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A more general way of combining ab initio quantum mechanical calculations and classical mechanical free energy perturbation method to measure the general energetics of enzyme-catalyzed reactions and the same reaction in solution is described. Estimating the free energy to assemble the reacting group was one of the more important conditions of the method for the accurate calculations of the reaction energies in solution. Moreover, the use of the RESP protocol was critical in calculating the charge distribution of the structures in the reaction pathway.

MNDO and ab initio SCF calculations predict a single energy minimum for each of the large fullerenes with Goldberg type I(sub h) symmetry, which corresponds to an icosahedrally shaped structure with facets obtained from nearly planar hexagonal sheets and vertices located at the pentagons. Higher energy shown by the spherically shaped structures disfavors spherically shaped fullerenes. The observed trends are explained on the basis of force field estimates and Huckel calculations.

TheATOMIC protocol is a quantum-chemical thermochemistry protocoldesigned to obtain accurate atomization energies and derived heatsof formation. It reduces errors of computationally tractable compositeschemes through the use of bond separation reactions, which are implementedin a consistent ab initio framework. The present work explores possiblesimplification of previously introduced ATOMIC models. While coupledcluster calculations with singles and doubles excitations and perturbationaltreatments of connected triples excitations [CCSD(T)] are still requiredfor high accuracy, basis-set truncations are possible in the CCSD-MP2and CCSD(T)-CCSD components. The resulting models B4, B5, and B6show root-mean-square (RMS) errors ofonly 0.21 to 0.46 kcal/mol for the AE set, which is a benchmark comprisingcomplete-basis-set CCSD(T)(full) atomization energies of 73 neutral,closed-shell molecules composed of H, C, N, O, and F atoms. The evaluationof connected triples excitations can be avoided at medium levels ofaccuracy if the complete-basis-set MP2 energy is augmented with anempirically calibrated fraction of the difference between MP3 (orCCSD) and MP2 energies, calculated with small basis sets. The correspondingEMP3and ECCSDmodels show RMS errors of 1.01and 0.70 kcal/mol, respectively. Spin-component scaling is an optionto rely entirely on the MP2 level of theory and still cut the RMSerror of 4.38 kcal/mol by roughly a factor of 2 and achieve an accuracycomparable to accurate density functionals, such as M05-2X. The proposednew models are additionally tested with the HOF benchmark, a subsetof G3/99 heats of formation that includes only neutral closed-shellmolecules composed of H, C, N, O, and F atoms. The assessment showsthat a number of experimental reference values are in error and shouldbe replaced with more recent data. Results obtained with the new modelsare compared to original HOF (G3/99) reference data, to updated referencedata, and to accurate ATOMIC/A theoretical data. [ABSTRACT FROM AUTHOR]

Research was conducted to examine the base-catalyzed hydrolysis of formamide in the gas phase and in aqueous solution by means of a combination of statistical mechanical and quantum chemical techniques. The main goal is to study the aqueous-phase reaction and to analyze the influence of bulk solvent. Results are in satisfactory agreement with available experimental data for the solution-phase reaction.

The recently proposed ATOMIC protocol is a fully ab initiothermochemicalprotocol that rests upon the concept of bond separation reactions(BSRs) to correct for systematic errors of composite wave functionapproaches. It achieves high accuracy for atomization energies andderived heats of formation if basis set requirements for all contributingcomponents are balanced carefully. The present work explores the potentialof density functionals as possible replacements of composite wavefunction approaches in the ATOMIC protocol. Twenty density functionalsare examined for their accuracy in thermochemical predictions basedon calculated bond-separation energies and precomputed high-leveldata for the small parent molecules entering BSRs. The best densityfunctionals outperform CCSD (coupled cluster with singles and doublesexcitations), but none reaches the accuracy of well-balanced compositewave function approaches that consider quasiperturbational connectedtriples excitations at least with small basis sets. Some functionalsshow unexpected problems with bond separation reactions and are analyzedfurther with a model of empirically calibrated bond additivity corrections.Finally, the benefit of adding empirical dispersion terms to commondensity functionals is analyzed in the context of BSR-corrected thermochemistry. [ABSTRACT FROM AUTHOR]

Density functionals are often used in ab initio thermochemistry to provide optimized geometries for single-point evaluations at a high level and to supply estimates of anharmonic zero-point energies (ZPEs). Their use is motivated by relatively high accuracy at a modest computational expense, but a thorough assessment of geometry-related error seems to be lacking. We have benchmarked 53 density functionals, focusing on approximations of the first four rungs and on relatively small basis sets for computational efficiency. Optimized geometries of 279 neutral first-row molecules (H, C, N, O, F) are judged by energy penalties relative to the best available geometries, using the composite model ATOMIC/B 5 as energy probe. Only hybrid functionals provide good accuracy with root-mean-square errors around 0.1 kcal/mol and maximum errors below 1.0 kcal/mol, but not all of them do. Conspicuously, first-generation hybrids with few or no empirical parameters tend to perform better than highly parameterized ones. A number of them show good accuracy already with small basis sets (6-31G(d), 6-311G(d)). As is standard practice, anharmonic ZPEs are estimated from scaled harmonic values. Statistics of the latter show less performance variation among functionals than observed for geometry-related error, but they also indicate that ZPE error will generally dominate. We have selected PBE0-D3/6-311G(d) for the next version of the ATOMIC protocol (ATOMIC-2) and studied it in more detail. Empirical expressions have been calibrated to estimate bias corrections and 95% uncertainty intervals for both geometry-related error and scaled ZPEs.

ATOMIC is a thermochemistry protocol geared toward larger molecules with first-row atoms. It implements Pople's concept of bond separation reactions in an ab initio fashion and so enhances the accuracy of midlevel composite models for atomization energies. Recently we have introduced ATOMIC(hc), a model for applications to hydrocarbons, that estimates bias and uncertainty for each of the components contributing to the ATOMIC bottom-of-the-well atomization energy ( Bakowies , D. J. Chem. Theory Comput. 2019 , 15 , 5230 - 5251 ). Here we scrutinize the remaining components of the ATOMIC protocol, including midlevel composite models to approximate the complete-basis set (CBS) limit of CCSD(T) as well as zero-point energies (ZPEs) and thermal enthalpy increments that are evaluated from scaled harmonic MP2 frequencies. Potential errors relating to imperfections in MP2 geometries and ZPEs are estimated using auxiliary information obtained from geometry optimizations and frequency calculations at the density functional (B3LYP) level. Overall corrections to and uncertainties of enthalpies of formation are obtained from summation and error propagation, respectively. The error and uncertainty model is validated with accurate data from the Active Thermochemical Tables (ATcT) and compared to earlier statistical assessments for the G3/99 benchmark. The proposed model is a welcome alternative to statistical assessment, first because it does not depend on comparison with experiment, second because it recognizes the expected scaling of error with system size, and third because it provides a detailed account of the importance of various contributions to overall error and uncertainty. The evaluation of ZPEs from scaled harmonic frequencies expectedly emerges as the leading source of uncertainty if highly accurate composite models are used to treat the electronic problem, but uncertainties are usually balanced with those arising from computationally more attractive B level (B 1 ...B 6 ) models to estimate the CBS limit of CCSD(T). ATOMIC(hc) enthalpies of formation, complete with uncertainty estimates, are reported for 161 hydrocarbons ranging in size from methane (CH 4 ) to [8]circulene (C 32 H 16 ) and tetra- tert -butyltetrahedrane (C 20 H 36 ). Experimental data are available for 127 molecules but cannot be reconciled with theory in 37 cases. Theory helps to identify the more accurate among conflicting experimental values in 11 cases and emerges as a valuable complement to experiment also for larger molecules, provided that fair estimates of uncertainty are available.

The reliability of popular density functionals was studied for the description of torsional profiles of 36 molecules: glyoxal, oxalyl halides, and their thiocarbonyl derivatives. HF and 18 functionals of varying complexity, from local density to range-separated hybrid approximations and double-hybrid, have been considered and benchmarked against CCSD(T)-level rotational profiles. For molecules containing heavy halogens, most functionals fail to reproduce barrier heights accurately and a number of functionals introduce spurious minima. Dispersion corrections show no improvement. Calibrated torsion-corrected atom-centered potentials rectify the shortcomings of PBE and also improve on σ-hole based intermolecular binding in dimers and crystals.