Methyl substituent effects in [H(n)X...XH(n)](+) three-electron-bonded radical cations (X = F, O, N, Cl, S, P; n = 1 - 3). An ab initio theoretical study

A molecular dynamics and quantum mechanical investigation of intermolecular interaction and electron-transfer mechanism between copper-containing nitrite reductase and redox partner pseudoazurin

Much of biological electron transfer occurs between proteins. These molecular processes usually involve molecular recognition and intermolecular electron transfer (inter-ET). The inter-ET reaction between copper-containing nitrite reductase (CuNiR) and partner protein pseudoazurin (PAz) is the first step in denitrification, which is affected by intermolecular association. However, the transient interaction between CuNiR and PAz and the indistinct inter-ET pathway pose challenges for people to understand the biological functions of the CuNiR-PAz complex. Thus, molecular dynamics simulation and quantum mechanical calculation were used to investigate the question in this study. The interaction of the interface residues was determined through hydrogen bonds, root-mean-square deviation, root-mean-square fluctuation, the dynamics cross-correlation matrix, and molecular mechanics Poisson-Boltzmann surface area of molecular dynamics simulations. The interactions among the residues Glu89, Gly200, Asp205, Asn91, Glu204, Thr92, and Met141 on CuNiR and the residues Lys109, Ala15, Lys10, Asn9, Ile110, Met84, and Met16 on PAz are responsible for the stabilization of the complex. The binding free energy is up to -25.33 kcal mol^-1. We compared the wild-type and mutant (M84A) interfacial optimized complex models at the CAM-B3LYP level with Grimme dispersion corrections (GD3) to confirm Met84 as a relay station for promoting the inter-ET. Additionally, to test whether Met84 may combine with the adjacent Met141 to form a special two-center, three-electron (S∴S)⁺ structure to promote the inter-ET, QM/MM was further performed to discuss the possibility of generating an electron stepping stone. Our study will promote a deep understanding of the stable protein-protein interaction, and the identified inter-residue interaction will be theoretical guidance for enhancing the catalytic activity of CuNiR in denitrification.

Nature of the Three-Electron Bond

We analyze the properties of 15 3-electron bonds, which include σ-3-electron-bonds, such as dihalide radical anions and di-noble gas radical cations, π-3-electron-bonds as in hydrazine radical cations, and doubly-π-(3e)-bonded species such as O₂, FeO⁺, S₂, etc. The primary analytical tool is the breathing-orbital valence-bond (BOVB) method, which enables us to quantify the charge shift resonance energy (RE_CS) of the three electrons, and the bond dissociation energies (D_e). BOVB is tested reliable against MRCI calculations. Our findings show that in all 3-electron bonds, none of the VB structures have by themselves any bonding. In fact, in each VB structure, the three electrons maintain Pauli repulsion, while the entire bonding energy arises from resonance due to the charge shift between the two or more constituent VB structures. Hence, 3e-bonds are charge shift bonds (CSBs). The CSB character is probed by calculating the Laplacian (L) of the 3e-bond. Thus, much like the CSBs in electron-pair bonds, such as F₂ or the central bond in [1.1.1]propellane, here too L is positive, thus showing the excess kinetic energy of the shared density due to the Pauli repulsion in the 3-electron VB structures. The RE_CS values for 3-electron bonds are invariably larger than the corresponding bond energies. For the doubly-π-(3e)-bonded species, RE_CS is very large, exceeding 100 kcal mol^-1. As such, it is fitting to conclude that σ- and π-3-electron-bonds find their natural place in the CSB family along with two-electron CSBs, with which they share identical energetic and topological characteristics. Experimental manifestations/tests of 3e-CSBs are proposed.

Two-Center/Three-Electron Sigma Half-Bonds in Main Group and Transition Metal Chemistry

First proposed in a classic Linus Pauling paper, the two-center/three-electron (2c/3e) σ half-bond challenges the extremes of what may or may not be considered a chemical bond. Two electrons occupying a σ bonding orbital and one electron occupying the antibonding σ* orbital results in bond orders of ∼0.5 that are characteristic of metastable and exotic species, epitomized in the fleetingly stable He2(+) ion. In this Account, I describe the use of coordination chemistry to stabilize such fugacious three-electron bonded species at disparate ends of the periodic table. A recent emphasis in the chemistry of metal-metal bonds has been to prepare compounds with extremely short metal-metal distances and high metal-metal bond orders. But similar chemistry can be used to explore metal-metal bond orders less than one, including 2c/3e half-bonds. Bimetallic compounds in the Ni2(II,III) and Pd2(II,III) oxidation states were originally examined in the 1980s, but the evidence collected at that time suggested that they did not contain 2c/3e σ bonds. Both classes of compounds have been re-examined using EPR spectroscopy and modern computational methods that show the unpaired electron of each compound to occupy a M-M σ* orbital, consistent with 2c/3e Ni-Ni and Pd-Pd σ half-bonds. Elsewhere on the periodic table, a seemingly unrelated compound containing a trigonal bipyramidal Cu3S2 core caused a stir, leaving prominent theorists at odds with one another as to whether the compound contains a S-S bond. Due to my previous experience with 2c/3e metal-metal bonds, I suggested that the Cu3S2 compound could contain a 2c/3e S-S σ half-bond in the previously unknown oxidation state of S2(3-). By use of the Cambridge Database, a number of other known compounds were identified as potentially containing S2(3-) ligands, including a noteworthy set of cyclopentadienyl-supported compounds possessing diamond-shaped Ni2E2 units with E = S, Se, and Te. These compounds were subjected to extensive studies using X-ray absorption spectroscopy, X-ray photoelectron spectroscopy, density functional theory, and wave function-based computational methods, as well as chemical oxidation and reduction. The compounds contain E-E 2c/3e σ half-bonds and unprecedented E2(3-) "subchalcogenide" ligands, ushering in a new oxidation state paradigm for transition metal-chalcogen chemistry.

Odd-electron-bonded sulfur radical cations: X-ray structural evidence of a sulfur-sulfur three-electron σ-bond

The one-electron oxidations of 1,8-chalcogen naphthalenes Nap(SPh)2 (1) and Nap(SPh)(SePh) (2) lead to the formation of persistent radical cations 1(•+) and 2(•+) in solution. EPR spectra, UV-vis absorptions, and DFT calculations show a three-electron σ-bond in both cations. The former cation remains stable in the solid state, while the latter dimerizes upon crystallization and returns to being radical cations upon dissolution. This work provides conclusive structural evidence of a sulfur-sulfur three-electron σ-bond (in 1(•+)) and a rare example of a persistent heteroatomic three-electron σ-bond (in 2(•+)).

Isolation and reversible dimerization of a selenium-selenium three-electron σ-bond

Three-electron σ-bonding that was proposed by Linus Pauling in 1931 has been recognized as important in intermediates encountered in many areas. A number of three-electron bonding systems have been spectroscopically investigated in the gas phase, solution and solid matrix. However, X-ray diffraction studies have only been possible on simple noble gas dimer Xe∴Xe and cyclic framework-constrained N∴N radical cations. Here, we show that a diselena species modified with a naphthalene scaffold can undergo one-electron oxidation using a large and weakly coordinating anion, to afford a room-temperature-stable radical cation containing a Se∴Se three-electron σ-bond. When a small anion is used, a reversible dimerization with phase and marked colour changes is observed: radical cation in solution (blue) but diamagnetic dimer in the solid state (brown). These findings suggest that more examples of three-electron σ-bonds may be stabilized and isolated by using naphthalene scaffolds together with large and weakly coordinating anions.

Do single-electron lithium bonds exist? Prediction and characterization of the H3C⋯Li–Y (Y=H, F, OH, CN, NC, and CCH) complexes

A new kind of single-electron lithium bonding complexes H(3)C...LiY (Y=H, F, OH, CN, NC, and CCH) was predicted and characterized in the present paper. Their geometries (C(3v)) with all real harmonic vibrational frequencies were obtained at the MP2/aug-cc-pVTZ level. For each H(3)C...LiY complex, single-electron Li bond is formed between the unpaired electron of CH(3) radical and positively charged Li atom of LiY molecule. Due to the formation of the single-electron Li bond, the C-H bonds of the CH(3) radical bend opposite to the LiY molecule and the Li-Y bond elongates. Abnormally, the three H(3)C...LiY (Y=CN, NC, and CCH) complexes exhibit blueshifted Li-Y stretching frequencies along with the elongated Li-Y bonds. Natural bond orbital analyses suggest ca. 0.02 electron transfer from the methyl radical (CH(3)) to the LiY moiety. In the single occupied molecular orbitals of the H(3)C...LiY complexes, it is also seen that the electron could of the CH(3) radical approaches the Li atom. The single-electron Li bond energies are 5.20-6.94 kcal/mol for the H(3)C...LiY complexes at the CCSD(T)aug-cc-pVDZ+BF (bond functions) level with counterpoise procedure. By comparisons with some related systems, it is concluded that the single-electron Li bonds are stronger than single-electron H bonds, and weaker than conventional Li bonds and pi-Li bonds.

Photoreactions in the gas-phase complexes of Mg(*+)-dioxanes

Photoreactions in the gas-phase complexes Mg(*+)(1,4-dioxane) (1) and Mg(*+)(1,3-dioxane) (1M) have been examined in the wavelength region of 230-440 nm. Photoproduct assignments are facilitated with the help of deuterium substitution experiments. The main energy relaxation channel for both photoexcited complexes is the evaporation of Mg(*+). Also observed from 1 are rich photoproducts with m/z 28, 41, 54-58, 67, 69, and 88; the most abundant one at m/z 54 is designated to Mg(*+)(O=CH(2)). In marked contrast, the photolysis of 1M yields only Mg(*+)(O=CH(2)) other than Mg(*+). Density functional calculations are performed to obtain optimized geometries and potential energy surfaces of 1 and 1M. Although Mg(*+)(chair-1,4-C(4)H(8)O(2)) (1a) and Mg(*+)(boat-1,4-C(4)H(8)O(2)) (1b) are comparable in energy, the much better agreement of the experimental action spectrum of Mg(*+)(1,4-C(4)H(8)O(2)) with the calculated absorption spectrum of 1a than with that of 1b indicates the predominance of 1a in the source due to the stability of the chair-1,4-dioxane. For photoreactions, the C-O bond is found to be much more prone to rupture than the C-C bond due to the coordination of O to Mg(+) in the parent complexes. Photoreaction mechanisms are discussed in terms of two key insertion complexes, which rationalize all of the observed photoproducts.

Kinetics, Mechanism, and Thermochemistry of the Gas Phase Reaction of Atomic Chlorine with Dimethyl Sulfoxide

A laser flash photolysis-resonance fluorescence technique has been employed to study the kinetics of the reaction of chlorine atoms with dimethyl sulfoxide (CH3S(O)CH3; DMSO) as a function of temperature (270-571 K) and pressure (5-500 Torr) in nitrogen bath gas. At T = 296 K and P > or = 5 Torr, measured rate coefficients increase with increasing pressure. Combining our data with literature values for low-pressure rate coefficients (0.5-3 Torr He) leads to a rate coefficient for the pressure independent H-transfer channel of k1a = 1.45 x 10(-11) cm3 molecule(-1) s(-1) and the following falloff parameters for the pressure-dependent addition channel in N2 bath gas: k(1b,0) = 2.53 x 10(-28) cm6 molecule(-2) s(-1); k(1b,infinity) = 1.17 x 10(-10) cm3 molecule(-1) s(-1), F(c) = 0.503. At the 95% confidence level, both k1a and k1b(P) have estimated accuracies of +/-30%. At T > 430 K, where adduct decomposition is fast enough that only the H-transfer pathway is important, measured rate coefficients are independent of pressure (30-100 Torr N2) and increase with increasing temperature. The following Arrhenius expression adequately describes the temperature dependence of the rate coefficients measured at over the range 438-571 K: k1a = (4.6 +/- 0.4) x 10(-11) exp[-(472 +/- 40)/T) cm3 molecule(-1) s(-1) (uncertainties are 2sigma, precision only). When our data at T > 430 K are combined with values for k1a at temperatures of 273-335 K that are obtained by correcting reported low-pressure rate coefficients from discharge flow studies to remove the contribution from the pressure-dependent channel, the following modified Arrhenius expression best describes the derived temperature dependence: k1a = 1.34 x 10(-15)T(1.40) exp(+383/T) cm3 molecule(-1) s(-1) (273 K < or = T < or = 571 K). At temperatures around 330 K, reversible addition is observed, thus allowing equilibrium constants for Cl-DMSO formation and dissociation to be determined. A third-law analysis of the equilibrium data using structural information obtained from electronic structure calculations leads to the following thermochemical parameters for the association reaction: delta(r)H(o)298 = -72.8 +/- 2.9 kJ mol(-1), deltaH(o)0 = -71.5 +/- 3.3 kJ mol(-1), and delta(r)S(o)298 = -110.6 +/- 4.0 J K(-1) mol(-1). In conjunction with standard enthalpies of formation of Cl and DMSO taken from the literature, the above values for delta(r)H(o) lead to the following values for the standard enthalpy of formation of Cl-DMSO: delta(f)H(o)298 = -102.7 +/- 4.9 kJ mol(-1) and delta(r)H(o)0 = -84.4 +/- 5.8 kJ mol(-1). Uncertainties in the above thermochemical parameters represent estimated accuracy at the 95% confidence level. In agreement with one published theoretical study, electronic structure calculations using density functional theory and G3B3 theory reproduce the experimental adduct bond strength quite well.

Experimental and Computational Studies of Intracomplex Reactions in Mg+(Primary, Secondary Alkylamine) Complexes Induced by Photoexcitation of Mg+

We report herein a comprehensive study of photoinduced reactions in complexes of Mg+ with primary (n-propyl- and isopropylamine) and secondary amines (dipropyl- and diisopropylamine) in the spectral range of 230-440 nm. Similar to the methyl- and ethylamine complexes studied previously, N-H bond activation of these complexes is very unfavorable. Instead, the C(alpha)-C, C-N, and C(alpha)-H bond-cleavage photoproducts are observed after photoexcitation of the Mg+ complexes (3(2)P<--3(2)S). For Mg+(primary amine) complexes, for example, Mg+-NH2CH2CH2CH3, and Mg+-NH2CH(CH3)2, the photoproducts resulting from C(alpha)--C rupture prevail after P(z) and charge-transfer excitations, whereas the Mg+ photofragment is predominant upon P(x,y) excitation. However, with further N-alkyl substitution, as in Mg+(secondary amine) complexes, for example, Mg+-NH(CH2CH2CH3)2 and Mg+-NH[CH(CH3)2]2, a novel intracomplex C-C coupling photoreaction dominates on P(x,y) excitation of Mg+, which is believed to arise from Mg+* insertion into the C-N bond. With P(z) and charge-transfer excitation, the Mg-R elimination photoproducts, arising from C(alpha)-C bond cleavage, predominate. The energetics and possible mechanisms of the intracomplex photoreactions are analyzed in detail with the help of extensive quantum mechanics calculations.

Stability, Metastability, and Unstability of Three-Electron-Bonded Radical Anions. A Model ab Initio Theoretical Study

The stability of O therefore O, N therefore N, S therefore S, P therefore P, and Si therefore Si three-electron bonds in anionic radicals isoelectronic to dihalogen radical anions is studied by means of ab initio calculations on model systems. The difficulty of generating the dissociation energy profiles of such anions and their rearrangement to neutral species is solved by a practical method which consists of calculating the neutral and anionic energy profiles separately and shifting the curves with respect to each other to match the experimental energy gap between the asymptotes. Here the neutral and anionic reaction profiles are calculated at the CASPT2 and MP2 levels, respectively. The calculations predict that the O therefore O bond is likely to be observed in anions of the type [RO therefore OR](*-), where R is any alkyl substituent or carbon chain. The anion Si(2)H(6)(*-) is found to be a metastable species, with a fair barrier to electron detachment. The barrier is much smaller for N(2)H(4)(*-) and P(2)H(4)(*-), thus precluding experimental observation. However, these species can be stabilized by electron-attractor substituents, the effect of which can be quantitatively estimated by means of the parent anion's diagrams and some fast complementary calculations. An example is given with the [CF(3)HN therefore NHCF(3)](*-) anionic complex.