Charge sensitivity analysis in force-field-atom resolution

Stachowicz, Anna; Styrcz, Anna; Korchowiec, Jacek

doi:10.1007/s00894-011-1006-7

Cited by 13 publications

(29 citation statements)

References 38 publications

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“…This makes it likely (but not guaranteed) that the physical model employed 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 conformation-independent charges 217, 249-251 (vs. inclusion of conformation-dependent charge fluxes); (9) the decoupling of the van der Waals from the charge model [252][253][254][255] (i.e. use of QM-derived charges along with a standardized van der Waals atom-type set).…”

Section: Discussionmentioning

confidence: 99%

“…Importantly, 2016H66 also addresses point 9. In many current small-molecule force fields 11,22,43,44,252,253,256 , QM-derived (thus also in principle structure-dependent) atomic charges are used along within standardized van der Waals atom-type sets, a situation that is somewhat reminiscent of the separate optimization of van der Waals parameters and charges in the design of the 53A6 set 63 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 dynamics (time-dependence) of the system, whereas D and η are transport parameters which characterize precisely this dynamics. The dynamic information is thus implicitly added by the physical model.…”

Section: Discussionmentioning

confidence: 99%

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A GROMOS-Compatible Force Field for Small Organic Molecules in the Condensed Phase: The 2016H66 Parameter Set

Horta

Merz

Fuchs

et al. 2016

J. Chem. Theory Comput.

144

287

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This article reports on the calibration and validation of a new GROMOS-compatible parameter set 2016H66 for small organic molecules in the condensed phase. The calibration is based on 62 organic molecules spanning the chemical functions alcohol, ether, aldehyde, ketone, carboxylic acid, ester, amine, amide, thiol, sulfide, and disulfide, as well as aromatic compounds and nucleic-acid bases. For 57 organic compounds, the calibration targets are the experimental pure-liquid density ρliq and the vaporization enthalpy ΔHvap, as well as the hydration free energy ΔGwat and the solvation free energy ΔGche in cyclohexane, at atmospheric pressure and at (or close to) room temperature. The final root-mean-square deviations (RMSD) for these four quantities over the set of compounds are 32.4 kg m(-3), 3.5 kJ mol(-1), 4.1 kJ mol(-1), and 2.1 kJ mol(-1), respectively, and the corresponding average deviations (AVED) are 1.0 kg m(-3), 0.2 kJ mol(-1), 2.6 kJ mol(-1), and 1.0 kJ mol(-1), respectively. For the five nucleic-acid bases, the parametrization is performed by transferring the final 2016H66 parameters from analogous organic compounds followed by a slight readjustment of the charges to reproduce the experimental water-to-chloroform transfer free energies ΔGtrn. The final RMSD for this quantity over the five bases is 1.7 kJ mol(-1), and the corresponding AVED is 0.8 kJ mol(-1). As an initial validation of the 2016H66 set, seven additional thermodynamic, transport, and dielectric properties are calculated for the 57 organic compounds in the liquid phase. The agreement with experiment in terms of these additional properties is found to be reasonable, with significant deviations typically affecting either a specific chemical function or a specific molecule. This suggests that in most cases, a classical force-field description along with a careful parametrization against ρliq, ΔHvap, ΔGwat, and ΔGche results in a model that appropriately describes the liquid in terms of a wide spectrum of its physical properties.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

A GROMOS-Compatible Force Field for Small Organic Molecules in the Condensed Phase: The 2016H66 Parameter Set

Horta

Merz

Fuchs

et al. 2016

J. Chem. Theory Comput.

144

287

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“…The details of this formalism can be found in the literature [41,42,60]. Here, only a short overview is given.…”

Section: Theoretical Backgroundmentioning

confidence: 99%

“…It is derived from DFT and was originally formulated to extract chemically relevant information from ab initio calculations in different resolutions. We have recently parameterized its semiempirical variant in force-field atoms resolution [42,43]. It allows efficient calculating of equilibrium charge distribution and a set of reactivity indices by a single matrix inversion step.…”

Section: Introductionmentioning

confidence: 99%

Nucleophilic properties of purine bases: inherent reactivity versus reaction conditions

Stachowicz‐Kuśnierz

Korchowiec

2015

Struct Chem

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In the present study, nucleophilic properties of adenine and guanine are examined by means of density functional theory. H? is used as a model electrophile. Two modes of H ? attack on the bases are considered: on the neutral molecule and on the anion. Solvent effects are modeled by means of polarizable continuum model. Regioselectivity of attack is studied by analyzing two contributions. The first one is the energetic ordering of the tautomers. The second is the relative inherent reactivity of nucleophilic sites in the bases. Atomic softnesses calculated by means of charge sensitivity analysis are employed for this purpose. The most reactive sites in various tautomers are identified on the ground of Li-Evans model. For adenine, it is demonstrated that both in basic and in neutral pH N7 atom possesses the most nucleophilic character. In polar solvents, N7 substitution is also most favored energetically. In basic pH and nonpolar solvents as well as in the gas phase, N9 substitution is slightly more probable. For guanine, a mixture of N7-and N9-substituted products can be expected in basic pH. In neutral pH, inherent reactivity and energy trends are opposite to each other; therefore, the substitution does not occur. Experimentally observed products of reactions with various electrophiles and in various conditions confirm the results obtained in this study.

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“…In our previous article [21], we have determined CSA parameters based on original Wiener's AMBERff84 [27] atomic types. Two population analyses were used independently to calculate the reference ab initio charge distribution of training molecules, namely Mulliken Population Analysis (MPA) [28] and electrostatic potential fitting (ChelpG scheme) [29,30] calculated at HF/6-31G* level of theory.…”

Section: Introductionmentioning

confidence: 99%