Mono-silicon isoelectronic replacement in CAl4: van't hoff/le bel carbon or not?

In cluster studies, the isoelectronic replacement strategy has been successfully used to introduce new elements into a known structure while maintaining the desired topology. The well-known penta-atomic 18 valence electron (ve) species and its Al⁻/Si or Al/Si⁺ isoelectronically replaced clusters CAl₃Si⁻, CAl₂Si₂, , and , all possess the same anti-van't Hoff/Le Bel skeletons, that is, nontraditional planar tetracoordinate carbon (ptC) structure. In this article, however, we found that such isoelectronic replacement between Si and Al does not work for the 16ve-CAl₄ with the traditional van't Hoff/Le Bel tetrahedral carbon (thC) and its isoelectronic derivatives CAl₃X (X = Ga/In/Tl). At the level of CCSD(T)/def2-QZVP//B3LYP/def2-QZVP, none of the global minima of the 16ve mono-Si-containing clusters CAl₂SiX⁺ (X = Al/Ga/In/Tl) maintains thC as the parent CAl₄ does. Instead, X = Al/Ga globally favors an unusual ptC structure that has one long C─X distance yet with significant bond index value, and X = In/Tl prefers the planar tricoordinate carbon. The frustrated formation of thC in these clusters is ascribed to the CSi bonding that prefers a planar fashion. Inclusion of chloride ion would further stabilize the ptC of CAl₂SiAl⁺ and CAl₂SiGa⁺. The unexpectedly disclosed CAl₂SiAl⁺ and CAl₂SiGa⁺ represent the first type of 16ve-cationic ptCs with multiple bonds. © 2019 Wiley Periodicals, Inc.     

Ion‐Pair SN2 Reaction of OH− and CH3Cl: Activation Strain Analyses of Counterion and Solvent Effects

We have theoretically studied the non‐identity S_N2 reactions of M_nOH^(n?1)+CH₃Cl (M⁺=Li⁺, Na⁺, K⁺, and MgCl⁺; n=0, 1) in the gas phase and in THF solution at the OLYP/6‐31++G(d,p) level using polarizable continuum model (PCM) implicit solvation. We want to explore and understand the effect of the metal counterion M⁺ and solvation on the reaction profile and the stereoselectivity of these processes. To this end, we have explored the potential energy surfaces of the backside (S_N2‐b) and frontside (S_N2‐f) pathways. To explain the computed trends, we have carried out analyses with an extended activation strain model (ASM) of chemical reactivity that includes the treatment of solvation effects.     

Aspartate: An interesting model for analyzing dipole-ion and ion pair interactions through its oppositely charged amine and acid groups

Anionic species of aspartic acid, Asp⁻, having a zwitterionic backbone and a deprotonated side chain, appears to be a good example for analyzing dipole-ion and ion pair interactions. Density functional theory calculations were herein performed to investigate the low energy conformers of Asp⁻ embedded in a dielectric continuum modeling an aqueous environment, through a scan of the potential energy as a function of the side chain (χ₁, χ₂) torsion angles. The most energetically favorable conformers having g⁺g⁻ and g⁻g⁺ side chain orientations are found to be stabilized by charge-enhanced intramolecular H-bonding involving the positively charged () and the two negatively charged (COO⁻) groups. These conformers were further used to analyze Asp⁻ + nW clusters (W: water, n = 1 or 3), and Asp⁻/Asp⁻ pair formation. COO⁻ groups were found to be the most attractive sites for hosting a water molecule (binding energy: −6.0 ± 1.5 kcal/mol), compared to groups (binding energy: −4.7 ± 1.1 kcal/mol). Energy separation between g⁺g⁻ and g⁻g⁺ conformers increases upon explicit hydration. Asp⁻/Asp⁻ ion pairs, stabilized by the interaction between the group of a partner and the COO⁻ group of the other, shows a quite constant binding energy (−8.1 ± 0.2 kcal/mol), whatever the pair type, and the relative orientation of the two interacting partners. This study suggests a first step to achieve a more realistic image of intermolecular interactions in aqueous environment, especially upon increasing concentration. It can also be considered as a preliminary attempt to assess the interactions of the Lys⁺…Asp⁻/Glu⁻ ion pairs stabilizing intra- and interchain interactions in proteins.     

Substitutional carbon defects in silicon: A quantum mechanical characterization through the infrared and Raman spectra

The infrared (IR) and Raman spectra of eight substitutional carbon defects in silicon are computed at the quantum mechanical level by using a periodic supercell approach based on hybrid functionals, an all electron Gaussian type basis set and the CRYSTAL code. The single substitutional C _s case and its combination with a vacancy (C _sV and C _sSiV) are considered first. The progressive saturation of the four bonds of a Si atom with C is then examined. The last set of defects consists of a chain of adjacent carbon atoms C, with i = 1–3. The simple substitutional case, C _s, is the common first member of the three sets. All these defects show important, very characteristic features in their IR spectrum. One or two C related peaks dominate the spectra: at 596 cm⁻¹ for C _s (and C _sSiV, the second neighbor vacancy is not shifting the C _s peak), at 705 and 716 cm⁻¹ for C _sV, at 537 cm⁻¹ for C and C (with additional peaks at 522, 655 and 689 for the latter only), at 607 and 624 cm⁻¹, 601 and 643 cm⁻¹, and 629 cm⁻¹ for SiC, SiC, and SiC, respectively. Comparison with experiment allows to attribute many observed peaks to one of the C substitutional defects. Observed peaks above 720 cm⁻¹ must be attributed to interstitial C or more complicated defects.     

Four faces of the interaction between ions and aromatic rings

Non‐covalent interactions between ions and aromatic rings play an important role in the stabilization of macromolecular complexes; of particular interest are peptides and proteins containing aromatic side chains (Phe, Trp, and Tyr) interacting with negatively (Asp and Glu) and positively (Arg and Lys) charged amino acid residues. The structures of the ion–aromatic‐ring complexes are the result of an interaction between the large quadrupole moment of the ring and the charge of the ion. Four attractive interaction types are proposed to be distinguished based on the position of the ion with respect to the plane of the ring: perpendicular cation–π (CP_⊥), co‐planar cation–π (CP_∥), perpendicular anion–π (AP_⊥), and co‐planar anion–π (AP_∥). To understand more than the basic features of these four interaction types, a systematic, high‐level quantum chemical study is performed, using the X^– + C₆H₆, M⁺ + C₆H₆, X^– + C₆F₆, and M⁺ + C₆F₆ model systems with X⁻ = H⁻, F⁻, Cl⁻, HCOO⁻, CH₃COO⁻ and M⁺ = H⁺, Li⁺, Na⁺, , CH₃ , whereby C₆H₆ and C₆F₆ represent an electron‐rich and an electron‐deficient π system, respectively. Benchmark‐quality interaction energies with small uncertainties, obtained via the so‐called focal‐point analysis (FPA) technique, are reported for the four interaction types. The computations reveal that the interactions lead to significant stabilization, and that the interaction energy order, given in kcal mol⁻¹ in parentheses, is CP_⊥ (23–37) > AP_⊥ (14–21) > CP_∥ (9–22) > AP_∥ (6–16). A natural bond orbital analysis performed leads to a deeper qualitative understanding of the four interaction types. To facilitate the future quantum chemical characterization of ion–aromatic‐ring interactions in large biomolecules, the performance of three density functional theory methods, B3LYP, BHandHLYP, and M06‐2X, is tested against the FPA benchmarks, with the result that the M06‐2X functional performs best. © 2017 Wiley Periodicals, Inc.     

A Density Functional Theory Study on Nonlinear Optical Properties of Double Cage Excess Electron Compounds: Theoretically Design M[Cu(Ag)@(NH3)n](M = Be,Mg and Ca; n = 1–3)

In this work, we investigated the nonlinear optical (NLO) properties of excess electron electride molecules of M[Cu(Ag)@(NH₃)_n](M = Be, Mg and Ca; n = 1–3) using density functional theory (DFT). This electride molecules consist of an alkaline-earth (Be, Mg and Ca) together with transition metal (Cu and Ag) doped in NH₃ cluster. The natural population analysis of charge and their highest occupied molecular orbital suggests that the M[Cu(Ag)@(NH₃)_n] compound has excess electron like alkaline-earth metal form double cage electrides molecules, which exhibit a large static first hyperpolarizability () (electron contribution part) and one of which owns a peak value of 216,938 (a.u.) for Be[Ag@(NH₃)₂] and vibrational harmonic first hyperpolarizability () (nuclear contribution part) values and the ratio of /, namely, η values from 0.02 for Be[Ag@(NH₃)] to 0.757 for Mg[Ag@(NH₃)₃]. The electron density contribution in different regions on values mainly come from alkaline-earth and transition metal atoms by first hyperpolarizability density analysis, and also explains the reason why values are positive and negative. Moreover, the frequency-dependent values β(−2ω,ω,ω) are also estimated to make a comparison with experimental measures. © 2018 Wiley Periodicals, Inc.     

Ion‐Pair SN2 Substitution: Activation Strain Analyses of Counter‐Ion and Solvent Effects

The ion‐pair S_N2 reactions of model systems M_nF^n?1+CH₃Cl (M⁺=Li⁺, Na⁺, K⁺, and MgCl⁺; n=0, 1) have been quantum chemically explored by using DFT at the OLYP/6‐31++G(d,p) level. The purpose of this study is threefold: 1) to elucidate how the counterion M⁺ modifies ion‐pair S_N2 reactivity relative to the parent reaction F^?+CH₃Cl; 2) to determine how this influences stereochemical competition between the backside and frontside attacks; and 3) to examine the effect of solvation on these ion‐pair S_N2 pathways. Trends in reactivity are analyzed and explained by using the activation strain model (ASM) of chemical reactivity. The ASM has been extended to treat reactivity in solution. These findings contribute to a more rational design of tailor‐made substitution reactions.     

Entropic Contributions to Sodium Solvation and Solvent Stabilization upon Electrochemical Sodium Deposition from Diglyme and Propylene Carbonate Electrolytes

The formation of an appropriate solid electrolyte interphase (SEI) at the anode of a sodium battery is crucially dependent on the electrochemical stability of solvent and electrolyte at the redox potential of Na/Na⁺ in the respective system. In order to determine entropic contributions to the relative stability of the electrolyte solution, we measure the reaction entropy of Na metal deposition for diglyme (DG) and propylene carbonate (PC) based electrolyte solutions by electrochemical microcalorimetry at single electrodes. We found a large positive reaction entropy for Na⁺ deposition in DG of Δ_R 234 J mol⁻¹ K⁻¹ (c.f.: Δ_R 83 J mol⁻¹ K⁻¹), which signals substantial entropic destabilization of Na⁺ in DG by about 0.73 eV, thus increasing the stability of solvent and electrolyte relative to Na⁺ reduction. We attribute this strong entropic destabilization to a highly negative solvation entropy of Na⁺, due to the low dielectric constant and high freezing entropy of DG.     

Effects of zero point vibration on the reaction dynamics of water dimer cations following ionization

Reactions of water dimer cation following ionization have been investigated by means of a direct ab initio molecular dynamics method. In particular, the effects of zero point vibration and zero point energy (ZPE) on the reaction mechanism were considered in this work. Trajectories were run on two electronic potential energy surfaces (PESs) of : ground state (²A″‐like state) and the first excited state (²A′ ‐ like state). All trajectories on the ground‐state PES lead to the proton‐transferred product: H₂O⁺(Wd)‐H₂O(Wa) → OH(Wd)‐H₃O⁺(Wa), where Wd and Wa refer to the proton donor and acceptor water molecules, respectively. Time of proton transfer (PT) varied widely from 15 to 40 fs (average time of PT = 30.9 fs). The trajectories on the excited‐state PES gave two products: an intermediate complex with a face‐to‐face structure (H₂O‐OH₂)⁺ and a PT product. However, the proton was transferred to the opposite direction, and the reverse PT was found on the excited‐state PES: H₂O(Wd)‐H₂O⁺ (Wa) → H₃O⁺(Wd)‐OH(Wa). This difference occurred because the ionizing water molecule in the dimer switched between the ground and excited states. The reaction mechanism of and the effects of ZPE are discussed on the basis of the results. © 2017 Wiley Periodicals, Inc.     

Ab initio potential energy surface and vibration–rotation energy levels of germanium dicarbide,GeC2

The accurate ground‐state potential energy surface of germanium dicarbide, GeC₂, has been determined from ab initio calculations using the coupled‐cluster approach. The core–electron correlation, higher‐order valence‐electron correlation, and scalar relativistic effects were taken into account. The potential energy surface of GeC₂ was shown to be extraordinarily flat near the T‐shaped equilibrium configuration. The potential energy barrier to the linear CCGe configuration was predicted to be 1218 cm⁻¹. The vibration–rotation energy levels of some GeC₂ isotopologues were calculated using a variational method. The vibrational bending mode ν₃ was found to be highly anharmonic, with the fundamental wavenumber being only 58 cm⁻¹. Vibrational progressions due to this mode were predicted for the , , and states of GeC₂. © 2018 Wiley Periodicals, Inc.     

Ab initio structure and vibration-rotation dynamics of germylene,GeH2

Accurate structure and potential energy surface of germylene, GeH₂, in its ground electronic state ¹A₁ were determined from ab initio calculations using the coupled-cluster approach in conjunction with the correlation-consistent basis sets up to sextuple-zeta quality. The Born-Oppenheimer equilibrium structural parameters for the ¹A₁ state are estimated to be r_e(GeH) = 1.5793 Å and ∠_e(HGeH) = 91.19^∘. The term value T_e for the lowest excited electronic state ã³B₁ of GeH₂ is predicted to be 9140 cm^–1. The vibration-rotation energy levels for the ¹A₁ state of the ⁷⁴GeH₂, ⁷⁴GeD₂, ⁷²GeH₂, and ⁷⁰GeH₂ isotopologues were determined using a variational approach and compared with the experimental data. The role of the core-electron correlation, higher-order valence-electron correlation, scalar relativistic, spin-orbit, and adiabatic effects for prediction of the structure and vibration-rotation dynamics of the GeH₂ molecule is discussed. © 2019 Wiley Periodicals, Inc.     

Mechanism of the O2(1Δg) generation from the Cl2/H2O2 basic aqueous solution explored by the combined ab initio calculation and nonadiabatic dynamics simulation

In the present work, mechanism of the O₂(¹Δ_g) generation from the reaction of the dissolved Cl₂ with H₂O₂ in basic aqueous solution has been explored by the combined ab initio calculation and nonadiabatic dynamics simulation, together with different solvent models. Three possible pathways have been determined for the O₂(¹Δ_g) generation, but two of them are sequentially downhill processes until formation of the OOCl⁻ complex with water, which are of high exothermic character. Once the complex is formed, singlet molecular oxygen is easily generated by its decomposition along the singlet-state pathway. However, triplet molecular oxygen of O₂() can be produced with considerable probability through nonadiabatic intersystem crossing in the ¹Δ_g/ intersection region. It has been found that the coupled solvent, heavy-atom, and nonadiabatic effects have an important influence on the quantum yield of the O₂(¹Δ_g) generation. © 2018 Wiley Periodicals, Inc.     

Fluxional bonds in quasi-planar and half-sandwich (M = K,Rb, and Cs)

Detailed molecular orbital and bonding analyses reveal the existence of both fluxional σ- and π-bonds in the global minima C_s ( 1 ) and C_s MB₁₈ ( 3 ) and transition states C_s ( 2 ) and C_s ( 4 ) of dianion and monoanions (M = K, Rb, and Cs). It is the fluxional bonds that facilitate the fluxional behaviors of the quasi-planar and half-sandwich which possess energy barriers smaller than the difference of the corresponding zero-point corrections. © 2019 Wiley Periodicals, Inc.     

Double-Gyroid Nanostructure Formation by Aggregation-Induced Atropisomerization and Co-Assembly of Ionic Liquid-Crystalline Amphiphiles

We report a new molecular-design principle for creating double-gyroid nanostructured molecular assemblies based on atropisomerization. Ionic amphiphiles containing two imidazolium rings close to each other were designed and synthesized. NMR data revealed that the rotation of the imidazolium rings is restricted, with an activation energy as high as 63 kJ mol⁻¹ in DMSO-d₆ solution (DFT prediction for a model compound in the vacuum: 90–100 kJ mol⁻¹). Due to the restricted rotation, the amphiphiles feature “double” atropisomeric axes in their ionic segments and form three stable atropisomers: meso, R, and S. These isomers co-organize into -type bicontinuous cubic liquid-crystalline mesophases through nanosegregation of the ionic and non-ionic parts. Considering the intrinsic characteristic of -type bicontinuous cubic structures that they are composed of intertwined right- and left-handed single gyroids, we propose that the simultaneous presence of both R- and S-atropisomers is an important contributor to the formation of double-gyroid structures.     

Harnessing Plasticity in an Amine-Borane as a Piezoelectric and Pyroelectric Flexible Film

We demonstrate that trimethylamine borane can exhibit desirable piezoelectric and pyroelectric properties. The material was shown to be able operate as a flexible film for both thermal sensing, thermal energy conversion and mechanical sensing with high open circuit voltages (>10 V). A piezoelectric coefficient of d₃₃≈10–16 pC N⁻¹, and pyroelectric coefficient of p≈25.8 μC m⁻² K⁻¹ were achieved after poling, with high pyroelectric figure of merits for sensing and harvesting, along with a relative permittivity of 6.3.     

Modular and Selective Arylation of Aryl Germanes (C−GeEt3) over C−Bpin,C−SiR3 and Halogens Enabled by Light-Activated Gold Catalysis

Selective C –C couplings are powerful strategies for the rapid and programmable construction of bi- or multiaryls. To this end, the next frontier of synthetic modularity will likely arise from harnessing the coupling space that is orthogonal to the powerful Pd-catalyzed coupling regime. This report details the realization of this concept and presents the fully selective arylation of aryl germanes (which are inert under Pd⁰/Pd^II catalysis) in the presence of the valuable functionalities C−BPin, C−SiMe₃, C−I, C−Br, C−Cl, which in turn offer versatile opportunities for diversification. The protocol makes use of visible light activation combined with gold catalysis, which facilitates the selective coupling of C−Ge with aryl diazonium salts. Contrary to previous light-/gold-catalyzed couplings of Ar–N₂⁺, which were specialized in Ar–N₂⁺ scope, we present conditions to efficiently couple electron-rich, electron-poor, heterocyclic and sterically hindered aryl diazonium salts. Our computational data suggest that while electron-poor Ar–N₂⁺ salts are readily activated by gold under blue-light irradiation, there is a competing dissociative deactivation pathway for excited electron-rich Ar–N₂⁺, which requires an alternative photo-redox approach to enable productive couplings.     

A Computational Analysis of the Intrinsic Plasticity of Five-Coordinate Cu(II) Complexes and the Factors Leading to the Breakdown of the Orbital Directing Effect in Paddlewheel Secondary Building Units

Quantum chemical calculations on model copper paddlewheel (CPW) complexes of general formula [Cu₂(μ₂-O₂CR)₄L₂] establish two local coordination geometries at the metal centers depending on the balance between equatorial and axial ligand fields. When the equatorial field is stronger than the axial field (large ligand field asymmetry), dominates the stereochemical activity of the d⁹ shell resulting in a relatively rigid, “orbitally directed” planar or square pyramidal structure. However, if the axial field is significantly increased, or the equatorial field moderately weakened, a small ligand field asymmetry results and both and are involved in the stereochemical activity. This results in a “plastic,” distorted trigonal bipyramidal geometry where the former axial ligand moves into one of the original four equatorial positions. Linkers already used to synthesize zinc-dabco MOFs (dabco = 1,4-diazabicyclo[2.2.2]octane) are shown to generate plastic CPW secondary building unit analogs with potential implications for conferring breathing behavior for MOFs which would currently be assumed to be rigid. © 2019 Wiley Periodicals, Inc.     

One Way Traffic: Base-to-Backbone Hole Transfer in Nucleoside Phosphorodithioate

The directionality of the hole-transfer processes between DNA backbone and base was investigated by using phosphorodithioate [P(S⁻)=S] components. ESR spectroscopy in homogeneous frozen aqueous solutions and pulse radiolysis in aqueous solution at ambient temperature confirmed initial formation of G^.+-P(S⁻)=S. The ionization potential of G-P(S⁻)=S was calculated to be slightly lower than that of guanine in 5′-dGMP. Subsequent thermally activated hole transfer from G^.+ to P(S⁻)=S led to dithiyl radical (P-2S^.) formation on the μs timescale. In parallel, ESR spectroscopy, pulse radiolysis, and density functional theory (DFT) calculations confirmed P-2S^. formation in an abasic phosphorodithioate model compound. ESR investigations at low temperatures and higher G-P(S⁻)=S concentrations showed a bimolecular conversion of P-2S^. to the σ²-σ*¹-bonded dimer anion radical [-P-2S 2S-P-]⁻ [ΔG (150 K, DFT)=−7.2 kcal mol⁻¹]. However, [-P-2S 2S-P-]⁻ formation was not observed by pulse radiolysis [ΔG° (298 K, DFT)=−1.4 kcal mol⁻¹]. Neither P-2S^. nor [-P-2S 2S-P-]⁻ oxidized guanine base; only base-to-backbone hole transfer occurs in phosphorodithioate.