Mechanisms of acetylcholinesterase protection against sarin and soman by adenosine A1 receptor agonist N6-cyclopentyladenosine.

Organophosphorus nerve agents (NAs) irreversibly inhibit acetylcholinesterase (AChE), the enzyme responsible for breaking down the neurotransmitter acetylcholine (ACh). The over accumulation of ACh after NA exposure leads to cholinergic toxicity, seizure, and death. Current medical countermeasures effectively mitigate peripheral symptoms, however; the brain is often unprotected. Alternative acute treatment with the adenosine A1 receptor agonist N6-cyclopentyladensosine (CPA) has previously been demonstrated to prevent AChE inhibition as well as to suppress neuronal activity. The mechanism of AChE protection is unknown. To elucidate the feasibility of potential CPA-AChE interaction mechanisms, we applied a truncated molecular model approach and density functional theory. The candidate mechanisms studied are reversible enzyme inhibition, enzyme reactivation, and NA blocking prior to enzyme conjugation. Our thermodynamic data suggest that CPA can compete with the NAs sarin and soman for the active site of AChE, but may, in contrast to NAs, undergo back-reaction. We found a strong interaction between CPA and NA conjugated AChE, making enzyme reactivation unlikely but possibly allowing for CPA protection through the prevention of NA aging. The data also indicates that there is an affinity between CPA and unbound NAs. The results from this study support the hypothesis that CPA counters NA toxicity via multiple mechanisms and is a promising therapeutic strategy that warrants further development.

Below-Room-Temperature C-H Bond Breaking on an Inexpensive Metal Oxide: Methanol to Formaldehyde on CeO2(111).

Upgrading of primary alcohols by C-H bond breaking currently requires temperatures of >200 °C. In this work, new understanding from simulation of a temperature-programmed reaction study with methanol over a CeO2(111) surface shows C-H bond breaking and the subsequent desorption of formaldehyde, even below room temperature. This is of particular interest because CeO2 is a naturally abundant and inexpensive metal oxide. We combine density functional theory and kinetic Monte Carlo methods to show that the low-temperature C-H bond breaking occurs via disproportionation of adjacent methoxy species. We further show from calculations that the same transition state with comparable activation energy exists for other primary alcohols; with ethanol, 1-propanol, and 1-butanol explicitly calculated. These findings indicate a promising class of transition states to search for in seeking low-temperature C-H bond breaking over inexpensive oxides.

Direct Neutron Spectroscopy Observation of Cerium Hydride Species on a Cerium Oxide Catalyst.

Ceria has recently shown intriguing hydrogenation reactivity in catalyzing alkyne selectively to alkenes. However, the mechanism of the hydrogenation reaction, especially the activation of H2, remains experimentally elusive. In this work, we report the first direct spectroscopy evidence for the presence of both surface and bulk Ce-H species upon H2 dissociation over ceria via in situ inelastic neutron scattering spectroscopy. Combined with in situ ambient-pressure X-ray photoelectron spectroscopy, IR, and Raman spectroscopic studies, the results together point to a heterolytic dissociation mechanism of H2 over ceria, leading to either homolytic products (surface OHs) on a close-to-stoichiometric ceria surface or heterolytic products (Ce-H and OH) with the presence of induced oxygen vacancies in ceria. The finding of this work has significant implications for understanding catalysis by ceria in both hydrogenation and redox reactions where hydrogen is involved.

Dehydrogenation of methanol to formaldehyde catalyzed by pristine and defective ceria surfaces.

We have explored the dehydrogenation of methoxy on pristine and defective (111), (100), and (110) ceria surfaces with density functional methods. Methanol conversion is used as a probe reaction to understand structure sensitivity of the oxide catalysis. Differences in reaction selectivity have been observed experimentally as a function of crystallographically exposed faces and degree of reduction. We find that the barrier for carbon-hydrogen cleavage in methoxy is similar for the pristine and defective (111), (100), and (110) surfaces. However, there are large differences in the stability of the surface intermediates on the different surfaces. The variations in experimentally observed product selectivities are a consequence of the interplay between barrier controlled bond cleavage and desorption processes. Subtle differences in activation energies for carbon-hydrogen cleavage on the different crystallographic faces of ceria could not be correlated with structural or electronic descriptors.

ReaxFF study of the oxidation of lignin model compounds for the most common linkages in softwood in view of carbon fiber production.

Lignin is an underused but major component of biomass. One possible area of utilization is the production of carbon fiber. A necessary processing step is the stabilization of lignin fiber (typically in an oxygen environment) before high temperature treatment. We investigate oxidative, thermal conversion of lignin using computational methods. Dilignol model compounds for the most common (seven) linkages in softwood are chosen to represent the diverse structure of lignin. We perform molecular dynamics simulation where the potential energy surface is described by a reactive force field (ReaxFF). We calculate overall activation energies for model conversion and reveal initial mechanisms of formaldehyde formation. We record fragmentation patterns and average carbon oxidation numbers at various temperatures. Most importantly, we identify mechanisms for stabilizing reactions that result in cyclic and rigid connections in softwood lignin fibers that are necessary for further processing into carbon fibers.

Mercury methylation by HgcA: theory supports carbanion transfer to Hg(II).

Many proteins use corrinoid cofactors to facilitate methyl transfer reactions. Recently, a corrinoid protein, HgcA, has been shown to be required for the production of the neurotoxin methylmercury by anaerobic bacteria. A strictly conserved Cys residue in HgcA was predicted to be a lower-axial ligand to Co(III), which has never been observed in a corrinoid protein. Here, we use density functional theory to study homolytic and heterolytic Co-C bond dissociation and methyl transfer to Hg(II) substrates with model methylcobalamin complexes containing a lower-axial Cys or His ligand to cobalt, the latter of which is commonly found in other corrinoid proteins. We find that Cys thiolate coordination to Co facilitates both methyl radical and methyl carbanion transfer to Hg(II) substrates, but carbanion transfer is more favorable overall in the condensed phase. Thus, our findings are consistent with HgcA representing a new class of corrinoid protein capable of transferring methyl groups to electrophilic substrates.

Pyrolysis pathways of sulfonated polyethylene, an alternative carbon fiber precursor.

Polyethylene is an emerging precursor material for the production of carbon fibers. Its sulfonated derivative yields ordered carbon when pyrolyzed under inert atmosphere. Here, we investigate its pyrolysis pathways by selecting n-heptane-4-sulfonic acid (H4S) as a model compound. Density functional theory and transition state theory were used to determine the rate constants of pyrolysis for H4S from 300 to 1000 K. Multiple reaction channels from two different mechanisms were explored: (1) internal five-centered elimination (Ei5) and (2) radical chain reaction. The pyrolysis of H4S was simulated with kinetic Monte Carlo (kMC) to obtain thermogravimetric (TGA) plots that compared favorably to experiment. We observed that at temperatures <550 K, the radical mechanism was dominant and yielded the trans-alkene, whereas cis-alkene was formed at higher temperatures from the internal elimination. The maximum rates of % mass loss became independent of initial È®H radical concentration at 440-480 K. Experimentally, the maximum % mass loss occurred from 440 to 460 K (heating rate dependent). Activation energies derived from the kMC-simulated TGAs of H4S (26-29 kcal/mol) agreed with experiment for sulfonated polyethylene (~31 kcal/mol). The simulations revealed that in this region, decomposition of radical HOSÈ®2 became competitive to α-H abstraction by HOSÈ®2, making È®H the carrying radical for the reaction chain. The maximum rate of % mass loss for internal elimination was observed at temperatures >600 K. Low-scale carbonization utilizes temperatures <620 K; thus, internal elimination will not be competitive. E(i)5 elimination has been studied for sulfoxides and sulfones, but this represents the first study of internal elimination in sulfonic acids.

Direct ΔMBPT(2) method for ionization potentials, electron affinities, and excitation energies using fractional occupation numbers.

A direct method (D-ΔMBPT(2)) to calculate second-order ionization potentials (IPs), electron affinities (EAs), and excitation energies is developed. The ΔMBPT(2) method is defined as the correlated extension of the ΔHF method. Energy differences are obtained by integrating the energy derivative with respect to occupation numbers over the appropriate parameter range. This is made possible by writing the second-order energy as a function of the occupation numbers. Relaxation effects are fully included at the SCF level. This is in contrast to linear response theory, which makes the D-ΔMBPT(2) applicable not only to single excited but also higher excited states. We show the relationship of the D-ΔMBPT(2) method for IPs and EAs to a second-order approximation of the effective Fock-space coupled-cluster Hamiltonian and a second-order electron propagator method. We also discuss the connection between the D-ΔMBPT(2) method for excitation energies and the CIS-MP2 method. Finally, as a proof of principle, we apply our method to calculate ionization potentials and excitation energies of some small molecules. For IPs, the ΔMBPT(2) results compare well to the second-order solution of the Dyson equation. For excitation energies, the deviation from equation of motion coupled cluster singles and doubles increases when correlation becomes more important. When using the numerical integration technique, we encounter difficulties that prevented us from reaching the ΔMBPT(2) values. Most importantly, relaxation beyond the Hartree-Fock level is significant and needs to be included in future research.

Computational investigation of the pyrolysis product selectivity for α-hydroxy phenethyl phenyl ether and phenethyl phenyl ether: analysis of substituent effects and reactant conformer selection.

Using computational methods, we determine product selectivities for the pyrolysis of two model compounds for the ß-O-4 linkage in lignin: phenethyl phenyl ether (PPE) and α-hydroxy phenethyl phenyl ether (α-hydroxy PPE). We investigate the dependence of the product selectivities on the number of reactant conformers included. Utilizing density functional theory in combination with transition state theory, we obtain rate constants for hydrogen abstraction reactions by the key chain-carrying radicals, which determine the product selectivity within a steady-state kinetic model. The inclusion of the energetically second lowest reactant conformer of PPE and α-hydroxy PPE has a large effect on the product selectivity. The final product selectivity computed for PPE agrees well with experiment. We find that the α-hydroxy substituent affects energetic as well as entropic contributions to the rate constant differently for alternative pathways of hydrogen abstraction and, thereby, significantly alters product distributions.

Role of carbon-carbon phenyl migration in the pyrolysis mechanism of ß-O-4 lignin model compounds: phenethyl phenyl ether and α-hydroxy phenethyl phenyl ether.

We investigate phenyl shift and subsequent ß-scission reactions for PhCHXCH·OPh [X = H, OH], which are part of the pyrolysis mechanism of phenethyl phenyl ether (PPE) and α-hydroxy PPE. PPE and its derivatives are model compounds for the most common linkage in lignin, the ß-O-4 linkage. We use density functional theory to locate transition states and equilibrium structures and kinetic Monte Carlo in combination with transition-state theory for kinetic simulations. Oxygen-carbon and carbon-carbon phenyl shift reactions proceed through cyclic intermediates with similar barriers. However, while subsequent ß-scission of the oxygen-carbon shift products proceeds with virtually no barrier, the activation energy for ß-scission of the carbon-carbon shift products exceeds 15 kcal/mol. We found that about 15% of ß-radical conversion can be attributed to carbon-carbon shift for PPE and α-hydroxy PPE at 618 K. Whereas the oxygen-carbon shift reaction has been established as an integral part of the pyrolysis mechanism of PPE and its derivatives, participation of the carbon-carbon shift reaction has not been shown previously.

Computational study of bond dissociation enthalpies for substituted ß-O-4 lignin model compounds.

The biopolymer lignin is a potential source of valuable chemicals. Phenethyl phenyl ether (PPE) is representative of the dominant ß-O-4 ether linkage. DFT is used to calculate the Boltzmann-weighted carbon-oxygen and carbon-carbon bond dissociation enthalpies (BDEs) of substituted PPE. These values are important for understanding lignin decomposition. Exclusion of all conformers that have distributions of less than 5% at 298 K impacts the BDE by less than 1 kcal mol(-1). We find that aliphatic hydroxyl/methylhydroxyl substituents introduce only small changes to the BDEs (0-3 kcal mol(-1)). Substitution on the phenyl ring at the ortho position substantially lowers the C-O BDE, except in combination with the hydroxyl/methylhydroxyl substituents, for which the effect of methoxy substitution is reduced by hydrogen bonding. Hydrogen bonding between the aliphatic substituents and the ether oxygen in the PPE derivatives has a significant influence on the BDE. CCSD(T)-calculated BDEs and hydrogen-bond strengths of ortho-substituted anisoles, when compared with M06-2X values, confirm that the latter method is sufficient to describe the molecules studied and provide an important benchmark for lignin model compounds.

Kinetic analysis of the phenyl-shift reaction in ß-O-4 lignin model compounds: a computational study.

The phenyl-shift reaction for the ß-radical of phenethyl phenyl ether (PhCH(2)CHOPh, ß-PPE) is an integral step in the pyrolysis of PPE, which is a model compound for the ß-O-4 linkage in lignin. We investigated the influence of natural occurring substituents (hydroxy, methoxy) on the reaction rate by calculating relative rate constants using density functional theory in combination with transition state theory, including anharmonic correction for low-frequency modes. The phenyl-shift reaction proceeds through an oxaspiro[2.5]octadienyl radical intermediate and the overall rate constants were computed invoking the steady-state approximation (its validity was confirmed). Substituents on the phenethyl ring have only little influence on the rate constants. If a methoxy substituent is located in the para position of the phenyl ring adjacent to the ether oxygen, the energies of the intermediate and second transition state are lowered, but the overall rate constant is not significantly altered. This is a consequence of the dominating first transition from reactant to intermediate in the overall rate constant. In contrast, o- and di-o-methoxy substituents significantly accelerate the phenyl-migration rate compared to ß-PPE.

Computational study of bond dissociation enthalpies for lignin model compounds. Substituent effects in phenethyl phenyl ethers.

Lignin is an abundant natural resource that is a potential source of valuable chemicals. Improved understanding of the pyrolysis of lignin occurs through the study of model compounds for which phenethyl phenyl ether (PhCH(2)CH(2)OPh, PPE) is the simplest example representing the dominant beta-O-4 ether linkage. The initial step in the thermal decomposition of PPE is the homolytic cleavage of the oxygen-carbon bond. The rate of this key step will depend on the bond dissociation enthalpy, which in turn will depend on the nature and location of relevant substituents. We used modern density functional methods to calculate the oxygen-carbon bond dissociation enthalpies for PPE and several oxygen-substituted derivatives. Since carbon-carbon bond cleavage in PPE could be a competitive initial reaction under high-temperature pyrolysis conditions, we also calculated substituent effects on these bond dissociation enthalpies. We found that the oxygen-carbon bond dissociation enthalpy is substantially lowered by oxygen substituents situated at the phenyl ring adjacent to the ether oxygen. On the other hand, the carbon-carbon bond dissociation enthalpy shows little variation with different substitution patterns on either phenyl ring.

Computational prediction of alpha/beta selectivities in the pyrolysis of oxygen-substituted phenethyl phenyl ethers.

Phenethyl phenyl ether (PPE; PhCH 2CH 2OPh) is the simplest model for the most common beta-O-4 linkage in lignin. Previously, we developed a computational scheme to calculate the alpha/beta product selectivity in the pyrolysis of PPE by systematically exploiting error cancellation in the computation of relative rate constants. The alpha/beta selectivity is defined as the selectivity between the competitive hydrogen abstraction reaction paths on the alpha- and beta-carbons of PPE. We use density functional theory and employ transition state theory where we include diagonal anharmonic correction in the vibrational partition functions for low frequency modes for which a semiclassical expression is used. In this work we investigate the effect of oxygen substituents (hydroxy, methoxy) in the para position on the phenethyl ring of PPE on the alpha/beta selectivities. The total alpha/beta selectivity increases when substituents are introduced and is larger for the methoxy than the hydroxy substituent. The strongest effect of the substituents is observed for the alpha-pathway of the hydrogen abstraction by the phenoxyl chain carrying radical for which the rate increases. For the beta pathway and the abstraction by the R-benzyl radical (R = OH,OCH 3) the rate decreases with the introduction of the substituents. These findings are compared with results from recent experimental studies.

Electron transport in open systems from finite-size calculations: Examination of the principal layer method applied to linear gold chains.

We describe the occurrence of computational artifacts when the principal layer method is used in combination with the cluster approximation for the calculation of electronic transport properties of nanostructures. For a one-dimensional gold chain, we observe an unphysical band in the band structure. The artificial band persists for large principal layers and for large buffer sizes. We demonstrate that the assumption of equality between Hamiltonian elements of neighboring layers is no longer valid and that a discontinuity is introduced in the potential at the layer transition. The effect depends on the basis set. When periodic boundary conditions are imposed and the k-space sampling is converged, the discontinuity disappears and the principal layer method can be correctly applied by using a linear combination of atomic orbitals as basis set.

Kinetic analysis of the pyrolysis of phenethyl phenyl ether: computational prediction of alpha/beta-selectivities.

We calculated an overall alpha/beta-selectivity for the pyrolysis of phenethyl phenyl ether as a composite of the alpha/beta-selectivities in the hydrogen abstraction reactions by the phenoxyl and by the benzyl radical that is in excellent agreement with experiment. The difference between the individual selectivities for these radicals is explained by analyzing the electronic structure of the transition states. Spin delocalization of the single electron favors the alpha-pathways. An opposing effect occurs for polarized transition states, such as the transition states for the hydrogen abstraction by the electrophilic phenoxyl radical, where the adjacent ether oxygen in phenethyl phenyl ether stabilizes the beta-transition states. These results indicate that theory will be able to provide excellent predictions of alpha/beta-product selectivities for more complicated lignin model compounds bearing multiple substituents. We have developed a scheme to predict alpha/beta-product selectivities in the pyrolysis of model compounds for the beta-ether linkage in lignin. The approach is based on computation of the relative rate constant, which profits from error cancellation in the individual rate constants. The Arrhenius prefactors depend strongly on the description of the low-frequency modes for which anharmonic contributions are important. We use density functional theory in combination with transition-state theory in this analysis. Diagonal anharmonic effects for individual low-frequency modes are included by employing a second-order Wigner-Kirkwood expansion in a semiclassical expression for the vibrational partition function. The composite alpha/beta-product selectivity is obtained by applying quasi-steady-state kinetic analysis for the intermediate radicals.

Correlated one-particle method: numerical results.

In a previous paper a correlated one-particle method was formulated, where the effective Hamiltonian was composed of the Fock operator and a correlation potential. The objective was to define a correlated one-particle theory that would give all properties that can be obtained from a one-particle theory. The Fock-space coupled-cluster method was used to construct the infinite-order correlation potential, which yields correct ionization potentials (IP's) and electron affinities (EA's) as the negative of the eigenvalues. The model, however, was largely independent of orbital choice. To exploit the degree of freedom of improving the orbitals, the Brillouin-Brueckner condition is imposed, which leads to an effective Brueckner Hamiltonian. To assess its numerical properties, the effective Brueckner Hamiltonian is approximated through second order in perturbation. Its eigenvalues are the negative of IP's and EA's correct through second order, and its eigenfunctions are second-order Brueckner orbitals. We also give expressions for its energy and density matrix. Different partitioning schemes of the Hamiltonian are used and the intruder state problem is discussed. The results for ionization potentials, electron affinities, dipole moments, energies, and potential curves are given for some sample molecules.

Independent particle theory with electron correlation.

We formulate an effective independent particle model where the effective Hamiltonian is composed of the Fock operator and a correlation potential. Within the model the kinetic energy and the exchange energy can be expressed exactly leaving the correlation energy functional as the remaining unknown. Our efforts concentrate on finding a correlation potential such that exact ionization potentials and electron affinities can be reproduced as orbital energies. The equation-of-motion coupled-cluster approach enables us to define an effective Hamiltonian from which a correlation potential can be extracted. We also make the connection to electron propagator theory. The disadvantage of the latter is the inherit energy dependence of the potential resulting in a different Hamiltonian for each orbital. Alternatively, the Fock space coupled-cluster approach employs an effective Hamiltonian which is energy independent and universal for all orbitals. A correlation potential is extracted which yields the exact ionization potentials and electron affinities and a set of associated molecular orbitals. We also describe the close relationship to Brueckner theory.