Calculated Bond Dissociation Energies Research Articles

Antioxidant Capacity of Free and Peptide Tryptophan Residues Determined by the ORAC (Oxygen Radical Absorbance Capacity) Assay Is Modulated by Radical-Radical Reactions and Oxidation Products.

The ORAC (Oxygen Radical Absorbance Capacity) assay is commonly employed for determining the antioxidant capacity of bioactive peptides. To gain insights into the meaning of this index for peptides containing a single Trp, we studied the consumption of this residue and fluorescein (FLH, the probe of ORAC method), induced by radicals generated by AAPH (2,2'-Azo-bis(2-amidinopropane) dihydrochloride) thermolysis. ORAC values were rationalized from kinetics and computational calculations of bond dissociation energies (BDE) of the N-H bond (indole ring of Trp). Free Trp, di- and tri- peptides, and three larger peptides were studied. Solutions containing 70 nM FLH, 1-5 μM free Trp or peptides, and 10 mM AAPH were incubated at 37 °C in phosphate buffer. Kinetic studies showed that FLH minimally affected Trp consumption. However, a clear protection of FLH, characterized by pseudo-lag times, was evidenced, reflecting radical-radical reactions and FLH repairing. Peptides showed similar ORAC values (~1.9-2.8 Trolox equivalents), while BDE varied between 91.9 and 103.5 kcal. These results, added to the protection of FLH observed after total consumption of Trp, indicate a lack of discrimination of the assay for the chemical structure of peptides and the contribution of oxidation products to the index.

Molecular Insights into Antioxidant Efficiency of Melanin: A Sustainable Antioxidant for Natural Rubber Formulations.

N-(1,3-Dimethyl butyl)-N'-phenyl-p-phenylenediamine (6-PPD) is a worldwide antioxidant commonly added to delay the thermo-oxidative degradation of tire rubbers. Unfortunately, 6PPD and its transformation product 6PPD-quinone are toxic to aquatic organisms (e.g., coho salmon). Herein, we explore the free radical scavenging activity and protective mechanism of melanin (MLN) on natural rubber's (NR's) oxidative resistance using molecular dynamics (MD) and quantum mechanical (QM) calculations. The relationship between the molecular structure and the chemical nature of the antioxidant molecules via transition state calculations is explored to unravel the reaction mechanisms of antioxidants interacting with peroxy radicals (ROO·) of NR with the estimation of reaction barriers. Following this, the radical scavenging activity of antioxidants was quantified via a hydrogen atom transfer mechanism and bond dissociation energy calculations. Parallel MD simulations were considered to study the interfacial interactions of antioxidant molecules with polymer chains and fillers with a quantifiable structure-property correlation. Given these results, the nanocomposite (NR-MLN-SiO2) with natural antioxidant melanin manifested outstanding antioxidant properties by preferentially bagging the ROO· radicals, thus improving NR's thermal-oxidative aging relative to 6-PPD. The MD results revealed that the intermolecular interactions at the NR/antioxidant interface benefited the antioxidant MLN to bind tightly to the NR in NR-MLN-SiO2 composite, thus exhibiting improved dispersion, O2 barrier properties, and thermo-oxidative stability, which could extend the service life of NR products (e.g., tires). In addition, as a sustainable antioxidant, MLN could replace toxic antioxidants like 6-PPD. More importantly, the QM/MD simulations provided a fundamental understanding of the mechanistic pathways of antioxidant molecules in NR composites, which are conducive to designing high-performance and sustainable green elastomers.

Probabilistic Approach to Low Strain Rate Atomistic Simulations of Ultimate Tensile Strength of Polymer Crystals.

Molecular dynamics simulations of the tensile ultimate properties of polymer crystals require the use of empirical potentials that model bond dissociation. However, fully reactive potentials are computationally expensive such that reactive simulations cannot reach the low strain rates of typical experiments. Here, we present a hybrid approach that uses the simplicity of a classical, nonreactive potential, information from bond dissociation energy calculations, and a probabilistic expression that mimics bond breaking. The approach is demonstrated for poly(p-phenylene terephthalamide) and, with one tunable parameter, the calculated tensile ultimate stress matches that obtained using a fully reactive simulation at high strain rates. Then, the hybrid simulations are run at much lower strain rates where the ultimate tensile stress is strain rate-independent and consistent with the expected experimental range.

Can Dative Bond Between two Anions Possible?

Formation of a genuine chemical bond between two similar charged fragments is beyond expectation. Any such interaction generally lies in the realm of non-covalent interaction. Herein, formation of a strong dative covalent bond between two anionic fragments is reported for the first time. Calculation using ab initio coupled cluster theory reveals the formation of unprecedented strong H3Be- ← X- (X- = CH3-, CN-, OH-, F-) dative covalent bond. The calculated bond dissociation energies in polar solvents are significant which indicates the possibility of their experimental realization.

Quest of Quadruple Bonding Between Two Main-Group Atoms in AeB- and AeC (Ae=Ca, Sr, Ba) and the Role of d Orbitals of Heavier Alkaline-Earth Atoms in Covalent Interactions.

Quantum chemical calculations using ab initio methods at the MRCI+Q(6,8)/def2-QZVPP and CCSD(T)/def2-QZVPP levels as well as density functional theory are reported for the diatomic molecules AeB- and isoelectronic AeC (Ae=Ca, Sr, Ba). The boride anions AeB- have an electronic triplet (3 Σ- ) ground state. The quintet (5 Σ- ) state is 5.8-12.3 kcal/mol higher in energy and the singlet (1 Δ) state is 13.1-15.3 kcal/mol above the triplet. The isoelectronic AeC molecules are also predicted to have a low-lying triplet (3 Σ- ) state but the quintet (5 Σ- ) state is only 2.2 kcal/mol (SrC) and 2.9 kcal/mol (CaC) above the triplet state. The triplet (3 Σ- ) and quintet (5 Σ- ) states of BaC are nearly isoenergetic. All systems have rather strong bonds. The calculated bond dissociation energies of the triplet (3 Σ- ) state are between De =38.3-41.7 kcal/mol for AeB- and De =49.4-57.5 kcal/mol for AeC. The barium species have always the strongest bonds whereas the calcium and strontium compounds have similar BDEs. The bonding analysis indicates that there is little charge migration in AeB- in the direction Ae→B- where the alkaline earth atoms carry positive charges between 0.09 e-0.22 e. The positive charges at the Ae atoms are much larger in AeC where the charge migration Ae→C is between 0.90 e-0.91 e. A detailed analysis of the interatomic interactions with the EDA-NOCV method shows that all diatomic species AeB- and AeC are built from dative interactions between Ae (1 S, ns2 ) and B- or C (3 P, 2 s2 2pπ 1 2pπ' 1 ). The eventually formed bonds in AeC are better described in terms of interactions between the ions Ae+ (2 S, ns1 )+C- (4 S, 2 s2 2pπ 1 2pπ' 1 2pσ 1 ). Inspection of the orbital interactions suggests that the alkaline earth atoms Ca, Sr, Ba use mainly their (n-1)d AOs besides the (n)s AOs for the covalent bonds. This creates a second energetically low-lying σ-bonding MO in the molecules, which feature valence orbitals with the order ϕ1 (σ-bonding)<ϕ2 (σ-bonding)<ϕ3 (degenerate π-bonding). All four occupied valence MOs of AeB- and AeC are bonding orbitals. Since the degenerate π orbitals ϕ3 are only singly occupied, the formal bond order is three.

Potential of derivation of a series of C6–C14 1-alkene skeletal oxidation mechanisms on the basis of reaction rate rules

Olefins, accounting for one-fifth proportion of gasoline fuel, are also essential intermediates in the combustion of large hydrocarbons and vital precursors of large polycyclic aromatic hydrocarbons and soot. The unsaturated C = C bond of alkenes renders a more complex low-temperature reaction scheme compared with their corresponding n-alkanes. Thus, it is of great necessity to obtain a thorough knowledge of the chemical kinetics of alkenes. However, the studies on the chemical kinetics of long-chain olefins are far from sufficient. In this work, a collection of skeletal oxidation mechanisms for 1-alkenes from 1-hexene (C6H12-1) to 1-tetradecene (C14H28-1) were constructed in light of recent advances in skeletal mechanism construction for fuels sharing similar structures based on reaction rate rules. For each 1-alkene, the skeletal mechanism includes ∼54 species and ∼216 reactions. Meanwhile, the effect of the C = C double bond was evaluated by conducting a bond dissociation energy calculation to assist the skeletal mechanism construction and derivation. It is discovered that the allylic position is preferred for H-atom abstraction reactions owing to its lowest bond dissociation energy among different locations for all heavy 1-alkenes. Furthermore, the reactions of OH addition to the C = C bond become important at low temperatures, which competes with the H-atom abstraction reactions. This results in the lower reactivity of 1-alkenes compared with corresponding n-alkanes at low temperatures. The acquired skeletal mechanisms were validated against extensive experimental data including laminar flame speeds, ignition delay times in shock tubes, and key species concentrations in jet-stirred reactors, flow reactors, and premixed laminar flames. The good agreements between experiments and simulations demonstrate the prediction capability of all the skeletal mechanisms of 1-alkenes although minor discrepancies exist in the concentration predictions for C2–C3 species, which might stem from a highly reduced C2–C3 sub-mechanism being utilized in the present mechanism.

Inorganic Acids, Fluoridated Ethanol’s, and Some Fluoridated Saturated Hydrocarbons’ Stability and Bond Dissociation Energy Values.

The energetics of chemical processes can be assessed using bond dissociation energy values. The objective of this work is to calculate the hydrogen-halogen (H-X) and carbon- fluorine (C-F) bond dissociation energy values for some energetic materials including fluorinated ethanols, some fluorinated saturated hydrocarbons, and some inorganic acids. Bond dissociation energy values for 40 different compounds are reported in this work. All calculated bond dissociation energy is reported for standard conditions, 1 atm pressure and 298 K temperature. Bond dissociation energy values are listed in tables 1,2 and 3.

Inter-Alkali-Metal Dative Bond in the MMN3 - (M=Alkali Metal) Cluster.

Alkali metals are generally Lewis acids. On the contrary, Lewis basic character of alkali metals forming donor - acceptor complexes is a very rare phenomenon. In this contribution, I have theoretically designed an anionic cluster MMN3 - (M=alkali metals) on the basis of experimentally known reagent, alkali salt of azide ion MN3 , which shows unprecedented M:- →M donor-acceptor interaction. To the best of author's knowledge, the characterization of such donor-acceptor interaction among alkali metals is unprecedented. Formation of the 2c-2e donor-acceptor bonds have been confirmed by quantum theory of atoms in molecules and electron localization function analyses. The calculated bond dissociation energies are significant suggesting their possible spectroscopic identification.

Theoretical and Experimental Investigation of Autoxidation Propensity of Selected Drugs in Solution State.

The C-H bond dissociation energy (BDE) of drug molecules is often used to estimate their relative propensities to undergo autoxidation. BDE calculations based on electronic structures provide a convenient means to estimate the risk for a given compound to degrade via autoxidation. This study aimed to verify the utility of calculated C-H BDEs of a range of drug molecules in predicting their autoxidation propensities, in the solution state. For the autoxidation study, 2,2'-azobis (2-methylpropionitrile) was employed as the solution state stressor, and the experimental reaction rate constants were determined employing ultraperformance liquid chromatographic (UPLC) methods. Reaction rates in the solution state were compared to the calculated C-H BDE values of the respective compounds. The results indicated a poor correlation for compounds in the solution state, and their relative stabilities could not be explained with C-H BDE. On the other hand, a favorable relationship was observed between the relative extent of ionization and the autoxidation rates of the selected compounds. In the solution state, factors such as the type and extent of drug ionization, degree and type of solvation have been shown to contribute to differences in reactivity. By applying the computational method involving the effect of H-atom abstraction and potential ionization sites in the molecule, the calculated C-H BDE should relate better to the experimental autoxidation rates.

Free radical mechanism of toxic organic compound formations from o-chlorophenol.

Organic free radical intermediates are pivotal to our understanding of toxic chemicals formation from chlorophenols that widely exist in thermal processes. However, in most cases, multiple free radical intermediates exist and produce complex spectra that are hard to deconvolute. Identification of free radical intermediates is the current difficulty for detailed formation mechanisms of toxic products from chlorophenols. In this study, a universal bottom-up method was developed to identify the organic free radical intermediates. Candidate organic free radicals were firstly speculated according to the critical parameters obtained from experimental electron paramagnetic resonance (EPR) spectra and the calculated bond dissociation energies of precursors. Their theoretical spectra were then used retrospectively to justify the accordance with the experimental EPR spectra. Identification of the organic free radicals provides straightforward evidence for the formation pathways of pollutants from chlorophenol. Internal factors influencing formation of radical intermediates and the toxic products were also studied, including the ortho effect of the precursor, spin densities of the organic free radical intermediates, and steric hindrance effects of the molecular intermediates. In combination of the experimental results and theoretical calculations, detailed formation mechanisms of toxic pollutants intermediating by organic free radicals from thermal oxidation of chlorophenol were strongly evidenced.

Evaluation of Free Radical Quenching Ability of Quinoline Acids through in vitro and Theoretical Studies

Drugs based antioxidants are commonly suggested as targets while designing new medicines. All sorts of pharmaceutical drug development benefit from the extremely desirable quinoline moiety with antioxidant. In this work, the scavenging behaviour of four quinoline derivatives (Q1-Q4) towards DPPH, H2O2, ABTS and superoxide activity were investigated. According to the in vitro inhibition concentration (IC50), quinoline derivative Q1 showed high antioxidant potential. Additionally, the theoretical DFT gas phase calculations of HOMO-LUMO, MEP, NPA and NBO are used to study the conjugating systems in radicals and showed that the N-H site acts more favourable than the O-H site for the radical attack. The calculated bond dissociation energy (BDE) values demonstrated that compound Q1 follows the HAT mechanism and while the calculated ionization potential (IP) and proton dissociation energy (PDE) values showed that Q4 follows the SET-PT route. The results of these two mechanisms demonstrated that radical quenching activity occurs at the N-H and O-H sites. The spin density demonstrates that both radicals are delocalized uniformly across the molecule.

Initial unimolecular decomposition of 3,4-bis(3-fluorodinitromethylfuroxan-4-yl) furoxan from quantum mechanics and ReaxFF molecular dynamics simulation

High-energy-density materials (HEDMs) have a wide range of applications in many usages. Recently synthesized 3,4-bis(3-fluorodinitromethylfuroxan-4-yl) furoxan (BFTF-1), composed of furoxan rings and fluorodinitromethyl groups, has shown advanced properties comparing to other existed HEDMs, such as density and enthalpy of formation. Understanding the decomposition mechanism for BFTF-1 could provide insights into future designs of HEDMs, and the initial decompositions are critical steps in the mechanism. In the present study, we employed quantum mechanics calculations and reactive molecular dynamics simulations to explore the initial decomposition steps. The electronic structural analysis and bond dissociation energy calculations suggested that the nitro moieties in the fluorodinitromethyl groups and the furoxan rings could begin the bond breaking process in BFTF-1. The reactive molecular dynamics simulation showed that the increase of the nitro moieties was concurrent with the decrease of BFTF-1, proving the nitro moieties were the first product for the decomposition of BFTF-1. The present study laid the ground for the theoretical understanding of decomposition mechanisms for BFTF-1 and shed light on further designs of advanced HEDMs.

Benchmark Density Functional Theory Approach for the Calculation of Bond Dissociation Energies of the M-O2 Bond: A Key Step in Water Splitting Reactions.

A very fascinating aspect in quantum chemical research is to determine the accurate and cost-effective methods for the calculation of electronic and structural properties through a benchmark study. The current study focuses on the performance evaluation of density functional theory methods for the accurate measurement of bond dissociation energies (BDEs) of chemically important M–O2 bonds in water splitting reactions. The BDE measurement has got noteworthy attention due to its importance in all areas of chemistry. For BDE measurements of M–O2 bonds in five metal complexes with oxygen molecules, 14 density functionals (DFs) are chosen from seven classes of DFs with two series of mixed basis sets. A combination of pseudopotential and Pople basis sets [LANL2DZ & 6-31G(d) and SDD & 6-31+G(d)] are used as a series of mixed basis sets. The B3LYP-GD3BJ functional with LANL2DZ & 6-31G(d) gives outstanding results due to low deviations, error, and the best Pearson’s correlation (R) between the experimental and theoretical data. Our study suggested an efficient, low-cost, precise, and accurate B3LYP-GD3BJ/LANL2DZ & 6-31G(d) level of theory for BDE of the M–O2 bond, which may be useful for chemists working in the field of energy generation and utilization.

Effect of methyl substituents, ring size, and oxygen on bond dissociation energies and ring-opening kinetics of five- and six-membered cyclic acetals

The demand for clean and highly efficient fuels stimulates the development of novel fuels for the next generation. With the emergence of new catalytic methods, the selective synthesis of cyclic acetals made them promising fuel candidates. The present work provides systematic and consistent calculations of bond dissociation energies for 1,3-dioxolane and 1,3-dioxane and their substituted derivatives. Rate constants of subsequent ring-opening reactions of the formed fuel radicals have been calculated to facilitate the understanding of initial fuel consumption pathways. We found that the CH bond on the carbon that is in between two oxygens will always be the weakest bond to be broken. The inclusion of two oxygens in the ring slightly changes the strain in the ring structure. However, the trend that the BDEs increase from five to six-membered ring species still exists in cyclic acetals. The reason is a smaller eclipsing strain in the five-membered radicals relative to the parent molecules. For the subsequent ring-opening reactions of the formed radicals, the radical site and the position of the substitution have a major impact. The results of our study facilitate a deeper understanding of the effect of methyl substituents, ring size, and oxygen on the reactivity of five- and six-membered cyclic acetals as well as provide accurate kinetic data for the mechanism development of these potential fuels.

Calculating bond dissociation energies of X-H (X=C, N, O, S) bonds of aromatic systems via density functional theory: a detailed comparison of methods.

In this study, the performance of 17 different density functional theory functionals was compared for the calculation of the bond dissociation energy (BDE) values of X−H (X=C, N, O, S) bonds of aromatic compounds. The effect of the size of the basis set (expansions of 6-31(G)) was also assessed for the initial geometry and zero-point energy calculations, followed by the single-point BDE calculations with different model chemistries with the 6-311 + (3df,2p) basis set. It was found that the size of the basis set for geometry optimization has a much smaller effect on the accuracy of BDE than the choice of functional for the following single-point calculations. The M06-2X, M05-2X and M08−HX functionals yielded highly accurate BDE values compared to experimental data (with the average mean unsigned error MUE = 1.2–1.5 kcal mol−1), performing better than any of the other functionals. The results suggest that geometry optimization may be performed with B3LYP functional and a small basis set, whereas the M06-2X, M05-2X and M08-HX density functionals with a suitably large basis set offer the best method for calculating BDEs of ArX−H (X=C, N, O, S) bonds.

Supramolecular Template-Assisted Catalytic [2+2] Photocycloaddition in Homogeneous Solution

Supramolecular Template-Assisted Catalytic [2+2] Photocycloaddition in Homogeneous Solution

Experimental and Theoretical Study of Gamma Radiolysis and Dose Rate Effect of o-Cresol Formaldehyde Epoxy Composites.

Gamma radiolysis behaviors and mechanisms of silica-filled o-cresol formaldehyde epoxy are studied at 2.20 × 10-5 to 1.95 × 10-1 Gy/s. The radiolysis-induced changes in chemical structures do not severely affect its thermostability. The slightly deteriorated mechanical strength at temperature exceeding 100 °C is accompanied by the declining glass transition temperature (from 185.9 to 172.2 °C) and enhanced damping ability. The gas yields of hydrogen, methane, and carbon dioxide manifest a remarkable dose rate effect. Based on the Schwarzschild law, their yields at an extremely low dose rate are accurately predicted by the established master curves. Besides, the latent radiolysis of gas products and postradiation effect are found with caution. The radiation-caused residual spin species are proved to be composed of silica defects and a phenoxy-type free radical with a tert-butyl group, according to the experimental results, theoretical calculations, and spectra simulations. The lower vertical ionization potential (7.6 eV) and adiabatic ionization potential (7.1 eV) are primarily due to the ionization of the benzene ring moiety with the tert-butyl group, which is likely to suffer from radiolysis. The calculated bond dissociation energy (260.8-563.5 kJ/mol) of the typical chemical bonds of epoxy is consistent with its radiolytic vulnerability and degradation mechanisms.

Cover Feature: TET‐Like Oxidation in 5‐Methylcytosine and Derivatives: A Computational and Experimental Study (ChemBioChem 23/2021)

The reactivity of a biomimetic iron (IV)-oxo complex (the sun) towards a number of methylated cytosine and uracil substrates (the orbiting planets) was investigated. The reaction rates (corresponding to the orbital periods) are in very good agreement with the calculated bond dissociation energies. 5mC, T and 5miC possess a different reactivity than the solely N-methylated compounds 1mC and 1mU or the dimethylated compounds 1,5dimC and 1,5dimU. The image was created by coauthor R. Janßen. More information can be found in the Full Paper by L. J. Daumann et al.

Estimation of the reducing power and electrochemical behavior of few flavonoids and polyhydroxybenzophenones substantiated by bond dissociation energy: a comparative analysis.

Oxidative stress that damages cellular components affects various organs including the brain. It is thus believed to play an active role in neurodegenerative diseases, wherein the intrinsic antioxidant enzymes metabolize toxic intermediates. For therapeutic purpose, instead of antioxidant enzymes, small organic compounds as antioxidants may be more effective. Here, reducing power and electrochemical behavior of some flavanols, flavanonols, flavones, flavonols and O-methylated flavonols have been estimated and confirmed by the calculated bond dissociation energy. Compared to other classes, flavonols exhibited increased reducing power that decreased with methylation of the oxygen atom in the B-ring. Gossypetin emerged as the most effective of these flavonols. Generally, compounds with two hydroxyl groups in two consecutive positions of the phenyl ring and an enolic group in the C-ring with more preference for the hydroxyl group in the ortho position with respect to each other in the catechol moiety showed major activity. 5 position of the A-ring showed the least effect on the activity. The present understanding therefore may be applied for identifying compounds to be used as scaffold for designing potent antioxidants.

Constituents of Chamaecrista diphylla (L.) Greene Leaves with Potent Antioxidant Capacity: A Feature-Based Molecular Network Dereplication Approach.

Chamaecrista diphylla (L.) Greene (Fabaceae/Caesalpiniaceae) is a herbaceous plant that is widely distributed throughout the Americas. Plants from this genus have been used in traditional medicine as a laxative, to heal wounds, and to treat ulcers, snake and scorpion bites. In the present study, we investigated the chemical composition of Chamaecrista diphylla leaves through a mass spectrometry molecular network approach. The oxygen radical absorbance capacity (ORAC) for the ethanolic extract, enriched fractions and isolated compounds was assessed. Overall, thirty-five compounds were annotated for the first time in C. diphylla. Thirty-two of them were reported for the first time in the genus. The isolated compounds 9, 12, 24 and 33 showed an excellent antioxidant capacity, superior to the extract and enriched fractions. Bond dissociation energy calculations were performed to explain and sustain the antioxidant capacity found. According to our results, the leaves of C. diphylla represent a promising source of potent antioxidant compounds.