Search

Differential mobility spectrometry (DMS) uses high-frequency oscillating electrical fields to harness the differential mobility of ions for separating complex sample mixtures prior to detection. To increase the resolving power, a dynamic microsolvation environment is often created by introducing solvent vapors. Here, relatively large clusters are formed at low-field conditions which then evaporate to form smaller clusters at high-field conditions. The kinetics of these processes as the electrical field strength oscillates are not well studied. Here, we develop a computational framework to investigate how the different reactions (cluster association, cluster dissociation, and fast conformational changes) behave at different field strengths. We aim to better understand these processes, their effect on experimental outcomes, and whether DMS model accuracy is improved via incorporating their description. We find that cluster association and dissociation reactions for typical ion–solvent pairs are fast compared to the time scale of the varying separation fields usually used. However, low solvent concentration, small dipole moments, and strong ion–solvent binding can result in reaction rates small enough that a lag is observed in the ion's DMS response. This can yield differences of several volts in the compensation voltages required to correct ion trajectories for optimal transmission. We also find that the proposed kinetic approach yields generally better agreement with experiment than using a modified Boltzmann weighting scheme. Thus, this work provides insights into the chemical dynamics occurring within the DMS cell while also increasing the accuracy of dispersion plot predictions. [ABSTRACT FROM AUTHOR]

Unidirectional double-hydrogen (2H) and triple-hydrogen (3H) rearrangement reactions occur upon electron-ionization-induced fragmentation of trans-2-(4-N,N-dimethylaminobenzyl)-1-indanol (1), trans-2-(4-methoxybenzyl)-1-indanol (2), 4-(4-N,N-dimethylaminophenyl)-2-butanol (3), and related compounds, as reported some 35 years ago (Kuck, D.; Filges, U. Org. Mass Spectrom.1988, 23, 643–653). These unusual intramolecular redox processes were found to dominate the mass spectra of long-lived, metastable ions. The present report provides independent evidence for the structures of the product ions formed by the 2H and 3H rearrangement in an ion trap instrument. The radical cations 1•+ and 3•+ as well as ionized 1-(4-N,N-dimethylaminophenyl)-5-(4-methoxyphenyl)-3-pentanol, 5•+, were generated by electrospray ionization from anhydrous acetonitrile solutions. The 2H and 3H fragment ions were obtained by collision-induced dissociation and characterized by IR ion spectroscopy and density functional theory calculations. Comparison of the experimental and calculated infrared ion spectra enabled the identification of the 2H rearrangement product ion, C9H14N+ (m/z 136), as an N,N-dimethyl-para-toluidinium ion bearing the extra proton ortho to the amino group, a tautomer which was calculated to be 31 kJ/mol less stable than the corresponding N-protonated form. The 3H rearrangement product ion, C8H13N•+ (m/z 123), formerly assumed to be a distonic ammonium ion bearing a cyclohexadienyl radical, was now identified as a conventional radical cation, ionized N,N-dimethyl-2,3-dihydro-para-toluidine. Thus, the 3H rearrangement represents an intramolecular transfer hydrogenation between a secondary alcohol and an ionized aromatic ring. Based on these structural assignments, more detailed mechanisms for the unidirectional 2H and 3H rearrangement reactions are proposed. [ABSTRACT FROM AUTHOR]

Glycerophospholipids (GPs) are highly abundant in eukaryotic cells and take part in numerous fundamental physiological processes such as molecular signaling. The GP composition of samples is often analyzed using mass spectrometry (MS), but identification of some structural features, for example, differentiation of stereospecific numbering (sn) isomers by well-established tandem MS (MS2) methods, is challenging. In particular, the formation of 1,3-dioxolane over 1,3-dioxane intermediates proposed to be responsible for the sn-selectivity of these tandem MS strategies has not been validated by spectroscopic methods. In this work, we present infrared multiple photon dissociation (IRMPD) spectra of phosphatidylcholine (PC) ions [PC 4:0/4:0 + H/Na/K]+ and [PC 4:0/4:0 + Na/K - 183]+ fragments generated by electrospray ionization (ESI)-MS and collision-induced dissociation (CID), respectively. IRMPD spectra of protonated, sodiated, and potassiated PC 4:0/4:0 differ in the phosphate- and ester-related bands, which are increasingly shifted to lower wavenumbers with higher adduct masses. Comparison of calculated and experimental IR spectra indicates the presence of multiple, two and one isomer(s) for [PC 4:0/4:0 + H]+, [PC 4:0/4:0 + Na]+, and [PC 4:0/4:0 + K]+, respectively. Isomers exhibiting pronounced sn-1 ester-ion interactions are computationally predicted to be energetically preferred for all species and are in line with experimental results. IRMPD spectra of [PC 4:0/4:0 + Na/K - 183]+ are presented and shed the first light on the fragment ion structures, rationalizing MS-based lipidomics strategies that aim to characterize the sn-isomerism of GPs. [ABSTRACT FROM AUTHOR]

We investigate the gas-phase structures and fragmentation pathways of model compounds of anthracene derivatives of the general formula CcHhN1 utilizing tandem mass spectrometry and computational methods. We vary the substituent alkyl chain length, composition, and degree of branching. We find substantial experimental and theoretical differences between the linear and branched congeners in terms of fragmentation thresholds, available pathways, and distribution of products. Our calculations predict that the linear substituents initially isomerize to form lower energy branched isomers prior to loss of the alkyl substituents as alkenes. The rate-determining chemistry underlying these related processes is dominated by the ability to stabilize the alkene loss transition structures. This task is more effectively undertaken by branched substituents. Consequently, analyte lability systematically increased with degree of branching (linear < secondary < tertiary). The resulting anthracen-9-ylmethaniminium ion generated from these alkene loss reactions undergoes rate-limiting proton transfer to enable expulsion of either hydrogen cyanide or CNH. The combination of the differences in primary fragmentation thresholds and degree of radical-based fragmentation processes provide a potential means of distinguishing compounds that contain branched alkyl chain substituents from those with linear ones. [ABSTRACT FROM AUTHOR]

Infrared multiple photon dissociation (IR-MPD) spectroscopy in conjunction with density functional theory (DFT) calculations has been employed to study the activation of molecular oxygen and ethylene co-adsorbed on a free gold dimer cation Au2+. Both studied complexes, Au2O2(C2H4)+ and Au2O2(C2H4)2+, show distinct features of both intact O2 and ethylene co-adsorbed on the cluster. However, the ethylene C=C double bond is activated, increasing in length by up to 0.07 Å compared with the free molecule, and the red shift of the O–O vibration frequency increases with the number of adsorbed ethylene molecules, indicating a small but increasing activation of the O–O bond. The small O2 activation and the rather weak interaction between O2 and C2H4 are also reflected in the calculated electronic structure of the co-adsorption complexes which shows only a small occupation of the empty anti-bonding O2 2π*2p orbital as well as the localization of most of the Kohn–Sham orbitals on O2 and C2H4, respectively, with only limited mixing between O2 and C2H4 orbitals. The results are compared with theoretical studies on neutral AuxO2(C2H4) (x = 3, 5, 7, 9) complexes. [ABSTRACT FROM AUTHOR]

Dinitrogen (N2) activation by metal hydride species is of fundamental interest and practical importance while the role of hydrogen in N2 activation is not well studied. Herein, the structures of Co3Dn− (n = 0–4) clusters and their reactions with N2 have been studied by using a combined experimental and computational approach. The mass spectrometry experiments identified that the Co3Dn− (n = 2–4) clusters could adsorb N2 while the Co3Dn− (n = 0 and 1) clusters were inert. The photoelectron imaging spectroscopy indicated that the electron detachment energies of Co3D2–4− are smaller than those of Co3D0,1−, which characterized that it is easier to transfer electrons from Co3D2–4− than from Co3D0,1− to activate N2. The density functional theory calculations generally supported the experimental observations. Further analysis revealed that the H atoms in the Co3Hn− (n = 2–4) clusters generally result in higher energies of the Co 3d orbitals in comparison with the Co3Hn− (n = 0 and 1) systems. By forming chemical bonds with H atoms, the Co atoms of Co3H2–4− are less negatively charged with respect to the naked Co3− system, which leads to higher N2 binding energies of Co3H2–4N2− than that of Co3N2−. [ABSTRACT FROM AUTHOR]

We have used trapped ion mobility spectrometry (TIMS) to obtain highly accurate experimental collision cross sections (CCS) for the fullerene C80− and the endohedral metallofullerenes La2@C80−, Sc3N@C80−, and Er3N@C80− in molecular nitrogen. The CCS values of the endohedral fullerenes are 0.2% larger than that of the empty cage. Using a combination of density functional theory and trajectory calculations, we were able to reproduce these experimental findings theoretically. Two effects are discussed that contribute to the CCS differences: (i) a small increase in fullerene cage size upon endohedral doping and (ii) charge transfer from the encapsulated moieties to the cage thus increasing the attractive charge-induced dipole interaction between the (endohedral) fullerene ion and the nitrogen bath gas molecules. [ABSTRACT FROM AUTHOR]

Nitrogen-centered and β-carbon–centered hydrogen-deficient peptide radicals are considered to be intermediates in the matrix-assisted laser desorption/ionization in-source decay (MALDI-ISD)–induced Cα–C bond cleavage of peptide backbones when using an oxidizing matrix. To understand the general mechanism of Cα–C bond cleavage by MALDI-ISD, I study the fragmentation of model peptides and investigate the fragment formation pathways using calculations with density functional theory and transition state theory. The calculations indicate that the nitrogen-centered radical immediately undergoes Cα–C bond cleavage, leading to the formation of an a•/x fragment pair. In contrast, the dissociation of the β-carbon–centered radical is kinetically feasible under MALDI-ISD conditions, leading to the formation of an a/x• fragment pair. To discriminate these processes, I focus on the yield of d fragments, which originate from a• radicals through radical-induced side-chain loss, not from a fragments. The Cα–C bond cleavage on the C-terminal side of the carbamidomethylated cysteine residue is found to produce d fragments instead of a fragments. According to the calculation of the rate constant, the corresponding fragmentation occurs within 1 ns. The intense signal arising from d fragments and the lack of or weak signal from a fragments strongly suggest that the Cα–C bond cleavage occurs through a nitrogen-centered radical intermediate. In addition to the side-chain loss, the resulting a• radical undergoes hydrogen atom abstraction by the matrix. The results for a deuterium-labeled peptide indicate that the matrix abstracts a hydrogen atom from either the amide nitrogen or the β-carbon. [ABSTRACT FROM AUTHOR]

Because of the high stability and inertness of the U=O bonds, activation and/or functionalization of UO22+ and UO2+ remain challenging tasks. We show here that collision-induced dissociation (CID) of the uranyl-propiolate cation, [UVIO2(O2C-C≡CH)]+, can be used to prepare [UVIO2(C≡CH)]+ in the gas phase by decarboxylation. Remarkably, CID of [UVIO2(C≡CH)]+ caused elimination of CO to create [OUVICH]+, thus providing a new example of a well-defined substitution of an "yl" oxo ligand of UVIO22+ in a unimolecular reaction. Relative energies for candidate structures based on density functional theory calculations suggest that the [OUVICH]+ ion is a uranium-methylidyne product, with a U≡C triple bond composed of one σ-bond with contributions from the U df and C sp hybrid orbitals, and two π-bonds with contributions from the U df and C p orbitals. Upon isolation, without imposed collisional activation, [OUVICH]+ appears to react spontaneously with O2 to produce [UVO2]+. [ABSTRACT FROM AUTHOR]

Collisional activation fragmentation of protonated phosphorothioates leads to skeletal rearrangement and formation of aryl sulfenylium cation (R-PhS+) via successive eliminations of CH3OH and CH3O-P=O. To better understand this unusual fragmentation reaction, isotope-labeling experiments and density functional theory (DFT) calculations were carried out to investigate two mechanistic pathways. In route 1, a direct intramolecular transfer of the R-phenyl group occurs from the oxygen atom to the sulfur atom on thiophosphoryl to form methoxyl S-(3-methyl-4-methylsulfanyl-phenyl) phosphonium thiolate (a4), which subsequently dissociates to form the m/z 169 cation. In route 2, the sulfur atom of the thiophosphoryl group undergoes two stepwise transfer (1,4-migration to the ortho-carbon atom of the phenyl ring followed by 1,2-migration to the ipso-carbon atom) to form an intermediate isomer, which undergoes the subsequent dissociation to form the m/z 169 cation. DFT calculations suggested that route 2 was more favorable than route 1 from the point view of kinetics.Graphical Abstract [ABSTRACT FROM AUTHOR]

We investigate the tandem mass spectrometry of regiospecifically labeled, deprotonated sucrose analytes. We utilize density functional theory calculations to model the pertinent gas-phase fragmentation chemistry of the prevalent glycosidic bond cleavages (B1-Y1 and C1-Z1 reactions) and compare these predictions to infrared spectroscopy experiments on the resulting B1 and C1 product anions. For the C1 anions, barriers to interconversion of the pyranose [α-glucose-H]−, C1 anions to entropically favorable ring-open aldehyde-terminated forms were modest (41 kJ mol−1) consistent with the observation of a band assigned to a carbonyl stretch at ~ 1680-1720 cm−1. For the B1 anions, our transition structure calculations predict the presence of both deprotonated 1,6-anhydroglucose and carbon 2-ketone ((4S,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)dihydro-2H-pyran-3(4H)-one) anion structures, with the latter predominating. This hypothesis is supported by our spectroscopic data which show diagnostic bands at 1600, 1674, and 1699 cm−1 (deprotonated carbon 2-ketone structures), and at ~ 1541 cm−1 (both types of structure) and RRKM rate calculations. The deprotonated carbon 2-ketone structures are also the lowest energy product B1 anions.ᅟ [ABSTRACT FROM AUTHOR]

The present work explores the structures of species formed by dehydrogenation of methane (CH4) and perdeuterated methane (CD4) by the 5d transition metal cation osmium (Os+). Using infrared multiple photon dissociation (IRMPD) action spectroscopy and density functional theory (DFT), the structures of the [Os,C,2H]+ and [Os,C,2D]+ products are explored. This study complements previous work on the related species formed by dehydrogenation of methane by four other 5d transition metal cations (M+ = Ta+, W+, Ir+, and Pt+). Osmium cations are formed in a laser ablation source, react with methane pulsed into a reaction channel downstream, and the resulting products spectroscopically characterized through photofragmentation using the Free-Electron Laser for IntraCavity Experiments (FELICE) in the 300-1800 cm−1 range. Photofragmentation was monitored by the loss of H2/D2. Comparison of the experimental spectra and DFT calculated spectra leads to identification of the ground state carbyne hydride, HOsCH+ (2A′) as the species formed, as previously postulated theoretically. Further, a full description of the systematic spectroscopic shifts observed for deuterium labeling of these complexes, some of the smallest systems to be studied using IRMPD action spectroscopy, is achieved. A full rotational contour analysis explains the observed linewidths as well as the observation of doublet structures in several bands, consistent with previous observations for HIrCH+ (2A′).ᅟ [ABSTRACT FROM AUTHOR]

We characterize the primary fragmentation reactions of three isomeric lithiated D-hexose sugars (glucose, galactose, and mannose) utilizing tandem mass spectrometry, regiospecific labeling, and theory. We provide evidence that these three isomers populate similar fragmentation pathways to produce the abundant cross-ring cleavage peaks (0,2A1 and 0,3A1). These pathways are highly consistent with the prior literature (Hofmeister et al. J. Am. Chem. Soc. 113, 5964-5970, 1991, Bythell et al. J. Am. Soc. Mass Spectrom. 28, 688-703, 2017, Rabus et al. Phys. Chem. Chem. Phys. 19, 25643-25652, 2017) and the present labeling data. However, the structure-specific energetics and rate-determining steps of these reactions differ as a function of precursor sugar and anomeric configuration. The lowest energy water loss pathways involve loss of the anomeric oxygen to furnish B1 ions. For glucose and galactose, the lithiated α-anomers generate ketone structures at C2 in a concerted reaction involving a 1,2-migration of the C2-H to the anomeric carbon (C1). In contrast, the β-anomers are predicted to form 1,3-anhydroglucose/galactose B1 ion structures. Initiation of the water loss reactions from each anomeric configuration requires distinct reactive conformers, resulting in different product ion structures. Inversion of the stereochemistry at C2 has marked consequences. Both lithiated mannose forms expel water to form 1,2-anhydromannose B1 ions with the newly formed epoxide group above the ring. Additionally, provided water loss is not instantaneous, the α-anomer can also isomerize to generate a ketone structure at C2 in a concerted reaction involving a 1,2-migration of the C2-H to C1. This product is indistinguishable to that from α-glucose. The energetics and interplay of these pathways are discussed.ᅟ [ABSTRACT FROM AUTHOR]

The stable model of a double (±)charge-assisted halogen bridge has been built on the basis of searches of the Crystal Structure Database. The model, investigated by DFT theory, consists of quinuclidine-like cation derivatives and a set of simple anions. These charged fragments form halogen-bonded complexes of which the energy of complexation in some cases reaches 100 kcal/mol. Even for such strong interactions, the QTAIM characteristics are similar to those of the more classic, relatively weak halogen bonds. An important effect of complexation is the charge transfer measured by means of QTAIM and NBO. It can also be supposed, on the basis of detailed structural and QTAIM analysis, that the delocalization of the charge in a quinuclidine moiety occurs through space and not necessarily along formal bonds. The analysis of only partially charged and fully neutral counterparts of a double (±)charge-assisted halogen bridge shows significantly weaker bonding, being less than 10 kcal/mol. [ABSTRACT FROM AUTHOR]

A detailed theoretical investigation of specific rotation is carried out in solution for nine flexible molecules of biological importance. Systematic search for the main conformers is followed by time-dependent density functional theory (TD-DFT) calculations of specific rotation employing a wide range of basis sets. Due to conformational flexibility of the compounds under study, the possibility of basis set size reduction without deterioration of the results is investigated. The increasing size (d-)aug-cc-pVXZ (X = D, T, Q) bases of Dunning et al., and the ORP basis set, recently developed to efficiently provide molecular specific rotation, are used for this purpose. The polarizable continuum model is employed at all steps of the investigation. Comparison of the present results with the available data obtained in a vacuum reveals considerable differences, the values in solution being much closer to the experimental specific rotation data available. The ORP basis set proves to be competitive with the d-aug-cc-pVDZ set of Dunning in specific rotation calculations carried out in solution. While having the same number of functions, the former yields, in general, results considerably closer to the reference triple-ζ values. We can thus recommend the ORP basis set to study the optical rotation in conformationally flexible molecules in solution. [ABSTRACT FROM AUTHOR]

Salicylideneanilines are characterized by a tautomer equilibrium, between an enol and a keto form of different colors, at the origin of their remarkable thermochromic, solvatochromic, and photochromic properties. The enol form is usually the most stable but appropriate choice of substituents and conditions (solvent, crystal, host compound) can displace the equilibrium toward the keto form so that there is a need for fast prediction of the keto:enol abundance ratio. Here we demonstrate the reliability of a combined theoretical-experimental method, based on comparing simulated and measured UV/visible absorption spectra, to determine this keto/enol ratio. The calculations of the excitation energies, oscillator strengths, and vibronic structures of both enol and keto forms are performed for all excited states absorbing in the relevant (visible and near-UV) wavelength range at the time-dependent density functional theory level by accounting for solvent effects using the polarizable continuum model. This approach is illustrated for two salicylideneaniline derivatives, which are present, in solution, under the form of keto-enol mixtures. The results are compared to those of chemometric analysis as well as ab initio predictions of the reaction free enthalpies. [ABSTRACT FROM AUTHOR]

Metal complexes have many proven applications in the caging and photochemical release of biologically active compounds. Photocaging groups derived from Ru(II) traditionally have been composed of ancillary ligands that are planar and bi- or tridentate, such as 2,2'-bipyridine (bpy), 2,2':6',2"-terpyridine (tpy), and 1,10-phenanthroline (phen). Complexes bearing ancillary ligands with denticities higher than three represent a new class of Ru(II)-based photocaging groups that are grossly underdeveloped. Because high-denticity ancillary ligands provide the ability to increase the structural rigidity and control the stereochemistry, our groups initiated a research program to explore the applications of such ligands in Ru(II)-based photocaging. Ru(TPA), bearing the tetradentate ancillary ligand tris(2-pyridylmethyl)amine (TPA), has been successfully utilized to effectively cage nitriles and aromatic heterocycles. Nitriles and aromatic heterocycles caged by the Ru(TPA) group show excellent stability in aqueous solutions in the dark, and the complexes can selectively release the caged molecules upon irradiation with light. Ru(TPA) is applicable as a photochemical agent to offer precise spatiotemporal control over biological activity without undesired toxicity. In addition, Ru(II) polypyridyl complexes with desired photochemical properties can be synthesized and identified by solid-phase synthesis, and the resulting complexes show properties to similar to those of complexes obtained by solution-phase synthesis. Density functional theory (DFT) calculations reveal that orbital mixing between the π* orbitals of the ancillary ligand and the Ru-N dσ* orbital is essential for ligand photodissociation in these complexes. Furthermore, the introduction of steric bulk enhances the photoliability of the caged molecules, validating that steric effects can largely influence the quantum efficiency of photoinduced ligand exchange in Ru(II) polypyridyl complexes. Recently, two new photocaging groups, Ru(cyTPA) and Ru(1-isocyTPQA), have been designed and synthesized for caging of nitriles and aromatic heterocycles, and these complexes exhibit unique photochemical properties distinct from those derived from Ru(TPA). Notably, the unusually greater quantum efficiency for the ligand exchange in [Ru(1-isocyTPQA)(MeCN)2](PF6)2, Φ400 = 0.033(3), uncovers a trans-type effect in the triplet metal-to-ligand charge transfer (3MLCT) state that enhances photoinduced ligand exchange in a new manner. DFT calculations and ultrafast transient spectroscopy reveal that the lowest-energy triplet state in [Ru(1-isocyTPQA)(MeCN)2](PF6)2 is a highly mixed 3MLCT/3ππ* excited state rather than a triplet metal-centered ligand-field (3LF) excited state; the latter is generally accepted for ligand photodissociation. In addition, Mulliken spin density calculations indicate that a majority of the spin density in [Ru(1-isocyTPQA)(MeCN)2](PF6)2 is localized on the isoquinoline arm, which is opposite to the cis MeCN, rather than on the ruthenium center. This significantly weakens the Ru-N6 (cis MeCN) bond, which then promotes the ligand photodissociation. This newly discovered effect gives a clearer perception of the interplay between the 3MLCT and 3LF excited states of Ru(II) polypyridyl complexes, which may be useful in the design and applications of ruthenium complexes in the areas of photoactivated drug delivery and photosensitizers. [ABSTRACT FROM AUTHOR]

The transformation of methane into methanol or higher alcohols at moderate temperature and pressure conditions is of great environmental interest and remains a challenge despite many efforts. Extended surfaces of metallic nickel are inactive for a direct CH4 → CH3OH conversion. This experimental and computational study provides clear evidence that low Ni loadings on a CeO2(111) support can perform a direct catalytic cycle for the generation of methanol at low temperature using oxygen and water as reactants, with a higher selectivity than ever reported for ceria-based catalysts. On the basis of ambient pressure X-ray photoemission spectroscopy and density functional theory calculations, we demonstrate that water plays a crucial role in blocking catalyst sites where methyl species could fully decompose, an essential factor for diminishing the production of CO and CO2, and in generating sites on which methoxy species and ultimately methanol can form. In addition to water-site blocking, one needs the effects of metal-support interactions to bind and activate methane and water. These findings should be considered when designing metal/oxide catalysts for converting methane to value-added chemicals and fuels. [ABSTRACT FROM AUTHOR]

C-N cross-coupling is an important class of reactions with far-reaching impacts across chemistry, materials science, biology, and medicine. Transition metal complexes can elegantly orchestrate diverse aminations but typically require demanding reaction conditions, precious metal catalysts, or oxygen-sensitive procedures. Here, we introduce a mild nickel-catalyzed C-N cross-coupling methodology that operates at room temperature using an inexpensive nickel source (NiBr2·3H2O), is oxygen tolerant, and proceeds through direct irradiation of the nickel-amine complex. This operationally robust process was employed for the synthesis of diverse C-N-coupled products (40 examples) by irradiating a solution containing an amine, an aryl halide, and a catalytic amount of NiBr2·3H2O with a commercially available 365 nm LED at room temperature without added photoredox catalyst and the amine substrate serving additional roles as the ligands and base. Density functional theory calculations and kinetic isotope effect experiments were performed to elucidate the observed C-N cross-coupling reactivity. [ABSTRACT FROM AUTHOR]

We report a new formal oxidation state for neptunium in a crystallographically characterizable molecular complex, namely Np2+ in [K(crypt)][NpIICp″3] [crypt = 2.2.2-cryptand, Cp″ = C5H3(SiMe3)2]. Density functional theory calculations indicate that the ground state electronic configuration of the Np2+ ion in the complex is 5f46d1. [ABSTRACT FROM AUTHOR]

This work addresses the need for chemical tools that can selectively form cross-links. Contemporary thiol-selective cross-linkers, for example, modify all accessible thiols, but only form cross-links between a subset. The resulting terminal "dead-end" modifications of lone thiols are toxic, confound cross-linking-based studies of macromolecular structure, and are an undesired, and currently unavoidable, byproduct in polymer synthesis. Using the thiol pair of Cu/Zn-superoxide dismutase (SOD1), we demonstrated that cyclic disulfides, including the drug/nutritional supplement lipoic acid, efficiently cross-linked thiol pairs but avoided dead-end modifications. Thiolatedirected nucleophilic attack upon the cyclic disulfide resulted in thiol-disulfide exchange and ring cleavage. The resulting disulfide-tethered terminal thiolate moiety either directed the reverse reaction, releasing the cyclic disulfide, or participated in oxidative disulfide (cross-link) formation. We hypothesized, and confirmed with density functional theory (DFT) calculations, that mono-S-oxo derivatives of cyclic disulfides formed a terminal sulfenic acid upon ring cleavage that obviated the previously rate-limiting step, thiol oxidation, and accelerated the new rate-determining step, ring cleavage. Our calculations suggest that the origin of accelerated ring cleavage is improved frontier molecular orbital overlap in the thiolate-disulfide interchange transition. Five- to seven-membered cyclic thiosulfinates were synthesized and efficiently cross-linked up to 104-fold faster than their cyclic disulfide precursors; functioned in the presence of biological concentrations of glutathione; and acted as cell-permeable, potent, tolerable, intracellular cross-linkers. This new class of thiol cross-linkers exhibited click-like attributes including, high yields driven by the enthalpies of disulfide and water formation, orthogonality with common functional groups, water-compatibility, and ring strain-dependence. [ABSTRACT FROM AUTHOR]

The hydrosilylation reaction is one of the largest-scale application of homogeneous catalysis and is widely used to enable the commercial manufacture of silicon products. However, considerable issues including disposable platinum consumption, undesired side reactions and unacceptable catalyst residues still remain. Here, we synthesize a heterogeneous partially charged single-atom platinum supported on anatase TiO2 (Pt1 δ+/TiO2) catalyst via an electrostatic-induction ion exchange and twodimensional confinement strategy, which can catalyze hydrosilylation reaction with almost complete conversion and produce exclusive adduct. Density functional theory calculations reveal that unexpected property of Pt1 δ+/TiO2 originates from atomic dispersion of active species and unique partially positive charge Ptδ+ electronic structure that conventional nanocatalysts do not possess. The fabrication of single-atom Pt1 δ+/TiO2 catalyst accomplishes a reasonable use of Pt through recycling and maximum atom-utilized efficiency, indicating the potential to achieve a green hydrosilylation industry. [ABSTRACT FROM AUTHOR]

We describe an unusual in-plane type of porphyrin core distortion, tetragonal elongation (TE), observed experimentally in diboron porphyrins. The vibrational spectra of several of these complexes exhibit shifts that we have assigned to this TE distortion by comparing experimental spectra with DFT computational findings. The influence of TE in porphyrin systems was isolated using DFT analysis of the well-known model compounds Ni(II)porphine and Zn(II)porphine, with the macrocycle ring constrained to eliminate the influence of out-of-plane (OOP) distortions. A significant down-shift in frequencies was observed for porphyrin normal vibrational modes, particularly the in-plane A1g/B1g modes that are dominated by contributions from stretching and bending of Cα-Cm coordinates. In contrast, TE had little effect on the v(Pyrhalfring) and δ(Pyrdef) modes, though the lowered symmetry of the system resulted in significant splitting of the B2u and B3u modes. The impact of the TE distortion upon the diboron porphyrin vibrational spectrum was probed experimentally using Raman spectroscopy of B2O2(BCl3)2(TTP), B2OF2(TTP), and B2OPhOH2(TTP) (TTP = 5,10,15,20-(tetra-p-tolyl)porphyrin). Comparing the experimentally obtained spectral signatures to the computational findings allowed us to assign the large shifts observed for the v2 and v3 modes to the TE distortion in diboron porphyrins. [ABSTRACT FROM AUTHOR]

Manipulating physical properties using the spin degree of freedom constitutes a major part of modern condensed matter physics and is a key aspect for spintronics devices. Using the newly discovered two-dimensional van der Waals ferromagnetic CrI3 as a prototype material, we theoretically demonstrated a giant magneto band-structure (GMB) effect whereby a change of magnetization direction significantly modifies the electronic band structure. Our density functional theory calculations and model analysis reveal that rotating the magnetic moment of CrI3 from out-of-plane to in-plane causes a direct-to-indirect bandgap transition, inducing a magnetic field controlled photoluminescence. Moreover, our results show a significant change of Fermi surface with different magnetization directions, giving rise to giant anisotropic magnetoresistance. Additionally, the spin reorientation is found to modify the topological states. Given that a variety of properties are determined by band structures, our predicted GMB effect in CrI3 opens a new paradigm for spintronics applications. [ABSTRACT FROM AUTHOR]

Bottom-up fabrication techniques enable atomically precise integration of dopant atoms into the structure of graphene nanoribbons (GNRs). Such dopants exhibit perfect alignment within GNRs and behave differently from bulk semiconductor dopants. The effect of dopant concentration on the electronic structure of GNRs, however, remains unclear despite its importance in future electronics applications. Here we use scanning tunneling microscopy and first-principles calculations to investigate the electronic structure of bottom-up synthesized N = 7 armchair GNRs featuring varying concentrations of boron dopants. First-principles calculations of freestanding GNRs predict that the inclusion of boron atoms into a GNR backbone should induce two sharp dopant states whose energy splitting varies with dopant concentration. Scanning tunneling spectroscopy experiments, however, reveal two broad dopant states with an energy splitting greater than expected. This anomalous behavior results from an unusual hybridization between the dopant states and the Au(111) surface, with the dopant-surface interaction strength dictated by the dopant orbital symmetry. [ABSTRACT FROM AUTHOR]

The 19F chemical shift is a sensitive NMR probe of structure and electronic environment in organic and biological molecules. In this report, we examine chemical shift parameters of 4F-, 5F-, 6F-, and 7F-substituted crystalline tryptophan by magic angle spinning (MAS) solid-state NMR spectroscopy and density functional theory. Significant narrowing of the 19F lines was observed under fast MAS conditions, at spinning frequencies above 50 kHz. The parameters characterizing the 19F chemical shift tensor are sensitive to the position of the fluorine in the aromatic ring and, to a lesser extent, the chirality of the molecule. Accurate calculations of 19F magnetic shielding tensors require the PBE0 functional with a 50% admixture of a Hartree-Fock exchange term, as well as taking account of the local crystal symmetry. The methodology developed will be beneficial for 19F-based MAS NMR structural analysis of proteins and protein assemblies. [ABSTRACT FROM AUTHOR]

A systematic theoretical study on the effect of H2S on mercury (Hg) adsorption on activated carbon was conducted by density functional calculation. The form and amount of sulfur species formed by H2S adsorption dominate the pattern of Hg adsorption on activated carbon surface. C–S species is more active to improve Hg adsorption than C–S–C species. C–S species can improve the chemisorption of Hg by enhancing the activity of neighboring C sites. Increasing the amount of C–S species can further enhance the interaction of Hg with C sites, and leads to the formation of HgS. The adsorption of HgS on activated carbon surface is highly thermally favorable, and belongs to chemisorption. C–S species is able to facilitate the adsorption of HgS, and makes HgS adsorbing more likely in molecular adsorption pattern. HgS complex is the most stable form of Hg adsorption on activated carbon surface with H2S. [ABSTRACT FROM AUTHOR]

The formation of biimidazoldiium structures by the introduction of methyl substituents on the N atoms at the 3 and 3′ positions of 2,2′-biimidazoles led to increments in the Stokes shift of these structures. Based on time-dependent density functional theory (TDDFT) calculations, the imidazolium rings become distorted and the N atoms of the imidazolium rings underwent structural changes through sp2 to sp2 rehybridization in the excited states. [ABSTRACT FROM AUTHOR]

Mixed lead–tin hybrid perovskite alloy CH3NH3(Pb1–xSnx)I3 attracted significant attention lately because of the reduction of its band gap below both end compounds, which makes it a promising bottom cell material in all-perovskite tandem solar cells. The effect is a consequence of a strongly nonlinear dependence of the alloy band gap on chemical composition. Here, we use electronic structure calculations at different levels of theory (density functional theory (DFT), hybrid DFT, and QSGW, with and without spin–orbit interactions) to investigate the presently elusive origin of this effect. Contrary to current conflicting studies, our results show that neither spin–orbit interactions nor the composition induced changes of the crystal structure and ordering of atoms contributes to the nonlinearity of the band gap. We find that the strong nonlinearity is primarily a consequence of chemical effects, i.e., the mismatch in energy between s and p atomic orbitals of Pb and Sn, which form the band edges of the alloy. These results unravel the nature of the band gap bowing in Sn/Pb hybrid perovskite alloys and offer a relatively simple way to estimate evolution of the band gap in other hybrid perovskite alloys. [ABSTRACT FROM AUTHOR]

Predicting crystal structure has always been a challenging problem for physical sciences. Recently, computational methods have been built to predict crystal structure with success but have been limited in scope and computational time. In this paper, we review computational methods such as density functional theory and machine learning methods used to predict crystal structure. We also explored the breadth versus accuracy of building a model to predict across any crystal structure using machine learning. We extracted 24 913 unique chemical formulas existing between 290 and 310 K from the Pearson Crystal Database. Of these 24 913 formulas, there exists 10 711 unique crystal structures referred to as entry prototypes. Common entries might have hundreds of chemical compositions, while the vast majority of entry prototypes is represented by fewer than ten unique compositions. To include all data in our predictions, entry prototypes that lacked a minimum number of representatives were relabeled as “Other”. By selecting the minimum numbers to be 150, 100, 70, 40, 20, and 10, we explored how limiting class sizes affected performance. Using each minimum number to reorganize the data, we looked at the classification performance metrics: accuracy, precision, and recall. Accuracy ranged from 97 ± 2 to 85 ± 2%; average precision ranged from 86 ± 2 to 79 ± 2%, while average recall ranged from 73 ± 2 to 54 ± 2% for minimum-class representatives from 150 to 10, respectively. [ABSTRACT FROM AUTHOR]

We report the catalyzed atomic layer deposition (ALD) of silicon oxide using Si2Cl6, H2O, and various alkylamines. The density functional theory (DFT) calculations using the periodic slab model of the SiO2 surface were performed for the selection of alternative Lewis base catalysts with high catalytic activities. During the first half-reaction, the catalysts with less steric hindrance such as pyridine would be more effective than bulky alkylamines despite lower nucleophilicity. On the other hand, during the second half-reaction, the catalysts with a high nucleophilicity such as triethylamine (Et3N) would be more efficient because the steric hindrance is less critical. The in situ process monitoring shows that the calculated atomic charge is a good indicator for expecting the catalyst activity in the ALD reaction. The use of Et3N in the second half-reaction was essential to improving the growth rate as well as the step coverage of the film because the Et3N-catalyzed process deposited a SiO2 film with a step coverage of 98% that is better than 93% of the pyridine-catalyzed process. The adsorption of pyridine, ammonia (NH3), or trimethylamine (Me3N) salts was more favorable than that of Et3N, n-Pr3N, or iPr3N salts. Therefore, Et3N was expected to incorporate less amine salts in the film as compared to pyridine, and the compositional analyses confirmed that the concentrations of Cl and N by the Et3N-catalyzed process were significantly lower than those by the pyridine-catalyzed process. [ABSTRACT FROM AUTHOR]

The efficacy of S-omeprazole as a proton pump inhibitor compared with that of its enantiomer R-omeprazole is studied using density functional theoretical calculations. The pharmacokinetic studies suggest that the efficacy of S-omeprazole presumably depends on metabolic pathway and excretion from the human body. The density functional theory calculations at SMDwater-B3LYP-D3/6-311+G(d,p)/LANL2DZ//B3LYP/6-31G(d)/LANL2DZ with triradicaloid model active species, [Por•+FeIV(SH)O], of CYP2C19 enzyme with high-spin quartet and low-spin doublet states demonstrate C-H bond activation mechanism through a two-state rebound process for the hydroxylation of R-omeprazole and S-omeprazole. The calculated activation free energy barriers for the hydrogen abstraction are 15.7 and 17.5 kcal/mol for R-omeprazole and S-omeprazole, respectively. The hydroxylation of R-omeprazole and S-omeprazole is thermodynamically favored; however, the hydroxylated intermediate of S-omeprazole further disintegrates to metabolite 5-O-desmethylomeprazole with a higher kinetic barrier. We have examined the sulfoxidation of S-omeprazole to omeprazole sulfone metabolite by CYP3A4, and the observed activation free energy barrier is 9.9 kcal/mol. The computational results reveal that CYP2C19 exclusively metabolizes R-omeprazole to hydroxyomeprazole, which is hydrophilic and can easily excrete, whereas CYP3A4 metabolizes S-omeprazole to lipophilic sulfone; hence, the excretion of this metabolite would be relatively slower from the body. The spin density analysis and molecular orbital analysis performed using biorthogonalization calculations indicate that R-omeprazole favors high-spin pathway for metabolism process whereas S-omeprazole prefers the low-spin pathway. [ABSTRACT FROM AUTHOR]

Achieving both bond dissociation energies (BDEs) and their trends for the R-X bonds with R = Me, Et, i-Pr, and t-Bu reliably is nontrivial. Density functional theory (DFT) methods with traditional exchange-correlation functionals usually have large error on both the BDEs and their trends. The M06-2X functional gives rise to reliable BDEs, but the relative BDEs are determined not as accurately. More demanding approaches such as some double-hybrid functionals, for example, G4 and CCSD(T), are generally required to achieve the BDEs and their trends reliably. The fixed-node diffusion quantum Monte Carlo method (FN-DMC) is employed to calculated BDEs of these R-X bonds with X = H, CH3, OCH3, OH, and F in this work. The single Slater-Jastrow wave function is adopted as trial wave function, and pseudopotentials (PPs) developed for quantum Monte Carlo calculations are chosen. Error of these PPs is modest in wave function methods, while it is more pronounced in DFT calculations. Our results show that accuracy of BDEs with FN-DMC is similar to that of M06-2X and G4, and trends in BDEs are calculated more reliably than M06-2X. Both BDEs and trends in BDEs of these bonds are reproduced reasonably with FN-DMC. FN-DMC using PPs can thus be applied to BDEs and their trends of similar chemical bonds in larger molecules reliably and provide valuable information on properties of these molecules. [ABSTRACT FROM AUTHOR]

In this work, DFT calculations are performed in order to provide a basis for the assemblage of Gd-based supramolecular magnetic hyperalkali complexes that combine strong donor character and outstanding magnetic response. When the Gd atom is decorated with the lithiated superalkali moieties Li3O and Li4O, the calculated vertical ionization potential (VIP) is observed to drop to 3.75 eV for the Gd(Li3O)4 cluster, and 3.58 eV for the Gd(Li4O)3 cluster, which are below the VIP of cesium (3.99 eV) calculated at the same level of theory. A recipe earlier proposed for obtaining hyperalkali molecules is verified. By using the hypermetalated cluster Li4O in number that matches exactly the formal valence of Gd, we observe the lowest VIP, where the next excess electron provides the enhancement of the donor character besides stabilizing the cluster. The results indicate a new concept for designing highly reactive molecules. [ABSTRACT FROM AUTHOR]

Motivated by the fact that Fe2O3 nanoparticles are used in the treatment of cancer, we have examined the role of ligands on the magnetic properties of these particles by focusing on (Fe2O3)4 as a prototype system with H as ligands. Using the Broken-Symmetry Density Functional Theory, we observed a strong collective superexchange in the hydrogenated Fe8O12H8 cluster. The average antiferromagnetic exchange coupling constant between the four iron-iron oxo-bridged pairs was found to be -178 cm-1, whereas coupling constants between hydroxo-bridged pairs were much smaller. We found that despite the apparent symmetry of the iron atom framework, it is not reasonable to assume this symmetry when fitting the exchange coupling constants. We also analyzed the geometrical and magnetic properties of Fe8O12Hn for n = 0-12 and found that hydrogenating oxo-bridges would generally inhibit the Fe-O-Fe antiferromagnetic superexchange interactions. Antiferromagnetic lowest total energy states become favorable only when specific distributions of hydrogen atoms are realized. The (HO)4-Fe4(all spin-up)-O4-Fe4(all spin-down)-(OH)4 configuration in Fe8O12H8 presents such an example. This symmetric configuration can be considered a superdiatomic system. [ABSTRACT FROM AUTHOR]

In the solid state, (±)-3-methyl-2-phenylbutyramide 1 spontaneously resolves into a conglomerate (Form I) that crystallizes in a racemic form (Form II) upon melting followed by vapor crystallization, a rarely reported phenomenon. An additional racemic polymorph, Form III, has been characterized, and the thermodynamic relationship between the three forms established by a variety of computational and experimental methods including grinding, slurry crystallization, and seeding techniques. Both racemic Forms II and III are metastable and readily convert to the more stable conglomerate, Form I. Density functional theory calculations of the different polymorphs of 1 show that the enantiomers of 1 (R & S) are more stable than both racemic forms. [ABSTRACT FROM AUTHOR]

The stiffness tensor and elastic anisotropy characteristics for the crystalline hydrogen maleates of l-isoleucinium, l-leucinium, and l-norvalinium with l-norvaline have been calculated using the periodic DFT calculations and atom-centered basis sets. The H-bond orientations have been compared with spatial directions of the minimum and maximum values of Young’s modulus, shear modulus, and linear compressibility. In spite of the similar layered structures, l-isoleucinium and l-leucinium hydrogen maleates show significant difference in elastic moduli anisotropy. The flexibility of l-leucinium hydrogen maleate is explained by the relatively high universal elastic anisotropy index and the large anisotropy ratios of elastic moduli. In its turn, this index is determined by the almost coincidental Young’s modulus maximum direction and the orientation of the strongest H-bonds. [ABSTRACT FROM AUTHOR]

The formation mechanism of vinyl acetate in the reaction of acetylene and acetic acid, which was catalyzed by ordered mesoporous carbon (OMC) supported zinc acetate, was investigated using density functional theory (DFT). Since the surface functional groups of carbon support influence the reaction significantly and play an important role in catalysis designing, we calculate the elementary steps on pristine ordered mesoporous carbon and carbon modified with carboxyl, carbonyl, and hydroxyl, respectively. After calculation, we find that carbonyl shifts to the epoxy group, which indicates the instability of carbonyl on the catalyst support. We propose the possible reaction mechanism and find that the reaction mechanism is not exactly the same with different functional groups. A remarkably acetate shift will occur in the existence of carboxyl and the activation barrier of rate-limiting steps in this case is also reduced, while the hydroxyl and epoxy groups will increase the barrier to some extent. Therefore, when designing the industrial catalysis for this reaction, we can modify the surface of catalysis support directionally, to enhance the reaction efficiency. [ABSTRACT FROM AUTHOR]

Kamlet-Taft (KT) parameters were measured for four nonaqueous hydrogen bond donor (HBD)-hydrogen bond acceptor (HBA) solvent-pair mixtures: methanol-cyclopentanone, methanol-cyclohexanone, ethanol-cyclopentanone, and ethanol-cyclohexanone to define their solvent polarity as a function of composition. KT mixed-solvent polarities differed greatly from molar average property values. The preferential solvation (PS) model was used to correlate solvent polarity and showed that local compositions of 1:1 (HBD-HBA) complex molecules were highly asymmetric. Trends of KT parameters of both cyclohexanone and cyclopentanone mixtures were similar, although the specific hydrogen bonding interactions of HBD-HBA complex molecules in cyclohexanone mixtures were stronger than those of cyclopentanone mixtures according to density functional theory calculations, infrared spectroscopy, and solution macroscopic properties. Application of the PS model to pharmaceuticals showed that the solvent-pair mixtures have wide-working composition ranges (~0 < xHBA < ~ 1) for aspirin, ibuprofen, niflumic acid, p-amino-benzoic, p-hydroxy-benzoic and salicyclic acid, limited composition ranges (ΔxHBA ≈ 0.7) for benzoic acid and temazepam, and narrow composition ranges (ΔxHBA ≈ 0.3) for others. By comparing mixed-solvent polarity with polarity of solvents being used for material, petroleum, and biomass processing, it can be concluded that cyclic ketone-alcohol mixtures have many applications. [ABSTRACT FROM AUTHOR]

The development of highly active and selective metal catalysts for efficient oxidation of hydrocarbons and identification of the reactive intermediates in the oxidation catalysis are long-standing challenges. In the rapid hydrocarbon oxidation catalyzed by ruthenium(IV) and -(III) porphyrins, the putative Ru(V)-oxo intermediates remain elusive. Herein we report that arylruthenium(III) porphyrins are highly active catalysts for hydrocarbon oxidation. Using catalyst [RuIII(TDCPP)(Ph)(OEt2)] (H2TDCPP = 5,10,15,20-tetrakis(2,6-dichlorophenyl)porphyrin), the oxidation of C-H bonds of various hydrocarbons with oxidant m-CPBA at room temperature gave alcohols/ketones in up to 99% yield within 1 h; use of [nBu4N]IO4 as a mild alternative oxidant avoided formation of lactone from cyclic ketone in C-H oxidation, and the catalytic epoxidation with up to 99% yield and high selectivity (no aldehydes as side product) was accomplished within 5 min. UV-vis, electrospray ionization-mass spectrometry, resonance Raman, electron paramagnetic resonance, and kinetic measurements and density functional theory calculations lend evidence for the formation of Ru(V)-oxo intermediate [RuV(TDCPP)(O)(Ph)]. [ABSTRACT FROM AUTHOR]

We investigate the structure and binding energy of alkanethiolate self-assembled monolayers (SAMs) on Pd (111), Pd (100), and Pd (110) facets at different coverages. Dispersion-corrected density functional theory calculations are used to correlate the binding energy of alkanethiolates with alkyl chain length and coverage. The equilibrium coverage of thiolate layers strongly prefers 1/3 monolayer (ML) on the Pd (111) surface. The coverage of thiolates varies with chemical potential on Pd (100) and Pd (110), increasing from 1/3 to 1/2 ML on (100) and from 1/4 to 1/2 ML on (110) as the thiol chemical potential is increased. Higher coverages are driven by attractive dispersion interactions between the extended alkyl chains, such that transitions to higher coverages occur at lower thiol chemical potentials for longer chain thiolates. Stronger adsorption to the Pd (100) surface causes the equilibrium Wulff construction of Pd particles to take on a cubic shape upon saturation with thiols. The binding of H, O, and CO adsorbates is weakened as the thiolate coverage is increased, with saturation coverages causing unfavorable binding of O and CO on Pd (100) and weakened binding on other facets. Temperature-dependent CO diffuse reflectance infrared Fourier transform spectroscopy experiments are used to corroborate the weakened binding of CO in the presence of thiolate SAMs of varying surface density. Preliminary results of multiscale modeling efforts on the Pd-thiol system using a reactive force field, ReaxFF, are also discussed. [ABSTRACT FROM AUTHOR]

The catalytic [5 + 1] annulation/5-exo-cyclization reaction of amidines with diynes is reported herein. This protocol provides highly atom-economical access to fabricate two nitrogen-containing heterocycles in one step with high efficiency and selectivity. Significantly, this reaction represents the first example of using diyne as a one-carbon reaction partner in C–H functionalization. Kinetic isotope effects suggested that the catalytic cycle of this reaction is initiated by the cleavage of the ortho C–H bond in the N-phenyl ring of amidines, which is likely involved in the rate-limiting step. Calculations based on density functional theory (DFT) indicated that C–H activation and the formation of Rh(V) species via 5-exo-cyclization could be vital processes for this cascade transformation. [ABSTRACT FROM AUTHOR]

In this work, we compare the results obtained with 89 computational methods for predicting noncovalent bond lengths in weakly bound complexes. Evaluations for the performance in noncovalent interaction energies and covalent bond lengths obtained from five other data sets are included. The overall best performing density functional is the ωB97M-V method, achieving balanced results across all three categories. For noncovalent geometries, the best methods include B97M-V, B3LYP-D3(BJ) and DSD-PBEPBE-D3(BJ). The effects of systematic improvement of the density functional approximation and of dispersion corrections are also discussed. [ABSTRACT FROM AUTHOR]

Reactions of copper oxide cluster cations, CunOm+ (n = 3-7; m ≤ 5), with ammonia, NH3, are studied at near thermal energies using a guided ion beam tandem mass spectrometer. The single-collision reactions of specific clusters such as Cu4O2+, Cu5O3+, Cu6O3+, Cu7O3+, and Cu7O4+ give rise to the release of H2O after NH3 adsorption efficiently and result in the formation of CunOm-1NH+. These CunOm+ clusters commonly have Cu average oxidation numbers of 1.0-1.4. On the other hand, the formation of CunOm-1H2+, i.e., the release of HNO, is dominantly observed for Cu7O5+ with a higher Cu oxidation number. Density functional theory calculations are performed for the reaction Cu5O3+ + NH3 → Cu5O2NH+ + H2O as a typical example of H2O release. The calculations show that this reaction occurs almost thermoneutrally, consistent with the experimental observation. Further, our experimental studies indicate that the multiple-collision reactions of Cu5O3+ and Cu7O4+ with NH3 lead to the production of Cu5+ and Cu7O+, respectively. This suggests that the desirable NH3 oxidation to N2 and H2O proceeds on these clusters. [ABSTRACT FROM AUTHOR]

The mechanism for dioxygen activation using the biomimetic model complex of [NiFe]-hydrogenase, [NiLFe(η5-C5Me5)]+ [L = N,N′-diethyl-3,7-diazanonane-1,9-dithiolato] was established using density functional theory (DFT) and artificial force-induced reaction (AFIR) methods. Our computational results suggest that O2 binds to the FeII center in an end-on fashion and forms a high-valent iron complex, NiFe-peroxo (NiIIFeIV(η²-O2)), which has been experimentally observed. The O-O bond cleavage occurs in the presence of borohydride (BH4-) through hydrogen atom transfer (HAT). Once the HAT occurs, the generated BH3 radical anion (BH3•-) binds to the terminal oxygen of NiFe-OOH, giving rise to BH3OH- and NiIIFeIV═O. The second HAT from BH4- to the oxygen of NiIIFeIV═O leads to BH3OH- and Fe-reduced NiIIFeII complex. Importantly, the dioxygen activation is triggered by HAT, not by proton transfer or hydride transfer. The O2 is activated by the Fe center, and the oxidation state of Fe varies during the process, while the oxidation state of Ni is conserved. These mechanistic insights into O2 activation are essential in understanding the formation of the inactive state and reactivation process in hydrogenase. [ABSTRACT FROM AUTHOR]

The disproportionation of formic acid to methanol catalyzed by a half-sandwich iridium complex, [Cp*Ir(bpy-Me)OH2]2+, was computationally investigated by using density functional theory. A newly proposed mechanism features three interrelated catalytic cycles, the dehydrogenation of formic acid to CO2 and H2, the hydrogenation of formic acid to formaldehyde with the formation of water, and the hydrogenation of formaldehyde to methanol. Methanol assisted proton transfer and direct C-O bond cleavage after hydroxyl deprotonation in two competitive pathways for the formation of formaldehyde are the rate-determining steps in the whole catalytic reaction. Calculation results indicate that the formation of formaldehyde from methanediol through direct cleavage of a C-O bond after hydroxyl deprotonation has a free energy barrier of 25.9 kcal/mol, which is 1.9 kcal/mol more favorable than methanol assisted proton transfer. [ABSTRACT FROM AUTHOR]

Accurate double-hybrid density functional theory and isodesmic-type reaction schemes are utilized to report accurate estimates of the heats of formation (ΔfH) for all 24 isolated-pentagon-rule isomers of the third most abundant fullerene, C84. Kinetic stabilities of these C84 isomers are also considered via C-C bond cleavage rates (Pcleav) calculated using density functional theory. Our results show that the relative abundance of C84 fullerene isomers observed in arc discharge synthesis is the result of both thermochemical and kinetic factors. This provides timely insight regarding the characterization of several C84 isomers that have been obtained experimentally to date. For instance, the established assignments of C84 isomers of (using the Fowler-Manolopoulos numbering scheme) 22 [D2(IV)], 23 [D2d(II)], 19 [D3d], 24 [D6h], 11 [C2(IV)], and 4 [D2d(I)] are consistent with the relative ΔfH and Pcleav values for these structures. However, our thermochemical and kinetic stabilities of Cs isomers 14, 15, and 16 indicate that the two experimentally isolated Cs isomers are 15 and 16, contrary to some previous assignments. Of the remaining isolated isomers of symmetry C2 and D2, definitive assignment was not possible with consideration of only ΔfH and Pcleav. [ABSTRACT FROM AUTHOR]

Magnetically induced current densities and ring-current pathways have been calculated at density functional theory (DFT) and second-order Møller-Plesset perturbation theory (MP2) levels of theory for a set of expanded porphyrins consisting of five or six pyrrolic rings. The studied molecules are sapphyrin, cyclo[6]pyrrole, rubyrin, orangarin, rosarin, and amethyrin. Different functionals have been employed to assess the functional dependence of the ring-current strength susceptibility. Vertical singlet and triplet excitation energies have been calculated at the second-order approximate coupled cluster (CC2), expanded multiconfigurational quasi-degenerate perturbation theory (XMC-DPT2), and time-dependent density functional theory levels. The lowest electronic transition of the antiaromatic molecules was found to be pure magnetic transitions providing an explanation for the large paratropic contribution to the total current density. Rate constants for different nonradiative deactivation channels of the lowest excited states have been calculated yielding lifetimes and quantum yields of the lowest excited singlet and triplet states. The calculations show that the spin-orbit interaction between the lowest singlet (S0) and triplet (T1) states of the antiaromatic molecules is strong, whereas for the aromatic molecule the spin-orbit coupling vanishes. The experimentally detected fluorescence from S2 to S0 of amethyrin has been explained. The study shows that there are correlations between the aromatic character and optical properties of the investigated expanded porphyrins. [ABSTRACT FROM AUTHOR]

XPS and NEXAFS spectra of four stable C40 isomers [29(C2), 31(Cs), 38(D2), and 39(D5d)] have been investigated theoretically. We combined density functional theory and the full core hole potential method to simulate C 1s XPS and NEXAFS spectra for nonequivalent carbon atoms of four stable C40 fullerene isomers. The NEXAFS showed obvious dependence on the four C40 isomers, and XPS spectra are distinct for all four isomers, which can be employed to identify the four stable structures of C40. Furthermore, the individual components of the spectra according to different categories have been investigated, and the relationship between the spectra and the local structures of C atoms was also explored. [ABSTRACT FROM AUTHOR]

VNn+ clusters were generated by laser ablation and analyzed by mass spectrometry. The results showed that VN8+, VN9+, and VN10+ clusters were formed, and the mass peak of VN8+ is dominant in the spectrum. The VN8+ cluster was further investigated by a photodissociation experiment with 266 nm photons. Density functional theory calculations were conducted at the M06-2X/6-311+G(d,p) level to search for stable structures of VNn+ (n = 8, 9, and 10) and their neutral counterparts. The theoretical calculations revealed that the most stable structure of VN8+ is in the form of V(N2)4+ with D4h symmetry. The binding energy from the calculation is in good agreement with that obtained from the photodissociation experiments. The global minimum structures of VN8, VN9+/0, and VN10+/0 contain a similar substructure of the N4 ring and exhibit energy properties. The most stable structure of VN9+ is in the form of (η²-N4)V+N(N2)2 with C1 symmetry, while that of VN10+ is in the form of (η4-N4)V+(N2)3 with Cs symmetry. For neutral VN8, VN9, and VN10, (η4-N4)V(N2)2, (η4-N4)V(N3)(N2), and (η4-N4)V(N2)3 are their ground-state structures, with decomposition into one V atom, and corresponding quantities of N2 can release energies of about 50.20, 96.28, and 57.76 kcal/mol, respectively. [ABSTRACT FROM AUTHOR]