Differences In Stabilization Energies Research Articles

Layer spacing gradient (NaLi)1−xCoO2 for electrochemical Li extraction

Layer spacing gradient (NaLi)1−xCoO2 for electrochemical Li extraction

OH-Initiated Reactions of para-Coumaryl Alcohol Relevant to the Lignin Pyrolysis. Part II. Kinetic Analysis.

Monolignols are precursor units and primary products of lignin pyrolysis. The currently available global (lumped) and semidetailed kinetic models, however, are lacking the comprehensive decomposition kinetics of these key intermediates in order to advance toward the fundamentally based detailed chemical-kinetic models of biomass pyrolysis. para-Coumaryl alcohol (HOPh-CH═CH-CH2OH, p-CMA) is the simplest of the three basic monolignols containing a typical side-chain double bond and both alkyl and phenolic type OH groups. The two other monomers additionally contain one and two methoxy groups, respectively, attached to the benzene ring. Previously, we developed a detailed fundamentally based mechanism for unimolecular decomposition of p-CMA (as well as its truncated allyl and cinnamyl alcohol models) and explored its reactivity toward H radicals generated during pyrolysis. The reactions of p-CMA with pyrolytic OH radicals is another set of key reactions particularly important for understanding the formation mechanisms of a wide variety of oxygenates in oxygen-deficit (anaerobic) conditions and the role of the lignin side groups in pyrolysis pathways. In Part I of the current study (J. Phys. Chem. A, 2019, 123, 2570-2585), we reported a detailed potential energy (enthalpy) surface analysis of the reaction OH + p-CMA with suggestions for a variety of chemically activated, unimolecular, and bimolecular reaction pathways. In Part II of our work, we provide a detailed kinetic analysis of the major reaction channels to evaluate their significance and possible impacts on product distributions. Temperature- and pressure-dependent rate constants are calculated using the quantum Rice-Ramsperger-Kassel method and the master equation analysis for falloff and stabilization. Enthalpies of formation, entropies, and heat capacities are calculated using density functional theory and higher-level composite methods for stable molecules, radicals, and transition-state species. A significant difference between well depths for the chemically activated adduct radicals, [p-CMA-OH]*, is found for the α- and β-carbon addition reactions to generate the 1,3- and 1,2-diol radicals, respectively. This is due to the synergistic effect from conjugation of the proximal radical center with the aromatic ring and the strong H-bonding interaction between vicinal OH groups in the β-adduct (1,2-diol radical). Both adducts undergo isomerization and low-energy transformations, however, with different kinetic efficiencies because of the difference in stabilization energies. Reaction pathways include dissociation, intramolecular abstraction, atom and group transfers, and elimination. Of particular interest is a roaming-like low-energy dehydration reaction to form O-centered intermediate radicals. The kinetic analysis demonstrated the feasible formation of various products detected in pyrolysis experiments, suggesting that the gas-phase reactions of OH radicals can be a key process to form major products and complex oxygenates during lignin pyrolysis. Our preliminary experiments involving pyrolysis of the vaporized monomers support this basic statement. A novel mechanism for the formation of benzofuran, identified in experimentation, is also provided based on the potential conversions of hydroxyphenylacetaldehyde and corresponding isomers, which are kinetically favored products.

Quantum-chemical investigation on 5-fluorouracil anticancer drug

DFT with B3LYP/6-311++G(d,p) level were used for all calculations in this work. In biological system, 5-FU-3H2O has the highest stabilization energy compared to 5-FU-3NH3, 5-FU dimer, and 5-FU monomer. The chemical interactions of 2′-deoxyribose radical with uracil and 5-FU radicals to form 2′-deoxyuridine and 2′-deoxy-5-fluorouridine show that the difference in stabilization energies, ΔE, for their formation are quite low which facilitates the exchange reactions in DNA structure. Size, shape density distributions, and chemical reactivity sites of 5-FU were obtained by mapping electron density isosurface with electronic surface. Additionally, the intermolecular hydrogen bonding in 5-FU (sugar-phosphate) backbone system was simulated by NBO analysis to describe the role of intermolecular hydrogen bonding on the structure and chemical reactivity of 5-FU in biological systems. Molecular docking study of the interaction between 5-FU and human serum albumin (HSA) indicated that 5-FU binds to HSA with low affinity and low specificity compared to other anticancer drugs.

Structure and Energetics of Complexes of B12N12 with Hydrogen Halides-SAPT(DFT) and MP2 Study.

Molecular complexes of a fullerene analogue B12N12 with hydrogen halides (HCl, HBr, and HI) were studied with symmetry-adapted perturbation theory with density-functional theory applied for a description of monomers (SAPT(DFT)), Møller-Plesset theory to the second order (MP2), and its spin-component-scaled variant (SCS-MP2) in a limit of a complete basis set. For each halide five symmetry-distinct minimum structures of the complex have been found on the potential energy hypersurface, with interaction energies ranging from -6 to -18 kJ/mol. The natural bond orbital and the atom-in-molecules analysis of noncovalent bonds resulted in a division of these configurations into three categories: hydrogen-bonded, halogen-bonded, and those of a mixed type, involving simultaneously a hydrogen bonding and a π-hole bonding between halogen and boron atoms. A comparison of various approaches for the calculation of interaction energies shows that the SCS-MP2 supermolecular method gives results which are in a close agreement with SAPT(DFT), while the MP2 interaction energies are systematically more negative than the SAPT values. The ability of the B12N12 nanocage to bind hydrogen halides through several active sites on its surface puts under question the selectivity of the binding necessary in crystal engineering, especially for the hydrogen bromide and hydrogen iodide cases, which show small differences in stabilization energies for their minimum structures. The directionality of noncovalent bonds is explained on grounds of the anisotropy of some SAPT components, like electrostatics and induction, as well as by the σ-hole and π-hole models.

Thermodynamic analysis of lysozyme adsorbed to silica.

The structural stability of hen egg white lysozyme in solution and adsorbed to small colloidal silica particles at various surface concentrations was investigated using hydrogen-deuterium (H/D) exchange in combination with mass spectrometry (HDX-MS) and differential scanning calorimetry (DSC). The combination of HDX-MS and DSC allows a full thermodynamic analysis of the lysozyme structure as both the enthalpy and the Gibbs free energy can be derived from the various measurements. Moreover, both HDX-MS and DSC provide information on the relative structural heterogeneity of lysozyme in the adsorbed state compared to that in solution. Results demonstrated that at high surface coverage, the structural stability of lysozyme was only marginally affected by adsorption to silica particles whereas the unfolding enthalpy decreased by more than 10%, meaning that the entropy of lysozyme increased with a similar value upon adsorption. Furthermore, the structural heterogeneity increased considerably. At lower surface concentrations, the structural heterogeneity increased further whereas the enthalpy of unfolding decreased. Further analyses of the HDX-MS experiments clearly indicated that folding/unfolding of lysozyme occurs through a two-domain process. These two domains had a similar amount of structural elements and a difference in stabilization energy of 8 kJ/mol, regardless if lysozyme was in solution or adsorbed to silica.

A comparison of the B3LYP and MP2 methods in the calculation of phosphate complexes

Hydrogen-bond complexes of dihydrogen phosphate and dimethyl phosphate anions with orthosilicic acid, water, and ionic complexes with sodium cations are investigated with the density functional (B3LYP/6-31G(d,p) and B3LYP/6-31+G(d,p)) theory and the second-order perturbation (MP2/6-31+G(d,p)) theory. The geometries and IR spectra of the complexes obtained with the B3LYP/6-31+G(d,p) and MP2/6-31+G(d,p) level calculations are found to be very similar. Inclusion of diffuse functions in the basis set significantly improves the reproducibility of the experimental data. The BSSE corrections significantly reduce the differences in stabilization energies obtained at different levels of theory, and as expected are the largest with the least flexible basis set calculations.

Hydration change during the aging of phosphorylated human butyrylcholinesterase: importance of residues aspartate-70 and glutamate-197 in the water network as probed by hydrostatic and osmotic pressures

Wild-type human butyrylcholinesterase (BuChE) and Glu-197-->Asp and Asp-70-->Gly mutants (E197D and D70G respectively) were inhibited by di-isopropyl phosphorofluoridate under standard conditions of pH, temperature and pressure. The effect of hydrostatic and osmotic pressures on the aging process (dealkylation of an isopropyl chain) of phosphorylated enzymes [di-isopropylated (DIP)-BuChE] was investigated. Hydrostatic pressure markedly increased the rate of aging of wild-type enzyme. The average activation volume (DeltaV( not equal)) for the dealkylation reaction was -170 ml/mol for DIP wild-type BuChE. On the other hand, hydrostatic pressure had little effect on the aging of the DIP mutants (DeltaV( not equal)=-2.6 ml/mol for E197D and -2 ml/mol for D70G), suggesting that the transition state of the aging process was associated with an extended hydration and conformational change in wild-type BuChE, but not in the mutants. The rate of aging of wild-type and mutant enzymes decreased with osmotic pressure, allowing very large positive osmotic activation volumes (DeltaV not equal osm) to be estimated, thus probing the participation of water in the aging process. Molecular dynamics simulations performed on the active-site gorge of the wild-type DIP adduct showed that the isopropyl chain involved in aging was highly solvated, supporting the idea that water is important for stabilizing the transition state of the dealkylation reaction. Wild-type BuChE was inhibited by soman (pinacolyl methylphosphonofluoridate). Electrophoresis performed under high pressure [up to 2.5 kbar (1 bar=10(5) Pa)] showed that the soman-aged enzyme did not pass through a pressure-induced, molten-globule transition, unlike the native wild-type enzyme. Likewise, this transition was not seen for the native E197D and D70G mutants, indicating that these mutants are resistant to the penetration of water into their structure. The stability energetics of native and soman-aged wild-type BuChE were determined by differential scanning calorimetry. The pH-dependence of the midpoint transition temperature of endotherms indicated that the high difference in stabilization energy between aged and native BuChE (DeltaDeltaG=23.7 kJ/mol at pH 8.0) is mainly due to the salt bridge between protonated His-438 and PO(-), with pK(His-438)=8.3. A molecular dynamics simulation on the MIP adduct showed that there is no water molecule around the ion pair. The 'hydrostatic versus osmotic pressure' approach probed the importance of water in aging, and also revealed that Asp-70 and Glu-197 are the major residues controlling both the dynamics and the structural organization of the water/hydrogen-bond network in the active-site gorge of BuChE. In wild-type BuChE both residues function like valves, whereas in the mutant enzymes the water network is slack, and residues Gly-70 and Asp-197 function like check valves, i.e. forced penetration of water into the gorge is not easily achieved, thereby facilitating the release of water.

Photooxygenation of Tetrabenzo[a,cd,j,lm]Perylene and Tribenzo[a,h,rst]Phenanthra[10,1,2-cde]Pentaphene

Abstract The photooxygenation of tetrabenzo[a,cd,j,lm]perylene (TBP) and tribenzo[a,h,rst]phenanthra[10,1,2-cde]pentaphene (TBPP) due to exposure to visible-light was investigated by measuring the absorption spectra and applying semi-empirical molecular orbital methods. Regardless of similarity in molecular structure, TBPP undergoes photooxygenation, but TBP does not. The energy correlation diagrams were obtained by calculations of the heats of formation for TBP, TBPP and their endo-peroxides. The experimental results were explained in terms of difference in stabilization energy.

RNA/DNA hybrid duplexes with identical nearest-neighbor base-pairs have identical stability

Energetic behaviors of eight pairs of RNA/DNA hybrid duplexes with identical nearest neighbors have been investigated by UV melting analysis. In the pairs with identical nearest-neighbor pairs, the melting curve traces at the same strand concentration were very similar. The average difference in stabilization energy of these pairs was 4%, which was about expected within experimental error. These results indicate that the nearest-neighbor model is valid for predicting the stability of RNA/DNA hybrid duplexes as well as RNA/RNA and DNA/DNA duplexes.

The role of solvent models in stabilizing nonclassical ions

A molecular dynamics simulation is performed for a system of classical and nonclassical 2-norbornyl cations surrounded by a model solvent. Comparison of the energies of stabilization of the two ions due to the model solvent medium indicates that the difference in stabilization energies of the two ions is less than 1 kcal/mol.

The mechanism of the vapor‐phase chlorination of benzene derivatives

AbstractThe title reaction, displaying peculiar characteristics as to relative rates and isomer distributions, has been studied in detail. Prior to this study, different mechanisms had been advanced by several groups. Kinetic features (isomer patterns, relative and absolute rates, reaction orders, influences of additives, H/D isotope effects) strongly point to a free‐radical (chain) process, in which (1) is a crucial step. This abstraction reaction, endothermal by about 6 kcal/mol, apparently proceeds via a transition state closely resembling the free aryl radical. Relative rates and isomer distributions therefore reflect differences in stabilization energies, or in DH°(Ar – H). With high arene–Cl2 intake ratios or, more pronounced, with CCl4 as the reagent, aryl radicals also lead to biaryl, where arene successfully competes with the halogenating agent. This interpretation is quantitatively supported by our observation that “added,˝” recognizable aryl radicals yield the same chlorination–arylation product ratio, and by the results of competitive chlorination of benzene and chloroform over a temperature range of 200°C, where the latter study substantiates the value DH0(C6H5 – H) ≈ 109 kcal/mol.

CNDO/2 Studies on Ion Solvation by Methanol

CNDO/2 calculations are presented for the solvation of the ions H+, Li+, Na+, F−, and Cl− by methanol. The results are compared with previous calculations for solvation by water and with the experimental data of Kebarle. Predicted stabilization energies are grossly overestimated but differences in stabilization energies agree well with the experimental data.

A chemical diffusion model for partitioning of transition elements in oxide scales on alloys

Abstract A mechanism based on lattice diffusion of cations is proposed to account for segregation of transition elements in scales on oxidized ferrous alloys. From considerations of diffusion paths through close-packed oxide lattices, the mobility of a cation is related to the difference in stabilization energies for octahedral and for tetrahedral sites, as estimated from crystal field theory. The proposed correlation between crystal field preference energy and cation mobility is substantiated by reference to experimental oxidation rates for certain transition elements. The ranking order established for ease of diffusion of cations through close-packed oxide lattices is then shown to agree with the measured distribution of elements in scales formed on iron-chromium alloys by oxidation at 600°C in CO2-based gas. The model also accords with previously published data on partitioning in oxides.

Conjugation and hyperconjugation: a survey with emphasis on isovalent hyperconjugation

Various aspects and examples of conjugation and hyperconjugation are surveyed, and the desirability of an explicit classification of both conjugation and hyperconjugation into two major types, isovalent and sacrificial (ordinary) is emphasized. The existence of a third type, pluvalent conjugation, is also mentioned. Further, the desirability of a subclassification of isoconjugation and isohyperconjugation each into three sub-types (dative, non-dative, and homodative, in orderof increasing conjugative stabilization) is pointed out, with examples. Sacrificial conjugation and hyperconjugation are usually non-dative, but some examples of dative conjugation and hyperconjugation are cited. The intrinsic jointness of the inductive and mesomeric effects (both of which are forms of resonance) in homodative isoconjugation and isohyperconjugation is emphasized. Homodative alkyl isohyperconjugation in carbonium ions is discussed extensively, with especial reference to McCaulay's Conference paper. Some hitherto incompletely published theoretical evidence, supported by experimental spectroscopic evidence, that the ethylene positive ion is partially twisted in its ground state, is presented; the twist is due to incipient isohyperconjugation. Definitions of the term hyperconjugation are considered with some care. It is suggested that the Baker-Nathan effect (in so far as it refers to differences between C-H and C-C hyperconjugation) should not itself be described as hyperconjugation, but rather as differential hyperconjugation. It is pointed out that there are no obvious theoretical reasons for expecting radical differences in stabilization energy or in magnitude of electron between C-C and C-H hyperconjugation. Finally, the writer wishes to apologize if he has sometimes gone astray in this paper because of the superficiality of his acquaintance with the vast literature of organic chemistry.