Performance of SM6, SM8, and SMD on the SAMPL1 Test Set for the Prediction of Small-Molecule Solvation Free Energies

Marenich, Aleksandr V.; Cramer, Christopher J.; Truhlar, Donald G.

doi:10.1021/jp809094y

Cited by 490 publications

(401 citation statements)

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“…A number of continuum and explicit-solvent methods were tested, most of them in the prospective mode, 17,[30][31][32] while results with two other methods were included retrospectively. 33,34 We have analyzed the sensitivity of the LIE model to several parameters that we believe are important for the accuracy of the model and for calibration of a continuum model based on these results. These include continuum corrections to infinity, charging method, solute flexibility, and internal energy terms.…”

Section: Introductionmentioning

confidence: 99%

Rapid Prediction of Solvation Free Energy. 1. An Extensive Test of Linear Interaction Energy (LIE)

Sulea

Corbeil

Purisima

2010

J. Chem. Theory Comput.

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Abstract:The present study provides a comprehensive systematic analysis on the applicability of the linear interaction energy (LIE) approximation to the prediction of gas-to-water transfer (hydration) free energy. The study is based on molecular dynamics simulations in explicit solvent for an extensive and diverse hydration data set comprising 564 neutral compounds with measured hydration free energies, including a "traditional" data set and the more challenging drug-like SAMPL1 data set. A highly correlative LIE model was achieved without empirical scaling of the solute-solvent interaction energy terms along with a cavity term calibrated to the experiment. This model was particularly accurate for the "traditional" data set and of acceptable accuracy for the SAMPL1 data set, with mean-unsigned-errors below 1 kcal/mol and slightly above 2 kcal/mol, respectively. We have analyzed the sensitivity of the LIE model to several parameters such as continuum correction terms applied outside the explicit water shell, the impact of various charging methods, the applicability of single-conformer representation of the solute, and the inclusion of internal energy terms. The parameters with the greatest sensitivity are the charging methods used, with AM1BCC-SP (without AM1 geometry optimization) charges favored over AM1BCC-OPT and RESP charges. The inclusion of the change in intramolecular van der Waals and electrostatic energies between the solution and gas phases can also lead to improved prediction accuracies. Functional group based error analysis identified several chemical classes as minor outliers with systematic errors. A direct comparison of the LIE and free energy perturbation (FEP) approaches using the same force field and charging method shows that the LIE approximation is at least as accurate as the FEP approach with a reduction of computing time by at least 1 order of magnitude.

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Section: Introductionmentioning

confidence: 99%

Rapid Prediction of Solvation Free Energy. 1. An Extensive Test of Linear Interaction Energy (LIE)

Sulea

Corbeil

Purisima

2010

J. Chem. Theory Comput.

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“…55 Then, DFT calculations at the M06-2X/6-31G(d) level, as implemented in Gaussian09 package, were also performed. 56 These semiempirical and DFT calculations involved full geometry optimizations followed by vibrational frequency calculations under the effect of a polarizable continuum model of water (dielectric constant: 78.4), using COSMO 57 for PM6-DH+ and using SMD 58 with radii and non-electrostatic terms from Please do not adjust margins…”

Section: Relative Stability Of Cis and Trans Conformers For All Monommentioning

confidence: 99%

Proline cis–trans isomerization and its implications for the dimerization of analogues of cyclopeptide stylostatin 1: a combined computational and experimental study

López-Martínez

Flores-Morales

Cruz

et al. 2016

Phys. Chem. Chem. Phys.

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dCis and trans proline conformers are often associated with dramatic changes in the biological function of peptides. A slow equilibrium between cis and trans Ile-Pro amide bond conformers occurs in constrained derivatives of the native marine cyclic heptapeptide stylostatin 1 (cyclo-(NSLAIPF)); a potential anticancer agent. In this work, four cyclopeptides, cyclo-(NSTAIPF), cyclo-(KSTAIPF), cyclo-(RSTAIPF) and cyclo-(DSTAIPF), which are structurally related to stylostatin 1, are experimentally and computationally examined in order to assess the effect of residue mutations on the cis-trans conformational ratio and the apparent capacity to form dimeric aggregates. Primarily, cyclo-(KSTAIPF) and cyclo-(RSTAIPF) showed specific trends in circular dichroism, MALDI-TOF and HPLC purification experiments which suggests the occurrence of peptide dimerization. Meanwhile, NMR spectrum of cyclo- (KSTAIPF) indicates that this cyclopeptide exists in the two slow-exchange families of conformations mentioned above. Molecular dynamics simulations combined with quantum mechanical calculations have shed light on the factors governing the cis/trans conformational ratio. In particular, we have found that residue mutations affect the internal hydrogen bond pattern which ultimately tunes the cis/trans conformational ratio and that only trans conformers are capable of aggregating due to the shape complementarity of the two subunits.

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“…To consider the solvent effect on reaction, single-point calculations with self-consistent reaction field [28][29][30] based on the integral equation formalism polarizable continuum model (IEFPCM) 31 with UAKS radii and cavity-dispersion-solventstructure terms in Truhlar and co-workers' SMD solvation model 32 for xylene and N,N-dimethylformamide (DMF) were applied for all gas-phase optimized structures at B3LYP/ 6-311++G(d,p) and MP2/6-311++G(d,p) levels. 33,34 For all cited energies, ZPE corrections were taken into account.The basis set superposition error (BSSE) corrections for species were estimated using the counterpoise method.…”

Section: Computational Detailsmentioning

confidence: 99%

Theoretical Mechanism Studies on the Enantioselectivity of aza-MBH-type Reaction of Nitroalkene to N-tosylimine Catalyzed by Thiourea-tertiary Amine

Lu¹,

Wang²,

Wang³

2013

Bulletin of the Korean Chemical Society

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The enantioselective aza-Morita Baylis Hillman reaction of nitroalkene and N-tosylimine catalyzed by thiourea-tertiary amine has been investigated using density functional theory. Enantioselectivity is dominated by the cooperative effect of non-covalent and weak covalent interactions imposed by different units of catalyst. As Lewis base, the tertiary amine unit activates nitroalkene via weak covalent bond. The weak covalent interaction orients the reaction in a major path with smaller variations of this bond. The aromatic ring unit activates N-tosylimine via π-π stacking. The non-covalent interaction selects the major path with smaller changes of the efficient packing areas. Thiourea unit donates more compact H-bonded network for species of the major path. The calculated ee value in xylene solution phase (97.6%) is much higher than that in N,NDimethylformamide (27.2%). Our conclusion is also supported by NBO analysis.

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Performance of SM6, SM8, and SMD on the SAMPL1 Test Set for the Prediction of Small-Molecule Solvation Free Energies

Cited by 490 publications

References 63 publications

Rapid Prediction of Solvation Free Energy. 1. An Extensive Test of Linear Interaction Energy (LIE)

Rapid Prediction of Solvation Free Energy. 1. An Extensive Test of Linear Interaction Energy (LIE)

Proline cis–trans isomerization and its implications for the dimerization of analogues of cyclopeptide stylostatin 1: a combined computational and experimental study

Theoretical Mechanism Studies on the Enantioselectivity of aza-MBH-type Reaction of Nitroalkene to N-tosylimine Catalyzed by Thiourea-tertiary Amine

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