interaction energy of -9.70 kcal mol-1, while the strongest stacking between two palladium chelates and two nickel chelates has CCSD(T)/CBS energies of -9.21 kcal mol-1 and -9.50 kcal mol-1, respectively. The strongest parallel chelate-chelate stacking was found for palladium chelates, with a LC-ωPBE-D3BJ/aug-cc-pVDZ energy of -6.51 kcal mol-1. The geometries of the potential surface minima are not the same for the three metals. The geometries of the minima are governed by electrostatic interactions, which are the ones determining the positions of the energy minima. Electrostatic interactions are governed by different electrostatic potentials above the metals, which are very positive for nickel, slightly positive for palladium, and slightly negative for platinum.
•Chelate rings in square-planar transition-metal complexes stack with aromatic rings.•Chelate rings stack with other isolated or fused chelate rings in the CSD structures.•Binding energies for these ...interactions exceed that for two benzene molecules.•These interactions are important for crystal packing and supramolecular structures.
Analysis of crystal structure data deposited in the Cambridge Structural Database (CSD) has shown that aromatic rings tend to stack with square planar transition metal complexes when they contain chelate rings. In these interactions, the orientation between chelate and aryl ring is a parallel-displaced orientation, like stacking interactions between aromatic molecules. In fused systems containing chelate and aryl rings, the aryl rings prefer to stack with the chelate rather than with other aryl rings. Quantum chemical calculations show that chelate-aryl stacking is stronger than aryl-aryl stacking. Interaction energies of six-membered chelates of the acetylacetonato type with benzene exceed −6kcal/mol (CCSD(T)/CBS), more that twice as strong as that for two benzene molecules. Further analysis of the CSD has shown that chelate rings, both isolated and fused stack with other chelate rings. These chelate-chelate stacking interactions can have both face-to-face and parallel-displaced geometries, unlike the stacking interactions between aromatic molecules, for which face-to-face geometry is not typical. Chelate-chelate stacking is stronger than aryl-aryl stacking and stronger even than chelate-aryl stacking. Stacking energies between six-membered chelates of acetylacetonato type exceed −9kcal/mol, while those between five-membered dithiolene chelates are even stronger. Calculated interaction energies and analysis of supramolecular structures have shown that chelate-chelate and chelate-aryl stacking must be considered in understanding the packing and organization of supramolecular systems and crystal engineering.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK, ZRSKP
Carbon monoxide (CO) is an important biological gasotransmitter in living cells. Precise spatial and temporal control over release of CO is a major requirement for clinical application. To date, the ...most reported carbon monoxide releasing materials use expensive fabrication methods and require harmful and poorly designed tissue-penetrating UV irradiation to initiate the CO release precisely at infected sites. Herein, we report the first example of utilizing a green light-responsive CO-releasing polymer P synthesized via ring-opening metathesis polymerization. Both monomer M and polymer P were very stable under dark conditions and CO release was effectively triggered using minimal power and low energy wavelength irradiation (550 nm, ≤28 mW). Time-dependent density functional theory (TD-DFT) calculations were carried out to simulate the electronic transition and insight into the nature of the excitations for both L and M. TD-DFT calculations indicate that the absorption peak of M is mainly due to the excitation of the seventh singlet excited state, S7. Furthermore, stretchable materials using polytetrafluoroethylene (PTFE) strips based on P were fabricated to afford P-PTFE, which can be used as a simple, inexpensive, and portable CO storage bandage. Insignificant cytotoxicity as well as cell permeability was found for M and P against human embryonic kidney cells.
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Two-dimensional (2D) halogen-bonded organic frameworks were readily engineered by strong and directional effects of the primary Br O and the secondary Br π halogen bonding interactions from the ...tetrabromobenzene-1,4-dicarboxylic acid (H
2
Br
4
BDC) building molecule involving 100% supramolecular yields. The 2D assembly can function as a host layered framework for the intercalation of various guest solvents including acetone (ATN), ethanol (EtOH), dimethyl sulfoxide (DMSO), and ethylene glycol (EG) resulting in a 1 : 2 host : guest complexation stoichiometry
viz.
H
2
Br
4
BDC·2S (S = ATN (
1
ATN
), EtOH (
2
EtOH
), DMSO (
3
DMSO
), and EG (
4
EG
)). All the solvates show remarkable similarities in their 2D layered sheets and the bilayer distance significantly responds to the size, shape, molecular conformation, and strength of the hydrogen bonding capability of the intercalated solvent molecules. The transition between solvate formation and desolvation was found to be facile and reversible upon the desolvation-resolvation process. The estimated Br O halogen bonding energy of the solvates is in the −0.6 to −1.7 kcal mol
−1
range, which was determined by quantum-mechanical calculations based on density functional theory (DFT) calculations. Furthermore, to quantitatively identify the host-guest intermolecular interactions of these solvates, they were visually compared by Hirshfeld surface analysis.
2D halogen-bonded organic frameworks were readily engineered by strong and directional effects of the primary Br O and the secondary Br π halogen bonding interactions from the tetrabromobenzene-1,4-dicarboxylic acid building molecule involving 100% supramolecular yields.
In the study of hydrogen bonds between noncoordinated and metal-coordinated ethylenediamine and a water molecule, the data in the Cambridge Structural Database (CSD) were analyzed and DFT ...calculations were performed. For coordinated ethylenediamine in the CSD, the analyzed distributions of d OH distances show a maximum in the range of 2.0–2.1 Å, while the angle α shows a maximum in the range of 150–160°. The DFT calculations were done for octahedral geometries of cobalt(III), copper(II), and nickel(II) complexes and square-planar geometry of palladium(II) complexes. The coordination of ethylenediamine to the metal ions strengthens its hydrogen bond with the water molecule. Namely, noncoordinated ethylenediamine and the water molecule have an interaction energy of −2.3 kcal/mol, while for coordinated ethylenediamine, the interacting energy spans from −4.0 to −28.0 kcal/mol depending on the metal ion and charge of the complex. The hydrogen bond energies have a good correlation with the calculated electrostatic potential on the interacting hydrogen atom. The coordination number and oxidation states of the metal have a significant influence on the electrostatic potential on the interacting hydrogen atom and the energy of hydrogen bonds.
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Accurate values for the energies of stacking interactions of nickel‐ and copper‐based six‐membered chelate rings with benzene are calculated at the CCSD(T)/CBS level. The results show that ...calculations made at the ωB97xD/def2‐TZVP level are in excellent agreement with CCSD(T)/CBS values. The energies of Cu(C3H3O2)(HCO2) and Ni(C3H3O2)(HCO2) chelates stacking with benzene are −6.39 and −4.77 kcal mol−1, respectively. Understanding these interactions might be important for materials with properties that are dependent on stacking interactions.
Stacks of energy: Energies of stacking interactions between benzene and metal chelates are calculated at the CCSD(T)/CBS level of theory. A copper chelate is found to stack more favorably with benzene than a nickel chelate. The energies of these interactions are significantly higher than that of benzene–benzene stacking. These results might be important for tuning the magnetic and electrical properties of organic–inorganic materials.
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Important interactions: The interactions between two benzene molecules in the parallel orientation are studied by means of crystallographic and computational methods. The results may have interesting ...applications in the study of systems containing aromatic molecules, including biomolecules and pharmaceuticals. The figure shows the minimum of a benzene dimer at a large offset (optimized geometry with an interaction energy of 2.01 kcal mol−1).
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