Geometry optimization of molecular structures in solution by the polarizable continuum model

Barone, Vincenzo; Cossi, Maurizio; Tomasi, Jacopo

doi:10.1002/(sici)1096-987x(199803)19:4<404::aid-jcc3>3.0.co;2-w

Cited by 1,635 publications

(478 citation statements)

References 81 publications

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“…The electrostatic part, which is charge-method dependent, can be evaluated using several different models, such as finite difference Poisson-Boltzmann (FDPB), dielectric screening Poisson-Boltzmann (DSPB), [14][15] the Generalized Born (GB), [16][17][18][19][20][21] and the conductor-like screening models. [22][23][24] The nonpolar part can be simply estimated using the total solvation accessible surface area (SAS), according to the formula ∆G ) γ A + b, where g and b are constants, and A is SAS. For WSAS, the two contributions are considered simultaneously, and the electrostatic part is taken into account implicitly using different atom types.…”

Section: Resultsmentioning

confidence: 99%

Solvation Model Based on Weighted Solvent Accessible Surface Area

et al. 2001

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We have developed a fast procedure to predict solvation free energies for both organic and biological molecules. This solvation model is based on weighted solvent accessible surface area (WSAS). Least-squares fittings have been applied to optimize the weights of SAS for different atom types in order to reproduce the experimental solvation free energies. Good agreement with experimental results has been obtained. For the 184-molecule set (model I), for which there are experimental solvation free energies in 1-octanol, we have achieved an average error of 0.36 kcal/mol, better than that of the SM5.42R universal solvation model 1 by Li et al. For the 245-molecule set (model II) that has experimental aqueous solvation free energies, our WSAS model achieves an average error of 0.48 kcal/mol, marginally larger than that of Li's model (0.46 kcal/mol). We have used a 401-molecule set, the largest training set (model IV) that we know of solvation model development, to derive the SAS weights in order to reproduce the experimental solvation free energies in water. For this model, we have achieved an average unsigned error of 0.54 kcal/mol and an RMS error of 0.79 kcal/mol.The advantage of this model lies in its simplicity and independence of charge models. We have successfully applied this model to predict the relative binding free energies for the five binding modes of HIV-1RT/ efavirenz. The most favorable binding mode, which has an RMSD of 1.1 Å (for 54 C R around the binding site) compared to the crystal structure, has a binding free energy at least 10 kcal/mol more negative than the other binding modes. Moreover, the solvation free energies with WSAS have a high correlation (the correlation coefficient is 0.92) to the solvation free energies calculated by the Poisson-Boltzmann/surface area (PBSA) model. As an efficient and fast approach, WASA is also attractive for protein modeling and protein folding studies. We have applied this model to predict the solvation free energies of the 36-mer villin headpiece subdomain in its native structure, a compact folding intermediate, and a random coil. The rank order of the solvation free energies and the free energies for the three kinds of conformational clusters are in reasonable agreement with those found by MM-PBSA, a widely used solvation free energy model.

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Section: Resultsmentioning

confidence: 99%

Solvation Model Based on Weighted Solvent Accessible Surface Area

et al. 2001

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“…24 At this level, the optimized Sn-P peri-distances in 1-4 are appreciably overestimated compared to those observed in the solid by up to 0.2 Å (Table S7, ESI). All four compounds were reoptimised using the PCM implementation of Tomasi and co-workers, 40 using the same methods and basis sets previously employed (and employing the parameters of THF to model a moderately polar environment). Little change was observed for the unpolar structure 1, with the Sn-P distance remaining substantially overestimated.…”

Section: Synthesismentioning

confidence: 99%

Sterically Restricted Tin Phosphines, Stabilized by Weak Intramolecular Donor–Acceptor Interactions

et al. 2014

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(4)). The degree of intramolecular P-Sn bonding within the series was investigated by X-ray crystallography, solution and solid-state NMR spectroscopy and density functional theory (DFT/B3LYP/SBKJC/PCM) calculations. All members of the series adopt a conformation such that the phosphorus lone-pair is located directly opposite the tin centre, promoting an intramolecular donor-acceptor P→Sn type interaction. The extent of covalent bonding between Sn and P is found to be much greater in triorganotin chlorides 2-4 compared with triphenyl derivative 1. Coordination of a highly electronegative chlorine atom naturally increases the Lewis acidity of the tin centre, enhancing the lp(P)−σ*(Sn−Y) donoracceptor 3c-4e type interaction, as indicated by conspicuously short Sn-P peri-distances and significant 1 J( 31 P, 119 Sn) spin-spin coupling constants (SSCCs) in the range 740-754 Hz. Evidence supporting the presence of this interaction was also found in solidstate NMR spectra of some of the compounds which exhibit an indirect spin-spin coupling on the same order of magnitude as observed in solution. DFT calculations confirm the increased covalent bonding between P and Sn in 2-4, with notable WBIs of ca. 0.35 obtained, compared to 0.1 in 1.

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“…Zero-point vibrational corrections and thermal corrections to the Gibbs free energy were determined from the harmonic vibrational frequencies. To take the solvent effect into account, singlet-point solvent calculations were performed at the optimized gas-phase geometries using the CPCM [50,51] solvation method with dielectric constant (e) of dichloromethane being 8.93. The UAHF (united atom Hartree-Fock) radii were used for all the atoms.…”

Section: Methodsmentioning

confidence: 99%