A simple additive model for polarizabilities: Application to amino acids

Kassimi, N. El-Bakali; Thakkar, Ajit J.

doi:10.1016/j.cplett.2009.03.016

Cited by 20 publications

(5 citation statements)

References 28 publications

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“…As benchmark, we take the polarizabilities derived, using the Clausius-Mossotti equation, from experimental measurements of molar refraction in aqueous solution at λ = 589 nm and T = 25 °C . The differences between experimental and calculated values are within 6%, a good result given that calculations do not account for wavelength dispersion or solvent effects. , Our results are also in good agreement with other additive models of dipole polarizabilities …”

Section: Results and Discussionsupporting

confidence: 69%

“…44,45 Our results are also in good agreement with other additive models of dipole polarizabilities. 46 The isotropic polarizabilities computed via the transferable groups (shown in Table 2 In order to confirm the validity of the transferable functional groups, we computed the polarizability of some molecules, for example -alanine and -aminoisobutyric acid, that contain the same functional groups but that are outside the set used to construct the database. The results in Table 3 indicate that the transferable groups pass this test as well, again with good comparison against experimental values, when available.…”

Section: Atomic and Functional Group Polarizabilities In Amino Acid Mmentioning

confidence: 99%

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Distributed Atomic Polarizabilities of Amino Acids and their Hydrogen-Bonded Aggregates

2015

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With the purpose of rational design of optical materials, distributed atomic polarizabilities of amino acid molecules and their hydrogen-bonded aggregates are calculated in order to identify the most efficient functional groups, able to buildup larger electric susceptibilities in crystals.Moreover, we carefully analyze how the atomic polarizabilities depend on the one-electron basis set or the many-electron Hamiltonian, including both wave function and density functional theory methods. This is useful for selecting the level of theory that best combines high accuracy and low computational costs, very important in particular when using the cluster method to estimate susceptibilities of molecular-based materials.KEYWORDS: distributed polarizability, quantum theory of atoms in molecules, electron density distribution, linear optical properties, hydrogen bonding.2

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Section: Results and Discussionsupporting

confidence: 69%

Section: Atomic and Functional Group Polarizabilities In Amino Acid Mmentioning

confidence: 99%

Distributed Atomic Polarizabilities of Amino Acids and their Hydrogen-Bonded Aggregates

2015

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“…1)" rend="display" xml:id="FD1">

R_{p} = \sum_{a} R_{a} M_{a} / \sum_{a} M_{a}

of the contributions of the amino acid refractivities R a , experimentally measured and tabulated for 589 nm and 25 ºC in 45 and reproduced in 43 . The data are supported by ab initio calculations of mean residue polarizabilities 106–108 . M a is the residue molecular weight.…”

Section: Methodsmentioning

confidence: 54%

The Molecular Refractive Function of Lens γ-Crystallins

Zhao

Brown

Magone

et al. 2011

Journal of Molecular Biology

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γ-crystallins constitute the major protein component in the nucleus of the vertebrate eye lens. Present at very high concentrations, they exhibit extreme solubility and thermodynamic stability to prevent scattering of light and the formation of cataracts. However, functions beyond this structural role have remained mostly unclear. Here, we calculate molecular refractive index increments of crystallins. We show that all lens γ-crystallins have evolved a significantly elevated molecular refractive index increment, which is far above those of most proteins, including non-lens members of the βγ-crystallin family from different species. The same trait has evolved in parallel in crystallins of different phyla, including in the S-crystallins of cephalopods. A high refractive index increment can lower the crystallin concentration required to achieve a suitable refractive power of the lens, and thereby reduce their propensity to aggregate and form cataract. To produce a significant increase of the refractive index increment, a substantial global shift in the amino acid composition is required, which can naturally explain the highly unusual amino acid composition of γ-crystallins and their functional homologues. This function provides a new perspective for interpreting their molecular structure.

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“…While the knowledge of protein amino acid sequences was extremely sparse in the 1960s, this is usually not a limitation anymore for contemporary studies. Strengthening the strategy of a compositional prediction are modern ab initio computations of the mean polarizabilities of amino acids, which were found to be in good agreement with the tabulated data of McMeekin and colleagues (24)(25)(26). Thus, where dn/dc cannot be experimentally measured for practical reasons, it might be valuable to obtain an estimate from the compositional prediction rather than using an average value for all proteins.…”

Section: Introductionmentioning

confidence: 66%

On the Distribution of Protein Refractive Index Increments

Zhao

Brown

Schuck

2011

Biophysical Journal

426

397

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The protein refractive index increment, dn/dc, is an important parameter underlying the concentration determination and the biophysical characterization of proteins and protein complexes in many techniques. In this study, we examine the widely used assumption that most proteins have dn/dc values in a very narrow range, and reappraise the prediction of dn/dc of unmodified proteins based on their amino acid composition. Applying this approach in large scale to the entire set of known and predicted human proteins, we obtain, for the first time, to our knowledge, an estimate of the full distribution of protein dn/dc values. The distribution is close to Gaussian with a mean of 0.190 ml/g (for unmodified proteins at 589 nm) and a standard deviation of 0.003 ml/g. However, small proteins <10 kDa exhibit a larger spread, and almost 3000 proteins have values deviating by more than two standard deviations from the mean. Due to the widespread availability of protein sequences and the potential for outliers, the compositional prediction should be convenient and provide greater accuracy than an average consensus value for all proteins. We discuss how this approach should be particularly valuable for certain protein classes where a high dn/dc is coincidental to structural features, or may be functionally relevant such as in proteins of the eye.

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A simple additive model for polarizabilities: Application to amino acids

Cited by 20 publications

References 28 publications

Distributed Atomic Polarizabilities of Amino Acids and their Hydrogen-Bonded Aggregates

Distributed Atomic Polarizabilities of Amino Acids and their Hydrogen-Bonded Aggregates

The Molecular Refractive Function of Lens γ-Crystallins

On the Distribution of Protein Refractive Index Increments

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