Atomic charges from IR intensity parameters: theory, implementation and application

2012 ◽  
Vol 131 (3) ◽  
Author(s):  
Alberto Milani ◽  
Matteo Tommasini ◽  
Chiara Castiglioni
1988 ◽  
Vol 31 (3) ◽  
pp. 425-431 ◽  
Author(s):  
Stephen M. Camarata ◽  
Lisa Erwin

This paper presents a case study of a language-impaired child who signaled the distinction between English singular and plural using suprasegmental cues rather than the usual segmental form used within the parent language. Acoustic analyses performed within the first study in the paper revealed that the suprasegmental features used to maintain this distinction included various duration, fundamental frequency, and intensity parameters. Acoustic analyses Were also performed on a set of matched two- and four-item plural forms within a second study. The results of these analyses indicated that the same acoustic parameters were used to distinguish two-item plural forms from four-item plural forms. This case of linguistic creativity is offered as further evidence in support of the model of language acquisition that emphasizes the active role children take in the acquisition process. Additionally, the phonological, morphological, and psycholinguistic factors that may contribute to such rule invention are discussed.


2018 ◽  
Author(s):  
Maximiliano Riquelme ◽  
Alejandro Lara ◽  
David L. Mobley ◽  
Toon Vestraelen ◽  
Adelio R Matamala ◽  
...  

<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>


2018 ◽  
Author(s):  
Alejandro Lara ◽  
Maximiliano Riquelme ◽  
Esteban Vöhringer-Martinez

<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>


2019 ◽  
Author(s):  
Maximiliano Riquelme ◽  
Esteban Vöhringer-Martinez

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.


Foods ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 254
Author(s):  
Aislinn M. Richardson ◽  
Andrey A. Tyuftin ◽  
Kieran N. Kilcawley ◽  
Eimear Gallagher ◽  
Maurice G. O’Sullivan ◽  
...  

Determining minimum levels of fat and sucrose needed for the sensory acceptance of sponge cake while increasing the nutritional quality was the main objective of this study. Sponge cakes with 0, 25, 50 and 75% sucrose replacement (SR) using a combination of inulin and Rebaudioside A (Reb A) were prepared. Sensory acceptance testing (SAT) was carried out on samples. Following experimental results, four more samples were prepared where fat was replaced sequentially (0, 25, 50 and 75%) in sucrose-replaced sponge cakes using pureed butter beans (Pbb) as a replacer. Fat-replaced samples were investigated using sensory (hedonic and intensity) and physicochemical analysis. Texture liking and overall acceptability (OA) were the only hedonic sensory parameters significantly affected after a 50% SR in sponge cake (p < 0.05). A 25% SR had no significant impact on any hedonic sensory properties and samples were just as accepted as the control sucrose sample. A 30% SR was chosen for further experiments. After a 50% fat replacement (FR), no significant differences were found between 30% sucrose-replaced sponge cake samples in relation to all sensory (hedonic and intensity) parameters investigated. Flavour and aroma intensity attributes such as buttery and sweet and, subsequently, liking and OA of samples were negatively affected after a 75% FR (p < 0.05). Instrumental texture properties (hardness and chewiness (N)) did not discriminate between samples with increasing levels of FR using Pbb. Moisture content increased significantly with FR (p < 0.05). A simultaneous reduction in fat (42%) and sucrose was achieved (28%) in sponge cake samples without negatively affecting OA. Optimised samples contained significantly more dietary fibre (p < 0.05).


2000 ◽  
Vol 113 (9) ◽  
pp. 3930-3930
Author(s):  
Tianhai Zhu ◽  
Jiabo Li ◽  
Gregory D. Hawkins ◽  
Christopher J. Cramer ◽  
Donald G. Truhlar

2013 ◽  
Vol 807-809 ◽  
pp. 2366-2370
Author(s):  
Hua Ping Yang ◽  
Ming Li ◽  
Zheng Xin Yan ◽  
Dong Zhi Yan

The coal molecule model and the absorption model of coal and methane were established according to Van der Walls force. The coal molecule model and the absorption model of coal and methane were optimized and obtained absorption energy and equilibrium structure with the DFT method with 6-311G++ basic sets. The effects of coal molecule on the absorption position, absorption energy and absorption distance of CH4 were presented by analyzing the Mulliken atomic charges of coal molecules.


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