Accurate relative pKa calculations for carboxylic acids using complete basis set and Gaussian-n models combined with continuum solvation methods

The complete basis set methods CBS-4, CBS-QB3, and CBS-APNO, and the Gaussian methods G2 and G3 were used to calculate the gas phase energy differences between six different carboxylic acids and their respective anions. Two different continuum methods, SM5.42R and CPCM, were used to calculate the free energy differences of solvation for the acids and their anions. Relative pKa values were calculated for each acid using one of the acids as a reference point. The CBS-QB3 and CBS-APNO gas phase calculations, combined with the CPCM/HF/6-31+G(d)//HF/6-31G(d) or CPCM/HF/6-31+G(d)//HF/6-31+G(d) continuum solvation calculations on the lowest energy gas phase conformer, and with the conformationally averaged values, give results accurate to ½ pKa unit. © 2001 American Institute of Physics.

Theoretical Calculations of Acid Dissociation Constants: A Review Article

Acid dissociation constants, or pKa values, are essential for understanding many fundamental reactions in chemistry. These values reveal the deprotonation state of a molecule in a particular solvent. There is great interest in using theoretical methods to calculate the pKa values for many different types of molecules. These include molecules that have not been synthesized, those for which experimental pKa determinations are difficult, and for larger molecules where the local environment changes the usual pKa values, such as for certain amino acids that are part of a larger polypeptide chain. Chemical accuracy in pKa calculations is difficult to achieve, because an error of 1.36 kcal/mol in the change of free energy for deprotonation in solvent results in an error of 1 pKa unit. In this review the most valuable methods for determining accurate pKa values in aqueous solution are presented for educators interested in explaining or using these methods for their students.

Experimentation with different thermodynamic cycles used for pKa calculations on carboxylic acids using Complete Basis Set and Gaussian-n Models combined with CPCM Continuum Solvation Methods

Complete basis set and Gaussian-n methods were combined with Barone and Cossi's implementation of the polarizable conductor model (CPCM) continuum solvation methods to calculate pKa values for six carboxylic acids. Four different thermodynamic cycles were considered in this work. An experimental value of −264.61 kcal/mol for the free energy of solvation of H+, ΔGs(H+), was combined with a value for Ggas(H+) of −6.28 kcal/mol, to calculate pKa values with cycle 1. The complete basis set gas-phase methods used to calculate gas-phase free energies are very accurate, with mean unsigned errors of 0.3 kcal/mol and standard deviations of 0.4 kcal/mol. The CPCM solvation calculations used to calculate condensed-phase free energies are slightly less accurate than the gas-phase models, and the best method has a mean unsigned error and standard deviation of 0.4 and 0.5 kcal/mol, respectively. Thermodynamic cycles that include an explicit water in the cycle are not accurate when the free energy of solvation of a water molecule is used, but appear to become accurate when the experimental free energy of vaporization of water is used. This apparent improvement is an artifact of the standard state used in the calculation. Geometry relaxation in solution does not improve the results when using these later cycles. The use of cycle 1 and the complete basis set models combined with the CPCM solvation methods yielded pKa values accurate to less than half a pKa unit. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001

Accurate pKa Calculations for Carboxylic Acids Using Complete Basis Set and Gaussian-n Models Combined with CPCM Continuum Solvation Methods”

Complete Basis Set and Gaussian-n methods were combined with CPCM continuum solvation methods to calculate pKa values for six carboxylic acids. An experimental value of −264.61 kcal/mol for the free energy of solvation of H+, ΔGs(H+), was combined with a value for Ggas(H+) of −6.28 kcal/mol to calculate pKa values with Cycle 1. The Complete Basis Set gas-phase methods used to calculate gas-phase free energies are very accurate, with mean unsigned errors of 0.3 kcal/mol and standard deviations of 0.4 kcal/mol. The CPCM solvation calculations used to calculate condensed-phase free energies are slightly less accurate than the gas-phase models, and the best method has a mean unsigned error and standard deviation of 0.4 and 0.5 kcal/mol, respectively. The use of Cycle 1 and the Complete Basis Set models combined with the CPCM solvation methods yielded pKa values accurate to less than half a pKa unit.

Comparison of Experimental and Theoretical Structures of a Transition State Analogue Used for the Induction of Anti-Cocaine Catalytic Antibodies

Comparison of the crystal structure of a transition state analogue that was used to raise catalytic antibodies for the benzoyl ester hydrolysis of cocaine with structures calculated by ab initio, semiempirical, and solvation semiempirical methods reveals that modeling of solvation is crucial for replicating the crystal structure geometry. Both SM3 and SM2 calculations, starting from the crystal structure TSA I, converged on structures similar to the crystal structure. The 3-21G(*)/HF, 6-31G*/HF, PM3, and AM1 calculations converged on structures similar to each other, but these gas-phase structures were significantly extended relative to the condensed phase structures. Two transition states for the hydrolysis of the benzoyl ester of cocaine were located with the SM3 method. The gas phase calculations failed to locate reasonable transition state structures for this reaction. These results imply that accurate modeling of the potential energy surfaces for the hydrolysis of cocaine requires solvation methods.

Quantum Mechnical Investion of Cyclic 3',5'- Adenosine Monophosphate, the Second Hormonal Messenger

Full geometry optimizations using the PM3, AM1, 3-21G∗/HF and 6-31G∗/HF levels of theory were conducted on the syn and anti conformations of cyclic3′,5′-adenosine monophosphate (cAMP). Comparison of the anti crystal structures with the semiempirical and ab initio results revealed that the ab initio results agree well with the experimental results. The results of semiempirical calculations are in qualitative agreement with experimental and ab initio values, with the exception of the glycosyl torsion angle for the anti conformer. Sugar puckering, which is not handled properly by semiempirical methods for unconstrained sugars, nucleosides, nucleotides and nucleotide base pairs, is modeled reasonably well by the semiempirical methods for cAMP. This improvement results from the constraints introduced by the cyclization of AMP to form the phosphodiester.

AM1 and PM3 Calculations of the Potential Energy Surfaces for CH2OH Reactions with NO and NO2

The AM1 and PM3 molecular orbital methods have been utilized to investigate the reactions of CH20H with NO and NO2 PM3 and AM1 calculated heats of formation differ from experimental values by 8.6 and 18.8 kcal mol-', respectively. The dominant reaction of CH20H with NO is predicted to produce the adduct HOCH2N0, supporting the hypothesis of Pagsberg, Munk, Anastasi, and Simpson. Calculated activation energies for the NO2 system predict the formation of the adducts HOCH2N02 and HOCH20N0. In addition, the PM3 calculations predict that the abstraction reaction producing CH20 and HN02 is more likely than one producing CH20 and HONO from reactions of CH20H with NO2.

Prediction of Accurate Anharmonic Experimental Vibrational Frequencies for Water Clusters, (H2O)n, n = 2−5

Accurate anharmonic experimental vibrational frequencies for water clusters consisting of 2−5 water molecules have been predicted on the basis of comparing different methods with MP2/aug-cc-pVTZ calculated and experimental anharmonic frequencies. The combination of using HF/6-31G* scaled frequencies for intramolecular modes and anharmonic frequencies for intermolecular modes gives excellent agreement with experiment for the water dimer and trimer and are as good as the expensive anharmonic MP2 calculations. The water trimer, the cyclic Ci and S4 tetramers, and the cyclic pentamer all have unique peaks in the infrared spectrum between 500 and 800 cm-1 and between 3400 and 3700 cm-1. Under the right experimental conditions these different clusters can be uniquely identified using high-resolution IR spectroscopy.