Publications by authors named "Masoud Darvish Ganji"

11 Publications

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Understanding structural and molecular properties of complexes of nucleobases and Au13 golden nanocluster by DFT calculations and DFT-MD simulation.

Sci Rep 2021 Jan 11;11(1):435. Epub 2021 Jan 11.

Department of Chemistry, Qaemshahr Branch, Islamic Azad University, Qaemshahr, Iran.

The characterization of the complexes of biomolecules and nanostructures is highly interesting and benefits the rational development and design of nano-materials and nano-devices in nano-biotechnology. In this work, we have used dispersion corrected density functional theory (DFT-D) as well as DFT based molecular dynamics simulations to provide an atomistic understanding of interaction properties of DNA nucleobases and Au13 nanocluster. Various active sites of interacting molecules considering their relative orientation and distance are explored. Our goal is to stimulate the binding characteristics between two entities and evaluate this through the interaction energy, the charge transfer, the electronic structure, and the specific role of the molecular properties of the nucleobase-Au13 system. The primary outcomes of this comprehensive research illuminated that nucleic bases have potent affinity for binding to the Au cluster being chemisorption type and following the trend: Adenine > Cytosine > Guanine > Thymine. The AIM analysis indicated that the binding nature of the interacting species was predominantly partial covalent and high polar. We discuss the bearing of our findings in view of gene-nanocarrier, biosensing applications as well as nanodevices for sequencing of DNA.
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http://dx.doi.org/10.1038/s41598-020-80161-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7801688PMC
January 2021

Molecular simulation of efficient removal of HS pollutant by cyclodextrine functionalized CNTs.

Sci Rep 2019 07 23;9(1):10605. Epub 2019 Jul 23.

Department of Nanochemistry, Faculty of Pharmaceutical Chemistry, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.

DFT-D3 calculations were carried out to investigate interaction of HS and CH between numerous functionalized CNTs (f-CNTs), including hydroxyl, carboxyl, and cyclodextrin groups as potential candidates for selective adsorption and elimination of toxic pollutants. It was found that pristine CNTs as well as nanotube surface of functionalized CNTs cannot stably adsorb the HS molecule (adsorption energy of -0.17 eV). However, HS adsorption was significantly enhanced with different magnitudes upon the functionalization of CNT. For f-CNTs, HS adsorption was accompanied by releasing energies in the range between -0.34 to -0.54 eV where the upper limit of this range belongs to the cyclodextrin-functionalized CNT (CD-CNT) as the consequence of the existence of both dispersion and electrostatic interactions between the adsorbate and substrate. Findings also demonstrated a significantly weaker interaction between CH and CD-CNT in comparison to the HS molecule with adsorption energy of -0.14 eV. Electronic properties of the selected substrates revealed no significant changes in the inherent electronic properties of the CNTs after functionalizing and adsorbing the gas molecules. Moreover, DFTB-MD simulation demonstrated high adsorption capacity as well as CD-CNT ability for HS molecules against the CH one under ambient condition.
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http://dx.doi.org/10.1038/s41598-019-46816-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6650489PMC
July 2019

Reactive molecular dynamic simulations on the gas separation performance of porous graphene membrane.

Sci Rep 2017 11 29;7(1):16561. Epub 2017 Nov 29.

Department of Nanochemistry, Faculty of Pharmaceutical Chemistry, Pharmaceutical Sciences Branch, Islamic Azad University, Tehran, Iran.

The separation of gases molecules with similar diameter and shape is an important area of research. For example, the major challenge to set up sweeping carbon dioxide capture and storage (CCS) in power plants is the energy requisite to separate the CO from flue gas. Porous graphene has been proposed as superior material for highly selective membranes for gas separation. Here we design some models of porous graphene with different sizes and shape as well as employ double layers porous graphene for efficient CO/H separation. The selectivity and permeability of gas molecules through various nanopores were investigated by using the reactive molecular dynamics simulation which considers the bond forming/breaking mechanism for all atoms. Furthermore, it uses a geometry-dependent charge calculation scheme that accounts appropriately for polarization effect which can play an important role in interacting systems. It was found that H-modified porous graphene membrane with pore diameter (short side) of about 3.75 Å has excellent selectivity for CO/H separation. The mechanism of gas penetration through the sub-nanometer pore was presented for the first time. The accuracy of MD simulation results validated by valuable DFT method. The present findings show that reactive MD simulation can propose an economical means of separating gases mixture.
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http://dx.doi.org/10.1038/s41598-017-14297-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5707435PMC
November 2017

Enantioseparation performance of CNTs as chiral selectors for the separation of ibuprofen isomers: a dispersion corrected DFT study.

J Mater Chem B 2017 Sep 9;5(33):6920-6929. Epub 2017 Aug 9.

Department of Organic Chemistry, Faculty of Chemistry, University of Mazandran, Babolsar, Iran.

The enantioseparation of chiral drugs has been of great interest in the modern pharmaceutical industry since the majority of bioorganic compounds are chiral. In this work, we have investigated the ability of pristine and defected (10, 5) chiral carbon nanotubes (CNTs) in enantioseparation of chiral R-/S-ibuprofen isomers. The interactions between the two enantiomers of ibuprofen and the outer surface and inner side wall of the chiral CNTs have been evaluated. We utilized dispersion-corrected density functional theory (DFT) calculations within the framework of the GGA-PBE scheme for the systems under study. The results indicated that the inner side walls of the defected (10, 5) CNTs exhibited the highest energy difference (ΔU) between the pairs of considered enantiomers with the energy difference of about 1.4 kcal mol, indicating that these nanotubes are a promising candidate in enantioseparation processes. The effect of solvation has also been considered in the calculations and it was found that changing the dielectric properties of the medium cannot affect the overall interactions between the drug and CNT. The electronic properties of the considered systems did not change upon the interaction between the incorporated molecules and the type of interaction was found to be dispersion-governed physisorption.
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http://dx.doi.org/10.1039/c7tb00755hDOI Listing
September 2017

Hydrogen purification performance of a nanoporous hexagonal boron nitride membrane: molecular dynamics and first-principle simulations.

Phys Chem Chem Phys 2017 May;19(19):12032-12044

Department of Nanochemistry, Faculty of Pharmaceutical Chemistry, Pharmaceutical Sciences Branch, Islamic Azad University (IAUPS), Tehran, Iran.

Membranes have attracted much attention for the efficient separation of gas mixtures, due to their specific structural and unique properties. In this work, density functional theory (DFT) and molecular dynamic (MD) simulations have been employed to evaluate the performance of nanoporous hexagonal boron nitride (h-BN) monolayers for hydrogen purification. Various porous membranes were designed, and full structural relaxation was carried out by using DFT calculations and then MD simulations to investigate the H purification performance of the nanoporous h-BN membranes. It was found that the selectivity for H gas over N gas was highly sensitive to the type and width of the pores. The h-BN membrane containing pores with short and long sides both of about 3 Å (pore 1B-3N) demonstrated optimal selectivity for H molecules, while the permeability of the pore 5B-5N + 4H membrane (short side of about 4.4 Å) was much higher than that of other counterparts. Furthermore, DFT calculations were performed to validate the MD simulation observations as well as to explain the selectivity performance of the most desirable pore membrane. We demonstrated that the 1B-3N pore is a far superior membrane to other counterparts and exhibits an excellent potential for applications in hydrogen purification, clean energy combustion, and the design of novel membranes for gas separation.
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http://dx.doi.org/10.1039/c7cp01665dDOI Listing
May 2017

First-principles vdW-DF study on the enhanced hydrogen storage capacity of Pt-adsorbed graphene.

J Mol Model 2014 May 29;20(5):2230. Epub 2014 Apr 29.

Department of Mechanical Engineering, Semnan University, Semnan, Iran.

Ab initio vdW calculations with the DFT level of theory were used to investigate hydrogen (H₂) adsorption on Pt-adsorbed graphene (Pt-graphene). We have explored the most energetically favorable sites for single Pt atom adsorption on the graphene surface. The interaction of H₂ with the energetically favorable Pt-graphene system was then investigated. We found that H₂ physisorbs on pristine graphene with a binding energy of -0.05 eV, while the binding energy is enhanced to -1.98 eV when H₂ binds Pt-adsorbed graphene. We also found that up to four H₂ molecules can be adsorbed on the Pt-graphene system with a -0.74 eV/H₂ binding energy. The effect of graphene layer stretching on the Pt-graphene capacity/ability for hydrogen adsorption was evaluated. Our results show that the number of H₂ molecules adsorbed on the Pt-graphene surface rises to six molecules with a binding energy of approximately -0.29 eV/H₂. Our first-principles results reveal that the Young's modulus was slightly decreased for Pt adsorption on the graphene layer. The first-principles calculated Young's modulus for the H₂-adsorbed Pt-graphene system demonstrates that hydrogen adsorption can dramatically increase the Young's modulus of such systems. As a result, hydrogen adsorption on the Pt-graphene system might enhance the substrate strength.
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http://dx.doi.org/10.1007/s00894-014-2230-8DOI Listing
May 2014

Density functional theory study of epoxy polymer chains adsorbing onto single-walled carbon nanotubes: electronic and mechanical properties.

J Mol Model 2013 Aug 23;19(8):3127-34. Epub 2013 Apr 23.

Department of Mechanical Engineering, Semnan University, Semnan, Iran.

We performed first principles calculations based on density functional theory (DFT) to investigate the effect of epoxy monomer content on the electronic and mechanical properties of single-walled carbon nanotubes (SWCNTs). Our calculation results reveal that interfacial interaction increases with increasing numbers of epoxy monomers on the surface of SWCNTs. Furthermore, density of states (DOS) results showed no orbital hybridization between the epoxy monomers and nanotubes. Mulliken charge analysis shows that the epoxy polymer carries a positive charge that is directly proportional to the number of monomers. The Young's modulus of the nanotubes was also studied as a function of monomer content. It was found that, with increasing number of monomers on the nanotubes, the Young's modulus first decreases and then approaches a constant value. The results of a SWCNT pullout simulation suggest that the interfacial shear stress of the epoxy/SWCNT complex is approximately 68 MPa. These results agreed well with experimental results, thus proving that the simulation methods used in this study are viable.
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http://dx.doi.org/10.1007/s00894-013-1852-6DOI Listing
August 2013

First-principles vdW-DF investigation on the interaction between the oxazepam molecule and C₆₀ fullerene.

J Mol Model 2013 Apr 24;19(4):1929-36. Epub 2013 Jan 24.

Department of Chemistry, Qaemshahr Branch, Islamic Azad University, Qaemshahr, Iran.

The interaction between oxazepam and C₆₀ fullerene was explored using first-principles vdW-DF calculations. It was found that oxazepam binds weakly to the fullerene cage via its carbonyl group. The binding of oxazepam to C₆₀ is affected drastically by nonlocal dispersion interactions, while vdW forces affect the corresponding geometries only a little. Furthermore, aqueous solution affects the geometries of the oxazepam approaching to fullerene slightly, while oxazepam binds slightly farther away from the nanocage. The results presented provide evidence for the applicability of the vdW-DF method and serve as a practical benchmark for the investigation of host-guest interactions in biological systems.
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http://dx.doi.org/10.1007/s00894-013-1758-3DOI Listing
April 2013

Boron nitride nanotube based nanosensor for acetone adsorption: a DFT simulation.

J Mol Model 2013 Mar 20;19(3):1259-65. Epub 2012 Nov 20.

Department of Chemistry, Qaemshahr Branch, Islamic Azad University, Qaemshahr, Iran.

We have investigated the adsorption properties of acetone on zigzag single-walled BNNTs using density functional theory (DFT) calculations. The results obtained show that acetone is strongly bound to the outer surface of a (5,0) BNNT on the top site directly above the boron atom, with a binding energy of -96.16 kJ mol(-1) and a B-O binding distance of 1.654 Å. Our first-principles calculations also predict that the ability of zigzag BNNTs to adsorb acetone is significantly stronger than the corresponding ability of zigzag CNTs. A comparative investigation of BNNTs with different diameters indicated that the ability of the side walls of the tubes to adsorb acetone decreases significantly for nanotubes with larger diameters. Furthermore, the stability of the most stable acetone/BNNT complex was tested using ab initio molecular dynamics simulation at room temperature.
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http://dx.doi.org/10.1007/s00894-012-1668-9DOI Listing
March 2013

Simple benzene derivatives adsorption on defective single-walled carbon nanotubes: a first-principles van der Waals density functional study.

J Mol Model 2013 Mar 1;19(3):1059-67. Epub 2012 Nov 1.

Center of Nano-Science, Qaemshahr Branch, Islamic Azad University, Qaemshahr, Iran.

We have investigated the interaction between open-ended zig-zag single-walled carbon nanotube (SWCNT) and a few benzene derivatives using the first-principles van der Waals density functional (vdW-DF) method, involving full geometry optimization. Such sp (2)-like materials are typically investigated using conventional DFT methods, which significantly underestimate non-local dispersion forces (vdW interactions), therefore affecting interactions between respected molecules. Here, we considered the vdW forces for the interacting molecules that originate from the interacting π electrons of the two systems. The -0.54 eV adsorption energy reveals that the interaction of benzene with the side wall of the SWCNT is typical of the strong physisorption and comparable with the experimental value for benzene adsorption onto the graphene sheet. It was found that aromatics are physisorbed on the sidewall of perfect SWCNTs, as well as at the edge site of the defective nanotube. Analysis of the electronic structures shows that no orbital hybridization between aromatics and nanotubes occurs in the adsorption process. The results are relevant in order to identify the potential applications of noncovalent functionalized systems.
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http://dx.doi.org/10.1007/s00894-012-1652-4DOI Listing
March 2013

Theoretical investigation of methane adsorption onto boron nitride and carbon nanotubes.

Sci Technol Adv Mater 2010 Aug 10;11(4):045001. Epub 2010 Sep 10.

Department of Chemistry, Islamic Azad University, Ghaemshahr Branch, Mazandaran, Iran.

Methane adsorption onto single-wall boron nitride nanotubes (BNNTs) and carbon nanotubes (CNTs) was studied using the density functional theory within the generalized gradient approximation. The structural optimization of several bonding configurations for a CH molecule approaching the outer surface of the (8,0) BNNT and (8,0) CNT shows that the CH molecule is preferentially adsorbed onto the CNT with a binding energy of -2.84 kcal mol. A comparative study of nanotubes with different diameters (curvatures) reveals that the methane adsorptive capability for the exterior surface increases for wider CNTs and decreases for wider BNNTs. The introduction of defects in the BNNT significantly enhances methane adsorption. We also examined the possibility of binding a bilayer or a single layer of methane molecules and found that methane molecules preferentially adsorb as a single layer onto either BNNTs or CNTs. However, bilayer adsorption is feasible for CNTs and defective BNNTs and requires binding energies of -3.00 and -1.44 kcal mol per adsorbed CH molecule, respectively. Our findings indicate that BNNTs might be an unsuitable material for natural gas storage.
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http://dx.doi.org/10.1088/1468-6996/11/4/045001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5090341PMC
August 2010