Beyond the Halogen Bond: Examining the Limits of Extended Polybromide Networks through Quantum‐Chemical Investigations

The bonding environments of some polybromide monoanions and networks were examined by quantum‐chemical methods to investigate electronic interactions between dibromine–dibromine contacts. Examination of thermodynamic parameters and a bond critical point analysis give strong evidence for such bonding modes, which have been previously treated disparately in the literature. The thermodynamic stability of large polybromides up to [Br₃₇]^? was also predicted by these methods.     

Path Length Determines the Tunneling Decay of Substituted Carbenes

Quantum mechanical tunneling of atoms allows chemical reactions to proceed through barriers too high for thermally activated processes. This causes hydroxycarbenes to decay rapidly and at a temperature‐independent rate even at 11 K. In methylhydroxycarbene, tunneling causes decay through a mechanism that reveals a high but thin barrier rather than an alternative with a lower but broader barrier. No accurate estimates of the widths of such barriers and the lengths of tunneling paths were available. Herein, such a measure is provided by calculating the length of the tunneling paths by using instanton theory. Potential energies are provided by density functional theory verified by explicitly correlated coupled cluster CCSD(T) energies. Our results explain the decay efficiency in the known cases and suggest new substitutions to tune the effects of barrier widths and heights. Fluorination and replacement of the hydroxyl group by a thiol group change the qualitative character of the decay. Methylaminocarbene is predicted to be stable for thousands of years.     

High‐resolution mass spectrometry and hydrogen/deuterium exchange study of mitorubrin azaphilones and nitrogenized analogues

Azaphilones represent numerous groups of wild fungal secondary metabolites that exhibit exceptional tendency to bind to nitrogen atoms in various molecules, especially those containing the amine group. Nitrogenized analogues of mitorubrin azaphilones, natural secondary metabolites of Hypoxylon fragiforme fungus, have been detected in the fungal methanol extract in very low concentrations. Positive electrospray ionization interfaced with high‐resolution mass spectrometry was applied for confirmation of the elemental composition of protonated species. Collision‐induced dissociation (CID) experiments have been performed, and fragmentation mechanisms have been proposed. Additional information regarding both secondary metabolite analogue families has been reached by application of gas‐phase proton/deuterium (H/D) exchanges performed in the collision cell of a triple quadrupole mass spectrometer. An incomplete H/D exchange with one proton less than expected was observed for both protonated mitorubrin azaphilones and their nitrogenized analogues. By means of the density functional theory, an appropriate explanation of this behavior was provided, and it revealed some information concerning gas‐phase H/D exchange mechanism and protonation sites. Copyright © 2012 John Wiley & Sons, Ltd.     

Manganese,Iron, Cobalt,and Nickel Oxo‐, Peroxo‐, and Superoxoclusters: A Density Functional Theory Study

The 3d‐transition‐metal dioxo‐, peroxo‐, and superoxoclusters with the general composition MO₂, M(O₂), and MOO (M=Mn, Fe, Co, and Ni) were studied by DFT by the B1LYP functional. The dioxides in their ground states represent the global minima for the M+O₂ system. Both ground‐state dioxides and the lowest‐energy peroxides are in their (d‐only) highest spin states. The ⁶A₁ state of Co(O₂) exceeds the d‐only spin‐multiplicity value (quartet), being nearly isoenergetic with the ⁴A₁ state of Co(O₂). The energy gain on transforming the peroxides to the corresponding dioxides decreases in the order Mn(O₂)>Fe(O₂)>Co(O₂)>Ni(O₂) and varies in the range 0.27–1.8 eV. The dissociation energy to M+O₂ for all studied peroxides is less than 1 eV being the lowest (0.47 eV) for Mn(O₂). The Mn and Fe peroxides need less than 0.3 eV to rupture one of the MO bonds to form the corresponding superoxide. Mn and Fe superoxides are less stable than the corresponding peroxides; the superoxide of Co is more stable than its peroxide, while Ni superoxide is unstable—its energy is above the limit of dissociation to Ni+O₂. According to the electrostatic potential maps, the oxygen atoms in the peroxides are more nucleophilic than those in the dioxides and superoxides, in which the terminal oxygen atom is more nucleophilic than the M‐bonded oxygen atom. This result differs from the expectations based on charge‐distribution analysis.     

The Generalized Energy‐Based Fragmentation Approach with an Improved Fragmentation Scheme: Benchmark Results and Illustrative Applications

We propose an improved fragmentation scheme for the generalized energy‐based fragmentation (GEBF) approach, which improves the accuracy of the GEBF approach in total energy calculations and intermolecular interactions. The main modification is to introduce some two‐fragment‐centered primitive subsystems, which are neglected in the previous GEBF implementation. Numerical calculations demonstrate that the present GEBF approach can provide more accurate ground‐state energies and intermolecular interactions. The present GEBF approach with the M06‐2X functional and the cc‐pVTZ basis set are employed to investigate the structures and binding energies in two dimeric species, which are related to pseudopolymorphism of a phenyleneethynylene‐based π‐conjugated molecule. A comparison of the binding free energies in a dimeric species and its corresponding model without C? H???F contacts reveal that the substitution of fluorine atoms weakens the binding of monomers in the dimeric species formed by intermolecular O? H???O hydrogen bonds, but strengthens the binding in the dimer formed by the π–π stacking interaction. Therefore, the C? H???F contacts in these two dimeric species are demonstrated to play a less significant role.     

Quantum chemical calculations of N@Cn endofullerenes (n ≤ 60)

The geometric parameters and energy characteristics of small endofullerenes N@C_n (n = 20, 24, 30, 32, 40, 50) and N@C₆₀ in the quartet ground state were calculated by the B3LYP/6-31G* method. The N atom is located at the center of the carbon cage in all molecules except N@C₃₀, where it is bound to the cage wall. Encapsulation of nitrogen atom has little effect on the fullerene cage geometry for n = 40, 50, and 60. No significant charge transfer from the N endo-atom to the cage was revealed for all the N@C_n endofullerenes studied. The calculated spin density on the nitrogen endo-atom increases as the size (n) of the carbon cage increases. The relative stabilities of C_n fullerenes and corresponding endofullerenes N@C_n are discussed. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 1, pp. 15–20, January, 2006.     

Synthesis and photochemical properties of azidohemicyanine

Photochemical activity of azidohemicyanine (1-methyl-4-(4-azidostyryl)quinolinium iodide) was predicted by quantum chemical calculations and confirmed experimentally. The azidohemicyanine, which was synthesized, is characterized by a long-wavelength absorption band (LWAB) in the spectral region 350–500 nm with a maximum at 417 nm; it decomposes with a quantum yield of 0.84±0.17 upon irradiation within the LWAB, the quantum yield being independent of the presence of oxygen. The reaction products identified by ESI mass spectrometry include the corresponding primary amine as well as azo, hydrazo, nitroso, and nitro compounds, some of them are unidentified. The azidohemicyanine possesses the longest-wavelength visible light sensitivity among aromatic azides known so far. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 7, pp. 1402–1408, July, 2008.     

Mechanism of Redox‐Active Ligand‐Assisted Nitrene‐Group Transfer in a ZrIV Complex: Direct Ligand‐to‐Ligand Charge Transfer Preferred

The mechanism of the nitrene‐group transfer reaction from an organic azide to isonitrile catalyzed by a Zr^IV d⁰ complex carrying a redox‐active ligand was studied by using quantum chemical molecular‐modeling methods. The key step of the reaction involves the two‐electron reduction of the azide moiety to release dinitrogen and provide the nitrene fragment, which is subsequently transferred to the isonitrile substrate. The reducing equivalents are supplied by the redox‐active bis(2‐iso‐propylamido‐4‐methoxyphenyl)‐amide ligand. The main focus of this work is on the mechanism of this redox reaction, in particular, two plausible mechanistic scenarios are considered: 1) the metal center may actively participate in the electron‐transfer process by first recruiting the electrons from the redox‐active ligand and becoming formally reduced in the process, followed by a classical metal‐based reduction of the azide reactant. 2) Alternatively, a non‐classical, direct ligand‐to‐ligand charge‐transfer process can be envisioned, in which no appreciable amount of electron density is accumulated at the metal center during the course of the reaction. Our calculations indicate that the non‐classical ligand‐to‐ligand charge‐transfer mechanism is much more favorable energetically. Utilizing a series of carefully constructed putative intermediates, both mechanistic scenarios were compared and contrasted to rationalize the preference for ligand‐to‐ligand charge‐transfer mechanism.     

BrSSCl和SSBrCl相对稳定性的理论研究

采用量子化学中的密度泛函理论，在B3LYP／6-311 G(3df)水平上全优化得到了S2BrCl分子线型和分叉型2种异构体的平衡结构，同时对可能发生的分子内原子迁移过程的过渡态进行了考察。计算结果表明，从能量角度看，线型的BrSSCl为稳定构型。采用统计热力学及过渡态理论，研究了Z种平衡结构之间相互转化的热力学和动力学性质。根据计算结果，无论是Cl迁移还是Br迁移，分子内的原子迁移都需要较高的活化能，并且迁移速度较慢。     

Tunneling Assists the 1,2‐Hydrogen Shift in N‐Heterocyclic Carbenes

At room temperature, 1,2‐hydrogen‐transfer reactions of N‐heterocyclic carbenes, like the imidazol‐2‐ylidene to give imidazole is shown to occurr almost entirely (>90 %) by quantum mechanical tunneling (QMT). At 60 K in an Ar matrix, for the 2, 3‐dihydrothiazol‐2‐ylidene→thiazole transformation, QMT is shown to increase the rate about 10⁵ times. Calculations including small‐curvature tunneling show that the barrier for intermolecular 1,2‐hydrogen‐transfer reaction is small, and QMT leads to a reduced rate of the forward reaction because of nonclassical reflections even at room temperature. A small barrier also leads to smaller kinetic isotope effects because of efficient QMT by both H and D. QMT does not always lead to faster reactions or larger KIE values, particularly when the barrier is small.     

How Does CuII Convert into CuI? An Unexpected Ring‐Mediated Single‐Electron Reduction

Cu(x)O (x=1,2) nanomaterials with tailored composition and properties-a hot topic in sustainable technologies-may be fabricated from molecular sources through bottom-up processes that involve unexpected changes in the metal oxidation state and open intriguing challenges on the copper redox chemistry. How copper(II) sources may lead to copper(I) species in spite of the absence of any explicit reducing agent, and even in the presence of oxygen, is one such question-to date unanswered. Herein, we study copper "reduction without reductants" within one molecule and reveal that the actual reducing agent is abstracted atomic hydrogen. By investigating the fragmentation of a copper(II) precursor for copper oxide nanostructures by combined ESI-MS with multiple collisional experiments (ESI/MS(n)) and theoretical calculations, we highlight a copper-promoted C-H bond activation, leading to reduction of the metal center and formation of a Cu(I)-C-NCCN six-membered ring. Such a novel ring system is the structural motif for a new family of cyclic copper(I) adducts, which show a bonding scheme, herein reported for the first time, that may shed unprecedented light on copper chemistry. Beyond the relevance for the preparation of copper oxide nanostructures, the hydrogen-abstraction/proton-delivery/electron-gain mechanism of copper(II) reduction disclosed herein appears to be a general property of copper and might help to understand its redox reactivity.     

Atomic properties of selected biomolecules: quantum topological atom types of hydrogen,oxygen, nitrogen and sulfur occurring in natural amino acids and their derivatives

Molecular electron densities are generated at B3LYP/6-311+G(2d,p)//HF/6-31G(d) level for 57 molecules, including one conformation of each naturally occurring amino acid and smaller derived molecules. The electron densities are partitioned into atomic fragments according to the approach of quantum chemical topology (QCT). A set of 547 unique topological atoms is obtained, containing 421 hydrogens, 63 oxygens, 57 nitrogens and 6 sulfurs. Each atom is described by seven properties: volume, kinetic energy, monopole, dipole, quadrupole, octupole and hexadecapole moment. Cluster analysis groups atoms into atom types based on their similarity expressed in the discrete 7D space of atomic properties. Using a separation criterion we distinguish seven hydrogen, six oxygen, two nitrogen and six sulfur atom types.     

Controlling Molecular Conductance: Switching Off π Sites through Protonation

Conductance switching through chemical modification of a molecular bridge is a major goal in molecular electronics, with the potential to lead to molecule‐based functional devices. In terms of switching speed, mechanisms that rely on only minor rearrangements of molecular structures are particularly promising. We demonstrate, based on density functional theory calculations combined with a coherent tunneling approach, how protonation and deprotonation of amine‐substituted or amine‐bridged model molecular wires can switch off and on π‐sites and thus: a) remove or introduce interference features in the electron transmission, and b) decrease or increase coupling along a chain. This mechanism may also be relevant for interactions between molecular bridges and metal cations, for example, in sensor applications.     

The E2 state of FeMoco: Hydride Formation versus Fe Reduction and a Mechanism for H2 Evolution

The iron-molybdenum cofactor (FeMoco) is responsible for dinitrogen reduction in Mo nitrogenase. Unlike the resting state, E₀, reduced states of FeMoco are much less well characterized. The E₂ state has been proposed to contain a hydride but direct spectroscopic evidence is still lacking. The E₂ state can, however, relax back the E₀ state via a H₂ side-reaction, implying a hydride intermediate prior to H₂ formation. This E₂→E₀ pathway is one of the primary mechanisms for H₂ formation under low-electron flux conditions. In this study we present an exploration of the energy surface of the E₂ state. Utilizing both cluster-continuum and QM/MM calculations, we explore various classes of E₂ models: including terminal hydrides, bridging hydrides with a closed or open sulfide-bridge, as well as models without. Importantly, we find the hemilability of a protonated belt-sulfide to strongly influence the stability of hydrides. Surprisingly, non-hydride models are found to be almost equally favorable as hydride models. While the cluster-continuum calculations suggest multiple possibilities, QM/MM suggests only two models as contenders for the E₂ state. These models feature either i) a bridging hydride between Fe₂ and Fe₆ and an open sulfide-bridge with terminal SH on Fe₆ ( E₂-hyd ) or ii) a double belt-sulfide protonated, reduced cofactor without a hydride ( E₂-nonhyd ). We suggest both models as contenders for the E₂ redox state and further calculate a mechanism for H₂ evolution. The changes in electronic structure of FeMoco during the proposed redox-state cycle, E₀→E₁→E₂→E₀, are discussed.