Controlling Electron Delocalization in Vanadium-Based Hybrid Bronzes through Molecular Templation

We show that the conductivity of hybrid vanadium bronzes—mixed-valence organic–inorganic vanadium oxides—can be tuned over six orders of magnitude through judicious choice of molecular component. By systematically varying the steric profile, charge density, and propensity to hydrogen bond across a series of eight diammonium-based molecules, we engender multiple distinct motifs of V−O connectivity within the two-dimensional vanadium oxide layers of a family of bulk crystalline hybrid materials. A combination of single-crystal and powder X-ray diffraction analysis, variable-temperature electrical transport measurements, and a range of spectroscopic methods, including UV/Visible diffuse reflectance, X-ray photoelectron, and electron paramagnetic resonance are employed to probe how vanadium oxide layer topology correlates with electron localization. Specifically, alkylammonium molecules yield hybrids featuring more corrugated layers that contain V−O tetrahedra as well as a higher ratio of corner-sharing to edge-sharing polyhedra and that exhibit highly localized electronic behavior, while alkyl bipyridinium molecules yield more regular layers with polyhedral edge-sharing that show substantially delocalized electronic behavior. This work allows for the development of design principles based on structure–property relationships and brings the charge transport capabilities of hybrid vanadium bronzes to more technologically relevant levels.     

NIR Clusteroluminescence of Non-conjugated Phenolic Resins Enabled by Through-Space Interactions

Clusteroluminescence (CL) and through-space interactions (TSIs) of non-conjugated molecules have drawn more attention due to their unique photophysical behaviors that are different from largely conjugated luminogens. However, achieving red and even near-infrared (NIR) emission from such systems is still challenging due to the intrinsic drawbacks of non-conjugated molecules and the lack of theories for structure–property relationships. In this work, six phenolic resins are designed and synthesized based on two molecule-engineering strategies: increasing the number of TSIs units and introducing electron-donating/-withdrawing groups. All phenolic resins are verified as luminogens with CL property (CLgens), and the first example of CLgens with NIR emission (maximum emission wavelength ≥680 nm) and high absolute quantum yield (47 %) is reported. Experiments and theoretical analysis reveal that two TSIs types, through-space locally excited state and through-space charge transfer state, play essential roles in achieving CL from these non-conjugated polymers, which could be manipulated via changing structural conformation and electron density or altering electron transition behaviors. This work not only provides an approach to manipulate TSIs and CL of non-conjugated polymers but also endows commercially available phenolic resins with high practical value as luminescence materials.     

Relationship between Hammett's parameters and in silico density functional with tandem mass ESI‐CID fragmentation: Dihydropyridines as prototypes

Over the years, with the instrumental analysis evolution, the relationships between the carried‐out results with the data of theoretical analysis in silico and the Hammett's parameters have been reported. They have been very useful for chemical characterization of small organic molecules. Thus, this work aims at showing the feasibility and limitations for Hammett's and density functional theory applications in electrospray ionization–collision‐induced dissociation (ESI‐CID) fragmentation provision. For this, 13 dihydropyrimidinones para, meta, and orto monosubstituted were studied using ESI and CID in positive mode. As a result, it was observed that the main fragmentation includes the isocyanate and ethanol loses at low energy. Nevertheless, at higher energies, radical ions formed by McLafferty rearrangement were observed. The Hammett plots were correlated fragmentation profiles, showing good linearity for the [M + H]⁺, which does not occur to radical ions and carbocation's. These tendencies had demonstrated that the stability of protonate and activation energy of secondary ions changes with the pKa. The density functional theory studies indicated that, both nitrogen atoms in the dihydropyrimidinone's prototypes are capable of being protonated. However, the activation energy of fragmentation products is not changed. Therefore, this work has shown information, which can be useful to understand tandem mass spectrometry in ESI‐CID conditions for small organic molecules series. This is the first step for normalization of fragmentation pathway.     

Effects of unidirectional and mutual interactions between microstructures and azo dyes as “kinetic” probe molecules on cis→trans isomerization rate constants in aqueous P85 and F88 triblock copolymer solutions

Rate constants of the thermal cis → trans isomerization of azo dyes have been studied in aqueous P85 and F88 triblock copolymer solutions by means of microsecond flash photolysis. Inflection points or maxima of the nonlinear Arrhenius plots indicate microstructure changes around the “kinetic” probe molecules. Unidirectional interactions of micelle formation on reactivity are reflected by discontinuous change of rate constants at temperatures near the critical micellization temperatures (cmT) determined by means of probe‐free methods. Mutual interactions have been identified by means of significant differences between cmT and temperatures, where rate constants change discontinuously. The type of interactions depends on the properties of probe molecules and amphiphiles. Systems as studied in this work might be models of more complex biological reaction systems with temperature‐dependent microstructure changes. © 2007 Wiley Periodicals, Inc. 40: 59–65, 2007     

Molecular modeling study on surface,thermal, mechanical and gas diffusion properties of chitosan

The motivation of this work is to provide reliable and accurate modeling studies of the physical (surface, thermal, mechanical and gas diffusion) properties of chitosan (CS) polymer. Our computational efforts have been devoted to make a comparison of the structural bulk properties of CS with similar type of polymers such as chitin and cellulose through cohesive energy density, solubility parameter, hydrogen bonding, and free volume distribution calculations. Atomistic modeling on CS polymer using molecular mechanics (MM) and molecular dynamics (MD) simulations has been carried out in three dimensionally periodic and effective two dimensionally periodic condensed phases. From the equilibrated structures, surface energies were computed. The equilibrium structure of the films shows an interior region of mass density close to the value in the bulk state. Various components of energetic interactions have been examined in detail to acquire a better insight into the interactions between bulk structure and the film surface. MD simulation (NPT ensemble) has also been used to obtain polymer specific volume as a function of temperature. It is demonstrated that these V–T curves can be used to locate the volumetric glass transition temperature (T_g) reliably. The mechanical properties of CS have been obtained using the strain deformation method. Diffusion coefficients of O₂, N₂, and CO₂ gas molecules at 300 K in CS have been estimated. The calculated properties of CS are comparable with the experimental values reported in the literature. © 2007 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 45: 1260–1270, 2007     

Method and algorithm of obtaining the molecular intrinsic characteristic contours (MICCs) of organic molecules

The molecular intrinsic characteristic contour (MICC) is defined as the set of all the classical turning points of electron movement in a molecule. Studies on the MICCs of some medium organic molecules, such as dimethylether, acetone, and some homologues of alkanes, alkenes, and alkynes, as well as the electron density distributions on the MICCs, are shown for the first time. Results show that the MICC is an intrinsic approach to shape and size of a molecule. Unlike the van der Waals hard-sphere model, the MICC is a smooth contour, and it has a clear physical meaning. Detailed investigations on the cross-sections of MICCs have provided a kind of important information about atomic size changing in the process of forming molecules. Studies on electron density distribution on the MICC not only provide a new insight into molecular shape, but also show that the electron density distribution on the boundary surface relates closely with molecular properties and reactivities. For the homologues of alkanes, Rout(H), Dmin, and Dmax (the minimum and maximum of electron density on the MICC), all have very good linear relationships with minus of the molecular ionization potential. This work may serve as a basis for exploring a new reactivity indicator of chemical reactions and for studying molecular shape properties of large organic and biological molecules.     

Molecular photochromic systems: a theoretical and experimental investigation on zinc(II) dithizonate

Zinc(II)‐dithizone based molecular systems [Zn(HDz)₂] are intriguing candidates for the development of optical devices thanks to their interesting photochromic and nonlinear optical properties. In the present work, the behavior of Zn(HDz)₂ in different solvents was investigated by a combined theoretical and experimental approach. In particular, solutions of both dithizone (H₂Dz) and Zn(HDz)₂ were analyzed by optical absorption spectroscopy and nuclear magnetic resonance (NMR) techniques, with particular attention to structure–properties relationships. Density functional and time‐dependent density functional calculations were performed on the stable and the activated forms of the complex, obtaining information on the energetics of their interconversion, as well as on the nature of their electronic excitations. Copyright © 2007 John Wiley & Sons, Ltd.     

Electron transport in Nano‐Gold–Silicon interfaces

The electron transport characteristics of gold–silicon interfaces are studied using a combined ab initio approach of the Green's function for electron transfer and quantum density functional theory (DFT) for finite and extended systems. The Kohn–Sham Hamiltonian of an extended cluster or molecule and the density of states (DOS) of bulk Si and Au are used to construct the interface Hamiltonian to obtain the DOS, electron transmission, and current–voltage characteristics of the interface. Diode behavior is observed with electron conduction when the gold side is positively biased with a threshold of 0.8 V. The presence of molecules trapped at the interface and the geometry of the metal atoms strongly affect the conductance, implying difficult or even impossible theory–experiment validations. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Adenosine Reagentless Electrochemical Aptasensor Using a Phosphorothioate Immobilization Strategy

This work deals with the characterization of a phosphorothioate anchoring strategy for aptamer molecules linked to gold, in the context of electrochemical sensors, using adenosine aptamer as model system. Surface density of immobilized phosphorothioate oligonucleotide sequences has been explored for a range of oligonucleotide concentrations (0.055–55 μM), finding a consequent variation of molecular surface density (3.5×10¹¹–2.8×10¹³ molecules/cm²). Most suitable aptamer concentration for adenosine recognition was also explored and found to be around 5.5 μM. As proof of concept of phosphorothioate strategy, electrochemical response to adenosine concentration was measured using a ferrocene‐labeled oligonucleotide sequence, and phosphorothioate anchoring thermal stability was compared to thiol immobilization.     

Toward understanding the nature of internal rotation barriers with a new energy partition scheme: ethane and n-butane

On the basis of an alternative energy partition scheme where density-based quantification of the steric effect was proposed [Liu, S. B. J. Chem. Phys. 2007, 126, 244103], the origin of the internal rotation barrier between the eclipsed and staggered conformers of ethane and n-butane is systematically investigated in this work. Within the new scheme, the total electronic energy is decomposed into three independent components, steric, electrostatic, and fermionic quantum. The steric energy defined in this way is repulsive, exclusive, and extensive and intrinsically linked to Bader's atoms in molecules approach. Two kinds of differences, adiabatic (with optimal structure) and vertical (with fixed geometry), are considered for the molecules in this work. We find that in the adiabatic case the eclipsed conformer possesses a larger steric repulsion than the staggered conformer for both molecules, but in the vertical cases the staggered conformer retains a larger steric repulsion. For ethane, a linear relationship between the total energy difference and the fermionic quantum energy difference is discovered. This linear relationship, however, does not hold for n-butane, whose behaviors in energy component differences are found to be more complicated. The impact of basis set and density functional choices on energy components from the new energy partition scheme has been investigated, as has its comparison with another definition of the steric effect in the literature in terms of the natural bond orbital analysis through the Pauli Exclusion Principle. In addition, profiles of conceptual density functional theory reactivity indices as a function of dihedral angle changes have been examined. Put together, these results suggest that the new energy partition scheme provides insights from a different perspective of internal rotation barriers.     

Sorption and diffusion of normal alkanes through poly(ethylene‐co‐vinyl acetate) membranes

The transport behavior of uncrosslinked and crosslinked poly(ethylene‐co‐vinyl acetate) membranes has been investigated using normal alkanes as probe molecules, in the temperature range of 30–60 °C. Benzoyl peroxide was used for crosslinking the matrix. It has been observed that, a critical concentration of crosslinker is necessary for maximum solvent uptake, followed by a decrease at higher concentration. The effect of free volume on liquid transport was investigated by positron annihilation lifetime spectroscopy. The mechanism of transport has been found to deviate from the regular Fickian behavior. The dependence of the transport coefficients on crosslink density, nature of penetrants, and temperature was studied. The polymer–solvent interaction parameter, enthalpy, and entropy of sorption have also been estimated from the transport data. The affine and phantom models for chemical crosslinks were used to predict the nature of crosslinks. Finally, the experimental sorption data were compared with theoretical predictions. © 2007 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 45: 2470–2480, 2007     

Exploring sets of molecules from patents and relationships to other active compounds in chemical space networks

Patents from medicinal chemistry represent a rich source of novel compounds and activity data that appear only infrequently in the scientific literature. Moreover, patent information provides a primary focal point for drug discovery. Accordingly, text mining and image extraction approaches have become hot topics in patent analysis and repositories of patent data are being established. In this work, we have generated network representations using alternative similarity measures to systematically compare molecules from patents with other bioactive compounds, visualize similarity relationships, explore the chemical neighbourhood of patent molecules, and identify closely related compounds with different activities. The design of network representations that combine patent molecules and other bioactive compounds and view patent information in the context of current bioactive chemical space aids in the analysis of patents and further extends the use of molecular networks to explore structure–activity relationships.     

Quantum topology phase diagrams for molecules,clusters, and solids

The need to make more quantitative use of the total electronic charge density distribution is demonstrated in this short perspective. This is framed in the perspective of the ground breaking early work of Bader and coworkers, along with mathematicians who captured the essential nature of a molecule in a suitably compact form in real space. We see that this simple form is the Poincaré–Hopf relation for molecules and clusters and the Euler–Hopf relation in solids. Thom's theory of elementary catastrophes combined with the Poincaré–Hopf relation provides the inspiration for the new quantum topology. An alternative use of the Poincaré–Hopf relation, molecular recognition, is discussed. Quantum topology is then used to create a topology phase diagram for both molecules and solids. The author adds their perspectives of the huge potential of the quantum topology approach by demonstrating the ease with which new theoretical ideas can be generated. © 2013 Wiley Periodicals, Inc.     

Description of self-diffusion coefficients of gases,liquids and fluids at high pressure based on molecular simulation data

The purpose of this work is to evaluate the potential of modeling the self-diffusion coefficient (SDC) of real fluids in all fluid states based on Lennard–Jones analytical relationships involving the SDC, the temperature, the density and the pressure. For that, we generated an equation of state (EOS) that interrelates the self-diffusion coefficient, the temperature and the density of the Lennard–Jones (LJ) fluid. We fit the parameters of such LJ–SDC–EOS using recent wide ranging molecular simulation data for the LJ fluid. We also used in this work a LJ pressure–density–temperature EOS that we combined with the LJ–SDC–EOS to make possible the calculation of LJ–SDC values from given temperature and pressure. Both EOSs are written in terms of LJ dimensionless variables, which are defined in terms of the LJ parameters ɛ and σ. These parameters are meaningful at molecular level. By combining both EOSs, we generated LJ corresponding states charts which make possible to conclude that the LJ fluid captures the observed behavioral patterns of the self-diffusion coefficient of real fluids over a wide range of conditions. In this work, we also performed predictions of the SDC of real fluids in all fluid states. For that, we assumed that a given real fluid behaves as a Lennard–Jones fluid which exactly matches the experimental critical temperature T_c and the experimental critical pressure P_c of the real fluid. Such an assumption implies average true prediction errors of the order of 10% for vapors, light supercritical fluids, some dense supercritical fluids and some liquids. These results make possible to conclude that it is worthwhile to use the LJ fluid reference as a basis to model the self-diffusion coefficient of real fluids, over a wide range of conditions, without resorting to non-LJ correlations for the density–temperature–pressure relationship. The database considered here contains more than 1000 experimental data points. The database practical reduced temperature range is from 0.53 to 2.4, and the practical reduced pressure range is from 0 to 68.4.     

Structure–activity relationship and the mechanism of analgesia of the analgesic drug 3-methyl-fentanyl and its analogs

The semiempirical self-consistent field MO (CNDO /2) calculations have been undertaken for 13 compounds involving 3-methyl-fentanyl and its analogs. Various quantum chemical indices were obtained. The relationships between the biological activity and quantum chemical indices of molecules of these compounds were investigated and it was found that there are remarkable relationships between the activity and some important quantum chemical indices such as the α-electron density of β substituent and the electron density of piperidyl nitrogen. The nature of interaction between the analgesics' molecule and the receptor was discussed on the basis of the relationships between the activity and quantum chemical indices and it was proposed that the β-substituent functions not only as a hydrophobic group, but also its electronic property has important effect on the activity. It may act as an electron acceptor and form acceptor–donor complex with receptor through the charge transfer process. The piperidyl nitrogen interacts with receptor forming quaternary ammonium ion and acting as positive charge center, and its electron density also has an important effect on the activity. The amide oxygen and nitrogen may be other active centers which function as donors when they interact with the receptor. The influence on activity through introduction of the hydroxyl group to the β-position of the 1-substituent of the piperdyl ring has also been discussed.     

Partitioning of atomization energy

The present work provides a technique for partitioning the atomization energy of a molecule into diatomic contributions. The method is largely based on the redistribution of the kinetic energy term in Mayer's energy partitioning and uses free‐atom energies as a reference. The comparison of Mayer's original method, the alternative Ichikawa–Yoshida approach, and the new atomization energy partitioning (AEP) shows that the new approach has advantages in describing trends in diatomic energies in molecules with triple bonds, as well as for hydrogen bonds. The proposed AEP is a viable alternative to Mayer's energy partitioning method. © 2007 Wiley Periodicals, Inc. Int. J. Quantum Chem, 2008