New developments in the polarizable continuum model for quantum mechanical and classical calculations on molecules in solution

Cossi, Maurizio; Scalmani, Giovanni; Rega, Nadia; Barone, Vincenzo

doi:10.1063/1.1480445

Cited by 2,291 publications

(1,581 citation statements)

References 62 publications

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“…The minimum character of the stationary points obtained by geometry optimizations was checked by vibrational frequency calculations. The solvent effects were considered implicitly by the polarizable continuum model (PCM) 28,29,30 . The solvation energies could be calculated only on the optimised geometries of the isolated structures, since the starting unequilibrated structures in most cases failed to converge with PCM.…”

Section: Quantum Chemical Methodsmentioning

confidence: 99%

Experimental and theoretical investigation of the complexation of methacrylic acid and diisopropyl urea

Pogány

Razali

Székely

2017

Spectrochimica Acta Part A: Molecular and Biomolecular Spectros

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The present paper explores the complexation ability of methacrylic acid which is one of the most abundant functional monomer for the preparation of molecularly imprinted polymers. Host-guest interactions and the mechanism of complex formation between methacrylic acid and potentially genotoxic 1,3-diisopropylurea were investigated in the pre-polymerization solution featuring both experimental (NMR, IR) and in silico density functional theory (DFT) tools. The continuous variation method revealed the presence of higher-order complexes and the appearance of self-association which were both taken into account during the determination of the association constants. The quantum chemical calculations -performed at B3LYP 6-311++G(d,p) level with basis set superposition error (BSSE) corrections -are in agreement with the experimental observations, reaffirming the association constants and justifying the validity of computational investigation of such systems. Furthermore, natural bond orbital analysis was carried out to appraise the binding properties of the complexes.

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Section: Quantum Chemical Methodsmentioning

confidence: 99%

Experimental and theoretical investigation of the complexation of methacrylic acid and diisopropyl urea

Pogány

Razali

Székely

2017

Spectrochimica Acta Part A: Molecular and Biomolecular Spectros

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“…These utilize a combination of Hartree-Fock exchange and density functional theory (DFT) exchange correlation. Initial geometries were obtained using the 6-31+G* basis set and the polarized continuum model [72][73][74][75] (PCM) with integral equation formalism. This allows for the calculation of the analytical gradients of the solute-solvent surface.…”

Section: Ii2 Computational Detailsmentioning

confidence: 99%

Theoretical Comparison ofp-Nitrophenyl Phosphate and Sulfate Hydrolysis in Aqueous Solution: Implications for Enzyme-Catalyzed Sulfuryl Transfer

Kamerlin

2011

J. Org. Chem.

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Both phosphoryl and sulfuryl transfer are ubiquitous in biology, being involved in a wide range of processes, ranging from cell division to apoptosis. Additionally, it is becoming increasingly clear that enzymes that can catalyze phosphoryl transfer can often cross-catalyze sulfuryl-transfer (and vice versa).However, while there have been extensive experimental and theoretical studies performed on phosphoryl transfer, the body of available research on sulfuryl transfer is comparatively much smaller.The present work presents a direct theoretical comparison of p-nitrophenyl phosphate and sulfate monoester hydrolysis, both of which are considered prototype systems for probing phosphoryl and sulfuryl transfer respectively. Specifically, free energy surfaces have been generated using density functional theory, by initial geometry optimization in PCM using the 6-31+G* basis set and the B3LYP density functional, followed by single point calculations using the larger 6-311+G** basis set and the COSMO continuum model. The resulting surfaces have been then used to identify the relevant transition states, either by further unconstrained geometry optimization, or from the surface itself where possible.Additionally, configurational entropies were evaluated using a combination of the quasiharmonic approximation and the restraint release approach and added to the calculated activation barriers as a correction. Finally, the overall activation entropy was estimated by approximating the solvent contribution to the total activation entropy using the Langevin dipoles solvation model. We have reproduced both the experimentally observed activation barriers and the observed trend in the activation entropies with reasonable accuracy, as well providing a comparison of calculated and observed 15 N and 18 O kinetic isotope effects. We demonstrate that, counterintuitively, the hydrolysis of the p-nitrophenyl sulfate proceeds through a more expa show that the solvation effects upon moving from the ground state to the transition state are quite different for both reactions, suggesting that the enzymes that catalyze these reactions would need active 4 sites with quite different electrostatic preorganization for the efficient catalysis of either reaction (despite which many enzymes can catalyze both phosphoryl and sulfuryl transfer). We believe that such a comparative study is an important foundation for understanding the molecular basis for phosphatesulfate cross promiscuity within members of the alkaline phosphatase superfamily.

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“…To estimate the influence of relativistic effects, a non-relativistic pseudopotential [32] with the accompanying basis set by Schwerdtfeger and Wesendrup was used [33]. Solvent effects were taken into account by calculating selfconsistent polarizable continuum model (PCM) single points at the previously obtained structures with methanol as a solvent [34,35]. Gibbs free energies were obtained by adding vibrational and thermal corrections to the result of the PCM single point calculations.…”

Section: Computational Detailsmentioning

confidence: 99%

Homogeneous Gold Catalysis: Mechanism and Relativistic Effects of the Addition of Water to Propyne

et al. 2010

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Homogeneous catalysis employing gold compounds is a rapidly developing field. Au(III) catalysts in particular are interesting, since they exhibit catalytic properties unseen in other metals. In this study we report for the first time the complete mechanism of the nucleophilic addition of water to triple bonds that have not specifically been activated. The effect that the coordination of solvent molecules has on the course of the catalytic cycle is demonstrated, and the importance of hydrogen bonds to guide the substrate through the mechanism is highlighted. The influence of relativistic effects, which are particularly important for very heavy metals such as gold, is investigated, and it is concluded that the catalytic activity of gold could be seen as a relativistic effect.

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New developments in the polarizable continuum model for quantum mechanical and classical calculations on molecules in solution

Cited by 2,291 publications

References 62 publications

Experimental and theoretical investigation of the complexation of methacrylic acid and diisopropyl urea

Experimental and theoretical investigation of the complexation of methacrylic acid and diisopropyl urea

Theoretical Comparison ofp-Nitrophenyl Phosphate and Sulfate Hydrolysis in Aqueous Solution: Implications for Enzyme-Catalyzed Sulfuryl Transfer

Homogeneous Gold Catalysis: Mechanism and Relativistic Effects of the Addition of Water to Propyne

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