On the stability of the elusive HO3 radical

The dissociation of HO(3) into OH + O(2) has been studied in a systematic and consistent way using the multireference configuration interaction method. Upon extrapolation of the calculated raw energies to the complete basis set limit and using jointly with a recent realistic estimate of the zero-point vibrational energy, the energy for OO-OH bond-breaking in the trans isomer is predicted to be of D(0) = (2.4 ± 0.1) kcal mol(-1), where the uncertainty reflects only the one inherent to the extrapolation. The average value so obtained falls short of the commonly accepted experimental counterpart by 0.5 kcal mol(-1). Reasons for the deviation are advanced, as well as an estimate of the binding energy for the cis-HO(3) isomer which is predicted to have a somewhat smaller binding energy than trans-HO(3), but likewise the latter dissociates without a barrier to the same products.     

An experimental and theoretical evaluation of the reactions of silver hyponitrite with phosphorus halides. In search of the elusive phosphorus-containing hyponitrites

In the reaction of F2PBr, F2P(O)Br, (C6F5)2PBr, (CH3)2P(S)Br, and (CH3)2P(O)Cl with silver hyponitrite (AgON=NOAg), nitrous oxide (N2O) and mu-oxo phosphorus species were obtained in all cases rather than the plausible hyponitrite alternative. Theoretical calculations of the geometries and expected decomposition pathways of the phosphorus-containing hypothetical hyponitrites were carried out at the B3LYP/6-311+G(2df)//B3LYP/6-31+G(d) level. The cis-hyponitrite, XON=NOX (X=PF2, OPF2), is predicted to concertedly decompose to N2 plus phosphorus-containing radicals (OPF2, O2PF2) or to N2O plus the mu-oxo phosphorus species, X-O-X, (X=PF2, OPF2) with the former pathway having a smaller activation barrier (4.6 kcal/mol, X=PF2; 10.5 kcal/mol, X=OPF2). On the other hand, trans-hyponitrite can only decompose to N2 plus the phosphorus-containing radicals, because there is a very high barrier for rearrangement to cis-hyponitrite. These results are in disagreement with experiment, because only the mu-oxo phosphorus species are observed. Reconciliation between experiment and theory is made for X=OPF2 when a silver cation is included in the calculations. In THF (as a model for neat F2P(O)Br), the silver cation is predicted to reverse the order of the two transition states through stronger interactions with the oxygen atoms in the transition state of the N2O-producing pathway. Thus, Ag(I) is predicted to be not only catalytic for X=OPF2 but also product-specific toward the mu-oxo products.     

Kinetics of the NCCO + NO2 reaction

The kinetics of the NCCO + NO(2) reaction was studied by transient infrared laser absorption spectroscopy. The total rate constant of the reaction was measured to be k = (2.1 ± 0.1) × 10(-11) cm(3) molecule(-1) s(-1) at 298 K. Detection of products and consideration of possible secondary chemistry shows that CO(2) + NO + CN is the primary product channel. The rate constants of the NCCO + CH(4) and NCCO + C(2)H(4) reactions were also measured, obtaining upper limits of k (NCCO + CH(4)) ≤ 7.0 × 10(-14) cm(3) molecule(-1) s(-1) and k (NCCO + C(2)H(4)) ≤ 5.0 × 10(-15) cm(3) molecule(-1) s(-1). Ab initio calculations on the singlet and triplet potential energy surfaces at B3LYP/6-311++G**//CCSD(T)/6-311++G** levels of theory show that the most favorable reaction pathway occurs on the singlet surface, leading to CO(2) + NO + CN products, in agreement with experiment.     

The elusive 5'-deoxyadenosyl radical in coenzyme-B12-mediated reactions

Vitamin B(12) and its biologically active counterparts possess the only examples of carbon-cobalt bonds in living systems. The role of such motifs as radical reservoirs has potential application in future catalytic and electronic nanodevices. To fully understand radical generation in coenzyme B(12) (dAdoCbl)-dependent enzymes, however, major obstacles still need to be overcome. In this work, we have used Car-Parrinello molecular dynamics (CPMD) simulations, in a mixed quantum mechanics/molecular mechanics (QM/MM) framework, to investigate the initial stages of the methylmalonyl-CoA-mutase-catalyzed reaction. We demonstrate that the 5'-deoxyadenosyl radical (dAdo(?)) exists as a distinct entity in this reaction, consistent with the results of extensive experimental and some previous theoretical studies. We report free energy calculations and first-principles trajectories that help understand how B(12) enzymes catalyze coenzyme activation and control highly reactive radical intermediates.     

In search of radical intermediates in the reactions catalyzed by lysine 2,3-aminomutase and lysine 5,6-aminomutase

High-level ab initio calculations have been used to study radical intermediates in the reactions catalyzed by lysine 2,3-aminomutase (2,3-LAM) and lysine 5,6-aminomutase (5,6-LAM). The reactions of these enzymes with the substrate analogues 4-oxalysine (4-OL), 4-thialysine (4-TL), or trans-4,5-dehydrolysine (t-4,5-DL) are rationalized in terms of stabilization provided by the substituent to the adjacent radical center. Large changes in the exothermicity accompanying the initial H-abstraction are observed relative to the lysine reference values that follow the series 4-OL < 4-TL < t-4,5-DL. These changes have the primary effect of increasing the endothermicity for subsequent ring-closure to form the putative aziridinylcarbinyl radical intermediate. Such stabilization is consistent with experimental observations of the substrate-derived radical (S*) in the reaction of 2,3-LAM with 4-TL as well as the ability of t-4,5-DL to act as an irreversible inhibitor of 2,3-LAM. Our calculations suggest that 4-TL and trans-3,4-dehydrolysine may also permit experimental characterization of S* radicals in the reactions catalyzed by 5,6-LAM. Strategies for modifying PLP are presented that might lead to the first observation of the aziridinylcarbinyl radical intermediate (I*) in the aminomutase-catalyzed reactions.     

In search of the plastic enzyme

Photozymes are novel polyelectrolytes made from mixtures of hydrophobic and hydrophilic comonomers. They often contain a relatively high concentration of bound chromophores as photon harvesting or antenna groups, which transport excitation energy to organic substrates located in the interior of the macromolecular coil in aqueous solution. Previous studies have shown that the photocatalytic behavior of these polymers has many similarities to natural enzymes which carry out thermal reactions in biological systems. Mechanistic studies of four photozyme reactions are discussed: (1) the oxidation of perylene to perylenequinones; (2) the dehalogenation of hexachloro- and pentachlorobenzene; (3) the high-yield synthesis of Vitamin D; and (4) the selective photolysis of aliphatic and aromatic ketones.     

In search for axions

In this report the present status of axions in our understanding of particle physics and cosmology is given. A brief review of axion theory is presented and constraints on axion properties from laboratory searches and astrophysical and cosmological arguments are discussed.     

In search of structural invariants

Graph theory has been used for modeling chemical structures, that is, chemical compounds, intermediates, changes, reactions and mechanisms. Among the most important such applications are: (1) structure-property relationships (SAR); (2) design of compounds of desired properties; (3) enumeration and construction of compounds of certain classes; (4) unique representation of compounds (for documentation needs). Here, we outline selected accomplishments of the past, show some current efforts and point to directions which may lead to further advancements in chemical graph theory.Dedicated to Linus Pauling (Nobel Prize for Peace 1962 and Nobel Prize for Chemistry 1954) in appreciation of his outstanding contributions to structural chemistry and his untiring efforts to end war.     

Theoretical studies on the mechanisms of NCCO + O2 reaction

The mechanisms of the reaction of NCCO with molecular oxygen are investigated at the G3MP2//B3LYP/6-311G(d,p) levels for the first time. The calculation results show that two mechanisms are involved, namely, O attack on α atom mechanism and O attack on β atom mechanism, with six products yielded. The most feasible channel is the addition of O₂ to β atom in NCCO radical leading to the energy-rich intermediate IM1, NCC(O)OO, which can isomerize to a four-center-structure IM3, and then undergoes C–C and O–C bond fission to form P1(NCO + CO₂) finally. The barriers are 27.3 and 25.4 kcal/mol, respectively. For other channels involved in the two mechanisms, with less stable initial adducts and higher barrier, they are less conceivable dynamically and thermochemically.     

Rate constants for the reactions of HCCCO and NCCO radicals with molecular oxygen

Reactions of HCCCO and NCCO radicals with O₂ have been studied by a combination of pulsed laser photolysis and photoionization mass spectrometry. HCCCO was produced by 193‐nm photolysis of methylpropiolate or 3‐butyn‐2‐one, and NCCO was formed by 193‐nm photolysis of acetylcyanide. The rate constants obtained at 298 ± 3 K were (6.5 ± 0.7) × 10^?12 cm³ molecule^?1 s^?1 for the HCCCO + O₂ reaction, and no pressure dependence was observed between 1.5 and 16 Torr of N₂ as a bath gas. Because HCO and HCCO radicals were observed as reaction products, it was confirmed that the reaction proceeds by a two‐body reaction. On the other hand, the rate constants of NCCO with O₂ depended on the total pressure and were (5.4–8.8) × 10^?13 cm³ molecule^?1 s^?1 for total pressures 2.0–15.5 Torr of N₂, confirming that the reaction proceeds by a three‐body process. © 2001 John Wiley & Sons, Inc. Int J Chem Kinet 33: 440–448, 2001     

Theoretical study on mechanisms and kinetics of NCCO + O2 reaction

Mechanisms and kinetics of the NCCO + O2 reaction have been investigated using the extrapolated full coupled cluster theory with the complete basis set limit (FCC/CBS) and multichannel RRKM theory. Energetically, the most favorable reaction route involves the barrierless addition of the oxygen atom to one of the carbon atoms of NCCO and the subsequent isomerization-decomposition via the four-center intermediate and transition state, leading to the final products NCO and CO2. At 298 K, the calculated overall rate constant is strongly pressure-dependent, which is in good agreement with the available experimental values. It is predicted that the high-pressure limit rate constants exhibit negative temperature dependence below 350 K. The dominant products are NCO and CO2 at low pressures (ca. <10 Torr) and the NCCO(O2) radical at higher pressures, respectively.     

In search of an RNA replicase ribozyme

The theory that an RNA world played a pivotal role in life's evolutionary past has prompted investigations into the scope of RNA catalysis. These efforts have attempted to demonstrate the plausibility of an RNA-based genetic system, which would require RNA molecules that catalyze their own replication. The mechanistic features of modern protein polymerases have been used to guide the laboratory evolution of catalytic RNAs (ribozymes) that exhibit polymerase-like activity. Ribozymes have been developed that recognize a primer-template complex in a general way and catalyze the template-directed polymerization of mononucleotides. These experiments demonstrate that RNA replicase behavior is likely within the catalytic repertoire of RNA, although many obstacles remain to be overcome in order to demonstrate that RNA can catalyze its own replication in a manner that could have sustained a genetic system on the early Earth.     

In search of efficient 5-endo-dig cyclization of a carbon-centered radical: 40 years from a prediction to another success for the Baldwin rules

Despite being predicted to be stereoelectronically favorable by the Baldwin rules, efficient formation of a C-C bond through a 5-endo-dig radical cyclization remained unknown for more than 40 years. This work reports a remarkable increase in the efficiency of this process upon beta-Ts substitution, which led to the development of an expedient approach to densely functionalized cyclic 1,3-dienes. Good qualitative agreement between the increased efficiency and stereoselectivity for the 5-endo-dig cyclization of Ts-substituted vinyl radicals and the results of density functional theory analysis further confirms the utility of computational methods in the design of new radical processes. Although reactions of Br atoms generated through photochemical Ts-Br bond homolysis lead to the formation of cyclic dibromide side products, the yields of target bromosulfones in the photochemically induced reactions can be increased by recycling the dibromide byproduct into the target bromosulfones through a sequence of addition/elimination reactions at the exocyclic double bond. Discovery of a relatively efficient radical 5-endo-dig closure, accompanied by a C-C bond formation, provides further support to stereoelectronic considerations at the heart of the Baldwin rules and fills one of the last remaining gaps in the arsenal of radical cyclizations.     

In search of ionic liquids incorporating azolate anions

Twenty-eight novel salts with tetramethyl-, tetraethyl-, and tetrabutylammonium and 1-butyl-3-methylimidazolium cations paired with 3,5-dinitro-1,2,4-triazolate, 4-nitro-1,2,3-triazolate, 2,4-dinitroimidazolate, 4,5-dinitroimidazolate, 4,5-dicyanoimidazolate, 4-nitroimidazolate, and tetrazolate anions have been prepared and characterized by using differential scanning calorimetry (DSC), thermogravimetric analysis (TGA), and single-crystal X-ray crystallography. The effects of cation and anion type and structure on the physicochemical properties of the resulting salts, including several ionic liquids, have been examined and discussed. Ionic liquids (defined as having m.p.<100 degrees C) were obtained with all combinations of the 1-butyl-3-methylimidazolium cation ([C(4)mim](+)) and the heterocyclic azolate anions studied, and with several combinations of tetraethyl or tetrabutylammonium cations and the azolate anions. The [C(4)mim](+) azolates were liquid at room temperature exhibiting large liquid ranges and forming glasses on cooling with glass-transition temperatures in the range of -53 to -82 degrees C (except for the 3,5-dinitro-1,2,4-triazolate salt with m.p. 33 degrees C). Six crystal structures of the corresponding tetraalkylammonium salts were determined and the effects of changes to the cations and anions on the packing of the structure have been investigated.     

In search of the germanium halomethylidyne (Ge=C-X; X=F,Cl,Br) free radicals: Ab initio studies of their spectroscopic signatures

A variety of ab initio methods have been used to calculate the X (2)Pi and A (2)Sigma(+) state spectroscopic parameters of the GeCX (X=F,Cl,Br) free radicals. The theoretical methods and basis sets were tested on GeCH, for which extensive experimental data are available, and found to give predictions sufficiently reliable to guide experimental searches for spectra. In all cases, the linear Ge=C-X species was found to be the global minimum on the potential energy surface, with the bent X-Ge=C ((2)A(')) isomer as a local minimum much higher (62-36 kcal/mol) in energy. In both the ground and excited states, the GeC moiety is very similar to that of GeCH, with a double bond in the lower state and a triple bond in the excited state, indicating that halogenation does not radically perturb the energetics or structure of germanium methylidyne. Ground state GeCX radicals have suitable rotational constants for microwave studies, although they suffer from only modest dipole moments. Matrix infrared experiments are most likely to detect the nu(1) fundamentals in the 1450-1100 cm(-1) region or the nu(3) fundamentals at the transition between the mid- and far-infrared regions. We have used the ab initio values for the Renner-Teller parameter, the average bending frequency, and the spin-orbit coupling constant to calculate the ground state energy levels, which will be helpful in the interpretation of A-X single vibronic level emission spectra, if they can be observed. The electronic absorption spectra of the (2)Pi(32) spin component of the 0(0) (0) bands of all three radicals have been calculated assuming typical jet-expansion conditions and should be useful in future laser-induced fluorescence, resonance enhanced multiphoton ionization, or cavity ringdown searches for the electronic band systems.