Co-reporter:Ethan Zars;Joseph Schell;Marco A. Delarosa
Journal of Solution Chemistry 2017 Volume 46( Issue 3) pp:643-662
Publication Date(Web):2017 March
DOI:10.1007/s10953-017-0593-z
We recently described a dynamical approach to the equilibrium problem that involves the formulation of the kinetic rate equations for each species. The equilibrium concentrations are determined by evolving the initial concentrations via this dynamical system to their steady state values. This dynamical approach is particularly attractive because it can be extended easily to very large multi-equilibria systems and the effects of ionic strength also are easily included. Here we describe mathematical methods for the determination of steady state concentrations of all species with the consideration of their activities using several approximations of Debye–Hückel theory of electrolyte solutions. We describe the equations for a system that consists of a triprotic acid H3A and its conjugate bases. With these equations, two types of multi-equilibria systems were studied and compared to experimental data. The first system is exemplified by case studies of solutions of acetate-buffered acetic acid and the second system is exemplified by the hydroxide titration of citric acid. The discussion focuses on the effect of ionic strength on pH and on the amplification of acidity by ionic strength. Ionic strength effects are shown to cause significant deviations from the widely used Henderson–Hasselbalch equation.
Co-reporter:X.J. Yang, R. Glaser, Aigen Li, J.X. Zhong
New Astronomy Reviews 2017 Volume 77(Volume 77) pp:
Publication Date(Web):1 April 2017
DOI:10.1016/j.newar.2017.01.001
The unidentified infrared emission (UIE) features at 3.3, 6.2, 7.7, 8.6, 11.3 and 12.7 µ m are ubiquitously seen in a wide variety of astrophysical regions in the Milky Way and nearby galaxies as well as distant galaxies at redshifts z ≳ 4. The UIE features are characteristic of the stretching and bending vibrations of aromatic hydrocarbon materials. The 3.3 µ m feature which results from the C–H stretching vibration in aromatic species is often accompanied by a weaker feature at 3.4 µ m. The 3.4 µ m feature is often thought to result from the C–H stretch of aliphatic groups attached to the aromatic systems. The ratio of the observed intensity of the 3.3 µ m aromatic C–H feature (I3.3) to that of the 3.4 µ m aliphatic C–H feature (I3.4) allows one to estimate the aliphatic fraction (e.g., NC, aliph/NC, arom, the number of C atoms in aliphatic units to that in aromatic rings) of the carriers of the UIE features, provided that the intrinsic oscillator strengths (per chemical bond) of the 3.3 µ m aromatic C–H stretch (A3.3) and the 3.4 µ m aliphatic C–H stretch (A3.4) are known. In this review we summarize the computational results on A3.3 and A3.4 and their implications for the aromaticity and aliphaticity of the UIE carriers. We use density functional theory and second-order perturbation theory to derive A3.3 and A3.4 from the infrared vibrational spectra of seven polycyclic aromatic hydrocarbon (PAH) molecules with various aliphatic substituents (e.g., methyl-, dimethyl-, ethyl-, propyl-, butyl-PAHs, and PAHs with unsaturated alkyl chains). The mean band strengths of the aromatic (A3.3) and aliphatic (A3.4) C–H stretches are derived and then employed to estimate the aliphatic fraction of the carriers of the UIE features by comparing the ratio of the intrinsic band strength of the two stretches (A3.4/A3.3) with the ratio of the observed intensities (I3.4/I3.3). We conclude that the UIE emitters are predominantly aromatic, as revealed by the observationally-derived mean ratio of ⟨I3.4/I3.3⟩ ≈ 0.12 and the computationally-derived mean ratio of ⟨A3.4/A3.3⟩ ≈ 1.76 which suggest an upper limit of NC, aliph/NC, arom ≈ 0.02 for the aliphatic fraction of the UIE carriers.
Co-reporter:Rainer Glaser, Roman Hillebrand, Wei Wycoff, Cory Camasta, and Kent S. Gates
The Journal of Organic Chemistry 2015 Volume 80(Issue 9) pp:4360-4369
Publication Date(Web):April 17, 2015
DOI:10.1021/acs.joc.5b00080
1H and 13C NMR spectra of allyl isothiocyanate (AITC) were measured, and the exchange dynamics were studied to explain the near-silence of the ITC carbon in 13C NMR spectra. The dihedral angles α = ∠(C1–C2–C3–N4) and β = ∠(C2–C3–N4–C5) describe the conformational dynamics (conformation change), and the bond angles γ = ∠(C3–N4–C5) and ε = ∠(N4–C5–S6) dominate the molecular dynamics (conformer flexibility). The conformation space of AITC contains three minima, Cs-M1 and enantiomers M2 and M2′; the exchange between conformers is very fast, and conformational effects on 13C chemical shifts are small (νM1 – νM2 < 3 ppm). Isotropic chemical shifts, ICS(γ), were determined for sp, spx, and sp2 N-hybridization, and the γ dependencies of δ(N4) and δ(C5) are very large (10–33 ppm). Atom-centered density matrix propagation trajectories show that every conformer can access a large region of the potential energy surface AITC(γ,ε,...) with 120° < γ < 180° and 155° < ε < 180°. Because the extreme broadening of the 13C NMR signal of the ITC carbon is caused by the structural flexibility of every conformer of AITC, the analysis provides a general explanation for the near-silence of the ITC carbon in 13C NMR spectra of organic isothiocyanates.
Co-reporter:Rainer E. Glaser, Marco A. Delarosa, Ahmed Olasunkanmi Salau, and Carmen Chicone
Journal of Chemical Education 2014 Volume 91(Issue 7) pp:1009-1016
Publication Date(Web):May 15, 2014
DOI:10.1021/ed400808c
Mathematical methods are described for the determination of steady-state concentrations of all species in multiequilibria systems consisting of several acids and their conjugated bases in aqueous solutions. The main example consists of a mixture of a diprotic acid H2A, a monoprotic acid HB, and their conjugate bases. The reaction equations lead to a system of autonomous ordinary differential equations for the species concentrations. The traditional equilibrium approach is briefly reviewed. Single variable polynomials are determined that are satisfied by the equilibrium proton concentrations. The remaining species are then given explicitly by rational functions of these proton concentrations, the equilibrium constants, and the initial concentrations of the other species. A quintic polynomial was derived to determine the equilibrium proton concentration for the example system. It is shown to reduce to a quartic polynomial in the absence of the second acid HB. An alternative dynamical approach to the equilibrium problem is described that involves the formulation of the kinetic rate equations for each species, which together constitute a nonlinear system of ordinary differential equations. The equilibrium concentrations are determined by evolving the initial concentrations via this dynamical system to their steady state. This dynamical approach is particularly attractive because it can easily be extended to determine equilibrium concentrations for arbitrarily large multiequilibria systems. With the equations provided here and some knowledge of computing software, the fast and accurate computation of equilibrium concentrations becomes feasible for the education of upper-division undergraduate and graduate students as well as for the study of research problems. This dynamical method also serves to introduce students to nonlinear dynamical systems, which are essential for the study of dynamic problems in chemistry, for example, oscillatory reactions.Keywords: Acids/Bases; Computer-Based Learning; Equilibrium; Graduate Education/Research; Interdisciplinary/Multidisciplinary; Mathematics/Symbolic Mathematics; Upper-Division Undergraduate;
Co-reporter:Rainer Glaser ;Cory Camasta
Inorganic Chemistry 2013 Volume 52(Issue 20) pp:11806-11820
Publication Date(Web):October 3, 2013
DOI:10.1021/ic4011967
The results are reported of an ab initio study of bromine dioxide BrO2, 1, and of the T-shaped trans- and cis-dihydroxides 2 and 3 of dihydrogen bromate (HO)2BrO. The thermochemistry has been explored of potential synthetic routes to (HO)2BrO involving water addition to BrO2, hydroxyl addition to bromous acid HOBrO, 4, protonation/reduction of bromic acid HOBrO2, 5, via tautomers 6–8 of protonated bromic acid, and by reduction/protonation of bromic acid via radical anion [HOBrO2]−, 9. The potential energy surface analyses were performed at the MP2(full)/6-311G* level (or better) and with the consideration of aqueous solvation at the SMD(MP2(full)/6-311G*) level (or better), and higher-level energies were computed at levels up to QCISD(full,T)/6-311++G(2df,2pd)//MP2. The addition of RO radical to bromous acid or bromite esters and the reduction of protonated bromic acid or protonated bromate esters are promising leads for possible synthetic exploration. Spin density distributions and molecular electrostatic potentials were computed at the QCISD(full)/6-311G*//MP2(full)/6-311G* level to characterize the electronic structures of 1–3. Both radicals employ maximally occupied (pseudo) π-systems to transfer electron density from bromine to the periphery. While the formation of the (3c-5e) π-system suffices to avoid hypervalency in 1, the formation of the (4c-7e) π-system in 2 or 3 still leaves the bromine formally hypervalent and (HO)2BrO requires delocalization of bromine density into σ*-SMOs over the trans O–Br–O moiety. Molecular orbital theory is employed to describe the mechanisms for the avoidance of hypervalency and for spin delocalization and spin polarization. The (4c-7e) π-system in 2 is truly remarkable in that it contains five π-symmetric spin molecular orbitals (SMO) with unique shapes.
Co-reporter:Rainer Glaser, Laura Ulmer, and Stephanie Coyle
The Journal of Organic Chemistry 2013 Volume 78(Issue 3) pp:1113-1126
Publication Date(Web):January 17, 2013
DOI:10.1021/jo302527k
The results are reported of an ab initio study of the addition of LiAlH4 to acetonitrile and malononitrile at the MP2(full)/6-311+G* level considering the effects of electron correlation at higher levels up to QCISD(T)/6-311++G(2df,2pd) and including ether solvation. All imide (RCH2CH═N–) and enamide (RCH–CH═NH ↔ RCH═CHN–H) adducts feature strong interactions between the organic anion and both Li+ and AlH3. The relative stabilities of the tautomeric LAH adducts are compared to the tautomer preference energies of the LiH adducts and of the hydride adducts of the nitriles. Alane affinities were determined for the lithium ion pairs formed by LiH addition to the nitriles. The results show that alane binding greatly affects the imide–enamide equilibria and that alane complexation might even provide a thermodynamic preference for the imide intermediate. While lithium enamides of malononitrile are much more stable than lithium imides, alane binding dramatically reduces the enamide preference so that both tautomers are present at equilibrium. Implications are discussed regarding to the propensity for multiple hydride reductions and with regard to the mechanism of reductive nitrile dimerization. A detailed mechanism is proposed for the formation of 2-aminonicotinonitrile (2ANN) in the LAH reduction of malononitrile.
Co-reporter:Jian Yin, Rainer Glaser, and Kent S. Gates
Chemical Research in Toxicology 2012 Volume 25(Issue 3) pp:620
Publication Date(Web):March 5, 2012
DOI:10.1021/tx2005458
Tirapazamine (TPZ, 1, 3-amino-1,2,4-benzotriazine 1,4-N,N-dioxide), the radical anion 2 formed by one-electron reduction of 1, and neutral radicals 3 and 4 formed by protonation of 2 at O(N4) or O(N1), respectively, and their N–OH homolyses 3 → 5 + ·OH and 4 → 6 + ·OH have been studied with configuration interaction theory, perturbation theory, and density functional theory. A comprehensive comparative analysis is presented of structures and electronic structures and with focus on the development of an understanding of the spin-density distributions of the radical species. The skeletons of radicals 3 and 4 are distinctly nonplanar, several stereoisomeric structures are discussed, and there exists an intrinsic preference for 3 over 4. The N-oxides 1, 5, and 6 have closed-shell singlet ground states and low-lying, singlet biradical (SP-1, SP-6) or biradicaloid (SP-5) excited states. The doublet radicals 2, 3, and 4 are heavily spin-polarized. Most of the spin density of the doublet radicals 2, 3, and 4 is located in one (N,O)-region, and in particular, 3 and 4 are not C3-centered radicals. Significant amounts of spin density occur in both rings in the singlet biradical(oid) excited states of 1, 5, and 6. The dipole moment of the N2–C3(X) bond is large, and the nature of X provides a powerful handle to modulate the N2–C3 bond polarity with opposite effects on the two NO regions. Our studies show very low proton affinities of radical anion 2 and suggest that the pKa of radical [2+H] might be lower than 6. Implications are discussed regarding the formation of hydroxyl from 3 and/or 4, regarding the ability of 5 and 6 to react with carbon-centered radicals in a manner that ultimately leads to oxygen transfer, and regarding the interpretation of the EPR spectra of reduced TPZ species and of their spin-trap adducts.
Co-reporter:Jian Yin, Rainer Glaser, and Kent S. Gates
Chemical Research in Toxicology 2012 Volume 25(Issue 3) pp:634
Publication Date(Web):March 5, 2012
DOI:10.1021/tx200546u
The initial steps of the activation of tirapazamine (TPZ, 1, 3-amino-1,2,4-benzotriazine 1,4-N,N-dioxide) under hypoxic conditions consist of the one-electron reduction of 1 to radical anion 2 and the protonation of 2 at O(N4) or O(N1) to form neutral radicals 3 and 4, respectively. There are some questions, however, as to whether radicals 3 and/or 4 will then undergo N–OH homolyses 3 → 5 + ·OH and 4 → 6 + ·OH or, alternatively, whether 3 and/or 4 may react by dehydration and form aminyl radicals via 3 → 11 + H2O and 4 → 12 + H2O or phenyl radicals via 3 → 17 + H2O. These outcomes might depend on the chemistry after the homolysis of 3 and/or 4, that is, dehydration may be the result of a two-step sequence that involves N–OH homolysis and formation of ·OH aggregates of 5 and 6 followed by H-abstraction within the ·OH aggregates to form hydrates of aminyls 11 and 12 or of phenyl 17. We studied these processes with configuration interaction theory, perturbation theory, and density functional theory. All stationary structures of OH aggregates of 5 and 6, of H2O aggregates of 11, 12, and 17, and of the transition state structures for H-abstraction were located and characterized by vibrational analysis and with methods of electron and spin-density analysis. The doublet radical 17 is a normal spin-polarized radical, whereas the doublet radicals 11 and 12 feature quartet instabilities. The computed reaction energies and activation barriers allow for dehydration in principle, but the productivity of all of these channels should be low for kinetic and dynamic reasons. With a view to plausible scenarios for the generation of latent aryl radical species without dehydration, we scanned the potential energy surfaces of 2–4 as a function of the (O)N1–Y (Y = C5a, N2) and (O)N4–Z (Z = C4a, C3) bond lengths. The elongation of any one of these bonds by 0.5 Å requires less than 25 kcal/mol, and this finding strongly suggests the possibility of bimolecular reactions of the spin-trap molecules with 2–4 concomitant with triazene ring-opening.
Co-reporter:Rainer Glaser and Kaitlan Prugger
Journal of Agricultural and Food Chemistry 2012 Volume 60(Issue 7) pp:1776-1787
Publication Date(Web):February 8, 2012
DOI:10.1021/jf2037906
The results are reported of a theoretical study of iodomethane (H3C–I, 1) and chloropicrin (Cl3C–NO2, 2), of the heterodimers 3–6 formed by aggregation of 1 and 2, and of their addition products 7 and 8 and their possible fragmentation reactions to 9–18. Mixtures of iodomethane and chloropicrin are not expected to show chemistry resulting from their reactions with each other. The structures and stabilities are discussed of the iodine-bonded molecular aggregates (IBMA) 3 and 4 and of the hydrogen- and iodine-bonded molecular aggregates (IHBMA) 5 and 6. The mixed aggregates 3–5 are bound on the free enthalpy surface relative to the homodimers of 1 and 2, and the IBMA structures 3 and 4 are most stable. This result suggests that the mixture of chloropicrin and iodomethane in the pesticide Midas is a good choice to reduce the volatility of iodomethane because of thermodynamically stabilizing iodine bonding.
Co-reporter:Rainer Glaser and Mary Jost
The Journal of Physical Chemistry A 2012 Volume 116(Issue 32) pp:8352-8365
Publication Date(Web):August 7, 2012
DOI:10.1021/jp301329g
The results are reported of an ab initio study of the thermochemistry and of the kinetics of the HOBrO disproportionation reaction 2HOBrO (2) ⇄ HOBr (1) + HBrO3 (3), reaction (R4′), in gas phase (MP2(full)/6-311G*) and aqueous solution (SMD(MP2(full)/6-311G*)). The reaction energy of bromous acid disproportionation is discussed in the context of the coupled reaction system R2–R4 of the FKN mechanism of the Belousov–Zhabotinsky reaction and considering the acidities of HBr and HOBrO2. The structures were determined of ten dimeric aggregates 4 of bromous acid, (HOBrO)2, of eight mixed aggregates 5 formed between the products of disproportionation, (HOBr)(HOBrO2), and of four transition states structures 6 for disproportionation by direct O-transfer. It was found that the condensation of two HOBrO molecules provides facile access to bromous acid anhydride 7, O(BrO)2. A discussion of the potential energy surface of Br2O3 shows that O(BrO)2 is prone to isomerization to the mixed anhydride 8, BrO–BrO2, and to dissociation to 9, BrO, and 10, BrO2, and their radical pair 11. Hence, three possible paths from O(BrO)2 to the products of disproportionation, HOBr and HOBrO2, are discussed: (1) hydrolysis of O(BrO)2 along a path that differs from its formation, (2) isomerization of O(BrO)2 to BrO–BrO2 followed by hydrolysis, and (3) O(BrO)2 dissociation to BrO and BrO2 and their reactions with water. The results of the potential energy surface analysis show that the rate-limiting step in the disproportionation of HOBrO consists of the formation of the hydrate 12a of bromous acid anhydride 7 via transition state structure 14a. The computed activation free enthalpy ΔGact(SMD) = 13.6 kcal/mol for the process 2·2a → [14a]‡ → 12a corresponds to the reaction rate constant k4 = 667.5 M–1 s–1 and is in very good agreement with experimental measurements. The potential energy surface analysis further shows that anhydride 7 is kinetically and thermodynamically unstable with regard to hydrolysis to HOBr and HOBrO2 via transition state structure 14b. The transition state structure 14b is much more stable than 14a, and, hence, the formation of the “symmetrical anhydride” from bromous acid becomes an irreversible reaction for all practical purposes because 7 will instead be hydrolyzed as a “mixed anhydride” to afford HOBr and HOBrO2. The mixed anhydride 8, BrO–BrO2, does not play a significant role in bromous acid disproportionation.
Co-reporter:Wenjuan Zhang, Shaofeng Liu, Wenhong Yang, Xiang Hao, Rainer Glaser, and Wen-Hua Sun
Organometallics 2012 Volume 31(Issue 23) pp:8178-8188
Publication Date(Web):November 5, 2012
DOI:10.1021/om300778g
Stoichiometric reactions of YCl3(THF)3 with potassium 2-((arylimino)methyl)quinolin-8-olates or 2-(1-(arylimino)ethyl)quinolin-8-olates in THF solution gave the mononuclear LYCl2(DMSO)2 complexes 1–5 in the presence of DMSO and a representative dinuclear complex 6 in the absence of DMSO. All yttrium complexes were fully characterized by NMR measurements and elemental analysis, and the crystal structures of complexes 1 and 4–6 were determined by single-crystal X-ray diffraction. The structures indicate coordination number seven around the yttrium center and pentagonal bipyramidal geometries. The complexes all feature diapical YCl2 moieties and one tridentate organic ligand in the equatorial plane. Upon reaction of the yttrium precatalysts 1–6 with LiCH2Si(CH3)3 alone or with LiCH2Si(CH3)3 together with BnOH, the ring-opening polymerization (ROP) of ε-caprolactone (ε-CL) occurred with high efficiency. Depending on conditions, the ROP of ε-CL produced polycaprolactone with narrow molecular distribution and in a living manner. Theoretical studies of the chlorine/CH2SiMe3 and Me3SiCH2/BnO ligand exchange reactions suggest that the replacement of the apical ligands can proceed without significantly affecting the equatorial ligands. These results suggest that one of the apical Y–CH2SiMe3 bonds within the LY(CH2SiMe3)2 intermediate catalyzes the polymerization in the BnOH-free process. Most polymers generated by BnOH-assisted catalysis possess Mn values that are similar to Mn,cal values based on Y–OBn, suggesting that one apical Y–OBn bond of the diapical LY(OBn)(CH2SiMe3) intermediate catalyzes most or all of the ring polymerization of ε-CL.
Co-reporter:Rainer Glaser ;Xinsen Sun
Journal of the American Chemical Society 2011 Volume 133(Issue 34) pp:13323-13336
Publication Date(Web):August 5, 2011
DOI:10.1021/ja109457j
Results are presented of ab initio studies at levels MP2(full)/6-31G* and MP2(full)/6-311G** of the hydrolysis of trimethylaluminum (TMA, 1) to dimethylaluminumhydroxide (DMAH, 2) and of the intramolecular 1,2-elimination of CH4 from 2 itself to form methylaluminumoxide 3, from its dimeric aggregate 4 to form hydroxytrimethyldialuminoxane 5 and dimethylcyclodialuminoxane 6, and from its TMA aggregate 7 to form 8 and/or 9, the cyclic and open isomers of tetramethyldialuminoxane, respectively. Each methane elimination creates one new Lewis acid site, and dimethylether is used as a model oxygen-donor molecule to assess the most important effects of product stabilization by Lewis donor coordination. It is found that the irreversible formation of aggregate 4 (ΔG298 = −29.2 kcal/mol) is about three times more exergonic than the reversible formation of aggregate 7 (ΔG298 = −9.9 kcal/mol), that the reaction free enthalpies for the formations of 5 (ΔG298 = −9.0 kcal/mol) and 6 (ΔG298 = −18.8 kcal/mol) both are predicted to be quite clearly exergonic, and that there is a significant thermodynamic preference (ΔG298 = −7.2 kcal/mol) for the formation of 6 over ring-opening of 5 to hydroxytrimethyldialuminoxane 10. The mechanism for oligomerization is discussed based on the bonding properties of dimeric aggregates and involves the homologation of HO-free aluminoxane with DMAH (i.e., 9 to 13), and any initially formed hydroxydialuminoxane 10 is easily capped to trialuminoxane 13. Our studies are consistent with and provide support for Sinn’s proposal for the formation of oligoaluminoxanes, and in addition, the results point to the crucial role played by the kinetic stability of 5 and the possibility to form cyclodialuminoxane 6. Dialuminoxanes 9 and 10 are reversed-polarity heterocumulenes, and intramolecular O→Al dative bonding competes successfully with Al complexation by Lewis donors. Intramolecular O→Al dative bonding is impeded in cyclodialuminoxane 6, and the dicoordinate oxygen in 6 is a strong Lewis donor. Ethylene polymerization catalysts contain highly oxophilic transition metals, and our studies suggest that these transition metal catalysts should discriminate strongly in favor of cycloaluminoxane-O donors even if these are present only in small concentrations in the methylaluminoxane (MAO) cocatalyst.
Co-reporter:Stephanie Coyle and Rainer Glaser
The Journal of Organic Chemistry 2011 Volume 76(Issue 10) pp:3987-3996
Publication Date(Web):April 28, 2011
DOI:10.1021/jo200411f
The thermal (E)/(Z)-isomerization of 3-methyl-4-pyrimidinimine, 3MePMI, has been studied in the gas phase at MP2/6-31G* and with the inclusion of medium effects using the polarizable continuum method, PCM(MP2/6-31G*), and the solvation model density method, SMD(MP2/6-31G*). For the free molecule and for 3MePMI in each of 14 solvents, the structures were determined of the (E)- and (Z)-isomers, of the transition state structure for isomerization ITS by asymmetric N-inversion, and of the second-order saddle point structure (SOSP) associated with in-plane N-inversion. The results predict a reduction of the (E)-isomer preference energy of 3MePMI, an increase of the deformation energy ΔEdef = E(SOSP) – E(ITS), and an increase of the activation barrier Eact(Z → E) with increasing solvent polarity. Electronic effects associated with N-inversion are analyzed using molecular orbital theory, results of population analysis, and electrostatic potential maps. The molecular dipole moments are superior parameters for the description of electronic relaxation in the imine basin during N-inversion. In particular, the analysis of dipole moments explains the compatibility of the increase of local CN polarity during N-inversion with the negative solvation effect on the activation barrier.
Co-reporter:Rainer Glaser, Yongqiang Sui, Ujjal Sarkar and Kent S. Gates
The Journal of Physical Chemistry A 2008 Volume 112(Issue 21) pp:4800-4814
Publication Date(Web):May 22, 2008
DOI:10.1021/jp8011987
Radicals resulting from one-electron reduction of (N-methylpyridinium-4-yl) methyl esters have been reported to yield (N-methylpyridinium-4-yl) methyl radical, or N-methyl-γ-picoliniumyl for short, by heterolytic cleavage of carboxylate. This new reaction could provide the foundation for a new structural class of bioreductively activated, hypoxia-selective antitumor agents. N-methyl-γ-picoliniumyl radicals are likely to damage DNA by way of H-abstraction and it is of paramount significance to assess their H-abstraction capabilities. In this context, the benzylic C−H homolyses were studied of toluene (T), γ-picoline (P, 4-methylpyridine), and N-methyl-γ-picolinium (1c, 1,4-dimethylpyridinium). With a view to providing capacity for DNA intercalation the properties also were examined of the annulated derivatives 2c (1,4-dimethylquinolinium), 3c (9,10-dimethylacridinium), and 4c (1,4-dimethylbenzo[g]quinolinium). The benzylic C−H homolyses were studied with density functional theory (DFT), perturbation theory (up to MP4SDTQ), and configuration interaction methods (QCISD(T), CCSD(T)). Although there are many similarities between the results obtained here with DFT and CI theory, a number of significant differences occur and these are shown to be caused by methodological differences in the spin density distributions of the radicals. The quality of the wave functions is established by demonstration of internal consistencies and with reference to a number of observable quantities. The analysis of spin polarization emphasizes the need for a clear distinction between “electron delocalization” and “spin delocalization” in annulated radicals. Aside from their relevance for the rational design of new antitumor drugs, the conceptional insights presented here also will inform the understanding of ferromagnetic materials, of spin-based signaling processes, and of spin topologies in metalloenzymes.
Co-reporter:Ming Qian;Shuo Yang;Hong Wu
Journal of The American Society for Mass Spectrometry 2007 Volume 18( Issue 11) pp:2040-2057
Publication Date(Web):2007 November
DOI:10.1016/j.jasms.2007.08.018
The results are reported of mass-spectrometric studies of the nucleobases adenine 1h (1, R = H), guanine 2h, and cytosine 3h. The protonated nucleobases are generated by electrospray ionization of adenosine 1r (1, R = ribose), guanosine 2r, and deoxycytidine 3d (3, R = deoxyribose) and their fragmentations were studied with tandem mass spectrometry. In contrast to previous EI-MS studies of the nucleobases, NH3 elimination does present a major path for the fragmentations of the ions [1h + H]+, [2h + H]+, and [3h + H]+. The ion [2h + H − NH3]+ also was generated from the acyclic precursor 5-cyanoamino-4-oxomethylene-dihydroimidazole 13h and from the thioether derivative 14h of 2h (NH2 replaced by MeS). The analyses of the modes of initial fragmentation is supported by density functional theoretical studies. Conjugate acids 15–55 were studied to determine site preferences for the protonations of 1h, 2h, 3h, 13h, and 14h. The proton affinity of the amino group hardly ever is the substrate’s best protonation site, and possible mechanisms for NH3 elimination are discussed in which the amino group serves as the dissociative protonation site. The results provide semi-direct experimental evidence for the existence of the pyrimidine ring-opened cations that we had proposed on the basis of theoretical studies as intermediates in nitrosative nucleobase deamination.
Co-reporter:Rainer Glaser, Nathan Knotts, Ping Yu, Linghui Li, Meera Chandrasekhar, Christopher Martin and Charles L. Barnes
Dalton Transactions 2006 (Issue 23) pp:2891-2899
Publication Date(Web):02 May 2006
DOI:10.1039/B515739K
Extraordinary high degrees of polar order can be achieved by a rational design that involves the polar stacking of parallel beloamphiphile monolayers (PBAM). This strategy is exemplified by the acetophenone azines MCA (4-methoxy-4′-chloroacetophenone azine) and DCA (4-decoxy-4′-chloroacetophenone azine). The beloamphiphile design aims to achieve strong lateral interactions by way of arene–arene, azine–azine, arene–azine and halogen-bonding interactions. Dipole-induced interactions and halogen bonding dominate interlayer interactions and halogen bonding is shown to effect the layer stacking. Crystals of DCA contain PBAMs with perfect polar order and perfect polar layer stacking, while crystals of MCA features perfect polar order only in one of two layers and layer stacking is polar but not entirely perfect. We report the synthesis of the beloamphiphile DCA, its crystal structure, and we present a comparative discussion of the structures and intermolecular interactions of MCA and DCA. Absorbance and photoluminescence measurements have been carried out for solutions of DCA and for DCA crystals. DCA exhibits a broad emission centered at 2.5 eV when excited with UV radiation. The nonlinear optical response was studied by measuring second harmonic generation (SHG). Strong SHG signals have been observed due to the polar alignment and the DCA crystal's NLO response is 34 times larger than that of urea. Optimization of the beloamphiphile and systematic SAR studies of the polar organic crystals, which are now possible for the very first time, will further improve the performance of this new class of functional organic materials. The materials are organic semiconductors and show promise as blue emitters, as nonlinear optical materials and as OLED materials.
Co-reporter:Michael Lewis Dr. Dr.
Chemistry - A European Journal 2002 Volume 8(Issue 8) pp:
Publication Date(Web):16 APR 2002
DOI:10.1002/1521-3765(20020415)8:8<1934::AID-CHEM1934>3.0.CO;2-0
The results of a theoretical study of the one-, two- and three-water hydrolyses of carbodiimide and the one- and two-water hydrolyses of methyleneimine are presented. All structures were optimized and characterized at the MP2(full)/6-31G* level of theory. Energies for the one-water hydrolysis of carbodiimide were determined at numerous higher levels of theory, up to the QCISD(T)(fc)/6-311+G(3df,2p)//MP2(full)/6-31G* level. The ΔE0(ΔG298) activation barriers for the rate-determining steps of the one-, two- and three-water hydrolyses of carbodiimide, respectively, are 44.8 (46.3), 29.3 (32.3) and 22.9 (26.2) kcal mol−1 at the MP2(full)/6-31G* level. The consideration of a second water molecule catalyzes the hydrolysis by 15.5 kcal mol−1 on the E0 surface and by 14.0 kcal mol−1 on the G298 surface with respect to the one-water hydrolysis. Placement of a third water molecule opposite the site of proton transfer catalyzes the reaction by an additional 6.4 kcal mol−1 on the E0 surface and by 6.1 kcal mol−1 on the G298 surface. The catalytic effect of the third water molecule results from the synergistic effects of rehybridization and charge relaxation in the transition state. The charge relaxation in the transition state is illustrated through natural population analysis calculations on the pre-coordination complexes and the transition state structures. We also consider the placement of the third water molecule in the proton transfer chain and we show this to be of little catalytic relevance. The activation barriers determined for the one- and two-water hydrolyses of methyleneimine are ΔG298=51.9 and ΔG298=35.5 kcal mol−1, respectively, and they are larger than for carbodiimide. The results are compared with the hydrolyses of carbon dioxide and formaldehyde.
Co-reporter:Graeme Day ;Noriyuki Shimomura;Atsushi Takamuku;Kazuhiko Ichikawa
Chemistry - A European Journal 2000 Volume 6(Issue 6) pp:
Publication Date(Web):15 MAR 2000
DOI:10.1002/(SICI)1521-3765(20000317)6:6<1078::AID-CHEM1078>3.0.CO;2-R
The electronic excitations of the low-valence bismuth cluster cations Bi53+, Bi82+, and Bi95+ have been studied with experimental and theoretical techniques. The UV-visible spectra of the bismuth ions were measured in acidic chloroaluminate melts (mixture of 1-methyl-3-benzyl imidazolium chloride and AlCl3). The spectra of the Bi53+ and Bi82+ ions agree fairly well with previous reports, but also revealed additional low-energy absorptions. Ab initio methods were employed to assign the experimentally observed electronic transitions of these homopolyatomic bismuth cations. Structures were optimized at the RHF, MP2, and B3LYP levels of theory by using split-valence LANL2DZ basis sets that were augmented with one and two sets of pure d functions. The computed structures agree well with the results of neutron diffraction analyses of melts. Electronically excited states of the three clusters were treated by using the CI-Singles theory. The results of these calculations were used to explain the observed UV-visible spectra. The observed electronic excitations in the UV-visible range are all found to result from transitions involving the molecular orbitals formed by 6p-atomic-orbital overlap. This leads to the necessity of using basis sets that include d-type functions, which allow for an adequate description of the bonding that results from such p-orbital overlap. Spin-orbit coupling becomes increasingly important with increasing atomic number and its consideration is necessary when describing the electronic transitions in clusters of heavy atoms. The calculations show that singlet-triplet transitions, which are made accessible by strong spin-orbit coupling, are responsible for some of the observed absorptions.
Co-reporter:Ming Qian, Shuo Yang, Hong Wu, Papiya Majumdar, Nathan Leigh, Rainer Glaser
Journal of the American Society for Mass Spectrometry (November 2007) Volume 18(Issue 11) pp:2040-2057
Publication Date(Web):1 November 2007
DOI:10.1016/j.jasms.2007.08.018
The results are reported of mass-spectrometric studies of the nucleobases adenine 1h (1, R = H), guanine 2h, and cytosine 3h. The protonated nucleobases are generated by electrospray ionization of adenosine 1r (1, R = ribose), guanosine 2r, and deoxycytidine 3d (3, R = deoxyribose) and their fragmentations were studied with tandem mass spectrometry. In contrast to previous EI-MS studies of the nucleobases, NH3 elimination does present a major path for the fragmentations of the ions [1h + H]+, [2h + H]+, and [3h + H]+. The ion [2h + H − NH3]+ also was generated from the acyclic precursor 5-cyanoamino-4-oxomethylene-dihydroimidazole 13h and from the thioether derivative 14h of 2h (NH2 replaced by MeS). The analyses of the modes of initial fragmentation is supported by density functional theoretical studies. Conjugate acids 15–55 were studied to determine site preferences for the protonations of 1h, 2h, 3h, 13h, and 14h. The proton affinity of the amino group hardly ever is the substrate’s best protonation site, and possible mechanisms for NH3 elimination are discussed in which the amino group serves as the dissociative protonation site. The results provide semi-direct experimental evidence for the existence of the pyrimidine ring-opened cations that we had proposed on the basis of theoretical studies as intermediates in nitrosative nucleobase deamination.
![3-Aminobenzo[e][1,2,4]triazine 1,4-dioxide](http://img.cochemist.com/ccimg/27400/27314-97-2.png)
![3-Aminobenzo[e][1,2,4]triazine 1,4-dioxide](http://img.cochemist.com/ccimg/27400/27314-97-2_b.png)