[DBU‐H]+ and H2o as effective catalyst form for 2,3‐dihydropyrido[2,3‐d]pyrimidin‐4(1H)‐ones: A DFT Study

DFT investigations are carried out to explore the effective catalyst forms of DBU and H₂O and the mechanism for the formation of 2,3‐dihydropyrido[2,3‐d]‐pyrimidin‐4(1H)‐ones. Three main pathways are disclosed under unassisted, water‐catalyzed, DBU and water cocatalyzed conditions, which involves concerted nucleophilic addition and H‐transfer, concerted intramolecular cyclization and H‐transfer, and Dimroth rearrangement to form the product. The results indicated that the DBU and water cocatalyzed pathway is the most favored one as compared to the rest two pathways. The water donates one H to DBU and accepts H from 2‐amino‐nicotinonitrile ( 1 ), forming [DBU‐H]⁺‐H₂O as effective catalyst form in the proton migration transition state rather than [DBU‐H]⁺‐OH^?. The hydrogen bond between [DBU‐H]⁺···H₂O··· 1 ^? decreases the activation barrier of the rate‐determining step. Our calculated results open a new insight for the green catalyst model of DBU‐H₂O. © 2015 Wiley Periodicals, Inc.     

Structures and thermochemistry of ions formed by methane chemical ionization of Fe(CO)5. Site of protonation and determination of Fe?H and Fe?CO bond dissociation energies of HFe(CO)n+ ions

High-energy collisional activation mass spectrometry of HFe(CO)₅⁺ ions shows that Fe(CO)₅ is protonated on the iron atom rather than on one of the ligands. This finding is supported by ab initio quantum chemical calculations. The value of the proton affinity of Fe(CO)₅ was measured by high-pressure mass spectrometry to be 857 kJ mol^?1. The Fe? CO bond dissociation energies for HFe(CO)_n⁺ (n = 1–5) were measured by energy-variable low-energy collisional activation mass spectrometry. The Fe? H bond dissociation energies in HFe(CO)_n⁺ ions were also determined. A synergistic effect on the strengths of the Fe? H and Fe? CO bonds in HFe(CO)⁺ is noticed. It is demonstrated that the electronically unsaturated species HFe(CO)_n⁺ (n = 3, 4) formed in exothermic proton-transfer reactions with Fe(CO)₅ form adducts with CH₄. Adducts between C₂H₅⁺ or C₃H₅⁺ and Fe(CO)_n are observed. These adducts are probably formed in direct reactions between the respective carbocations and Fe(CO)₅.     

A comparison of the fragmentation pathways of [Cu(II)(Ma)(Mb)]•2+ complexes where Ma and Mb are peptides containing either a tryptophan or a tyrosine residue

[Cu^II(M_a)(M_b)]^?2+ complexes, where M_a and M_b are dipeptides or tripeptides each containing either a tryptophan (W) or tyrosine (Y) residue, have been examined by means of electrospray tandem mass spectrometry. Collision‐induced dissociations (CIDs) of complexes containing identical peptides having a tryptophan residue generated abundant radical cations of the peptides; by contrast, for complexes containing peptides having a tyrosine residue, the main fragmentation channel is dissociative proton transfer to give [M_a + H]⁺ and [Cu^II(M_b – H)]^?+. When there are two different peptides in the complex, each containing a tryptophan residue, radical cations are again the major products, with their relative abundances depending on the locations of the tryptophan residue in the peptides. In the CIDs of mixed complexes, where one peptide contains a tryptophan residue and the other a tyrosine residue, the main fragmentation channel is formation of the radical cation of the tryptophan‐containing peptide and not proton transfer from the tyrosine‐containing peptide to give a protonated peptide. Copyright © 2010 John Wiley & Sons, Ltd.     

Theoretical study of [Li(H2O)n]+ and [K(H2O)n]+ (n = 1−4) complexes

The geometries, successive binding energies, vibrational frequencies, and infrared intensities are calculated for the [Li(H₂O)_n]⁺ and [K(H₂O)_n]⁺ (n = 1?4) complexes. The basis sets used are 6-31G* and LANL 1DZ (Los Alamos ECP +DZ ) at the SCF and MP 2 levels. There is an agreement for calculated structures and frequencies between the MP 2/6-31G* and MP 2/LANL 1DZ basis sets, which indicates that the latter can be used for calculations of water complexes with heavier ions. Our results are in a reasonable agreement with available experimental data and facilitate experimental study of these complexes. © 1995 John Wiley & Sons, Inc.     

Competitive formation of M+˙ and [M + H]+ ions under fast atom bombardment conditions

The competitive formation of molecular ions M^+˙ and protonated molecules [M + H]⁺ under fast atom bombardment (FAB) conditions was examined using various kinds of organic compounds. The use of protic/hydrophilic matrices such as thioglycerol and glycerol resulted in relatively large values of the peak intensity ratio I([M + H]⁺)/I(M^+˙) compared with the use of relatively aprotic/hydrophobic matrices such as m-nitrobenzyl alcohol and o-nitrophenyl octyl ether. The change of matrix from thiol-containing such as thioglycerol and dithiothreitol to alcoholic such as glycerol and pentamethylene glycol increased the I([M + H]⁺)/I(M^+˙) ratio. Furthermore, the change of matrix increased the peak intensity ratio of the doubly charged ion [M + 2H]²⁺ to [M + H]⁺ in the FAB mass spectra of angiotensin I and gramicidin S. The addition of acids to the matrix solution increased the I([M + H]⁺)/I(M^+˙) ratio, although such an effect did not always occur. The acetylation of simple aniline compounds markedly increased the I([M + H]⁺)/I(M^+˙) ratio. It was concluded from these results that the hydrogen bonding interaction between hydroxyl groups(s) of the matrix and basic site(s) of analyte molecules in solution acts advantageously as a quasi-preformed state for [M + H]⁺ formation, and that the presence of significant proton acceptor(s) such as carbonyl group in analytes hinder the M^+˙ formation which may generally occur under FAB conditions. The formation of M^+˙ and [M + H]⁺ ions seemed to occur competitively, reflecting or according to the interaction or solvation states between the analyte and matrix molecules in solution and the structural characteristics of the analytes.     

Structure and fragmentation of [C6H13O]+ ions formed by chemical ionization

The structure and fragmentation of eight [C₆H₁₃O] ⁺ ions formed by protonation of C₆H₁₂O carbonyl compounds in the gas phase have been investigated using isotopic labeling and metastable ion studies to investigate the fragmentation reactions and collisional dissociation studies to probe ion structures. Protonated 3-methyl-2-pentanone and protonated 2-methyl-3-pentanone readily-interconvert by pinacolic-retro-pinacolic rearrangements; the remaining six ions represent stable ion structures, although in many cases fragmentation is preceded by pinacolic-type rearrangements. Unimolecular (metastable ion) fragmentation of the [C₆H₁₃O] ⁺ species occurs by elimination of H₂O, C₃H₆, C₄H₈ and C₂H₄O. The last three elimination reactions appear to occur through the intermediacy of a proton-bound complex of a carbonyl compound and an olefin, with the proton residing with the species of higher proton affinity on decomposition of the complex.     

Proton-bound cluster ions in ion mobility spectrometry

Gaseous oxygen and nitrogen bases, both singly and as binary mixtures, have been introduced into ion mobility spectrometers to study the appearance of protonated molecules, and proton-bound dimers and trimers. At ambient temperature it was possible to simultaneously observe, following the introduction of molecule A, comparable intensities of peaks ascribable to the reactant ion (H₂O)_nH⁺, the protonated molecule AH⁺ and AH⁺ · H₂O, and the symmetrical proton bound dimer A₂H⁺. Mass spectral identification confirmed the identifications and also showed that the majority of the protonated molecules were hydrated and that the proton-bound dimers were hydrated to a much lesser extent. No significant peaks ascribable to proton-bound trimers were obtained no matter how high the sample concentration. Binary mixtures containing molecules A and B, in some cases gave not only the peaks unique to the individual compounds but also peaks due to asymmetrical proton bound dimers AHB⁺. Such ions were always present in the spectra of mixtures of oxygen bases but were not observed for several mixtures of oxygen and nitrogen bases. The dimers, which were not observable, notable for their low hydrogen bond strengths, must have decomposed in their passage from the ion source to the detector, i.e. in a time less than ∼5 ms. When the temperature was lowered to −20 °C, trimers, both homogeneous and mixed, were observed with mixtures of alcohols. The importance of hydrogen bond energy, and hence operating temperature, in determining the degree of solvation of the ions that will be observed in an ion mobility spectrometer is stressed. The possibility is discussed that a displacement reaction involving ambient water plays a role in the dissociation.     

Fast atom bombardment mass spectrometry of ionic gold(I) and gold(III) carbene derivatives: An investigation of the formation of [M – H]+ species

Fast atom bombardment (FAB) mass spectrometry of the gold(I) and gold(III) derivatives, {Au[C(Y)–NHAr]₂}⁺X^? and {Au[C(Y)–NHAr]₂I₂} ⁺ X^? (Y =? OC₂H₅ or ? NHAr; X^? = CIO₄^? or BF₄^?; Ar = p-CH₃? C₆H₄) has led to the detection, for the alkoxyamino derivatives only, of [M–H]⁺˙ molecular species. The mechanism of the formation of these unusual species has been studied with respect to the oxidation state of gold, nature of the matrix, matrix acidity and ligand structure. The energetics of two possible alternative mechanisms has been studied by means of ab initio theoretical calculations. Both experimental and theoretical data indicate that [M–H]⁺˙ formation is due to the reaction of M⁺ with H⁺-philic and/or H˙-philic species produced from the matrix by FAB. Whatever the operative mechanism, the [M–H]⁺˙ formation is to be considered a FAB-induced oxidative process.     

Syntheses and metal ions recognition of dendritic calix[n]arenes (n = 6,8) amide derivative

Dendritic p-t-butylcalix[n]arene amide derivatives with terminal amino groups of the first and second generations were synthesized by using divergent methods from ammonolysis of ethyl calixarylacetate with 1,6-diaminohexane and Michael addition of methyl acrylate. Their structures were confirmed by IR, ¹H NMR. The recognition properties of these amide derivatives for several kinds of metal ions were studied with UV-Vis spectroscopy. The results showed a great affinity for soft Ag⁺ and UO₂ ²⁺ ions and formed 1:2 or 1:3 stoichiometric complexes. Translated from Chinese Journal of Applied Chemistry, 2006, 23(3) (in Chinese)     

Structure of ions [ZnNCR]+ and [Zn(NCR)2]+ (R = H,CH3) in the gas phase

Structures of [ZnNCR]⁺ and [Zn(NCR)₂]⁺ ions (R = H, Me), which are abundant in the mass spectra of many types of coordination compounds, were studied by the MNDO method. In all cases the most stable isomers correspond to the zinc ion coordinated with the nitrogen(s) of the nitrile ligand. For [Zn(NCR)₂]⁺, the N-Zn-N angles are ～108°.     

Electron impact studies. CXII—The properties of positive ions produced by charge stripping from negative ions. [C6H5O]+, [C6H5S]+ and [C7H7S]+

The dissociative spectrum of the [C₆H₅S]⁺ ion derived by charge inversion from [C₆H₅S]^?, shows a variety of fragmentations including the competitive losses of H?, C₃H₄ and the formation of [CHS]⁺. The spectrum of a deuteriated derivative shows that these three processes are preceded or accompanied by H/D scrambling. The corresponding [C₆H₅O]⁺ species also undergoes hydrogen scrambling prior to fragmentation. In marked contrast, the ion [p-MeC₆H₄S]⁺ does not undergo hydrogen randomization between the methyl and aryl groups, and positional integrity is retained during fragmentation. These results are compared with the properties of the same ions produced by conventional ionization.     

Self‐Assembled Multimetallic/Peptide Complexes: Structures and Unimolecular Reactions of [Mn(GlyGly−H)2n−1]+ and Mn+1(GlyGly−H2n]2+ Clusters in the Gas Phase

The unimolecular chemistry and structures of self‐assembled complexes containing multiple alkaline‐earth‐metal dications and deprotonated GlyGly ligands are investigated. Singly and doubly charged ions [M_n(GlyGly?H)_n‐1]⁺ (n=2–4), [M_n+1(GlyGly?H)_2n]²⁺ (n=2,4,6), and [M(GlyGly?H)GlyGly]⁺ were observed. The losses of 132 Da (GlyGly) and 57 Da (determined to be aminoketene) were the major dissociation pathways for singly charged ions. Doubly charged Mg²⁺ clusters mainly lost GlyGly, whereas those containing Ca²⁺ or Sr²⁺ also underwent charge separation. Except for charge separation, no loss of metal cations was observed. Infrared multiple photon dissociation spectra were the most consistent with the computed IR spectra for the lowest energy structures, in which deprotonation occurs at the carboxyl acid groups and all amide and carboxylate oxygen atoms are complexed to the metal cations. The N?H stretch band, observed at 3350 cm^?1, is indicative of hydrogen bonding between the amine nitrogen atoms and the amide hydrogen atom. This study represents the first into large self‐assembled multimetallic complexes bound by peptide ligands.     

Synthesis and structure of cis-[RuCl(bpzm)(κ1-P-dpim)(κ2-P,N-dpim)]Cl·(CHCl3)5. Stability of [Cl(HCCl3) n ]− aggregates

The reaction of [RuCl₂(cod)(bpzm)] [cod = 1,5-cyclooctadiene, bpzm = bis(pyrazol-1-yl)methane] with 2-diphenylphosphino-1-methylimidazole (dpim) and crystallisation from CHCl₃ yielded crystals of cis-[RuCl(κ²-N,N-bpzm)(κ¹-P-dpim)(κ²-P,N-dpim)][Cl(CHCl₃)₄]·CHCl₃, (1√(CHCl₃)₅), in which the Cl^?  counteranion was solvated by four CHCl₃ molecules and interacted with the most positive region of the cation. The structure of the anionic entity and the presence of non-covalent interactions were studied. Theoretical calculations allowed the evaluation of the stability of [Cl(CHCl₃) _n ]^?  aggregates. A pronounced stability was found for aggregates with n = 6 with an increasing charge transfer from the chloride ion to the CHCl₃ molecules from n = 1 to 6. A literature survey on the occurrence of anionic species [Cl(CXCl₃) _n (HB) _m ]^?  (X = H or D; HB = hydrogen bonds with the cation) in solid state structures was carried out and the findings correlated with the results of computational studies. A stabilisation effect of a Cl…Cl interaction was demonstrated by a natural bond orbitals (NBO) analysis.     

Silver–Ethene Complexes [Ag(η2‐C2H4)n][Al(ORF)4] with n=1, 2, 3 (RF=Fluorine‐Substituted Group)

Compounds including the free or coordinated gas‐phase cations [Ag(η²‐C₂H₄)_n]⁺ (n=1–3) were stabilized with very weakly coordinating anions [A]^? (A=Al{OC(CH₃)(CF₃)₂}₄, n=1 ( 1 ); Al{OC(H)(CF₃)₂}₄, n=2 ( 3 ); Al{OC(CF₃)₃}₄, n=3 ( 5 ); {(F₃C)₃CO}₃Al‐F‐Al{OC(CF₃)₃}₃, n=3 ( 6 )). They were prepared by reaction of the respective silver(I) salts with stoichiometric amounts of ethene in CH₂Cl₂ solution. As a reference we also prepared the isobutene complex [(Me₂C?CH₂)Ag(Al{OC(CH₃)(CF₃)₂}₄)] ( 2 ). The compounds were characterized by multinuclear solution‐NMR, solid‐state MAS‐NMR, IR and Raman spectroscopy as well as by their single crystal X‐ray structures. MAS‐NMR spectroscopy shows that the [Ag(η²‐C₂H₄)₃]⁺ cation in its [Al{OC(CF₃)₃}₄]^? salt exhibits time‐averaged D_3h‐symmetry and freely rotates around its principal z‐axis in the solid state. All routine X‐ray structures (2θ_max.<55°) converged within the 3σ limit at C?C double bond lengths that were shorter or similar to that of free ethene. In contrast, the respective Raman active C?C stretching modes indicated red‐shifts of 38 to 45 cm^?1, suggesting a slight C?C bond elongation. This mismatch is owed to residual librational motion at 100 K, the temperature of the data collection, as well as the lack of high angular data owing to the anisotropic electron distribution in the ethene molecule. Therefore, a method for the extraction of the C?C distance in [M(C₂H₄)] complexes from experimental Raman data was developed and meaningful C?C distances were obtained. These spectroscopic C?C distances compare well to newly collected X‐ray data obtained at high resolution (2θ_max.=100°) and low temperature (100 K). To complement the experimental data as well as to obtain further insight into bond formation, the complexes with up to three ligands were studied theoretically. The calculations were performed with DFT (BP86/TZVPP, PBE0/TZVPP), MP2/TZVPP and partly CCSD(T)/AUG‐cc‐pVTZ methods. In most cases several isomers were considered. Additionally, [M(C₂H₄)₃] (M=Cu⁺, Ag⁺, Au⁺, Ni⁰, Pd⁰, Pt⁰, Na⁺) were investigated with AIM theory to substantiate the preference for a planar conformation and to estimate the importance of σ donation and π back donation. Comparing the group 10 and 11 analogues, we find that the lack of π back bonding in the group 11 cations is almost compensated by increased σ donation.     

Low-energy fragmentations of five isomeric [H3, C,N, O2] +· ions

The low-energy fragmentation characteristics of the [H₃,C,N,O₂]^+· isomers [H₃CNO₂]^+· (a), [H₂C?N(O)OH]^+· (b), [H₃CONO]^+· (c), [HC(O)NHOH]^+· (d) and [HC(OH)?NOH]^+· (e) were studied in detail by metastable ion mass spectrometry. In agreement with most earlier observations, appearance energy measurements established the potential energy surface of the isomers a, b and c, showing the intricate interrelations between them. It was concluded that a isomerizes into b prior to fragmentation by loss of ^·OH and H₂O and into c before loss of ^·H and H₃CO^· moreover, the reverse reactions do not take place on the metastable time-frame. The dominant metastable process for isomers d and e (obtained via HCN loss from glyoxime) was generation of [H₂NOH]^+·. For isomer e this process was proposed to involved a rate-determining isomerization into d. It was concluded that isomers d and e do not intercommunicate with ions a, b and c prior to fragmentation. Neutralization-reionization mass spectrometry indicated that the enol form of formohydroxamic acid as well as the keto counterpart are stable in the gas phase.     

Novel C<Subscript>β</Subscript>–C<Subscript>γ</Subscript> Bond Cleavages of Tryptophan-Containing Peptide Radical Cations

In this study, we observed unprecedented cleavages of the C_β–C_γ bonds of tryptophan residue side chains in a series of hydrogen-deficient tryptophan-containing peptide radical cations (M^•+) during low-energy collision-induced dissociation (CID). We used CID experiments and theoretical density functional theory (DFT) calculations to study the mechanism of this bond cleavage, which forms [M – 116]⁺ ions. The formation of an α-carbon radical intermediate at the tryptophan residue for the subsequent C_β–C_γ bond cleavage is analogous to that occurring at leucine residues, producing the same product ions; this hypothesis was supported by the identical product ion spectra of [LGGGH – 43]⁺ and [WGGGH – 116]⁺, obtained from the CID of [LGGGH]^•+ and [WGGGH]^•+, respectively. Elimination of the neutral 116-Da radical requires inevitable dehydrogenation of the indole nitrogen atom, leaving the radical centered formally on the indole nitrogen atom ([Ind]^•-2), in agreement with the CID data for [WGGGH]^•+ and [W_1-CH3GGGH]^•+; replacing the tryptophan residue with a 1-methyltryptophan residue results in a change of the base peak from that arising from a neutral radical loss (116 Da) to that arising from a molecule loss (131 Da), both originating from C_β–C_γ bond cleavage. Hydrogen atom transfer or proton transfer to the γ-carbon atom of the tryptophan residue weakens the C_β–C_γ bond and, therefore, decreases the dissociation energy barrier dramatically.     

Inverse hydrogen migration in arginine-containing peptide ions upon electron transfer

Collisional electron transfer from gaseous Cs atoms was studied for singly and doubly protonated peptides Gly-Arg (GR) and Ala-Arg (AR) at 50- and 100-keV kinetic energies. Singly protonated GR and AR were discharged to radicals that in part rearranged by migration of a C_α hydrogen atom onto the guanidine group. The C_α-radical isomers formed were detected as stable anions following transfer of a second electron. In addition to the stabilizing rearrangements, the radicals underwent side-chain and backbone dissociations. The latter formed z fragments that were detected as the corresponding anions. Analysis of the (GR+H)^· radical potential energy surface using electronic structure theory in combination with Rice-Ramsperger-Kassel-Marcus calculations of rate constants indicated that the arginine C_α hydrogen atom was likely to be transferred to the arginine side-chain on the experimental timescale of ≤200 ns. Transfer of the Gly C_α-H was calculated to have a higher transition-state energy and was not kinetically competitive. Collisional electron transfer to doubly protonated GR and AR resulted in complete dissociation of (GR+2H)^+· and (AR+2H)^+· ions by loss of H, ammonia, and N-C_α bond cleavage. Electronic structure theory analysis of (GR+2H)^+· indicated the presence of multiple conformers and electronic states that differed in reactivity and steered the dissociations to distinct channels. Electron attachment to (GR+2H)²⁺ resulted in the formation of closely spaced electronic states of (GR+2H)^+· in which the electron density was delocalized over the guanidinium, ammonium, amide, and carboxyl groups. The different behavior of (GR+H)^· and (GR+2H)^+· is explained by the different timescales for dissociation and different internal energies acquired upon electron transfer.     

Changes in Dissociation Efficiency and Kinetics of Peptide Ions Induced by Basic Residues and Their Mechanistic Implication

With matrix-assisted laser desorption ionization (MALDI) time-of-flight (TOF) mass spectrometry, total abundance of product ions formed by dissociation inside (in-source decay, ISD) and outside (post-source decay, PSD) the source was measured for peptide ions [Y ₅ X + H]⁺, [XY ₅ + H]⁺, [Y ₂ XY ₃ + H]⁺, and [XY ₄ X + H]⁺ (X = tyrosine (Y), histidine (H), lysine (K), and arginine (R) with H for the ionizing proton). α-Cyano-4-hydroxycinammic acid was used as matrix. Product abundance became smaller in the presence of basic residues (H, K, and R), in the order Y > H ≈ K > R. In particular, product abundances in ISD of peptide ions with R were smaller than those with H or K by an order of magnitude, which, in turn, were smaller than that for [Y ₆ + H]⁺ by an order of magnitude. Product abundance was affected by the most basic residue when more than one basic residue was present. A kinetic explanation for the data was attempted under the assumption of quasi-thermal equilibrium for peptide ions in MALDI plume which undergoes expansion cooling. Dramatic disparity in product abundance was found to arise from small difference in critical energy and entropy. Results indicate similar transition structures regardless of basic residues present, where the ionizing proton keeps interacting with a basic site. Further implication of the results on the dissociation mechanism along b-y channels is discussed.     

Collisional activation spectra. Behavior of [C3H7O]+ and other [CnH2n+1O]+ ions

Collisional activation spectra have identified (i) as Stable ion structures. Evidence is presented for a variety of pathway for their formation, including anchimeric assistance and hydrogen migration in less stable isomers. The fragmentation behavior of a number of [C_nH_2n+1O]⁺ isomers of n = 2 to 5 shows that extensive rearrangements are common, but that some reactions appear to be useful for ion structure elucidation. One reaction identified is unusual in that it represents the decomposition of an even-electron ion to yied an odd-electron ion product in significant abundance.     

Proton transfer and isotope‐induced reaction in aniline cluster ions

The proton transfer (PT) and other intraclusters reactions occurring after electron ionization of aniline clusters (PhNH₂)_N are investigated by the time‐of‐flight mass spectrometry. The mass spectra are recorded for different expansion conditions leading to the generation of different cluster sizes. Several fragment ions are shown to originate from intracluster reactions, namely, [Ph]⁺, [PhNH₃]⁺ and [Ph–N–Ph]⁺. Reaction schemes are proposed for these ions starting with the PT process. The mass region beyond the monomer mass is dominated by cluster ions (PhNH₂)_n⁺ accompanied by satellites with ±H and +2H. In experiments with deuterated species, new fragment ions are identified. The aniline isotopomer d₅‐PhNH₂ yields the fragment ions (PhNH₂)_n?(N–Ph–NH₂)⁺. Analogical series is observed in experiments with d₇‐PhND₂, and additional fragments occur corresponding to (PhND₂)_n?(D₂N–ND–Ph–ND–ND₂)⁺ ions. The possible reaction pathways to these ions and the unusual isotope effects are discussed. Copyright © 2015 John Wiley & Sons, Ltd.