Clustering Six Electrons within “Dawson-Like” Polyoxometalate: An Open Route toward Its Post-functionalization

Super-reduction of polyoxometalates (POMs) in solution is of fundamental interest for designing innovative energy storage systems. In this article, we show that the “Dawson-like” POM can undergo a disproportionation process during its massive electron uptake, leading to species containing three metal-metal bonds as evidenced by X-ray diffraction, multi-nuclear magnetic resonance spectroscopy (¹H and ¹⁸³W NMR), extended X-ray absorption fine structure (EXAFS), UV/Vis, and voltammetry techniques. This result indicates that electron storing within metal-metal bonds is not a unique property of Keggin-type POM as postulated since the 70s. Besides, we demonstrate that the presence of an electron-rich triad in the “Dawson-like” POM allows its post-functionalization with additional tungstate ions, generating a chiral molecule that is also the largest W^IV-containing POMs known to date.     

Distorted Molecules: Perturbation Design,Preparation and Structures

The structure of a molecule can change considerably as its energy and thus its electron distribution within the time-domain of dynamic relaxation varies. Based on comparison of approriate measured data of related compounds and supported by quantum chemical calculations, therefore, charge-perturbed and/or sterically overcrowded molecules can be designed. Their preparation, handling, and structural characterization, frequently under extreme and especially largely aprotic conditions, provides some surprises. New structural principles become evident and old-fashioned ones are confirmed. Thus the contact-ion aggregates that form on ultrasonically supported reduction of unsaturated hydrocarbons with sodium metal partly contain dibenzene sodium sandwiches. Vicinal dimethylamino substituents or isoelectronic isopropyl groups cause steric overcrowding and facilitate oxidation to molecular cations by energetically favorable delocalization of the generated positive charge. Molecules and molecular ions in which an even number of π electrons are distributed over a σ skeleton containing an odd number of centers preferentially form cyanine subunits. This is demonstrated by the novel ethene dication and dianion salts with central C? C single bonds and molecular halves twisted relative to each other. Altogether in two years well over 50 structures have been determined. Much has been learned from them, especially about electron transfer and contact ion-pair formation in aprotic solvents. Nevertheless, we had to realize that answers to many questions, above all “what crystallizes, how, and why”, are still out of reach.     

Fracture behavior in nylon 6 fibers

A reaction rate model of fracture in polymer fibers is described. This model assumes that bond rupture is governed by absolute reaction rate theory with a stress-aided activation energy. It is demonstrated that the key in obtaining good agreement between the model and experiment lies in taking proper account of the variation of stress on the tie-chain molecules. The more taut chains rupture first, and the load is redistributed among the remaining unruptured tie chains. The effect of varying the temperature both in the model and in experiments on fracture in fibers is explored. Good agreement between predictions of the model and experiment is possible only with an undeterstanding of the distribution in stress on the tie chains. The distribution in stress on the chains was experimentally determined by monitoring the kinetics of bond rupture with electron paramagnetic resonance (EPR) spectroscopy. Temperature is found to have two effects on macroscopic strength. (1) The thermal energy aids the atomic stress in breaking the atomic bonds; as a consequence the rate of bond rupture of a family of bonds under a given molecular stress is increased. In this respect temperature might be viewed as decreasing the “strength” of a bond. (2) Temperature also serves to “loosen” the molecular structure and in this way modify the distribution in stress on the tie chains. To explain bond rupture and macroscopic fracture behavior quantitatively, account must be taken of both effects.     

The Studies of Microwave Effects on the Chemical Reactions

Microwave heating involves direct absorption of energy by functional groups that bear ionic conductivity or a dipole rotational-effect, and this energy is then released into the surrounding solution. This absorption of energy causes the functional groups involved to have higher reactivity to other surrounding reactants than when they are simply incubated with the reactants at the same temperature. In other word the enhanced rate of the reaction can be due to the reactant stirred by the molecular dipole rotation and molecules themselves acting as a stirring bar. In contrast to conventional heating, the salient feature of “dipole rotation” constitutes one efficient form of “molecular agitation” or “molecular stirring” many aspects of which can be explore in chemical reactions. We will discuss some of the useful applications of this “molecular agitation” by means of microwave irradiation. Using this unique technology, we have developed: 1) a method to control the cleavage sites of peptide bonds, especially those bonds connected to aspartic acid residues inside the native peptides and proteins, 2) a method to increase coupling efficiency in solid-phase peptide synthesis using a common microwave oven, 3) a novel procedure that increases the rate of alcalase-catalyzed reactions using microwave irradiation in peptide-bond formation with proline as a nucleophile and selective benzoylation of a pyranoside derivative, 4) a procedure to solubilize and hydrolyze retrograded starch, 5) a novel procedure to enhance the rate of saponification in a serum sample for very long chain fatty acid analysis.     

ORAL: All purpose molecular mechanics simulator and energy minimizer

A molecular mechanics energy minimizer is presented whose main features are the “floating blocks” and “isles” option, the “a-NOE” distance inequality constraints and the variable storage first derivative minimization method. The program possibilities are illustrated by examples of molecular docking, energy barrier estimation, modeling of infinite structures, and DNA bending simulations.     

To What Extent are “Atoms in Molecules” Structures of Hydrocarbons Reproducible from the Promolecule Electron Densities?

The “atoms in molecules” structures of 225 unsubstituted hydrocarbons are derived from both the optimized and the promolecule electron densities. A comparative analysis demonstrates that the molecular graphs derived from these two types of electron densities at the same geometry are equivalent for almost 90 % of the hydrocarbons containing the same number and types of critical points. For the remaining 10 % of molecules, it is demonstrated that by inducing small perturbations, through the variation of the used basis set or slight changes in the used geometry, the emerging molecular graphs from both densities are also equivalent. Interestingly, the (3, ?1) critical point between two “non‐bonded” hydrogen atoms, which triggered “H?H bonding” controversy is also observed in the promolecule densities of certain hydrocarbons. Evidently, the topology of the electron density is not dictated by chemical bonds or strong interactions and deformations induced by the interactions of atoms in molecules have a quite marginal role, virtually null, in shaping the general traits of the topology of molecular electron densities of the studied hydrocarbons, whereas the key factor is the underlying atomic densities.     

ETC: A Mechanistic Concept for Inorganic and Organic Chemistry

The concept of electron transfer catalysis (ETC), or more specifically “Double Activation Induced by Single Electron Transfer” (DAISET) gives an opportunity to connect experimental facts never previously correlated. The first activation results from the transfer of an electron to (or from) a molecular species; the second activation results from the build-up of a reaction chain able to reproduce the species formed in the first step. The starting point of this review is the S_RN 1 mechanism where principle and experimental diagnostic criteria are critically discussed. The thermal and photochemical exchange and substitution reactions of Pt^IV complexes are then reviewed together with the exchange reaction [AuCl₄]^?/Cl^?, reactions with Grignard reagents and other organometallic reagents, as well as the redox behavior of electronically excited organic compounds. Photochemical applications, including solar energy conversion are discussed. New aspects are also presented for the mechanistic problem “S_N 2 reaction or SET process?” Moreover, the concept has significance for S_H2 reactions at metal centers, molecule-induced homolyses, reactions of complexes, as well as electrochemical processes.–Unless otherwise specified, only double activation (DAISET) processes will be discussed in this article.     

Analyzing the electric response of molecular conductors using “electron deformation” orbitals and occupied‐virtual electron transfer

The concept of “electron deformation orbitals” (EDOs) is used to investigate the electric response of conducting metals and oligophenyl chains. These orbitals and their eigenvalues are obtained by diagonalization of the deformation density matrix (difference between the density matrices of the perturbed and unperturbed systems) and can be constructed as linear combinations of the unperturbed molecular orbitals within “frozen geometry” conditions. This form of the EDOs allows calculating the part of the electron deformation density associated to an effective electron transfer from occupied to virtual orbitals (valence to conduction band electron transfer in the band model of conductivity). It is found that the “electron deformation” orbitals pair off, displaying the same eigenvalue but opposite sign. Each pair represents an amount of accumulation/depletion of electron charge at different molecular regions. In the oligophenyl systems investigated only one pair contributes effectively to the charge flow between molecular ends, resulting from the promotion of electrons from occupied orbitals to close in energy virtual orbitals of appropriate symmetry and overlapping. Analysis of this pair along explains the differences in conductance of olygophenyl chains based on phenyl units. © 2014 Wiley Periodicals, Inc.     

DNA sequencing with titanium nitride electrodes

We construct a hydrogen‐bond based metal–molecule–metal junction, which contains two identical “reader” molecules, one single DNA base as a bridged molecule, and two titanium nitride electrodes. Hydrogen bonds are formed between “reader” molecules and DNA base, whereas titanium–sulfur bonds are formed between “reader” molecules and titanium nitride electrodes. We perform electronic structure calculations for both the bare bridged molecule and the full metal–molecule–metal system. The projected density of states shows that when the molecule is connected to the titanium nitride electrode, the energy levels of the bridged molecule are shifted, with an indirect effect on the hydrogen bonds. This is similar to the case for a gold electrode but with a more pronounced effect. We also calculate the current–voltage characteristics for the molecular junctions containing each DNA base. Results show that titanium nitride as an electrode can generate distinct conductance for each DNA base, providing an alternative electrode for DNA sequencing. © 2013 Wiley Periodicals, Inc.     

Toward a Consistent Interpretation of the QTAIM: Tortuous Link between Chemical Bonds,Interactions, and Bond/Line Paths

Currently, bonding analysis of molecules based on the Quantum Theory of Atoms in Molecules (QTAIM) is popular; however, “misinterpretations” of the QTAIM analysis are also very frequent. In this contribution the chemical relevance of the bond path as one of the key topological entities emerging from the QTAIM’s topological analysis of the one‐electron density is reconsidered. The role of nuclear vibrations on the topological analysis is investigated demonstrating that the bond paths are not indicators of chemical bonds. Also, it is argued that the detection of the bond paths is not necessary for the “interaction” to be present between two atoms in a molecule. The conceptual disentanglement of chemical bonds/interactions from the bonds paths, which are alternatively termed “line paths” in this contribution, dismisses many superficial inconsistencies. Such inconsistencies emerge from the presence/absence of the line paths in places of a molecule in which chemical intuition or alternative bonding analysis does not support the presence/absence of a chemical bond. Moreover, computational QTAIM studies have been performed on some “problematic” molecules, which were considered previously by other authors, and the role of nuclear vibrations on presence/absence of the line paths is studied demonstrating that a bonding pattern consistent with other theoretical schemes appears after a careful QTAIM analysis and a new “interpretation” of data is performed.     

Die horizontale Korrelation in π-Elektronensystemen und ihre Beschreibung durch Elektronenpaarfunktionen

Different types of pair functions (geminal products and their linear combinations) are tested with respect to their ability to describe the “horizontal correlation” of the π-electrons of butadiene. The validity of the π-electron approximation is not discussed and “full configuration interaction” within the limited LCAO basis is used as the standard to which the model calculations are referred. An APSG-function (APSG = antisymmetrized product of strongly orthogonal geminals) built up from equivalent (localized) geminals, which contains only one variational parameter is able to account for about 90% of the “horizontal correlation energy”. Both APSG and APIG functions constructed from delocalized geminals, are much less favorable. Criteria of the goodness of an approximate wave function are a) the energy b) comparison of its one- and two-particle density matrices with those obtained from “full CI”. The good results with the localized APSG function are related to the fact that electron correlation between electrons of opposite spin is (in this molecule) essential only within either of the “double bonds” of the “canonical structure”. The pertinent results are quite insensitive to different parametrization of the integrals.     

The “Inverted Bonds” Revisited: Analysis of “In Silico” Models and of [1.1.1]Propellane by Using Orbital Forces

This article dwells on the nature of “inverted bonds”, which refer to the σ interaction between two sp hybrids by their smaller lobes, and their presence in [1.1.1]propellane. Firstly, we study H₃C−C models of C−C bonds with frozen H-C-C angles reproducing the constraints of various degrees of “inversion”. Secondly, the molecular orbital (MO) properties of [1.1.1]propellane and [1.1.1]bicyclopentane are analyzed with the help of orbital forces as a criterion of bonding/antibonding character and as a basis to evaluate bond energies. Triplet and cationic states of [1.1.1]propellane species are also considered to confirm the bonding/antibonding character of MOs in the parent molecule. These approaches show an essentially non-bonding character of the σ central C−C interaction in propellane. Within the MO theory, this bonding is thus only due to π-type MOs (also called “banana” MOs or “bridge” MOs) and its total energy is evaluated to approximately 50 kcal mol⁻¹. In bicyclopentane, despite a strong σ-type repulsion, a weak bonding (15–20 kcal mol⁻¹) exists between both central C−C bonds, also due to π-type interactions, though no bond is present in the Lewis structure. Overall, the so-called “inverted” bond, as resulting from a σ overlap of the two sp hybrids by their smaller lobes, appears highly questionable.     

Observing the 3D Chemical Bond and its Energy Distribution in a Projected Space

Our curiosity-driven desire to “see” chemical bonds dates back at least one-hundred years, perhaps to antiquity. Sweeping improvements in the accuracy of measured and predicted electron charge densities, alongside our largely bondcentric understanding of molecules and materials, heighten this desire with means and significance. Here we present a method for analyzing chemical bonds and their energy distributions in a two-dimensional projected space called the condensed charge density. Bond “silhouettes” in the condensed charge density can be reverse-projected to reveal precise three-dimensional bonding regions we call bond bundles. We show that delocalized metallic bonds and organic covalent bonds alike can be objectively analyzed, the formation of bonds observed, and that the crystallographic structure of simple metals can be rationalized in terms of bond bundle structure. Our method also reproduces the expected results of organic chemistry, enabling the recontextualization of existing bond models from a charge density perspective.     

Pure through‐bond state in organic molecules for analysis of the relationship between intramolecular interactions and total energy

Ab initio configuration interaction through‐space/bond interaction analysis was proposed for the examination of specific intramolecular interactions including the effect of electron correlations. To test the effectiveness of our method, we applied it to rotational barrier in ethane. The results of our test suggest that the insensitivity of the ethane barrier to geometric relaxations is intimately connected with the cancellation of interactions through orbital overlaps and other factors. The orbital overlaps include exchange repulsion and hyperconjugation; other factors include classic Coulomb interaction and changes in bond orbital energy. The rotational state without the barrier (pure through‐bond state) can be achieved by deleting not only the “vicinal” interactions between the C? H bonds that belong to different methyl groups but also the “geminal” interactions within the methyl groups. Our mixing analysis of molecular orbitals supports the superiority of the staggered conformer by hyperconjugation. Moreover, it was demonstrated that our treatment could be applied to excited states as well as to the ground state, including electron correlation effects. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2003     

几个P-ylide反应机理的量子拓扑研究

采用MP2(FC)/6-311++G(d,p)对磷叶立德和类磷叶立德自由基反应机理进行了探讨.优化了中间体、过渡态和产物的几何构型,并采用内禀反应坐标法进行追踪.侧重从量子拓扑学的角度,对反应过程中各点进行电子密度拓扑分析,讨论了反应过程中化学键的断裂、生成和化学键的变化规律.上述两个反应都经历三员环过渡态,找到了这类反应的能量过渡态和结构过渡态.     

Entropic concepts in electronic structure theory

It is argued that some elusive “entropic” characteristics of chemical bonds, e.g., bond multiplicities (orders), which connect the bonded atoms in molecules, can be probed using quantities and techniques of Information Theory (IT). This complementary perspective increases our insight and understanding of the molecular electronic structure. The specific IT tools for detecting effects of chemical bonds and predicting their entropic multiplicities in molecules are summarized. Alternative information densities, including measures of the local entropy deficiency or its displacement relative to the system atomic promolecule, and the nonadditive Fisher information in the atomic orbital resolution(called contragradience) are used to diagnose the bonding patterns in illustrative diatomic and polyatomic molecules. The elements of the orbital communication theory of the chemical bond are briefly summarized and illustrated for the simplest case of the two-orbital model. The information-cascade perspective also suggests a novel, indirect mechanism of the orbital interactions in molecular systems, through “bridges” (orbital intermediates), in addition to the familiar direct chemical bonds realized through “space”, as a result of the orbital constructive interference in the subspace of the occupied molecular orbitals. Some implications of these two sources of chemical bonds in propellanes, π-electron systems and polymers are examined. The current–density concept associated with the wave-function phase is introduced and the relevant phase-continuity equation is discussed. For the first time, the quantum generalizations of the classical measures of the information content, functionals of the probability distribution alone, are introduced to distinguish systems with the same electron density, but differing in their current(phase) composition. The corresponding information/entropy sources are identified in the associated continuity equations.     

Quino[7,8-h]quinoline,a New Type of “Proton Sponge”

So far, “proton sponges” have been defined as bis(dialkylamino)arenes whose dialkylamino groups are in close spatial proximity.^[1] The unusual basicity of these compounds is ascribed to the destabilizing overlap of the lone electron pairs on the nitrogen atoms, to the formation of especially strong hydrogen bonds in the monoprotonated diamines, and to the hydrophobic shielding of these hydrogen bonds. In order to differentiate and assess the relative importance of these factors, we were interested in quino[7,8-h]quinoline 1 , whose nitrogen atoms exhibit a mutual orientation similar to that in 1,8-bis(dimethylamino)naphthalene 2 (“proton sponge”). In contrast to 2 , however, 1 lacks the hydrophobic shielding of the hydrogen bonds of its monoprotonated derivative. This shielding is considered to be responsible for the low rates of proton transfer, which make the “proton sponges” reported so far unsuitable as auxiliary bases in chemical reactions.