Nonbonding Electrons Research Articles

EXPLAINING THE GEOMETRY OF SIMPLE MOLECULES USING MOLECULAR ORBITAL ENERGY-LEVEL DIAGRAMS BUILT BY USING SYMMETRY PRINCIPLES

The built of qualitative energy-level molecular diagrams for different geometries of simple molecules allow to explain the preferred geometry. The diagrams are built using simple symmetry principles and explain, on basis of the number of nonbonding electrons, for example, why the molecule of water is bent and not linear and ammonia is pyramidal and not planar. This simple energy principle does not need to consider the Valence Shell Electron-Pair Repulsion theory (VSEPR theory) neither hybrid orbitals to explain the geometry of simple molecules. This discussion is more appropriate to inorganic chemistry courses where symmetry is a common topic.

Rotational Isomers of Diphenhydramine

Diphenhydramine (DP), an antihistaminic agent, may become colored and daker or more fluorescent during storage. Herein, we spectroscopically examined the causes of this phenomenon under various DP storage conditions and durations. The infrared vibration-rotation spectrum shows multiple Gauche (G)-type conformers with different intramolecular n→π* interaction strengths. The splitting pattern of the dimethylamino group protons in the 1H-NMR spectrum indicates that DP is mainly in the G-type with a small portion in the Trans (T)-type. The correlation between the red-shifted peak intensity in the UV•VIS absorbance spectrum and the coloring progression indicates a decreased intramolecular n→π* interaction of the G-type under elevated temperature during storage. Enhanced fluorescence detected in the Excitation•Fluorescence spectrum demonstrates G-type (quenching) to T-type (fluorescent) conformation conversion, which is due to activated internal rotation of the dimethylamino group under elevated storage temperature and electronic excitation in the phenyl groups under light irradiation during storage. A signal detected in the ESR spectrum corresponds to the G-type charge transfer (CT) structure wherein part of the nonbonding electron pair on the N atom is intramolecularly redistributed to the phenyl groups. The CT structure presents the G-type quenching characteristics, whereas weak CT bonding corresponds to coloring. The results indicate that the quenching G-type is converted to T-type by heat or light to become color faded and bright with enhanced fluorescence and that T-type is reverted to G-type after storage under cool and dark conditions or by vacuum distillation to lose fluorescence.

Oxidation of β-blockers by birnessite: Kinetics, mechanism and effect of metal ions

Manganese dioxides are ubiquitous in natural waters, soils, and sediments and play an important role in oxidative transformation of organic pollutants. This work presents the kinetics of the oxidation of selected β-blockers, betaxolol, metoprolol, and atenolol by birnessite (δ-MnO2) as a function of concentration of the β-blocker, dosage of δ-MnO2, and solution pH. The values of pseudo-first-order rate constants (kobs) of β-blockers decreased in the order betaxolol > atenolol > metoprolol, which was positively correlated with their acid dissociation constants (Ka). Effect of series of metal ions (Fe3+, Cr3+, Al3+, Pb2+, Cu2+, Zn2+, Ni2+, Cd2+, Mg2+, and Ca2+) on the degradation of β-blockers by δ-MnO2 was systematically examined. All of these metal ions inhibited the oxidation reaction under the same constant ionic strength. The inhibition efficiency was positively correlated with the logarithm of stability constant of metal ions in aqueous solution (logKMeOH). By LC-ESI-MS/MS analyses, the oxidation of β-blockers primarily involved hydroxylation and cleavage of the parent molecules to the short branched chain compounds. An electron transfer mechanism for the oxidation of β-blockers by δ-MnO2 was proposed. The oxidation was initiated by the electron transfer from the nonbonding electrons on nitrogen (N-electrons) of β-blockers to δ-MnO2, followed by transformation of radical intermediates. These findings will help to understand the oxidation processes of β-blockers and predict the effect of metal ions on the removal of pollutants by δ-MnO2 in the environment.

Water adsorption on α-V2O5 surface and absorption in V2O5∙nH2O xerogel: DFT study of electronic structure

Adsorption of water on (001)-terminated α-V2O5 surface has been investigated in the framework of density functional theory. According to our calculations, molecular adsorption is preferred, and two types of adsorption sites (Lewis acid center on V atom and Lewis base center on O atoms) have been found. Water adsorption on Lewis acid site does not change the electronic structure of V2O5 surface. Adsorption on Lewis base site is less favorable but reduces the band gap value by half (from 2.5 to 1.3 eV). The reason of this decreasing is the localization of the non-bonding 1b2 electron state of water molecule within the forbidden gap of V2O5 surface. The idealized structure of V2O5∙nH2O xerogel has been computationally studied at n = 0 and 1. It is proved that only Lewis base sites are suitable for water positions. At n = 1, the water absorption energy in xerogel is close to adsorption energy of water on the oxygen atoms of α-V2O5 surface. The presence of the non-bonding states of physically absorbed water in the forbidden gap is also found in the xerogel case. This results in decreasing of the band gap from 2.7 eV to 0.7 eV.

Photosensitized Degradation of Amitriptyline and Its Active Metabolite Nortriptyline in Aqueous Fulvic Acid Solution.

Amitriptyline is a frequently prescribed tricyclic antidepressant. Although amitriptyline and its active metabolite, nortriptyline, have been widely detected in natural waters, their environmental fate due to photodegradation is poorly understood. Here we describe a study conducted to investigate the photodegradation of amitriptyline and its active metabolite under simulated sunlight. Neither amitriptyline nor nortriptyline underwent direct photodegradation, but rapid photosensitized degradation did occur in fulvic acid (FA) solutions. The photodegradation of amitriptyline and nortriptyline followed pseudo-first-order kinetics with rate constants 0.24 and 0.16 h, respectively, at pH 8.0 in air-saturated FA solutions. The photodegradation of the substrates increased markedly with pH. The deprotonation of amitriptyline and nortriptyline facilitated the availability of nonbonding electrons on nitrogen (N-electrons). The excited triplet state of FA (FA*) was verified as the main reactive species responsible for the photosensitized degradation. An electron transfer mechanism for the interaction between substrates and FA* was proposed on the basis of a series of quenching experiments, kinetic model and photoproducts determination. Demethylation at the α-carbon of amine and hydroxylation were two primary photochemical processes initiated by the electron transfer reaction in the air-saturated FA solution; these were followed by generation of demethyl amine and mono-hydroxylation isomers. Our results suggest that indirect photodegradation is an important elimination process for amitriptyline and its active metabolite in natural waters.

Chemical Origin of Termination-Functionalized MXenes: Ti3C2T2 as a Case Study

MXenes represent a burgeoning family of two-dimensional (2D) functional materials with a variety of applications that highly rely on termination-mediated surface functionalization, but the understanding of termination is limited. Here, we take Ti3C2T2 (T = O, F, OH, and H) as an example of MXenes, to demonstrate how termination stabilizes the Ti3C2 monolayer matrix by saturating the nonbonding valence electrons of the surface Ti atom by the low-energy orbitals of the termination. This is achieved by orbitally resolved density of states analysis by simply yet efficiently manipulating the internal coordination of the octahedral crystal field to match exactly the Cartesian coordination. Highly degenerate 3d orbitals of surface Ti split in such a way that it exhibits pseudogaps whose widths predict a stability order Ti3C2O2 > Ti3C2F2 > Ti3C2(OH)2 > Ti3C2H2 > Ti3C2, consistent with Bader charge analysis, thermodynamic calculations, and experimental results. This new criterion could have implications in the gen...

Electrostatic Potential and a Simple Extended Electric Dipole Model of Hydrogen Fluoride as Probes of Non-Bonding Electron Pairs in the Cyclic Ethers 2,5-Dihydrofuran, Oxetane and Oxirane

The electrostatic potential near to the oxygen atom in each of the cyclic ethers 2,5-dihydrofuran, oxetane and oxirane has been calculated by using a distributed multipole analysis (DMA) of each molecule. The electrostatic potential energy V(φ) of a unit non-perturbing positive charge was calculated (via the DMA of the cyclic ether molecule) as a function of the angle φ between the C2 axis of the cyclic ether and a vector of length r from the O atom to the unit charge. The resulting potential energy functions each has two equivalent minima. The angles φmin at the minima are compared with the angles φ0 and φe made by the O⋯H bond with the C2 axes in the cyclic ether⋯HF complexes, as determined by rotational spectroscopy and ab initio calculations at the CCSD(T)-F12c/cc-pVTZ-F12 level of theory, respectively. An electrostatic model of cyclic ether⋯HF complexes in which the DMA of the cyclic ether interacts with a simple extended electric dipole representation of HF is also used to calculate the variation of the potential energy VHF(φ) of the HF molecule with φ. The angles φmin generated by this model are also compared with φ0 and φe. The extent to which the electrostatic potential and the extended electric dipole HF model can be used as probes for the directions of non-bonding electron pairs carried by O in these cyclic ethers is discussed.

Metal-ligand interaction in ternary AgxInxSy clusters – (TD)DFT study

Comprehensive studies on the impact of 1-propanethiol ligands on the structural and optical properties of the AgxInxSy clusters have been discussed in this work. The studies were performed within a density functional theory and the time-dependent density functional theory framework for a group of model structures including metal thiolate complexes as well as two groups of larger models as the Ag2In2S8 and Ag3In3S10 clusters. Obtained results revealed that optical properties of the AgxInxSy clusters are dominated by the nonbonding electrons and the n→π* transitions characterized by weak oscillator strengths and charge transfer nature. It was also shown that structural reconstruction related to detachment of the alkane chains may be responsible for formation of the non-emissive species due to the rearrangement of atoms and formation of the S-S bridges and its higher oligomers. All of the results are consistent with the experimental results gained by single particle spectroscopy putting a new light on the photo-physics of the ternary I-III-VI quantum dots.

Multifaceted adsorption of α-cyano-4-hydroxycinnamic acid on silver colloidal and island surfaces

The surface adsorption of organic nitrile compounds on the silver colloidal and island surfaces has been studied using surface-enhanced Raman scattering (SERS). α-Cyano-4-hydroxycinnamic acid (CHCA) with nitrile and carboxyl groups shows various surface adsorption on the silver surfaces. In acidic conditions, the surface adsorption of CHCA via the nitrile group with a more or less tilted geometry to the surface was found. When the solution pH increases, the carboxylate and nitrile groups of deprotonated CHCA participate in the surface adsorption, whereas the molecular plane of CHCA becomes more parallel to the surface. The ν(CN) band in SERS of CHCA is the indicator of the surface adsorption geometry. The strongly red-shifted and broadened ν(CN) band in SERS represents the surface adsorption via π-electrons of the CN bond (side-on geometry; π-coordination). Nitriles adsorbed on the surface via the nonbonding electron pair of the nitrogen atom (end-on geometry; σ-coordination) often cause the blue-shifts and small band broadening in ν(CN) in SERS. The surface adsorption geometry of organic nitriles based on many previous experimental results was further confirmed by the surface adsorption of CHCA on the silver island surfaces and dinitrile compounds on the silver colloidal surfaces.

Revisiting blood-brain barrier: A chromatographic approach

Drugs designed to reach a pharmacological CNS target must be effectively transported across the blood-brain barrier (BBB), a thin monolayer of endothelial cells tightly attached together between the blood and the brain parenchyma. Because of the lipidic nature of the BBB, several physicochemical partition models have been studied as surrogates for the passive permeation of potential drug candidates across the BBB (octanol-water, alkane-water, PAMPA...). In the last years, biopartition chromatography is gaining importance as a noncellular system for the estimation of biological properties in early stages of drug development. Microemulsions (ME) are suitable mobile phases, because of their ease of formulation, stability and adjustability to a large number of compositions mimicking biological structures. In the present work, several microemulsion liquid chromatographic (MELC) systems have been characterized by means of the Abraham’s solvation parameter model, in order to assess their suitability as BBB distribution or permeability surrogates. In terms of similarity between BBB and MELC systems (dispersion forces arising from solute non-bonded electrons, dipolarity/polarizability, hydrogen-bond acidity and basicity, and molecular volume), the passive permeability surface area product (log PS) for neutral (including zwitterions), fully and partially ionized drugs was found to be well correlated with the ME made of 3.3% SDS (w/v; surfactant) 0.8% heptane (w/v; oil phase) and 6.6% 1-butanol (w/v; co-surfactant) in 50mM aqueous phosphate buffer, pH 7.4.

Impact of Conjugation and Hyperconjugation on the Radical Stability of Allylic and Benzylic Systems: A Theoretical Study.

Resonantly stabilized radicals are some of the most investigated chemical species due to their preferential formation in a wide variety of chemical environments. Density functional theory and post-Hartree-Fock calculations were utilized to elucidate the chemical interactions that contribute to the stability of two ubiquitous, resonantly stabilized radicals, allyl and benzyl radicals. The relative stability of these radical species was quantified through bond dissociation energies and relative rotational energy barriers, with a difference of only 0.1 kcal/mol. To clarify and contextualize the energetic results, natural bond orbitals were used to evaluate the atomic spin density distribution in the given molecules. The benzyl radical was found to be ∼3 kcal/mol less stable than the allyl radical, which was attributed to the inability to efficiently delocalize the spin on a phenyl unit, starkly contrary to general chemistry knowledge. Increasing the degree of π-conjugation and hyperconjugation was shown to benefit allyl radicals to a greater degree than benzyl radicals, again due to more efficient radical delocalization in allyl radicals. This work highlights that more resonance structures do not always lead to a more stabilized radical species, and provides fundamental knowledge about how conjugation and hyperconjugation impact the stabilization of nonbonding electrons in these systems.

Edge-Corrected Mean-Field Hubbard Model: Principle and Applications in 2D Materials

This work reviews the current progress of tight-binding methods and the recent edge-modified mean-field Hubbard model. Undercoordinated atoms and nonbonding electrons exist widely in nanomaterials and in network-structural materials with their impact under-estimated. A quantum theory was proposed to calculate the under-coordinated effects on the electronic structure of materials by incorporating bond order-length-strength (BOLS) correlation theory to mean-field Hubbard model, i.e. BOLS-HM. Consistency between the BOLS-HM calculation and density functional theory (DFT) calculation on 2D materials verified that i) bond contractions and potential well depression occur at the edge of graphene, phosphorene, and antimonene nanoribbons; ii) the physical origin of the band gap opening of graphene, phosphorene, and antimonene nanoribbons lays in the enhancement of edge potentials and hopping integrals due to the shorter and stronger bonds between undercoordinated atoms; iii) the band gap of 2D material nanoribbons expand as the width decreases due to the increasing under-coordination effects of edges which modulates the conductive behaviors; and iv) nonbond electrons at the edges and atomic vacancies of 2D material accompanied with the broken bond contribute to the Dirac-Fermi polaron (DFP) with a local magnetic moment.

Construction of valence bond structures for {FeNO}7 nitrosyl heme and non-heme complexes

For {FeNO}7 nitrosyl heme and non-heme complexes, with 17 valence shell electrons, FeIINO, FeIINO* and FeIIINO− valence bond structures of the increased-valence type are generated primarily from Lewis valence bond structures by delocalizing non-bonding electrons into diatomic bonding molecular orbitals. Valence bond formulations for the reactions 2MbNO + 2H+ → 2metMb + N2O + H2O and cis MbNO + NO− + 2H+ → metMb + N2O + H2O are also presented.

Structural behavior of Tl-exchanged natrolite at high pressure depending on the composition of pressure-transmitting medium

The structural evolution of Tl-exchanged natrolite with idealized formula Tl2[Al2Si3O10]·2H2O, compressed in penetrating (water:ethanol 1:1) and non-penetrating (paraffin) media, was studied up to 4 GPa. The presence of Tl+ with non-bonded electron lone pairs, which can be either stereo-chemically active or passive, determines distinctive features of the high-pressure behavior of the Tl-form. The effective volume of assemblages Tl+(O,H2O) n depends on the E-pairs activity: single-sided coordination correlates with smaller volumes. At ambient conditions, there are two types of Tl positions, only one of them having a nearly single-sided coordination as a characteristic of stereo-activity of the Tl+ E pair. Upon the compression in paraffin, a phase transition occurs: a 5% volume contraction of flexible natrolite framework is accompanied by the conversion of all the Tl+ cations into stereo-chemically active state with a single-sided coordination. This effect requires the reconstruction of all the extra-framework subsystems with the inversion of the cation and H2O positions. The compression in water-containing medium leads to the increase of H2O content up to three molecules pfu through the filling of partly vacant positions. This hinders a single-sided coordination of Tl ions and preserves the configuration of their ion-molecular subsystem. It is likely that the extra-framework subsystem is responsible for the super-structure modulation.

Is the Metallic Phosphorus Carbide (β0-PC) Monolayer Stable? An Answer from a Theoretical Perspective.

Phosphorus carbide (PC) has been the subject of major research efforts in recent years. In this regard, very recently, a stoichiometric metallic phosphorus carbide (β0-PC) monolayer has been proposed as locally stable with one lone nonbonding electron in each C atom. Therefore, the ambiguity of coexistence of a nonbonding electron with metallic properties for β0-PC is reported and hence deserves further explanation. Herein, using first-principles calculations, we have explored the stability and electronic properties of β0-PC to resolve this ambiguity. The metallic behavior of β0-PC is explained on the basis of electron delocalization involving P and C atoms along a zigzag chain of β0-PC. We have also explored the possibility of getting a β0-PC monolayer via homogeneous doping of C (P) into phosphorene (graphene) and layer exfoliation of 3D bulk PC with β-InS-like structure, which has been experimentally synthesized.

Tetrel, pnictogen and chalcogen bonds identified in the gas phase before they had names: a systematic look at non-covalent interactions

The terms tetrel bond, pnictogen bond and chalcogen bond were coined recently to describe non-covalent interactions involving group 14, 15 and 16 atoms, respectively, acting as the electrophilic site that seeks a nucleophilic region of another molecule, for example a non-bonding electron pair or π-electron pair of a Lewis base. Many complexes containing these non-covalent bonds were identified and characterised in isolation in the gas phase by rotational and vibrational spectroscopy long before they were given these names. In this article, the geometries so determined for selected examples of complexes of each type are rationalised in terms of the molecular electrostatic surface potentials of the component molecules. Examples of chalcogen-bonded complexes considered are based mainly on sulfur dioxide, with the region near the sulfur atom as the electrophilic site that interacts with n-electron and π-electron pairs for a range of simple Lewis base molecules. For tetrel bonds, the examples discussed involve the carbon atom of carbon dioxide as the electrophilic centre, while for pnictogen bonds the central nitrogen of the closely related molecule nitrous oxide is chosen. Geometrical similarities within each series allow simple definitions of each type of non-covalent bond that are conformal with that recently advanced for the halogen bond, a related non-covalent interaction.

Supersolid Skin Mechanics of Water and Ice

Skins of water and ice perform anomalously in capacities of hydrophobicity, lubricity, mass density, thermal stability, viscoelasticity, and phonon frequency with yet little knowledge about the mechanism behind these anomalies. We present the recent progress in this regard from the perspective of molecular undercoordination induced O:H-O bond segmental cooperative relaxation and nonbonding electron polarization. The skin molecular undercoordination shortens the intramolecular H-O covalent bond spontaneously from 1.0 to 0.84 Ǻ, while the Coulomb repulsion between oxygen anions lengthens the intermolecular O:H nonbond from 1.70 to 2.71 Ǻ associated with strong polarization. The O:H-O resultant elongation depresses the mass density to 0.75g/cm3; the polarization results the skin high stress, hydrophobicity, lubricity, viscoelasticity; the H-O contraction shifts its stretching vibration frequency from the bulk value of 3150 to 3450 cm-1 at skin and to 3650 cm-1 of vapor; the O:H elongation shifts its stretching mode from 210 of bulk to 180 cm-1 at skin. Therefore, molecular undercoordination induced O:H-O bond relaxation and the associated polarization govern the performance of molecules at the skins of water and ice.

Roles of nitrogen functionalities in enhancing the excitation-independent green-color photoluminescence of graphene oxide dots.

Fluorescent graphene oxide dots (GODs) are environmentally friendly and biocompatible materials for photoluminescence (PL) applications. In this study, we employed annealing and hydrothermal ammonia treatments at 500 and 140 °C, respectively, to introduce nitrogen functionalities into GODs for enhancing their green-color PL emissions. The hydrothermal treatment preferentially produces pyridinic and amino groups, whereas the annealing treatment produces pyrrolic and amide groups. The hydrothermally treated GODs (A-GODs) present a high conjugation of the nonbonding electrons of nitrogen in pyridinic and amino groups with the aromatic π orbital. This conjugation introduces a nitrogen nonbonding (nN 2p) state 0.3 eV above the oxygen nonbonding state (nO 2p state; the valence band maximum of the GODs). The GODs exhibit excitation-independent green-PL emissions at 530 nm with a maximum quantum yield (QY) of 12% at 470 nm excitation, whereas the A-GODs exhibit a maximum QY of 63%. The transformation of the solvent relaxation-governed π* → nO 2p transition in the GODs to the direct π* → nN 2p transition in the A-GODs possibly accounts for the substantial QY enhancement in the PL emissions. This study elucidates the role of nitrogen functionalities in the PL emissions of graphitic materials and proposes a strategy for designing the electronic structure to promote the PL performance.

Efficient External Electric Field Manipulated Nonlinear Optical Switches of All-Metal Electride Molecules with Infrared Transparency: Nonbonding Electron Transfer Forms an Excess Electron Lone Pair

Focusing on the interesting new concept of all-metal electride, centrosymmetric molecules e–+M2+(Ni@Pb12)2–M2++e– (M = Be, Mg, and Ca) with two anionic excess electrons located at the opposite ends of the molecule are obtained theoretically. These novel molecular all-metal electrides can act as infrared (IR) nonlinear optical (NLO) switches. Whereas the external electric field (F) hardly changes the molecular structure of the all-metal electrides, it seriously deforms their excess electron orbitals and average static first hyperpolarizabilities (β0e(F)). For e–+Ca2+(Ni@Pb12)2–Ca2++e–, a small external electric field F = 8 × 10–4 au (0.04 V/A) drives a long-range excess electron transfer from one end of the molecule through the middle all-metal anion cage (Ni@Pb12)2– to the other end. This long-range electron transfer is shown by a prominent change of excess electron orbital from double lobes to single lobe, which forms an excess electron lone pair and electronic structure Ca2+(Ni@Pb12)2–Ca2++2e–. Therefor...

Preparation and Spectroscopic Studies of FC(O)SSCl

The hitherto unknown FC(O)SSCl molecule has been prepared by the reaction of ClC(O)SSCl with TlF under vacuum conditions. The molecule was characterized by its electron‐impact mass spectrum, the IR spectrum of a vapour‐phase sample, the Raman spectrum of the liquid, and also the matrix‐isolated FTIR spectra. FC(O)SSCl is composed of an equilibrium mixture of two conformers,syn‐gaucheandanti‐gauche, both in the vapour and liquid phases, with an approximate ratio of 80:20. The valence electronic properties of FC(O)SSCl were studied by photoelectron spectroscopy. The first ionization potential was observed at 10.14 eV, and the HOMO was assigned to the nonbonding electron lone pair located on the S atom bonded to the carbonyl group. A decrease in the dihedral angle of the S–S bond after ionization was predicted by quantum chemical calculations.