Discrete Molecules Research Articles

•OH oxidation of methionine in the presence of discrete water molecules: DFT, QTAIM and valence bond analyses

The first steps of the oxidation process of amino acid methionine (Met, CAS 63-68-3) by •OH radicals, leading to Met-OH• adduct and then to Met radical cation, were investigated theoretically over the last few years considering the aqueous environment as a continuum. In this work, following the same procedure that we used for the oxidation of dimethyl sulfide as reported by Domin et al. (J Phys Chem B, 121:9321), discrete water molecules, as well as relative positions, of the •OH radical to Met were taken from molecular dynamics calculations. The presence of water molecules strongly modifies the relative energies of Met-OH adducts and cations when water is properly modeled. Depending on the terminal functional groups and on the position of the •OH radical, several stable structures were found; however, the most stable radical is the N-centered or the S∴N radical cation. QTAIM analysis and valence bond (VB) treatment allowed for the characterization of the 2c∴3e nature of S∴N and S∴OH bonds. VB analysis estimated the probability of the heterolytic rupture of the •OH adduct that is modified by the presence of water molecules.

Conformation and dynamics of discrete poly(ethylene glycol) chains in nano-scale-thickness solution next to a gold substrate

The functions and applications of flexible molecules rely heavily on their properties, such as conformation and dynamics. Despite numerous studies on the properties of flexible molecules in various conditions, the properties of discrete molecules in a dilute solution of nano-scale thickness sandwiched between a solid substrate and a bulk solution have not been sufficiently studied. In this study, based on the quartz crystal microbalance with dissipation monitoring, we demonstrate a facile way to investigate the conformation and dynamics of discrete polymer chains in nano-scale thickness solution by estimating the specific values of exclude volume exponent v and pre-factor k in the modified Mark-Houwink equation, respectively. Using poly(ethylene glycol) (PEG) as an example, the results suggest that the properties of a PEG with a molecular weight of 2 k are not significantly affected by the solid substrate. Moreover, for PEGs with molecular weights of 6 k and 20 k, the changes in conformation and dynamics are minimal and significant, respectively, in comparison with those in bulk solution. The proposed method can be further extended to probe the conformation, dynamics, and related phenomena of linear neutral polymers, and polyelectrolytes (including biopolymers) with a high salt condition.

Synthesis and structural characterization of Zn(II) and Cd(II) ion directed coordination networks and their template-free fabrication to metal oxide nanomaterials

Using a tetradentate capping ligand, N,N,N-tris(2-pyridylmethyl)-amine (tpa) and acetylene dicarboxylic acid (H2adc), structural diversity is achieved with two group 12 divalent metal ions, Zn(II) and Cd(II). With a change in metal center, a discrete molecule [Zn2(tpa)2(adc)2].5H2O (1) and a water soluble coordination polymer [Cd(tpa)(adc)]n (2) are isolated under the same reaction conditions. Furthermore, the formation of supramolecular networks of higher dimensionality in 1 and 2 has different associations: hydrogen bonding interactions between lattice water molecules and the uncoordinated oxygen atoms of adc are primarily involved in 1, whereas π-π interactions between pyridyl moieties are responsible for it in 2. Both 1 and 2 are characterized by elemental analysis, IR spectroscopy, and thermogravimetric analysis (TGA), single crystal and powder X-ray diffraction. The exceptional thermal stability of 2 compared to 1 based on TGA is correlated to their structural differences. The template-free ecofriendly and efficient fabrication of 1 and 2 to the corresponding metal oxide nanomaterials (ZnO and CdO, respectively) was achieved via the direct calcination method but without any external reagent such as surfactants. Furthermore, a temperature-dependent (400–600 °C) diversification of size and morphology of both ZnO and CdO has established the value of such precursors.

Synthesis and characterization of asymmetric [Mo2O2(μ-S)2(S2)(L)] complexes (L = bipy, en, dien) and their heterogeneous reaction with propylene sulfide

Crystalline and amorphous molybdenum sulfide “MoSx” catalysts are well established in sulfur removal from petrochemicals in heterogeneous reactions. Accessibility of sulfido ligands on the catalyst surface is generally accepted as pre-requisite for catalytic initiation. Interest in study of discrete molecules with similar active sites for sulfur transfer reactions in organic reactions prompted synthesis of the asymmetric dinuclear complexes, [Mo2O2(μ-S)2(S2)(L)] (1, L = bipyridine (bipy); 2, L = ethylene diamine (en), 3, L = diethylenediamine (dien)) in facile ligand exchange reaction. A single crystal of 1 was obtained from DMF/ether solution as dark red plates and analyzed by X-ray diffraction. The complexes remove sulfur from propylene sulfide in a heterogeneous reaction at ambient temperature on the NMR scale. Reactivity expected to reflect the donation properties of L with the largest LMCT contribution rendering the most reactive sulfido ligand yielded surprising results. DFT calculations of the optimized minimal energy structures of all three complexes were performed and several possible isomeric structures evaluated. The optimal energy form of 1 compared well with its crystal structure and results from calculated structures of 2 and 3 agree with spectroscopic observations. The modest reactivity is in agreement with poor access to the disulfide as inferred by DFT structures of the complexes and the crystal structure of 1 where strong SS interactions were found along its b-axis.

Recent advances of application of porous molecular cages for enantioselective recognition and separation.

Porous materials with well-defined pore structures have received considerable attention in the past decades due to their unique structures and wide applications. Most porous materials such as zeolites, metal-organic frameworks, covalent organic frameworks, and porous organic polymers are extended to infinite frameworks or networks by robust covalent or coordination bonds. Porous molecular cages composed of discrete molecules with permanent cavities are an emerging class of porous material and the discrete molecules assemble into solids by weak intermolecular interaction. In comparison to porous extended solids such as metal-organic frameworks and covalent organic frameworks, porous molecular cage solids are generally soluble in organic solvents thus allowing solution processing, making them more convenient to apply in many fields. This review mainly focuses on the recent advances of application of porous molecular cages (porous organic cages and metal-organic cages) for enantioselective recognition and separation from 2010 to present, including gas chromatography, capillary electrochromatography, chiral fluorescent recognition, chiral potentiometric sensing, and enantioselective adsorption. Furthermore, the two important family members of porous molecular cages, porous organic cages and metal-organic cages, are also discussed.

Dialkyldithiocarbamate platinum(II) complexes of [Pt(S2CNR2)2] (R = iso-C3H7, iso-C4H9): Preparation, 13C CP-MAS NMR, molecular structure, supramolecular self-assembly and thermal behaviour

Two new dialkyldithiocarbamato platinum(II) complexes of [Pt(S2CNR)2], R = iso-C3H7 (1) and iso-C4H9 (2), have been prepared and characterised using 13C CP-MAS NMR. The crystal and molecular structures of the isolated compounds were established by single-crystal X-ray diffraction. The unit cell of 1 contains four centrosymmetric discrete molecules of [Pt{S2CN(iso-C3H7)2}2], of which the pairs are structurally inequivalent to each other (hereafter denoted as molecules 1a and 1b). At the supramolecular level, due to numerous intermolecular CH⋯S hydrogen bonds, the 1a molecules form linear polymeric ribbons, whose interaction with the 1b molecules results in a two-dimensional polymeric network. In the structure of 2, the construction of supramolecular zigzag chains by non-centrosymmetric molecules of [Pt{S2CN(iso-C4H9)2}2] is determined by intermolecular CH⋯Pt anagostic interactions. The thermal behaviour of crystalline compounds 1 and 2 was studied by simultaneous thermal analysis (STA), a combination of the TG and DSC techniques, under an argon atmosphere. In both cases, platinum(II) sulfide (PtS) was identified as the main end-product upon thermal decomposition of the complexes at 600 °C.

Structures and stabilities of glycine and water complexes

Structural elucidation, stability, properties and proton transfer processes of neutral and zwitterionic Gly(H2O)1-6 complexes are studied by ab initio calculations. Polarizable continuum model (PCM) is important for energy examination since solvent effects is sensitive to the energy. Glycine is fully solvated by five discrete water molecules under polarizable continuum model (PCM). The structure of neutral and zwitterionic Gly(H2O)1-6 complexes changes from a ring motif to a chain motif, and then to a cubic motif. The binding energy for neutral and zwitterionic Gly(H2O)1-6 complexes increases linearly as function of the number of water molecules increase, indicating Gly(H2O)1-6 complexes exhibit relatively higher stability. However, distortion of water molecules will cost more energy, leading to reduced binding energy per water molecule. The reduction is mainly attributed to the directivity and saturability of H-bonds. Importantly, we find the deprotonation of –NH2 for zwitterionic Gly(H2O)2-4 needs ~10 kcal/mol, which is consistent with the experiments.

Crystal structure of bis-[2-(1H-benzimidazol-2-yl-κN 3)aniline-κN]bis-(nitrato-κO)cadmium(II).

In the title compound, [Cd(NO3)2(C13H11N3)2], the CdII atom lies on a twofold rotation axis and is coordinated by four N atoms and two O atoms, provided by two bidentate 2-(1H-benzimidazol-2-yl)aniline ligands, and two nitrato O atoms, forming a distorted octa-hedral geometry [range of bond angles around the Cd atom = 73.82 (2)-106.95 (8)°]. In the ligand, the dihedral angle between the aniline ring and the benzimidazole ring system is 30.43 (7)°. The discrete complex mol-ecule is stabilized by an intra-molecular N-H⋯O hydrogen bond. In the crystal, inter-molecular N-H⋯O hydrogen bonds link the mol-ecules, forming a three-dimensional network.

Water molecules mediate zinc mobility in the bacterial zinc diffusion channel ZIPB

Regulated ion diffusion across biological membranes is vital for cell function. In a nanoscale ion channel, the active role of discrete water molecules in modulating hydrodynamic behaviors of individual ions is poorly understood because of the technical challenge of tracking water molecules through the channel. Here we report the results of a hydroxyl radical footprinting analysis of the zinc-selective channel ZIPB from the Gram-negative bacterium, Bordetella bronchiseptica Irradiating ZIPB by microsecond X-ray pulses activated water molecules to form covalent hydroxyl radical adducts at nearby residues, which were identified by bottom-up proteomics to detect residues that interact either with zinc or water in response to zinc binding. We found a series of residues exhibiting reciprocal changes in water accessibility attributed to alternating zinc and water binding. Mapping these residues to the previously reported crystal structure of ZIPB, we identified a water-reactive pathway that superimposed on a zinc translocation pathway consisting of two binuclear metal centers and an interim zinc-binding site. The cotranslocation of zinc and water suggested that pore-lining residues undergo a mode switch between zinc coordination and water binding to confer zinc mobility. The unprecedented details of water-mediated zinc transport identified here highlight an essential role of solvated waters in driving zinc coordination dynamics and transmembrane crossing.

Numerical Modelling of Self-Compacting Concrete Flow

With the appearance of Self-Compacting Concrete (SCC) that streams uninhibitedly, under the sole impact of gravity, the desire for issue free and unsurprising castings even in complex cases, spurged the recreation of solid stream as a way to demonstrate and anticipate solid functionality. To accomplish total and dependable structure loading up with smooth surfaces of the solid, the fortified formwork geometry must be perfect with the rheology of the new SCC. Anticipating stream conduct in the formwork and connecting the required rheological parameters to stream tests performed on the site will guarantee an improvement of the throwing procedure. In this theory, numerical reproduction of solid stream is explored, utilizing both discrete just as constant approaches. The discrete molecule model here fills in as a way to mimic subtleties and marvels concerning totals demonstrated as individual items. The here gave cases are reenacted round particles. Be that as it may, it is conceivable to utilize nonspherical particles too. Total surface harshness, size and viewpoint proportion might be modeles by molecule erosion, size and bunching a few circles into framing the ideal molecule shape. The consistent methodology has been utilized to mimic huge volumes of cement. The solid is displayed as a homogeneous material, specific impacts of totals, for example, blocking or isolation are not represented. Great correspondence was accomplished with a Bingham material model used to reenact solid research center tests (for example droop stream, L-box) and structure filling. Stream of cement in an especially clogged segment of a twofold tee chunk just as two lifts of a multi-layered full scale divider throwing were reenactedsucessfully. A huge scale quantitative investigation is performed rather easily with the constant methodology. Littler scale subtleties and marvels are better caught subjectively with the discrete molecule approach. As PC speed and limit always develops, recreation detail and test volume will be permitted to increment. A future converging of the homogeneous liquid model with the molecule way to deal with structure particles in the liquid will highlight the progression of concrete as the physical suspension that it speaks to. One single ellipsoidal molecule falling in a Newtonian liquid was considered as an initial step.

Photoacidity of the 7-Hydroxyflavylium Cation.

Theoretical descriptions of excited state proton transfer (ESPT) have had various degrees of success. This work presents a theoretical description of the photodissociation of the 7-hydroxyflavylium cation (7-HF), the fundamental chromophoric moiety of anthocyanin natural plant pigments. ESPT of 7-HF is promoted by a significant shift of charge away from the OH group in the first singlet excited state, leading smoothly to the excited conjugate base and a protonated water cluster. Several factors contribute to the consistency of the results of the present study: (1) the theoretical approach (TD-DFT with the B3-LYP functional and def2-TZVP basis set utilizing Grimme's D3 dispersion correction); (2) the modeling of the solvent effect combining hydrogen bonding of the photoacid to a cluster of discrete water molecules in a water-like continuum solvent (COSMO); (3) the large S1 -S2 energy gap of flavylium cations; and (4) the electrostatics of the ESPT in which a proton is transferred from a cationic photoacid to water without Coulombic interaction between the proton and the conjugate base.

Recent Progress in Inorganic Anions Templated Silver Nanoclusters: Synthesis, Structures and Properties.

Over recent years, research on the ligand-protected silver clusters have gained significant interest owing to their unique potential applications in catalysis, organic optoelectronics, and luminescent materials. However, the synthesis of structurally precise high-nuclearity silver nanoclusters is still challenging and become one of the prime interests of chemists. The controllable synthesis of high-nuclearity silver nanoclusters involves the ingenious use of capping ligands or/and templating agents. Thereinto, the main role of the templating agents is to promote the order arrangement of silver ions around them to form discrete molecules. Our lab has performed comprehensive studies on the ligand-protected silver clusters in the past eight years. This review highlights recent progress in the use of inorganic template anions, silver precursors, solvents, and the ligand types in synthesizing high-nuclearity silver nanoclusters. Furthermore, some interesting photo- and electrochemical properties revealed by silver clusters including luminescent thermochromism, electrical conductivity, and electrochemical reduction of H2 O2 have been also summarized.

Syntheses and magnetic properties of three transition metal complexes based on 4′-p-tolyl-2,2′:6′,2″-terpyridine and SCN−

Three transition metal complexes based on 4′-p-tolyl-2,2′:6′,2″-terpyridine (ttpy) and SCN−, [Mn2(ttpy)2(SCN)3Cl] (1), [Co2(ttpy)2(SCN)4]·H2O (2) and [Ni(ttpy)(SCN)2]2 (3), have been hydrothermally synthesized. The single-crystal X-ray diffraction analyses reveal that the three complexes display discrete molecules with three distinct structures caused by the different coordination geometry of the transition metal centers. Complex 1 contains two neutral independent components of mononuclear [Mn(ttpy)(SCN)2] and binuclear [Mn(ttpy)(SCN)Cl]2. Complex 2 shows an ion-pair bicomponent structure of [Co(ttpy)2]2+ and [Co(SCN)4]2−. Complex 3 shows a binuclear structure bridged by two end-to-end bridging SCN− anions. Magnetic properties of the three complexes have been investigated.

Organic-inorganic all-pseudocapacitive asymmetric energy storage devices

Two-dimensional transition metal carbides (MXenes) have shown extraordinary promise for pseudocapacitive energy storage under negative potential in aqueous electrolytes, yet they lack matching positive electrodes. Here, we report an organic compound namely 2,5-dihydroxy-1,4-benzoquinone (DBQ), adsorbed on reduced graphene oxide (rGO) sheets as a positive electrode, which can deliver high capacitance (~500 F/g, ~800 F/cm3 at 2 mV/s), rate performance (83 F/g or 133 F/cm3 at 10 V/s), and remarkable cycle life (83% after 100,000 cycles), which is the highest for any reported discrete organic molecule. First-principle calculations were used to further understand the charge storage mechanism, find the preferred orientation of the adsorbed molecules, and to pinpoint the origin of the high pseudocapacitance and long cycle life. Optimized compositions of DBQ@rGO were paired with pseudocapacitive Ti3C2Tx MXene to manufacture devices composed of two entirely different classes of materials, where they electrochemically complement each other to expand the voltage window (and thus energy density) in aqueous electrolytes. As manufactured devices delivered energy density of 40 W h/kg at a power density of 2.9 kW/kg and capacitance retention of over 90% after 10,000 cycles.

Electronic and Structural Factors Controlling the Spin Orientations of Magnetic Ions.

Magnetic ions M in discrete molecules and extended solids form MLn complexes with their first-coordinate ligand atoms L. The spin moment of M in a complex MLn prefers a certain direction in coordinate space because of spin-orbit coupling (SOC). In this minireview, we examine the structural and electronic factors governing the preferred spin orientations. Elaborate experimental measurements and/or sophisticated computational efforts are required to find the preferred spin orientations of magnetic ions, largely because the energy scale of SOC is very small. The latter is also the very reason why one can readily predict the preferred spin orientation of M by analyzing the SOC-induced highest occupied molecular orbital (HOMO)-lowest unoccupied molecular orbital (LUMO) interactions of the MLn complexes in terms of qualitative perturbation theory. The strength of this HOMO-LUMO interaction depends on the spin orientation, which is governed by the selection rules based on the minimum |ΔLz| value (i.e., the minimum difference in the magnetic quantum numbers) between the HOMO and LUMO. With the local z axis of MLn chosen as its n-fold rotational axis, the preferred spin orientation is parallel to the z axis (∥z) when |ΔLz| = 0 but perpendicular to the z axis (⊥z) when |ΔLz| = 1.

Fully Polarizable QM/Fluctuating Charge Approach to Two-Photon Absorption of Aqueous Solutions.

We present the extension of the quantum/classical polarizable fluctuating charge model to the calculation of single residues of quadratic response functions, as required for the computational modeling of two-photon absorption cross sections. By virtue of a variational formulation of the quantum/classical polarizable coupling, we are able to exploit an atomic orbital-based quasienergy formalism to derive the additional coupling terms in the response equations. Our formalism can be extended to the calculation of arbitrary order response functions and their residues. The approach has been applied to the challenging problem of one- and two-photon spectra of rhodamine 6G (R6G) in aqueous solution. Solvent effects on one- and two-photon spectra of R6G in aqueous solution have been analyzed by considering three different approaches, from a continuum (QM/PCM) to two QM/MM models (nonpolarizable QM/TIP3P and polarizable QM/FQ). Both QM/TIP3P and QM/FQ simulated OPA and TPA spectra show that the inclusion of discrete water solvent molecules is essential to increase the agreement between theory and experiment. QM/FQ has been shown to give the best agreement with experiments.

A Metalloligand Approach for the Self-Assembly of a Magnetic Two-Dimensional Grid-of-Grids

The efficient organization of discrete functional molecules into extended frameworks, while retaining their physical properties, is a mandatory requisite to move toward applications. Here we descri...

Chalcogen-Chalcogen Bonding Catalysis Enables Assembly of Discrete Molecules.

Despite the observation of noncovalent interactions between chalcogen atoms in X-ray crystal structures, catalysis that harnesses the power of such chalcogen-chalcogen bonding interactions to produce advanced molecules remains an unresolved problem. Here, we show that a class of extraordinary chalcogen-bonding catalysts enables assembly of discrete small molecules including three β-ketoaldehydes and one indole, leading to the construction of N-heterocycles in a highly efficient manner. The strong activation ability of these rationally designed catalysts provides a general solution to the intrinsic limitations of chalcogen bonding catalysis.

Disulfonated azo dyes: metal coordination and ion-pair separation in twelve MII compounds of Ponceau Xylidine and Crystal Scarlet.

The structures of seven divalent metal cation compounds of Ponceau Xylidine {PX; systematic name of dication: 4-[2-(3,4-dimethylphenyl)hydrazin-1-ylidene]-3-oxo-3,4-dihydronaphthalene-2,7-disulfonate}, also known as Acid Red 26, CI 16150, and of five divalent metal cation compounds of Crystal Scarlet {CS; systematic name of dication: 8-[2-(naphthalen-1-yl)hydrazin-1-ylidene]-7-oxo-7,8-dihydronaphthalene-1,3-disulfonate}, also known as Acid Red 44, CI 16250, are presented. These are hexaaquamagnesium(II) PX dimethylformamide (DMF) monosolvate, [Mg(H2O)6](C18H14N2O7S2)·C3H7NO, (I); heptaaquacalcium(II) PX 2.5-hydrate, [Ca(H2O)7](C18H14N2O7S2)·2.5H2O, (II); catena-poly[aqua(μ-DMF)tris(DMF)bis(μ3-PX)distrontium(II)], [Sr(C18H14N2O7S2)(C3H7NO)2(H2O)0.5]n, (III); the transition-metal series hexaaquametal(II) PX DMF monosolvate, [M(H2O)6](C18H14N2O7S2)·C3H7NO, where M (metal) = Co, (IV), Ni, (V), Cu, (VI), and Zn, (VII); heptaaquacalcium(II) CS monohydrate, [Ca(H2O)7](C20H13N2O7S2)·H2O, (VIII); octaaquastrontium(II) CS monohydrate, [Sr(H2O)8](C20H13N2O7S2)·H2O, (IX); catena-poly[[triaqua(DMF)barium(II)]-μ-CS], [Ba(C20H13N2O7S2)(C3H7NO)(H2O)3]n, (X); tetrakis(DMF)(CS)copper(II) monohydrate, [Cu(C20H13N2O7S2)(C3H7NO)4]·H2O, (XI); and catena-poly[[[aquatris(DMF)zinc(III)]-μ-CS] diethyl ether hemisolvate], {[Zn(C20H13N2O7S2)(C3H7NO)3(H2O)]·0.5C4H10O}n, (XII). In all cases, the structures obtained were solvates with dimethylformamide (DMF) and/or water present. The disulfonated naphthalene-based azo anions adopt hydrazone tautomeric forms. The structures of the Mg salt and of four transition-metal forms (M = Co, Ni, Cu and Zn) of PX are found to form an isostructural series. All have solvent-separated ion-pair (SSIP) type structures and the formula [M(H2O)6][PX]·DMF. The Ca salt of PX also has an SSIP structure, but has a higher hydration state, [Ca(H2O)7][PX]·2.5H2O. In contrast, the Sr salt of PX, [Sr(PX)(DMF)2(H2O)0.5]n forms a one-dimensional coordination polymer. Both the Ca and the Sr salt of CS have an SSIP structure, namely [Ca(H2O)7][CS]·H2O and [Sr(H2O)8][CS]·H2O, whilst the heavier Ba analogue, [Ba(CS)(DMF)(H2O)3]n, forms a one-dimensional coordination polymer. Unlike PX, two CS structures containing transition metals are found to be coordination complexes, [Cu(CS)(DMF)4]·H2O and {[Zn(CS)(DMF)3(H2O)]·0.5Et2O}n. This suggests that CS is a better ligand than PX for transition metals. The Cu complex forms discrete molecules with Cu in a square-pyramidal environment, whilst the Zn species is a one-dimensional coordination polymer based on octahedral Zn centres.

Selective Formation of a Mixed-Valence State from Linearly Bridged Oligo(aromatic diamines): Drastic Structural Change into a Folded Columnar Stack for Half-filled Polycations.

A method to obtain an organic mixed-valence state with long-range delocalization is proposed, which enables the selective generation of half-filled (n/2-charged) polycations from linearly bridged oligomers with n electron-donating units. When π-extended phenylenediamine units are connected by meta-xylylene-type spacers, the resulting oligomers adopt non-folded structures in the neutral state owing to the non-conjugating and flexible nature of the spacer, whereas the structure shows a drastic change into a one-dimensional columnar stack upon oxidation to the corresponding half-filled polycations. Although they are nano-sized discrete molecules, they can mimic the electronic structure of crystalline organic conductors in a mixed-valence state. The key for the oligomer design is adoption of the best-matched spacer that facilitates formation of the singly charged pimer in the dichromophoric system whereas the corresponding doubly charged π-dimer is disfavored.