PubMed Health⌕ Search

Biomedical subjects

Jay K Kochi

Publications and source records attributed to Jay K Kochi.

At least 19 recordsLinked to original sources
PubMed2006

Quinones as electron acceptors. X-ray structures, spectral (EPR, UV-vis) characteristics and electron-transfer reactivities of their reduced anion radicals as separated vs contact ion pairs.

Successful isolation of a series of pure (crystalline) salts of labile quinone anion radicals suitable for X-ray crystallographic analysis allows for the first time their rigorous structural distinction as "separated" ion pairs (SIPs) vs "contact" ion pairs (CIPs). The quantitative evaluation of the precise changes in the geometries of these quinones (Q) upon one-electron reduction to afford the anion radical (Q-*) is viewed relative to the corresponding (two-electron) reduction to the hydroquinone (H2Q) via the Pauling bond-length/bond-order paradigm. Structural consequences between such separated and contact ion pairs as defined in the solid state with those extant in solution are explored in the context of their spectral (EPR, UV-vis) properties and isomerization of tightly bound CIPs. Moreover, the SIP/CIP dichotomy is also examined in intermolecular interactions for rapid (self-exchange) electron transfer between Q-* and Q with second-order rate constants of kET approximately equal to 10(8) M-1 s-1, together with the spectral observation of the paramagnetic intermediates [Q,Q-*]leading to 1:1 adducts, as established by X-ray crystallography.

Anions↗
PubMed2006

The question of aromaticity in open-shell cations and anions as ion-radical offsprings of polycyclic aromatic and antiaromatic hydrocarbons.

Arene cation-radicals and anion-radicals result directly from the one-electron oxidation and reduction of many aromatic hydrocarbons, yet virtually nothing is known of their intrinsic (thermodynamic) stability and hence "aromatic character". Since such paramagnetic ion radicals lie intermediate between aromatic (Hückel) hydrocarbons with 4n + 2-electrons and antiaromatic analogues with 4n-electrons, we can now address the question of pi-delocalization in these odd-electron counterparts. Application of the structure-based "harmonic oscillator model of aromaticity" or the HOMA method leads to the surprising conclusion that the aromaticity of these rather reactive, kinetically unstable arene cation and anion radicals (as measured by the HOMA index) is actually higher than that of their (diamagnetic) parent-contrary to conventional expectations.

Journal Article↗
PubMed2006

Very fast electron migrations within p-doped aromatic cofacial arrays leading to three-dimensional (toroidal) pi-delocalization.

The charge-resonance phenomenon originally identified by Badger and Brocklehurst lies at the core of the basic understanding of electron movement and delocalization that is possible within p-doped aromatic (face-to-face) arrays. To this end, we now utilize a series of different aryl-donor groups (Ar) around a central platform to precisely evaluate the intramolecular electron movement among these tethered redox centers. As such, the unique charge-resonance (intervalence) absorption bands observed upon the one-electron oxidation or p-doping of various hexaarylbenzenoid arrays (Ar6C6) provide quantitative measures of the reorganization energy (lambda) and the electronic coupling element (H(ab)) that are required for the evaluation of the activation barrier (deltaG(ET)) for electron-transfer self-exchange according to Marcus-Hush theory. The extensive search for viable redox centers is considerably aided by the application of a voltammetric criterion that has led in this study to Ar = N,N-dialkyl-p-anilinyl, in which exceptionally low barriers are shown to lie in the range deltaG(ET) = 0.3-0.7 kcal mol(-1) for very fast electron hopping or peregrination around the hexagonal circuit among six equivalent Ar sites. Therefore, at transition temperatures T(t) > 0.5/R or roughly -20 degrees C, the electron-transfer dynamics become essentially barrierless since the whizzing occurs beyond the continuum of states and effectively achieves complete pi-delocalization.

Journal Article↗
PubMed2005

Characterizing the dimerizations of phenalenyl radicals by ab initio calculations and spectroscopy: sigma-bond formation versus resonance pi-stabilization.

Electronic-structure calculations for the self-association of phenalenyl radical (P*) predict the formation of dimeric species (sigma-P2) in which both moieties are connected by a sigma-bond with rP-P approximately 1.59 A and bond dissociation enthalpy of DeltaH(D) approximately 16 kcal mol(-1). Such an unusually weak sigma-bond is related to the loss of aromatic stabilization energy of approximately 34 kcal mol(-1) per phenalenyl moiety, largely owing to rehybridization. Ab initio calculations also reveal that the corresponding (one-electron) bond between phenalenyl radical and its closed-shell cation in sigma-P2+* is unstable relative to dissociation. Time-dependent DFT computations indicate the absence of any (strongly allowed) electronic transition in the visible region of the absorption spectrum of phenalenyl sigma-dimer. Such theoretical predictions are supported by experimental (ESR and UV-NIR) spectroscopic studies, in which the availability of a series of sterically hindered phenalenyl radicals allows definitive separations of the sigma-dimerization process from interference by pi-dimerization. As such, the thermodynamic parameters (determined from the temperature dependence of the ESR signals) with DeltaH(D) = 14 kcal mol(-1) and DeltaS(D) = 52 e.u. can be assigned to the formation of the colorless sigma-dimer. Similar results are obtained for all phenalenyl derivatives (provided their substitution patterns allow sigma-bond formation) to confirm the energetic preference of sigma-dimerization over pi-dimerization.

Journal Article↗
PubMed2005

Crystallographic view of fluidic structures for room-temperature ionic liquids: 1-butyl-3-methylimidazolium hexafluorophosphate.

Shock-induced crystallization of the supercooled ionic liquid 1-butyl-3-methylimidazolium hexafluorophosphate, C8H15N2+.PF6-, allows for the first time precise X-ray diffraction analysis directly pertinent to the fluid state. This intermediate-chain-length structure shows features of both short- and long-chain analogs. Two types of interplanar distances between imidazolium rings are observed. The anions are located in channels formed by the imidazolium rings and alkyl chains.

Journal Article↗
PubMed2005

Intermolecular electron-transfer mechanisms via quantitative structures and ion-pair equilibria for self-exchange of anionic (dinitrobenzenide) donors.

Definitive X-ray structures of "separated" versus "contact" ion pairs, together with their spectral (UV-NIR, ESR) characterizations, provide the quantitative basis for evaluating the complex equilibria and intrinsic (self-exchange) electron-transfer rates for the potassium salts of p-dinitrobenzene radical anion (DNB(-)). Three principal types of ion pairs, K(L)(+)DNB(-), are designated as Classes S, M, and C via the specific ligation of K(+) with different macrocyclic polyether ligands (L). For Class S, the self-exchange rate constant for the separated ion pair (SIP) is essentially the same as that of the "free" anion, and we conclude that dinitrobenzenide reactivity is unaffected when the interionic distance in the separated ion pair is r(SIP) > or =6 Angstroms. For Class M, the dynamic equilibrium between the contact ion pair (with r(CIP) = 2.7 Angstroms) and its separated ion pair is quantitatively evaluated, and the rather minor fraction of SIP is nonetheless the principal contributor to the overall electron-transfer kinetics. For Class C, the SIP rate is limited by the slow rate of CIP right arrow over left arrow SIP interconversion, and the self-exchange proceeds via the contact ion pair by default. Theoretically, the electron-transfer rate constant for the separated ion pair is well-accommodated by the Marcus/Sutin two-state formulation when the precursor in Scheme 2 is identified as the "separated" inner-sphere complex (IS(SIP)) of cofacial DNB(-)/DNB dyads. By contrast, the significantly slower rate of self-exchange via the contact ion pair requires an associative mechanism (Scheme 3) in which the electron-transfer rate is strongly governed by cationic mobility of K(L)(+) within the "contact" precursor complex (IS(CIP)) according to the kinetics in Scheme 4.

Journal Article↗
PubMed2005

"Separated" versus "contact" ion-pair structures in solution from their crystalline states: dynamic effects on dinitrobenzenide as a mixed-valence anion.

Qualitative structural concepts about dynamic ion pairs, historically deduced in solution as labile solvent-separated and contact species, are now quantified by the low-temperature isolation of crystalline (reactive) salts suitable for direct X-ray analysis. Thus, dinitrobenzenide anion (DNB(-)) can be prepared in the two basic ion-paired forms by potassium-mirror reduction of p-dinitrobenzene in the presence of macrocyclic polyether ligands: L(C) (cryptand) and L(E) (crown-ethers). The crystalline "separated" ion-pair salt isolated as K(L(C))(+)//DNB(-) is crystallographically differentiated from the "contact" ion-pair salt isolated as K(L(E))(+)DNB(-) by their distinctive interionic separations. Spectral analysis reveals pronounced near-IR absorptions arising from intervalence transitions that characterize dinitrobenzenide to be a prototypical mixed-valence anion. Most importantly, the unique patterns of vibronic (fine-structure) progressions that also distinguish the "separated" from the "contact" ion pair in the crystalline solid state are the same as those dissolved into THF solvent and ensure that the same X-ray structures persist in solution. Moreover, these distinctive NIR patterns are assigned with the aid of Marcus-Hush (two-state) theory to the "separated"ion pair in which the unpaired electron is equally delocalized between both NO(2)-centers in the symmetric ground state of dinitrobenzenide, and by contrast, the asymmetric electron distribution inherent to "contact"ion pairs favors only that single NO(2)-center intimately paired to the counterion. The labilities of these dynamic ion pairs in solution are thoroughly elucidated by temperature-dependent ESR spectral changes that provide intimate details of facile isomerizations, ionic separations, and counterion-mediated exchanges.

Journal Article↗
PubMed2004

Intermolecular pi-to-pi bonding between stacked aromatic dyads. Experimental and theoretical binding energies and near-IR optical transitions for phenalenyl radical/radical versus radical/cation dimerizations.

The high symmetry and stability of phenalenyl systems, both as the planar pi-radical (P*) and as the pi-cation (P+), are desirable characteristics of prototypical aromatic donor/acceptor pairs that encourage their use as (binary) models for the study of intermolecular interactions extant in stacked molecular arrays. Thus, quantitative ESR spectroscopy of the paramagnetic P* identifies its spontaneous self-association to the diamagnetic P2, previously characterized as the stacked pi-dimer by X-ray crystallography. Likewise, the rapid cross-association of P* with the closed-shell P+ leads to the stacked pi-dimer cation P2*+ with the "doubled" ESR spectrum diagnostic of complete (odd) electron delocalization. These pi-associations are confirmed by UV-vis studies that reveal diagnostic near-IR bands of both P2 and P2*+-strongly reminiscent of intermolecular charge-transfer absorptions in related aromatic (donor/acceptor) pi-associations. Ab initio molecular-orbital calculations for the pi-dimer P2 predict a binding energy of DeltaED = -11 kcal mol(-1), which is in accord with the experimental enthalpy change of DeltaHD = -9.5 kcal mol(-1) in dichloromethane solution. Most importantly, the calculations reproduce the intermonomer spacings and reveal the delicate interplay of attractive covalent and dispersion forces, balanced against the repulsions between filled orbitals. For comparison, the binding energy in the structurally related cationic pi-pimer P2*+ is calculated to be significantly larger with DeltaEP approximately -20 kcal mol(-1) (gas phase), owing to favorable electrostatic interactions not present in the neutral pi-dimer (which outweigh the partial loss of covalent interactions). As a result, our theoretical formulation can correctly account for the experimental enthalpy change in solution of DeltaHP = -6.5 kcal mol(-1) by the inclusion of differential ionic solvation in the formation of the pi-pimer.

Journal Article↗
PubMed2004

Crystallographic distinction between "contact" and "separated" ion pairs: structural effects on electronic/ESR spectra of alkali-metal nitrobenzenides.

The classic nitrobenzene anion-radical (NB(-*) or nitrobenzenide) is isolated for the first time as pure crystalline alkali-metal salts. The deliberate use of the supporting ligands 18-crown-6 and [2.2.2]cryptand allows the selective formation of contact ion pairs designated as (crown)M(+)NB(-*), where M(+) = K(+), Rb(+), and Cs(+), as well as the separated ion pair K(cryptand)(+)NB(-*)-both series of which are structurally characterized by precise low-temperature X-ray crystallography, ESR analysis, and UV-vis spectroscopy. The unusually delocalized structure of NB(-*) in the separated ion pair follows from the drastically shortened N-C bond and marked quinonoidal distortion of the benzenoid ring to signify complete (95%) electronic conjugation with the nitro substituent. On the other hand, the formation of contact ion pairs results in the substantial decrease of electronic conjugation in inverse order with cation size (K(+) > Rb(+)) owing to increased localization of negative charge from partial (NO(2)) bonding to the alkali-metal cation. Such a loss in electronic conjugation (or reverse charge transfer) may be counterintuitive, but it is in agreement with the distribution of odd-electron spin electron density from the ESR data and with the hypsochromic shift of the characteristic absorption band in the electronic spectra. Most importantly, this crystallographic study underscores the importance of ion-pair structure on the intrinsic property (and thus reactivity) of the component ions-as focused here on the nitrobenzenide anion.

Journal Article↗
PubMed2004

Donor-acceptor (electronic) coupling in the precursor complex to organic electron transfer: intermolecular and intramolecular self-exchange between phenothiazine redox centers.

Intermolecular electron transfer (ET) between the free phenothiazine donor (PH) and its cation radical (PH*+) proceeds via the [1:1] precursor complex (PH)(2)*+ which is transiently observed for the first time by its diagnostic (charge-resonance) absorption band in the near-IR region. Similar intervalence (optical) transitions are also observed in mixed-valence cation radicals with the generic representation: P(br)P*+, in which two phenothiazine redox centers are interlinked by p-phenylene, o-xylylene, and o-phenylene (br) bridges. Mulliken-Hush analysis of the intervalence (charge-resonance) bands afford reliable values of the electronic coupling element H(IV) based on the separation parameters for (P/P*+) centers estimated from some X-ray structures of the intermolecular (PH)(2)*+ and the intramolecular P(br)P*+ systems. The values of H(IV), together with the reorganization energies lambda derived from the intervalence transitions, yield activation barriers DeltaG(ET)() and first-order rate constants k(ET) for electron-transfer based on the Marcus-Hush (two-state) formalism. Such theoretically based values of the intrinsic barrier and ET rate constants agree with the experimental activation barrier (E(a)) and the self-exchange rate constant (k(SE)) independently determined by ESR line broadening measurements. This convergence validates the use of the two-state model to adequately evaluate the critical electronic coupling elements between (P/P*+) redox centers in both (a) intermolecular ET via the precursor complex and (b) intramolecular ET within bridged mixed-valence cation radicals. Important to intermolecular ET mechanism is the intervention of the strongly coupled precursor complex since it leads to electron-transfer rates of self-exchange that are 2 orders of magnitude faster (and activation barrier that is substantially lower) than otherwise predicted solely on the basis of Marcus reorganization energy.

Journal Article↗
PubMed2003

Stable (long-bonded) dimers via the quantitative self-association of different cationic, anionic, and uncharged pi-radicals: structures, energetics, and optical transitions.

Unusual dimers with wide interplanar separations, that is, very long bonds with d(D) approximately 3.05 A, are common to the spontaneous self-association of various organic pi-radicals in solution and in the crystalline solid state, independent of whether they are derived from negatively charged anion radicals of planar electron acceptors (TCNE-*, TCNQ-*, DDQ-*, CA-*), positively charged biphenylene cation-radical (OMB+*), or neutral phenalene radical (PHEN*). All dimeric species are characterized by intense absorption bands in the near-IR region that are diagnostic of the charge-transfer transitions previously identified with intermolecular associations of various electron-donor/acceptor dyads. The extensive delocalizations of a pair of pi-electrons accord with the sizable values of (i) the enthalpies (-Delta H(D)) and entropies (-Delta S(D)) of pi-dimerization measured by quantitative UV-vis/EPR spectroscopies and (ii) the electronic coupling element H(ab) evaluated from the strongly allowed optical transitions, irrespective of whether the diamagnetic dimeric species bear a double-negative charge as in (TCNE)(2)(2-), (TCNQ)(2)(2-), (DDQ)(2)(2-), (CA)(2)(2-) or a double-positive charge as in (OMB)(2)(2+) or are uncharged as in (PHEN)(2). These long-bonded dimers persist in solution as well as in the solid state and suffer only minor perturbations with Delta d(D) < 10% from extra-dimer forces that may be imposed by counterion electrostatics, crystal packing, and so forth. The characteristic optical transitions in such diamagnetic two-electron dimers are shown to be related to those in the corresponding paramagnetic one-electron pimers of the same pi-radicals with their parent acceptor, both in general accord with Mulliken theory.

Journal Article↗
PubMed2003

The charge-transfer motif in crystal engineering. Self-assembly of acentric (diamondoid) networks from halide salts and carbon tetrabromide as electron-donor/acceptor synthons.

Unusual strength and directionality for the charge-transfer motif (established in solution) are shown to carry over into the solid state by the facile synthesis of a series of robust crystals of the [1:1] donor/acceptor complexes of carbon tetrabromide with the electron-rich halide anions (chloride, bromide, and iodide). X-ray crystallographic analyses identify the consistent formation of diamondoid networks, the dimensionality of which is dictated by the size of the tetraalkylammonium counterion. For the tetraethylammonium bromide/carbon tetrabromide dyad, the three-dimensional (diamondoid) network consists of donor (bromide) and acceptor (CBr(4)) nodes alternately populated to result in the effective annihilation of centers of symmetry in agreement with the sphaleroid structural subclass. Such inherently acentric networks exhibit intensive nonlinear optical properties in which the second harmonics generation in the extended charge-transfer system is augmented by the effective electronic (HOMO-LUMO) coupling between contiguous CBr(4)/halide centers.

Journal Article↗
PubMed2003

Charge-transfer mechanism for electrophilic aromatic nitration and nitrosation via the convergence of (ab initio) molecular-orbital and Marcus-Hush theories with experiments.

The highly disparate rates of aromatic nitrosation and nitration, despite the very similar (electrophilic) properties of the active species: NO(+) and NO(2)(+) in Chart 1, are quantitatively reconciled. First, the thorough mappings of the potential-energy surfaces by high level (ab initio) molecular-orbital methodologies involving extensive coupled-cluster CCSD(T)/6-31G optimizations establish the intervention of two reactive intermediates in nitration (Figure 8) but only one in nitrosation (Figure 7). Second, the same distinctive topologies involving double and single potential-energy minima (Figures 6 and 5) also emerge from the semiquantitative application of the Marcus-Hush theory to the transient spectral data. Such a striking convergence from quite different theoretical approaches indicates that the molecular-orbital and Marcus-Hush (potential-energy) surfaces are conceptually interchangeable. In the resultant charge-transfer mechanism, the bimolecular interactions of arene donors with both NO(+) and NO(2)(+) spontaneously lead (barrierless) to pi-complexes in which electron transfer is concurrent with complexation. Such a pi-complex in nitration is rapidly converted to the sigma-complex, whereas this Wheland adduct in nitrosation merely represents a high energy (transition-state) structure. Marcus-Hush analysis thus demonstrates how the strongly differentiated (arene) reactivities toward NO(+) and NO(2)(+) can actually be exploited in the quantitative development of a single coherent (electron-transfer) mechanism for both aromatic nitrosation and nitration.

Journal Article↗
PubMed2003

Isolation of the latent precursor complex in electron-transfer dynamics. Intermolecular association and self-exchange with acceptor anion radicals.

Transient [1:1] complexes formed in the bimolecular interactions of electron acceptors (A) with their reduced anion radicals (A(-.)) are detected and characterized in solution for the first time. The recognition of such metastable intermediates as the heretofore elusive precursor complex (A(2)(-.)) in electron-transfer processes for self-exchange allows the principal parameters lambda (Marcus reorganization energy) and H(DA) (electronic coupling element) to be experimentally determined from the optical (charge-transfer) transitions inherent to these intermolecular complexes. The satisfactory correspondence of the theoretically predicted with the experimentally observed rate constants validates these ET parameters and the Marcus-Hush-Sutin methodology for strongly coupled redox systems lying in the (Robin-Day) Class II category. Most importantly, the marked intermolecular electronic interaction (H(DA)) within these precursor complexes must be explicitly recognized, since it dramatically affects the electron-transfer dynamics by effectively lowering the activation barrier. As such, the numerous calculations of the reorganization energy previously obtained from various self-exchange kinetics based on lambda = 4DeltaG must be reconsidered in the light of such a precursor complex, with the important result that ET rates can be substantially faster than otherwise predicted. On the basis of these studies, a new mechanistic criterion is proposed for various outer-sphere/inner-sphere ET processes based on the relative magnitudes of H(DA) and lambda.

Journal Article↗
PubMed2002

Molecular structures of cation...pi(arene) interactions for alkali metals with pi- and sigma-modalities.

The monovalent cations of Na(+), K(+), Rb(+), and Cs(+) derived from the highly electropositive alkali metals represent prototypical charged spheres that are mainly subject to relatively simple electrostatic and solvation (hydration) forces. We now find that the largest of these Rb(+) and Cs(+) are involved in rather strong cation...pi(arene) interactions when they are suitably disposed with the ambifunctional hexasubstituted benzene C(6)E(6). The ether tentacles (E = methoxymethyl) allow these cations to effect eta(1)-bonding to the benzene center in a manner strongly reminiscent of the classical sigma-arene complexes with positively charged electrophiles where Z(+) = CH(3)(+), Br(+), Cl(+), Et(3)Si(+), etc. The somewhat smaller potassium cation is involved in a similar M(+)...pi(arene) interaction that leads to eta(2)-bonding with the aromatic center in the pi-mode previously defined in the well-known series of silver(I)/arene complexes. We can find no evidence for significant Na(+)... pi(arene) interaction under essentially the same conditions. As such, the sigma-structure of the Rb(+) and Cs(+) complexes and pi-structure of the K(+) complex are completely integrated into the continuum of sigma-pi bondings of various types of electrophilic (cationic) acceptors with arene donors that were initially identified by Mulliken as charge-transfer.

Journal Article↗