Hexa- and octacoordinate carbon in hydrocarbon cages: theoretical design and characterization

A new series of hydrocarbon cages containing hexa- and octacoordinate carbon centers were designed theoretically by performing DFT calculations at the B3 LYP/6-311+G** level. Among these non-classical structures that were found to still obey the 8e rule, the two tetracations with octacoordinate carbons may be the first examples found in pure hydrocarbons. Structural characteristics, as well as thermodynamic and kinetic stabilities, were also investigated theoretically for these two octacoordinate tetracations. These hydrocarbon compounds containing hypercoordinate carbon centers provide a challenge for synthetic organic chemists.     

New structural motif of 18 valence electron molecules with a planar tetracoordinate heavier group 14 center: Unique stabilization effect of a π‐type skeleton

Proposing new valence electron counting rules and new structural motifs are both very important in chemistry. In this work, we unexpectedly found that by introducing a π‐type skeleton YCCY (Y = Al/Ga/In/Tl), a total of sixteen novel planar tetracoordinate heavier group 14 species, that is, ptM (M = Si/Ge/Sn/Pb) in neutral, can be designed as global minima. The underlying bonding situation contrasts sharply both with the well‐known 18ve‐ptC and the limited 18ve‐ptM, for which there is little multiple bonding character within the skeleton. The fact that each YCCY (Y = Al/Ga/In/Tl) can stabilize all heavier group 14 atoms in a planar tetracoordinate fashion strongly demonstrates the universality of such a π‐type skeleton. The present work firmly demonstrates that introducing the π‐type ligand skeleton can effectively enrich the planar tetracoordinate chemistry with the heavier group atoms.     

1,3‐Dipolar cycloadditions of Stone–Wales defective single‐walled carbon nanotubes: A theoretical study

The presence of Stone‐Wales defects in single‐walled carbon nanotubes (SWNTs) not only leads to new interesting properties, but also provides opportunities for tailoring physical and chemical properties, and expands their novel potential applications. With a two‐layered ONIOM method, 1,3‐dipolar cycloadditions (1,3‐DCs) of a series of 1,3‐dipoles (azomethine ylide, nitrone, nitrile imine, nitrile ylide, nitrile oxide, and methyl azide) with Stone‐Wales defective SWNTs have been investigated theoretically for the first time. The calculated results demonstrate that the bond c , rather than the previously focused central bond a , exhibits the highest chemical reactivity among the defective sites. More interestingly, bond c is even more reactive thermodynamically and kinetically than the perfect C? C bond in SWNTs, suggesting the feasibility of utilizing 1,3‐DC reactions to separate and purify perfect and defective SWNTs. The reactivity order for nonequivalent bonds in defective sites is different from that of [1+2] cycloaddition, indicating that the reactivity order for nonequivalent bonds depends on the kind of the chemical reactions. Except azomethine ylide, nitrile ylide and nitrile imine are found to be good candidates for 1,3‐DCs upon Stone‐Wales defective SWNTs. The SW‐ A and SW‐ B defective SWNTs show different chemical reactivity toward nitrile ylide, making it possible to purify and separate the SW‐ A and SW‐ B defective SWNTs. The SWNT diameters are found to moderately influence the 1,3‐DC reactivity of both perfect and Stone‐Wales defective SWNTs, implying that Stone‐Wales defective SWNTs with different diameter would be separated experimentally through 1,3‐DC chemistry. The above 1,3‐DC reactivity can be well understood in terms of the distortion/interaction theory, which means that instead of frontier molecular orbitals interaction energy, the distortion energy controls the chemical reactivity. © 2013 Wiley Periodicals, Inc.     

A New Approach to the Design of Neutral 10‐C‐5 Trigonal‐Bipyramidal Carbon Compounds: A “π‐Electron Cap” Effect

DFT (B3LYP, M06‐2X) and MP2 methods are applied to the design of a wide series of the potentially 10‐C‐5 neutral compounds based on 6‐azabicyclotetradecanes: XC¹(YCH₂CH₂CH₂)₃N 1 – 3 , XC¹(YC₆H₄CH₂)₃N 4 – 6 , XC¹[Y(tBuC₆H₃)CH₂]₃N 7 – 9 and carbatranophanes 10 – 25 (X=Me, F, Cl; Y=O, NH, CH₂, SiH₂; Z=O, CH₂, (CH₂)₂, (CH₂)₃). Carbatranophanes 10 – 25 are characterized by a sterical compression of their axial 3c–4e XC¹←N fragment with respect to that in the parent molecules 4 – 6 . A magnitude of the revealed effect depends on a valence surrounding of the central carbon atom C¹, the size and the nature of the side chains (Z) that link the “π‐electron cap” with a tetradecane backbone. This circumstance allowed us to obtain 10‐C‐5 structures with the configuration of the bonds around the C¹ atom, which corresponds to practically an ideal trigonal bipyramid. In these compounds, the values of the covalence ratio χ of approximately 0.6 for the coordination C¹←N contacts with a covalent contribution (atoms in molecules (AIM) and natural bond orbital (NBO)) are record in magnitude. These values lie close to a low limit of the interval of the χ_Si←D change (0.6–0.9) being characteristic of the dative and ionic‐covalent (by nature) Si←D bond (D=N, O) in the known 10‐Si‐5 silicon compounds.     

Pentaatomic planar tetracoordinate silicon with 14 valence electrons: A large‐scale global search of (n + m = 4; q = 0, ±1, −2; X,Y = main group elements from H to Br)

Designing and characterizing the compounds with exotic structures and bonding that seemingly contrast the traditional chemical rules are a never‐ending goal. Although the silicon chemistry is dominated by the tetrahedral picture, many examples with the planar tetracoordinate‐Si skeletons have been discovered, among which simple species usually contain the 17/18 valence electrons. In this work, we report hitherto the most extensive structural search for the pentaatomic ptSi with 14 valence electrons, that is, (n + m = 4; q = 0, ±1, ?2; X, Y = main group elements from H to Br). For 129 studied systems, 50 systems have the ptSi structure as the local minimum. Promisingly, nine systems, that is, , HSiY₃ (Y = Al/Ga), Ca₃SiAl^?, Mg₄Si^2?, C₂LiSi, Si₃Y₂ (Y = Li/Na/K), each have the global minimum ptSi. The former six systems represent the first prediction. Interestingly, in HSiY₃ (Y = Al/Ga), the H‐atom is only bonded to the ptSi‐center via a localized 2c–2e σ bond. This sharply contradicts the known pentaatomic planar‐centered systems, in which the ligands are actively involved in the ligand–ligand bonding besides being bonded to the planar center. Therefore, we proposed here that to generalize the 14e‐ptSi, two strategies can be applied as (1) introducing the alkaline/alkaline‐earth elements and (2) breaking the peripheral bonding. In light of the very limited global ptSi examples, the presently designed six systems with 14e are expected to enrich the exotic ptSi chemistry and welcome future laboratory confirmation. © 2014 Wiley Periodicals, Inc.     

Be2C Monolayer with Quasi‐Planar Hexacoordinate Carbons: A Global Minimum Structure

The design of new materials is an important subject in order to attain new properties and applications, and it is of particular interest when some peculiar topological properties such as reduced dimensionality and rule‐breaking chemical bonding are involved. In this work, we designed a novel two‐dimensional (2D) inorganic material, namely Be₂C monolayer, by comprehensive density functional theory (DFT) computations. In Be₂C monolayer, each carbon atom binds to six Be atoms in an almost planar fashion, forming a quasi‐planar hexacoordinate carbon (phC) moiety. Be₂C monolayer has good stability and is the lowest‐energy structure in 2D space confirmed by a global minima search based on the particle‐swarm optimization (PSO) method. As a semiconductor with a direct medium band gap, Be₂C monolayer is promising for applications in electronics and optoelectronics.     

Electronic Structure of Thiolate‐bridged Diiron Complexes and a Single‐electron Oxidation Reaction: A Combination of Experimental and Computational Studies

Single‐electron oxidation of a diiron‐sulfur complex [Cp*Fe(μ‐bdt)FeCp*] ( 1 , Cp*=η⁵‐C₅Me₅; bdt=benzene‐1,2‐dithiolate) to [Cp*Fe(μ‐bdt)FeCp*]⁺ ( 2 ) has been experimentally conducted. The bdt ligand with redox‐active character has been computationally proposed to be a dianion (bdt^2?) rather than previously proposed monoanion (bdt^·?) radical in 1 though it has un‐equidistant aromatic C? C bond lengths. The ground state of 1 is predicted to be two low‐spin ferrous ions (S_Fe=0) and 2 has a medium‐spin ferric ion (S_Fe=1/2) and a low‐spin ferrous center (S_Fe=0), and the oxidation of 1 to 2 is calculated to be a single‐metal‐based process. Both complexes have no significant antiferromagnetic coupling character.     

A linear three‐center four electron bonding identity nucleophilic substitution at carbon,boron, and phosphorus. A theoretical study in combination with van't Hoff modeling

We studied various identity nucleophilic substitution reactions based on an S_N2 reaction profile. With calculations and experimental geometries concerning the nature of the various complexes indicated as stable, intermediate, and transition state we were able to show the additional value of van't Hoff 's tetrahedron by changing its geometry via a trigonal pyramid into a trigonal bipyramid. The ratio of the apical and the corresponding tetrahedral bond distance is then 1.333. This value has been used in general as a calibration point for the understanding of the (in)stabilities of the complex formation on the S_N2 reaction coordinate. The relevance of this approach has been also proved for enzymatic reactions focused on carbon and phosphorus substrates. Furthermore, it could be established that identity proton‐in‐line displacements are fully comparable with the relocation of carbon in a nucleophilic substitution reaction as Cl^? + CH₃Cl. The significance of this information will afford new insight in the dynamics of a linear three‐center four‐electron complex. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

Orientational Preference of Long,Multicenter Bonds in Radical Anion Dimers: A Case Study of π‐[TCNB]22− and π‐[TCNP]22−

The similar shape and electronic structure of the radical anions of 1,2,4,5‐tetracyanopyrazine (TCNP) and 1,2,4,5‐tetracyanobenzene (TCNB) suggest a similar relative orientation for their long, multicenter carbon?carbon bond in π‐[TCNP]₂^2? and in π‐[TCNB]₂^2?, in good accord with the Maximin Principle predictions. Instead, the two known structures of π‐[TCNP]₂^2? have a D_2h(θ=0°) and a C₂(θ=30°) orientation (θ being the dihedral angle that determines the rotation of one radical anion relative to the other along the axis that passes through center of the two six‐membered rings). The only known π‐[TCNB]₂^2? structure has a C₂(θ=60°) orientation. The origin of these preferences was investigated for both dimers by computing (at the RASPT2/RASSCF(30,28) level) the variation with θ of the interaction energy (E_int) and the variation of the E_int components. It was found that: 1) a long, multicenter bond exists for all orientations; 2) the E_int(θ) angular dependence is similar in both dimers; 3) for all orientations the electrostatic component dominates the value of E_int(θ), although the dispersion and bonding components also play a relevant role; and 4) the Maximin Principle curve reproduces well the shape of the E_int(θ) curve for isolated dimers, although none of them reproduce the experimental preferences. Only after the (radical anion)^.? ??? cation⁺ interactions are also included in the model aggregate are the experimental data reproduced computationally.     

Cs[Cl3F10]: A Propeller‐Shaped [Cl3F10]− Anion in a Peculiar A[5]B[5] Structure Type

Reaction of CsF with ClF₃ leads to Cs[Cl₃F₁₀]. It contains a molecular, propeller‐shaped [Cl₃F₁₀]^? anion with a central μ₃‐F atom and three T‐shaped ClF₃ molecules coordinated to it. This anion represents the first example of a heteropolyhalide anion of higher ClF₃ content than [ClF₄]^? and is the first Cl‐containing interhalogen species with a μ‐bridging F atom. The chemical bonds to the central μ₃‐F atom are highly ionic and quite weak as the bond lengths within the coordinating XF₃ units (X = Cl, and also calculated for Br, I) are almost unchanged in comparison to free XF₃ molecules. Cs[Cl₃F₁₀] crystallizes in a very rarely observed A^[5]B^[5] structure type, where cations and anions are each pseudohexagonally close packed, and reside, each with coordination number five, in the trigonal bipyramidal voids of the other.     

A novel gas sensor from polymer‐grafted carbon black: responsiveness of electric resistance of conducting composite from LDPE and PE‐b‐PEO‐grafted carbon black in various vapors

The composite of low‐density polyethylene (LDPE) filled with carbon black (CB) having high dispersibility and stability was successfully obtained by the use of poly(ethylene‐block‐ethylene oxide) (PE‐b‐PEO)‐grafted CB. The response of the electric resistance of the composite against solvent vapors was examined. The electric resistance drastically increased by 10⁴–10⁶ times the initial resistance in a nonpolar solvent vapor such as cyclohexane, and carbon tetrachloride vapor at 40 °C and returned immediately to its initial resistance when the composite was transferred to dry air. However, the electric resistance increased only several times in the polar solvent vapor, such as water and alcohol, at the same temperature. The responsiveness of electric resistance is excellently reproducible and is also stable in cyclohexane vapor and dry air. The effect of temperature on the responsiveness against cyclohexane vapor is also discussed. It is concluded that the composite of LDPE filled with PE‐b‐PEO‐grafted CB could be a promising material to use when preparing gas sensors. Copyright © 2000 John Wiley & Sons, Ltd.     

Electron smearing in DFT calculations: A case study of doxorubicin interaction with single‐walled carbon nanotubes

To address the choice of an appropriate value of electron smearing to facilitate self‐consistent field (SCF) convergence, we studied the interaction of doxorubicin with short armchair and zigzag single‐walled carbon nanotube models with closed caps, at the PWC/DNP level of density functional theory. By gradually reducing the electron smearing value from a large and most commonly used one of 0.005 Ha to zero (Fermi occupation), we monitored the changes in close contacts between the interacting species, total energy of the molecular system, highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energy and isosurfaces, HOMO‐LUMO gap energy, and plots of electrostatic potential. It became evident that the commonly used smearing values of ≥0.001 Ha can alter the results significantly (for example, by one order of magnitude for HOMO–LUMO gap energy). We suggest the setting of electron smearing value at 0.0001 Ha, which does not imply too high computation cost and can guarantee the results close to the ones obtained with Fermi occupation. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Dynamic drag force based on iterative density mapping: A new numerical tool for three‐dimensional analysis of particle trajectories in a dielectrophoretic system

Dielectrophoresis is a widely used means of manipulating suspended particles within microfluidic systems. In order to efficiently design such systems for a desired application, various numerical methods exist that enable particle trajectory plotting in two or three dimensions based on the interplay of hydrodynamic and dielectrophoretic forces. While various models are described in the literature, few are capable of modeling interactions between particles as well as their surrounding environment as these interactions are complex, multifaceted, and computationally expensive to the point of being prohibitive when considering a large number of particles. In this paper, we present a numerical model designed to enable spatial analysis of the physical effects exerted upon particles within microfluidic systems employing dielectrophoresis. The model presents a means of approximating the effects of the presence of large numbers of particles through dynamically adjusting hydrodynamic drag force based on particle density, thereby introducing a measure of emulated particle–particle and particle–liquid interactions. This model is referred to as “dynamic drag force based on iterative density mapping.” The resultant numerical model is used to simulate and predict particle trajectory and velocity profiles within a microfluidic system incorporating curved dielectrophoretic microelectrodes. The simulated data are compared favorably with experimental data gathered using microparticle image velocimetry, and is contrasted against simulated data generated using traditional “effective moment Stokes‐drag method,” showing more accurate particle velocity profiles for areas of high particle density.     

Gas‐phase doubly charged complexes of cyclic peptides with copper in +1, +2 and +3 formal oxidation states: formation,structures and electron capture dissociation

Copper complexes with a cyclic D‐His‐β‐Ala‐L‐His‐L‐Lys and all‐L‐His‐β‐Ala‐His‐Lys peptides were generated by electrospray which were doubly charged ions that had different formal oxidation states of Cu(I), Cu(II) and Cu(III) and different protonation states of the peptide ligands. Electron capture dissociation showed no substantial differences between the D‐His and L‐His complexes. All complexes underwent peptide cross‐ring cleavages upon electron capture. The modes of ring cleavage depended on the formal oxidation state of the Cu ion and peptide protonation. Density functional theory (DFT) calculations, using the B3LYP with an effective core potential at Cu and M06‐2X functionals, identified several precursor ion structures in which the Cu ion was threecoordinated to pentacoordinated by the His and Lys side‐chain groups and the peptide amide or enolimine groups. The electronic structure of the formally Cu(III) complexes pointed to an effective Cu(I) oxidation state with the other charge residing in the peptide ligand. The relative energies of isomeric complexes of the [Cu(c‐HAHK + H)]²⁺ and [Cu(c‐HAHK ? H)]²⁺ type with closed electronic shells followed similar orders when treated by the B3LYP and M06‐2X functionals. Large differences between relative energies calculated by these methods were obtained for open‐shell complexes of the [Cu(c‐HAHK)]²⁺ type. Charge reduction resulted in lowering the coordination numbers for some Cu complexes that depended on the singlet or triplet spin state being formed. For [Cu(c‐HAHK ? H)]²⁺ complexes, solution H/D exchange involved only the N–H protons, resulting in the exchange of up to seven protons, as established by ultra‐high mass resolution measurements. Contrasting the experiments, DFT calculations found the lowest energy structures for the gas‐phase ions that were deprotonated at the peptide C_α positions. Copyright © 2012 John Wiley & Sons, Ltd.