Tam Minh Nguyen

Tam Minh Nguyen
Ton Duc Thang University | TDT

PhD

About

80
Publications
9,639
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
968
Citations
Citations since 2017
56 Research Items
725 Citations
2017201820192020202120222023050100150200
2017201820192020202120222023050100150200
2017201820192020202120222023050100150200
2017201820192020202120222023050100150200

Publications

Publications (80)
Article
Increasing interest has been paid for hydrogen adsorption on atomically controlled nanoalloys due to their potential applications in catalytic processes and energy storage. In this work, we investigate the interaction of H2 with small-sized Ag n Cr (n = 1-12) using density functional theory calculations. It is found that the cluster structures are...
Article
Inhibiting the biological activity of SARS-CoV-2 Mpro can prevent viral replication. In this context, a hybrid approach using knowledge- and physics-based methods was proposed to characterize potential inhibitors for SARS-CoV-2 Mpro. Initially, supervised machine learning (ML) models were trained to predict a ligand-binding affinity of ca. 2 millio...
Article
In the present study, the performance of a new model of organic photodiodes (OPDs) are reported by incorporating silver nanowires (AgNWs) with vanadyl 3,10,17,24-tetra-tert-butyl-1,8,15,22 tetrakis(dimethylamino)-29H,31H phthalocyanine (VTP) and [6,6]-phenyl C71 butyric acid methyl ester (PC71BM) as the photoactive layer. The influence of the prese...
Article
Full-text available
A theoretical study of geometric and electronic structures, stability and magnetic properties of both neutral and anionic Ge16M0/- clusters with M being a first-row 3d transition metal atom, is performed using quantum chemical approaches. Both the isoelectronic Ge16Sc- anion and neutral Ge16Ti that have a perfect Frank-Kasper tetrahedral T d shape...
Article
For the purpose of discovering potential inhibitors of β-amyloid (BACE1), which is a crucial element in Alzheimer’s disease (AD) pathogenesis, an in silico study of naturally occurring compounds was performed using precise computational approaches. Autodock4 package was preliminary used to predict the binding affinities to BACE1 of more than four t...
Article
Au102+ has been found very stable showing a superatomic behavior with a highly symmetrical geometry and can be considered as the smallest copy of the golden pyramid Au20. In this work, we further explore superatomic clusters as analogues of more complex molecules by doping Au102+ cluster with 3d transition metal atom. It is found that, in similarit...
Article
AutoDock Vina (Vina) achieved a very high docking-success rate, , but give a rather low correlation coefficient, , for binding affinity with respect to experiments. This low correlation can be an obstacle for ranking of ligand-binding affinity, which is the main objective of docking simulations. In this context, we evaluated the dependence of Vina...
Article
Full-text available
The umbrella sampling (US) simulation is demonstrated to be an efficient approach for determining the unbinding pathway and binding affinity to the SARS-CoV-2 Mpro of small molecule inhibitors. The accuracy of US is in the same range as the linear interaction energy (LIE) and fast pulling of ligand (FPL) methods. In detail, the correlation coeffici...
Article
Full-text available
Correction for ‘The binary aluminum scandium clusters Al x Sc y with x + y = 13: when is the icosahedron retained?’ by Ngo Tuan Cuong et al. , RSC Adv. , 2021, 11 , 40072–40084. DOI: 10.1039/D1RA06994B.
Article
Full-text available
Geometrical and electronic structures of the 13-atom clusters Al x Sc y with x + y = 13, as well as their thermodynamic stabilities were investigated using DFT calculations. Both anionic and neutral isomers of Al x Sc y were found to retain an icosahedral shape of both Al13 and Sc13 systems in which an Al atom occupies the endohedral central positi...
Article
The spread of severe acute respiratory syndrome coronavirus 2 novel coronavirus (SARS-CoV-2) worldwide has caused the coronavirus disease 2019 (COVID-19) pandemic. A hundred million people were infected, resulting in several millions of death worldwide. In order to prevent viral replication, scientists have been aiming to prevent the biological act...
Preprint
Full-text available
AutoDock Vina (Vina) achieved a very high docking-success rate, p ̂, but give a rather low correlation coefficient, R, for binding affinity with respect to experiments. This low correlation can be an obstacle for ranking of ligand-binding affinity, which is the main objective of docking simulations. In this context, we evaluated the dependence of V...
Preprint
AutoDock Vina (Vina) achieved a very high docking-success rate, p ̂, but give a rather low correlation coefficient, R, for binding affinity with respect to experiments. This low correlation can be an obstacle for ranking of ligand-binding affinity, which is the main objective of docking simulations. In this context, we evaluated the dependence of V...
Article
Full-text available
The winged-helix domain of the methyl methanesulfonate and ultraviolet-sensitive 81 ( w MUS81) is a potential cancer drug target. In this context, marine fungi compounds were indicated to be able to prevent w MUS81 structure via atomistic simulations. Eight compounds such as D197 ( Tryptoquivaline U ), D220 ( Epiremisporine B ), D67 ( Aspergiolide...
Article
Full-text available
Binary clusters of transition-metal and noble-metal elements have been gathering momentum for not only advanced fundamental understanding but also potential as elementary blocks of novel nanostructured materials. In this regard, the geometries, electronic structures, stability, and magnetic properties of Cr-doped Cun, Agn, and Aun clusters (n = 2–2...
Preprint
Full-text available
According to the previous benchmark, Autodock Vina (Vina) achieved a very high successful-docking rate, p ̂, but give a rather a low correlation coefficient, R, for binding affinity with respect to experiment. This low correlation can be an obstacle for ranking of ligand-binding affinity, which is a main objective of docking simulations. The accura...
Preprint
According to the previous benchmark, Autodock Vina (Vina) achieved a very high successful-docking rate, p ̂, but give a rather a low correlation coefficient, R, for binding affinity with respect to experiment. This low correlation can be an obstacle for ranking of ligand-binding affinity, which is a main objective of docking simulations. The accura...
Article
Full-text available
Preventing the biological activity of SARS-CoV-2 main protease using natural compounds is of great interest. In this context, using a combination of AutoDock Vina and fast pulling of ligand simulations, eleven marine fungi compounds were identified that probably play as highly potent inhibitors for preventing viral replication. In particular, four...
Article
Full-text available
The COVID-19 pandemic has killed millions of people worldwide since its outbreak in December 2019. The pandemic is caused by the SARS-CoV-2 virus whose main protease (Mpro) is a promising drug target since it plays a key role in viral proliferation and replication. Currently, developing an effective therapy is an urgent task, which requires accurat...
Article
Full-text available
The coronavirus disease (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly spread worldwide recently, leading to global social and economic disruption. Although the emergently approved vaccine programs against SARS-CoV-2 have been rolled out globally, the number of COVID-19 daily cases and deaths...
Article
Abietanes are natural products that were isolated from Salvia clinopodioides. In this work, the HOO• antiradical activity of ten abietanes was thoroughly evaluated by using computational methods for the first time. It was found that the studied abietanes could exhibit moderate HOO• antiradical activity. Considerable antioxidant activity of the abie...
Article
Full-text available
The World Health Organization has designated Zika virus (ZIKV) as a dangerous, mosquito-borne flaviviral pathogen that was recently found to be responsible for a dramatically increased number of microcephaly cases and other congenital abnormalities in fetuses and newborns. There is neither a vaccine to prevent nor a drug to treat ZIKA virus infecti...
Article
Salvia species are frequently used in traditional medicine and are a source of diterpenoid antioxidants. In this study, the hydroperoxide radical scavenging activity of seven known abietane diterpenoids (ADs), isolated from Salvia barrelieri, are investigated using a quantum chemical approach. The ADs are 7-oxoroyleanone-12-methyl ether (1), 7a-ace...
Preprint
The coronavirus disease (COVID-19) pandemic caused by a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly spread worldwide recently, leading to a global social and economic disruption. Although the emergently approved vaccine programs against SARS-CoV-2 have been rolled out globally, the number of COVID-19 daily cases and dea...
Article
A series of host molecules have been designed and characterized for use in phosphorescent organic light-emitting diode devices. The parent host molecule was modified by adding nitrogen-containing groups at different positions. The triplet (T1) and first singlet excited (S1) states energies, frontier orbital energy levels, reorganization energies an...
Article
SARS-CoV-2 rapidly infects millions of people worldwide since December 2019. There is still no effective treatment for the virus, resulting in the death of more than one million patients. Inhibiting the activity of SARS-CoV-2 main protease (Mpro), 3C-like protease (3CLP), is able to block the viral replication and proliferation. In this context, ou...
Preprint
COVID-19 pandemic has killed millions of people worldwide since its outbreak in Dec 2019. The pandemic is caused by the SARS-CoV-2 virus whose main protease (Mpro) is a promising drug target since it plays a key role in viral proliferation and replication. Currently, designing an effective therapy is an urgent task, which requires accurately estima...
Preprint
div> SARS-CoV-2 rapidly infects millions of people worldwide since December 2019. There is still no effective treatment for the virus, resulting in the death of more than one million of patients. Inhibiting the activity of SARS-CoV-2 main protease (Mpro), 3C-like protease (3CLP), is able to block the viral replication and proliferation. In this co...
Article
The interaction between carbon monoxide and metal-based catalysts is important in several reactions such as CO hydrogenation, CO oxidation, and CO2 reduction. Consequently, CO adsorption on metal surfaces and nanoparticles has been largely investigated. Current understanding of the microscopic mechanism that governs the metal‒CO binding has been en...
Article
Full-text available
Novel hydroanthraquinones isolated from marine algal-derived endophytic fungus Talaromyces islandicus EN-501 exhibited promising antioxidant properties in preliminary studies, raising the prospect of adapting these compounds for therapeutic use in diseases caused by oxidative stress. For medicinal applications it is beneficial to develop a full und...
Article
Full-text available
A pentagonal hetero-prismatic structural motif was found for singly transition metal doped M@Ge5E5⁺ clusters, where the transition metal atom is located at the centre of a (5/5) Ge5E5 prism in which Ge is mixed with either P or As atoms. Structural characterization indicates that each (5/5) Ge5E5 prism is established by joining of two Ge3E2 and Ge2...
Article
Full-text available
Diterpenes that were isolated from Crossopetalum gaumeri (Loes.) Lundell (Celastraceae) plants are reported to exhibit a range of biological activities, in particular as radical scavengers. Thus further insight into the antioxidant activity of diterpenes in physiological environments is much needed but not studied yet. In this study, the antioxidan...
Preprint
Background: Understanding the genetic diversity in threatened species that occur in forest remnants is necessary to establish efficient strategies for the species conservation, restoration and management. Panax vietnamensis Ha et Grushv. is medicinally important, endemic and endangered species of Vietnam. However, genetic diversity and structure of...
Preprint
Full-text available
Background: Understanding the genetic diversity in threatened species that occur in forest remnants is necessary to establish efficient strategies for the species conservation, restoration and management. Panax vietnamensis Ha et Grushv. is medicinally important, endemic and endangered species of Vietnam. However, genetic diversity and structure of...
Preprint
Full-text available
Background: Understanding the genetic diversity in endangered species that occur in forest remnants is necessary to establish efficient strategies for the species conservation, restoration and management. Panax vietnamensis Ha et Grushv. is medicinally important, endemic and endangered species of Vietnam. However, genetic diversity and structure of...
Preprint
Full-text available
Background: Understanding the genetic diversity in threatened species that occur in forest remnants is necessary to establish efficient strategies for the species conservation, restoration and management. Panax vietnamensis Ha et Grushv. is medicinally important, endemic and endangered species of Vietnam. However, genetic diversity and structure of...
Article
Ramalin, which is isolated from the Antarctic lichen (Ramalina terebrata), has potential anti-inflammatory, anti-cancer and antioxidant activities. In this study, the HO and HOO radical scavenging of ramalin was evaluated in water and pentyl ethanoate (lipid mimetic) environments in silico by using kinetic calculations. It was found that the radica...
Article
Full-text available
p>An examination of the first-row transition metal doped boron clusters, B<sub>14</sub>M (M = Sc, Ti, V, Cr, Mn, Fe, Co, Ni, and Cu) in the neutral state, is carried out using DFT quantum chemical calculations. The lowest-energy equilibrium structures of the clusters considered are identified at TPSSh/ 6-311+G(d) level. It is found that the structu...
Article
Full-text available
Structures of the binary Al n Si m clusters in both neutral and cationic states were investigated using DFT and TD-DFT (B3LYP/6-311+G(d)) and (U)CCSD(T)/cc-pvTZ calculations. Silicon-doped aluminum clusters are characterized by low spin ground states. For small sizes, the Si dopant prefers to be located at vertices having many edges. For larger siz...
Article
A systematic investigation on structure, relative stabilities, dissociation behavior and bonding of the singly and doubly Ni doped boron clusters BnNim with n = 2 −22 and m = 1 – 2, was carried out using density functional theory calculations. Calculated results indicate that for n < 14, the BnNim structures are generally formed by capping Ni atom(...
Article
Ten conjugated polymers (polypyrrole, polyfuran, polythiophene, polyborole, polycyclopentadiene, polysilole, polyphosphole, polycyclopentadienethione, polycyclopentadieneone, poly(p-phenylene)) have been investigated using density functional theory (DFT) and semi-empirical method. BP86-30% HF hybrid functional with CEP-31G* basis set combined with...
Article
Binary BnAln clusters (n = 1–7) were investigated using both DFT/TPSSh and G4 calculations. B and Al atoms do not mix together but prefer to be assembled in two separated but interacting Bn and Aln components. Large electron donation from Al to B atoms induces a donor-acceptor stabilization. Planar B3Al3 is a σ aromatic compound. B4Al4 exhibits two...
Article
Quantum chemical computations of thermochemical parameters of several series of small pure and doped silicon clusters are reviewed. We analyzed the performance of the coupled-cluster theory with energies extrapolated up to complet basis set, CCSD(T)/CBS and the composite G4 method in determining the total atomization energies (TAE), standard heats...
Article
Acetylcholinesterase (AChE) is considered as one of the most favored drug targets for Alzheimer’s disease. The effects of different force fields (FFs) on ranking affinity of acetylcholinesterase inhibitors were obtained using the fast pulling of ligand (FPL) method in steered-molecular dynamics (SMD) simulations. GROMOS, AMBER, CHARMM, and OPLS-AA...
Article
Full-text available
Remarkably strong effects of the aromatic B3 cycle in stabilizing tubular silicon clusters were observed for the first time. The doped cluster B3@Si12+ presents a novel structural motif for silicon clusters in which a B3 cycle is encapsulated into a (6 x 2) Si12 prism giving raise to a high symmetry stable tubular structure (D3h). A large amount of...
Article
Full-text available
An investigation on structure, stability, and magnetic properties of singly doped Au19M (M=Cr, Mn, and Fe) clusters is carried out by means of density functional theory calculations. The studied clusters prefer forming magnetic versions of the unique tetrahedral Au20. Stable sextet Au19Cr is identified as the least reactive species and can be quali...
Article
The absolute free energy difference of binding (ΔG) between neuraminidase and its inhibitor was evaluated using fast pulling of ligand (FPL) method over steered molecular dynamics (SMD) simulations. The metric was computed through linear interaction approximation. Binding nature was described by free energy differences of electrostatic and van der...
Article
An extensive replica exchange molecular dynamics (REMD) simulation was performed to investigate the progress patterns of the inhibition of (−)-epigallocatechin-3-gallate (EGCG) on the Aβ16-22 hexamer. Structural variations of the oligomers without and with EGCG were monitored and analyzed in detail. It has been found that EGCG prevents the formatio...
Article
The geometrical evolution, electronic structure and thermodynamic stability of a series of singly-doped SinP and doubly-doped SinP2 silicon clusters with n = 1-10, in the neutral, cationic and anionic states were systematically investigated using DFT computations. The global minimum structures were identified using different search approaches. The...
Article
The interaction of carbon monoxide with platinum alloy nanoparticles is an important problem in the context of fuel cell catalysis. In this work, molybdenum doped platinum clusters are studied in the gas phase, in order to obtain a better understanding of the fundamental nature of the Pt-CO interaction in the presence of a dopant atom. For this pur...
Article
Full-text available
Two quantum chemical methods which are the time-dependent density functional theory (TD-DFT) and the complete active space CASPT2/CASSCF have been used in modeling absorption spectra of silver clusters Ag n (n = 2, 3, 4, 6, 8). There is an overall good agreement between TD-DFT and CASPT2 results for transition energies. The absorption spectra of th...
Article
A systematic investigation on structure, dissociation behavior, chemical bonding, and magnetic property of Cr-doped Cun clusters (n = 9-16) is carried out using the mean of density functional theory calculations. It is found that CrCu12 is a crucial size, preferring an icosahedral Cu12 cage with the central Cr dopant. Smaller cluster sizes appear a...
Article
The structure of cobalt doped silicon clusters, Si_nCo^+ (n = 5−8) and Si_nCo_2^+ (n = 8−12), is investigated in a combined infrared multiple photon dissociation spectroscopy and density functional theory study. The singly doped clusters have exohedral structures in which the Co atom substitutes an atom of bare Si_(n+1)^+ clusters. In the doubly do...
Article
We investigated the structures of the singly and doubly magnesium-doped silicon clusters in both neutral and cationic states, SinMgm0/+, with n = 1-10 and m = 1 and 2. Total atomization energies (TAEs), heats of formation (ΔHf), and binding energies (Ebs) were determined using the composite G4 method. The Ebs of the Mg-doped clusters are decreased...
Article
A theoretical investigation of the geometry, stability and aromaticity of boron clusters doped by two Sc and Ti atoms was carried out using DFT calculations. The Sc and Ti atoms form the bimetallic boron cycles not only with the eight-membered ring B82- but also with the isoelectronic species B7N and B6C2 rings yielding the planar B82-, B7N and B6C...
Article
We study CoxCryOm+ (x + y = 2, 3 and 1 ≤ m ≤ 4) clusters by means of density-functional-theory calculations. It is found that the clusters grow preferentially through maximizing the number of metal-oxygen bonds with a favor on Cr sites. The size- and composition-dependent magnetic behavior is discussed in relation with the local atomic magnetic mom...
Article
Full-text available
The smallest triple ring tubular silicon cluster Mn2@Si15 is reported for the first time. Theoretical structural identification shows that the Mn2@Si15 tubular structure whose triple ring is composed by three five-membered Si rings in anti-prism motif, is stable in high symmetry (D5h) and singlet ground state (1A1’). The dimer Mn2 is placed inside...
Article
We revisit the singlet-triplet energy gap (ΔEST ) of silicon trimer and evaluate the gaps of its derivatives by attachment of a cation (H(+) , Li(+) , Na(+) , and K(+) ) using the wavefunction-based methods including the composite G4, coupled-cluster theory CCSD(T)/CBS, CCSDT and CCSDTQ, and CASSCF/CASPT2 (for Si3 ) computations. Both (1) A1 and (3...
Article
Full-text available
Stabilized fullerene and tubular forms can be produced in boron clusters Bn in small sizes from n ~ 14 upon doping by transition metal atoms. B14Fe and B16Fe are stable tubes whereas B18Fe and B¬20Fe are stable fullerenes. The magnetic moment in B18Fe is completely quenched. Their formation and stability suggest the use of dopants to induce differe...
Article
We determined the geometries and chemical bonding phenomena of the B27 system in its dicationic, cationic, neutral, anionic and dianionic states using DFT computations. In both cationic and neutral states, the triple ring tubular forms correspond to the lowest-energy isomers, especially in B27(+). The cation B27(+) represents the first stable hollo...
Article
The boron oxide dianions Bn(BO)n2– (n = 4–12) are studied using DFT (B3LYP) method. Geometries of the global minima of Bn(BO)n2– with n = 4–12 are found to be analogous to those of boron hydrides. All boron oxides considered exhibit large HOMO-LUMO gaps and high vertical detachment energies. Similar to BnHn2–, the enhanced thermodynamic stabilities...
Article
The stability of mass-selected pure cobalt oxide and chromium doped cobalt oxide cluster cations, Con[Formula: see text] and Con-1[Formula: see text] (n = 2, 3; m = 2-6 and n = 4; m = 3-8), has been investigated using photodissociation mass spectrometry. Oxygen-rich Con[Formula: see text] clusters (m ⩾ n + 1 for n = 2, 4 and m ⩾ n + 2 for n = 3) pr...
Article
We revisited the aromaticity of silicon tetramer Si4, Si42+ and isoelectronic four-membered rings without and with a planar tetracoordinate carbon dopant (Si4C2+). Electron localizability indicators and magnetic ring currents were used to probe bonding patterns. Comparison with Al42�, Si2Al2, Al4C2� and Si2Al2C was performed. The 14 (Si42+), 16 (Si...
Article
The structures of neutral cobalt doped silicon clusters have been assigned by a combined experimental and theoretical study. Size-selective infrared spectra of neutral SinCo (n = 10-12) clusters are measured using a tunable IR-UV two-color ionization scheme. The experimental infrared spectra are compared with calculated spectra of low energy struct...
Article
Total atomization energies and heats of formation of small silicon clusters Sin and their ions are calculated using G4 (n = 2-13) and CCSD(T)/CBS (aug-cc-pV(n+d) Z for n = 2-6) methods. Experimental data for Si-n were available with large uncertainties. A new ground state structure for Si-11(-) was located. Using Delta H-f degrees (Si, 298 K) - 451...
Article
A systematic examination of the aluminum doped silicon clusters, SinAlm with n = 1 – 11 and m = 1 – 2, in both neutral and anionic states, is carried out using quantum chemical calculations. Lowest-energy equilibrium structures of the clusters considered are identified on the basis of G4 energies. High accuracy total atomization energies and thermo...
Article
A systematic investigation of the boron-doped silicon clusters SinB with n ranging from 1 to 10 in the neutral, anionic, and cationic states is performed using quantum chemical calculations. Lowest-energy minima of the clusters considered are identified on the basis of the B3LYP, G4, and CCSD(T) energies. Total atomization energies and thermochemic...
Article
Full-text available
We investigate the molecular and electronic structure and thermochemical properties of the cationic boron clusters B n + with n = 2–20, using both MO and DFT methods. Several functionals are used along with the MP2, G3, G3B3, G4, and CCSD(T)/CBS methods. The latter is the high accuracy reference. While the TPSS, TPSSh, PW91, PB86, and PBE functiona...
Article
We report on a combined experimental and theoretical study of the ionization energies and structures of small lithium doped silicon clusters, Si(n)Li(m) with n = 5-11 and m = 3-6. Photoionization efficiency curves are measured in the 4.68-6.24 eV range and subsequently compared with calculated values of both vertical and adiabatic ionization energi...
Article
We reinvestigate the structures of neutral boron clusters Bn, with n = 14–20. G3B3 calculations confirm that a transition between 2D and 3D shape occurs at B20, which has a tubular form. In disagreement with Boustani et al. (Phys. Rev. B, 83 (2011) 193405), we find a planar B19 cluster. Standard heats of formation are obtained and used to evaluate...