Transition metals as electron traps. I. Structures,energetics, electron capture,and electron‐transfer‐induced dissociations of ternary copper–peptide complexes in the gas phase

Electron‐induced dissociations of gas‐phase ternary copper‐2,2′‐bipyridine complexes of Gly‐Gly‐Gly and Gly‐Gly‐Leu were studied on a time scale ranging from 130 ns to several milliseconds using a combination of charge‐reversal (⁺CR^?) and electron‐capture‐induced dissociation (ECID) measured on a beam instrument and electron capture dissociation (ECD) measured in a Penning trap. Charge‐reduced intermediates were observed on the short time scale in the ⁺CR^? and ECID experiments but not in ECD. Ion dissociations following electron transfer or capture mostly occurred by competitive bpy or peptide ligand loss, whereas peptide backbone fragmentations were suppressed in the presence of the ligated metal ion. Extensive electron structure theory calculations using density functional theory and large basis sets provided optimized structures and energies for the precursor ions, charge‐reduced intermediates, and dissociation products. The Cu complexes underwent substantial structure changes upon electron capture. Cu was calculated to be pentacoordinated in the most stable singly charged complexes of the [Cu(peptide ? H)bpy]^{+ ?} type where it carried a ～+ 1 atomic charge. Cu coordination in charge‐reduced [Cu(peptide ? H)bpy] intermediates depended on the spin state. The themodynamically more stable singlet states had tricoordinated Cu, whereas triplet states had a tetracoordinated Cu. Cu was tricoordinated in stable [Cu(peptide ? H)bpy]^{? ?} products of electron transfer. [Cu(peptide)bpy]^{2 + ?} complexes contained the peptide ligand in a zwitterionic form while Cu was tetracoordinated. Upon electron capture, Cu was tri‐ or tetracoordinated in the [Cu(peptide)bpy]⁺ charge‐reduced analogs and the peptide ligands underwent prototropic isomerization to canonical forms. The role of excited singlet and triplet electronic states is assessed. Copyright © 2009 John Wiley & Sons, Ltd.     

Contra-thermodynamic behavior in intermolecular hydrogen transfer of alkylperoxy radicals.

Quantum chemical investigation of bimolecular hydrogen transfer involving alkylperoxy radicals, a key reaction family in the free-radical oxidation of hydrocarbons, was performed to establish structure-reactivity relationships. Eight different reactions were investigated featuring four different alkane substrates (methane, ethane, propane and isobutane) and two different alkylperoxy radicals (methylperoxy and iso-propylperoxy). Including forward and reverse pairs, sixteen different activation energies and enthalpies of reaction were used to formulate structure-reactivity relationships to describe this chemistry. We observed that the enthalpy of formation of loosely bound intermediate states has a strong inverse correlation with the overall heat of reaction and that this results in unique contra-thermodynamic behavior such that more exothermic reactions have higher activation barriers. A new structure-reactivity relationship was proposed that fits the calculated data extremely well: E(A)=E(o)+alphaDeltaH(rxn) where alpha=-0.10 for DeltaH(rxn)<0, and alpha=1.10 for DeltaH(rxn)>0 and E(o)=3.05 kcal mol(-1).     

Mechanism for the Nonadiabatic Photooxidation of Benzene to Phenol: Orientation‐Dependent Proton‐Coupled Electron Transfer

An efficient catalytic one‐step conversion of benzene to phenol was achieved recently by selective photooxidation under mild conditions with 2,3‐dichloro‐5,6‐dicyano‐p‐benzoquinone (DDQ) as the photocatalyst. Herein, high‐level electronic structure calculations in the gas phase and in acetonitrile solution are reported to explore the underlying mechanism. The initially populated ¹ππ* state of DDQ can relax efficiently through a nearby dark ¹nπ* doorway state to the ³ππ* state of DDQ, which is found to be the precursor state involved in the initial intermolecular electron transfer from benzene to DDQ. The subsequent triplet‐state reaction between DDQ radical anions, benzene radical cations, and water is computed to be facile. The formed DDQH and benzene‐OH radicals can undergo T₁→S₀ intersystem crossing and concomitant proton‐coupled electron transfer (PCET) to generate the products DDQH₂ and phenol. Two of the four considered nonadiabatic pathways involve an orientation‐dependent triplet PCET process, followed by intersystem crossing to the ground state (S₀). The other two first undergo a nonadiabatic T₁→S₀ transition to produce a zwitterionic S₀ complex, followed by a barrierless proton transfer. The present theoretical study identifies novel types of nonadiabatic PCET processes and provides detailed mechanistic insight into DDQ‐catalyzed photooxidation.     

The Stability of α‐Hydroperoxyalkyl Radicals

High‐level ab initio and Born–Oppenheimer molecular dynamic calculations have been carried out on a series of hydroperoxyalkyl (α‐QOOH) radicals with the aim of investigating the stability and unimolecular decomposition mechanism into QO+OH of these species. Dissociation was shown to take place through rotation of the C?O(OH) bond rather than through elongation of the CO?OH bond. Through the C?O(OH) rotation, the unpaired electron of the radical overlaps with the electron density on the O?OH bond, and from this overlap the C=O π bond forms and the O?OH bond breaks spontaneously. The CH₂OOH, CH(CH₃)OOH, CH(OH)OOH, and α‐hydroperoxycycloheptadienyl radical were found to decompose spontaneously, but the CH(CHO)OOH has a decomposition energy barrier of 5.95 kcal mol^?1 owing to its steric and electronic features. The systems studied in this work provide the first insights into how structural and electronic effects govern the stabilizing influence on elusive α‐QOOH radicals.     

A C‐linked Glycomimetic in the Gas Phase and in Solution: Synthesis and Conformation of the Disaccharide Manα(1,6)‐C‐ManαOPh

The effect of carbon is subtle but sweet : The flexible C‐linkage in the newly synthesised C‐glycosyl mimetic, Manα(1,6)‐C‐ManαOPh allows OH? π bonding, both in the gas phase and in aqueous solution. This interaction is absent in the O‐linked disaccharide (see figure).

     

Combining UV photodissociation action spectroscopy with electron transfer dissociation for structure analysis of gas‐phase peptide cation‐radicals

We report the first example of using ultraviolet (UV) photodissociation action spectroscopy for the investigation of gas‐phase peptide cation‐radicals produced by electron transfer dissociation. z ‐Type fragment ions ^●Gly‐Gly‐Lys⁺, coordinated to 18‐crown‐6‐ether (CE), are generated, selected by mass and photodissociated in the 200–400 nm region. The UVPD action spectra indicate the presence of valence‐bond isomers differing in the position of the C_α radical defect, (α‐Gly)‐Gly‐Lys⁺(CE), Gly‐(α‐Gly)‐Lys⁺(CE) and Gly‐Gly‐(α‐Lys⁺)(CE). The isomers are readily distinguishable by UV absorption spectra obtained by time‐dependent density functional theory (TD‐DFT) calculations. In contrast, conformational isomers of these radical types are calculated to have similar UV spectra. UV photodissociation action spectroscopy represents a new tool for the investigation of transient intermediates of ion‐electron reactions. Specifically, z ‐type cation radicals are shown to undergo spontaneous hydrogen atom migrations upon electron transfer dissociation. Copyright © 2015 John Wiley & Sons, Ltd.     

Ab Initio Study on the Mechanism of the Atmospheric Reaction OH+O3→HO2+O2

The atmospheric reaction (1) OH + O₃→HO₂ + O₂ was investigated theoretically by using MP2, QCISD, QCISD(T), and CCSD(T) methods with various basis sets. At the highest level of theory, namely, QCISD, the reaction is direct, with only one transition state between reactants and products. However, at the MP2 level, the reaction proceeds through a two‐step mechanism and shows two transition states, TS1 and TS2 , separated by an intermediate, Int . The different methodologies employed in this paper consistently predict the barrier height of reaction (1) to be within the range 2.16–5.11 kcal mol^?1, somewhat higher than the experimental value of 2.0 kcal mol^?1.     

Synthesis and Structure of α/δ‐Hybrid Peptides—Access to Novel Helix Patterns in Foldamers

Origami peptides : A novel class of foldamers consisting of α/δ‐hybrid peptides has been investigated theoretically and experimentally by exploiting the rigidity of the side chain of a new δ‐amino acid prepared from D ‐glucose and D ‐xylose with a furanose side chain (see figure).

     

An Ab Initio Study on the Mechanism of the Atmospheric Reaction NH2+O3→H2NO+O2

The atmospheric reaction NH₂+O₃→H₂NO+O₂ has been investigated theoretically by using MP2, QCISD, QCISD(T), CCSD(T), CASSCF, and CASPT2 methods with various basis sets. At the MP2 level of theory, the hypersurface of the potential energy (HPES) shows a two step reaction mechanism. Therefore, the mechanism proceeds along two transition states (TS1 and TS2), separated by an intermediate designated as Int. However, when the single‐reference higher correlated QCISD and the multiconfigurational CASSCF methodologies have been employed, the minimum structure Int and TS2 are not found on the HPES, which thus confirms a direct reaction mechanism. Single‐reference high correlated and multiconfigurational methods consistently predict the barrier height of the reaction to be within the range of 3.9 to 6.6 kcal mol^?1, which is somewhat higher than the experimental value. ¹ The calculated reaction enthalpy is ?67.7 kcal mol^?1.     

Formation of Octameric Methylaluminoxanes by Hydrolysis of Trimethylaluminum and the Mechanisms of Catalyst Activation in Single‐Site α‐Olefin Polymerization Catalysis

Hydrolysis of trimethylaluminum (TMA) leads to the formation of methylaluminoxanes (MAO) of general formula (MeAlO)_n(AlMe₃)_m. The thermodynamically favored pathway of MAO formation is followed up to n=8, showing the major impact of associated TMA on the structural characteristics of the MAOs. The MAOs bind up to five TMA molecules, thereby inducing transition from cages into rings and sheets. Zirconocene catalyst activation studies using model MAO co‐catalysts show the decisive role of the associated TMA in forming the catalytically active sites. Catalyst activation can take place either by Lewis‐acidic abstraction of an alkyl or halide ligand from the precatalyst or by reaction of the precatalyst with an MAO‐derived AlMe₂⁺ cation. Thermodynamics suggest that activation through AlMe₂⁺ transfer is the dominant mechanism because sites that are able to release AlMe₂⁺ are more abundant than Lewis‐acidic sites. The model catalyst system is demonstrated to polymerize ethene.     

Role of weak C—H…O and strong N—H…O intermolecular interactions on the high‐symmetry molecular packing of trans‐cyclohexane‐1,4‐dicarboxamide

An unpredicted fourfold screw N—H…O hydrogen bond C(4) motif in a primary dicarboxamide (trans‐cyclohexane‐1,4‐dicarboxamide, C₈H₁₄N₂O₂) was investigated by single‐crystal X‐ray diffraction and IR and Raman spectroscopies. Electron‐density topology and intermolecular energy analyses determined from ab initio calculations were employed to examine the influence of weak C—H…O hydrogen‐bond interactions on the peculiar arrangement of molecules in the tetragonal P4₃2₁2 space group. In addition, the way in which the co‐operative effects of those weak bonds might modify their relative influence on molecular packing was estimated from cluster calculations. Based on the results, a structural model is proposed which helps to rationalize the unusual fourfold screw molecular arrangement.     

Estimation of peptide N–Cα bond cleavage efficiency during MALDI‐ISD using a cyclic peptide

Matrix‐assisted laser desorption/ionization in‐source decay (MALDI‐ISD) induces N–C_α bond cleavage via hydrogen transfer from the matrix to the peptide backbone, which produces a c′/z? fragment pair. Subsequently, the z? generates z′ and [z + matrix] fragments via further radical reactions because of the low stability of the z?. In the present study, we investigated MALDI‐ISD of a cyclic peptide. The N–C_α bond cleavage in the cyclic peptide by MALDI‐ISD produced the hydrogen‐abundant peptide radical [M + 2H]⁺? with a radical site on the α‐carbon atom, which then reacted with the matrix to give [M + 3H]⁺ and [M + H + matrix]⁺. For 1,5‐diaminonaphthalene (1,5‐DAN) adducts with z fragments, post‐source decay of [M + H + 1,5‐DAN]⁺ generated from the cyclic peptide showed predominant loss of an amino acid with 1,5‐DAN. Additionally, MALDI‐ISD with Fourier transform‐ion cyclotron resonance mass spectrometry allowed for the detection of both [M + 3H]⁺ and [M + H]⁺ with two ¹³C atoms. These results strongly suggested that [M + 3H]⁺ and [M + H + 1,5‐DAN]⁺ were formed by N–C_α bond cleavage with further radical reactions. As a consequence, the cleavage efficiency of the N–C_α bond during MALDI‐ISD could be estimated by the ratio of the intensity of [M + H]⁺ and [M + 3H]⁺ in the Fourier transform‐ion cyclotron resonance spectrum. Because the reduction efficiency of a matrix for the cyclic peptide cyclo(Arg‐Gly‐Asp‐D‐Phe‐Val) was correlated to its tendency to cleave the N–C_α bond in linear peptides, the present method could allow the evaluation of the efficiency of N–C_α bond cleavage for MALDI matrix development. Copyright © 2016 John Wiley & Sons, Ltd.     

Studying the Origin of the Antiferromagnetic to Spin‐Canting Transition in the β‐p‐NCC6F4CNSSN. Molecular Magnet

The crystal structure of the spin‐canted antiferromagnet β‐p‐NCC₆F₄CNSSN^. at 12 K (reported in this work) was found to adopt the same orthorhombic space group as that previously determined at 160 K. The change in the magnetic properties of these two crystal structures has been rigorously studied by applying a first‐principles bottom‐up procedure above and below the magnetic transition temperature (36 K). Calculations of the magnetic exchange pathways on the 160 K structure reveal only one significant exchange coupling (J(d1)=?33.8 cm^?1), which generates a three‐dimensional diamond‐like magnetic topology within the crystal. The computed magnetic susceptibility, χ(T), which was determined by using this magnetic topology, quantitatively reproduces the experimental features observed above 36 K. Owing to the anisotropic contraction of the crystal lattice, both the geometry of the intermolecular contacts at 12 K and the microscopic J_AB radical–radical magnetic interactions change: the J(d1) radical–radical interaction becomes even more antiferromagnetic (?43.2 cm^?1) and two additional ferromagnetic interactions appear (+7.6 and +7.3 cm^?1). Consequently, the magnetic topologies of the 12 and 160 K structures differ: the 12 K magnetic topology exhibits two ferromagnetic sublattices that are antiferromagnetically coupled. The χ(T) curve, computed below 36 K at the limit of zero magnetic field by using the 12 K magnetic topology, reproduces the shape of the residual magnetic susceptibility (having subtracted the contribution to the magnetization arising from spin canting). The evolution of these two ferromagnetic J_AB contributions explains the change in the slope of the residual magnetic susceptibility in the low‐temperature region.     

Quantum‐Transport Characteristics of a p–n Junction on Single‐Layer TiS3

By using density functional theory and non‐equilibrium Green′s function‐based methods, we investigated the electronic and transport properties of a TiS₃ monolayer p–n junction. We constructed a lateral p–n junction on a TiS₃ monolayer using Li and F adatoms. An applied bias voltage caused significant variability in the electronic and transport properties of the TiS₃ p–n junction. In addition, the spin‐dependent current–voltage characteristics of the constructed TiS₃ p–n junction were analyzed. Important device characteristics were found, such as negative differential resistance and rectifying diode behaviors for spin‐polarized currents in the TiS₃ p–n junction. These prominent conduction properties of the TiS₃ p–n junction offer remarkable opportunities for the design of nanoelectronic devices based on a recently synthesized single‐layered material.     

Theoretical study of thermal rearrangements of α‐silylalcohols: Effects of substituents attached to the silicon atom on the reactions

To investigate the effects of substituents attached to the silicon atom on the thermal rearrangement reactions of α‐silyl alcohols, the thermal rearrangement reactions of dimethylsilyl methanol (CH₃)₂SiHCH₂OH and vinylsilyl methanol CH₂?CHSiH₂CH₂OH were studied by ab initio calculations at the G3 level. Geometries of various stationary points were fully optimized at the MP2(full)/6‐31G(d) and MP2(full)/6‐311G(d,p) levels, and harmonic vibrational frequencies were calculated at the same levels. The reaction paths were investigated and confirmed by intrinsic reaction coordinate (IRC) calculations at the MP2(full)/6‐31G(d) level. The results show that two dyotropic reactions could occur when (CH₃)₂SiHCH₂OH or CH₂?CHSiH₂CH₂OH is heated. One is Brook rearrangement reaction (reaction A), and the dimethylsilyl or vinylsilyl groups migrates from carbon atom to oxygen atom coupled with a simultaneous migration of a hydrogen atom from oxygen atom to carbon atom passing through a double three‐membered ring transition state, forming dimethylmethoxylsilane (CH₃)₂SiHOCH₃ or methoxylvinylsilane CH₂?CHSiH₂OCH₃; the other is a hydroxyl group migration (reaction B) from carbon atom to silicon atom, coupled with a simultaneous migration of a hydrogen atom from silicon atom to carbon atom, via a double three‐membered ring transition state, forming trimethylsilanol (CH₃)₃SiOH or methylvinylsilanol CH₃SiH(OH)CH?CH₂. The G3 barriers of the reactions A and B were computed to be 312.8 and 241.4 kJ/mol for (CH₃)₂SiHCH₂OH, and 317.6 and 233.7 kJ/mol for CH₂?CHSiH₂CH₂OH, respectively. On the basis of the MP2(full)/6‐31G(d) optimized parameters, vibrational frequencies, and G3 energies, the reaction rate constants k(T) and equilibrium constants K(T) were calculated using canonical variational transition state theory (CVT) with centrifugal‐dominant small‐curvature tunneling (SCT) approximation over a temperature range of 400–1800 K. The influences of methyl and vinyl groups attached to the silicon atom on reactions are discussed. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Theoretical Study on Electron Transfer Matrix Element in Oxidation of α—Amino Carbon—Centered Radical by O2

As a successive work of our previous paper,^1the electron transfer matrix element(Vrp)in the oxidation of the simplified model molecule of α-amino carbon-centered radical by O2 has been investigated with ab initio calculation at the level of UHF/6-31 G**.Based on the optimized geometries of the reactgant and the ion-pair complex obtained previously,the reaction heat and the iuner reorganization energy have been obtained by constructing the potential energy curves of reactant and product states considering the solvent effect with the conductor-like screening model(COSMO).The solvent reorganization energy has been estimated using Lippert-Mataga relationship.The calculated results show that the value of Vrp is several times larger than that of RT,which means that the model reaction is an adiabatic one.Theoretical investigation indicates that the solvent effect on the direct electron transfer (ET) process of oxidation of α-amino carbon-centered radical by oxygen is remarkable.     

Theoretical Study on Reactivity of Electron Transfer in Model—System of Oxidation of α—Amino Carbon—centered Radical by O2

Electron transfer reaction between a simplified model model molecule of α－amino carbon-centered radical and O2 has studied with ab initio calculations at the MP2/6-31 G^**//UHF/6-31 G^** level,The reactant complex and the ion pair complex have been optimized and employed to perform calculation of the reaction heat and the reorganization energy,Solvent effects have been considered by applyning the conductor-like screening model,Theoretical results show that the highly endothermic charge separation process ,in which one electron transfers from the α－amino carbon-centered radical to O2,so as to form an ion pair complex,is difficult to occur in gas-phase,By apply-ing an external electronic field to prepare the charge-locallized molecular orbitals,the charge-separated state has been obtained using the initial-guess-induced self-consistent field technique,The theoretical investigations indicate that the solvent effect in the process of the oxidation of α-animo carbon-centered radical by O2 is remarkable.From the rate constant estima-tion ,it can be predicted that the oxidation of the model donor molecule by O2 can proceed,but not very fast.A peroxyl radi-cal compound has been found to be a competitive intermediate in the oxidation process.