Distinguishment of Weak Interactions of Hydrogen Atoms Bound to Carbon Atoms: X-Ray Crystal Structural and Hirshfeld Surface Analyses of 2-Hydroxy-7-methoxy-3-(2,4,6-trimethylbenzoyl)naphthalene with the 2-Methoxylated Homologue

X-ray crystal and Hirshfeld surface analyses of 2-hydroxy-7-methoxy-3-(2,4,6-trimethylbenzoyl)naphthalene and its 2-methoxylated homologue show quantitatively and visually distinct molecular contacts in crystals and minute differences in the weak intermolecular interactions. The title compound has a helical tubular packing, where molecules are piled in a two-folded head-to-tail fashion. The homologue has a tight zigzag molecular string lined up behind each other via nonclassical intermolecular hydrogen bonds between the carbonyl oxygen atom and the hydrogen atom of the naphthalene ring. The dnorm index obtained from the Hirshfeld surface analysis quantitatively demonstrates stronger molecular contacts in the homologue, an ethereal compound, than in the title compound, an alcohol, which is consistent with the higher melting temperature of the former than the latter. Stabilization through the significantly weak intermolecular nonclassical hydrogen bonding interactions in the homologue surpasses the stability imparted by the intramolecular C=O…H–O classical hydrogen bonds in the title compound. The classical hydrogen bond places the six-membered ring in the concave of the title molecule. The hydroxy group opposingly disturbs the molecular aggregation of the title compound, as demonstrated by the distorted H…H interactions covering the molecular surface, owing to the rigid molecular conformation. The position of effective interactions predominate over the strength of the classical/nonclassical hydrogen bonds in the two compounds.

Electron Density Geometry and the Quantum Theory of Atoms in Molecules

A novel form of charge density analysis, that of isosurface curvature redistribution, is formulated and applied to the toy problem of carbonyl oxygen activation in formaldehyde. The isosurface representation of the electron charge density allows us to incorporate the rigorous geometric constraints of closed surfaces towards the analysis and chemical interpretation of the charge density response to perturbations. Visual inspection of 2D isosurface motion resulting from applied external electric fields reveals how isosurface curvature flows within and between atoms, and that a molecule can be uniquely and completely partitioned into chemically significant regions of positive and negative curvature. These concepts reveal that carbonyl oxygen activation proceeds primarily through curvature and charge redistribution within rather than between Bader atoms. Using gradient bundle analysis—the partitioning of formaldehyde into infinitesimal volume elements bounded by QTAIM zero flux surfaces—the observations from visual isosurface inspection are verified. The results of the formaldehyde carbonyl analysis are then shown to be transferable to the substrate carbonyl in the ketosteroid isomerase enzyme, laying the groundwork for extending this approach to the problems of enzymatic catalysis.

Exploring Orthogonality between Halogen and Hydrogen Bonding Involving Benzene

The concept of orthogonality between halogen and hydrogen bonding, brought out by Ho and coworkers some years ago, has become a widely accepted idea within the chemists’ community. While the original work was based on a common carbonyl oxygen as acceptor for both interactions, we explore here, by means of M06-2X, M11, ωB97X, and ωB97XD/aug-cc-PVTZ DFT calculations, the interdependence of halogen and hydrogen bonding with a shared π-electron system of benzene. The donor groups (specifically NCBr and H2O) were placed on either or the same side of the ring, according to a double T-shaped or a perpendicular geometry, respectively. The results demonstrate that the two interactions with benzene are not strictly independent on each other, therefore outlining that the orthogonality between halogen and hydrogen bonding, intended as energetical independence between the two interactions, should be carefully evaluated according to the specific acceptor group.

Electron Density Geometry and the Quantum Theory of Atoms in Molecules

A novel form of charge density analysis, that of isosurface curvature redistribution, is formulated and applied to the toy problem of carbonyl oxygen activation in formaldehyde. The isosurface representation of the electron charge density allows us to incorporate the rigorous geometric constraints of closed surfaces towards the analysis and chemical interpretation of the charge density response to perturbations. Visual inspection of 2D isosurface motion resulting from applied external electric fields reveals how isosurface curvature flows within and between atoms, and that a molecule can be uniquely and completely partitioned into chemically significant regions of positive and negative curvature. These concepts reveal that carbonyl oxygen activation proceeds primarily through curvature and charge redistribution within rather than between Bader atoms. Using gradient bundle analysis—the partitioning of formaldehyde into infinitesimal volume elements bounded by QTAIM zero flux surfaces—the observations from visual isosurface inspection are verified. The results of the formaldehyde carbonyl analysis are then shown to be transferable to the substrate carbonyl in the ketosteroid isomerase enzyme, laying the groundwork for extending this approach to the problems of enzymatic catalysis.

Electron Density Geometry and the Quantum Theory of Atoms in Molecules

A novel form of charge density analysis, that of isosurface curvature redistribution, is formulated and applied to the toy problem of carbonyl oxygen activation in formaldehyde. The isosurface representation of the electron charge density allows us to incorporate the rigorous geometric constraints of closed surfaces towards the analysis and chemical interpretation of the charge density response to perturbations. Visual inspection of 2D isosurface motion resulting from applied external electric fields reveals how isosurface curvature flows within and between atoms, and that a molecule can be uniquely and completely partitioned into chemically significant regions of positive and negative curvature. These concepts reveal that carbonyl oxygen activation proceeds primarily through curvature and charge redistribution within rather than between Bader atoms. Using gradient bundle analysis—the partitioning of formaldehyde into infinitesimal volume elements bounded by QTAIM zero flux surfaces—the observations from visual isosurface inspection are verified. The results of the formaldehyde carbonyl analysis are then shown to be transferable to the substrate carbonyl in the ketosteroid isomerase enzyme, laying the groundwork for extending this approach to the problems of enzymatic catalysis.

Inhibiting wax deposition using palm oil additives

Among the flow assurance problems that the petroleum industry faces, the deposition of paraffin waxes on to the wall of the pipeline is the most challenging. The challenge arises when the crude oil temperature decreases below the wax appearance temperature which prompts wax crystallization in the crude oil. An efficient method in remedying paraffin wax deposition is the utilization of chemical inhibitors. However, currently used chemical inhibitors are costly and environmentally harmful if a spillage occurs. Therefore, the use of biodegradable or environmentally friendly inhibitors as potential chemical inhibitors is being studied by various researchers. This study investigated oleic acid, poly (ethylene-co-vinyl acetate) (EVA) and triethanolamine (TEA) as inhibitors that perform based on the van der Waals intermolecular interaction between the main wax component molecule eicosane C20H42 using molecular dynamics simulations Material Studio 8.0 software package. In order to analyse the desired structural property which is the radial distribution function (RDF), COMPASS force field was used. The RDF and g(r) function portrayed the functional atoms which aid in inhibiting the agglomeration and crystallization of the wax crystal formation. The presence of a carbonyl oxygen in oleic acid plays a vital role to inhibit the wax formation through the van der Waals interaction between active hydrogen atoms in eicosane molecule. Therefore, the chances of wax inhibition in eicosane are higher by introducing oleic acid as an inhibitor as compared to EVA and TEA. The results were then validated experimentally utilizing a cold finger technique under static condition.

Humidity-Sensing Properties of an 1D Antiferromagnetic Oxalate-Bridged Coordination Polymer of Iron(III) and Its Temperature-Induced Structural Flexibility

A novel one-dimensional (1D) oxalate-bridged coordination polymer of iron(III), {[NH(CH3)(C2H5)2][FeCl2(C2O4)]}n (1), exhibits remarkable humidity-sensing properties and very high proton conductivity at room temperature (2.70 × 10−4 (Ω·cm)−1 at 298 K under 93% relative humidity), in addition to the independent antiferromagnetic spin chains of iron(III) ions bridged by oxalate groups (J = −7.58(9) cm−1). Moreover, the time-dependent measurements show that 1 could maintain a stable proton conductivity for at least 12 h. Charge transport and magnetic properties were investigated by impedance spectroscopy and magnetization measurements, respectively. Compound 1 consists of infinite anionic zig-zag chains [FeCl2(C2O4)]nn− and interposed diethylmethylammonium cations (C2H5)2(CH3)NH+, which act as hydrogen bond donors toward carbonyl oxygen atoms. Extraordinarily, the studied coordination polymer exhibits two reversible phase transitions: from the high-temperature phase HT to the mid-temperature phase MT at T ~213 K and from the mid-temperature phase MT to the low-temperature phase LT at T ~120 K, as revealed by in situ powder and single-crystal X-ray diffraction. All three polymorphs show large linear thermal expansion coefficients.

Crystal structures and hydrogen-bonding analysis of a series of benzamide complexes of zinc(II) chloride

Ionic co-crystals are co-crystals between organic molecules and inorganic salt coformers. Co-crystals of pharmaceuticals are of interest to help control polymorph formation and potentially improve stability and other physical properties. We describe the preparation, crystal structures, and hydrogen bonding of five different 2:1 benzamide or toluamide/zinc(II) chloride co-crystal salts, namely, bis(benzamide-κO)dichloridozinc(II), [ZnCl2(C7H7NO)2], dichloridobis(2-methylbenzamide-κO)zinc(II), [ZnCl2(C8H9NO)2], dichloridobis(3-methylbenzamide-κO)zinc(II), [ZnCl2(C8H9NO)2], dichloridobis(4-methylbenzamide-κO)zinc(II), [ZnCl2(C8H9NO)2], and dichloridobis(4-hydroxybenzamide-κO)zinc(II), [ZnCl2(C7H7NO2)2]. All of the complexes contain hydrogen bonds between the amide N—H group and the amide carbonyl oxygen atoms or the chlorine atoms, forming extended networks.

Crystal structures of bis-{N-[1-(pyridin-2-yl-κN)ethylidene]nicotine hydrazide-κ2N’,O}cobalt(II)bis(perchlorate) dihydrate and bis-{N'-[1-(pyridin-2-yl-κN)ethylidene]nicotinohydrazide-κ2N',O}copper(II) perchlorate

Complexes of Co(II), [Co(C26H24N8O2)]·(ClO4)2·(H2O)2 (1), and Cu(II), [Cu(C26H23N8O2)]·(ClO4) (2), have been synthesized. The prepared two compounds were characterized by elemental analysis, infrared and their structures were determined by single-crystal X-ray diffraction. The compound 1 crystallizes in the triclinic space group P-1 with the following unit cell parameters: a = 8.880 (5) Å, b = 10.529 (5) Å, c = 18.430 (5) Å, α = 99.407 (5)°, β = 102.174 (5)°, γ = 100.652 (5)°, V = 1618.2 (13) Å3, Z = 2, T = 293(2), μ(MoKα) = 0.77 mm-1, Dcalc = 1.582 g/cm3, 16135 reflections measured (5.050° ≤ 2q ≤ 59.152°), 7648 unique, Rint = 0.034 which were used in all calculations. The final R1 was 0.066 (I ≥ 2σ(I)) and wR2 was 0.22 (all data). The compound 2 crystallizes in the monoclinic space group P21/c with the following unit cell parameters : a = 11.652 (5) Å, b = 16.540 (5) Å, c = 14.512 (5) Å, β = 93.495 (5)°, V = 2791.6 (18) Å3, Z = 4, T = 293(2), μ(MoKα) = 1.05 mm-1, Dcalc = 1.768 g/cm3, 15592 reflections measured (5.624° ≤ 2θ ≤ 58.804°), 6630 unique, Rint = 0.025 which were used in all calculations. The final R1 was 0.050 (I ≥ 2σ(I)) and wR2 was 0.144 (all data). In both complexes, the ligand acts in a tridentate fashion. In the structure of the mononuclear complex 1, the Co(II) cation is coordinated by two ligand molecules. The basal plane around the Co(II) cation is occupied by two pyridine nitrogen atoms and two carbonyl oxygen atoms. Two imino nitrogen atoms occupy the apical positions of the distorted square-pyramidal geometry. The mononuclear 2 consists of a Cu(II) coordinated by one ligand and one monodeprotonated ligand molecule. The metal center lies in a distorted square bipyramidal environment. The basal plane around the Cu(II) is occupied by two pyridine nitrogen atoms and two carbonyl oxygen atoms, the apical position being occupied by the two imino nitrogen atoms.