scholarly journals Ab Initio Electronic Dielectric “Constant” of Proteins: A Baseline for Electrostatic Interaction in Biomolecular Systems

2021 ◽  
Author(s):  
Puja Adhikari ◽  
Rudolf Podgornik ◽  
Bahaa Jawad ◽  
Wai-Yim Ching
Keyword(s):  
Dielectric Constant ◽  
Ab Initio ◽  
Electrostatic Interactions ◽  
Size Structure ◽  
Dielectric Constants ◽  
Computational Method ◽  
Molecular Heterogeneity ◽  
Bathing Solution ◽  
Theoretical Approaches ◽  
Small Proteins

<p>The protein dielectric constant reflects the molecular heterogeneity of the proteins and can be decomposed into different components depending on the size, structure, composition, locality, and environment of the protein in general. The long history of its computation and measurement attest to the vital importance of electrostatic interactions in protein physics that engendered diverse theoretical approaches based often on scattered methodologies with various adjustable parameters. We present a new robust computational method anchored in rigorous <i>ab initio</i> quantum mechanical calculation of explicit atomistic models, without any indeterminate parameters to compute and gain insight into the <i>electronic component</i> of the static dielectric constants of small proteins under different conditions. We implement the new methodology to the 20 canonical amino acids individually, a polypeptide RGD-4C (1FUV) in different environments, and the SD1 domain in the Spike protein of SARS-COV-2. The calculated electronic dielectric constants for 1FUV and SD1 in vacuum are 28.06 and 50.02 respectively. They decrease in the presence of aqueous bathing solution.</p>

scholarly journals Ab Initio Electronic Dielectric “Constant” of Proteins: A Baseline for Electrostatic Interaction in Biomolecular Systems

2021 ◽  
Author(s):  
Puja Adhikari ◽  
Rudolf Podgornik ◽  
Bahaa Jawad ◽  
Wai-Yim Ching
Keyword(s):  
Dielectric Constant ◽  
Ab Initio ◽  
Electrostatic Interactions ◽  
Size Structure ◽  
Dielectric Constants ◽  
Computational Method ◽  
Molecular Heterogeneity ◽  
Bathing Solution ◽  
Theoretical Approaches ◽  
Small Proteins

<p>The protein dielectric constant reflects the molecular heterogeneity of the proteins and can be decomposed into different components depending on the size, structure, composition, locality, and environment of the protein in general. The long history of its computation and measurement attest to the vital importance of electrostatic interactions in protein physics that engendered diverse theoretical approaches based often on scattered methodologies with various adjustable parameters. We present a new robust computational method anchored in rigorous <i>ab initio</i> quantum mechanical calculation of explicit atomistic models, without any indeterminate parameters to compute and gain insight into the <i>electronic component</i> of the static dielectric constants of small proteins under different conditions. We implement the new methodology to the 20 canonical amino acids individually, a polypeptide RGD-4C (1FUV) in different environments, and the SD1 domain in the Spike protein of SARS-COV-2. The calculated electronic dielectric constants for 1FUV and SD1 in vacuum are 28.06 and 50.02 respectively. They decrease in the presence of aqueous bathing solution.</p>

scholarly journals First-Principles Simulation of Dielectric Function in Biomolecules

Materials ◽  
2021 ◽  
Vol 14 (19) ◽  
pp. 5774
Author(s):  
Puja Adhikari ◽  
Rudolf Podgornik ◽  
Bahaa Jawad ◽  
Wai-Yim Ching
Keyword(s):  
Size Structure ◽  
Simulation Method ◽  
Van Der Waals Interactions ◽  
Molecular Heterogeneity ◽  
Dielectric Spectra ◽  
Dielectric Absorption ◽  
Small Proteins ◽  
Atomistic Models ◽  
Two Peaks ◽  
Insight Into

The dielectric spectra of complex biomolecules reflect the molecular heterogeneity of the proteins and are particularly important for the calculations of electrostatic (Coulomb) and electrodynamic (van der Waals) interactions in protein physics. The dielectric response of the proteins can be decomposed into different components depending on the size, structure, composition, locality, and environment of the protein in general. We present a new robust simulation method anchored in rigorous ab initio quantum mechanical calculations of explicit atomistic models, without any indeterminate parameters to compute and gain insight into the dielectric spectra of small proteins under different conditions. We implement this methodology to a polypeptide RGD-4C (1FUV) in different environments, and the SD1 domain in the spike protein of SARS-COV-2. Two peaks at 5.2–5.7 eV and 14.4–15.2 eV in the dielectric absorption spectra are observed for 1FUV and SD1 in vacuum as well as in their solvated and salted models.

scholarly journals Comment on “investigation of dielectric constants of water in a nano-confined pore” by H. Zhu, F. Yang, Y. Zhu, A. Li, W. He, J. Huang and G. Li, RSC Adv., 2020, 10, 8628

RSC Advances ◽  
2021 ◽  
Vol 11 (9) ◽  
pp. 5179-5181
Author(s):  
Sayantan Mondal ◽  
Biman Bagchi
Keyword(s):  
Dielectric Constant ◽  
Dielectric Constants ◽  
Static Dielectric Constant ◽  
Inherent Anisotropy ◽  
Nanoconfined Water

Neglects of inherent anisotropy and distinct dielectric boundaries may lead to completely erroneous results. We demonstrate that such mistakes can give rise to gross underestimation of the static dielectric constant of cylindrically nanoconfined water.

DIELECTRIC CONSTANT AND SEEBECK COEFFICIENT FOR SEMICONDUCTORS: THERMODYNAMIC AND DFT STUDIES

2013 ◽  
Vol 12 (06) ◽  
pp. 1350057 ◽  
Author(s):  
HSIU-YA TASI ◽  
CHAOYUAN ZHU
Keyword(s):  
Boundary Condition ◽  
Dielectric Constant ◽  
Seebeck Coefficient ◽  
Gas Phase ◽  
Present Method ◽  
Dielectric Constants ◽  
Semiconductor Materials ◽  
Electronic Polarizability ◽  
Seebeck Coefficients ◽  
Good Agreement

Dielectric constants and Seebeck coefficients for semiconductor materials are studied by thermodynamic method plus ab initio quantum density functional theory (DFT). A single molecule which is formed in semiconductor material is treated in gas phase with molecular boundary condition and then electronic polarizability is directly calculated through Mulliken and atomic polar tensor (APT) density charges in the presence of the external electric field. This electronic polarizability can be converted to dielectric constant for solid material through the Clausius–Mossotti formula. Seebeck coefficient is first simulated in gas phase by thermodynamic method and then its value divided by its dielectric constant is regarded as Seebeck coefficient for solid materials. Furthermore, unit cell of semiconductor material is calculated with periodic boundary condition and its solid structure properties such as lattice constant and band gap are obtained. In this way, proper DFT function and basis set are selected to simulate electronic polarizability directly and Seebeck coefficient through chemical potential. Three semiconductor materials Mg 2 Si , β- FeSi 2 and SiGe are extensively tested by DFT method with B3LYP, BLYP and M05 functionals, and dielectric constants simulated by the present method are in good agreement with experimental values. Seebeck coefficients simulated by the present method are in reasonable good agreement with experiments and temperature dependence of Seebeck coefficients basically follows experimental results as well. The present method works much better than the conventional energy band structure theory for Seebeck coefficients of three semiconductors mentioned above. Simulation with periodic boundary condition can be generalized directly to treat with doped semiconductor in near future.

scholarly journals A note on some further determinations of the dielectric constants of organic bodies and electrolytes at very low temperatures

1898 ◽  
Vol 62 (379-387) ◽  
pp. 250-266 ◽  
Keyword(s):  
Dielectric Constant ◽  
Low Temperatures ◽  
Tuning Fork ◽  
Dielectric Constants ◽  
The Past ◽  
Method Of Measurement ◽  
The Given ◽  
Past Summer

In several previous communications we have described the investigations made by us on the dielectric constants of various frozen organic bodies and electrolytes at very low temperatures. In these researches we employed a method for the measurement of the dielectric constant which consisted in charging and discharging a condenser, having the given body as dielectric, through a galvanometer 120 times in a second by means of a tuning-fork interrupter. During the past summer we have repeated some of these determinations and used a different method of measurement and a rather higher frequency. In the experiments here described we have adopted Nernst’s method for the measurement of dielectric constants, using for this purpose the apparatus as arranged by Dr. Nernst which belongs to the Davy-Faraday Laboratory.

Contributions to Silicon-Hydrogen Bond-Stretching Frequency in Amorphous Si Alloys

1992 ◽  
Vol 258 ◽  
Author(s):  
Z. Jing ◽  
J. L. Whitten ◽  
G. Lucovsky
Keyword(s):  
Experimental Data ◽  
Hydrogen Bond ◽  
Dielectric Constant ◽  
Ab Initio ◽  
Effective Dielectric Constant ◽  
Bond Energies ◽  
Calculated Frequency ◽  
Bond Stretching ◽  
Amorphous Si ◽  
Good Agreement

ABSTRACTWe have performed ab initio calculations and determined the bond-energies and vibrational frequencies of Si-H groups that are: i) attached to Si-atoms as their immediate, and also more distant neighbors; and ii) attached to three O-atoms as their immediate neighbors, but are connected to an all Si-atom matrix. These arrangements simulate bonding geometries on Si surfaces, and the calculated frequency for i) is in good agreement with that of an Si-H group on an Si surface. To compare these results with a-Si:H alloys it is necessary to take into account an additional factor: the effective dielectric constant of the host. We show how to do this, demonstrating the way results of the ab initio calculations should then be compared with experimental data.

Epitaxial Growth and Anisotropic Dielectric Properties of La-Doped Bi4Ti3O12 Thin Films

2007 ◽  
Vol 124-126 ◽  
pp. 177-180
Author(s):  
Jang Sik Lee ◽  
Q.X. Jia
Keyword(s):  
Thin Films ◽  
Dielectric Constant ◽  
Dielectric Properties ◽  
Bottom Electrode ◽  
Dielectric Constants ◽  
The Other ◽  
Field Range ◽  
Anisotropic Dielectric ◽  
Dielectric Nonlinearity ◽  
La Doped

To investigate the anisotropic dielectric properties of layer-structured bismuth-based ferroelectrics along different crystal directions, we fabricate devices along different crystal orientations using highly c-axis oriented Bi3.25La0.75Ti3O12 (BLT) thin films on (001) LaAlO3 (LAO) substrates. Experimental results have shown that the dielectric properties of the BLT films are highly anisotropic along different crystal directions. The dielectric constants (1MHz at 300 K) are 358 and 160 along [100] and [110], respectively. Dielectric nonlinearity is also detected along these crystal directions. On the other hand, a much smaller dielectric constant and no detectable dielectric nonlinearity in a field range of 0-200 kV/cm are observed for films along [001] when c-axis oriented SRO is used as the bottom electrode.

Development of the trappe force field for ammonia

2010 ◽  
Vol 75 (5) ◽  
pp. 577-591 ◽  
Author(s):  
Ling Zhang ◽  
J. Ilja Siepmann
Keyword(s):  
Dielectric Constant ◽  
Nitrogen Atom ◽  
Force Field ◽  
Electrostatic Interactions ◽  
Hydrogen Atoms ◽  
Site Model ◽  
Lennard Jones ◽  
Hydrogen Position ◽  
Partial Charges ◽  
Vapor Liquid

The transferable potentials for phase equilibria (TraPPE) force field is extended through the development of a non-polarizable five-site ammonia model. In this model, the electrostatic interactions are represented by three positive partial charges placed at the hydrogen position and a compensating partial charge placed on an M site that is located on the C3 molecular axis and displaced from the nitrogen atom toward the hydrogen atoms. The repulsive and dispersive interactions are represented by placing a single Lennard–Jones site at the position of the nitrogen atom. Starting from the five-site model by Impey and Klein (Chem. Phys. Lett. 1984, 104, 579), this work optimizes the Lennard–Jones parameters and the magnitude of the partial charges for three values of the M site displacement. This parameterization is done by fitting to the vapor–liquid coexistence curve of neat ammonia. The accuracy of the three resulting models (differing in the displacement of the M site) is assessed through computation of the binary vapor–liquid equilibria with methane, the structure and the dielectric constant of liquid ammonia. The five-site model with an intermediate displacement of 0.08 Å for the M site yields a much better value for the dielectric constant, whereas differences in the other properties are quite small.

Fabrication of low dielectric constant polyimide/TiO2 nanofibers with enhanced UV-light shielding properties

2018 ◽  
Vol 31 (8) ◽  
pp. 986-995
Author(s):  
Lei Wang ◽  
Guifen Gong ◽  
Junyao Shen ◽  
Jinsong Leng
Keyword(s):  
Dielectric Constant ◽  
Light Absorption ◽  
Composite Nanofibers ◽  
Uv Light ◽  
Dielectric Constants ◽  
Low Dielectric Constant ◽  
Number Density ◽  
Tio2 Nanofibers ◽  
Low Dielectric ◽  
Mechanical Tensile

Polyimide (PI)/titanium dioxide (TiO2) composite nanofibers (NFs) with average diameters of 200–250 nm were synthesized via electrospinning. The total number density of dipoles decreased significantly, owing to the porous structures and compact interface between TiO2 NPs and PI matrix. All PI/TiO2 NFs maintain low dielectric constants and losses. For example, the dielectric constants of PI/TiO2-6% NFs are all lower than 2.6, being exposed to temperatures from 25°C to 200°C. Meantime, the dielectric losses of PI/TiO2-6% NFs are below 0.005. For ultraviolet (UV)-light shielding performance, the PI/TiO2 NFs exhibited good UV-light shielding and corresponding anti-photoaging properties. The reason can be ascribed from high UV-light absorption and scattering ability in the TiO2 NPs. The best UV-light absorption (average: 3.71) and corresponding absorption decay (15.13%) were achieved for optimized PI/TiO2-6% NFs. Other fundamental characteristics, such as the thermal stability, mechanical tensile property, and hydrophobicity, were also investigated. Such low dielectric constant PI/TiO2 composite NFs can be alternatively chosen under a longtime UV-light exposing condition.

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