BDE261: a comprehensive set of high-level theoretical bond dissociation enthalpies

Using atomic clustering based on structural and electronic descriptors that consider surrounding environment to evaluate local properties of DFT functionals

We developed a method for evaluating the accuracies of the local properties of DFT functionals in detail using a clustering method based on machine learning and structural/electronic descriptors. We generated 36 clusters consistent with human intuition using 30,436 carbon atoms from the QM9 dataset. The results were used to evaluate 13C NMR chemical shifts calculated using 84 DFT functionals. Carbon atoms were grouped based on their similar environments, reducing errors within these groups. This enables more accurate assessment of the accuracy using a specific DFT functional. Therefore, the present atomic clustering provides more detailed insight into accuracy verification.

The influence of substituents in governing the strength of the P-X bonds of substituted halophosphines R1R2P-X (X = F and Cl)

In this study, the gas-phase homolytic P-F and P-Cl bond dissociation energies (BDEs) of a set of thirty fluorophosphine (R1R2P-F) and thirty chlorophosphine-type (R1R2P-Cl) molecules have been obtained using the high-level W2 thermochemical protocol. For the R1R2P-F species, the P-F BDEs (at 298 K) differ by up to 117.0 kJ mol-1, with (H3Si)2P-F having the lowest BDE (439.5 kJ mol-1) and F2P-F having the largest BDE (556.5 kJ mol-1). In the case of the chlorophosphine-type molecules, the difference in BDEs is considerably smaller (i.e., 72.6 kJ mol-1), with (NC)2P-Cl having the lowest P-Cl BDE (299.8 kJ mol-1) and (HO)2P-Cl having the largest (372.4 kJ mol-1). We have further analyzed the effect of substituents in governing the P-F and P-Cl BDEs by considering the effect of substituents in the parent halogenated precursors (using molecule stabilization enthalpies) and the effect of substituents in the product radicals (using radical stabilization enthalpies). Finally, we have also assessed the performance of a wide range of DFT methods for their ability to compute the gas-phase P-F and P-Cl BDEs contained in this dataset. We find that, overall, the double hybrid functional DSD-PBEB95 offers the best performance for both bond types, with mean absolute deviations of just 2.1 (P-F BDEs) and 2.2 (P-Cl BDEs) kJ mol-1.

Bond dissociation energies of ethyl valerate and tripropionin

CONTEXT

Due to the expected decrease in the availability of conventional oils, numerous studies are currently underway to find complementary sources of energy. Among the explored avenue is that of biofuels. Ethyl valerate (ETV) and tripropionin (TPP) are two biofuels whose thermal decomposition has not received the attention it deserves. Herein, we have evaluated the bond dissociation enthalpies (BDHs) to predict how easy it is to break some bonds in these compounds, and subsequently contribute to revealing the initiation step in their combustion reactions. Our computations consistently predict C4-C5 and C1-C2 bonds in ETV and TPP as the weakest bonds, likely to break first and initiate the thermal decomposition of these two compounds, respectively. The conformational changes in ETV and TPP have only a small influence on the BDHs of 1 kcal/mol at M06-2X/6-311 + G(3df,2p). B3LYP and ωB97XD appear to be the most affordable methods for estimating BDHs at 6-31G(d,p) as they give good results for ETV (RMSD: 2.94 kcal/mol and 3.22 kcal/mol) and performed better than CBS-QB3 (RMSD: 3.64 kcal/mol). Using a larger basis set, the M06-2X (RMSD: 3.61 kcal/mol) and ωB97XD (RMSD: 3.51 kcal/mol) functionals are found to provide the most accurate predictions at 6-311 + G(3df,2p) as compared to G4MP2.

METHODS

BDHs of ETV and TPP are computed using density functional theory (DFT) and quantum chemistry composite methods at 6-31G(d,p) and 6-311 + G(3df,2p) levels. Because of its reliability and accuracy in thermochemical calculations, the G4MP2 theory is used as a reference to gauge the performance of DFT methods. All the calculations were carried out using the Gaussian 09 program.

Experimental and theoretical study of the mechanism and rate constants of the sequential 5-exo-trig spirocyclization involving vinyl, aryl and N-alkoxyaminyl radicals

In this research the sequential generation and cyclization of N-alkoxyaminyl radicals to produce 1-azaspiro[4.4]nonane, a prominent scaffold in organic and medicinal chemistry, was studied. Competition experiments in benzene at 80 °C with brominated oxime ethers using Bu₃SnH as chain transfer and AIBN as the initiator generated vinyl or aryl radicals which were captured by oxime ethers, allowing approximate 5-exo-trig cyclization constants at 4.6 × 10⁸ s^-1 and 9.9 × 10⁸ s^-1 respectively to be established. Similar results were obtained by kinetic studies using the transition state theory (TST) from ab initio calculations with density functional theory (DFT) using the M06-2X, B3LYP, mPW1PW91 and TPSSh functionals in combination with the 6-311+G(d, p) basis set. Additionally, it was found that the 5-exo-trig cyclization of the N-alkoxyaminyl radical onto CC double bonds is a reversible process whose constants were determined to be in the range of 6.2 × 10⁰ s^-1 and 3.5 × 10⁶ s^-1 at 80 °C, depending on the nature of the substituents. The calculation of the radical stabilization energy (RSE) shows that the N-alkoxyaminyl radical is a very stable species and its reactivity in the addition on alkenes is governed by its nucleophilic character and the stability of the carbon-centered radical formed after cyclization. The reduction constant of the N-alkoxyaminyl radical with Bu₃SnH in the gas phase at 80 °C was also estimated to be 3.4 × 10⁰ M^-1 s^-1 through computational calculations. This information facilitates the rational planning of cascades and other methodologies applied to the construction of carbocyclic and aza-heterocyclic compounds.

Autoxidation of Formaldehyde with Oxygen-A Comparison of Reaction Channels

The autoxidation of formaldehyde through initiation by triplet oxygen is studied via two initial steps: (1) H-atom abstraction and (2) 3O2 addition reaction. The reaction energy profiles show that the reactions are thermodynamically and kinetically demanding. A comparison of the pathways of these initial reactions and the search for a less energy-demanding pathway is presented. The presence of a Brønsted acid has no effect on the energetics of the reaction, while the presence of a single water molecule catalyst enhances the initial reactions. The H-atom abstraction reaction from formaldehyde results in formyl and hydroperoxy radicals. These radicals on further reaction with the second equivalent of 3O2 lead to a CO + 2HO2 product channel. The 3O2 addition reaction to formaldehyde results in a triplet biradical intermediate which further leads to performic acid, the precursor in the synthesis of carboxylic acids from aldehydes. In the presence of water molecules, performic acid is formed in a single kinetic step, and this leads to a CO2 + OH + HO2 product channel upon subsequent reaction with 3O2 in a thermodynamically favorable reaction. The results show that the less established 3O2 addition reaction to aldehydes is a viable route for autoxidation in the absence of purpose-built initiators, in addition to the well-established H-atom abstraction route.

BSE49, a diverse, high-quality benchmark dataset of separation energies of chemical bonds

We present an extensive and diverse dataset of bond separation energies associated with the homolytic cleavage of covalently bonded molecules (A-B) into their corresponding radical fragments (A. and B.). Our dataset contains two different classifications of model structures referred to as "Existing" (molecules with associated experimental data) and "Hypothetical" (molecules with no associated experimental data). In total, the dataset consists of 4502 datapoints (1969 datapoints from the Existing and 2533 datapoints from the Hypothetical classes). The dataset covers 49 unique X-Y type single bonds (except H-H, H-F, and H-Cl), where X and Y are H, B, C, N, O, F, Si, P, S, and Cl atoms. All the reference data was calculated at the (RO)CBS-QB3 level of theory. The reference bond separation energies are non-relativistic ground-state energy differences and contain no zero-point energy corrections. This new dataset of bond separation energies (BSE49) is presented as a high-quality reference dataset for assessing and developing computational chemistry methods.

The Chemical Bond: When Atom Size Instead of Electronegativity Difference Determines Trend in Bond Strength

We have quantum chemically analyzed element−element bonds of archetypal H_nX−YH_n molecules (X, Y=C, N, O, F, Si, P, S, Cl, Br, I), using density functional theory. One purpose is to obtain a set of consistent homolytic bond dissociation energies (BDE) for establishing accurate trends across the periodic table. The main objective is to elucidate the underlying physical factors behind these chemical bonding trends. On one hand, we confirm that, along a period (e. g., from C−C to C−F), bonds strengthen because the electronegativity difference across the bond increases. But, down a period, our findings constitute a paradigm shift. From C−F to C−I, for example, bonds do become weaker, however, not because of the decreasing electronegativity difference. Instead, we show that the effective atom size (via steric Pauli repulsion) is the causal factor behind bond weakening in this series, and behind the weakening in orbital interactions at the equilibrium distance. We discuss the actual bonding mechanism and the importance of analyzing this mechanism as a function of the bond distance.

IRMPD Spectroscopy of Homo- and Heterochiral Asparagine Proton-Bound Dimers in the Gas Phase

We investigate gas-phase structures of homo- and heterochiral asparagine proton-bound dimers with infrared multiphoton dissociation (IRMPD) spectroscopy and quantum-chemical calculations. Their IRMPD spectra are recorded at room temperature in the range of 500-1875 and 3000-3600 cm-1. Both varieties of asparagine dimers are found to be charge-solvated based on their IRMPD spectra. The location of the principal intramolecular H-bond is discussed in light of harmonic frequency analyses using the B3LYP functional with GD3BJ empirical dispersion. Contrary to theoretical analyses, the two spectra are very similar.

Exceptionally Long Covalent CC Bonds-A Local Vibrational Mode Study

For decades one has strived to synthesize a compound with the longest covalent C−C bond applying predominantly steric hindrance and/or strain to achieve this goal. On the other hand electronic effects have been added to the repertoire, such as realized in the electron deficient ethane radical cation in its D3d form. Recently, negative hyperconjugation effects occurring in diamino-o-carborane analogs such as di-N,N-dimethylamino-o-carborane have been held responsible for their long C−C bonds. In this work we systematically analyzed CC bonding in a diverse set of 53 molecules including clamped bonds, highly sterically strained complexes such as diamondoid dimers, electron deficient species, and di-N,N-dimethylamino-o-carborane to cover the whole spectrum of possibilities for elongating a covalent C−C bond to the limit. As a quantitative intrinsic bond strength measure, we utilized local vibrational CC stretching force constants ka(CC) and related bond strength orders BSO n(CC), computed at the ωB97X-D/aug-cc-pVTZ level of theory. Our systematic study quantifies for the first time that whereas steric hindrance and/or strain definitely elongate a C−C bond, electronic effects can lead to even longer and weaker C−C bonds. Within our set of molecules the electron deficient ethane radical cation, in D3d symmetry, acquires the longest C−C bond with a length of 1.935 Å followed by di-N,N-dimethylamino-o-carborane with a bond length of 1.930 Å. However, the C−C bond in di-N,N-dimethylamino-o-carborane is the weakest with a BSO n value of 0.209 compared to 0.286 for the ethane radical cation; another example that the longer bond is not always the weaker bond. Based on our findings we provide new guidelines for the general characterization of CC bonds based on local vibrational CC stretching force constants and for future design of compounds with long C−C bonds.

Reactive Compression Molding Post-Inverse Vulcanization: A Method to Assemble, Recycle, and Repurpose Sulfur Polymers and Composites

Inverse vulcanization provides dynamic and responsive materials made from elemental sulfur and unsaturated cross-linkers. These polymers have been used in a variety of applications such as energy storage, infrared optics, repairable materials, environmental remediation, and precision fertilizers. In spite of these advances, there is a need for methods to recycle and reprocess these polymers. In this study, polymers prepared by inverse vulcanization are shown to undergo reactive compression molding. In this process, the reactive interfaces of sulfur polymers are brought into contact by mechanical compression. Upon heating these molds at relatively low temperatures (≈100 °C), chemical bonding occurs at the polymer interfaces by S-S metathesis. This method of processing is distinct from previous studies on inverse vulcanization because the polymers examined in this study do not form a liquid phase when heated. Neither compression nor heating alone was sufficient to mold these polymers into new architectures, so this is a new concept in the manipulation of sulfur polymers. Additionally, high-level ab initio calculations revealed that the weakest S-S bond in organic polysulfides decreases linearly in strength from a sulfur rank of 2 to 4, but then remains constant at about 100 kJ mol^-1 for higher sulfur rank. This is critical information in engineering these polymers for S-S metathesis. Guided by this insight, polymer repair, recycling, and repurposing into new composites was demonstrated.

Kinetic and Theoretical Study of the Atmospheric Aqueous-Phase Reactions of OH Radicals with Methoxyphenolic Compounds

Methoxyphenols, which are emitted through biomass burning, are an important species in atmospheric chemistry. In the present study, temperature-dependent aqueous-phase OH radical reactions of six methoxyphenols and two related phenols have been investigated through laser flash photolysis and the density functional theory. The rate constants obtained were in a range of (1.1-1.9) × 10¹⁰ L mol^-1 s^-1 with k(3-MC) > k(Cre) ≈ k(Syr) ≈ k(MEP) > k(Res) > k(3-MP) > k(2-EP) ≈ k(2-MP). We derived the parameters of these reactions from the obtained T-dependent rate constants and found a mean Arrhenius activation energy of 16.9 kJ mol^-1. The diffusion rate constants were calculated for each case and compared to the measured ones. Generally, the rate constants are found to be close to fully diffusion-controlled (k_diff = (1.4-1.5) × 10¹⁰ L mol^-1 s^-1 for all reactions). A structure-function relationship was established through the measurement result, which could be used for predicting unknown rate constants of other phenolic compounds. All of these findings are expected to enhance the predictive capabilities of models, such as the chemical aqueous-phase radical mechanism.

Modelling the Effect of Conformation on Hydrogen-Atom Abstraction from Peptides

Computational quantum chemistry is used to examine the effect of conformation on the kinetics of hydrogen-atom abstraction by HO• from amides of glycine and proline as peptide models. In accord with previous findings, it is found that there are substantial variations possible in the conformations and the corresponding energies, with the captodative effect, hydrogen bonding, and solvation being some of the major features that contribute to the variations. The ‘minimum-energy-structure-pathway’ strategy that is often employed in theoretical studies of peptide chemistry with small models certainly provides valuable fundamental information. However, one may anticipate different reaction outcomes in structurally constrained systems due to modified reaction thermodynamics and kinetics, as demonstrated explicitly in the present study. Thus, using a ‘consistent-conformation-pathway’ approach may indeed be more informative in such circumstances, and in this regard theory provides information that would be difficult to obtain from experimental studies alone.

How to computationally calculate thermochemical properties objectively, accurately, and as economically as possible

We have developed the WnX series of quantum chemistry composite protocols for the computation of highly-accurate thermochemical quantities with advanced efficiency and applicability. The W1X-type methods have a general accuracy of ~3–4 kJ mol−1 and they can currently be applied to systems with ~20–30 atoms. Higher-level methods include W2X, W3X and W3X-L, with the most accurate of these being W3X-L. It can be applied to molecules with ~10–20 atoms and is generally accurate to ~1.5 kJ mol−1. The WnX procedures have opened up new possibilities for computational chemists in pursue of accurate thermochemical values in a highly-productive manner.

Unification of the W1X and G4(MP2)-6X Composite Protocols

We have devised the composite procedures WG and WGh to unify the W1X and the (computationally more economical) G4(MP2)-6X protocols. The WG procedure employs a combination of MP2, MP2-F12, CCSD-F12b, and CCSD(T) to approximate the all-electron scalar-relativistic CCSD(T)/CBS energy. In addition, it incorporates features such as the scaling of the energy components and an empirical "higher-level-correction" term. The WGh protocol represents a somewhat more economical variant of WG with partial removal of diffuse functions. Our benchmark shows that, in general, both WG and WGh have similar performance to that for W1X-2, with WGh (predictably) performing somewhat less well for electron affinities. In terms of computational efficiency, WG is approximately an order of magnitude less costly than W1X-2, while WGh gives not only a further slight savings in computer time but also a notably reduced disk requirement.

Radical Reaction Control in the AdoMet Radical Enzyme CDG Synthase (QueE): Consolidate, Destabilize, Accelerate

Controlling radical intermediates and thus catalysing and directing complex radical reactions is a central feature of S-adensosylmethionine (SAM)-dependent radical enzymes. We report ab initio and DFT calculations highlighting the specific influence of ion complexation, including Mg2+ , identified as a key catalytic component on radical stability and reaction control in 7-carboxy-7-deazaguanine synthase (QueE). Radical stabilisation energies (RSEs) of key intermediates and radical clock-like model systems of the enzyme-catalysed rearrangement of 6-carboxytetrahydropterin (CPH4), reveals a directing role of Mg2+ in destabilising both the substrate-derived radical and corresponding side reactions, with the effect that the experimentally-observed rearrangement becomes dominant over possible alternatives. Importantly, this is achieved with minimal disruption of the thermodynamics of the substrate itself, affording a novel mechanism for an enzyme to both maintain binding potential and accelerate the rearrangement step. Other mono and divalent ions were probed with only dicationic species achieving the necessary radical conformation to facilitate the reaction.

The stability of nitrogen-centered radicals

Radical stabilization energies (RSEs) for a wide variety of nitrogen-centered radicals and their protonated counterparts have been calculated at G3(MP2)-RAD and G3B3 level. The calculated RSE values can be rationalized through the combined effects of resonance delocalization of the unpaired spin, electron donation through adjacent alkyl groups or lone pairs, and through inductive electron donation/electron withdrawal. The influence of ring strain effects as well as the synergistic combination of individual substituent effects (captodatively stabilized N-radicals) have also been explored. In symmetric N-radicals the substituents may also affect the relative ordering of electronic states. In most cases the π-type radical (unpaired spin distribution perpendicular to the plane of the N-radical) is found to be most stable. Closed shell precursors of biological and pharmaceutical relevance, for which neither experimental nor theoretical results on radical stabilities exist, have been included.

Outcome-changing effect of polarity reversal in hydrogen-atom-abstraction reactions

We have examined hydrogen-atom-abstraction reactions for combinations of electrophilic/nucleophilic radicals with electrophilic/nucleophilic substrates. We find that reaction between an electrophilic radical and a nucleophilic substrate is relatively favorable, and vice versa, but the reactions between a radical and a substrate that are both electrophilic or both nucleophilic are relatively unfavorable, consistent with the literature reports of Roberts. As a result, the regioselectivity for the abstraction from a polar substrate can be reversed by reversing the polarity of the attacking radical. Our calculations support Roberts' polarity-reversal-catalysis concept and suggest that addition of a catalyst of appropriate electrophilicity/nucleophilicity can lead to an enhancement of the reaction rate of approximately 5 orders of magnitude. By exploiting the control over regioselectivity associated with the polar nature of the radical and the substrate, we demonstrate the possibility of directing the regioselectivity of hydrogen abstraction from amino acid derivatives and simultaneously providing a significant rate acceleration.

Antioxidant properties can be tuned in the presence of an external electric field: accurate computation of O–H BDE with range-separated density functionals

The effect of external electric field on the antioxidant properties of gallic and caffeic acids is studied. The performance of range-separated functionals in reproducing the O–H BDE is tested in the presence of an external electric field.

Theoretical study on homolytic C(sp2)–O cleavage in ethers and phenols

The C(sp²)–O BDEs and the substituent effect of ethers/phenols were investigated in detail by the wB97 method.

Modeling spin-forbidden monomer self-initiation reactions in spontaneous free-radical polymerization of acrylates and methacrylates

A spin-forbidden reaction is a reaction in which the total electronic spin-state changes. The standard transition-state theory that assumes a reaction occurs on a single potential energy surface with spin-conservation cannot be applied to a spin-forbidden reaction directly. In this work, we derive the crossing coefficient based on the Wentzel-Kramers-Brillouin (WKB) theory to quantify the effect of intersystem crossing on the kinetics of spin-forbidden reactions. Acrylates and methacrylates, by themselves, can generate free radicals that initiate polymerization at temperatures above 120 °C. Previous studies suggest that a triplet diradical is a key intermediate in the self-initiation. The formation of a triplet diradical from two closed-shell monomer molecules is a spin-forbidden reaction. This study provides a quantitative analysis of singlet-triplet spin crossover of diradical species in self-initiation of acrylates and methacrylates, taking into account the effect of intersystem crossing. The concept of crossing control is introduced and demonstrated computationally to be a new likely route to generate monoradicals via monomer self-initiation in high temperature polymerization.

Quantum chemistry structures and properties of 134 kilo molecules

Computational de novo design of new drugs and materials requires rigorous and unbiased exploration of chemical compound space. However, large uncharted territories persist due to its size scaling combinatorially with molecular size. We report computed geometric, energetic, electronic, and thermodynamic properties for 134k stable small organic molecules made up of CHONF. These molecules correspond to the subset of all 133,885 species with up to nine heavy atoms (CONF) out of the GDB-17 chemical universe of 166 billion organic molecules. We report geometries minimal in energy, corresponding harmonic frequencies, dipole moments, polarizabilities, along with energies, enthalpies, and free energies of atomization. All properties were calculated at the B3LYP/6-31G(2df,p) level of quantum chemistry. Furthermore, for the predominant stoichiometry, C7H10O2, there are 6,095 constitutional isomers among the 134k molecules. We report energies, enthalpies, and free energies of atomization at the more accurate G4MP2 level of theory for all of them. As such, this data set provides quantum chemical properties for a relevant, consistent, and comprehensive chemical space of small organic molecules. This database may serve the benchmarking of existing methods, development of new methods, such as hybrid quantum mechanics/machine learning, and systematic identification of structure-property relationships.

Inherent and transferable stabilization energies of carbon- and heteroatom-centred radicals on the same relative scale and their applications

Accurate G3(MP2)-RAD calculations are used to predict 264 R-H, R-CH3, R-Cl and R-R bond dissociation energies for a wide-ranging test set of carbon and non-carbon centred R˙ radicals. The data are used to calculate a set of inherent and transferrable radical stabilization energies, denoted RSEEt, which ranks the inherent stability of the 66 radicals studied on the same relative scale, irrespective of the nature of the radical centre. The Pauling electronegativity parameter for each radical is also calculated from the same data, along with the radical's inherent bonding ability D[R-R]calc. This latter quantity is defined as the R-R bond dissociation energy expected in the absence of direct steric or resonance interactions that are present in R-R but absent in R-CH3 and R-Cl. We show that the differences between D[R-R] and D[R-R]calc are typically very small except when R is sterically bulky, or there is a chain of (hyper)conjugation across the R-R bond. In such cases the difference between D[R-R] and D[R-R]calc provides a convenient means of quantifying the stabilization or destabilization of R-R due to these interactions. The predictability of the scheme is demonstrated by using these radical stabilities to calculate R-R' bond dissociation energies for 234 combinations of the 66 radicals studied, chosen to exclude steric or resonance interactions in the R-R' bond. The predicted bond energies lie within an average of 1.6 kcal mol(-1) from directly measured or calculated literature values.

W3X: A Cost-Effective Post-CCSD(T) Composite Procedure

We have formulated the W3X procedure by incorporating cost-effective post-CCSD(T) components (up to the CCSDT(Q) level) into the W1X-1 protocol, the latter representing a recently reported economical yet accurate approximation to CCSD(T)/CBS. For medium-sized systems, W3X is moderately more computationally demanding than W1X-1, but it is significantly less costly than the W3.2lite and (especially) W3.2 procedures. Because of the use of the cost-effective W1X-1 method as the underlying CCSD(T) component, W3X is also less expensive than the W2.2 protocol, which does not incorporate post-CCSD(T) excitations. We find that, for single-reference systems (the G2/97 set and most of the W4-11 set), W3X is comparable in accuracy to the underlying W1X-1 protocol, as might have been expected. For the more challenging cases of the multireference systems within the W4-11 set, the dissociation of F2 and the automerization of cyclobutadiene, W3X provides improved performance compared with the CCSD(T)-based procedures (W1X-1 and W2.2). Highly multireference chromium oxides CrO, CrO2, and CrO3 are still somewhat challenging for W3X (and even for the higher-level W3.2lite and W3.2 procedures), but the inclusion of the economical post-CCSD(T) terms in W3X already leads to a significant improvement over W1X-1. Thus, W3X provides a cost-effective means for treating systems with significant (but perhaps not excessive) multireference character that are otherwise not well-described by CCSD(T)-based methods.