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Computational Design of Materials for Applications (Drugs, Photonics)

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biophysics".

Deadline for manuscript submissions: closed (30 June 2022) | Viewed by 4220

Special Issue Editor

Special Issue Information

Dear Colleagues,

Computational science (or scientific computation) is a rapidly growing multidisciplinary field that uses advanced computing capabilities, algorithms, and techniques to unravel and solve complex problems. It is now commonly considered a third node of science, complementing experiment and theory. It is also an area of science which spans many disciplines (chemistry, physics, biology, mathematics), but which at its core involves the development of models and simulations to understand natural systems. It uses computer to advance science, largely modeling and simulating the physical world.

Possible areas of application which are rapidly attracting considerable interest, due to its potential practical use, are photonics and medicine. Through the use of methods based on principles of chemistry and/or physics, incorporated into efficient computer programs and exploiting the rapidly growing computational power, a series of phenomena which are associated (I) with properties of matter and (II) the evolution of important biological processes, which are of vital importance for the human life, are unraveled.

In the context of the present contribution, well-established computational methods with broad application and impact in the study of molecular materials, nanomaterials and biomolecular systems, such as ab initio, molecular dynamics/mechanics, and QM/MM, will be briefly presented. Through a series of representative case studies, it will be clearly shown that the combination and use of these computational techniques provides an effective and valuable tool for the study of a series of issues (e.g., novel photonic materials acting as switches, molecular conductors, molecular wires, optical materials, nonlinear optical materials, drug design in combating diseases, study of the toxicity of chemical molecules and compounds, unraveling of protein structures) which are of medical importance.

Possible Areas of Investigation: The proposed project aims to explore and to focus on new areas within the field of material science. These involve: i) computational science for the development of a systematic and integrated approach for the design of novel nanophotonic materials, and structure–property relationships; ii) elucidation of mechanisms at nanolevel for an efficient development of low-cost and environmentally friendly materials for photonic applications; iii) computational medicinal chemistry; iv) molecular descriptors of molecules of pharmacological interest and analysis of pharmacological activities; and v) toxicity of nanomaterials.

Dr. Avramopoulos Aggelos
Guest Editor

Manuscript Submission Information

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Keywords

  • Properties of matter
  • Molecular materials
  • Molecular and optical properties
  • Physics and chemistry of materials
  • Nanomaterials
  • Biomaterials with applications in drug design
  • Advanced computational techniques
  • Molecular drug design

Published Papers (2 papers)

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16 pages, 3214 KiB  
Article
Role of Monovalent Ions in the NKCC1 Inhibition Mechanism Revealed through Molecular Simulations
by Pavel Janoš and Alessandra Magistrato
Int. J. Mol. Sci. 2022, 23(23), 15439; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms232315439 - 06 Dec 2022
Cited by 1 | Viewed by 1457
Abstract
The secondary active Na-K-Cl cotransporter 1 (NKCC1) promotes electroneutral uptake of two chloride ions, one sodium ion and one potassium ion. NKCC1 regulates Cl homeostasis, thus being implicated in transepithelial water transport and in neuronal excitability. Aberrant NKCC1 transport is linked to [...] Read more.
The secondary active Na-K-Cl cotransporter 1 (NKCC1) promotes electroneutral uptake of two chloride ions, one sodium ion and one potassium ion. NKCC1 regulates Cl homeostasis, thus being implicated in transepithelial water transport and in neuronal excitability. Aberrant NKCC1 transport is linked to a variety of human diseases. The loop diuretic drugs bumetanide, furosemide, azosemide and ethacrynic acid target NKCC1, but are characterized by poor selectivity leading to severe side effects. Despite its therapeutic importance, the molecular details of the NKCC1 inhibition mechanism remain unclear. Using all-atom simulations, we predict a putative binding mode of these drugs to the zebrafish (z) and human (h) NKCC1 orthologs. Although differing in their specific interactions with NKCC1 and/or monovalent ions, all drugs can fit within the same cavity and engage in hydrophobic interactions with M304/M382 in z/hNKCC1, a proposed ion gating residue demonstrated to be key for bumetanide binding. Consistent with experimental evidence, all drugs take advantage of the K+/Na+ ions, which plastically respond to their binding. This study not only provides atomic-level insights useful for drug discovery campaigns of more selective/potent NKCC1 inhibitors aimed to tackle diseases related to deregulated Cl homeostasis, but it also supplies a paradigmatic example of the key importance of dynamical effects when drug binding is mediated by monovalent ions. Full article
(This article belongs to the Special Issue Computational Design of Materials for Applications (Drugs, Photonics))
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9 pages, 1793 KiB  
Article
Computational Design of Radical Recognition Assay with the Possible Application of Cyclopropyl Vinyl Sulfides as Tunable Sensors
by Liliya T. Sahharova, Evgeniy G. Gordeev, Dmitry B. Eremin and Valentine P. Ananikov
Int. J. Mol. Sci. 2021, 22(14), 7637; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22147637 - 16 Jul 2021
Cited by 3 | Viewed by 1969
Abstract
The processes involving the capture of free radicals were explored by performing DFT molecular dynamics simulations and modeling of reaction energy profiles. We describe the idea of a radical recognition assay, where not only the presence of a radical but also the nature/reactivity [...] Read more.
The processes involving the capture of free radicals were explored by performing DFT molecular dynamics simulations and modeling of reaction energy profiles. We describe the idea of a radical recognition assay, where not only the presence of a radical but also the nature/reactivity of a radical may be assessed. The idea is to utilize a set of radical-sensitive molecules as tunable sensors, followed by insight into the studied radical species based on the observed reactivity/selectivity. We utilize this approach for selective recognition of common radicals—alkyl, phenyl, and iodine. By matching quantum chemical calculations with experimental data, we show that components of a system react differently with the studied radicals. Possible radical generation processes were studied involving model reactions under UV light and metal-catalyzed conditions. Full article
(This article belongs to the Special Issue Computational Design of Materials for Applications (Drugs, Photonics))
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