How to compute isomerization energies of organic molecules with quantum chemical methods
ABSTRACT The reaction energies for 34 typical organic isomerizations including oxygen and nitrogen heteroatoms are investigated with modern quantum chemical methods that have the perspective of also being applicable to large systems. The experimental reaction enthalpies are corrected for vibrational and thermal effects, and the thus derived "experimental" reaction energies are compared to corresponding theoretical data. A series of standard AO basis sets in combination with second-order perturbation theory (MP2, SCS-MP2), conventional density functionals (e.g., PBE, TPSS, B3-LYP, MPW1K, BMK), and new perturbative functionals (B2-PLYP, mPW2-PLYP) are tested. In three cases, obvious errors of the experimental values could be detected, and accurate coupled-cluster [CCSD(T)] reference values have been used instead. It is found that only triple-zeta quality AO basis sets provide results close enough to the basis set limit and that sets like the popular 6-31G(d) should be avoided in accurate work. Augmentation of small basis sets with diffuse functions has a notable effect in B3-LYP calculations that is attributed to intramolecular basis set superposition error and covers basic deficiencies of the functional. The new methods based on perturbation theory (SCS-MP2, X2-PLYP) are found to be clearly superior to many other approaches; that is, they provide mean absolute deviations of less than 1.2 kcal mol-1 and only a few (<10%) outliers. The best performance in the group of conventional functionals is found for the highly parametrized BMK hybrid meta-GGA. Contrary to accepted opinion, hybrid density functionals offer no real advantage over simple GGAs. For reasonably large AO basis sets, results of poor quality are obtained with the popular B3-LYP functional that cannot be recommended for thermochemical applications in organic chemistry. The results of this study are complementary to often used benchmarks based on atomization energies and should guide chemists in their search for accurate and efficient computational thermochemistry methods.
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ABSTRACT: The gas and solution phase relative thermodynamic stabilities of the 89 perfluorooctane sulfonic acid (PFOS) congeners play an important role in assessing whether synthetic conditions for commercial mixtures are under thermodynamic or kinetic control, and in calculating various physico-chemical properties for these important industrial compounds and environmental contaminants. In the present study, 4,272 gas and solvent phase (water and n-octanol) calculations were conducted at various levels of semiempirical (PM6), density functional (B3LYP, B97D, PBE1PBE [PBE0], and M062X functionals with the 6-311++G(d,p) basis set), and second order Moller-Plesset perturbation (MP2/6-311++G(d,p)//B3LYP/6-311++G(d,p)) theory and the SMD, IEFPCM-UFF, and CPCM implicit solvation models on the 89 PFOS congeners in both their acid and anionic forms. The B3LYP functional consistently and incorrectly predicts substantially increasing thermodynamic stability of PFOS isomers with increasing linearity of the perfluoroalkyl chains. By comparison, PM6, M062X, and MP2 calculations more closely reflect the expected patterns of thermodynamic stability for branched versus linear PFOS congeners.Nature Precedings 12/2010; DOI:10.1038/npre.2010.5353.1
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ABSTRACT: Gas phase standard state (298.15 K, 1 atm) isomerization energies were calculated using the M062X functional with the QZVP, 6-311++G(d,p), 6-311++G(2d,2p), and cc-pVTZ basis sets against the 24 reactions in the ISOL set of benchmark isomerization energies for large organic molecules. The M062X functional appears to offer comparable isomerization energy prediction performance to the best performing currently available dispersion corrected functionals against this benchmark dataset.Nature Precedings 11/2010; DOI:10.1038/npre.2010.5183.1
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ABSTRACT: The purpose of this study was to examine the feasibility of a hybrid orthosis for walking after spinal cord injury (SCI) that coordinates the locking and unlocking of knee and ankle joints of a reciprocating gait orthosis (RGO), while injecting propulsive forces and controlling unlocked joints with functional neuromuscular stimulation (FNS). The effectiveness of the hybrid system relative to gait stability and posture were determined in this simulation study. A three-dimensional computer model of a hybrid orthosis system (HOS) combining FNS with a RGO incorporating feedback control of muscle activation and coordinated joint locking was developed in Working Model 3D. The simulated hybrid orthosis system achieved gait speeds, stride lengths, and cadences of 0.51 +/- 0.03 m/s, 0.85 +/- 0.04 m, and 72 +/- 4 steps/min respectively, exceeding the performance of other hybrid systems. Forward trunk tilt was found to be necessary during initial step from standing and pro-swing, but posture and stability were significantly improved over FNS-only systems. The results of the model shows that a HOS that coordinates knee and ankle joint locking with electrical stimulation to the paralyzed muscles holds significant advantages over brace- and FNS-only walking systems in terms of enhanced trunk stability and posture.Conference proceedings: ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Conference 02/2004; 6:4041-4. DOI:10.1109/IEMBS.2004.1404128