Syntheses, characterizations, crystal structures and Hirshfeld surface analyses of methyl 4-[4-(di-fluorometh-oxy)phen-yl]-2,7,7-trimethyl-5-oxo-1,4,5,6,7,8-hexa-hydro-quinoline-3-carboxyl-ate, isopropyl 4-[4-(di-fluoro-meth-oxy)phen-yl]-2,6,6-trimethyl-5-oxo-1,4,5,6,7,8-hexa-hydro-quinoline-3-carboxyl-ate and tert-butyl 4-[4-(di-fluoro-meth-oxy)phen-yl]-2,6,6-trimethyl-5-oxo-1,4,5,6,7,8-hexa-hydro-quinoline-3-carboxyl-ate.

The crystal structures and Hirshfeld surface analyses of three similar compounds are reported. Methyl 4-[4-(di-fluoro-meth-oxy)phen-yl]-2,7,7-trimethyl-5-oxo-1,4,5,6,7,8-hexa-hydro-quinoline-3-carboxyl-ate, (C21H23F2NO4), (I), crystallizes in the monoclinic space group C2/c with Z = 8, while isopropyl 4-[4-(di-fluoro-meth-oxy)phen-yl]-2,6,6-trimethyl-5-oxo-1,4,5,6,7,8-hexa-hydro-quinoline-3-carb-oxyl-ate, (C23H27F2NO4), (II) and tert-butyl 4-[4-(di-fluoro-meth-oxy)phen-yl]-2,6,6-trimethyl-5-oxo-1,4,5,6,7,8-hexa-hydro-quinoline-3-carboxyl-ate, (C24H29F2NO4), (III) crystallize in the ortho-rhom-bic space group Pbca with Z = 8. In the crystal structure of (I), mol-ecules are linked by N-H⋯O and C-H⋯O inter-actions, forming a tri-periodic network, while mol-ecules of (II) and (III) are linked by N-H⋯O, C-H⋯F and C-H⋯π inter-actions, forming layers parallel to (002). The cohesion of the mol-ecular packing is ensured by van der Waals forces between these layers. In (I), the atoms of the 4-di-fluoro-meth-oxy-phenyl group are disordered over two sets of sites in a 0.647 (3): 0.353 (3) ratio. In (III), the atoms of the dimethyl group attached to the cyclo-hexane ring, and the two carbon atoms of the cyclo-hexane ring are disordered over two sets of sites in a 0.646 (3):0.354 (3) ratio.

Energy, water, and protein folding: A molecular dynamics-based quantitative inventory of molecular interactions and forces that make proteins stable.

Protein folding energetics can be determined experimentally on a case-by-case basis but it is not understood in sufficient detail to provide deep control in protein design. The fundamentals of protein stability have been outlined by calorimetry, protein engineering, and biophysical modeling, but these approaches still face great difficulty in elucidating the specific contributions of the intervening molecules and physical interactions. Recently, we have shown that the enthalpy and heat capacity changes associated to the protein folding reaction can be calculated within experimental error using molecular dynamics simulations of native protein structures and their corresponding unfolded ensembles. Analyzing in depth molecular dynamics simulations of four model proteins (CI2, barnase, SNase, and apoflavodoxin), we dissect here the energy contributions to ΔH (a key component of protein stability) made by the molecular players (polypeptide and solvent molecules) and physical interactions (electrostatic, van der Waals, and bonded) involved. Although the proteins analyzed differ in length, isoelectric point and fold class, their folding energetics is governed by the same quantitative pattern. Relative to the unfolded ensemble, the native conformations are enthalpically stabilized by comparable contributions from protein-protein and solvent-solvent interactions, and almost equally destabilized by interactions between protein and solvent molecules. The native protein surface seems to interact better with water than the unfolded one, but this is outweighed by the unfolded surface being larger. From the perspective of physical interactions, the native conformations are stabilized by van de Waals and Coulomb interactions and destabilized by conformational strain arising from bonded interactions. Also common to the four proteins, the sign of the heat capacity change is set by interactions between protein and solvent molecules or, from the alternative perspective, by Coulomb interactions.

Enantioselective Adsorption on Magnetic Surfaces.

From the beginning of molecular theory, the interplay of chirality and magnetism has intrigued scientists. There is still the question if enantiospecific adsorption of chiral molecules occurs on magnetic surfaces. Enantiomer discrimination was conjectured to arise from chirality-induced spin separation within the molecules and exchange interaction with the substrate's magnetization. Here, it is shown that single helical aromatic hydrocarbons undergo enantioselective adsorption on ferromagnetic cobalt surfaces. Spin and chirality sensitive scanning tunneling microscopy reveals that molecules of opposite handedness prefer adsorption onto cobalt islands with opposite out-of-plane magnetization. As mobility ceases in the final chemisorbed state, it is concluded that enantioselection must occur in a physisorbed transient precursor state. State-of-the-art spin-resolved ab initio simulations support this scenario by refuting enantio-dependent chemisorption energies. These findings demonstrate that van der Waals interaction should also include spin-fluctuations which are crucial for molecular magnetochiral processes.

van der Waals interaction energies for ferric ion sensors using prismatic and cylindrical pore approximations for a MOF pore.

Using the Lennard-Jones potential, we determine analytical expressions for van der Waals interaction energies between a point and a rectangular prism-shaped pore, writing them in terms of standard elementary functions. The parameter values for a new ferric ion sensor are used to compare these calculations with the cylindrical pore approximation for the interactions between an ion and a metal organic framework (MOF) pore. The results using the prismatic pore approximation predict the same qualitative outcomes as a cylindrical pore approximation. However, the prismatic approximation predicts lower magnitudes for both the interaction potential energy minimum and the force maximum, since the average distance from the centre-line to the surface of the prism is greater. We suggest that in some circumstances it is sufficient to use the simpler cylindrical approximation, provided that the cylinder radius is chosen so that the cross-sectional area is equal to the area of the prism pore opening. However, atoms at the nodes should remain approximated by semi-infinite lines. We also determine the interaction between a second ferric ion and a blocked MOF pore; as expected, the second ferric ion experiences a force away from the pore, implying that approaching ferric ions can only occupy vacant MOF pores.

Crystal structure and Hirshfeld surface analysis of 2,2'-[(3,5-di-tert-butyl-4-hy-droxy-phen-yl)methanedi-yl]bis-(3-hy-droxy-5,5-di-methyl-cyclo-hex-2-en-1-one).

In the title compound, C31H44O5, mol-ecules are connected by O-H⋯O and C-H⋯O hydrogen bonds, forming hydrogen-bonded zigzag chains running along the b axis and parallel to the (001) plane. The mol-ecular packing is stabilized by van der Waals inter-actions between these chains along the a and c axes. The inter-molecular inter-actions in the crystal structure were qu-anti-fied and analysed using Hirshfeld surface analysis.

Exploring Alternative Pathways to Target Bacterial Type II Topoisomerases Using NBTI Antibacterials: Beyond Halogen-Bonding Interactions.

Novel bacterial topoisomerase inhibitors (NBTIs) are a new class of antibacterial agents that target bacterial type II topoisomerases (DNA gyrase and topoisomerase IV). Our recently disclosed crystal structure of an NBTI ligand in complex with DNA gyrase and DNA revealed that the halogen atom in the para position of the phenyl right hand side (RHS) moiety is able to establish strong symmetrical bifurcated halogen bonds with the enzyme; these are responsible for the excellent enzyme inhibitory potency and antibacterial activity of these NBTIs. To further assess the possibility of any alternative interactions (e.g., hydrogen-bonding and/or hydrophobic interactions), we introduced various non-halogen groups at the p-position of the phenyl RHS moiety. Considering the hydrophobic nature of amino acid residues delineating the NBTI's binding pocket in bacterial topoisomerases, we demonstrated that designed NBTIs cannot establish any hydrogen-bonding interactions with the enzyme; hydrophobic interactions are feasible in all respects, while halogen-bonding interactions are apparently the most preferred.

Crystal structure and Hirshfeld surface analysis of isopropyl 4-[2-fluoro-5-(tri-fluoro-meth-yl)phen-yl]-2,6,6-trimethyl-5-oxo-1,4,5,6,7,8-hexa-hydro-quinoline-3-carboxyl-ate.

In the title compound, C23H25F4NO3, the 1,4-di-hydro-pyridine ring adopts a distorted boat conformation, while the cyclo-hexene ring is almost showing a half-chair conformation. In the crystal, inter-molecular N-H⋯O hydrogen bonds connect the mol-ecules into chains with graph-set motif C(6) parallel to the a-axis. These chains are linked together by C-H⋯O and C-H⋯F inter-actions, forming a three-dimensional network. In addition, C-H⋯π inter-actions link the mol-ecules into layers parallel to the (100) plane. A Hirshfeld surface analysis was performed to further investigate the inter-molecular inter-actions.

Anharmonicity Reveals the Tunability of the Charge Density Wave Orders in Monolayer VSe2.

VSe2 is a layered compound that has attracted great attention due to its proximity to a ferromagnetic state that is quenched by its charge density wave (CDW) phase. In the monolayer limit, unrelated experiments have reported different CDW orders with different transition temperatures, making this monolayer very controversial. Here we perform first-principles nonperturbative anharmonic phonon calculations in monolayer VSe2 in order to estimate the CDW order and the corresponding transition temperature. They reveal that monolayer VSe2 develops two independent charge density wave orders that compete as a function of strain. Variations of only 1.5% in the lattice parameter are enough to stabilize one order or the other. Moreover, we analyze the impact of external Lennard-Jones interactions, showing that these can act together with anharmonicity to suppress the CDW orders. Our results solve previous experimental contradictions, highlighting the high tunability and substrate dependency of the CDW orders of monolayer VSe2.

Synthesis, characterization, crystal structure and Hirshfeld surface analysis of isobutyl 4-[4-(di-fluoro-meth-oxy)phen-yl]-2,6,6-trimethyl-5-oxo-1,4,5,6,7,8-hexa-hydro-quinoline-3-carboxyl-ate.

In the title compound, C24H29F2NO4, which crystallizes in the ortho-rhom-bic Pca21 space group with Z = 4, the 1,4-di-hydro-pyridine ring adopts a distorted boat conformation, while the cyclo-hexene ring is in a distorted half-chair conformation. In the crystal, the mol-ecules are linked by N-H⋯O and C-H⋯O inter-actions, forming supra-molecular chains parallel to the a axis. These chains pack with C-H⋯π inter-actions between them, forming layers parallel to the (010) plane. The cohesion of the crystal structure is ensured by van der Waals inter-actions between these layers. Hirshfeld surface analysis shows the major contributions to the crystal packing are from H⋯H (56.9%), F⋯H/H⋯F (15.7%), O⋯H/H⋯O (13.7%) and C⋯H/H⋯C (9.5%) contacts.

Cycloalkyl Groups as Building Blocks of Artificial Carbohydrate Receptors: Studies with Macrocycles Bearing Flexible Side-Arms.

The cyclopentyl group was expected to act as a building block for artificial carbohydrate receptors and to participate in van der Waals contacts with the carbohydrate substrate in a similar way as observed for the pyrrolidine ring of proline in the crystal structures of protein-carbohydrate complexes. Systematic binding studies with a series of 1,3,5-trisubstituted 2,4,6-triethylbenzenes bearing various cycloalkyl groups as recognition units provided indications of the involvement of these groups in the complexation process and showed the influence of the ring size on the receptor efficiency. Representatives of compounds that exhibit a macrocyclic backbone and flexible side arms were now chosen as further model systems to investigate whether the previously observed effects represent a general trend. Binding studies with these macrocycles towards ß-D-glucopyranoside, an all-equatorial substituted carbohydrate substrate, included 1H NMR spectroscopic titrations and microcalorimetric investigations. The performed studies confirmed the previously observed tendency and showed that the compound bearing cyclohexyl groups displays the best binding properties.

Mapping the Binding Energy of Layered Crystals to Macroscopic Observables.

Van der Waals (vdW) integration of two dimensional (2D) crystals into functional heterostructures emerges as a powerful tool to design new materials with fine-tuned physical properties at an unprecedented precision. The intermolecular forces governing the assembly of vdW heterostructures are investigated by first-principles models, yet translating the outcome of these models to macroscopic observables in layered crystals is missing. Establishing this connection is, therefore, crucial for ultimately designing advanced materials of choice-tailoring the composition to functional device properties. Herein, components from both vdW and non-vdW forces are integrated to build a comprehensive framework that can quantitatively describe the dynamics of these forces in action. Specifically, it is shown that the optical band gap of layered crystals possesses a peculiar ionic character that works as a quantitative indicator of non-vdW forces. Using these two components, it is then described why only a narrow range of exfoliation energies for this class of materials is observed. These findings unlock the microscopic origin of universal binding energy in layered crystals and provide a general protocol to identify and synthesize new crystals to regulate vdW coupling in the next generation of heterostructures.

Crystal structure and Hirshfeld surface analysis of 4-(3-meth-oxy-phen-yl)-2,6-di-phenyl-pyridine.

The title compound, C24H19NO, was obtained via the reaction of (1E,2E)-3-(3-meth-oxy-phen-yl)-1-phenyl-prop-2-en-1-one with ethyl 2-oxo-propano-ate, using NH4I as a catalyst. The compound crystallizes in the monoclinic space group I2/a. In the mol-ecule, the four rings are not in the same plane, the pyridine ring being inclined to the benzene rings by 17.26 (6), 56.16 (3) and 24.50 (6)°. In the crystal, mol-ecules are linked by C-H⋯π inter-actions into a three-dimensional network. To further analyse the inter-molecular inter-actions, a Hirshfeld surface analysis was performed. Hirshfeld surface analysis indicates that the most abundant contributions to the crystal packing are from H⋯H (50.4%), C⋯H/H⋯C (37.9%) and O⋯H/H⋯O (5.1%) inter-actions.

Crystal structure and Hirshfeld surface analysis of ethyl 2'-amino-5-bromo-3'-cyano-6'-methyl-2-oxo-spiro-[indoline-3,4'-pyran]-5'-carboxyl-ate.

The crystal used for structure determination contained, along with the title compound, C17H14BrN3O4, an admixture [0.0324 (11)] of its 7-bromo isomer. The 2,3-di-hydro-1H-indole ring system is nearly planar, while the conformation of the 4H-pyran ring is close to a flattened boat. The mean planes of these fragments form a dihedral angle of 86.67 (9)°. The carboxyl-ate group lies near the plane of 4H-pyran, its orientation is stabilized by an intra-molecular C-H⋯O contact. In the crystal, the mol-ecules are connected into layers by N-H⋯N and N-H⋯O hydrogen bonds. The most important contributions to the crystal packing are from H⋯H (33.1%), O⋯H/H⋯O (16.3%), N⋯H/H⋯N (12.1%), Br⋯H/H⋯Br (11.5%) and C⋯H/H⋯C (10.6%) inter-actions.

Synthesis, characterization, crystal structure and Hirshfeld surface analysis of a hexa-hydro-quinoline derivative: tert-butyl 4-([1,1'-biphen-yl]-4-yl)-2,6,6-trimethyl-5-oxo-1,4,5,6,7,8-hexa-hydro-quinoline-3-carboxyl-ate.

The title compound, C29H33NO3, crystallizes with three mol-ecules (A, B and C) in the asymmetric unit. They differ in the twist of the phenyl and benzene rings of the 1,1'-biphenyl ring with respect to the plane of the 1,4-di-hydro-pyridine ring. In all three mol-ecules, the 1,4-di-hydro-pyridine ring adopts a distorted boat conformation. The cyclo-hexene ring has an envelope conformation in mol-ecules A and B, while it exhibits a distorted half-chair conformation for both the major and minor components in the disordered mol-ecule C. In the crystal, mol-ecules are linked by C-H⋯O and N-H⋯O hydrogen bonds, forming layers parallel to (100) defining R 1 4(6) and C(7) graph-set motifs. Additional C-H⋯π inter-actions consolidate the layered structure. Between the layers, van der Waals inter-actions stabilize the packing, as revealed by Hirshfeld surface analysis. The greatest contributions to the crystal packing are from H⋯H (69.6% in A, 69.9% in B, 70.1% in C), C⋯H/H⋯C (20.3% in A, 20.6% in B, 20.3% in C) and O⋯H/H⋯O (8.6% in A, 8.6% in B, 8.4% in C) inter-actions.

Crystal structures and Hirshfeld surface analyses of 2-amino-4-(4-bromo-phen-yl)-6-oxo-1-phenyl-1,4,5,6-tetra-hydro-pyridine-3-carbo-nitrile hemi-hydrate and 1,6-di-amino-2-oxo-4-phenyl-1,2-di-hydro-pyridine-3,5-dicarbo-nitrile.

In 2-amino-4-(4-bromo-phen-yl)-6-oxo-1-phenyl-1,4,5,6-tetra-hydro-pyridine-3-carbo-nitrile hemihydrate, C18H14BrN3O·0.5H2O, (I), pairs of mol-ecules are linked by pairs of N-H⋯N hydrogen bonds, forming dimers with an R 2 2(12) ring motif. The dimers are connected by N-H⋯Br and O-H⋯O hydrogen bonds, and C-Br⋯π inter-actions, forming layers parallel to the (010) plane. 1,6-Di-amino-2-oxo-4-phenyl-1,2-di-hydro-pyridine-3,5-dicarbo-nitrile, C13H9N5O, (II), crystallizes in the triclinic space group P with two independent mol-ecules (IIA and IIB) in the asymmetric unit. In the crystal of (II), mol-ecules IIA and IIB are linked by inter-molecular N-H⋯N and N-H⋯O hydrogen bonds into layers parallel to (001). These layers are connected along the c-axis direction by weak C-H⋯N contacts. C-H⋯π and C-N⋯π inter-actions connect adjacent mol-ecules, forming chains along the a-axis direction. In (I) and (II), the stability of the packing is ensured by van der Waals inter-actions between the layers. In (I), Hirshfeld surface analysis showed that the most important contributions to the crystal packing are from H⋯H (37.9%), C⋯H/H⋯C (18.4%), Br⋯H/H⋯Br (13.3%), N⋯H/H⋯N (11.5%) and O⋯H/H⋯O (10.0%) inter-actions, while in (II), H⋯H inter-actions are the most significant contributors to the crystal packing (27.6% for mol-ecule IIA and 23.1% for mol-ecule IIB).

Energetic basis of hydrogen bond formation in aqueous solution.

The thermodynamic forces driving the formation of H-bonds in macromolecules have long been the subject of speculation, theory and experiment. Comparison of the energetic parameters of AT and GC base pairs in DNA duplexes has recently led to the realisation that formation of a 'naked' hydrogen bond, i.e. without other accompanying Van der Waals close contacts, is a non-enthalpic process driven by the entropy increase resulting from release of tightly bound water molecules from the component polar groups. This unexpected conclusion finds a parallel in the formation of ionic bonds, for example between the amino groups of DNA binding proteins and the oxygens of DNA phosphate groups that are also non-enthalpic and entropy driven. The thermodynamic correspondence between these two types of polar non-covalent bonding implies that the non-enthalpic nature of base pairing in DNA is not particular to that specific structural circumstance.

Crystal structure and Hirshfeld surface analysis of 2,2'-(phenyl-aza-nedi-yl)bis-(1-phenyl-ethan-1-one).

The whole mol-ecule of the title compound, C22H19NO2, is generated by twofold rotational symmetry. The N atom exhibits a trigonal-planar geometry and is located on the twofold rotation axis. In the crystal, mol-ecules are linked by C-H⋯O contacts with R 2 2(12) ring motifs, and C-H⋯π inter-actions, resulting in ribbons along the c-axis direction. van der Waals inter-actions between these ribbons consolidate the mol-ecular packing. Hirshfeld surface analysis indicates that the greatest contributions to the crystal packing are from H⋯H (45.5%), C⋯H/H⋯C (38.2%) and O⋯H/H⋯O (16.0%) inter-actions.

Crystal structure and Hirshfeld surface analysis of 4-bromo-2-[3-methyl-5-(2,4,6-tri-methyl-benz-yl)oxazolidin-2-yl]phenol.

The title compound, C20H24BrNO2, is chiral at the carbon atoms on either side of the oxygen atom of the oxazolidine ring and crystallizes as a racemate. The 1,3-oxazolidine ring adopts an envelope conformation with the N atom in an endo position. The mean plane of the oxazolidine ring makes dihedral angles of 77.74 (10) and 45.50 (11)°, respectively, with the 4-bromo-phenol and 1,3,5-tri-methyl-benzene rings. In the crystal, adjacent mol-ecules are connected via C-H⋯O hydrogen bonds and C-H⋯π inter-actions into layers parallel to the (200) plane. The packing is strengthened by van der Waals inter-actions between parallel mol-ecular layers. A Hirshfeld surface analysis shows that H⋯H (58.2%), C⋯H/H⋯C (18.9%), and Br⋯H/H⋯Br (11.5%) inter-actions are the most abundant in the crystal packing.

Moiré Modulation of Van Der Waals Potential in Twisted Hexagonal Boron Nitride.

When a twist angle is applied between two layered materials (LMs), the registry of the layers and the associated change in their functional properties are spatially modulated, and a moiré superlattice arises. Several works explored the optical, electric, and electromechanical moiré-dependent properties of such twisted LMs but, to the best of our knowledge, no direct visualization and quantification of van der Waals (vdW) interlayer interactions has been presented, so far. Here, we use tapping mode atomic force microscopy phase-imaging to probe the spatial modulation of the vdW potential in twisted hexagonal boron nitride. We find a moiré superlattice in the phase channel only when noncontact (long-range) forces are probed, revealing the modulation of the vdW potential at the sample surface, following AB and BA stacking domains. The creation of scalable electrostatic domains, modulating the vdW potential at the interface with the environment by means of layer twisting, could be used for local adhesion engineering and surface functionalization by affecting the deposition of molecules or nanoparticles.

Spray drying of non-chemically prepared nanofibrillated cellulose: Improving water redispersibility of the dried product.

Despite increasing interest in using nanofibrillated cellulose (NFC) as food thickener and emulsifier, poor water redispersibility of dried NFC, which is form suitable for practical utilization, significantly limits such applications. Studies are lacking on preparation of dried NFC with superior redispersibility. The present study therefore proposed and examined strategies to improve water redispersibility of spray dried NFC via the use of selected co-carriers, i.e., gum Arabic with/without xanthan gum, carboxymethyl cellulose or pectin. Synergistic interactions between NFC and co-carriers, as confirmed by X-ray diffraction (XRD) patterns and Fourier transform infrared (FTIR) spectra, helped prevent NFC agglomeration during spray drying. All reconstituted spray-dried NFC/co-carriers suspensions exhibited shear-thinning and gel-like behaviors, thus supporting the use of such suspensions as thickener and emulsifier. Spray-dried NFC with 80% gum Arabic and 20% xanthan gum (SD-NFC/GA20XG) resulted in suspension with highest viscosity; the suspension also performed best at recovering viscous characteristics of NFC. Water thickened by SD-NFC/GA20XG had strongest shear-thinning behavior, indicating that SD-NFC/GA20XG suspension resulted in smoothest mouth feel and easiest swallowing. Such observations were supported by XRD patterns of SD-NFC/GA20XG, which suggested that its relative crystallinity was the lowest. Its FTIR spectra also showed the highest intensity of -OH bending and carbonyl bands, which are directly related to water adsorption capability of NFC. Use of reconstituted SD-NFC/GA20XG as emulsifier also resulted in highest stability for oil-in-water (O/W) Pickering emulsion during storage for up to 30 days.