Desorption reaction of ferric ions adsorbed on cellulosic materials by acids

Factors affecting the desorption reaction of ferric ions adsorbed on cellulose and oxidized poly(vinyl alcohol) fibers by acids were investigated. The desorbing effect generally increased with increasing acid concentration, treating temperature, and treating time, although the magnitude of this effect varied somewhat from one acid to another. Oxalic acid, hydrochloric acid, sulfuric acid, sulfurous acid, and phosphoric acid are examples of those acids which show large desorbing effects. Scission of the cellulose chain was also observed under the desorption conditions used for such acids. The desorption reaction may be divided into two stages, an initial fast reaction and a subsequent slow reaction; the activation energies were calculated for each reaction, and values of 7–10 kcal/mole and 5–6 kcal/mole were obtained for cellulose and oxidized poly(vinyl alcohol) fibers, respectively.     

SCF LCAO MO studies on the hydration of ions: The system F− · 2H2O

The energy surface of the dihydrated fluoride anion (F·2H₂O)^–1 is studied for a number of different geometry points near the equilibrium structure within the SCF LCAO MO framework, using an extended gaussian basis set to approximate the molecular wavefunctions. For the first and second hydration step of the fluoride anion the corresponding hydration energies are calculated to beB ₁ ^scf =24.1 kcal/mole andB ₂ ^SCF =20.8 kcal/mole (experimental measurements: 23.3 kcal/mole and 16.6 kcal/mole, respectively). The hydration energies and equilibrium bond distances obtained for the dihydrated fluoride anion (F·2H₂O)^– are compared with those found for the monohydrate (FHOH)^– and with corresponding results of the dihydrated lithium cation (Li · 2H₂O)⁺. The system (F·2H₂O)^– is taken as a very simple model to discuss some basic features of the hydration process of small ions and to study the influence of a negative ion on an adjacent hydrogen bond.We would like to thank our technical staff for valuable help in carrying out these calculations.     

Quantum chemical studies on electrophilic addition

The geometries of the 2-aminoethyl cation and the isomeric protonated aziridine have been optimized using ab initio molecular orbital calculations employing the split-valence shell 4-31G basis set. The protonated aziridine is computed to be the more stable ion by 46.5 kcal/mole (4-31G level) and 44.9 kcal/mole (double-zeta basis set). The profile to interconversion is found to have a barrier of less than 15 kcal/mole (relative to the 2-aminoethyl cation) and this profile is compared with those computed for the similar ions XCH₂CH ₂ ⁺ where X=OH, F, SH and Cl.     

Quasiclassical trajectory studies of H(D)+HBr(DBr) abstraction and exchange reactions

The abstraction and exchange reaction dynamics for H(D)+HBr(DBr) systems have been investigated on three LEPS potential-energy surfaces whose features are in accord with the surface topography suggested by recent molecular-beam and thermal experiments (abstraction barrier less than 1.0 kcal/mole, exchange reaction barriers of =5.0 kcal/mole, and no attractive wells with a depth greater than 0.209 kcal/mole). The surfaces differ primarily in the magnitude of the abstraction barrier which varies from 0.19 to 1.01 kcal/mole. Reaction cross sections have been computed on each surface as a function of relative collision energy from the results of 139000 quasiclassical trajectoris. Comparison of these results with measured relative abstraction cross sections suggests that the true abstraction barrier is very small, perhaps between 0.0 and 0.25 kcal/mole. However, thermal rate coefficients computed on the - best- surface at 300 K are about a factor of 2 larger than the most recently measured values. The calculated (H,D)/(D,H) isotope ratio at 300 K lies between the two reported experimental results. The computed thermal activation energy for abstraction is 835 cal/mole, which is in good agreement with a very early measurements but a factor of 2.5 less than the most recently reported experimental result. These results suggest that the molecular-beam and thermal rate measurements are inconsistent. The average fraction of the available energy which is partitioned into internal product modes <f_E> is found to be nearly independent of relative collision energy and the small topographical differences present in the potential surfaces used in these calculations. We find <f_E> = 0.40. In all reactions, the differential scattering cross sections are peaked in the backward direction for the molecular products, indicating a rebound mechanism.     

Atomic and molecular forms of oxygen on Ag(331). Theoretical analysis using the DFT method

Oxygen adsorption on Ag(331) is analyzed in a cluster approximation using the density functional theory (DFT) method. Adsorption centers (AC) for the bridge (S2) and three-center (S3) coordinations of oxygen are identified on the stepwise face Ag(331) and the Ag-O bond energies at these centers are calculated. For atomic adsorption, the Ag-O bond strength varies from 50 to 65 kcal/mole, depending on AC. The heat of molecular adsorption DH = 5 kcal/mole for S2(L1-L2) type AC. The molecule is oriented parallel to Ag(110) between the terraces with R(O-O) = 1.34 å Calculations showed that the ground state of the O₂Ag20(331) system is a triplet, but a part of spin density is delocalized on silver atoms, so that the spin density on oxygen ρ_s(O) = 0.46 (ρ_s = 1.0 for the free O₂ molecule). The energy of the singlet state is 9 kcal/mole greater than that of the ground state.     

Rearrangement of 3-membered 1,1,2-trifluorobromonium and iodonium ions and comparison of trifluorochloronium to fluorocarbenium ions

Reactions of chlorine (Cl(2)) with 4-halo-1,1,2-trifluorobut-1-enes (1, 2, or 3) give open-ion intermediates A and E that are in equilibrium. The open-chloronium ions (E) rearrange to a five-membered-ring halonium ion during ionic chlorination of 3 when the number-4 halo-substituent is iodine. Three-membered-ring bromonium and iodonium ions from alkenes 1, 2, or 3 are rather symmetrical and similar in structure. Quantum chemical calculations show that five-membered-ring halonium ion intermediates are 11 to 27 kcal/mol more stable than the three-membered-ring halonium ions or the open-ions A and E. The five-membered-ring intermediates lead to rearranged products. Rearranged products increase as the number-4 halogen (Z) becomes more nucleophilic (Z: Cl < Br < I). Open chloronium ions from ionic chlorination of terminal fluorovinyl alkenes are compared to the open ions generated by protons to similar alkenes.     

Doubly charged protonated a ions derived from small peptides

Protonated a(2) and a(3) (therefore doubly charged) ions in which both charges lie on the peptide backbone are formed in collision-induced dissociations of [La(III)(peptide)(CH(3)CN)(m)](3+) complexes. Abundant (a(3)+H)(2+) ions are formed from triproline (PPP) and peptides with a proline residue at the N-terminus; these peptides are the most effective in producing ions of the type (a(2)+H)(2+) and (a(3)+H)(2+). A systematic study of the effect of the location of the proline residue and other residues of aliphatic amino acids on the generation of protonated a ions is reported. Density functional theory calculations at B3LYP/6-311++G(d,p) gave the proton affinity of the a(3) ion derived from PPP to be 167.6 kcal mol(-1), 2.6 kcal mol(-1) higher than that of water. The protonated a(2) ions of diglycine and diproline and a(3) ions of triglycine have lower proton affinities and are only observed in lower abundances, possibly due to proton transfer to water in ion-molecule reactions.     

A theoretical study of the internal rotation and inversion in hydroxymethyl radical (CH2OH)

Ab initio SCF calculation shows that the hydroxymethyl radical (CH₂OH) is non-planar, supporting the ESR experimental evidence. The out-of-plane angle of the CH₂ group is calculated to be 25° with a barrier of 0.4 kcal/mole. The rotational barriers of the hydroxy-group of the non-planar radical are calculated to be 1.8 kcal/mole (trans) and 3.5 kcal/mole (cis), respectively.     

Kinetics of the I2-catalyzed isomerization of allyl chloride to cis- and trans-1-chloro-1-propene. The stabilization energy of the chloroallyl radical

The I₂-catalyzed isomerization of allyl chloride to cis- and trans- l-chloro-l-propene was measured in a static system in the temperature range 225–329°C. Propylene was found as a side product, mainly at the lower temperatures. The rate constant for an abstraction of a hydrogen atom from allyl chloride by an iodine atom was found to obey the equation log [k,/M^?1 sec^?1] = (10.5 ± 0.2) ?; (18.3 ± 10.4)/θ, where θ is 2.303RT in kcal/mole. Using this activation energy together with 1 ± 1 kcal/mole for the activation energy for the reaction of HI with alkyl radicals gives DH⁰ (CH₂CHCHCl? H) = 88.6 ± 1.1 kcal/mole, and 7.4 ± 1.5 kcal/mole as the stabilization energy (SE) of the chloroallyl radical. Using the results of Abell and Adolf on allyl fluoride and allyl bromide, we conclude DH⁰ (CH₂CHCHF? H) = 88.6 ± 1.1 and DH⁰ (CH₂CHCHBr? H) = 89.4 ± 1.1 kcal/ mole; the SE of the corresponding radicals are 7.4 ± 2.2 and 7.8 ± 1.5 kcal/mole. The bond dissociation energies of the C? H bonds in the allyl halides are similar to that of propene, while the SE values are about 2 kcal/mole less than in the allyl radical, resulting perhaps more from the stabilization of alkyl radicals by α-halogen atoms than from differences in the unsaturated systems.     

Free energy of solvation of simple ions: molecular-dynamics study of solvation of Cl- and Na+ in the ice/water interface

Molecular-dynamics simulations of Cl(-) and Na(+) ions are performed to calculate ionic solvation free energies in both bulk simple point-charge/extended water and ice 1 h at several different temperatures, and at the basal ice 1 h/water interface. For the interface we calculate the free energy of "transfer" of the ions across the ice/water interface. For the ions in bulk water in the NPT ensemble at 298 K and 1 atm, results are found to be in good agreement with experiments, and with other simulation results. Simulations performed in the NVT ensemble are shown to give equivalent solvation free energies, and this ensemble is used for the interfacial simulations. Solvation free energies of Cl(-) and Na(+) ions in ice at 150 K are found to be approximately 30 and approximately 20 kcal mol(-1), respectively, less favorable than for water at room temperature. Near the melting point of the model the solvation of the ions in water is the same (within statistical error) as that measured at room temperature, and in the ice is equivalent and approximately 10 kcal mol(-1) less favorable than the liquid. The free energy of transfer for each ion across ice/water interface is calculated and is in good agreement with the bulk observations for the Cl(-) ion. However, for the model of Na(+) the long-range electrostatic contribution to the free energy was more negative in the ice than the liquid, in contrast with the results observed in the bulk calculations.     

Isomerization of azomethine- and azo-compounds and their protonated species

Barriers of rotation and inversion, respectively, have been calculated for the species H₂CNH (I), H₂CNCH₃ (II), NHNH (III), NHNCH₃ (IV) and their protonated species. For any unprotonated molecule the barrier of inversion is consistently lower than the barrier of rotation. Tile inversion barriers are: 27.8 (I), 23.8 (II), 51.9 (III) and 46.1 (IV) kcal/mole. In the case of azomethine species, protonation results in an increased rotational barrier (from 50.8 to 74.7 kcal/mole for II). In the case of azo species barriers of inversion are lowered on protonation (from 51.9 to 30.1 for II and from 46.1 to 24.4 kcal/mole for IV). All barriers are given with reference to the trans-isomer (azo). Proton affinities for the azomethine species are higher than those of the corresponding azo species (223.3 for 1, 199.9 kcal/mole for II).     

Theoretical study on germanium cyanide radical GeCN and its ions

A detailed theoretical study is performed on the hitherto unknown germanium cyanide radical and its ions. The (2)Pi state GeCN lies 5.0 kcal/mol lower than the (2)Pi state GeNC at the coupled-cluster theory including single and double excitations and perturbative inclusion of triple excitations [CCSD(T)]/6-311++G(3df)//quadratic configuration interaction with single and double excitations (QCISD)/6-311G(d)+zero-point vibrational energy (ZPVE) level. For interconversion between them, two electronic state pathways (2)A(') and (2)A(") are located, with the latter being 0.7 kcal/mol more favorable than the former. On the (2)A(") path, the GeCN-->GeNC and GeNC-->GeCN conversion barriers are 14.5 and 9.5 kcal/mol, respectively. The detailed singlet and triplet potential-energy surfaces of both the cationic and anionic GeCN species are also investigated. On the ground-state electronic hypersurface, singlet GeNC(+) is 4.6 kcal/mol more stable than singlet GeCN(+), whereas triplet GeNC(-) is 10.0 kcal/mol less stable than triplet GeCN(-). The relative energy difference between the GeCN(0,+/-) and GeNC(0,+/-) can be well correlated with the number of vacant orbitals on the Ge atom. The stability of the neutral and ionic CGeN and cyclic cGeCN is also discussed. The predicted structures, spectroscopies, ionization, and affinity energies as well as the Renner-Teller properties are expected to provide reliable estimates for future characterization of the potential GeCN and GeNC radicals as well as their ionic counterparts both in the laboratory and in the interstellar space.     

Fixed-node diffusion Monte Carlo study of the structures of m-benzyne

Diffusion Monte Carlo (DMC) calculations are performed on the monocyclic and bicyclic forms of m-benzyne, which are the equilibrium structures at the CCSD(T) and CCSD levels of coupled cluster theory. We employed multiconfiguration self-consistent field trial wave functions which are constructed from a carefully selected eight-electrons-in-eight-orbitals complete active space [CAS(8,8)], with configuration state function coefficients that are reoptimized in the presence of a Jastrow factor. The DMC calculations show that the monocyclic structure is lower in energy than the bicyclic structure by 1.9(2) kcal/mole, which is in excellent agreement with the best coupled cluster results.     

AB initio SCF LCAO MO study of the HOH…Cl− hydrogen bond

Ab initio SCF LCAO MO calculations for the [H₂O…Cl]^? complex have been performed. The energy of the linear hydrogen bond has been found to be lower than the energy of the bifurcated one. The difference of the energies is about 3 kcal/mole. The calculated equilibrium distance between the oxygen and chlorine atoms equals 5.75 au. The interaction energy of the chlorine anion and the rigid water molecule amounts to ?19 kcal/mole. The optimization of the OH bond length in the complex (linear hydrogen bond) leads to an interaction energy of ?19.5 kcal/mole (the experimental value equals ?13.1 kcal/mole). As a result of the hydrogen bond formation the OH bond length increases by 0.08 au.     

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.     

CNDO/2 and INDO calculations of a reaction pathway for the sigmatropic [1, 5] H-shift in cyclopentadiene

CNDO/2 and INDO calculations have been carried out in order to construct a suitable model for the activated complex during the reaction. In this reaction model the migrating hydrogen atom moves along an edge of the cyclopentadiene ring. An analysis of this situation suggests a partial electron transfer from the migrating hydrogen to the nascent cyclopentadienyl system. This charge transfer is discussed in terms of aromaticity. The calculated activation enthalpies are 10 kcal/mole (CNDO/2) and 17 kcal/mole (INDO), whereas the experimental value is ca. 24 kcal/mole [1].     

Formation and thermal-induced decay of radical ions in polymer matrices

The formation of radical ions in γ-irradiated polymethyl-methacrylate (PMMA) matrices at 77°K and thermal-induced reaction of these radical ions were of studied by optical absorption spectroscopic measurements. The radical ions of stilbene and pyrene were investigated. These radical ions decay according to second-order kinetics, which means that the neutralization reaction of the cationic species and anionic species participates in the decay process. The kinetic plots consist of two straight lines; that is, fast and slow decay processes are concerned. The activation energies were estimated to be E_fast = 2.4 kcal/mol and E_slow = 6.4 kcal/mol, respectively. The probability of recombination reaction depends on the distance between cationic and anionic species.     

Ab initioMO calculations on the acidities of water and methanol,and hydrogen bond energies of the conjugate ions with a water molecule

The acidities, deprotonation energies, of water and methanol were calculated by the use of the ab initio self-consistent-field (SCF ) molecular orbital (MO ) method with electron correlation computed by the thirdorder Møller–Plesset perturbation method and configuration interaction with double excitations. Zero-point vibrational energy correction translational energy change, and the PV work term were included to evaluate the accurate acidities. The calculated acidity difference including these corrections was 7 kcal/mol, which is somewhat smaller than the experimental ones (9.5–12.5 kcal/mol) recently determined. The hydrogen bond energies of the conjugate ions (OH^? and CH₃O^?) with a water molecule were calculated to be 2.3 kcal/mol near the Hartree–Fock limit; this energy only amounts to 25% of the (total) hydration energy difference between the two negative ions. The aqueous solvation effect on the acidity scale was discussed.