Light-Modulated Self-Blockage of a Urea Binding Site in a Stiff-Stilbene Based Anion Receptor

Anion binding to a receptor based on stiff-stilbene, which is equipped with a urea hydrogen bond donating group and a phosphate or phosphinate hydrogen bond accepting group, can be controlled by light. In one photoaddressable state (E isomer) the urea binding site is available for binding, while in the other (Z isomer) it is blocked because of an intramolecular interaction with its hydrogen bond accepting motif. This intramolecular interaction is supported by DFT calculations and ¹H NMR titrations reveal a significantly lower anion binding strength for the state in which anion binding is blocked. Furthermore, the molecular switching process has been studied in detail by UV/Vis and NMR spectroscopy. The presented approach opens up new opportunities toward the development of photoresponsive anion receptors.     

Aromaticity in linear polyacenes: generalized population analysis and molecular quantum similarity approach

The relative aromaticity of benzenoid rings in the linear polyacenes is investigated using two novel aromaticity approaches. According to the first, the aromaticity of individual benzene rings was gauged by the values of six-center bond indices (SCI) calculated within the so-called Generalized Population Analysis (GPA). In the second approach, the same goal is addressed using the theory of Molecular Quantum Similarity (MQS). Both independent approaches are found to correlate very well, and both point toward decreasing aromaticity in any linear polyacenes upon going from the outer to inner rings.     

Adhesion from tethered ligand-receptor bonds with microsecond lifetimes

According to classical thermodynamics, biological ligand-receptor bonds should have a median lifetime of about 2 ms, and nearly half should have lifetimes of nanoseconds to microseconds. As a result, it is clear that many "weak" bonds are indispensable for cellular adhesion, signaling, and other critical events. However, the forces required to rupture such weak bonds and the adhesion they provide between surfaces are largely unknown because of their propensity to dissociate rapidly from a measuring probe. To measure such weak bond forces quantitatively, we followed nature's example of adhering surfaces with many weak ligand-receptor bonds. Analogously to how multiplicity promotes stronger adhesion between cellular membranes, multiple bonds created significant adhesion between model cellular surfaces. Specifically, we used an automated surface forces apparatus to measure the adhesion between complementary surfaces bearing dense populations of streptavidin receptors and flexible PEG tethers that each anchored a weakly binding ligand (HABA, or 2-(4-hydroxyphenylazo) benzoic acid). We show that this short-lived bond (<100 mus) leads to low forces of dissociation and only a small fraction being simultaneously bound. These results are significant because the HABA-streptavidin bond energy ( approximately 10.5kBT) is similar to the average found in nature (14.7kBT). The measurements exemplify how a single ligand-receptor bond may fall apart and rejoin many times before completing a cellular function yet can still exhibit strength in numbers.     

A new look at the ylidic bond in phosphorus ylides and related compounds: energy decomposition analysis combined with a domain-averaged fermi hole analysis

Geometries and bond dissociation energies of the ylide compounds H2CPH3, H2CPMe3, H2CPF3, (BH2)2CPH3, H2CNH3, H2CAsH3, H2SiPH3, and (BH2)2SiPH3 have been calculated using ab initio (MP2, CBS-QB3) and DFT (B3LYP, BP86) methods. The nature of the ylidic bond R2E1-E2X3 was investigated with an energy decomposition analysis and with the domain-averaged Fermi hole (DAFH) analysis. The results of the latter method indicate that the peculiar features of the ylidic bond can be understood in terms of donor-acceptor interactions between closed-shell R2E1 and E2X3 fragments. The DAFH analysis clearly shows that there are two bonding contributions to the ylidic bond. The strength of the donor and acceptor contributions to the attractive orbital interactions can be estimated from the energy decomposition analysis (EDA) calculations, which give also the contributions of the electrostatic attraction and the Pauli repulsion of the chemical bonding. The EDA and DAFH results clearly show that the orbital interactions take place through the singlet ground state of the R2E1 fragment where the donor orbital of E1 yields pi-type back-donation while the E2X3 lone-pair orbital yields sigma-type bonding. Both bonds are polarized toward E2X3 when E2 = P, while the sigma-type bonding remains more polarized at E2X3 when E2 = N, As. This shows that the phosphorus ylides exhibit a particular bonding situation which is clearly different from that of the nitrogen and arsenic homologues. With ylides built around a P-C linkage, the pi-acceptor strength of phosphorus and the sigma-acceptor strength at carbon contribute to a double bond which is enhanced by electrostatic contributions. The strength of the sigma and pi components and the electrostatic attraction are then fine-tuned by the substituents at C and P, which yields a peculiar type of carbon-phosphorus bonding. The EDA data reveal that the relative strength of the ylidic bond may be determined not only by the R2E1 --> E2X3 pi back-donation, but also by the electrostatic contribution to the bonding. The calculations of the R2E1-E2X3 bond dissociation energy using ab initio methods predict that the order of the bond strength is H2C-PMe3 > H2C-PF3 > H2C-PH3 > (BH2)2C-PH3 > H2C-AsH3 > H2C-NH3 approximately H2Si-PH3 approximately (BH2)2Si-PH3. The DFT methods predict a similar trend, but they underestimate the bond strength of (BH2)2CPH3.     

Thinking Like a Chemist: Intuition in Thermoelectric Materials

The coupled transport properties required to create an efficient thermoelectric material necessitates a thorough understanding of the relationship between the chemistry and physics in a solid. We approach thermoelectric material design using the chemical intuition provided by molecular orbital diagrams, tight binding theory, and a classic understanding of bond strength. Concepts such as electronegativity, band width, orbital overlap, bond energy, and bond length are used to explain trends in electronic properties such as the magnitude and temperature dependence of band gap, carrier effective mass, and band degeneracy and convergence. The lattice thermal conductivity is discussed in relation to the crystal structure and bond strength, with emphasis on the importance of bond length. We provide an overview of how symmetry and bonding strength affect electron and phonon transport in solids, and how altering these properties may be used in strategies to improve thermoelectric performance.     

A theoretical study of the hydrogen bond donor capability and co-operative effects in the hydrogen bond complexes of the diaza-aromatic betacarbolines

In this work, we present a quantum mechanical investigation on the hydrogen bond interactions of N(9)-methyl-9H-pyrido[3,4-b]indole, MBC, and N(2)-methyl-9H-pyrido[3,4-b]indole, BCA, with different hydrogen bond donors. Thus, it has been analysed the influence that the hydrogen bond donor strength and the co-operative effect of the increasing number of donor molecules have on the shape of the potential energy surfaces versus the N···H distances, r(N–H). To rationalize the nature of the interactions, the Bader theory has been applied and the characteristics of the bond critical points analysed. The results show that two different hydrogen bond complexes can be formed depending on the donor capabilities or the number of donor molecules included in the calculations. The topological parameters from the Bader theory are used to justify the statement that the analysed interactions can be classified as weak or partially covalent hydrogen bond interactions, respectively. As experimentally observed, weak hydrogen bond donors form weak hydrogen bond complexes, called HBC. Upon the increase of the donor strength the N···H proton is shifted nearest to the nitrogen atom giving rise to the observation of a stronger hydrogen bond complex, the proton transfer complex, PTC. The most outstanding result of these studies is the fact that the formation of the PTC can also be managed just by changing the number of donor molecules, that is, by a co-operative effect of the hydrogen bonds.     

Synthesis and properties of oligonucleotides with iodo-substituted aromatic aglycons: investigation of possible halogen bonding base pairs

Ab initio calculations of halogen bond energies of artificial base pairs constructed between iodinated aromatic nucleobase mimics and nitrogen-containing acceptor molecules such as pyridine and imidazole suggest that modified base pairs are converted to optimized planar base pairs with weak Delta E values of -0.19 to -3.93 kcal/mol. To evaluate the contribution of halogen bonding toward duplex stabilization of such modified nucleobase mimics introduced into artificial base pairs, we synthesized three C-nucleoside analogues 1-3 with several iodinated aromatic rings and an imidazole nucleoside derivative 4 and incorporated them into oligodeoxynucleotides. Hybridization studies of modified oligodeoxynucleotides incorporating iodoaromatic bases showed their unique universal base-like ability; however, no indication of halogen bond formation was observed. A more sophisticated design is required for the development of new base pairs stabilized by halogen bonding.     

Ligand field parameters in pentaammine complexes of chromium(III) with a carbon-oxygen or phosphorus-oxygen donor

Summary Coordination of oxyphosphorus ligands to pentaamminechromium(III) lowers the ligand field strength of the ammines to a much greater extent than trichloroacetate. This presumably signifies a weaker metal-nitrogen bond, and may contribute to the reluctance of the amines in aminophosphonate ligands to coordinate.     

Hydrogen bonding without borders: an atoms-in-molecules perspective

It is shown that the electron density at the hydrogen bond critical point increases approximately linearly with increasing stabilization energy in going from weak hydrogen bonds to moderate and strong hydrogen bonds, thus serving as an indicator of the nature and gradual change of strength of the hydrogen bond for a large number of test intermolecular complexes.     

The interaction of molecular oxygen with active sites of graphite: a theoretical study

The adsorption of molecular oxygen at defective edge sites of zigzag and armchair graphite surfaces has been investigated by adopting cluster models in conjunction with density functional theory. Several different types of chemisorbed O₂ species are identified. It was found that the defect edge sites exhibit the significant catalytic role toward the adsorption and activation of molecular oxygen. The O₂ molecule is not only able to strongly bind to these edge sites, but the O–O bond strength is obviously weakened. Moreover, the calculated adsorption energy for O₂ adsorbed on the clean graphite basal surface is fairly consistent with the weak interaction nature of O₂ with the surface observed in the experiment, indicating one-layer cluster model is an effective way to study O₂ adsorption on graphite surface in terms of accuracy and computational cost, which is in agreement with previous experience. Whereas, we note that the local detailed arrangement of edge carbon atoms can play an important effect on the adsorption of O₂ on defect surfaces.     

Rotational Spectroscopy Probes Water Flipping by Full Fluorination of Benzene

The topology of the interaction of water with benzene changes drastically upon full H→F substitution on the aromatic ring: the weak O−H⋅⋅⋅π hydrogen bond is replaced by a O⋅⋅⋅π linkage, of about the same strength. Hexafluorobenzene–water appears to be the prototype system to investigate this kind of weak bond. The pulsed Fourier transform microwave technique has been used for the detection of the rotational spectra of the normal species and five isotopologues which unambiguously led to the identification of the geometry. Quantum mechanical calculations have been performed to interpret the experimental evidence.     

Predicting Trigger Bonds in Explosive Materials through Wiberg Bond Index Analysis

Understanding the explosive decomposition pathways of high‐energy‐density materials (HEDMs) is important for developing compounds with improved properties. Rapid reaction rates make the detonation mechanisms of HEDMs difficult to understand, so computational tools are used to predict trigger bonds—weak bonds that break, leading to detonation. Wiberg bond indices (WBIs) have been used to compare bond densities in HEDMs to reference molecules to provide a relative scale for the bond strength to predict the activated bonds most likely to break to trigger an explosion. This analysis confirms that X?NO₂ (X=N,C,O) bonds are trigger linkages in common HEDMs such as TNT, RDX and PETN, consistent with previous experimental and theoretical studies. Calculations on a small test set of substituted tetrazoles show that the assignment of the trigger bond depends upon the functionality of the material and that the relative weakening of the bond correlates with experimental impact sensitivities.     

Ligand effects on hydrogen atom transfer from hydrocarbons to three-coordinate iron imides

A new β-diketiminate ligand with 2,4,6-tri(phenyl)phenyl N-substituents provides protective bulk around the metal without exposing any weak C-H bonds. This ligand improves the stability of reactive iron(III) imido complexes with Fe═NAd and Fe═NMes functional groups (Ad = 1-adamantyl; Mes = mesityl). The new ligand gives iron(III) imido complexes that are significantly more reactive toward 1,4-cyclohexadiene than the previously reported 2,6-diisopropylphenyl diketiminate variants. Analysis of X-ray crystal structures implicates Fe═N-C bending, a longer Fe═N bond, and greater access to the metal as potential reasons for the increase in C-H bond activation rates.     

Molecular description of indigo oxidation mechanisms initiated by OH and OOH radicals

In this work, we report a quantum chemistry mechanistic study of the hydroxyl (?OH) and hydroperoxyl (?OOH) radicals initiated oxidation of indigo, within the density functional theory framework. All possible hydrogen abstraction and radical addition reaction pathways have been considered. We find that the reaction between a free indigo molecule and an ?OH radical occurs mainly through two competing mechanisms: H-abstraction from an NH site and ?OH addition to the central C═C double bond. Although the latter is favored, both channels occur, the indigo chromophore group structure is modified, and thus the color is changed. This mechanism adequately accounts for the loss of chromophore in urban air, including indoor air such as in museums and in urban areas. Regarding the reactivity of indigo toward ?OOH radicals, only ?OOH-addition to the central double bond is thermodynamically feasible. The corresponding transition state free energy value is about 10 kcal/mol larger than the one for the ?OH initiated oxidation. Therefore, even considering that the ?OOH concentration is considerably larger than the one of ?OH, this reaction is not expected to contribute significantly to indigo oxidation under atmospheric conditions.     

Energy landscapes of biomolecular adhesion and receptor anchoring at interfaces explored with dynamic force spectroscopy

Beyond covalent connections within protein and lipid molecules, weak noncovalent interactions between large molecules govern properties of cellular structure and interfacial adhesion in biology. These bonds and structures have limited lifetimes and so will fail under any level of force if pulled on for the right length of time. As such, the strength of interaction is the level of force most likely to disrupt a bond on a particular time scale. For instance, strength is zero on time scales longer than the natural lifetime for spontaneous dissociation. On the other hand, if driven to unbind or change structure on time scales shorter than needed for diffusive relaxation, strength will reach an adiabatic limit set by the maximum gradient in a potential of mean force. Over the enormous span of time scales between spontaneous dissociation and adiabatic detachment, theory predicts that bond breakage under steadily rising force occurs most frequently at a force determined by the rate of loading. Moreover, the continuous plot (spectrum) of strength expressed on a scale of loge(loading rate) provides a map of the prominent barriers traversed in the energy landscape along the force-driven pathway and reveals the differences in energy between barriers. Illustrated with results from recent laboratory measurements, dynamic strength spectra provide a new view into the inner complexity of receptor-ligand interactions and receptor lipid anchoring.     

Intramolecular xh⋯π hydrogen bonds. a quantum study of the conformation of ortho-ethylenic phenols and anilines

IR evidence suggests the occurrence of a weak hydrogen bond between the XH (X = N, O) bond and the π bond of ortho-ethylenic substituents in anilines and phenols. A quantum mechanical (PCILO) study of the conformational maps has been performed for a series of compounds and confirms the generality of this phenomenon and the role of the charge transfer π→ XH* excitation. The strength of the hydrogen bond depends on the position of the double bond in the o chain; it is stronger for o-(β,γ-ethylenic) derivatives than for o-(α,β) and o-(γ,σ) analogs. The steric influence of methyl substituents is illustrated. The role of XH ? π bond in the photochemical behaviour of these molecules is discussed.     

Density functional calculations on the conversion of azide and carbon monoxide to isocyanate and dinitrogen by a nickel to sulfur rebound mechanism

Density functional calculations (B3 LYP & BP86) on a model system for the reaction between carbon monoxide and [Ni(N(3))('S(3)')](-) ('S(3)'(2-)=bis(2-mercaptophenyl)sulfide (2-)) predict a three-step mechanism. First, CO attacks the nickel to generate a pseudo "square-pyramidal" complex, in which CO, N(3) (-), and two sulfides are basal and the central S atom of the 'S(3)'(2-) ligand backs away from Ni to form a weak Ni-S apical bond. Then, CO inserts into the Ni-N bond and the weak apical Ni--S bond rebounds to its original strength as the nickel forms a square-planar intermediate. Finally, in a one-step process N(2) leaves as the remaining N atom and carbonyl rearrange to produce the nickel isocyanate product [Ni(NCO)('S(3)')](-).     

Characterization of a closed-shell fluorine-fluorine bonding interaction in aromatic compounds on the basis of the electron density

A bond path linking two saturated fluorine atoms is found to be ubiquitous in crowded difluorinated aromatic compounds. The bond path is shown to persist for a range of internuclear distances (2.3-2.8 A) and a range of relative orientations of the two C-F internuclear axes. The F. . .F bonding is shown to exhibit all the hallmarks of a closed-shell weak interaction. The presence of such a bond path can impart as much as 14 kcal/mol of local stabilization to the molecule in which it exists, a stabilization that can be offset or even overwhelmed by destabilization of other regions in the molecule. Several other weak closed-shell interactions were also found and characterized including F. . .C, F. . .O, and C. . .C interactions, hydrogen bonding, dihydrogen bonding, and hydrogen-hydrogen bonding. This study represents another example of the usefulness and richness of the bond path concept and of the theory of atoms in molecules in general.     

Adhesion of polyelectrolyte multilayers: sealing and transfer of microchamber arrays

Polyelectrolyte multilayer (PEM) films with array of responsive microchambers are promising candidates for site-specific release of chemicals in small and precisely defined quantities on demand. It requires effective sealing of the microchambers toward a support to prevent leakage of a cargo. In this paper, we study the pressure-induced adhesion of poly(allylammonium)-poly(4-styrenesulfonate) (PAH-PSS) multilayers assembled on different templates toward the poly(4-styrenesulfonate)-poly(diallyldimethylammonium) multilayer. The tensile bond strength increases from 0.4 to 3.5 MPa upon the increase of PAH-PSS bilayers from 10 to 40, if assembled on a silicon template. Weaker tensile bond strength of 0.35 MPa between the PAH-PSS multilayer and a poly(methylmethacrylate) (PMMA) template results in adhesive break at this interface and allows mechanical removal of the template. The successful PEM transfer is demonstrated for templates of various geometrical patterns, while the tensile break of a multilayer film happens for the others.