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Article: Theoretical study of chemical reactivity descriptors of some repurposed drugs for COVID-19.

Morad, Razieh / Akbari, Mahmood / Maaza, Malik

MRS advances

2023 , Page(s) 1–5

Language	English
Publishing date	2023-05-31
Publishing country	United States
Document type	Journal Article
ISSN	2059-8521
ISSN	2059-8521
DOI	10.1557/s43580-023-00590-6
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: First principle study of silver nanoparticle interactions with antimalarial drugs extracted from

Akbari, Mahmood / Morad, Razieh / Maaza, Malik

Journal of nanoparticle research : an interdisciplinary forum for nanoscale science and technology

2020 Volume 22, Issue 11, Page(s) 331

Abstract: Silver nanoparticles have a great potential in a broad range of applications such as drug-delivery carriers because of their antiviral and antibacterial properties. In this study, the coating properties of silver nanoparticle (size range of 1.6 nm) with ... ...

Abstract	Silver nanoparticles have a great potential in a broad range of applications such as drug-delivery carriers because of their antiviral and antibacterial properties. In this study, the coating properties of silver nanoparticle (size range of 1.6 nm) with three common anti-malarial drugs, Artemisinin, Artemether, and Artesunate have been studied by using the quantum mechanical and classical atomistic molecular dynamics simulation in order to use as the drug delivery to treat malaria and COVID-19 diseases. The optimized structure, frequencies, charge distribution, and the electrostatic potential maps of the three drug molecules were simulated by using the density functional theory (DFT) at the B3LYP/6-311++g(d,p) level of theory. Then, molecular dynamics simulation was used to study the coating of AgNP with each of these drugs. The affinity of interaction was obtained as Artesunate > Artemether > Artemisinin which is in agreement with the DFT results on the adsorption of drugs on the Ag(111) slab.
Keywords	covid19
Language	English
Publishing date	2020-10-27
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2017013-0
ISSN	1572-896X ; 1388-0764
ISSN (online)	1572-896X
ISSN	1388-0764
DOI	10.1007/s11051-020-05058-4
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Article ; Online: Ionome mapping and amino acid metabolome profiling of Phaseolus vulgaris L. seeds imbibed with computationally informed phytoengineered copper sulphide nanoparticles.

Botha, Nandipha L / Cloete, Karen J / Šmit, Žiga / Isaković, Kristina / Akbari, Mahmood / Morad, Razieh / Madiba, Itani / David, Oladipupo Moyinoluwa / Santos, Luis P M / Dube, Admire / Pelicon, Primoz / Maaza, Malik

Discover nano

2024 Volume 19, Issue 1, Page(s) 8

Abstract: This study reports the effects of a computationally informed and avocado-seed mediated Phyto engineered CuS nanoparticles as fertilizing agent on the ionome and amino acid metabolome of Pinto bean seeds using both bench top and ion beam analytical ... ...

Abstract	This study reports the effects of a computationally informed and avocado-seed mediated Phyto engineered CuS nanoparticles as fertilizing agent on the ionome and amino acid metabolome of Pinto bean seeds using both bench top and ion beam analytical techniques. Physico-chemical analysis of the Phyto engineered nanoparticles with scanning-electron microscopy, transmission electron microscopy, X-ray diffraction, and Fourier Transform Infrared Spectroscopy confirmed the presence of CuS nanoparticles. Molecular dynamics simulations to investigate the interaction of some active phytocompounds in avocado seeds that act as reducing agents with the nano-digenite further showed that 4-hydroxybenzoic acid had a higher affinity for interacting with the nanoparticle's surface than other active compounds. Seeds treated with the digenite nanoparticles exhibited a unique ionome distribution pattern as determined with external beam proton-induced X-ray emission, with hotspots of Cu and S appearing in the hilum and micropyle area that indicated a possible uptake mechanism via the seed coat. The nano-digenite also triggered a plant stress response by slightly altering seed amino acid metabolism. Ultimately, the nano-digenite may have important implications as a seed protective or nutritive agent as advised by its unique distribution pattern and effect on amino acid metabolism.
Language	English
Publishing date	2024-01-04
Publishing country	Switzerland
Document type	Journal Article
ISSN	2731-9229
ISSN (online)	2731-9229
DOI	10.1186/s11671-023-03953-y
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Article ; Online: Comparing the nature of quantum plasmonic excitations for closely spaced silver and gold dimers.

Jamshidi, Zahra / Asadi-Aghbolaghi, Narges / Morad, Razieh / Mahmoudi, Erfan / Sen, Souloke / Maaza, Malik / Visscher, Lucas

The Journal of chemical physics

2022 Volume 156, Issue 7, Page(s) 74102

Abstract: In the new field of quantum plasmonics, plasmonic excitations of silver and gold nanoparticles are utilized to manipulate and control light-matter interactions at the nanoscale. While quantum plasmons can be described with atomistic detail using Time- ... ...

Abstract	In the new field of quantum plasmonics, plasmonic excitations of silver and gold nanoparticles are utilized to manipulate and control light-matter interactions at the nanoscale. While quantum plasmons can be described with atomistic detail using Time-Dependent Density Functional Theory (DFT), such studies are computationally challenging due to the size of the nanoparticles. An efficient alternative is to employ DFT without approximations only for the relatively fast ground state calculations and use tight-binding approximations in the demanding linear response calculations. In this work, we use this approach to investigate the nature of plasmonic excitations under the variation of the separation distance between two nanoparticles. We thereby provide complementary characterizations of these excitations in terms of Kohn-Sham single-orbital transitions, intrinsic localized molecular fragment orbitals, scaling of the electron-electron interactions, and probability of electron tunneling between monomers.
Language	English
Publishing date	2022-02-19
Publishing country	United States
Document type	Journal Article
ZDB-ID	3113-6
ISSN	1089-7690 ; 0021-9606
ISSN (online)	1089-7690
ISSN	0021-9606
DOI	10.1063/5.0079258
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Article ; Online: First principle simulation of coated hydroxychloroquine on Ag, Au and Pt nanoparticles.

Morad, Razieh / Akbari, Mahmood / Rezaee, Parham / Koochaki, Amin / Maaza, Malik / Jamshidi, Zahra

Scientific reports

2021 Volume 11, Issue 1, Page(s) 2131

Abstract: From the first month of the COVID-19 pandemic, the potential antiviral properties of hydroxychloroquine (HCQ) and chloroquine (CQ) against SARS-CoV-2 suggested that these drugs could be the appropriate therapeutic candidates. However, their side effects ... ...

Abstract	From the first month of the COVID-19 pandemic, the potential antiviral properties of hydroxychloroquine (HCQ) and chloroquine (CQ) against SARS-CoV-2 suggested that these drugs could be the appropriate therapeutic candidates. However, their side effects directed clinical tests towards optimizing safe utilization strategies. The noble metal nanoparticles (NP) are promising materials with antiviral and antibacterial properties that can deliver the drug to the target agent, thereby reducing the side effects. In this work, we applied both the quantum mechanical and classical atomistic molecular dynamics approaches to demonstrate the adsorption properties of HCQ/CQ on Ag, Au, AgAu, and Pt nanoparticles. We found the adsorption energies of HCQ/CQ towards nanoparticles have the following trend: PtNP > AuNP > AuAgNP > AgNP. This shows that PtNP has the highest affinity in comparison to the other types of nanoparticles. The (non)perturbative effects of this drug on the plasmonic absorption spectra of AgNP and AuNP with the time-dependent density functional theory. The effect of size and composition of NPs on the coating with HCQ and CQ were obtained to propose the appropriate candidate for drug delivery. This kind of modeling could help experimental groups to find efficient and safe therapies.
MeSH term(s)	Adsorption ; Antiviral Agents/chemistry ; Antiviral Agents/therapeutic use ; COVID-19/drug therapy ; Gold/chemistry ; Humans ; Hydroxychloroquine/chemistry ; Hydroxychloroquine/therapeutic use ; Metal Nanoparticles/chemistry ; Molecular Dynamics Simulation ; Pandemics ; Platinum/chemistry ; Quantum Theory ; SARS-CoV-2/physiology ; Silver/chemistry
Chemical Substances	Antiviral Agents ; Silver (3M4G523W1G) ; Platinum (49DFR088MY) ; Hydroxychloroquine (4QWG6N8QKH) ; Gold (7440-57-5)
Language	English
Publishing date	2021-01-22
Publishing country	England
Document type	Comparative Study ; Journal Article
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-021-81617-6
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Toward visual chiral recognition of amino acids using a wide-range color tonality ratiometric nanoprobe.

Jafar-Nezhad Ivrigh, Zahra / Fahimi-Kashani, Nafiseh / Morad, Razieh / Jamshidi, Zahar / Hormozi-Nezhad, Mohammad Reza

Analytica chimica acta

2022 Volume 1231, Page(s) 340386

Abstract: Chiral recognition has long been a challenging issue to deal with in biological systems, drug design and food authentication. Implementing nanoparticle-based probes with intrinsic or induced chirality in this field has addressed several issues concerning ...

Abstract	Chiral recognition has long been a challenging issue to deal with in biological systems, drug design and food authentication. Implementing nanoparticle-based probes with intrinsic or induced chirality in this field has addressed several issues concerning sensitivity, reliability, rapidness and the cost of chiral sensing platforms. Yet, research into chiral nanoprobes that can be used for visual monitoring of chiral substances is still in its infancy. As part of this study, a visual chiral recognition platform has been developed in which a combination of blue-emitting carbon dots (BCDs) and mercaptopropionic acid-capped CdTe quantum dots (MPA-QDs) with inherent chiroptical activity were employed for enantiomeric detection. The ratiometric probe displayed unique fluorescence response patterns in the presence of arginine (Arg) and histidine (His) enantiomers. Upon addition of l-amino acids, successive enhancement and quenching of emission intensity as well as a red-shift in emission wavelength of MPA-QDs were observed. The emission color of the nanoprobe changed from green to pink-red and green to brick-red red by increasing the concentration of L-Arg and L-His, respectively. In contrast, their d-amino acid equivalents have a negligible influence on the emission color and fluorescence signal of the developed nanoprobe. Due to the enantioselective vibrant color changes of the nanoprobe, RGB analysis was applied for the determination of enantiomeric excess (ee) in racemic mixture with satisfactory results, allowing smartphone-based onsite visual evaluation of ee (%). Circular dichroism, lifetime, size distribution and ζ-potential measurements were employed to study the chiroselective responses. First-principle calculations were also carried out with density functional theory (DFT) to confirm the experimental observation. Furthermore, chiroselective response patterns of the ratiometric nanoprobe were manipulated to construct a logic gate system mimicking AND, OR, and INHIBIT functions. The capability of the proposed chiral platform in visual monitoring of the fraction of enantiomers in racemic mixtures has a great potential for rapid and onsite visual discrimination of chiral compounds in the field of clinical diagnostics and drug analysis.
MeSH term(s)	Amines ; Amino Acids ; Arginine ; Cadmium Compounds ; Carbon ; Fluorescent Dyes/chemistry ; Histidine ; Quantum Dots/chemistry ; Reproducibility of Results ; Tellurium
Chemical Substances	Amines ; Amino Acids ; Cadmium Compounds ; Fluorescent Dyes ; Histidine (4QD397987E) ; Carbon (7440-44-0) ; Arginine (94ZLA3W45F) ; Tellurium (NQA0O090ZJ) ; cadmium telluride (STG188WO13)
Language	English
Publishing date	2022-09-16
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1483436-4
ISSN	1873-4324 ; 0003-2670
ISSN (online)	1873-4324
ISSN	0003-2670
DOI	10.1016/j.aca.2022.340386
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: First principle simulation of coated hydroxychloroquine on Ag, Au and Pt nanoparticles

Razieh Morad / Mahmood Akbari / Parham Rezaee / Amin Koochaki / Malik Maaza / Zahra Jamshidi

Scientific Reports, Vol 11, Iss 1, Pp 1-

2021 Volume 9

Abstract: Abstract From the first month of the COVID-19 pandemic, the potential antiviral properties of hydroxychloroquine (HCQ) and chloroquine (CQ) against SARS-CoV-2 suggested that these drugs could be the appropriate therapeutic candidates. However, their side ...

Abstract	Abstract From the first month of the COVID-19 pandemic, the potential antiviral properties of hydroxychloroquine (HCQ) and chloroquine (CQ) against SARS-CoV-2 suggested that these drugs could be the appropriate therapeutic candidates. However, their side effects directed clinical tests towards optimizing safe utilization strategies. The noble metal nanoparticles (NP) are promising materials with antiviral and antibacterial properties that can deliver the drug to the target agent, thereby reducing the side effects. In this work, we applied both the quantum mechanical and classical atomistic molecular dynamics approaches to demonstrate the adsorption properties of HCQ/CQ on Ag, Au, AgAu, and Pt nanoparticles. We found the adsorption energies of HCQ/CQ towards nanoparticles have the following trend: PtNP > AuNP > AuAgNP > AgNP. This shows that PtNP has the highest affinity in comparison to the other types of nanoparticles. The (non)perturbative effects of this drug on the plasmonic absorption spectra of AgNP and AuNP with the time-dependent density functional theory. The effect of size and composition of NPs on the coating with HCQ and CQ were obtained to propose the appropriate candidate for drug delivery. This kind of modeling could help experimental groups to find efficient and safe therapies.
Keywords	Medicine ; R ; Science ; Q
Subject code	620
Language	English
Publishing date	2021-01-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: First Principle Simulation of Coated Hydroxychloroquine on Ag, Au and Pt Nanoparticle as a Potential Candidate for Treatment of SARS-CoV-2 (COVID-19)

Rezaee, Parham / Akbari, Mahmood / Morad, Razieh / Koochaki, Amin / Maaz, Malik / Jamshidi, Zahra

Abstract: The {\it{in vitro}} antiviral activity of Hydroxychloroquine (HCQ) and chloroquine (CQ) against SARS-CoV-2 from the first month of pandemic proposed these drugs as the appropriate therapeutic candidate, although their side effect directed the clinical ... ...

Abstract	The {\it{in vitro}} antiviral activity of Hydroxychloroquine (HCQ) and chloroquine (CQ) against SARS-CoV-2 from the first month of pandemic proposed these drugs as the appropriate therapeutic candidate, although their side effect directed the clinical test toward optimizing the safe utilization strategies. The noble metal nanoparticles (NP) as promising materials with antiviral and antibacterial properties can deliver the drug to the target agent and decrease the side effect. In this work, we have applied quantum mechanical and classical atomistic molecular dynamics computational approaches to demonstrate the adsorption properties of HCQ on Ag, Au, AgAu, and Pt nanoparticles. The adsorption energies (less than -30 kcal/mole) were established for HCQ, and the (non)perturbative effects of this drug on the plasmonic absorption spectra of AgNP and AuNP have characterized with time-dependent density functional theory. The effect of size and compositions of nanoparticle on the coating with HCQ and CQ have obtained and proposed the appropriate candidate for drug delivery. This kind of modeling could help the experimental groups to find the efficient and safe therapies.
Keywords	covid19
Publisher	ArXiv
Document type	Article
Database	COVID19

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Book ; Online: First Principle Simulation of Coated Hydroxychloroquine on Ag, Au and Pt Nanoparticle as a Potential Candidate for Treatment of SARS-CoV-2 (COVID-19)

Rezaee, Parham / Akbari, Mahmood / Morad, Razieh / Koochaki, Amin / Maaz, Malik / Jamshidi, Zahra

2020

Abstract	The {\it{in vitro}} antiviral activity of Hydroxychloroquine (HCQ) and chloroquine (CQ) against SARS-CoV-2 from the first month of pandemic proposed these drugs as the appropriate therapeutic candidate, although their side effect directed the clinical test toward optimizing the safe utilization strategies. The noble metal nanoparticles (NP) as promising materials with antiviral and antibacterial properties can deliver the drug to the target agent and decrease the side effect. In this work, we have applied quantum mechanical and classical atomistic molecular dynamics computational approaches to demonstrate the adsorption properties of HCQ on Ag, Au, AgAu, and Pt nanoparticles. The adsorption energies (less than -30 kcal/mole) were established for HCQ, and the (non)perturbative effects of this drug on the plasmonic absorption spectra of AgNP and AuNP have characterized with time-dependent density functional theory. The effect of size and compositions of nanoparticle on the coating with HCQ and CQ have obtained and proposed the appropriate candidate for drug delivery. This kind of modeling could help the experimental groups to find the efficient and safe therapies.
Keywords	Physics - Medical Physics ; Physics - Biological Physics ; Physics - Chemical Physics ; covid19
Subject code	541
Publishing date	2020-05-28
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Synthesis and Characterization of Thermally-Reduced Graphene

Razieh Jabari seresht / Mohsen Jahanshahi / Ali Morad Rashidi / Ali Asghar Ghoreyshi

Iranica Journal of Energy and Environment (IJEE), Vol 4, Iss 1, Pp 53-

2013 Volume 59

Abstract: Thermally-reduced graphene was obtained from reduction of graphene oxide (GO) via heat treatment under the hydrogen in the range of 300-1100°C. In order to find optimum tempreture, the synthesized graphene has been investigated by X-ray diffraction (XRD), ...

Abstract	Thermally-reduced graphene was obtained from reduction of graphene oxide (GO) via heat treatment under the hydrogen in the range of 300-1100°C. In order to find optimum tempreture, the synthesized graphene has been investigated by X-ray diffraction (XRD), FTIR spectroscopy as well as Raman spectroscopy. The result indicated that the reduced graphene at 900°C (GR900) had the highest quality in comparison with the other temperatures. Additionally, GR900 exhibited a sharp (002) peak corresponding to an interlayer distance of 3.39° A, which is close to that of conventional graphene (3.4°A). However, the structure of GR900 was also investigated by transmission electron microscopy (TEM), scanning electron microscopy (SEM) and the results supported the previous findings.
Keywords	Graphene ; Graphene oxide ; Thermal reduction ; X-ray diffraction ; FTIR spectroscopy ; Raman spectroscopy ; Environmental sciences ; GE1-350 ; Geography. Anthropology. Recreation ; G ; DOAJ:Environmental Sciences ; DOAJ:Earth and Environmental Sciences
Subject code	669
Language	English
Publishing date	2013-01-01T00:00:00Z
Publisher	IDOSI
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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