Browsing by Author "Mollaamin F., Monajjemi M."

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Aging Genome Modification and Editing using the CrisprCas9 system: Anti-Alzheimer Study by Docking Methods
(2023-06-15) Mollaamin F., Monajjemi M.
Cas-9 is an enzyme that uses CRISPR sequences as a guide for detecting and separating a part of the genome which are complementary to the CRISPR sequence. Cas9 (CRISPR-associated protein 9, formerly called Cas5, Csn1, or Csx12) plays an important role in the human immune system against DNA viruses and is also utilized in genetic engineering approaches. They are able to cut a part of the DNA sequence in genome editing. CRISPR-Cas-9 editing was established by Emmanuelle Charpentier and Jennifer Doudna (Nobel Prize in Chemistry in 2020). CRISPR has been edited for making transcription items that permit researchers to activate specific genes. There are two categories of CRISPR-Cas; category 1 consists of multiple Cas proteins for degrading foreign nucleic bases. Category 2 consists of a single huge Cas protein for the same role. Aging results from a lifetime of stochastic destruction of tissues and cellular ingredients. Increasing age parallel causes a decrease of immunity and any inflammation related to reflecting incidents of cellular and tissue damage as a function of a lifetime. The DNA sensing signaling is activated via wrong placed cytosolic, which initiates the innate immune responses. Micronuclei are completely related to aging and affect aging due to always occurring in several aging syndromes and cancer. Therefore, micronuclei may present a mechanistic link among genome instabilities, innate immune activation, and a few hallmarks of aging tissues with the different drug properties of Verubecestat, Donepezil, Memantine, galantamine, Tacrine, Exelon, Rivastigmine, 7-MEOTA, and Acyclovir. Among them, Tacrine was found to have the highest (negative) binding energy and was further subjected to molecular dynamics (MD) simulation analysis.
Application of DFT/TD-DFT Frameworks in the Drug Delivery Mechanism: Investigation of Chelated Bisphosphonate with Transition Metal Cations in Bone Treatment
(2023-03-01) Mollaamin F., Monajjemi M.; Mollaamin, F, Monajjemi, M
Carbon nanotubes (CNTs) are applied in a drug delivery system, which can be reacted with different structures such biomolecules. Bones have vital functions and are the locations of biochemical reactions in cells that might be exposed various diseases. As different metal ions are integral components of bone tissue with different functions in the physiological cellular medium as well as in bone treatment, they can be used differently as a basis or as a supplement for various materials in the field of bone repair. Therefore, this research aims to represent the recent progress in conjugated bisphosphonate (BP)-divalent transition metal ions of Mn2+, Fe2+, and Co2+ with an emphasis on the properties of interaction with a (6, 6) armchair carbon nanotube as a nanocarrier to exhibit the potential biomedical application of drug delivery. In this article, “CNT” linked to “BP“ of alendronic acid, ibandronic acid, neridronic acid, and pamidronic acid, which are chelated to transition metal cations of Mn2+, Fe2+, and Co2+, was investigated based on DFT insights for obtaining the electron charge density. Transition metals chelating with phosphonate groups, which are large with six O atoms with negative charges, are active in generating chelated complexes with the bisphosphonates [BPs- Mn2+/Fe2+/Co2+] through the status of drug design. In this work, B3LYP/6-311+G(d,p)/lanl2dz we have estimated the susceptibility of CNT for conjugating alendronic acid, ibandronic acid, neridronic acid, and pamidronic acid, which are chelated to transition metal cations of Mn2+, Fe2+, and Co2+ through NMR, NQR, IR, UV-VIS spectroscopy, and HOMO-LUMO analysis. Finally, the obtained results have confirmed that the possibility of applying CNT and BPs of alendronic acid, ibandronic acid, neridronic acid, and pamidronic acid becomes suitable in transition metal chelating for delivery application. The calculated HOMO–LUMO energy gaps for BPs of alendronic acid, ibandronic acid, neridronic acid, and pamidronic acid at the B3LYP/6-311+G (d,p) level have revealed that the energy gap reflects the chemical activity of the molecule.
Corrosion Inhibiting by Some Organic Heterocyclic Inhibitors Through Langmuir Adsorption Mechanism on the Al-X (X = Mg/Ga/Si) Alloy Surface: A Study of Quantum Three-Layer Method of CAM-DFT/ONIOM
(2023-06-01) Mollaamin F., Monajjemi M.
The physicochemical attributes of inhibitor → metal & metal alloys nanosheet can be one of the fundamental factors for recognizing determining and selecting the Langmuir adsorption through IR, NMR, NQR, NBO, UV–VIS, HOMO/LUMO, and charge distribution and other quantum attributes. Then, the fluctuation of occupancy of natural bond orbitals has been estimated for pyridine → Al–Al, pyridine → Al–Mg, pyridine → Al–Ga, pyridine → Al–Si; 2-picoline → Al–Al, 2-picoline → Al–Mg, 2-picoline → Al–Ga, 2-picoline → Al–Si; 3-picoline → Al–Al, 3-picoline → Al–Mg, 3-picoline → Al–Ga, 3-picoline → Al–Si, 4-picoline → Al–Al, 4-picoline → Al–Mg, 4-picoline → Al–Ga, 4-picoline → Al–Si, and 2,4-lutidine → Al–Al, 2,4-lutidine → Al–Mg, 2,4-lutidine → Al–Ga, and 2,4-lutidine → Al–Si through the Langmuir adsorption process due to concerning the nitrogen atom in the benzene ring of related heterocyclic compounds becoming close to the monolayer nanosurface of aluminum and its alloys. Nuclear magnetic resonance has certainly has focused on the aluminum shielding in the intra-atomic interaction with magnesium, gallium, and silicon and simultaneously interatomic interaction with nitrogen atoms in organic heterocyclic inhibitors through variety of high, medium, and low layers of ONIOM method. In addition, on the basis of the computed amounts of UV–VIS spectra for pyridine and its family adsorbing on the Al alloy surface, there are maximum adsorption bands between 150 and 240 nm. Two maximum adsorption bands for pyridine, 2-picoline, 3-picoline, and 4-picoline are at 200 nm and 250 nm. Besides, it has been observed two maximum adsorption bands for 2,4-lutidine around 170 nm and 210 nm, respectively.
Graphene Embedded with Transition Metals for Capturing Carbon Dioxide: Gas Detection Study Using QM Methods
(2023-03-01) Mollaamin F., Monajjemi M.; Mollaamin, F, Monajjemi, M
Carbon dioxide (CO2) adsorption on decorated graphene (GR) sheets with transition metals (TMs) including iron, nickel and zinc was investigated for removing this hazardous gas from the environment. TM-doped GR results in higher activity toward gas detecting than pristine graphene nanosheets. TM embedding restrains hydrogen evolution on the C sites, leaving more available sites for a CO2 decrease. The Langmuir adsorption model with ONIOM using CAM-B3LYP functional and LANL2DZ and 6-31+G (d,p) basis sets due to Gaussian 16 revision C.01 program on the complexes of CO2→(Fe, Ni, Zn) embedded on the GR was accomplished. The changes of charge density illustrated a more considerable charge transfer for Zn-embedded GR. The thermodynamic results from IR spectroscopy indicated that (Formula presented.) has the notable gap of Gibbs free energy adsorption with a dipole moment which defines the alterations between the Gibbs free energy of the initial compounds ((Formula presented.) and (Formula presented.)) and product compound ((Formula presented.)) through polarizability. Frontier molecular orbital and band energy gaps accompanying some chemical reactivity parameters represented the behavior of molecular electrical transport of the (Fe, Ni, Zn) embedding of GR for the adsorption of CO2 gas molecules. Our results have provided a favorable understanding of the interaction between TM-embedded graphene nanosheets and CO2.
In Silico-DFT Investigation of Nanocluster Alloys of Al-(Mg, Ge, Sn) Coated by Nitrogen Heterocyclic Carbenes as Corrosion Inhibitors
(2023-01-01) Mollaamin F., Monajjemi M.
Aluminum alloys with magnesium are broadly applied as structural materials for their high ductility and remarkable corrosion resistance. As the strongest alloys of this system have low stability specifications, the present research aims to investigate the probability of making strong of Al–Mg alloy by doping silicon, germanium and tin. This work presents an analysis of the influence of some organic heterocyclic inhibitors owing to Langmuir adsorption and DFT and TD-DFT method with different process parameters, on the corrosion resistance of aluminum alloy containing Al-X–Y (X = Mg, Y = Si, Ge, Sn). The ONIOM approach has been performed with a three-layered level of high by CAM-B3LYP theoretical function using 6–31 + G (2d,p) and LANL2DZ basis sets applying Gaussian 16 revision C.01; a medium semi-active part that consists of essential electronic contributions; and a low level part that has been handled using MM2 force field approaches. The physicochemical properties of inhibitor → metal alloy complexes are evaluated with the Langmuir adsorption through NMR, NBO, UV–VIS, HOMO/LUMO and DOS/PDOS graphs toward structural, electronic and thermodynamic properties and other quantum attributes. The fluctuation of occupancy of natural bond orbitals has been estimated for [pyridine,2-picoline,3-picoline,4-picoline, 2,4-lutidine → Al–Mg–(Si, Ge, Sn)] concerning the influence of nitrogen atom in the benzene ring of related heterocyclic compounds becoming close to the monolayer nanosurface of Al-X–Y (X = Mg, Y = Si, Ge, Sn) alloys. Furthermore, the results of partial electron density states (PDOS) have confirmed an obvious charge accumulation between the Al–Mg alloy and doped atoms of Si, Ge, and Sn through the recognition of the conduction band region. Based on the computed values of UV–VIS spectrums for pyridine, 2-picolone, 3-picoline, 4-picoline and 2,4-lutidine adsorbed on the Al–Mg-Y (Y = Si/Ge/Sn) alloys surface, there are maximum adsorption band wavelengths between 1000 nm and 4000 nm, respectively. In addition, it has been observed the sharpest peak in 2250 nm for all of these inhibitors adsorbed on the Al–Mg-Y (Y = Si/Ge/Sn) alloys surface. This study revealed that appropriate control of the coating process by Langmuir adsorption can illustrate inhibiting the aluminum alloys corrosion through an investigation of their structural, electronic and thermodynamic properties.
Molecular modelling framework of metal-organic clusters for conserving surfaces: Langmuir sorption through the TD-DFT/ONIOM approach
(2023-01-01) Mollaamin F., Monajjemi M.; Mollaamin, F, Monajjemi, M
The Langmuir adsorption model of some organic inhibitors containing benzotriazole (BTA), 8- hydroxyquinoline (8-HQ), and 2-mercaptobenzothiazole (2-MBT) onto the Al-X (X=Mg, Ga, Si) alloy surface.The ONIOM method has been accomplished with a three-layered step of high level of DFT method using EPR-III, 6-31+G (d,p) and LANL2DZ basis sets. NMR spectroscopy has indeed concentrated on the Al shielding in the intra-atomic interaction with Mg, Ga and Si and meanwhile interatomic interaction with other atoms in BTA, 8-HQ, and 2-MBT compounds. Aluminum-silicon binary alloy with highest changes in the shielding tensors of NMR spectrum produced by intra-atomic interaction directs us to the most penetration in the neighbor atoms created by interatomic reaction. IR computations based on comparing the amounts has exhibited that 2-MBT with high stability based on its active zone of sulfur atoms and high molecular size shows high corrosive inhibition as 2-MBT →Al-Ga>Al-Mg ≈ Al-Si. Furthermore, BTA with nitrogen atom and 8-HQ with oxygen atom can coat the Al-X (X=Mg/Ga/Si) alloys surface through Langmuir adsorption as BTA →Al-Ga>Al-Mg ≈ Al-Si, and 8-HQ →Al-Ga>Al-Mg ≈ Al-Si, respectively. Moreover, it has been observed that the inhibition yield is ordered as: Al-Ga> Al-Mg ≈ Al-Si.
Tailoring and functionalizing the graphitic-like GaN and GaP nanostructures as selective sensors for NO, NO, and NH adsorbing: a DFT study.
(2023-05-06T00:00:00Z) Mollaamin, Fatemeh, Monajjemi, Majid; Mollaamin, F, Monajjemi, M
Langmuir adsorption of gas molecules of NO, NO, and NH on the graphitic GaN and GaP sheets has been accomplished using density functional theory. The changes of charge density have shown a more important charge transfer for GaN compared to GaP which acts both as the electron donor while gas molecules act as the stronger electron acceptors through adsorption on the graphitic-like GaN surface. The adsorption of NO and NO molecules introduced spin polarization in the PL-GaN sheet, indicating that it can be employed as a magnetic gas sensor for NO and NO sensing.
Transition metal (X = Mn, Fe, Co, Ni, Cu, Zn)-doped graphene as gas sensor for CO and NO detection: a molecular modeling framework by DFT perspective.
(2023-03-29T00:00:00Z) Mollaamin, Fatemeh, Monajjemi, Majid; Mollaamin, F, Monajjemi, M
In this research, CO and NO adsorption on doped nanographene (NG) sheets with transition metals (Fe, Ni, Zn) and (Mn, Co, Cu), respectively, have been applied for scavenging of these toxic gases as the environmental pollutants. The values of changes of atomic charge density have illustrated a more significant charge transfer for Ni-doped C-NG through CO adsorption and a more remarkable charge transfer for Co-doped C-NG through NO adsorption. The data of NMR spectroscopy has depicted several fluctuations around the graph of Zn-doped on the nanographene surface. The thermodynamic results from IR spectroscopy have indicated that [Formula: see text] values are almost similar for doped metal transitions of Mn, Co, and Cu on the C-NG nanosheet, while [Formula: see text] has the largest gap of Gibbs free energy adsorption with dipole moment.
Tribocorrosion Framework of (Iron, Nickel, Zinc)-Doped Graphene Nanosheet: New Sights into Sulfur Dioxide and Hydrogen Sulfide Removal Using DFT/TD-DFT Methods
(2023-09-01) Mollaamin F., Monajjemi M.
Progress of largely selective and sensitive compounds is essential for removing two toxic gases of hydrogen sulfide (H2S) and sulfur dioxide (SO2).The effect of Iron (Fe), Nickel (Ni), and Zinc (Zn) doping of graphene (Gr) nanosheet (NS) on their adsorption for both H2S and SO2 gases has been investigated in this work using first-principles density-functional theory (DFT) computations. In this research, it has been investigated the ability of transition metals of iron, nickel, and zinc doping of Gr@NS for adsorption toxic gas of Sulfur Dioxide and Hydrogen Sulfide Removal. The Langmuir adsorption model with a three-layered ONIOM used CAM-B3LYP functional accompanying LANL2DZ and 6–31 + G (d,p) basis sets due to Gaussian 16 revision C.01 program on the complexes of H2S and SO2 → TM(Fe, Ni, Zn) doping of Gr nanosheet. The changes of charge density have shown the values of ∆Q Fe-doped = − 0.566 >> ∆Q Zn-doped = + 0.387 >>> ∆Q Ni-doped = + 0.605 for H2S adsorption and ∆Q Fe-doped = − 0.336 >> ∆Q Zn-doped = + 0.376 >>> ∆Q Ni-doped = + 0.618 for SO2 adsorption. Based on these amount of changes of charge density, H2S and SO2 have exhibited a significant charge transfer for Fe doping of graphene nanosheet compared to Ni- and Zn-doped Gr@NS. Based on NMR spectroscopy, it has been illustrated that the sharp peaks in the adsorption site are due to the Fe, Ni, and Zn doping on the surface of graphene nanosheet through H2S and SO2 adsorption. However, it has represented some fluctuations in the chemical shielding of isotropic and anisotropy behaviors around Zn-doped on the H2S/ SO2 → Zn-doped/Gr@NS. Moreover, it has exhibited the fluctuation of occupancy of NBO for H2S/SO2 → Fe-doped, H2S/SO2 → Ni-doped, and H2S/SO2 → Zn-doped graphene nanosheet through the Langmuir adsorption process by indicating the active sulfur atom in hydrogen sulfide (H2S) and sulfur dioxide (SO2) becoming close to the nanosheet. The amounts of ΔGadso through IR computations based on polarizability have exhibited that ΔGads,SO2→Fe-Co and ΔGads,H2S→Fe-Co have exhibited the most energy gap because of charge density transfer from sulfur atom in hydrogen sulfide (H2S) and sulfur dioxide (SO2) to Fe doping of Gr@NS, although, ΔGH2S/SO2→Zn-C0 > ΔGH2S/SO2→Ni-C0 > ΔGH2S/SO2→Fe-C0 . Frontier molecular orbitals of HOMO, LUMO, and band energy gap accompanying some chemical reactivity parameters have represented the attributes of molecular electrical transport of TM (Fe, Ni, Zn) doping of Gr nanosheet for adsorption of H2S and SO2 gases. Our results have provided a favorable understanding of the interaction between TM doping of Gr@NS nanosheet and H2S and SO2 molecules. A high performance of TM doping of Gr@NS as gas sensor is demonstrated by modeling the material’s transport characteristics by means of the Langmuir adsorption and three-layered ONIOM/DFT method. Furthermore, the results of partial electron density of states (PDOS) have confirmed an obvious charge accumulation between the graphene nanosheet and doped atoms of Fe, Ni, and Zn through adsorption of H2S and SO2 molecules on the surface due to the recognition of the conduction band region. Finally, this research can build up our knowledge about the electronic structure, relative stability, and surface bonding of various metal-doped graphene nanosheets, metal alloy surfaces, and other dependent mechanisms, like heterogeneous catalysis, friction lubrication, and biological systems.