scholarly journals Molecular Interpretation of Pharmaceuticals’ Adsorption on Carbon Nanomaterials: Theory Meets Experiments

Processes ◽  
2020 ◽  
Vol 8 (6) ◽  
pp. 642 ◽  
Author(s):  
Daniele Veclani ◽  
Marilena Tolazzi ◽  
Andrea Melchior
Keyword(s):  
Density Functional ◽  
Carbon Nanomaterials ◽  
Experimental Studies ◽  
Md Simulations ◽  
Spectroscopic Properties ◽  
Pharmaceutical Drugs ◽  
Mechanical Methods ◽  
Adsorption Processes ◽  
Carbon Based Nanomaterials

The ability of carbon-based nanomaterials (CNM) to interact with a variety of pharmaceutical drugs can be exploited in many applications. In particular, they have been studied both as carriers for in vivo drug delivery and as sorbents for the treatment of water polluted by pharmaceuticals. In recent years, the large number of experimental studies was also assisted by computational work as a tool to provide understanding at molecular level of structural and thermodynamic aspects of adsorption processes. Quantum mechanical methods, especially based on density functional theory (DFT) and classical molecular dynamics (MD) simulations were mainly applied to study adsorption/release of various drugs. This review aims to compare results obtained by theory and experiments, focusing on the adsorption of three classes of compounds: (i) simple organic model molecules; (ii) antimicrobials; (iii) cytostatics. Generally, a good agreement between experimental data (e.g. energies of adsorption, spectroscopic properties, adsorption isotherms, type of interactions, emerged from this review) and theoretical results can be reached, provided that a selection of the correct level of theory is performed. Computational studies are shown to be a valuable tool for investigating such systems and ultimately provide useful insights to guide CNMs materials development and design.

scholarly journals Understanding the Role of R266K Mutation in Cystathionine β-Synthase (CBS) Enzyme: An in Silico Study

2021 ◽  
Author(s):  
Aashish Bhatt ◽  
Md. Ehesan Ali
Keyword(s):  
Hydrogen Bonding ◽  
In Silico ◽  
Density Functional ◽  
Experimental Studies ◽  
Salt Bridge ◽  
Md Simulations ◽  
Enzymatic Activities ◽  
Wild Type ◽  
Long Distance

<div>Human cystathionine β-synthase (hCBS) is a unique pyridoxal 5’-phosphate (PLP) dependent enzyme that catalyses the condensation reactions in the transsulfuration pathways. The specific role of Heme in the enzymatic activities has not yet been established, however, several experimental studies indicated the bi-directional communications between the Heme and PLP. Performing classical molecular dynamics (MD) simulations upon developing the necessary force field parameters for the cysteine and histidine bound hexa-coordinated Heme, we have investigated <i>In Silico</i> dynamical aspects of the bi-directional communications. Furthermore, we have investigated the comparative aspects of electron density overlap across the communicating pathways adopting the density functional theory (DFT) in conjunction with the hybrid exchange correlation functional for the CSB<sup>WT</sup> (wild-type) and CBS<sup>R266K</sup> (mutated) case. The atomistic dynamical simulations and subsequent explorations of the electronic structure not only confirm the reported observations but provide an in-depth mechanistic understating of how the non-covalent hydrogen bonding interactions with Cys52 control the such long-distance communication. Our study also provides a convincing answer to the reduced enzymatic activities in the R266K hCBS in comparison to the wild-type enzymes. We further realized that the difference in hydrogen-bonding patterns as well as salt-bridge interactions play the pivotal role in such long distant bi-directional communications.</div>

Development of a 2NN-MEAM potential for boron

2021 ◽  
pp. 2050008
Author(s):  
Siamak Attarian ◽  
Shaoping Xiao
Keyword(s):  
Potential Function ◽  
Density Functional ◽  
Nearest Neighbor ◽  
Experimental Studies ◽  
Md Simulations ◽  
Mechanical And Thermal Properties ◽  
Functional Theory ◽  
Embedded Atom ◽  
The Density Functional Theory ◽  
Comprehensive Comparison

In this paper, we present the first work in developing a second nearest-neighbor modified embedded atom method (2NN-MEAM) potential function that can be used to model interatomic interactions in both [Formula: see text] boron and [Formula: see text] boron polymorphs. To fit the potential parameters by optimization, some physical properties and elastic constants of boron, calculated from the density functional theory, are adopted as the targets in the objective function. The developed potential is utilized in molecular dynamics (MD) simulations to calculate the physical, mechanical, and thermal properties of [Formula: see text] boron and [Formula: see text] boron. A comprehensive comparison is conducted between the MD simulations and various experimental studies if available to validate the developed potential function. It is concluded that the developed 2NN-MEAM potential can be practically employed in MD modeling and simulation of boron. This work will also enhance the future development of binary potentials for boron compounds to study boron-based composites via MD.

Adsorption of polyaromatic heterocycles on pyrophyllite surface by means of different theoretical approaches

2011 ◽  
Vol 8 (4) ◽  
pp. 429 ◽  
Author(s):  
C. Ignacio Sainz-Díaz ◽  
Misaela Francisco-Márquez ◽  
Annik Vivier-Bunge
Keyword(s):  
Adsorption Energy ◽  
Density Functional ◽  
Interlayer Space ◽  
External Surface ◽  
Experimental Studies ◽  
Atmospheric Pollutants ◽  
Interatomic Potentials ◽  
Dft Methods ◽  
Theoretical Approaches ◽  
Mechanical Methods

Environmental contextVolatile organic compounds can adsorb to the surfaces of silicates present in atmospheric aerosols, but the mechanisms and interactions are not well understood. We compare theoretical approaches for describing the adsorption of polyaromatic heterocycles to a model phyllosilicate surface. The enthalpy and spectroscopic data for this adsorption provide valuable information for future experimental studies on these atmospheric pollutants. AbstractThe adsorption of thiophene, benzothiophene and dibenzothiophene, as models of polyaromatic heterocycles, on the (001) surface of pyrophyllite, as a model of phyllosilicates, has been investigated by means of empirical interatomic potentials and quantum-mechanical methods based on Hartree–Fock and Density Functional Theory (DFT) approximations. Molecular Dynamic simulations have also been performed for this adsorption, exploring the different configurations that these polyaromatic heterocycles can adopt with respect to the surface. These adsorbates adopt more likely a planar disposition with respect to the phyllosilicate surface. Spectroscopic shifts of the main vibration frequencies upon adsorption of these heterocycles on the phyllosilicate surface have been identified. The adsorption energy calculated with different methods are compared and discussed in terms of adequacy of empirical potentials and DFT methods for describing the weak interactions observed. In addition to considering the (001) surface of pyrophyllite as an external surface of the mineral, the adsorption in the interlayer space was also explored obtaining a d(001) spacing of 12.64 Å. However, the adsorption energy is much lower than the cleavage energy of the interlayer space and it is clear that adsorption is more likely to occur on the external surface than in the interlayer space.

scholarly journals Molecular Docking of Olea europaea and Curcuma Longa Compounds as Potential Drug Agents for Targeting Main-Protease of SARS-nCoV2

2020 ◽  
Author(s):  
Rashid Saif ◽  
Muhammad Hassan Raza ◽  
Talha Rehman ◽  
Muhammad Osama Zafar ◽  
Saeeda Zia ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Structural Information ◽  
Curcuma Longa ◽  
Experimental Studies ◽  
Md Simulations ◽  
Binding Energies ◽  
Target Protein ◽  
Target Proteins ◽  
Main Protease

<p>One of the main reasons of rapidly growing cases of COVID-19 pandemic is the unavailability of approved therapeutic agents. Therefore, it is urgently required to find out the best drug/vaccine by all means. Aim of the current study is to test the anti-viral drug potential of many of the available olive and turmeric compounds that can be used as potential inhibitors against one of the target proteins of SARS-nCoV2 named Main protease (Mpro/3clpro). Molecular docking of thirty olive and turmeric compounds with target protein was performed using Molecular Operating Environment (MOE) software to determine the best ligand-protein interaction energies. The structural information of the viral target protein M pro/3CL pro and ligands were taken from PDB and PubChem database respectively. Out of the thirty drug agents, 6 ligands do not follow the Lipinski rule of drug likeliness by violating two or more rules while remaining 24 obey the rules and included for the downstream analysis. Ten ligands from olive and four from turmeric gave the best lowest binding energies, which are Neuzhenide, Rutin, Demethyloleoeuropein, Oleuropein, Luteolin-7-rutinoside, Ligstroside, Verbascoside, Luteolin-7-glucoside, Cosmosin, Curcumin, Tetrehydrocurcumin, Luteolin-4'-o-glucoside, Demethoxycurcumin and Bidemethoxycurcumin with docking scores of -10.91, -9.49, -9.48, -9.21, -9.18, -8.72, -8.51, -7.68, -7.67, -7.65, -7.42, -7.25, -7.02 and - 6.77 kcal/mol respectively. Our predictions suggest that these ligands have the potential inhibitory effects of M pro of SARS-nCoV2, so, these herbal plants would be helpful in harnessing COVID-19 infection as home remedy with no serious known side effects. Further, in-silico MD simulations and in-vivo experimental studies are needed to validate the inhibitory properties of these compounds against the current and other target proteins in SARS-nCoV2.<br></p>

scholarly journals Interactions of Carbon Nanotubes and Carbon Nanohorns with a Model Membrane Layer and Lung Surfactant In Vitro

2019 ◽  
Vol 2019 ◽  
pp. 1-10 ◽  
Author(s):  
Dorota Kondej ◽  
Tomasz R. Sosnowski
Keyword(s):  
Carbon Nanomaterials ◽  
Lung Surfactant ◽  
Surface Elasticity ◽  
Experimental Studies ◽  
Dynamic Surface ◽  
Carbon Nanohorns ◽  
Experimental Systems ◽  
Lipid Layers

A broader use of carbon nanomaterials increases the risk of their inhalation as aerosol dispersed in the air. Inhaled nanometer-sized particles are known to penetrate to the pulmonary region where they interact with the lung surfactant as the first barrier they meet and eventually penetrate to the surface of the cellular layer. This study presents the results of experimental studies of physicochemical interactions between several types of carbon nanomaterials (nanotubes and nanohorns of various size and surface properties) and lipid layers in two qualitatively different experimental systems: Langmuir trough and pulsated drop tensiometer, both providing complementary possibilities to study interfacial properties of the lipid-rich layer. Quantified alterations in mechanical properties if lipid films (equilibrium compressibility, dynamic surface elasticity, and viscosity) indicate that nanocarbons with different wettability may induce concentration-dependent frustration of the lung surfactant and biological membranes in vivo. The observed effects are discussed not only in relation to health effects from nanoparticle inhalation but also to potential medical applications of engineered carbon nanomaterials.

scholarly journals Molecular Docking of Olea europaea and Curcuma Longa Compounds as Potential Drug Agents for Targeting Main-Protease of SARS-nCoV2

2020 ◽  
Author(s):  
Rashid Saif ◽  
Muhammad Hassan Raza ◽  
Talha Rehman ◽  
Muhammad Osama Zafar ◽  
Saeeda Zia ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Structural Information ◽  
Curcuma Longa ◽  
Experimental Studies ◽  
Md Simulations ◽  
Binding Energies ◽  
Target Protein ◽  
Target Proteins ◽  
Main Protease

<p>One of the main reasons of rapidly growing cases of COVID-19 pandemic is the unavailability of approved therapeutic agents. Therefore, it is urgently required to find out the best drug/vaccine by all means. Aim of the current study is to test the anti-viral drug potential of many of the available olive and turmeric compounds that can be used as potential inhibitors against one of the target proteins of SARS-nCoV2 named Main protease (Mpro/3clpro). Molecular docking of thirty olive and turmeric compounds with target protein was performed using Molecular Operating Environment (MOE) software to determine the best ligand-protein interaction energies. The structural information of the viral target protein M pro/3CL pro and ligands were taken from PDB and PubChem database respectively. Out of the thirty drug agents, 6 ligands do not follow the Lipinski rule of drug likeliness by violating two or more rules while remaining 24 obey the rules and included for the downstream analysis. Ten ligands from olive and four from turmeric gave the best lowest binding energies, which are Neuzhenide, Rutin, Demethyloleoeuropein, Oleuropein, Luteolin-7-rutinoside, Ligstroside, Verbascoside, Luteolin-7-glucoside, Cosmosin, Curcumin, Tetrehydrocurcumin, Luteolin-4'-o-glucoside, Demethoxycurcumin and Bidemethoxycurcumin with docking scores of -10.91, -9.49, -9.48, -9.21, -9.18, -8.72, -8.51, -7.68, -7.67, -7.65, -7.42, -7.25, -7.02 and - 6.77 kcal/mol respectively. Our predictions suggest that these ligands have the potential inhibitory effects of M pro of SARS-nCoV2, so, these herbal plants would be helpful in harnessing COVID-19 infection as home remedy with no serious known side effects. Further, in-silico MD simulations and in-vivo experimental studies are needed to validate the inhibitory properties of these compounds against the current and other target proteins in SARS-nCoV2.<br></p>

scholarly journals Understanding the Role of R266K Mutation in Cystathionine β-Synthase (CBS) Enzyme: An in Silico Study

2021 ◽  
Author(s):  
Aashish Bhatt ◽  
Md. Ehesan Ali
Keyword(s):  
Hydrogen Bonding ◽  
In Silico ◽  
Density Functional ◽  
Experimental Studies ◽  
Salt Bridge ◽  
Md Simulations ◽  
Enzymatic Activities ◽  
Wild Type ◽  
Long Distance

<div>Human cystathionine β-synthase (hCBS) is a unique pyridoxal 5’-phosphate (PLP) dependent enzyme that catalyses the condensation reactions in the transsulfuration pathways. The specific role of Heme in the enzymatic activities has not yet been established, however, several experimental studies indicated the bi-directional communications between the Heme and PLP. Performing classical molecular dynamics (MD) simulations upon developing the necessary force field parameters for the cysteine and histidine bound hexa-coordinated Heme, we have investigated <i>In Silico</i> dynamical aspects of the bi-directional communications. Furthermore, we have investigated the comparative aspects of electron density overlap across the communicating pathways adopting the density functional theory (DFT) in conjunction with the hybrid exchange correlation functional for the CSB<sup>WT</sup> (wild-type) and CBS<sup>R266K</sup> (mutated) case. The atomistic dynamical simulations and subsequent explorations of the electronic structure not only confirm the reported observations but provide an in-depth mechanistic understating of how the non-covalent hydrogen bonding interactions with Cys52 control the such long-distance communication. Our study also provides a convincing answer to the reduced enzymatic activities in the R266K hCBS in comparison to the wild-type enzymes. We further realized that the difference in hydrogen-bonding patterns as well as salt-bridge interactions play the pivotal role in such long distant bi-directional communications.</div>

scholarly journals Understanding the Role of R266K Mutation in Cystathionine β-Synthase (CBS) Enzyme: An in Silico Study

2021 ◽  
Author(s):  
Aashish Bhatt ◽  
Md. Ehesan Ali
Keyword(s):  
Hydrogen Bonding ◽  
Electron Density ◽  
In Silico ◽  
Density Functional ◽  
Experimental Studies ◽  
Md Simulations ◽  
Wild Type ◽  
Long Distance ◽  
Transsulfuration Pathway

Human cystathionine β-synthase (hCBS) is a Heme containing unique pyridoxal 5’-phosphate (PLP) dependent enzyme that catalyzes the bio-chemical condensation reactions in the transsulfuration pathway. The role of Heme in the catalytic activities of enzyme has not yet been understood completely, even though various experimental studies have indicated its participation in the bi-directional electronic communication with the PLP center. Most probably Heme acts as the electron density reservoir for the catalytic reaction center but not as a redox electron source. Here, in this work, we investigated <i>In Silico</i> dynamical aspects of the bi-directional communications by performing classical molecular dynamics (MD) simulations upon developing the necessary force field parameters for the cysteine and histidine bound hexa-coordinated Heme. The comparative aspects of electron density overlap across the communicating pathways are also explored adopting the density functional theory (DFT) in conjunction with the hybrid exchange-correlation functional for the CSB<sup>WT</sup> (wild-type) and CBS<sup>R266K</sup> (mutated) case. The atomistic MD simulations and subsequent explorations of the electronic structures not only confirm the reported observations but provide an in-depth mechanistic understating of how the non-covalent hydrogen bonding interactions with Cys52 control such long-distance communication. Our study also provides a convincing answer to the reduced enzymatic activities in the R266K hCBS in comparison to the wild-type enzymes. We further realized that the difference in hydrogen-bonding patterns, as well as salt-bridge interactions, play a pivotal role in such long distant bi-directional communications.<br>

Computationally Assisted Design of High Signal-to-Noise Photoinduced Electron Transfer-Based Voltage-Sensitive Dyes

2020 ◽  
Author(s):  
Rishikesh Kulkarni ◽  
Anneliese Gest ◽  
Chun Kei Lam ◽  
Benjamin Raliski ◽  
Feroz James ◽  
...  
Keyword(s):  
Electron Transfer ◽  
Dft Calculations ◽  
Photoinduced Electron Transfer ◽  
Density Functional ◽  
Embryonic Stem ◽  
High Sensitivity ◽  
Md Simulations ◽  
High Signal ◽  
Signal To Noise ◽  
Green Fluorescent

<p>High signal-to-noise optical voltage indicators will enable simultaneous interrogation of membrane potential in large ensembles of neurons. However, design principles for voltage sensors with high sensitivity and brightness remain elusive, limiting the applicability of voltage imaging. In this paper, we use molecular dynamics (MD) simulations and density functional theory (DFT) calculations to guide the design of a bright and sensitive green-fluorescent voltage-sensitive fluorophore, or VoltageFluor (VF dye), that uses photoinduced electron transfer (PeT) as a voltage-sensing mechanism. MD simulations predict an 11% increase in sensitivity due to membrane orientation, while DFT calculations predict an increase in fluorescence quantum yield, but a decrease in sensitivity due to a decrease in rate of PeT. We confirm these predictions by synthesizing a new VF dye and demonstrating that it displays the expected improvements by doubling the brightness and retaining similar sensitivity to prior VF dyes. Combining theoretical predictions and experimental validation has resulted in the synthesis of the highest signal-to-noise green VF dye to date. We use this new voltage indicator to monitor the electrophysiological maturation of human embryonic stem cell-derived medium spiny neurons. </p>

Molecular Investigations of the Newly Synthesized Azomethines as Antioxidants: Theoretical and Experimental Studies

2019 ◽  
Vol 19 (6) ◽  
pp. 419-433 ◽  
Author(s):  
Siyamak Shahab ◽  
Masoome Sheikhi ◽  
Liudmila Filippovich ◽  
Evgenij Dikusar ◽  
Anhelina Pazniak ◽  
...  
Keyword(s):  
Density Functional ◽  
Energy Gap ◽  
Experimental Studies ◽  
Antioxidant Property ◽  
Nbo Analysis ◽  
Antioxidant Potential ◽  
Functional Theory ◽  
Homo And Lumo ◽  
Intramolecular Hydrogen ◽  
Activity Mechanism

: In this study, the antioxidant property of new synthesized azomethins has been investigated as theoretical and experimental. Methods and Results: Density functional theory (DFT) was employed to investigate the Bond Dissociation Enthalpy (BDE), Mulliken Charges, NBO analysis, Ionization Potential (IP), Electron Affinities (EA), HOMO and LUMO energies, Hardness (η), Softness (S), Electronegativity (µ), Electrophilic Index (ω), Electron Donating Power (ω-), Electron Accepting Power (ω+) and Energy Gap (Eg) in order to deduce scavenging action of the two new synthesized azomethines (FD-1 and FD-2). Spin density calculations and NBO analysis were also carried out to understand the antioxidant activity mechanism. Comparison of BDE of FD-1 and FD-2 indicate the weal antioxidant potential of these structures. Conclusion: FD-1 and FD-2 have very high antioxidant potential due to the planarity and formation of intramolecular hydrogen bonds.

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