Topology of the electron density of multicenter bonding in the anion TCNE2 2−

For TCNE₂ ^2? the role of bond paths in the electron density is emphasized to show that the anion contains multicenter bonding interactions across 4 central carbon atoms conferring inherent stability to it, consistent with experimental, and theoretical studies of other authors.     

Bond Fukui functions as descriptor of the electron density reorganization in π conjugated systems

The bond Fukui function is introduced and tested as a new reactivity index capable of predicting the evolution of bond breaking and formation processes during an organic reaction involving π conjugated systems. As an illustration, we examine many cases where substituted ethylenes and dienes may respond to different reagents to yield cycloaddition, Michael addition, and other reactions at double bonds.     

Pointing the way to the products? Comparison of the stress tensor and the second-derivative tensor of the electron density

The eigenvectors of the electronic stress tensor can be used to identify where new bond paths form in a chemical reaction. In cases where the eigenvectors of the stress tensor are not available, the gradient-expansion-approximation suggests using the eigenvalues of the second derivative tensor of the electron density instead; this approximation can be made quantitatively accurate by scaling and shifting the second-derivative tensor, but it has a weaker physical basis and less predictive power for chemical reactivity than the stress tensor. These tools provide an extension of the quantum theory of atoms and molecules from the characterization of molecular electronic structure to the prediction of chemical reactivity.     

How well can new-generation density functional methods describe stacking interactions in biological systems?

We compare the performance of four recently developed DFT methods (MPW1B95, MPWB1K, PW6B95, and PWB6K) and two previous, generally successful DFT methods (B3LYP and B97-1) for the calculation of stacking interactions in six nucleic acid bases complexes and five amino acid pairs and for the calculation of hydrogen bonding interactions in two Watson-Crick type base pairs. We found that the four newly developed DFT methods give reasonable results for the stacking interactions in the DNA base pairs and amino acid pairs, whereas the previous DFT methods fail to describe interactions in these stacked complexes. We conclude that the new generation of DFT methods have greatly improved performance for stacking interaction as compared to previously available methods. We recommend the PWB6K method for investigating large DNA or protein systems where stacking plays an important role.     

Food authentication in real life: How to link nontargeted approaches with routine analytics?

In times of increasing globalization and the resulting complexity of trade flows, securing food quality is an increasing challenge. The development of analytical methods for checking the integrity and, thus, the safety of food is one of the central questions for actors from science, politics, and industry. Targeted methods, for the detection of a few selected analytes, still play the most important role in routine analysis. In the past 5 years, nontargeted methods that do not aim at individual analytes but on analyte profiles that are as comprehensive as possible have increasingly come into focus. Instead of investigating individual chemical structures, data patterns are collected, evaluated and, depending on the problem, fed into databases that can be used for further nontargeted approaches. Alternatively, individual markers can be extracted and transferred to targeted methods. Such an approach requires (i) the availability of authentic reference material, (ii) the corresponding high-resolution laboratory infrastructure, and (iii) extensive expertise in processing and storing very large amounts of data. Probably due to the requirements mentioned above, only a few methods have really established themselves in routine analysis. This review article focuses on the establishment of nontargeted methods in routine laboratories. Challenges are summarized and possible solutions are presented.     

The response electron–electron repulsion energy and energy component analysis in CC/MBPT methods

Molecular properties are computed as responses to perturbations (energy derivatives) in coupled-cluster (CC)/many-body perturbation theory (MBPT) models. Here, the CC/MBPT energy derivative with respect to a general two-electron (2-e) perturbation is assembled from gradient theory for 2-e property evaluation, including the electron repulsion energy. The correlation energy (?E) is shown to be the sum of response kinetic (?T), electron–nuclear attraction (?V), and electron repulsion (?V _ee ) energies. Thus, evaluation of total V _ee for energy component analysis is simple: For total energy (E), total 1-e responses T and V, and nuclear–nuclear repulsion energy (V _NN ), V _ee  = E ? V _NN  ? T ? V is the true 2-e response value. Component energy analysis is illustrated in an assessment of steric repulsion in ethane’s rotational barrier. Earlier SCF-based results (Bader et al. in J Am Chem Soc 112:6530, 1990) are corroborated: The higher-energy eclipsed geometry is favored versus staggered in the two repulsion energies (V _NN and V _ee ), while decisively disfavored in electron–nuclear attraction energy (V). Our best quality calculations (CCSD/cc-pVQZ) attain practical Virial Theorem compliance (i.e., agreement among the kinetic energy, potential energy, and total energy representations) in assigning 2.70 ± 0.06 to the barrier height; ?195.80 kcal/mol is assigned to the drop in “steric” repulsion upon going to the eclipsed geometry. Steric repulsion is not responsible for any fraction of the ~3 kcal/mol barrier.     

What is the future of electrophoresis in large-scale genomic sequencing?

Although a finished human genome reference sequence is now available, the ability to sequence large, complex genomes remains critically important for researchers in the biological sciences, and in particular, continued human genomic sequence determination will ultimately help to realize the promise of medical care tailored to an individual's unique genetic identity. Many new technologies are being developed to decrease the costs and to dramatically increase the data acquisition rate of such sequencing projects. These new sequencing approaches include Sanger reaction-based technologies that have electrophoresis as the final separation step as well as those that use completely novel, nonelectrophoretic methods to generate sequence data. In this review, we discuss the various advances in sequencing technologies and evaluate the current limitations of novel methods that currently preclude their complete acceptance in large-scale sequencing projects. Our primary goal is to analyze and predict the continuing role of electrophoresis in large-scale DNA sequencing, both in the near and longer term.     

Palladium: a future key player in the nanomedical field?

Metal nanostructures offer invaluable possibilities for targeted drug delivery, detection/diagnosis and imaging. Whereas iron, gold, silver and platinum nanoarchitectures have largely dominated this field to date, several hurdles impede the widespread application of those nanopharmaceuticals in a clinical context. Therefore, technologies based on alternative metals are now being evaluated for their potential in medical applications. Palladium nanostructures are characterized by remarkable catalytic and optical properties. However, until recently, very few studies have taken advantage of these unique characteristics for applications in the biomedical field. Very recently, palladium nanostructures have been reported as prodrug activator, as photothermal agents and for anti-cancer/anti-microbial therapy. With only a handful of reports available, the pharmaceutical applications of palladium nanostructures reviewed here are in their infancy. Yet their interesting performance and toxicity profiles may qualify them as future key players in the nanomedical field.     

Congested molecules. Where is the steric repulsion? An analysis of the electron density by the method of interacting quantum atoms

The computed electron density of several congested saturated hydrocarbons and halogenated derivatives has been analyzed by the method of interacting quantum atoms (IQA). For all the molecules studied, the calculations show the existence of a bond path between the congested atoms and which, according to the Quantum Theory of Atoms in Molecules, indicates that there is a stabilizing interaction between these atoms. The bond path is found to exist up to interatomic distances well‐beyond the sum of the van der Waals radii. The IQA results indicate that steric hindrance is not a repulsive force between the congested atoms but that is the result of an increase in the intra‐atomic or self‐energy of the congested atoms. This increase in self‐energy is caused by the deformation of the atomic basin of the congested atoms. © 2013 Wiley Periodicals, Inc.     

Löwdin correlation energy density of the inhomogeneous electron liquid in some closed-shell molecules at equilibrium geometry

Using existing theoretical studies, we point out that the dominant variable in determining Löwdin correlation energies per electron E _c /N of isoelectronic series of molecules at equilibrium is the total number of electrons. This turns out to be E _c /N = ?0.033 ± 0.003 a.u. for CH₄, NH₃, H₂O and HF (N = 10), and E _c /N = ?0.039 ± 0.007 for some 20 Si-containing molecules in the series SiX _n Y _m . Following earlier work of March and Wind on atoms, some proposals are then made as to a possible explanation of such behaviour. A test is proposed, via low-order Møller–Plesset perturbation theory, as to whether the Löwdin correlation energy density ε _c (r) is, albeit approximately, a local functional ε _c (ρ) of the ground-state density for molecules at equilibrium. Such an LDA assumption would imply that ε _c (ρ) is quantitatively linear in ρ(r), for closed-shell molecules at equilibrium, at least for the light atomic components treated here. This, in turn implies that the dominant effect of the Löwdin correlation energy for closed-shell molecules at equilibrium is merely to shift the chemical potential.     

Aptasensors – the future of biosensing?

Aptamers are artificial nucleic acid ligands that can be generated against amino acids, drugs, proteins and other molecules. They are isolated from combinatorial libraries of synthetic nucleic acid by an iterative process of adsorption, recovery and reamplification. Aptamers, first reported in 1990, are attracting interest in the areas of therapeutics and diagnostics and offer themselves as ideal candidates for use as biocomponents in biosensors (aptasensors), possessing many advantages over state of the art affinity sensors. The properties of aptamers, their applicability to biosensor technology, current research and future prospects are addressed in this short review.     

Where does the electron go? Electron distribution and reactivity of peptide cation radicals formed by electron transfer in the gas phase

We report the first detailed analysis at correlated levels of ab initio theory of experimentally studied peptide cations undergoing charge reduction by collisional electron transfer and competitive dissociations by loss of H atoms, ammonia, and N-C alpha bond cleavage in the gas phase. Doubly protonated Gly-Lys, (GK + 2H) (2+), and Lys-Lys, (KK + 2H) (2+), are each calculated to exist as two major conformers in the gas phase. Electron transfer to conformers with an extended lysine chain triggers highly exothermic dissociation by loss of ammonia from the Gly residue, which occurs from the ground ( X ) electronic state of the cation radical. Loss of Lys ammonium H atoms is predicted to occur from the first excited ( A ) state of the charge-reduced ions. The X and A states are nearly degenerate and show extensive delocalization of unpaired electron density over spatially remote groups. This delocalization indicates that the captured electron cannot be assigned to reduce a particular charged group in the peptide cation and that superposition of remote local Rydberg-like orbitals plays a critical role in affecting the cation-radical reactivity. Electron attachment to ion conformers with carboxyl-solvated Lys ammonium groups results in spontaneous isomerization by proton-coupled electron transfer to the carboxyl group forming dihydroxymethyl radical intermediates. This directs the peptide dissociation toward NC alpha bond cleavage that can proceed by multiple mechanisms involving reversible proton migrations in the reactants or ion-molecule complexes. The experimentally observed formations of Lys z (+*) fragments from (GK + 2H) (2+) and Lys c (+) fragments from (KK + 2H) (2+) correlate with the product thermochemistry but are independent of charge distribution in the transition states for NC alpha bond cleavage. This emphasizes the role of ion-molecule complexes in affecting the charge distribution between backbone fragments produced upon electron transfer or capture.     

Can coacervation unify disparate hypotheses in the origin of cellular life?

Here, we review the recent progress in the characterisation and utilisation of coacervates as protocell models in the origin of life studies. We provide evidence that coacervation could have played a unique role during the origin of life, based on its ability to form from a range of different prebiotically relevant molecules; partition solutes; support and alter RNA catalysis and readily deform its shape. We discuss how these properties could have been important for the formation of the first membrane-bound cells, supporting RNA-peptide evolution and primitive metabolism, and in replicating and proliferating by growth and division processes.     

Do one-step mechanisms always involve simultaneous evolution of electron density? QTAIM/IQA analysis of the Curtius rearrangement

The Curtius rearrangement reaction is studied by using quantum theory of atoms in molecules (QTAIM) analysis of the electron density and the interacting quantum atoms (IQA) formalism. Although the rearrangements take place in one stage, two phases are distinguished when the rearranged atom is H: the first one corresponds to the separation of N₂, and the second one to the N-H/C-H bond rearrangement. The transition state (TS) for the reaction does not represent an intermediate between reagent and product for the migration but for the isolation of the N₂ molecule. When the migration is undergone by a fluorine atom, no electronic phases can be distinguished and the process is really concerted. As the migration happens closer to the TS, the TS is more similar to the product. The IQA analysis reveals different electron density evolutions for H and F migrations, and the scarce relevance (in terms of energy) of the point where BCPs appear or disappear.     

How well can density functional methods describe hydrogen bonds to pi acceptors?

We employed four newly developed density functional theory (DFT) methods for the calculation of five pi hydrogen bonding systems, namely, H2O-C6H6, NH3-C6H6, HCl-C6H6, H2O-indole, and H2O-methylindole. We report new coupled cluster calculations for HCl-C6H6 that support the experimental results of Gotch and Zwier. Using the best available theoretical and experimental results for all five systems, our calculations show that the recently proposed MPW1B95, MPWB1K, PW6B95, and PWB6K methods give accurate energetic and geometrical predictions for pi hydrogen bonding interactions, for which B3LYP fails and PW91 is less accurate. We recommend the most recent DFT method, PWB6K, for investigating larger pi hydrogen bonded systems, such as those that occur in molecular recognition, protein folding, and crystal packing.     

Overlapping electron density and the global delocalization of π-aromatic fragments as the reason of conductivity of the biphenylene network

Recently fabricated 2D biphenylene network is an astonishing solid-state material, which possesses unique metal-like conductive properties. At the same time, two-dimensional boron nitride network (2D-BN)—an isoelectronic and structural analogue of biphenylene network, is an insulator with a wide direct bandgap. This study investigates the relationship between the electronic properties and chemical bonding patterns for these species. It is shown that the insulating 2D-BN network possesses a strong localization of electron density on the nitrogen atoms. In turn, for a carbon-containing sheet, we found a highly delocalized electron density and an appreciable overlap of p_z orbitals of neighboring C₆ rings, which might be a reason for the conductive properties of the material.     

Towards an atomistic model for ORMOCER?-I: application of forcefield methods

ORMOCER^?s are an outstanding class of hybrid materials due to their tuneable properties, e.g. hardness, resistivity and refractive index. These materials are well-characterized with regard to their macroscopic properties, but understanding the system at the atomistic level still remains challenging. Understanding the material formation process at this level becomes especially important when three-dimensional nanoscale patterns are generated employing processes as laser-based multi-photon polymerization. We have developed an atomistic model based on the COMPASS forcefield to simulate the reference system ORMOCER^?-I. We chose representative compositions for the condensation reaction product as well as for the organically cross-linked polymerized product. In the first part of the study, the results of forcefield validation experiments and the development of the atomistic model for ORMOCER^?s are presented. The second part contains the results from molecular dynamics simulations at room temperature and under periodic boundary conditions, performed in order to test the feasibility of our model. The densities of the simulated materials are in very good agreement with experimentally determined densities for the unpolymerized as well as for the polymerized state, respectively.