Theoretical study of long oligothiophene dications: bipolaron vs polaron pair vs triplet state

A series of oligothiophene dications (from the sexithiophene dication to the 50-mer oligothiophene dication, nT2+, n = 6-50) were studied. Density functional theory (DFT) at the B3LYP/6-31G(d) level and, in some cases, also at BLYP/6-31Gd, was applied to study the singlet and triplet states of the whole series. We found that the singlet state is the ground state for all oligothiophene dications up to the 20-mer, and that the singlet and triplet states are degenerate for longer oligomers. Thus, the triplet state is never a pure ground state for these dications. We found that, for short oligothiophenes dication (e.g., 6T2+), the bipolaron state is the more important state, with only a small contribution made by the polaron pair state. For medium size oligothiophene dications (e.g., 14T2+), both the bipolaron state and the polaron-pair state contribute to the electronic structure. Finally, in long oligothiophene dications, such as 30T2+ and 50T2+, the contribution from the polaron pair state becomes dominant, and these molecules can be considered as consisting of two independent cation radicals or a polaron pair. Results from isodesmic reactions show that the stability of oligothiophene cation radicals over dications is inversely proportional to chain length. Small oligothiophene dications (n = 6-12) were studied at the CASSCF(m,m)/6-31G(d) (m = 4, 6, and 10) level. The major conclusions of this paper regarding the relative energy of the singlet state versus the triplet state and regarding the relative stability of the bipolaron versus the polaron pair were also supported by CASSCF calculations.     

A meta effect in organic photochemistry? The case of SN1 reactions in methoxyphenyl derivatives

The photochemistry of isomeric methoxyphenyl chlorides and phosphates has been examined in different solvents (and in the presence of benzene) and found to involve the triplet state. With the chlorides, C-Cl bond homolysis occurs in cyclohexane and is superseded by heterolysis in polar media, while the phosphate group is detached (heterolytically) only in polar solvents. Under such conditions, the isomeric triplet methoxyphenyl cations are the first formed intermediates from both precursors, but intersystem crossing (isc) to the singlets can take place. Solvent addition (forming the acetanilide in MeCN, the ethers in alcohols, overall a SN1 solvolysis) is a diagnostic reaction for the singlet cation, as reduction and trapping by benzene are for the corresponding triplet. Solvolysis is most important with the meta isomer, for which the singlet is calculated (UB3LYP/6-31 g(d)) to be the ground state of the cation (DeltaE = 4 kcal/mol) and isc is efficient (kisc ca. 1 x 108 s-1), and occurs to some extent with the para isomer (isoenergetic spin states, kisc ca. 1.7 x 106 s-1). The triplet is the ground state with the ortho isomer, and in that case isc does not compete, although trapping by benzene is slow because of the hindering of C1 by the substituent. The position of the substituent thus determines the energetic order of the cation spin states, in particular through the selective stabilization of the singlet by the m-methoxy group, a novel case of "meta effect".     

The almost bottleable triplet carbene: 2,6-dibromo-4-tert-butyl-2',6'-bis(trifluoromethyl)-4'-isopropyldiphenylcarbene.

Computations on 2,6-dibromo-4-tert-butyl-2',6'-bis(trifluoromethyl)-4'-isopropyldiphenylcarbene (1) using ab initio and density functional theory methods underscore the unusual stability of the triplet over the singlet state. At the B3LYP/6-311G(d,p) level, the triplet state had a slightly bent central C-C-C bond angle of 167 degrees, whereas this angle in the singlet was 134 degrees. The B3LYP singlet-triplet splitting (12.2 kcal/mol) was larger than that of the parent molecule (5.8 kcal/mol), diphenylcarbene (2), which also has a triplet ground state. The energy of a suitable isodesmic reaction showed the triplet and singlet states of (1) to be destabilized, by 6.3 and 12.5 kcal/mol, respectively, due to the combined effects of the CF3, Br, and alkyl substituents. The linear-coplanar form of (3)(1), which might facilitate dimerization or electrophilic attack at the more exposed diradical center, was prohibitively (35.9 kcal/mol) higher in energy. Our results confirm Tomioka's conclusion that the triplet diarylcarbene, ortho-substituted with bulky CF3 and Br substituents, is persistent due to steric protection of the diradical center. Dimerization and other possible reaction pathways are inhibited, not only by the bulky ortho substituents but also by the para alkyl groups. The increase in stability of the triplet ((3)(1)) state relative to the singlet ((1)(1)) state does not influence the reactivity directly.     

Phenyloxenium ions: more like phenylnitrenium ions than isoelectronic phenylnitrenes?

The geometries and energies of the electronic states of phenyloxenium ion 1 (Ph-O(+)) were computed at the multireference CASPT2/pVTZ level of theory. Despite being isoelectronic to phenylnitrene 4, the phenyloxenium ion 1 has remarkably different energetic orderings of its electronic states. The closed-shell singlet configuration ((1)A(1)) is the ground state of the phenyloxenium ion 1, with a computed adiabatic energy gap of 22.1 kcal/mol to the lowest-energy triplet state ((3)A(2)). Open-shell singlet configurations ((1)A(2), (1)B(1), (1)B(2), 2(1)A(1)) are significantly higher in energy (>30 kcal/mol) than the closed-shell singlet configuration. These values suggest a revision to the current assignments of the ultraviolet photoelectron spectroscopy bands for the phenoxy radical to generate the phenyloxenium ion 1. For para-substituted phenyloxenium ions, the adiabatic singlet-triplet energy gap (ΔE(ST)) is found to have a positive linear free energy relationship with the Hammett-like σ(+)(R)/σ(+) substituent parameters; for meta substituents, the relationship is nonlinear and negatively correlated. CASPT2 analyses of the excited states of p-aminophenyloxenium ion 5 and p-cyanophenyloxenium ion 10 indicate that the relative orderings of the electronic states remain largely unperturbed for these para substitutions. In contrast, meta-donor-substituted phenyloxenium ions have low-energy open-shell states (open-shell singlet, triplet) due to stabilization of a π,π* diradical state by the donor substituent. However, all of the other phenyloxenium ions and larger aryloxenium ions (naphthyl, anthryl) included in this study have closed-shell singlet ground states. Consequently, ground-state reactions of phenyloxenium ions are anticipated to be more closely related to closed-shell singlet arylnitrenium ions (Ar-NH(+)) than their isoelectronic arylnitrene (Ar-N) counterparts.     

The beta effect of silicon in phenyl cations

Irradiation of chloroanisoles, phenols, and N,N-dimethylanilines bearing a trimethylsilyl (TMS) group in the ortho position with respect to the chlorine atom caused photoheterolysis of the Ar-Cl bond and formation of the corresponding ortho-trimethylsilylphenyl cations in the triplet state. The beta effect of silicon on these intermediates has been studied by comparing the resulting chemistry in alcoholic solvents with that of the silicon-free analogues and by computational analysis (at the UB3LYP/6-311+G(2d,p) level in MeOH). TMS groups little affect the photophysics and the photocleavage of the starting phenyl chlorides, while stabilizing the phenyl cations, both in the triplet (ca. 4 kcal/mol per group) and, dramatically, in the singlet state (9 kcal/mol). As a result, although triplet phenyl cations are the first formed species, intersystem crossing to the more stable singlets is favored with chloroanisoles and phenols. Indeed, with these compounds, solvent addition to give aryl ethers (from the singlet) competed efficiently with reduction or arylation (from the triplet). In the case of the silylated 4-chloro-N,N-dimethylaniline, the triplet cation remained in the ground state and trapping by pi nucleophiles remained efficient, though slowed by the steric bulk of the TMS group. In alcohols, the silyl group was eliminated via a photoinduced protiodesilylation during the irradiation. Thus, the silyl group could be considered as a directing, photoremovable group that allowed shifting to the singlet phenyl cation chemistry and was smoothly eliminated in the same one-pot procedure.     

Carbene stabilization by aryl substituents. Is bigger better?

The geometries and relative stabilities of the singlet and triplet states of phenyl- (Cs), diphenyl- (C2), 1-naphthyl- (Cs), di(1-naphthyl)- (C2), and 9-anthryl-substituted (Cs) carbenes were investigated at the B3LYP/6-311+G(d,p) + ZPVE level of density functional theory. The singlet-triplet energy separations (DeltaEST), 2.7, 2.9, 3.4, 3.7, and 5.7 kcal/mol, respectively, after including an empirical correction (2.8 kcal/mol) based on the error in the computed singlet-triplet gap for methylene versus experiment, are in good agreement with available experimental values. Consistent with literature reports, triplet di(9-anthryl)carbene has a linear, D2d symmetrical, allene structure with 1.336 A C=C bond lengths and considerable biradical character. B3LYP favors such cumulene biradical structures and triplet spin states and predicts a large (>15 kcal/mol) "di(9-anthryl)carbene" singlet-triplet (biradical) energy gap. The resonance stabilization of both singlet and triplet carbenes increases modestly with the size of the arene substituent and overall, (di)arylcarbenes, both singlet and triplet, are better stabilized by bigger substituents. For example, methylene is stabilized more by a naphthyl than a phenyl group (singlets, 26.6 versus 24.4; and triplets, 20.9 versus 18.1 kcal/mol, respectively). The carbene geometries are affected by both steric effects and arene-carbene orbital interactions (sigma-p and p-pi). For instance, the central angles at the carbene are widened by a second arene group, which leads to increased s-character and shorter carbene bond lengths (i.e., C-C, C-H). In general, the aromaticity of the substituted rings in triplet carbenes is most affected by the presence of the unpaired electrons.     

(Sensitized) photolysis of diazonium salts as a mild general method for the generation of aryl cations. Chemoselectivity of the singlet and triplet 4-substituted phenyl cations

The photolysis of a series of 4-X-benzenediazonium tetrafluoroborates is studied in MeCN. Loss of nitrogen occurs from the singlet excited state with X=H, t-Bu, and NMe2 and leads to the singlet aryl cation. This adds to the solvent yielding the corresponding acetanilides. With other substituents, ISC competes with (X=Br, CN) or overcomes (X=COMe, NO2) fragmentation and the aryl cation is formed in part or completely in the triplet state. In neat MeCN, this either abstracts hydrogen from the solvent (in most cases inefficiently) or undergoes intersystem crossing to the more stable singlet that reacts as above. In the presence of pi nucleophiles (allyltrimethylsilane or benzene), the triplet aryl cation is efficiently trapped giving substituted allylbenzenes and biphenyls, respectively. By triplet sensitization by xanthone, the triplet cation and the products from it are obtained from the whole series considered. The direct or sensitized photodecomposition of diazonium fluoroborates, substituted with both electron-donating and -withdrawing substituents, in the presence of alkenes and arenes offers an access to an alternative arylation procedure.     

A theoretical study of the lowest-energy singlet and triplet electronic states p-iminophosphaalkyne and nitrilimine

The equilibrium geometries and fundamental vibrational frequencies of the two energetically lowest-lying electronic states of p-iminophosphaalkyne (HCPNH) and nitrilimine (HCNNH) were determined using a split-valence basis set with polarization functions on the heavy atoms. The most extensively correlated functions used in the geometry optimizations were of the Complete Active Space Self-Consistent Field (CASSCF) variety and included eight electrons distributed among seven active orbitals for HCPNH and six active orbitals for HCNNH. The effects on predicted geometry of the size of the CASSCF active space were investigated for HCPNH and are reported. Multi-Reference Configuration Interaction with Single and Double excitations calculations have been performed at the equilibrium geometries using larger basis sets to determine more accurately the relative energetics of the electronic states. It was found that nitrilimine has the expected singlet ground state, with the triplet lying 38.5 kcal mol⁻¹ higher in energy; however, p-iminophosphaalkyne has a triplet ground state, lying 9.7 kcal mol⁻¹ below the singlet.     

Early events in the photochemistry of 2-naphthyl azide from femtosecond UV/Vis spectroscopy and quantum chemical calculations: direct observation of a very short-lived singlet nitrene

Exposure of 2-naphthyl azide in acetonitrile at ambient temperature to femtosecond pulses of 266 nm light produces a transient absorption with maxima at 350 and 420 nm. The carrier of the 350 nm band decays more rapidly than that of the 420 nm band which has a lifetime of 1.8 ps. Analogous experiments with 1-chloro-2-naphthyl azide in methanol allow the assignment of the 350 nm band to a singlet excited state of 2-naphthyl azide and the carrier of the 420 nm band to singlet 2-naphthylnitrene. This reactive intermediate has the shortest lifetime of any singlet nitrene observed to date and is a true reactive intermediate. Computational studies at the RI-CC2 level of theory support these conclusions and suggest that initial excitation populates the S2 state of 2-naphthyl azide. The S2 state, best characterized as a pi --> (pi*, aryl) transition, has a geometry similar to S0. S2 of 2-naphthyl azide can then populate the S1 state, a pi --> (in-plane, pi*, azide) excitation, and in the S1 state, electron density is depleted along the proximal N-N bond. S1 is dissociative along that N-N coordinate to form the singlet nitrene, and with a barrier of only approximately 5 kcal/mol for N2 extrusion.     

Reaction of 4-oxo-2,3,5,6-tetrafluorocyclohexa-2,5-dienylidene with acetylene: a carbene to carbene reaction.

The EPR spectrum of triplet 4-oxo-2,3,5,6-tetrafluorocyclohexa-2,5-dienylidene 1 was recorded in solid argon at 15 K. Carbene 1 reacts with acetylene under the conditions of matrix isolation yielding triplet vinylmethylene 4, which was characterized by its IR, UV-vis, and EPR spectrum. Carbene 4 is photolabile and is converted to spiro compound 5 on irradiation with lambda > 515 nm. The reaction of triplet carbene 1 with acetylene to produce triplet carbene 4 is predicted to be exothermic by 55 kcal mol(-1) at the B3LYP/6-31G(d,p) level of theory. The cis isomer is calculated to be only 0.4 kcal mol(-1) less stable than trans-4 at this level of theory. According to our calculations, singlet carbene S-4 is not a minimum on the C(8)F(4)H(2)O potential energy surface; however, at the T-4 geometry, the lowest lying singlet state is predicted to be 20.7 kcal mol(-1) higher in energy. The subsequent photochemical cyclization of T-4 yielding spiro compound 5 is exothermic by 10.3 kcal mol(-1) relative to T-4 and by 31.1 kcal mol(-1) relative to S-4. 4-Ethinyl-2,3,5,6-tetrafluorocyclohexa-2,5-dienone 9, the C-H insertion product of 1 and acetylene, was not observed experimentally, although it is favored energetically by 4.3 kcal mol(-1) over 5.     

p-Phenylenecarbenonitrene and its halogen derivatives: how does resonance interaction between a nitrene and a carbene center affect the overall electronic configuration?

A series of para-conjugatively coupled phenylenecarbenonitrenes [(4-nitrenophenyl)methylene (3a), (4-nitrenophenyl)fluoromethylene (3b), (4-nitrenophenyl)chloromethylene (3c), and (4-nitrenophenyl)bromomethylene (3d)] were generated in argon matrix at low temperature (10 or 13 K) and characterized by IR and UV/vis spectroscopy. Density functional theory (B3LYP/6-31G(d)) and ab initio (MCSCF, CASPT2) methods were used to study the ground- and some low-lying excited states of 3a-d. The experimental and computational data suggest that 3a-d have singlet ground states (S0) and can be thought of as quinonoidal biradicals. In all cases, the lowest triplet (T1) and quintet (Q1) states lie about 2 kcal mol(-1) and 28-29 kcal mol(-1), respectively, higher in energy than S0. On the other hand the substituent is found to have a significant effect on the relative energy of the second excited triplet (T2) state. This state tends to become relatively more stable as the ability of the substituent to enforce a closed-shell configuration at the carbene subunit increases. Interestingly, the energy difference between the T2 and S0 states in 3a-d is found to depend linearly on the S-T gap of the corresponding phenylcarbenes 7a-d. This relationship is helpful in predicting when a substituted p-phenylenecarbenonitrene may have a triplet ground state instead of a singlet one.     

An Argon–Oxygen Covalent Bond in the ArOH+ Molecular Ion

The OH⁺ cation is a well‐known diatomic for which the triplet (³Σ^?) ground state is 50.5 kcal mol^?1 more stable than its corresponding singlet (¹Δ) excited state. However, the singlet forms a strong donor–acceptor bond to argon with a bond energy of 66.4 kcal mol^?1 at the CCSDT(Q)/CBS level, making the singlet ArOH⁺ cation 3.9 kcal mol^?1 more stable than the lowest energy triplet complex. Both singlet and triplet isomers of this molecular ion were prepared in a cold molecular beam using different ion sources. Infrared photodissociation spectroscopy in combination with messenger atom tagging shows that the two spin isomers exhibit completely different spectral signatures. The ground state of ArOH⁺ is the predicted singlet with a covalent Ar?O bond.     

Benzylic cations with triplet ground states: computational studies of aryl carbenium ions, silylenium ions, nitrenium ions, and oxenium ions substituted with meta pi donors

Density functional theory (B3LYP/6-31G(d,p)) was used to predict the effect of meta substitution on aryl cationic (Ar-X+) species, including aryloxenium ions, arylsilylenium ions, arylnitrenium ions, and arylcarbenium ions. Multireference second-order perturbation theory (CASPT2) calculations were used to benchmark the quantitative accuracy of the DFT calculations for representative systems. Substituting the meta positions on these species with pi donors stabilizes a pi,pi* diradical state analogous to the well-known m-xylylene diradical. Notably, the 3,5-bis(N,N-dimethylamino)benzyl cation is predicted to have a triplet ground state by 1.9 kcal/mol by DFT and to have essentially degenerate singlet-triplet states at the CASPT2(10,9) level of theory. Adding electron-withdrawing CF3 groups to the exocyclic carbon of this meta-disubstituted benzyl cation further increases the predicted singlet-triplet gap in favor of the triplet. Other aryl cationic species substituted with strong pi electron-donating groups in the meta positions are predicted to have low-energy or ground-state triplet states. Systems analogous to the naphthaquinodimethane diradicals are also reported.     

Dissociative addition of water to a main group 13 metal cluster: computational study of the reaction of gallium dimer with H2O

We have investigated the lowest triplet and singlet potential energy surfaces (PESs) for the reaction of Ga(2) dimer with water. Under thermal conditions, we predict formation of the triplet ground state addition complex Ga(2)···OH(2)((3)B(1)) involving Ga···O···Ga bridge interaction. At the coupled cluster CCSD(T)/AE (CCSD(T)/ECP) computational levels, Ga(2)···OH(2)((3)B(1)) is bound by 5.5 (5.7) kcal/mol with respect to the ground state reactants Ga(2)((3)Π(u)) + H(2)O. Identification of the addition complex is in agreement with the experimental evidence from matrix isolation infrared (IR) spectroscopy reported recently by Macrae and Downs. The located minimum energy crossing points (MECPs) between the triplet and singlet energy surfaces on the entrance channel of Ga(2) + H(2)O are not expected to be energetically accessible under the matrix conditions, consistent with the lack of occurrence of Ga(2) insertion into the O-H bond under such conditions. The computed energies and harmonic and anharmonic vibrational frequencies for the triplet and singlet Ga(2)(H)(OH) insertion isomers indicate the singlet double-bridged Ga(μ-H)(μ-OH)Ga isomer to be the most stable and support the experimental IR identification of this species. The energy barrier for elimination of H(2) from the second most stable singlet HGa(μ-OH)Ga insertion isomer found to be 13.9 (12.9) kcal/mol is also consistent with the available experimental data.     

Large substituent effect on the photochemical rearrangement of 1,6-(N-Aryl)aza-[60]fulleroids to 1,2-(N-Arylaziridino)-[60]fullerenes

Large substituent effects were observed in the rates and reaction mechanisms of the photochemical rearrangement of N-arylaza-[60]fulleroid 1 to N-arylaziridino-[60]fullerene 2, in which the difference of the rates between the fastest and the slowest (>2160-fold) was attained only by changing the aryl group from 1-naphthyl to 2-naphthyl. The decreasing order of the reaction rates in relation to the substituents was 1-naphthyl (1b) > 1-pyrenyl (1d) > phenyl (1a) > 2-naphthyl (1c). The reactions proceeded via triplet states of the fulleroids and a triplet sensitization of the reaction by rearranged product 2b was observed in the case of 1b. The slow reactions of 1a,c were interpretated by the participation of charge-separated species in the excited triplet states, which was supported by nanosecond transient absorption spectra.     

Tuning Ground States of Bis(triarylamine) Dications: From a Closed‐Shell Singlet to a Diradicaloid with an Excited Triplet State

Three bis(triarylamine) dications were isolated by using weakly coordinating anions. Their electronic structures in the ground state were investigated by various experiments in conjunction with theoretical calculations. The ground‐state electronic structures of these species were tunable by substituent effects, with two of them as closed‐shell singlets and one of them as an open‐shell singlet in the solid state. The excited state of the latter is thermally accessible, indicated by EPR and SQUID measurements. The work provides a new and stable diradicaloid structure motif with an excited triplet sate.     

Modeling the photochemistry of the reference phototoxic drug lomefloxacin by steady-state and time-resolved experiments, and DFT and post-HF calculations

The irradiation in water of 1-ethyl-6,8-difluoro-7(3-methylpiperazino)3-quinolone-2-carboxylic acid (lomefloxacin), a bactericidal agent whose use is limited by its serious phototoxicity (and photomutagenicity in the mouse), leads to formation of the aryl cation in position eight that inserts into the 1-ethyl chain. Trapping of the cation was examined and it was found that chloride and bromide straightforwardly add in position eight, but with iodide and with pyrrole the 1-(2-iodoethyl) and the 1-[2-(2-pyrrolyl)ethyl] derivatives are formed. Flash photolysis reveals the triplet of lomefloxacin, a short-lived species (lambda max=370 nm, tau=40 ns) that generates the triplet cation (lambda max=480 nm, tau approximately 120 ns). The last intermediate is quenched both by halides and by pyrrole. DFT and post-HF methods have shown that the triplet is the lowest state of the cation (Delta G(ST)=13.3 kcal mol(-1)) and intersystem crossing (ISC) to the singlet has no role because a less endothermic process occurs, that is, intramolecular hydrogen abstraction from the N-ethyl chain (9.2 kcal mol(-1)) that finally leads to cyclization. The halides form weak complexes with the triplet cation (kq from 4.9 x 10(8) for Cl(-) to 7.0 x 10(9) m(-1) s(-1) for I-). With Cl(-) and Br(-) ISC occurs in the complex along with C8--X bond formation. However, this latter process is slow with bulky iodide and with neutral pyrrole, and in these cases moderately endothermic electron transfer (ca. 7 kcal mol(-1)) yielding the 8-quinolinyl radical occurs. Hydrogen exchange leads to a new radical on the 1-ethyl chain and to the observed products. These findings suggest that the mutagenic activity of the DNA-intercalated drug involves attack of the photogenerated cation to the heterocyclic bases.     

Cyclization and rearrangement reactions of a(n) fragment ions of protonated peptides

a(n) ions are frequently formed in collision-induced dissociation (CID) of protonated peptides in tandem mass spectrometry (MS/MS) based sequencing experiments. These ions have generally been assumed to exist as immonium derivatives (-HN(+)═CHR). Using a quadrupole ion trap mass spectrometer, MS/MS experiments have been performed and the structure of a(n) ions formed from oligoglycines was probed by infrared spectroscopy. The structure and isomerization reactions of the same ions were studied using density functional theory. Overall, theory and infrared spectroscopy provide compelling evidence that a(n) ions undergo cyclization and/or rearrangement reactions, and the resulting structure(s) observed under our experimental conditions depends on the size (n). The a(2) ion (GG sequence) undergoes cyclization to form a 5-membered ring isomer. The a(3) ion (GGG sequence) undergoes cyclization initiated by nucleophilic attack of the carbonyl oxygen of the N-terminal glycine residue on the carbon center of the C-terminal immonium group forming a 7-membered ring isomer. The barrier to this reaction is comparatively low at 10.5 kcal mol(-1), and the resulting cyclic isomer (-5.4 kcal mol(-1)) is more energetically favorable than the linear form. The a(4) ion with the GGGG sequence undergoes head-to-tail cyclization via nucleophilic attack of the N-terminal amino group on the carbon center of the C-terminal immonium ion, forming an 11-membered macroring which contains a secondary amine and three trans amide bonds. Then an intermolecular proton transfer isomerizes the initially formed secondary amine moiety (-CH(2)-NH(2)(+)-CH(2)-NH-CO-) to form a new -CH(2)-NH-CH(2)-NH(2)(+)-CO- form. This structure is readily cleaved at the -CH(2)-NH(2)(+)- bond, leading to opening of the macrocycle and formation of a rearranged linear isomer with the H(2)C═NH(+)-CH(2)- moiety at the N terminus and the -CO-NH(2) amide bond at the C terminus. This rearranged linear structure is much more energetically favorable (-14.0 kcal mol(-1)) than the initially formed imine-protonated linear a(4) ion structure. Furthermore, the barriers to these cyclization and ring-opening reactions are low (8-11 kcal mol(-1)), allowing facile formation of the rearranged linear species in the mass spectrometer. This finding is not limited to 'simple' glycine-containing systems, as evidenced by the IRMPD spectrum of the a(4) ion generated from protonated AAAAA, which shows a stronger tendency toward formation of the energetically favorable (-12.3 kcal mol(-1)) rearranged linear structure with the MeHC═NH(+)-CHMe- moiety at the N terminus and the -CO-NH(2) amide bond at the C terminus. Our results indicate that one needs to consider a complex variety of cyclization and rearrangement reactions in order to decipher the structure and fragmentation pathways of peptide a(n) ions. The implications this potentially has for peptide sequencing are also discussed.     

Ab initio calculations of the reaction mechanisms for metal-nitride deposition from organo-metallic precursors onto functionalized self-assembled monolayers

An atomistic mechanism has been derived for the initial stages of the adsorption reaction for metal-nitride atomic layer deposition (ALD) from alkylamido organometallic precursors of Ti and Zr on alkyltrichorosilane-based self-assembled monolayers (SAMs). The effect of altering the terminal functional group on the SAM (including -OH, -NH2, -SH, and -NH(CH3)) has been investigated using the density functional theory and the MP2 perturbation theory. Reactions on amine-terminated SAMs proceed through the formation of a dative-bond complex with an activation barrier of 16-20 kcal/mol. In contrast, thiol-terminated SAMs form weak hydrogen-bonded intermediates with activation barriers between 7 and 10 kcal/mol. The deposition of Ti organometallic precursors on hydroxyl-terminated SAMs proceeds through the formation of stronger hydrogen-bonded complexes with barriers of 7 kcal/mol. Zr-based precursors form dative-bonded adducts with near barrierless transitions. This variety allows us to select a kinetically favorable substrate for a chosen precursor. The predicted order of reactivity of differently terminated SAMs and the temperature dependence of the initial reaction probability have been confirmed for Ti-based precursors by recent experimental results. We predict that the replacement of methyl groups by trifluoromethyl groups on the SAM backbone decreases the activation barrier for amine-terminated SAMs by 5 kcal/mol. This opens a route to alter the native reactivities of a given SAM termination, in this case making amine termination energetically viable. The surface distribution of SAM molecules has a strong effect on the adsorption kinetics of Ti-based precursors. Unimolecular side decomposition reactions were found to be kinetically competitive with adsorption at 400 K.     

In Search of Singlet Phosphinidenes

We have examined singlet-triplet energy separations in different phosphinidenes (RP) substituted by first- and second-row elements, making use of ab initio molecular orbital theory. Our main purpose is to find out the substituents that particularly favor the singlet electronic state. The QCISD(T)/6-311++G(3df,2p) + ZPE level has been applied to small molecules and the CISD(Q) and QCISD(T) with the 6-311G(d,p) basis set for all species considered. We have identified few factors that come into play rendering the singlet phosphinidene more stable than the triplet. The parent phosphinidene, PH, has a triplet ground state lying 28 kcal/mol below the closed-shell singlet excited state. The triplet ground state is mainly favored when negative hyperconjugation is involved. In the boryl-, alkyl-, and silyl-substituted phosphinidenes, the triplet state remains by far the ground state. When the substituents have pi-type lone pair electrons (i.e., -NX(2), -PX(2), -OX, -SX), the singlet state becomes stabilized by such an amount that both states have similar energies or even a change in ground state occurs. The most stabilized singlet ground states are attributed to PSF and PSCl. P and S have similar p-orbital sizes, making pi-delocalization easier. Implantation of alkyl and/or amino groups in the beta-position of amino- and phosphinophosphinidenes also contributes to a singlet stabilization. Bulky beta-groups also destabilize the triplet state by a steric effect. From a practical viewpoint, amino (P-NR(2)) and phosphino (P-PR(2)) derivatives bearing large alkyl groups (R) are the most plausible and feasible targets for preparing phosphinidenes possessing a closed-shell singlet ground state.