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  1. Article ; Online: Quantum mechanical investigations of mechanical and thermodynamic properties of SiC and ZrO

    Novir, Samaneh Bagheri / Aram, Mohammad Reza

    Journal of molecular modeling

    2021  Volume 27, Issue 9, Page(s) 269

    Abstract: The mechanical and thermodynamic properties of β and α structures of SiC and also monoclinic and cubic structures of ... ...

    Abstract The mechanical and thermodynamic properties of β and α structures of SiC and also monoclinic and cubic structures of ZrO
    Language English
    Publishing date 2021-08-30
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 1284729-X
    ISSN 0948-5023 ; 1610-2940
    ISSN (online) 0948-5023
    ISSN 1610-2940
    DOI 10.1007/s00894-021-04878-y
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  2. Article: Quantum mechanical studies of the adsorption of Remdesivir, as an effective drug for treatment of COVID-19, on the surface of pristine, COOH-functionalized and S-, Si- and Al- doped carbon nanotubes.

    Bagheri Novir, Samaneh / Aram, Mohammad Reza

    Physica. E, Low-dimensional systems & nanostructures

    2021  Volume 129, Page(s) 114668

    Abstract: Remdesivir has been recognized as an important medicine in the control of COVID-19 illness. Since carbon nanotubes were considered in the design of novel drug delivery vehicles, the interaction between simple CNT, functionalized CNT by carboxylic group ... ...

    Abstract Remdesivir has been recognized as an important medicine in the control of COVID-19 illness. Since carbon nanotubes were considered in the design of novel drug delivery vehicles, the interaction between simple CNT, functionalized CNT by carboxylic group and S-, Al-, and Si-doped CNT and Remdesivir drug were studied using density functional theory (DFT) and time dependent DFT (TDDFT) calculations. The results of this work show that the Si-doped CNT is the best drug delivery system for Remdesivir due to its better electronic, energetic, adsorption and thermodynamic properties.
    Language English
    Publishing date 2021-02-04
    Publishing country Netherlands
    Document type Journal Article
    ISSN 1386-9477
    ISSN 1386-9477
    DOI 10.1016/j.physe.2021.114668
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  3. Article: Quantum mechanical simulation of Chloroquine drug interaction with C60 fullerene for treatment of COVID-19.

    Bagheri Novir, Samaneh / Aram, Mohammad Reza

    Chemical physics letters

    2020  Volume 757, Page(s) 137869

    Abstract: Chloroquine (CQ) has been reported as an effective drug in the control of COVID-19 infection. Since C60 fullerene has been considered as a drug delivery system, the interaction between pristine fullerene and chloroquine drug and also the interaction ... ...

    Abstract Chloroquine (CQ) has been reported as an effective drug in the control of COVID-19 infection. Since C60 fullerene has been considered as a drug delivery system, the interaction between pristine fullerene and chloroquine drug and also the interaction between B, Al, Si doped fullerene and chloroquine drug have been investigated based on the density functional theory calculations. The results of this study show that the doped fullerene, especially Al and Si doped fullerene could be the better drug delivery vehicles for chloroquine drug because of their relatively better energetic and electronic properties with chloroquine.
    Keywords covid19
    Language English
    Publishing date 2020-08-09
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 1466293-0
    ISSN 0009-2614
    ISSN 0009-2614
    DOI 10.1016/j.cplett.2020.137869
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  4. Article ; Online: A quantum study on novel azo-dyes containing a fullerene C60 unit as a smart material for optoelectronic applications.

    Bagheri Novir, Samaneh / Aram, Mohammad Reza

    Journal of molecular modeling

    2020  Volume 26, Issue 10, Page(s) 258

    Abstract: Quantum chemical calculations of some novel azo-dyes containing a fullerene C60 unit as a smart material have been carried out with the aims to determine their cis and trans electronic properties and to describe the change of their quantum parameters as ... ...

    Abstract Quantum chemical calculations of some novel azo-dyes containing a fullerene C60 unit as a smart material have been carried out with the aims to determine their cis and trans electronic properties and to describe the change of their quantum parameters as a result of the trans/cis isomerization of these molecules. The effects of electron-withdrawing or electron-releasing groups on the R-position of these molecules on electronic, optical, spectroscopic, and other properties of these molecules have been considered with DFT and TDDFT calculations. The obtained results of the calculations show that compounds "b" and "c" with the strongest electron-releasing groups in the R-position of these molecules, particularly the trans isomers of these compounds, with higher chemical softness, higher electrophilicity index, higher thermodynamic properties, and higher charge transfer values, have the better electronic and optical properties and therefore the better chemical reactivity compared to the other compounds. Graphical abstract.
    Language English
    Publishing date 2020-09-04
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 1284729-X
    ISSN 0948-5023 ; 1610-2940
    ISSN (online) 0948-5023
    ISSN 1610-2940
    DOI 10.1007/s00894-020-04516-z
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  5. Article ; Online: Quantum mechanical simulation of Chloroquine drug interaction with C60 fullerene for treatment of COVID-19

    Bagheri Novir, Samaneh / Aram, Mohammad Reza

    Chemical Physics Letters

    2020  Volume 757, Page(s) 137869

    Keywords Physical and Theoretical Chemistry ; General Physics and Astronomy ; covid19
    Language English
    Publisher Elsevier BV
    Publishing country us
    Document type Article ; Online
    ZDB-ID 1466293-0
    ISSN 0009-2614
    ISSN 0009-2614
    DOI 10.1016/j.cplett.2020.137869
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article: Quantum mechanical simulation of Chloroquine drug interaction with C60 fullerene for treatment of COVID-19

    Bagheri Novir, Samaneh / Aram, Mohammad Reza

    Chem. Phys. Lett.

    Abstract: Chloroquine (CQ) has been reported as an effective drug in the control of COVID-19 infection. Since C60 fullerene has been considered as a drug delivery system, the interaction between pristine fullerene and chloroquine drug and also the interaction ... ...

    Abstract Chloroquine (CQ) has been reported as an effective drug in the control of COVID-19 infection. Since C60 fullerene has been considered as a drug delivery system, the interaction between pristine fullerene and chloroquine drug and also the interaction between B, Al, Si doped fullerene and chloroquine drug have been investigated based on the density functional theory calculations. The results of this study show that the doped fullerene, especially Al and Si doped fullerene could be the better drug delivery vehicles for chloroquine drug because of their relatively better energetic and electronic properties with chloroquine.
    Keywords covid19
    Publisher WHO
    Document type Article
    Note WHO #Covidence: #695247
    Database COVID19

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  7. Article ; Online: Density functional theory study of structural and electronic properties of trans and cis structures of thiothixene as a nano-drug.

    Noori Tahneh, Akram / Bagheri Novir, Samaneh / Balali, Ebrahim

    Journal of molecular modeling

    2017  Volume 23, Issue 12, Page(s) 356

    Abstract: The geometrical structure, electronic and optical properties, electronic absorption spectra, vibrational frequencies, natural charge distribution, MEP analysis and thermodynamic properties of the trans and cis structures of the drug thiothixene were ... ...

    Abstract The geometrical structure, electronic and optical properties, electronic absorption spectra, vibrational frequencies, natural charge distribution, MEP analysis and thermodynamic properties of the trans and cis structures of the drug thiothixene were investigated using density functional theory (DFT) and time-dependent DFT (TDDFT) methods with the B3LYP hybrid functional and 6-311 + G(d,p) basis set. The results of the calculations demonstrate that the cis structure of thiothixene has appropriate quantum properties that can act as an active medicine. The relative energies of trans and cis structures of thiothixene shows that the cis structure is more stable than the trans structure, with a small energy difference. TDDFT calculations show that the cis structure of thiothixene has the best absorption properties. The calculated NLO properties show that the NLO properties of the cis structure of thiothixene are higher than the trans structure, and the fact that the chemical hardness of the cis structure is lower than that of the trans structure that indicates that the reactivity and charge transfer of the cis isomer of thiothixene is higher than that of trans thiothixene. The molecular electrostatic potential (MEP) maps of both structures of thiothixene demonstrate that the oxygen atoms of the molecule are appropriate areas for electrophilic reactions. The vibrational frequencies of the two conformations of thiothixene demonstrate that both structures of thiothixene have almost similar modes of vibrations. The calculated thermodynamic parameters show that these quantities increase with enhancing temperature due to the enhancement of molecular vibrational intensities with temperature. Graphical abstract Trans/Cis isomerization of thiothixene drug.
    MeSH term(s) Antipsychotic Agents/chemistry ; Antipsychotic Agents/pharmacology ; Humans ; Models, Molecular ; Molecular Structure ; Schizophrenia/drug therapy ; Static Electricity ; Thermodynamics ; Thiothixene/chemistry ; Thiothixene/pharmacology
    Chemical Substances Antipsychotic Agents ; Thiothixene (7318FJ13YJ)
    Language English
    Publishing date 2017-11-25
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 1284729-x
    ISSN 0948-5023 ; 1610-2940
    ISSN (online) 0948-5023
    ISSN 1610-2940
    DOI 10.1007/s00894-017-3522-6
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  8. Article ; Online: Density functional theory study of new azo dyes with different π-spacers for dye-sensitized solar cells.

    Bagheri Novir, Samaneh / Hashemianzadeh, Seyed Majid

    Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy

    2015  Volume 143, Page(s) 20–34

    Abstract: Some of new azo-based metal-free dyes with different π-conjugation spacers, such as carbazole, fluorene, pyrrole, thiophene, furan and thiazole, have been investigated with density functional theory (DFT) and time-dependent DFT (TDDFT) calculations. ... ...

    Abstract Some of new azo-based metal-free dyes with different π-conjugation spacers, such as carbazole, fluorene, pyrrole, thiophene, furan and thiazole, have been investigated with density functional theory (DFT) and time-dependent DFT (TDDFT) calculations. Theoretical calculations allow us to quantify factors such as light harvesting efficiency (LHE), electron injection driving force (ΔG(inject)) and the weight of the LUMO orbital on the carboxylic group (QLUMO) related to the short-circuit photocurrent density (Jsc), and to evaluate both charge recombination between the semiconductor conduction band electrons and the oxidized dyes and/or electrolyte, and also the shift of the conduction band of the semiconductor as a result of the adsorption of the dyes onto the semiconductor surface, associated with the open-circuit photovoltage (Voc). According to the results, we could predict that how the π-conjugation spacers influence the Jsc as well as the Voc of DSSCs. Among these dyes, the carbazole and fluorene-based dyes (dyes 1 and 2) show the highest LHE, ΔG(inject), QLUMO, and the slowest recombination rate. Consequently, the obtained results show that the carbazole and fluorene-based dyes could have the better Jsc and Voc compared to the other dyes.
    MeSH term(s) Azo Compounds/chemistry ; Quantum Theory ; Solar Energy
    Chemical Substances Azo Compounds
    Language English
    Publishing date 2015-05-15
    Publishing country England
    Document type Journal Article
    ZDB-ID 210413-1
    ISSN 1873-3557 ; 0370-8322 ; 0584-8539 ; 1386-1425
    ISSN (online) 1873-3557
    ISSN 0370-8322 ; 0584-8539 ; 1386-1425
    DOI 10.1016/j.saa.2015.02.026
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  9. Article ; Online: The polythiophene molecular segment as a sensor model for H2O, HCN, NH3, SO3, and H2S: a density functional theory study.

    Shokuhi Rad, Ali / Esfahanian, Mehri / Ganjian, Etesam / Tayebi, Habib-Allah / Novir, Samaneh Bagheri

    Journal of molecular modeling

    2016  Volume 22, Issue 6, Page(s) 127

    Abstract: Studying the interaction of some atmospheric gases (H2O, HCN, NH3, SO3 and H2S) with 3PT oligomers is important in the development of polymeric sensors for gas detection. In the present study, we studied the relaxed geometries, interaction energies, ... ...

    Abstract Studying the interaction of some atmospheric gases (H2O, HCN, NH3, SO3 and H2S) with 3PT oligomers is important in the development of polymeric sensors for gas detection. In the present study, we studied the relaxed geometries, interaction energies, charge analysis, HOMO-LUMO orbital analysis, and UV-vis spectra of all interacted systems using first-principles density functional theory (DFT). All these analyses indicated the potential of polythiophene as an inexpensive polymeric sensor for the analytes mentioned. Interaction energy values of -19.90, -19.66, -14.01, -8.70, and -4.76 kJ mol(-1) were achieved for adsorption of SO3, H2O, NH3, HCN, and H2S on 3PT, respectively. Consequently, clarification of their physical parameters became the major focus of this study.
    Language English
    Publishing date 2016
    Publishing country Germany
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1284729-x
    ISSN 0948-5023 ; 1610-2940
    ISSN (online) 0948-5023
    ISSN 1610-2940
    DOI 10.1007/s00894-016-3001-5
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  10. Article ; Online: Deep analysis of N-cadherin/ADH-1 interaction: a computational survey.

    Eslami, Mahboobeh / Nezafat, Navid / Khajeh, Sahar / Mostafavi-Pour, Zohreh / Bagheri Novir, Samaneh / Negahdaripour, Manica / Ghasemi, Younes / Razban, Vahid

    Journal of biomolecular structure & dynamics

    2018  Volume 37, Issue 1, Page(s) 210–228

    Abstract: Due to the considerable role of N-cadherin in cancer metastasis, tumor growth, and progression, inhibition of this protein has been highly regarded in recent years. Although ADH-1 has been known as an appropriate inhibitor of N-cadherin in clinical ... ...

    Abstract Due to the considerable role of N-cadherin in cancer metastasis, tumor growth, and progression, inhibition of this protein has been highly regarded in recent years. Although ADH-1 has been known as an appropriate inhibitor of N-cadherin in clinical trials, its chemical nature and binding mode with N-cadherin have not been precisely specified yet. Accordingly, in this study, quantum mechanics calculations were used to investigate the chemical nature of ADH-1. These calculations clarify the molecular properties of ADH-1 and determine its reactive sites. Based on the results, the oxygen atoms are suitable for electrophilic reactivity, while the hydrogen atoms that are connected to nitrogen atoms are the favorite sites for nucleophilic reactivity. The higher electronegativity of the oxygen atoms makes them the most reactive portions in this molecule. Molecular docking and molecular dynamics (MD) simulation have also been applied to specify the binding mode of ADH-1 with N-cadherin and determine the important residues of N-cadherin involving in the interaction with ADH-1. Moreover, the verified model by MD simulation has been studied to extract the free energy value and find driving forces. These calculations and molecular electrostatic potential map of ADH-1 indicated that hydrophobic and electrostatic interactions are almost equally involved in the implantation of ADH-1 in the N-cadherin binding site. The presented results not only enable a closer examination of N-cadherin in complex with ADH-1 molecule, but also are very beneficial in designing new inhibitors for N-cadherin and can help to save time and cost in this field.
    MeSH term(s) Alcohol Dehydrogenase/chemistry ; Alcohol Dehydrogenase/metabolism ; Algorithms ; Cadherins/chemistry ; Cadherins/metabolism ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Ligands ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Protein Binding ; Quantum Theory ; Spectrum Analysis ; Structure-Activity Relationship ; Thermodynamics
    Chemical Substances Cadherins ; Ligands ; Alcohol Dehydrogenase (EC 1.1.1.1)
    Language English
    Publishing date 2018-01-19
    Publishing country England
    Document type Journal Article
    ZDB-ID 49157-3
    ISSN 1538-0254 ; 0739-1102
    ISSN (online) 1538-0254
    ISSN 0739-1102
    DOI 10.1080/07391102.2018.1424035
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