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.     

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.     

New insight into the electronic structure of iron(IV)‐oxo porphyrin compound I. A quantum chemical topological analysis

The electronic structure of iron‐oxo porphyrin π‐cation radical complex Por^·+Fe^IV?O (S? H) has been studied for doublet and quartet electronic states by means of two methods of the quantum chemical topology analysis: electron localization function (ELF) η(r) and electron density ρ(r). The formation of this complex leads to essential perturbation of the topological structure of the carbon–carbon bonds in porphyrin moiety. The double C?C bonds in the pyrrole anion subunits, represented by pair of bonding disynaptic basins V_i=1,2(C,C) in isolated porphyrin, are replaced by single attractor V(C,C)_i=1–20 after complexation with the Fe cation. The iron–nitrogen bonds are covalent dative bonds, N→Fe, described by the disynaptic bonding basins V(Fe,N)_i=1–4, where electron density is almost formed by the lone pairs of the N atoms. The nature of the iron–oxygen bond predicted by the ELF topological analysis, shows a main contribution of the electrostatic interaction, Fe^δ+···O^δ?, as long as no attractors between the C(Fe) and C(O) core basins were found, although there are common surfaces between the iron and oxygen basines and coupling between iron and oxygen lone pairs, that could be interpreted as a charge‐shift bond. The Fe? S bond, characterized by the disynaptic bonding basin V(Fe,S), is partially a dative bond with the lone pair donated from sulfur atom. The change of electronic state from the doublet (M = 2) to quartet (M = 4) leads to reorganization of spin polarization, which is observed only for the porphyrin skeleton (?0.43e to 0.50e) and S? H bond (?0.55e to 0.52e). © 2012 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.     

Activation Strain Analyses of Counterion and Solvent Effects on the Ion-Pair SN2 Reaction of and CH3Cl

We have computationally studied the bimolecular nucleophilic substitution (S_N2) reactions of M_nNH₂⁽ⁿ⁻¹⁾ + CH₃Cl (M⁺ = Li⁺, Na⁺, K⁺, and MgCl⁺; n = 0, 1) in the gas phase and in tetrahydrofuran solution at OLYP/6-31++G(d,p) using polarizable continuum model implicit solvation. We wish to explore and understand the effect of the metal counterion M⁺ and of solvation on the reaction profile and the stereochemical preference, that is, backside (S_N2-b) versus frontside attack (S_N2-f). The results were compared to the corresponding ion-pair S_N2 reactions involving F⁻ and OH⁻ nucleophiles. Our analyses with an extended activation strain model of chemical reactivity uncover and explain various trends in S_N2 reactivity along the nucleophiles F⁻, OH⁻, and , including solvent and counterion effects. © 2019 Wiley Periodicals, Inc.     

Analysis of tertiary phosphanes, arsanes, and stibanes as bridging ligands in dinuclear Group 9 complexes

The unusual bridging and semi‐bridging binding mode of tertiary phosphanes, arsanes, and stibanes in dinuclear low‐valent Group 9 complexes have been studied by density functional methods and bonding analyses. The influence of various parameters (bridging and terminal ligands, metal atoms) on the structural preferences and bonding of dinuclear complexes of the general composition [A¹ M¹(μ‐CH₂)₂(μ‐EX₃)M² A²] (M¹, M²=Co, Rh, Ir; A¹, A²=F, Cl, Br, I, κ²‐acac; E=P, As, Sb, X=H, F, CH₃) has been analyzed. A number of factors have been identified that favor bridging or semi‐bridging modes for the phosphane ligands and their homologues. A more symmetrical position of the bridging ligand EX₃ is promoted by more polar E? X bonding, but by less electronegative (softer) terminal anionic ligands. Among the Group 9 metal elements Co, Rh, and Ir, the computations clearly show that the 4d element rhodium exhibits the largest preference for a {M¹(μ‐EX₃)M²} bridge, in agreement with experimental observation. Iridium complexes should be valid targets, whereas cobalt does not seem to support well a symmetric bridging mode. Analyses of the Electron Localization Function (ELF) indicate a competition between a delocalized three‐center bridge bond and direct metal–metal bonding.     

Substituent effect on electron affinity,gas‐phase basicity,and structure of monosubstituted propynyl radicals and their anions: A theoretical study

The substituent effect of electron‐withdrawing groups on electron affinity and gas‐phase basicity has been investigated for substituted propynl radicals and their corresponding anions. It is shown that when a hydrogen of the α‐CH₃ group in the propynyl system is substituted by an electron‐withdrawing substituent, electron affinity increases, whereas gas‐phase basicity decreases. These results can be explained in terms of the natural atomic charge of the terminal acetylene carbon of the systems. The calculated electron affinities are 3.28 eV (?C?C? CH₂F), 3.59 eV (?C?C? CH₂Cl) and 3.73 eV (?C?C? CH₂Br), and the gas‐phase basicities of their anions are 359.5 kcal/mol (^?:C?C? CH₂F), 354.8 kcal/mol (:C?C? CH₂Cl) and 351.3 kcal/mol (^?:C?C? CH₂Br). It is concluded that the larger the magnitude of electron‐withdrawing, the greater is the electron affinity of radical and the smaller is the gas‐phase basicity of its anion. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009     

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.     

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.     

Inverse Ubbelohde effect in the short hydrogen bond of photosystem II: Relation between H/D isotope effect and symmetry in potential energy profile

The short hydrogen bond between tyrosine Y_z and D1‐His190 of photosystem II (PSII) was investigated using multicomponent quantum mechanics, where the quantum fluctuation of a hydrogen nucleus was incorporated into electronic structure calculation. Our computation demonstrated that the deuteration for hydrogen in the short hydrogen bond of PSII led to the reduction of the O…N distance. It indicated an inverse Ubbelohde effect typically recognized in strong and symmetric hydrogen‐bonding clusters such as FHF^– and . We confirmed that the relation between the geometric isotope effect and the symmetry of the potential energy profile of FHF^– was reasonably agreed with that of PSII. According to this agreement, the short hydrogen bond in PSII can be regarded as a short strong hydrogen bond. © 2016 Wiley Periodicals, Inc.     

Polar-Covalent Bonding Beyond the Zintl Picture in Intermetallic Rare-Earth Germanides

A comparative chemical bonding analysis for the germanides La₂MGe₆ (M=Li, Mg, Al, Zn, Cu, Ag, Pd) and Y₂PdGe₆ is presented, together with the crystal structure determination for M=Li, Mg, Cu, Ag. The studied compounds adopt the two closely related structure types oS72-Ce₂(Ga_0.1Ge_0.9)₇ and mS36-La₂AlGe₆, containing zigzag chains and corrugated layers of Ge atoms bridged by M species, with La/Y atoms located in the biggest cavities. Chemical bonding was studied by means of the quantum chemical position-space techniques QTAIM (quantum theory of atoms in molecules), ELI-D (electron localizability indicator), and their basin intersections. The new penultimate shell correction (PSC0) method was introduced to adapt the ELI-D valence electron count to that expected from the periodic table of the elements. It plays a decisive role to balance the Ge−La polar-covalent interactions against the Ge−M ones. In spite of covalently bonded Ge partial structures formally obeying the Zintl electron count for M=Mg²⁺, Zn²⁺, all the compounds reveal noticeable deviations from the conceptual 8−N picture due to significant polar-covalent interactions of Ge with La and M ≠ Li, Mg atoms. For M=Li, Mg a formulation as a germanolanthanate M[La₂Ge₆] is appropriate. Moreover, the relative Laplacian of ELI-D was discovered to reveal a chemically useful fine structure of the ELI-D distribution being related to polyatomic bonding features. With the aid of this new tool, a consistent picture of La/Y−M interactions for the title compounds was extracted.     

Comparative Analysis of Electron‐Density and Electron‐Localization Function for Dinuclear Manganese Complexes with Bridging Boron‐ and Carbon‐Centered Ligands

Bonding in borylene‐, carbene‐, and vinylidene‐bridged dinuclear manganese complexes [MnCp(CO)₂]₂X (X=B‐tBu, B=NMe₂, CH₂, C?CH₂) has been compared by analyses based on quantum theory of atoms in molecules (QTAIM), on the electron‐localization function (ELF), and by natural‐population analyses. All of the density functional theory based analyses agree on the absence of a significant direct Mn? Mn bond in these complexes and confirm a dominance of delocalized bonding via the bridging ligand. Interestingly, however, the topology of both charge density and ELF related to the Mn‐bridge‐Mn bonding depend qualitatively on the chosen density functional (except for the methylene‐bridged complex, which exhibits only one three‐center‐bonding attractor both in ??²ρ and in ELF). While gradient‐corrected functionals provide a picture with localized two‐center X? Mn bonding, increasing exact‐exchange admixture in hybrid functionals concentrates charge below the bridging atom and suggests a three‐center bonding situation. For example, the bridging boron ligands may be described either as substituted boranes (e.g., at BLYP or BP86 levels) or as true bridging borylenes (e.g., at BHLYP level). This dependence on the theoretical level appears to derive from a bifurcation between two different bonding situations and is discussed in terms of charge transfer between X and Mn, and in the context of self‐interaction errors exhibited by popular functionals.     

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.     

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.     

Formal Nickelate(−I) Complexes Supported by Group 13 Ions

Formal nickelate(?I) complexes bearing Group 13 metalloligands (M=Al and Ga) were isolated. These 17 e^? complexes were synthesized by one‐electron reduction of the corresponding Ni⁰→M^III precursors, and were investigated by single‐crystal X‐ray diffraction, EPR spectroscopy, and quantum chemical calculations. Collectively, the experimental and computational data support: 1) the strengthening of the Ni?M bond upon one‐electron reduction, and 2) the delocalization of the unpaired spin across the Ni and M atoms. An intriguing electronic configuration is revealed where three valence electrons occupy two σ‐type bonding interactions: Ni(3d )²→M and σ‐(Ni?M)¹. The latter is an unusual Ni?M σ‐bonding molecular orbital that comprises primarily the Ni 4p_z and M np_z/ns atomic orbitals.     

Triple Bonds Between Iron and Heavier Group 15 Elements in AFe(CO)3− (A=As,Sb, Bi) Complexes

Heteronuclear transition‐metal–main‐group‐element carbonyl complexes of AsFe(CO)₃^?, SbFe(CO)₃^?, and BiFe(CO)₃^? were produced by a laser vaporization supersonic ion source in the gas phase, and were studied by mass‐selected IR photodissociation spectroscopy and advanced quantum chemistry methods. These complexes have C_3v structures with all of the carbonyl ligands bonded on the iron center, and feature covalent triple bonds between bare Group 15 elements and Fe(CO)₃^?. Chemical bonding analyses on the whole series of AFe(CO)₃^? (A=N, P, As, Sb, Bi, Mc) complexes indicate that the valence orbitals involved in the triple bonds are hybridized 3d and 4p atomic orbitals of iron, leading to an unusual (dp–p) type of transition‐metal–main‐group‐element multiple bonding. The σ‐type three‐orbital interaction between Fe 3d/4p and Group 15 np valence orbitals plays an important role in the bonding and stability of the heavier AFe(CO)₃^? (A=As, Sb, Bi) complexes.     

Structural parameters of the ground states of the quasi‐stable diatomic anions CO−, BF−, and BCl− as obtained by conventional Ab Initio methods

The experimental electron affinity (EA) of CO(X¹Σ⁺) is ?1.5 eV, signifying the metastability of the CO^?(X²Π) anion. The electronic structure and bonding of CO^?, BF^?, and BCl^? vis‐à‐vis their neutral counterparts have been studied by conventional coupled‐cluster (CCSD(T)) and multireference (MRCI) methods. Our results are in agreement with experiment for the CO/CO^? system, indicating as well the metastable nature of the BF^?(X²Π) and BCl^?(X²Π) anions, their MRCI EAs being ?0.8 ± 0.1 and ?0.3 ± 0.1 eV, respectively. Our work clearly shows the usefulness of stationary state ab initio methods to the elucidation of metastable species. © 2015 Wiley Periodicals, Inc.     

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.