Isodesmic Reaction Schemes Research Articles

Photoionization of buckybowls: Sumanene and derivatives

The electronic structures of sumanene and several heterasumanenes have been calculated using high-level ab initio method: Green’s function method (OVGF). The vertical, valence ionization energies were calculated and gas phase photoelectron spectra simulated on the basis of those ionization energies. The Franck-Condon analysis of vibronic effects has also been performed and changes between molecular geometries in neutral and ionic state have been discussed Standard formation enthalpies for some sumanenes were calculated using isodesmic reaction scheme. The results help in the understanding of how is the electronic structure affected when molecule deviates from planar geometry and what is the influence of substituents in benzylic positions. We have demonstrated that the substituent effects affect not only geometry, but also the electronic structure (reflected in ionization energies). This can be used in preparing new functional materials for various applications.

Thermochemistry of Oxygen-Containing Organosilane Radicals and Uncertainty Estimations of Organosilane Group-Additivity Values.

Si-C-H-O-containing radicals are important intermediates during the combustion and pyrolysis of precursors applied for the gas-phase synthesis of silica nanoparticles. Despite the industrial importance of silica nanoparticles, a comprehensive thermodynamics database of organosilane species is still missing. This work presents thermochemical data of 91 Si-C-H-O radical species. Quantum-chemical calculations and isodesmic reaction schemes are used to determine the standard enthalpy of formation, entropy, and heat capacities covering the 298-2000 K temperature range. In addition, 90 group-additivity values (GAVs) are calculated, which cover all relevant group increments. A combinatorial approach is used to ensure that all possible group increments are considered. The theoretically calculated species are used as a training set to derive 90 GAVs of Si-C-H-O radical species for the first time. In addition, uncertainty contributions of GAVs were estimated. These uncertainty estimates also comprise GAVs that were previously derived to compute thermochemical data of stable Si-C-H species and radicals as well as stable Si-C-H-O compounds. Therefore, uncertainty contributions of GAVs for a whole set of 243 group increments used to predict thermochemical data of Si-organic species are reported.

SAMPL7 blind challenge: quantum-mechanical prediction of partition coefficients and acid dissociation constants for small drug-like molecules.

The physicochemical properties of a drug molecule determine the therapeutic effectiveness of the drug. Thus, the development of fast and accurate theoretical approaches for the prediction of such properties is inevitable. The participation to the SAMPL7 challenge is based on the estimation of logP coefficients and pKa values of small drug-like sulfonamide derivatives. Thereby, quantum mechanical calculations were carried out in order to calculate the free energy of solvation and the transfer energy of 22 drug-like compounds in different environments (water and n-octanol) by employing the SMD solvation model. For logP calculations, we studied eleven different methodologies to calculate the transfer free energies, the lowest RMSE value was obtained for the M06L/def2-TZVP//M06L/def2-SVP level of theory. On the other hand, we employed an isodesmic reaction scheme within the macro pKa framework; this was based on selecting reference molecules similar to the SAMPL7 challenge molecules. Consequently, highly well correlated pKa values were obtained with the M062X/6-311+G(2df,2p)//M052X/6-31+G(d,p) level of theory.

Large Stabilization Effects by Intramolecular Beryllium Bonds in Ortho-Benzene Derivatives.

Intramolecular interactions are shown to be key for favoring a given structure in systems with a variety of conformers. In ortho-substituted benzene derivatives including a beryllium moiety, beryllium bonds provide very large stabilizations with respect to non-bound conformers and enthalpy differences above one hundred kJ·mol−1 are found in the most favorable cases, especially if the newly formed rings are five or six-membered heterocycles. These values are in general significantly larger than hydrogen bonds in 1,2-dihidroxybenzene. Conformers stabilized by a beryllium bond exhibit the typical features of this non-covalent interaction, such as the presence of a bond critical point according to the topology of the electron density, positive Laplacian values, significant geometrical distortions and strong interaction energies between the donor and acceptor quantified by using the Natural Bond Orbital approach. An isodesmic reaction scheme is used as a tool to measure the strength of the beryllium bond in these systems in terms of isodesmic energies (analogous to binding energies), interaction energies and deformation energies. This approach shows that a huge amount of energy is spent on deforming the donor–acceptor pairs to form the new rings.

Regio and stereochemical probes of iodine interactions in diiodocyclododecanes

AbstractCyclododecane preferentially adopts a square‐like geometry, giving rise to corner and edge methylene (CH2) groups, whose hydrogens assume different orientations. In edge CH2 groups, hydrogens can be inward‐ (endo) and outward‐looking (exo) the ring. Herein, we have quantum‐chemically studied the replacement of two hydrogens in cyclododecane with iodines at the relative positions 1,4, 1,5, 1,6, and 1,7. Intramolecular interactions are only slightly unfavorable in 1,7‐diiodocyclododecane containing the organic iodines in the edge/endo positions, less than expected from steric considerations. This behavior was discussed in terms of transannular interactions, and a numerical estimation for the magnitude of the intramolecular interaction energy has been performed based on an isodesmic reaction scheme and by natural energy decomposition analysis. 1,5‐Diiodocyclododecane with both edge iodines in the endo orientation (occupying opposite faces of the ring) is strongly favored (by ca. 2.0 kcal mol−1) compared to the respective monosubstituted counterparts, due to highly stabilizing hyperconjugative interactions. Although halogen bonding involving anionic species is widely known, we show that organic halogens, in particular iodine, can be useful for stereochemical control in macrocycles.

Thermochemistry of organosilane compounds and organosilyl radicals

Si–C–H-containing radicals and stable species are present in the oxidation of silicon-organic compounds such as methyl and ethyl silanes, which are frequently-used precursors for the synthesis of silicon-based nanoparticles and coatings via combustion processes. Silicon-containing intermediates interact with flame radicals and thus play a major role in flame chemistry and influence flame propagation. Mechanistic understanding of these effects is hampered by very limited thermochemical properties available for relevant organosilane species. This paper presents quantum-chemical calculations and isodesmic reaction schemes for the determination of temperature-dependent heat of formation, entropy, and heat capacity of Si–C–H radicals and molecules, from which group additivity values (GAVs) were obtained from combinatorial considerations. The data for 22 stable Si–C–H species are revised using isodesmic reactions and the related 24 GAVs were refined by considering 19 additional stable Si–C–H species. In addition, quantum chemical calculations are made to calculate the thermochemistry of 61 radicals and used to derive 56 GAVs for Si–C–H containing radicals for the first time.

Effective Molecular Descriptors for Chemical Accuracy at DFT Cost: Fragmentation, Error-Cancellation, and Machine Learning.

Recent advances in theoretical thermochemistry have allowed the study of small organic and bio-organic molecules with high accuracy. However, applications to larger molecules are still impeded by the steep scaling problem of highly accurate quantum mechanical (QM) methods, forcing the use of approximate, more cost-effective methods at a greatly reduced accuracy. One of the most successful strategies to mitigate this error is the use of systematic error-cancellation schemes, in which highly accurate QM calculations can be performed on small portions of the molecule to construct corrections to an approximate method. Herein, we build on ideas from fragmentation and error-cancellation to introduce a new family of molecular descriptors for machine learning modeled after the Connectivity-Based Hierarchy (CBH) of generalized isodesmic reaction schemes. The best performing descriptor ML(CBH-2) is constructed from fragments preserving only the immediate connectivity of all heavy (non-H) atoms of a molecule along with overlapping regions of fragments in accordance with the inclusion-exclusion principle. Our proposed approach offers a simple, chemically intuitive grouping of atoms, tuned with an optimal amount of error-cancellation, and outperforms previous structure-based descriptors using a much smaller input vector length. For a wide variety of density functionals, DFT+ΔML(CBH-2) models, trained on a set of small- to medium-sized organic HCNOSCl-containing molecules, achieved an out-of-sample MAE within 0.5 kcal/mol and 2σ (95%) confidence interval of <1.5 kcal/mol compared to accurate G4 reference values at DFT cost.

The Driving Force for the Acylation of β-Lactam Antibiotics by L,D-Transpeptidase 2: Quantum Mechanics/Molecular Mechanics (QM/MM) Study.

β-lactam antibiotics, which are used to treat infectious diseases, are currently the most widely used class of antibiotics. This study focused on the chemical reactivity of five- and six-membered ring systems attached to the β-lactam ring. The ring strain energy (RSE), force constant (FC) of amide (C-N), acylation transition states and second-order perturbation stabilization energies of 13 basic structural units of β-lactam derivatives were computed using the M06-2X and G3/B3LYP multistep method. In the ring strain calculations, an isodesmic reaction scheme was used to obtain the total energies. RSE is relatively greater in the five-(1a-2c) compared to the six-membered ring systems except for 4b, which gives a RSE that is comparable to five-membered ring lactams. These variations were also observed in the calculated inter-atomic amide bond distances (C-N), which is why the six-membered ring lactams C-N bond are more rigid than those with five-membered ring lactams. The calculated ΔG# values from the acylation reaction of the lactams (involving the S-H group of the cysteine active residue from L,D transpeptidase 2) revealed a faster rate of C-N cleavage in the five-membered ring lactams especially in the 1-2 derivatives (17.58 kcal mol-1 ). This observation is also reflected in the calculated amide bond force constant (1.26 mDyn/A) indicating a weaker bond strength, suggesting that electronic factors (electron delocalization) play more of a role on reactivity of the β-lactam ring, than ring strain.

Kinetics and mechanism of 3-chloro-2-methyl-1-propene(3-ClMP) initiated by OH radical: an insight from DFT calculations[1

ABSTRACTIn this manuscript, OH-initiated gas phase reactions of 3-chloro-2-methyl-1-propene [CH2=C(CH3)CH2Cl] has been carried out by using density functional theory (DFT) method. We have chosen M06-2X hybrid density functional method along with 6-31 + G(d,p) basis set for optimisation and vibrational frequency calculations of all the relevant molecular species of the titled reaction. Energetic calculations have been further refined at CCSD(T) method along with cc-pVTZ basis set in order to obtain higher degree of precision of thermo-chemical and kinetic results. Energy profile is presented for all stationary points involved in the titled reaction and thermochemistry for all possible reaction channels (H-abstraction and OH-addition reactions) has been analysed. Canonical Transition State Theory (CTST) has been employed to determine the rate constants within the temperature range of 250–450 K and Our reported rate constant at 298 K are found to be close to the reported experimental rate constant. The atmospheric lifetime of the titled molecule has also been reported in this work. We have also reported standard enthalpies of formation of the titled molecule and generated product radicals by using group-balanced isodesmic reaction schemes.

Enthalpies of Formation of Hydrazine and Its Derivatives.

Enthalpies of formation, ΔfH298°, in both the gas and condensed phase, and enthalpies of sublimation or vaporization have been estimated for hydrazine, NH2NH2, and its 36 various derivatives using quantum chemical calculations. The composite G4 method has been used along with isodesmic reaction schemes to derive a set of self-consistent high-accuracy gas-phase enthalpies of formation. To estimate the enthalpies of sublimation and vaporization with reasonable accuracy (5-20 kJ/mol), the method of molecular electrostatic potential (MEP) has been used. The value of ΔfH298°(NH2NH2,g) = 97.0 ± 3.0 kJ/mol was determined from 75 isogyric reactions involving about 50 reference species; for most of these species, the accurate ΔfH298°(g) values are available in Active Thermochemical Tables (ATcT). The calculated value is in excellent agreement with the reported results of the most accurate models based on coupled cluster theory (97.3 kJ/mol, the average of six calculations). Thus, the difference between the values predicted by high-level theoretical calculations and the experimental value of ΔfH298°(NH2NH2,g) = 95.55 ± 0.19 kJ/mol recommended in the ATcT and other comprehensive reference sources is sufficiently large and requires further investigation. Different hydrazine derivatives have been also considered in this work. For some of them, both the enthalpy of formation in the condensed phase and the enthalpy of sublimation or vaporization are available; for other compounds, experimental data for only one of these properties exist. Evidence of accuracy of experimental data for the first group of compounds was provided by the agreement with theoretical ΔfH298°(g) value. The unknown property for the second group of compounds was predicted using the MEP model. This paper presents a systematic comparison of experimentally determined enthalpies of formation and enthalpies of sublimation or vaporization with the results of calculations. Because of relatively large uncertainty in the estimated enthalpies of sublimation, it was not always possible to evaluate the accuracy of the experimental values; however, this model allowed us to detect large errors in the experimental data, as in the case of 5,5'-hydrazinebistetrazole. The enthalpies of formation and enthalpies of sublimation or vaporization have been predicted for the first time for ten hydrazine derivatives with no experimental data. A recommended set of self-consistent experimental and calculated gas-phase enthalpies of formation of hydrazine derivatives can be used as reference ΔfH298°(g) values to predict the enthalpies of formation of various hydrazines by means of isodesmic reactions.

Performance of DFT, MP2, and composite ab initio methods for the prediction of enthalpies of formations of CHON compounds using isodesmic reactions

This paper assesses the performance of quantum chemical models with regard to the calculation of enthalpy of formation of CHON molecules using isodesmic reactions. The high accuracy of prediction of enthalpy of formation of CHON compounds can be achieved by the combination of isodesmic reaction scheme with composite ab initio methods. The best composite methods, such as G4, G4MP2, CBS-QB3, and CBS-APNO, can attain near chemical accuracy or better depending on reaction type. Other composite methods yield the same accuracy only in conjunction with isodesmic or homodesmotic reactions. The DFT and MP2 methods lead to good results if they are used with homodesmotic reactions. For CHO compounds, all composite methods demonstrate the high accuracy not only with isodesmic and homodesmotic reactions, but also with isogyric reactions. Moreover, the DFT and MP2 methods can also yield a high accuracy estimate of the enthalpy of formation when they are used with isodesmic or homodesmotic reactions. Four composite methods (G4, G3, CBS-APNO, and CBS-QB3) employed in conjunction with 45 isogyric reactions yield the enthalpy of formation of hydrazine (97.7±2.0kJ/mol) in agreement with the best approximating to CCSD(T)/CBS energy, thus calling into question the usually quoted experimental value of 95.5kJ/mol.

Cyclopentadienone Oxidation Reaction Kinetics and Thermochemistry for the Alcohols, Hydroperoxides, and Vinylic, Alkoxy, and Alkylperoxy Radicals.

Cyclopentadienone has one carbonyl and two olefin groups resulting in 4n + 2 π-electrons in a cyclic five-membered ring structure. Thermochemical and kinetic parameters for the initial reactions of cyclopentadienone radicals with O2 and the thermochemical properties for cyclopentadienone-hydroperoxides, alcohols, and alkenyl, alkoxy, and peroxy radicals were determined by use of computational chemistry. The CBS-QB3 composite and B3LYP density functional theory methods were used to determine the enthalpies of formation (ΔfH°298) using the isodesmic reaction schemes with several work reactions for each species. Entropy and heat capacity, S°(T) and Cp°(T) (50 K ≤ T ≤ 5000 K) are determined using geometric parameters, internal rotor potentials, and frequencies from B3LYP/6-31G(d,p) calculations. Standard enthalpies of formation are reported for parent molecules as cyclopentadienone, cyclopentadienone with alcohol, hydroperoxide substituents, and the cyclopentadienone-yl vinylic, alkoxy, and peroxy radicals corresponding to loss of a hydrogen atom from the carbon and oxygen sites. Entropy and heat capacity vs temperature also are reported for the parent molecules and for radicals. The thermochemical analysis shows The R(•) + O2 well depths are deep, on the order of 50 kcal mol(-1), and the R(•) + O2 reactions to RO + O (chain branching products) for cyclopentadienone-2-yl and cyclopentadienone-3-yl have unusually low reaction (ΔHrxn) enthalpies, some 20 or so kcal/mol below the entrance channels. Chemical activation kinetics using quantum RRK analysis for k(E) and master equation for falloff are used to show that significant chain branching as a function of temperature and pressure can occur when these vinylic radicals are formed.

Theoretical calculations of the relative pKa values of some selected aromatic arsonic acids in water using density functional theory

Article history: Received July 21, 2015 Received in revised form August 29, 2015 Accepted 8 October 2015 Available online 8 October 2015 With the focus on calculating the equilibrium constant (Ka) of arsonic acids (RAsO(OH)2) in aqueous media, the behavior of both neutral and negatively charged species of some arsonic acids have been considered through the isodesmic reaction scheme with polarized continuum model of solvation. The relative pKa values of a number of arsonic acids were calculated using density functional theory (DFT), with methylarsonic acid (CH3AsO(OH)2) used as a reference molecule. Various basis sets such as (6-31G(d), 6-31+G(d), 6-311++G(d,p) and 6311++G(2d,2p)) in conjunction with B3LYP computational method were examined. Finally the latter one was found to give better results. The results of applied B3LYP 6-311++G(2d,2p) method for pKa values of 25 arsonic acids in aqueous media showed good agreement with corresponding experimental pKa values. In this level of theory the average error was less than 0.3 pKa units. The type of substituent affected the acid strength, with electron withdrawing substituents lowering the pKa and electron releasing groups increasing it. © 2016 Growing Science Ltd. All rights reserved.

Theoretical determination of the redox electrode potential of cyanidin

The electrode potential of cyanidin was determined both by experimental (cyclic voltammetry) and theoretical methods, at HF/6-311G(d) level of theory. An isodesmic reaction scheme, involving 1,2-benzoquinone as reference molecules, has been proposed for the computation of electrode potential of cyanidin. The results of the ab initio computations are in reasonable agreement with available experimental measurements; the differences between experiment and theory are within the range of 0.02-0.05V. Geometric parameters of the six more stable conformers of cyanidin are computed, as well as properties like atomic charges and contribution to the HOMO (Highest Occupied Molecular Orbital) energies of each hydroxyl group of the cyanidin.

Theoretical Studies Regarding the Aromaticity of Some Non-Planar Circulenes

Abstract The aromatic character of three non-planar circulenes has been investigated at B3LYP/6-311+G(d,p) level of theory. Global aromaticity descriptors like HOMO-LUMO gap, enthalpy of formation and exaltation of magnetic susceptibility outline a possible aromatic character only for circulenes [4:64] and [7:67]. The viability of isodesmic reaction schemes -for evaluation of the enthalpies of formation- has been discussed. Local aromaticity descriptors like HOMA (Harmonic Oscillator Model of Aromaticity), NICS (Nucleus Independent Chemical Shift) and electronic delocalization indices have been calculated for each outer ring of circulenes.

Gas-phase equilibrium constants for the thermally initiated oxidation of hexafluoropropene with molecular oxygen

Equilibrium constants for a kinetic model of the thermally initiated gas-phase oxidation of hexafluoropropene have been calculated in the temperature range of 463–493 K based on the thermochemical properties of the reactive species. Standard molar enthalpies and entropies of formation as well as heat capacities of trifluoroacetyl fluoride, hexafluorocyclopropane, hexafluoropropene, and hexafluoropropene oxide were predicted using methods of quantum statistical mechanics. These along with literature data for remaining species involved allowed for calculating reaction enthalpies of individual steps of the proposed reaction mechanism. The calculations were performed at the G4 B3LYP/6-31G(2df,p) level of theory. The enthalpy of formation was determined using both the atomization method and isodesmic reaction schemes. All reactions apart from the decomposition of hexafluoropropene oxide were found to be exothermic. Only the hexafluoropropene oxide decomposition reaction was found to be noticeably reversible under the reaction conditions considered. This was confirmed through independent experimentation and kinetic model identification. Copyright © 2015 John Wiley & Sons, Ltd.

Energetic and structural study of bisphenols.

We have studied thermochemical, thermophysical and structural properties of bisphenols A, E, F, and AP. In particular, the standard enthalpies of sublimation and the standard enthalpies of formation in the gas phase at 298.15 K for all these species were experimentally determined. A computational study, through M05-2X density functional theory, of the various species shed light on structural effects and further confirmed, by means of the isodesmic reaction scheme, the excellent consistency of the experimental results. Our results reflect also the fact that energetic substituent effects are transferable from diphenylalkanes to bisphenols.

Thermochemistry of cyclic acetone peroxides

Two potentially initiating explosive peroxides, diacetonediperoxide (DADP) and triacetonetriperoxide (TATP), were studied in respect to their thermochemical properties. To get the internally self-consistent estimations of gas-phase enthalpy of formation of DADP and TATP, their values were calculated by combining Gaussian-4 (G4) theory with an isodesmic reaction scheme. The energies of combustion (ΔcU) were measured and the standard enthalpies of formation (ΔfH298°) of DADP and TATP were derived using the standard enthalpies of formation of the combustion products. The heat of explosion was measured for small low-pressed charges of the peroxides. The obtained enthalpies of formation of DADP and TATP were found to agree well with quantum chemical calculations and reasonably account for the observed derivative parameters: heats of decomposition, combustion, and detonation.

The DFT calculations of pKa values of the cationic acids of aniline and pyridine derivatives in common solvents

Abstract The theoretical pKa values of the derivatives of anilinium and pyridinium ions in 7 solvents are presented. For this purpose, the usage of isodesmic reaction scheme using the DFT/B3LYP approach with IEFPCM solvation was evaluated. We have shown that the suitable selection of reference species has the primary influence on the resulting data. For the studied anilinium ion derivatives the nonsubstituted anilinium ion seems to be a satisfactory reference system. The calculated values are in good accordance with the available experimental data with the RMS error of 1.00 and 0.99 pKa units in water and THF, respectively. The highest error in predicted pKa value is less than 2.0 pKa units in all cases. The chemical accuracy of the applied treatment is limited in the case of nitroaniline ions and the maximal therotetical uncertainty for derivatives of the pyridinium ion is within 2.1 pKa units. Our theoretical results enable us to predict the values of pKa for the solvents, where the experimental data are not completely available. Also the influence of the chemical structure on the accuracy of the applied method was discussed.

Enthalpies of formation of nitromethane and nitrobenzene: New experiments vs. quantum chemical calculations

Enthalpies of combustion of highly pure nitromethane and nitrobenzene have been measured with precise combustion calorimetry. Enthalpies of vaporisation for both compounds were collected and evaluated. A new, internally consistent experimental data set of ΔfHm°(g) values for nitromethane and nitrobenzene was compared with the results of one of the most accurate first-principles G4 method applied to both atomization and isodesmic reactions. It was shown that the values calculated using the atomization reaction procedure are underestimated by 6.6kJ·mol−1 for nitromethane and 9.1kJ·mol−1 for nitrobenzene. An isodesmic reaction scheme strongly supports the internal consistency of new experimental values. A simple “corrected atomization procedure” to derive reliable theoretical enthalpies of formation directly from the G4 atomization reaction values has been tested and recommended as the alternative to the bond separation and isodesmic reactions.