Atomic Charges of the Water Molecule and the Water Dimer

1998 ◽  
Vol 102 (39) ◽  
pp. 7686-7691 ◽  
Author(s):  
Per-Olof Åstrand ◽  
Kenneth Ruud ◽  
Kurt V. Mikkelsen ◽  
Trygve Helgaker
Keyword(s):  
Water Molecule ◽  
Water Dimer ◽  
Atomic Charges

scholarly journals Determining Partial Atomic Charges for Liquid Water: Assessing Electronic Structure and Charge Models

2020 ◽  
Author(s):  
Bowen Han ◽  
Christine Isborn ◽  
Liang Shi
Keyword(s):  
Electronic Structure ◽  
Dipole Moment ◽  
Charge Transfer ◽  
Liquid Water ◽  
Quantum Chemical ◽  
Water Dimer ◽  
Atomic Charges ◽  
Molecular Dipole ◽  
Molecular Dipole Moment ◽  
Partial Atomic Charges

Partial atomic charges provide an intuitive and efficient way to describe the charge distribution and the resulting intermolecular electrostatic interactions in liquid water. Many charge models exist and it is unclear which model provides the best assignment of partial atomic charges in response to the local molecular environment. In this work, we systematically scrutinize various electronic structure methods and charge models (Mulliken, Natural Population Analysis, CHelpG, RESP, Hirshfeld, Iterative Hirshfeld, and Bader) by evaluating their performance in predicting the dipole moments of isolated water, water clusters, and liquid water as well as charge transfer in the water dimer and liquid water. Although none of the seven charge models is capable of fully capturing the dipole moment increase from isolated water (1.85 D) to liquid water (about 2.9 D), the Iterative Hirshfeld method performs best for liquid water, reproducing its experimental average molecular dipole moment, yielding a reasonable amount of intermolecular charge transfer, and showing modest sensitivity to the local water environment. The performance of the charge model is dependent on the choice of the density functional and the quantum treatment of the environment. The computed molecular dipole moment of water generally increases with the percentage of the exact Hartree-Fock exchange in the functional, whereas the amount of charge transfer between molecules decreases. For liquid water, including two full solvation shells of surrounding water molecules (within about 5.5 A of the central water) in the quantum-chemical calculation converges the charges of the central water molecule. Our final pragmatic quantum-chemical charge assigning protocol for liquid water is the Iterative Hirshfeld method with M06-HF/aug-cc-pVDZ and a quantum region cutoff radius of 5.5 A.<br>

scholarly journals Rotational spectra of tetracyclic quinolizidine alkaloids: does a water molecule flip sparteine?

2017 ◽  
Vol 19 (27) ◽  
pp. 17553-17559 ◽  
Author(s):  
Alberto Lesarri ◽  
Ruth Pinacho ◽  
Lourdes Enríquez ◽  
José E. Rubio ◽  
Martín Jaraíz ◽  
...  
Keyword(s):  
Water Molecule ◽  
Water Dimer ◽  
Quinolizidine Alkaloids ◽  
Parent Molecule ◽  
Rotational Spectra

Flipping or not flipping? The sparteine–water dimer generated in a jet expansion retains the trans conformation of the parent molecule.

scholarly journals Determining Partial Atomic Charges for Liquid Water: Assessing Electronic Structure and Charge Models

2020 ◽  
Author(s):  
Bowen Han ◽  
Christine Isborn ◽  
Liang Shi
Keyword(s):  
Electronic Structure ◽  
Dipole Moment ◽  
Charge Transfer ◽  
Liquid Water ◽  
Quantum Chemical ◽  
Water Dimer ◽  
Atomic Charges ◽  
Molecular Dipole ◽  
Molecular Dipole Moment ◽  
Partial Atomic Charges

Partial atomic charges provide an intuitive and efficient way to describe the charge distribution and the resulting intermolecular electrostatic interactions in liquid water. Many charge models exist and it is unclear which model provides the best assignment of partial atomic charges in response to the local molecular environment. In this work, we systematically scrutinize various electronic structure methods and charge models (Mulliken, Natural Population Analysis, CHelpG, RESP, Hirshfeld, Iterative Hirshfeld, and Bader) by evaluating their performance in predicting the dipole moments of isolated water, water clusters, and liquid water as well as charge transfer in the water dimer and liquid water. Although none of the seven charge models is capable of fully capturing the dipole moment increase from isolated water (1.85 D) to liquid water (about 2.9 D), the Iterative Hirshfeld method performs best for liquid water, reproducing its experimental average molecular dipole moment, yielding a reasonable amount of intermolecular charge transfer, and showing modest sensitivity to the local water environment. The performance of the charge model is dependent on the choice of the density functional and the quantum treatment of the environment. The computed molecular dipole moment of water generally increases with the percentage of the exact Hartree-Fock exchange in the functional, whereas the amount of charge transfer between molecules decreases. For liquid water, including two full solvation shells of surrounding water molecules (within about 5.5 A of the central water) in the quantum-chemical calculation converges the charges of the central water molecule. Our final pragmatic quantum-chemical charge assigning protocol for liquid water is the Iterative Hirshfeld method with M06-HF/aug-cc-pVDZ and a quantum region cutoff radius of 5.5 A.<br>

scholarly journals Density functional theory meta GGA study of water adsorption in MIL-53(Cr)

2019 ◽  
Vol 34 (3) ◽  
pp. 227-232 ◽  
Author(s):  
E. Cockayne
Keyword(s):  
Density Functional Theory ◽  
Water Molecule ◽  
Density Functional ◽  
Critical Concentration ◽  
Metal Organic Framework ◽  
Water Dimer ◽  
Hydroxyl Group ◽  
Water Molecules ◽  
Generalized Gradient ◽  
Functional Theory

We use density functional theory meta-generalized gradient approximation TPSS + D3(BJ) + U + J calculations to investigate the energetics and geometry of water molecules in the flexible metal-organic framework material Materials of Institut Lavoisier (MIL)-53(Cr) as a function of cell volume. The critical concentration of water to cause the transition from the large pore (lp) to the narrow pore (np) structure is estimated to be about 0.13 water molecule per Cr. At a concentration x = 1 water molecule per Cr, the zero-temperature np and lp configurations each have a hydrogen bond between the H of each framework hydroxyl group and water oxygen (OW). At intermediate volumes, water dimer-like configurations are observed. A concentration x = 1.25 leads to hydrogen bonding between water molecules in the np phase that is absent for x = 1. Our results suggest possible mechanisms for pore closing in hydrated MIL-53(Cr).

Internal dynamics of cyclohexanol and the cyclohexanol–water adduct

2019 ◽  
Vol 21 (7) ◽  
pp. 3676-3682 ◽  
Author(s):  
Marcos Juanes ◽  
Weixing Li ◽  
Lorenzo Spada ◽  
Luca Evangelisti ◽  
Alberto Lesarri ◽  
...  
Keyword(s):  
Water Molecule ◽  
Water Dimer ◽  
Hydroxyl Group ◽  
Rotational Spectrum ◽  
Internal Dynamics

Two for a tango: the rotational spectrum of a cyclohexanol–water dimer evidences a concerted motion of the water molecule and the hydroxyl group of the ring.

Hydration Free Energies of Organic Molecules in the FreeSolv Database Calculated with Polarized Atom In Molecules Atomic Charges and the GAFF Force Field.

2018 ◽  
Author(s):  
Maximiliano Riquelme ◽  
Alejandro Lara ◽  
David L. Mobley ◽  
Toon Vestraelen ◽  
Adelio R Matamala ◽  
...  
Keyword(s):  
Force Field ◽  
Functional Groups ◽  
Electrostatic Interactions ◽  
Organic Molecules ◽  
Force Fields ◽  
Chemical Elements ◽  
Atomic Charges ◽  
Free Energies ◽  
Molecular Systems ◽  
Solvent Model

<div>Computer simulations of bio-molecular systems often use force fields, which are combinations of simple empirical atom-based functions to describe the molecular interactions. Even though polarizable force fields give a more detailed description of intermolecular interactions, nonpolarizable force fields, developed several decades ago, are often still preferred because of their reduced computation cost. Electrostatic interactions play a major role in bio-molecular systems and are therein described by atomic point charges.</div><div>In this work, we address the performance of different atomic charges to reproduce experimental hydration free energies in the FreeSolv database in combination with the GAFF force field. Atomic charges were calculated by two atoms-in-molecules approaches, Hirshfeld-I and Minimal Basis Iterative Stockholder (MBIS). To account for polarization effects, the charges were derived from the solute's electron density computed with an implicit solvent model and the energy required to polarize the solute was added to the free energy cycle. The calculated hydration free energies were analyzed with an error model, revealing systematic errors associated with specific functional groups or chemical elements. The best agreement with the experimental data is observed for the MBIS atomic charge method, including the solvent polarization, with a root mean square error of 2.0 kcal mol<sup>-1</sup> for the 613 organic molecules studied. The largest deviation was observed for phosphor-containing molecules and the molecules with amide, ester and amine functional groups.</div>

Partition Coefficients of Methylated DNA Bases Obtained from Free Energy Calculations with Molecular Electron Density Derived Atomic Charges.

2018 ◽  
Author(s):  
Alejandro Lara ◽  
Maximiliano Riquelme ◽  
Esteban Vöhringer-Martinez
Keyword(s):  
Electron Density ◽  
Partition Coefficients ◽  
Dna Bases ◽  
Atomic Charges ◽  
Free Energies ◽  
Solvation Model ◽  
Minimal Basis ◽  
Methylated Dna ◽  
Implicit Solvation Model ◽  
Good Agreement

<div> <div> <div> <p>Partition coefficients serve in various areas as pharmacology and environmental sciences to predict the hydrophobicity of different substances. Recently, they have been also used to address the accuracy of force fields for various organic compounds and specifically the methylated DNA bases. In this study atomic charges were derived by different partitioning methods (Hirshfeld and Minimal Basis Iterative Stockholder) directly from the electron density obtained by electronic structure calculations in vac- uum, with an implicit solvation model or with explicit solvation taking the dynamics of the solute and the solvent into account. To test the ability of these charges to describe electrostatic interactions in force fields for condensed phases the original atomic charges of the AMBER99 force field were replaced with the new atomic charges and combined with different solvent models to obtain the hydration and chloroform solvation free energies by molecular dynamics simulations. Chloroform-water partition coefficients derived from the obtained free energies were compared to experimental and previously reported values obtained with the GAFF or the AMBER-99 force field. The results show that good agreement with experimental data is obtained when the polarization of the electron density by the solvent has been taken into account deriving the atomic charges of polar DNA bases and when the energy needed to polarize the electron den- sity of the solute has been considered in the transfer free energy. These results were further confirmed by hydration free energies of polar and aromatic amino acid side chain analogues. Comparison of the two partitioning methods Hirsheld-I and Minimal Basis Iterative Stockholder (MBIS) revealed some deficiencies in the Hirshfeld-I method related to nonexistent isolated anionic nitrogen pro-atoms used in the method. Hydration free energies and partitioning coefficients obtained with atomic charges from the MBIS partitioning method accounting for polarization by the implicit solvation model are in good agreement with the experimental values. </p> </div> </div> </div>

SAMPL6 Octanol-Water Partition Coefficients from Alchemical Free Energy Calculations with MBIS Atomic Charges

2019 ◽  
Author(s):  
Maximiliano Riquelme ◽  
Esteban Vöhringer-Martinez
Keyword(s):  
Free Energy ◽  
Electron Density ◽  
Free Energy Calculations ◽  
Basis Set ◽  
Energetic Cost ◽  
Atomic Charges ◽  
Free Energies ◽  
Energy Calculations ◽  
Alchemical Free Energy ◽  
Alchemical Free Energy Calculations

In molecular modeling the description of the interactions between molecules forms the basis for a correct prediction of macroscopic observables. Here, we derive atomic charges from the implicitly polarized electron density of eleven molecules in the SAMPL6 challenge using the Hirshfeld-I and Minimal Basis Set Iterative Stockholder(MBIS) partitioning method. These atomic charges combined with other parameters in the GAFF force field and different water/octanol models were then used in alchemical free energy calculations to obtain hydration and solvation free energies, which after correction for the polarization cost, result in the blind prediction of the partition coefficient. From the tested partitioning methods and water models the S-MBIS atomic charges with the TIP3P water model presented the smallest deviation from the experiment. Conformational dependence of the free energies and the energetic cost associated with the polarization of the electron density are discussed.

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