Assessing the validity of DLPNO-CCSD(T) in the calculation of activation and reaction energies of ubiquitous enzymatic reactions

The domain-based local pair natural orbital coupled-cluster with single, double, and perturbative triples excitation (DLPNO-CCSD(T)) method was employed to portray the activation and reaction energies of four ubiquitous enzymatic reactions, and its performance was confronted to CCSD(T)/complete basis set (CBS) to assess its accuracy and robustness in this specific field. The DLPNO-CCSD(T) results were also confronted to those of a set of density functionals (DFs) to understand the benefit of implementing this technique in enzymatic quantum mechanics/molecular mechanics (QM/MM) calculations as a second QM component, which is often treated with DF theory (DFT). On average, the DLPNO-CCSD(T)/aug-cc-pVTZ results were 0.51 kcal·mol⁻¹ apart from the canonic CCSD(T)/CBS, without noticeable biases toward any of the reactions under study. All DFs fell short to the DLPNO-CCSD(T), both in terms of accuracy and robustness, which suggests that this method is advantageous to characterize enzymatic reactions and that its use in QM/MM calculations, either alone or in conjugation with DFT, in a two-region QM layer (DLPNO-CCSD(T):DFT), should enhance the quality and faithfulness of the results.     

Activation Energies and Reaction Energetics for 1,3‐Dipolar Cycloadditions of Hydrazoic Acid with C?C and C?N Multiple Bonds from High‐Accuracy and Density Functional Quantum Mechanical Calculations

The reactions of hydrazoic acid (HN₃) with ethene, acetylene, formaldimine (H₂CNH), and HCN were explored with the high‐accuracy CBS‐QB3 method, as well as with the B3LYP and mPW1K density functionals. CBS‐QB3 predicts that the activation energies for the reactions of hydrazoic acid with ethylene, acetylene, formaldimine, and HCN have remarkably similar activation enthalpies of 19.0, 19.0, 21.6, and 25.2 kcal/mol, respectively. The reactions are calculated to have reaction enthalpies of −21.5 for triazoline formation from ethene, and −63.7 kcal/mol for formation of the aromatic triazole from acetylene. The reaction to form tetrazoline from formaldimine has a reaction enthalpy of −8 kcal/mol (ΔG_rxn=+5.6 kcal/mol), and the formation of tetrazole from HCN has a reaction enthalpy of −23.0 kcal/mol. The trends in the energetics of these processes are rationalized by differences in σ‐bond energies in the transition states and adducts, and the energy required to distort hydrazoic acid to its transition‐state geometry. The density functionals predict activation enthalpies that are in relatively good agreement with CBS‐QB3, the results differing from CBS‐QB3 results by ca. 1–2 kcal/mol. Significant errors are revealed for mPW1K in predicting the reaction enthalpies for all reactions.     

Molecular enthalpies: 1. Ground-state thermodynamic and computed enthalpies of the norbornadiene cycle

The enthalpies of formation of norbornadiene, norbornene, norbornane, nortricyclane, and quadricyclane, which are experimentally known, have been calculated using the semiempirical programs MNDO, AM1, and PM3 and the empirical force-field method MMP2. MMP2 agrees most closely with experimental results. Of the semiempirical methods, PM3 agrees most closely with experimental results and is very good for the alkenes. Enthalpies of hydrogenation, calculable fromH _f, are inconclusive on the question of ground-state homoaromatic stabilization of norbornadiene.     

Toward a less costly but accurate calculation of the CCSD(T)/CBS noncovalent interaction energy

The popular method of calculating the noncovalent interaction energies at the coupled-cluster single-, double-, and perturbative triple-excitations [CCSD(T)] theory level in the complete basis set (CBS) limit was to add a CCSD(T) correction term to the CBS second-order Møller-Plesset perturbation theory (MP2). The CCSD(T) correction term is the difference between the CCSD(T) and MP2 interaction energies evaluated in a medium basis set. However, the CCSD(T) calculations with the medium basis sets are still very expensive for systems with more than 30 atoms. Comparatively, the domain-based local pair natural orbital coupled-cluster method [DLPNO-CCSD(T)] can be applied to large systems with over 1,000 atoms. Considering both the computational accuracy and efficiency, in this work, we propose a new scheme to calculate the CCSD(T)/CBS interaction energies. In this scheme, the MP2/CBS term keeps intact and the CCSD(T) correction term is replaced by a DLPNO-CCSD(T) correction term which is the difference between the DLPNO-CCSD(T) and DLPNO-MP2 interaction energies evaluated in a medium basis set. The interaction energies of the noncovalent systems in the S22, HSG, HBC6, NBC10, and S66 databases were recalculated employing this new scheme. The consistent and tight settings of the truncation parameters for DLPNO-CCSD(T) and DLPNO-MP2 in this noncanonical CCSD(T)/CBS calculations lead to the maximum absolute deviation and root-mean-square deviation from the canonical CCSD(T)/CBS interaction energies of less than or equal to 0.28 kcal/mol and 0.09 kcal/mol, respectively. The high accuracy and low cost of this new computational scheme make it an excellent candidate for the study of large noncovalent systems.     

Group Additive Values for the Gas‐Phase Standard Enthalpy of Formation,Entropy and Heat Capacity of Oxygenates

A complete and consistent set of 60 Benson group additive values (GAVs) for oxygenate molecules and 97 GAVs for oxygenate radicals is provided, which allow to describe their standard enthalpies of formation, entropies and heat capacities. Approximately half of the GAVs for oxygenate molecules and the majority of the GAVs for oxygenate radicals have not been reported before. The values are derived from an extensive and accurate database of thermochemical data obtained by ab initio calculations at the CBS‐QB3 level of theory for 202 molecules and 248 radicals. These compounds include saturated and unsaturated, α‐ and β‐branched, mono‐ and bifunctional oxygenates. Internal rotations were accounted for by using one‐dimensional hindered rotor corrections. The accuracy of the database was further improved by adding bond additive corrections to the CBS‐QB3 standard enthalpies of formation. Furthermore, 14 corrections for non‐nearest‐neighbor interactions (NNI) were introduced for molecules and 12 for radicals. The validity of the constructed group additive model was established by comparing the predicted values with both ab initio calculated values and experimental data for oxygenates and oxygenate radicals. The group additive method predicts standard enthalpies of formation, entropies, and heat capacities with chemical accuracy, respectively, within 4 kJ mol^?1 and 4 J mol^?1 K^?1 for both ab initio calculated and experimental values. As an alternative, the hydrogen bond increment (HBI) method developed by Lay et al. (T. H. Lay, J. W. Bozzelli, A. M. Dean, E. R. Ritter, J. Phys. Chem.­ 1995 , 99, 14514) was used to introduce 77 new HBI structures and to calculate their thermodynamic parameters (Δ_fH°, S°, C_p°). The GAVs reported in this work can be reliably used for the prediction of thermochemical data for large oxygenate compounds, combining rapid prediction with wide‐ranging application.     

Assessment of Gaussian-3X theory for chlorinated organic molecules. Enthalpies of formation of chlorobenzenes and predictions for polychlorinated aromatic compounds

The enthalpies of formation of chlorinated methanes, ethanes, ethylenes, phenols, and benzenes have been calculated at the G3X level of theory using the atomization energy procedure and the method of isodesmic reactions. By comparing the most reliable experimental data on chlorinated hydrocarbons recommended by Manion [Manion JA (2002) J Phys Chem Ref Data 31:123] with the G3X results, the accuracy of theoretical enthalpies of formation is estimated as ranging from ±4 to ±10 kJ/mol. Only for hexachloroethane, the difference between the experimental value and G3X result was outside this range and the experimental enthalpy of formation of hexachloroethane was called into question by theory. The G3X enthalpies of formation of all chlorobenzenes agree well with experimental data which were partly reanalyzed using recent experimental data on enthalpies of sublimation. Based on the G3X results, a set of self-consistent experimental data for chlorobenzenes is recommended. The enthalpies of formation of some polychlorinated dibenzo-p-dioxins were estimated using improved enthalpies of formation for chlorobenzenes. The possible inaccuracy of previously estimated values for polychlorinated aromatic compounds is discussed.     

A high‐accuracy theoretical study of the CHnP Systems n = 1–3

We have performed high‐level electronic structure computations on the most important species of the CH_nP systems n = 1–3 to characterize them and provide reliable information about the equilibrium and vibrationally averaged molecular structures, rotational constants, vibrational frequencies (harmonic and anharmonic), formation enthalpies, and vertical excitation energies. Those chemical systems are intermediates for several important reactions and also prototypical phosphorus‐carbon compounds; however, they are often elusive to experimental detection. The present results significantly complement their knowledge and can be used as an assessment of the experimental information when available. The explicitly correlated coupled‐cluster RCCSD(T)‐F12 method has been used for geometry optimizations and vibrational frequency calculations. Vibrational configuration interaction theory has been used to account for anharmonicity effects. Basis‐set limit extrapolations have been carried out to determine accurate thermochemical quantities. Electronic excited states have been calculated with coupled‐cluster approaches and also by means of the multireference configuration interaction method. © 2013 Wiley Periodicals, Inc.     

The reactions of dialkyl and diarylethoxysilanes with T6 silsesquioxane cages: X-ray crystallographic studies of the mono-T6D1 and bis-T6D2 insertion ring expansion products

Successful ring-expanding insertion reactions of T₆ silsesquioxane cages using dialkyl and diarylethoxysilanes have been performed to give the first reported mixed T₆D₁ and T₆D₂ silsesquioxane cages. The reactions of hexacyclohexylsilsesquioxane (T₆) with dialkyl and diaryldiethoxysilanes give predominantly T₆D₂ bis-insertion compounds while the reaction of T₆ with dimethylethoxysilane gives one T₆D₁ mono-insertion product and various T₆D₂ bis-insertion products as isolable components. Three of the ring-expanded products are chiral and it has been shown from their X-ray crystal structures that the pairs of enantiomers, formed as racemic mixtures, co-crystallise together. As well as comparing these structures with related ones in the literature, the possible mechanism of their formation is discussed.     

Experimental and computational thermochemistry of 1-phenylpyrrole and 1-(4-methylphenyl)pyrrole

The standard (p° = 0.1 MPa) molar enthalpies of formation, in the crystalline phase, of 1-phenylpyrrole and 1-(4-methylphenyl)pyrrole, at T = 298.15 K, were derived from the standard molar energies of combustion in oxygen, measured by static-bomb combustion calorimetry. For these compounds, the standard molar enthalpies of sublimation, at T = 298.15 K, were determined from the temperature–vapour pressure dependence, obtained by the Knudsen mass-loss effusion method. Using estimated values for the heat capacity differences between the gas and the crystal phases of the studied compounds, the standard (p° = 0.1 MPa) molar enthalpies, entropies, and Gibbs energies of sublimation, at T = 298.15 K, were derived. From the experimental values, the standard molar enthalpies of formation, in the gaseous phase, at T = 298.15 K, were calculated.Additionally, the enthalpies of formation of both compounds were estimated using the composite G3(MP2)//B3LYP approach together with adequate gas-phase working reactions. There is a very good agreement between computational and experimental results.     

The Heat of Formation of the Uranyl Dication: Theoretical Evaluation Based on Relativistic Density Functional Calculations

By using a set of model reactions, we estimated the heat of formation of gaseous UO₂²⁺ from quantum‐chemical reaction enthalpies and experimental heats of formation of reference species. For this purpose, we performed relativistic density functional calculations for the molecules UO₂²⁺, UO₂, UF₆, and UF₅. We used two gradient‐corrected exchange‐correlation functionals (revised Perdew–Burke–Ernzerhof (PBEN) and Becke–Perdew (BP)) and we accounted for spin‐orbit interaction in a self‐consistent fashion. Indeed, spin‐orbit interaction notably affects the energies of the model reactions, especially if compounds of U^IV are involved. Our resulting theoretical estimates for Δ_f (UO₂²⁺), 365±10 kcal mol^?1 (PBEN) and 370±12 kcal mol^?1 (BP), are in quantitative agreement with a recent experimental result, 364±15 kcal mol^?1. Agreement between the results of the two different exchange‐correlation functionals PBEN and BP supports the reliability of our approach. The procedure applied offers a general means to derive unknown enthalpies of formation of actinide species based on the available well‐established data for other compounds of the element in question.     

Thermodynamic data of the NZP compounds family

Summary The thermodynamic data for NZP compounds MZr₂(PO₄)₃ (M=Na, K, Rb, Cs, Zr_0.25) and Na₅D(PO₄)₃ (D=Ti, Zr) are reported. The heat capacities of the phosphates were measured between T=7 and T=640 K. The standard enthalpies entropies, and Gibbs functions of formation at T=298.15 K were derived. The obtained thermodynamic characteristics of phosphates of the NZP type structure and literature data are summarized. Thermodynamic functions of reactions of solid-state synthesis were calculated and the usability of ceramic technology for obtaining NZP compounds was proved.     

Ab initio chemical kinetics for reactions of H atoms with SiHx (x = 1–3) radicals and related unimolecular decomposition processes

Hydrogen atoms and SiH_x (x = 1–3) radicals coexist during the chemical vapor deposition (CVD) of hydrogenated amorphous silicon (a‐Si:H) thin films for Si‐solar cell fabrication, a technology necessitated recently by the need for energy and material conservation. The kinetics and mechanisms for H‐atom reactions with SiH_x radicals and the thermal decomposition of their intermediates have been investigated by using a high high‐level ab initio molecular‐orbital CCSD (Coupled Cluster with Single and Double)(T)/CBS (complete basis set extrapolation) method. These reactions occurring primarily by association producing excited intermediates, ¹SiH₂, ³SiH₂, SiH₃, and SiH₄, with no intrinsic barriers were computed to have 75.6, 55.0, 68.5, and 90.2 kcal/mol association energies for x = 1–3, respectively, based on the computed heats of formation of these radicals. The excited intermediates can further fragment by H₂ elimination with 62.5, 44.3, 47.5, and 56.7 kcal/mol barriers giving ¹Si, ³Si, SiH, and ¹SiH₂ from the above respective intermediates. The predicted heats of reaction and enthalpies of formation of the radicals at 0 K, including the latter evaluated by the isodesmic reactions, SiH_x + CH₄ = SiH₄ + CH_x, are in good agreement with available experimental data within reported errors. Furthermore, the rate constants for the forward and unimolecular reactions have been predicted with tunneling corrections using transition state theory (for direct abstraction) and variational Rice–Ramsperger–Kassel–Marcus theory (for association/decomposition) by solving the master equation covering the P,T‐conditions commonly employed used in industrial CVD processes. The predicted results compare well experimental and/or computational data available in the literature. © 2013 Wiley Periodicals, Inc.     

Additivity methods for prediction of thermochemical properties. The Laidler method revisited. 2. Hydrocarbons including substituted cyclic compounds

A revised parameterization of the extended Laidler method for predicting standard molar enthalpies of atomization and standard molar enthalpies of formation at T = 298.15 K for several families of hydrocarbons (alkanes, alkenes, alkynes, polyenes, poly-ynes, cycloalkanes, substituted cycloalkanes, cycloalkenes, substituted cycloalkenes, benzene derivatives, and bi and polyphenyls) is presented. Data for a total of 265 gas-phase and 242 liquid-phase compounds were used for the calculation of the parameters. Comparison of the experimental values with those obtained using the additive scheme led to an average absolute difference of 0.73 kJ · mol⁻¹ for the gas-phase standard molar enthalpy of formation and 0.79 kJ · mol⁻¹ for the liquid-phase standard molar enthalpy of formation. The database used to establish the parameters was carefully reviewed by using, whenever possible, the original publications. A worksheet to simplify the calculation of standard molar enthalpies of formation and standard molar enthalpies of atomization at T = 298.15 K based on the extended Laidler parameters defined in this paper is provided as supplementary material.     

Experimental standard molar enthalpies of formation of crystalline 3,5-dimethylpyrazole, 3,5-dimethyl-4-nitrosopyrazole, 1,3,5-trimethyl-4-nitrosopyrazole,and 3,5-dimethyl-1-phenyl-4-nitrosopyrazole

The standard (p^o =  0.1 MPa) molar enthalpies of combustion in oxygen, at T =  298.15 K, for crystalline 3,5-dimethylpyrazole (Me₂Pyr), 3,5-dimethyl-4-nitrosopyrazole (Me₂PyrNO), 1,3,5-trimethyl-4-nitrosopyrazole (Me₃PyrNO), and 3,5-dimethyl-1-phenyl-4-nitrosopyrazole (Me₂PhPyrNO) were measured by static-bomb calorimetry. These values were used to derive the standard molar enthalpies of formation of the crystalline compounds. The standard molar enthalpies of sublimation for these four compounds were measured by microcalorimetry.The experimental results obtained allow us to derive the values of the standard molar enthalpies of formation, in the gaseous state, for the monomeric compounds involved in this work. These last values are discussed comparatively with results previously obtained for some aromatic nitroso derivatives.     

Theoretical Studies of the Reactions CFxH3−xCOOR+Cl and CF3COOCH3+OH

The mechanism and kinetics of the reactions of CF₃COOCH₂CH₃, CF₂HCOOCH₃, and CF₃COOCH₃ with Cl and OH radicals are studied using the B3LYP, MP2, BHandHLYP, and M06‐2X methods with the 6‐311G(d,p) basis set. The study is further refined by using the CCSD(T) and QCISD(T)/6‐311++G(d,p) methods. Seven hydrogen‐abstraction channels are found. All the rate constants, computed by a dual‐level direct method with a small‐curvature tunneling correction, are in good agreement with the experimental data. The tunneling effect is found to be important for the calculated rate constants in the low‐temperature range. For the reaction of CF₃COOCH₂CH₃+Cl, H‐abstraction from the CH₂ group is found to be the dominant reaction channel. The standard enthalpies of formation for the species are also calculated. The Arrhenius expressions are fitted within 200–1000 K as k_T(1)=8.4×10^?20T ^2.63exp(381.28/T), k_T(2)=2.95×10^?21T ^3.13exp(?103.21/T), k_T(3)=1.25×10^?23T ^3.37exp(791.98/T), and k_T(4)=4.53×10^?22T ^3.07exp(465.00/T).     

Thermochemical study of 2- and 3-alkyl substituted thiophenes

The standard (p ⁰=0.1 MPa) molar enthalpies of formation, in the condensed phase, of nine linear-alkyl substituted thiophenes, six in position 2- and three in position 3-, at T=298.15 K, were derived from the standard massic energies of combustion, in oxygen, to yield CO₂(g) and H₂SO₄·115H₂O(aq), measured by rotating-bomb combustion calorimetry. The standard molar enthalpies of vaporization of these compounds were measured by high temperature Calvet Microcalorimetry, so their standard molar enthalpies of formation, in the gaseous phase, were derived. The results are discussed in terms of structural contributions to the energetics of the alkyl-substituted thiophenes, and empirical correlations are suggested for the estimation of the standard molar enthalpies of formation, at T=298.15 K, for 2- and 3-alkyl-substituted thiophenes, both in the condensed and in the gaseous phases.     

Thermochemical properties for n‐propyl,iso‐propyl,and tert‐butyl nitroalkanes,alkyl nitrites,and their carbon‐centered radicals

Density functional theory (DFT) based calculations are performed on a series of alkyl nitrites and nitroalkanes representing large‐scale primary, secondary, and tertiary nitro compounds and their radicals resulting from the loss of their skeletal hydrogen atoms. Geometries, vibration frequencies, and thermochemical properties [S°(T) and C°_p(T) (10 K ? T ? 5000 K)] are calculated at the B3LYP/6‐31G(d,p) DFT level. Δ_fH°₂₉₈ values are from B3LYP/6‐31G(d,p), B3LYP/6‐31+G(2d,2p), and the composite CBS‐QB3 levels. Potential energy barriers for the internal rotations have been computed at the B3LYP/6‐31G(d,p) level of theory, and the lower barrier contributions are incorporated into entropy and heat capacity data. The standard enthalpies of formation at 298 K are evaluated using isodesmic reaction schemes with several work reactions for each species. Recommended values derived from the most stable conformers of respective nitro‐ and nitrite isomers include ?30.57 and ?28.44 kcal mol^?1 for n‐propane‐, ?33.89 and ?32.32 kcal mol^?1 for iso‐propane‐, ?42.78 and ?41.36 kcal mol^?1 for tert‐butane‐nitro compounds and nitrites, respectively. Entropy and heat capacity values are also reported for the lower homologues: nitromethane, nitroethane, and corresponding nitrites. © 2010 Wiley Periodicals, Inc. Int J Chem Kinet 42: 181–199, 2010     

Thermodynamic properties of solutions of imidazolidine-2-thione and potassium isopropylxanthate in ethanol and characteristics of individual compounds

The enthalpies of solution of imidazolidine-2-thione and potassium isopropylxanthate in ethanol and their isobaric heat capacity in the range from 173 to (T _{m ? 100}) K were measured by calorimetry at 298.15 K. The standard enthalpies of formation, combustion, and melting of these compounds were estimated.     

Thermochemistry of 2-methylbenzoxazole and 2,5-dimethylbenzoxazole: an experimental and computational study

The standard (p° = 0.1 MPa) molar energies of combustion of 2-methylbenzoxazole and 2,5-dimethylbenzoxazole were measured by static-bomb combustion calorimetry. The standard molar enthalpies of vapourization, at T = 298.15 K, were obtained from high-temperature Calvet microcalorimetry. The experimental results enable the calculation of the standard molar enthalpies of formation in the gaseous state, at T = 298.15 K, for both compounds, being the results discussed in terms of structural and energetic contributions. The theoretically estimated gas-phase enthalpies of formation were calculated from high-level ab initio molecular orbital calculations at the G3(MP2)//B3LYP level of theory. The computed values compare very well with the experimental results obtained in this work and show that the 2,5-dimethylbenzoxazole is enthalpically the most stable compound. Furthermore, this composite approach was also used to obtain information about the gas-phase basicities, proton and electron affinities and adiabatic ionization enthalpies.     

Dual‐level direct dynamics study on the reactions of SH (SD) with F2

The dual‐level direct dynamics study is carried out in the reactions of SH (SD) + F₂, and enthalpies of formation for the species FSH (FSD) are evaluated using isodesmic reactions. Furthermore, the dynamics calculations are performed using the variational transition‐state theory (VTST) with interpolated single‐point energies (ISPE) method at the approximate QCISD(T)/6‐311++G(3df, 2pd)//MPW1K/6‐311G(d, p) level. Over the temperature range of 200–2000 K, theoretical rate constants evaluated using canonical variational transition state theory (CVT) are in good agreement with the available experimental values. The kinetic isotope effects for the title reactions are not obvious. © 2005 Wiley Periodicals, Inc. Int J Chem Kinet 37: 710–716, 2005