ngo thi Lan | Thai Nguyen University of Education (original) (raw)

Papers by ngo thi Lan

Research paper thumbnail of Density Functional Study of Size-Dependent Hydrogen Adsorption on AgnCr (n = 1–12) Clusters

Research paper thumbnail of Systematic Investigation of the Structure, Stability, and Spin Magnetic Moment of CrMn Clusters (M = Cu, Ag, Au, and n = 2–20) by DFT Calculations

ACS Omega

Binary clusters of transition-metal and noble-metal elements have been gathering momentum for not... more 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 Cu n , Ag n , and Au n clusters (n = 2−20) have been systematically studied by means of density functional theory calculations. It is found that the structural evolutions of CrCu n and CrAg n clusters are identical. The icosahedral CrCu 12 and CrAg 12 are crucial sizes for doped copper and silver species. Small CrAu n clusters prefer the planar geometries, while the larger ones appear as on the way to establish the tetrahedral CrAu 19. Our results show that while each noble atom contributes one s valence electron to the cluster shell, the number of chromium delocalized electrons is strongly size-dependent. The localization and delocalization behavior of 3d orbitals of the chromium decide how they participate in metallic bonding, stabilize the cluster, and give rise to and eventually quench the spin magnetic moment. Moreover, molecular orbital analysis in combination with a qualitative interpretation using the phenomenological shell model is applied to reveal the complex interplay between geometric structure, electronic structure, and magnetic moment of clusters. The finding results are expected to provide greater insight into how a host material electronic structure influences the geometry, stability, and formation of spin magnetic moments in doped systems.

Research paper thumbnail of A computationally affordable approach for accurate prediction of the binding affinity of JAK2 inhibitors

Journal of Molecular Modeling

Research paper thumbnail of Corrigendum to 'Estimation of the ligand-binding free energy of checkpoint kinase 1 via non-equilibrium MD simulations

Journal of molecular graphics & modelling, 2020

Research paper thumbnail of Design, synthesis, structure, in vitro cytotoxic activity evaluation and docking studies on target enzyme GSK-3β of new indirubin-3ʹ-oxime derivatives

Scientific Reports, 2020

The addition of chalcone and amine components into indirubin-3′-oxime resulted in 15 new derivati... more The addition of chalcone and amine components into indirubin-3′-oxime resulted in 15 new derivatives with high yields. Structures of new derivatives were also elucidated through 1D, 2D-NMR and HR-MS(ESI) spectra and X-ray crystallography. All designed compounds were screened for cytotoxic activity against four human cancer cell lines (HepG2, LU-1, SW480 and HL-60) and one human normal kidney cell line (HEK-293). Compound 6f exhibited the most marked cytotoxicity meanwhile cytotoxicity of compounds 6e, 6h and 6l was more profound toward cancer cell lines than toward normal cell. These new derivatives were further analyzed via molecular docking studies on GSK-3β enzyme. Docking analysis shows that most of the derivatives exhibited potential inhibition activity against GSK-3β with characteristic interacting residues in the binding site. The fast pulling of ligand scheme was then employed to refine the binding affinity and mechanism between ligands and GSK-3β enzyme. The computational r...

Research paper thumbnail of Estimation of the ligand-binding free energy of checkpoint kinase 1 via non-equilibrium MD simulations

Journal of Molecular Graphics and Modelling, 2020

This is a PDF file of an article that has undergone enhancements after acceptance, such as the ad... more This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. This version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. Please note that, during the production process, errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.

Research paper thumbnail of DFT investigation of Au9M2+ nanoclusters (M = Sc-Ni): The magnetic superatomic behavior of Au9Cr2+

Chemical Physics Letters, 2022

Research paper thumbnail of Correction: The binary aluminum scandium clusters AlxScy with x + y = 13: when is the icosahedron retained?

RSC Advances, 2022

Correction for ‘The binary aluminum scandium clusters AlxScy with x + y = 13: when is the icosahe... more Correction for ‘The binary aluminum scandium clusters AlxScy 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.

Research paper thumbnail of Magnetic domain-wall motion study under an electric field in a Finemet thin film on flexible substrate

Influence of applied in-plane elastic strains on the static magnetic configuration of a 530 nm ma... more Influence of applied in-plane elastic strains on the static magnetic configuration of a 530 nm magnetostrictive FeCuNbSiB thin film. The in-plane strains are induced via the application of a voltage to a piezoelectric actuator on which the film/substrate system was glued. A quantitative characterization of the voltage dependence of the induced-strain at the surface of the film was performed using a digital image correlation technique. MFM images at remanence (H=0 Oe and U=0 V) clearly reveal the presence of weak stripe domains. The effect of the voltage-induced strain shows the existence of a threshold value above, which the break of the stripe configuration set in. For a maximum strain of exx~0.5*10-3 we succeed in destabilizing the stripes configuration helping the setting up of a complete homogeneous magnetic pattern.

Research paper thumbnail of The binary aluminum scandium clusters AlxScy with x + y = 13: when is the icosahedron retained?

RSC Advances

The icosahedral structure of the AlxScy clusters with x + y = 13.

Research paper thumbnail of Prediction of AChE-ligand affinity using the umbrella sampling simulation

Journal of Molecular Graphics and Modelling

Acetylcholinesterase (AChE) is characterized as a key target for designing inhibitors to prevent ... more Acetylcholinesterase (AChE) is characterized as a key target for designing inhibitors to prevent Alzheimer's disease (AD). The binding free energy of a ligand to the AChE enzyme is a critical factor to screen the potential inhibitor in addition to pharmacokinetics and pharmacology estimation. The biased sampling or umbrella sampling (US) method emerges as a reliable technique to estimate the AChE-inhibitor affinity. The affinity is computed as the difference between the largest and smallest values of the free energy change, obtained by using a potential of mean force (PMF) analysis. The obtained affinities overestimate the experimental ones with a value of ∼4.10 kcal/mol. However, a very good correlation coefficient (R=0.94) between the computational and experimental values is observed. Consequently, the obtained precision is high since the mean error of the free energy value is of δ=1.17 kcal/mol. The binding affinity of a new ligand can be consistently appraised via the US technique. Therefore, the absolute binding free energy of a ligand to the AChE protein can be obtained via the linear regression with the root-mean-square errors (RMSE) of 0.98 kcal/mol. The small value of RMSE implies that ligands revealing the similar binding affinities are able to be discriminated through the US simulations. In addition, the derivatives of Cordyceps were recently reported that they are able to inhibit the AChE enzyme, resulting in an improvement in learning and cognitive ability for curing AD. The active metabolites of Cordyceps were thus evaluated as the potential inhibitors for the AChE enzyme, and the 5-Carboxy-2'-deoxyuridine compound can inhibit the activity of the AChE enzyme. These compounds are also passed the testing of Lipinski's rule of five, toxicity, crossing blood-brain barrier (BBB) ability, and human intestinal absorption.

Research paper thumbnail of Insights into the magnetic origin of CunCr (n= 9÷11) clusters: A superposition of magnetic and electronic shells

Vietnam Journal of Science and Technology

Interests in Cu-Cr sub-nanometer systems have been increasing due to the recently-found icosahedr... more Interests in Cu-Cr sub-nanometer systems have been increasing due to the recently-found icosahedral Cu12Cr cluster as a superatomic molecule, where the 3d-Cr and 4s-Cu electrons can phenomenologically form the 18-e molecular shell (1S21P61D10) of Cu12Cr. In this report, we set out to investigate the energetically-preferred geometries and stabilities of CunCr (n = 9÷11) clusters using the density-functional-theory calculations. It is found that not all of 3d-Cr electrons involve in the formation of the cluster shell and the remaining localized ones cause the magnetic moment of the clusters, which is different from what was believed.

Research paper thumbnail of Magnetic domain-wall motion study under an electric field in a thin film on flexible substrate

Journal of Magnetism and Magnetic Materials, 2014

We study the influence of applied in-plane elastic strains on the static magnetic configuration o... more We study the influence of applied in-plane elastic strains on the static magnetic configuration of a 530 nm magnetostrictive FeCuNbSiB ðFinemet s Þ thin film. The in-plane strains are induced via the application of a voltage to a piezoelectric actuator on which the film/substrate system was glued. A quantitative characterization of the voltage dependence of the induced-strain at the surface of the film was performed using a digital image correlation technique. Magnetic Force Microscopy (MFM) images at remanence (H ¼0 Oe and U ¼0 V) clearly reveal the presence of weak stripe domains. The effect of the voltage-induced strain shows the existence of a voltage threshold value for the strike configuration break. For a maximum strain of ε XX $ 0:5 Â 10 À 3 we succeed in destabilizing the stripes configuration helping the setting up of a complete homogeneous magnetic pattern.

Research paper thumbnail of Density Functional Study of Size-Dependent Hydrogen Adsorption on AgnCr (n = 1–12) Clusters

Research paper thumbnail of Systematic Investigation of the Structure, Stability, and Spin Magnetic Moment of CrMn Clusters (M = Cu, Ag, Au, and n = 2–20) by DFT Calculations

ACS Omega

Binary clusters of transition-metal and noble-metal elements have been gathering momentum for not... more 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 Cu n , Ag n , and Au n clusters (n = 2−20) have been systematically studied by means of density functional theory calculations. It is found that the structural evolutions of CrCu n and CrAg n clusters are identical. The icosahedral CrCu 12 and CrAg 12 are crucial sizes for doped copper and silver species. Small CrAu n clusters prefer the planar geometries, while the larger ones appear as on the way to establish the tetrahedral CrAu 19. Our results show that while each noble atom contributes one s valence electron to the cluster shell, the number of chromium delocalized electrons is strongly size-dependent. The localization and delocalization behavior of 3d orbitals of the chromium decide how they participate in metallic bonding, stabilize the cluster, and give rise to and eventually quench the spin magnetic moment. Moreover, molecular orbital analysis in combination with a qualitative interpretation using the phenomenological shell model is applied to reveal the complex interplay between geometric structure, electronic structure, and magnetic moment of clusters. The finding results are expected to provide greater insight into how a host material electronic structure influences the geometry, stability, and formation of spin magnetic moments in doped systems.

Research paper thumbnail of A computationally affordable approach for accurate prediction of the binding affinity of JAK2 inhibitors

Journal of Molecular Modeling

Research paper thumbnail of Corrigendum to 'Estimation of the ligand-binding free energy of checkpoint kinase 1 via non-equilibrium MD simulations

Journal of molecular graphics & modelling, 2020

Research paper thumbnail of Design, synthesis, structure, in vitro cytotoxic activity evaluation and docking studies on target enzyme GSK-3β of new indirubin-3ʹ-oxime derivatives

Scientific Reports, 2020

The addition of chalcone and amine components into indirubin-3′-oxime resulted in 15 new derivati... more The addition of chalcone and amine components into indirubin-3′-oxime resulted in 15 new derivatives with high yields. Structures of new derivatives were also elucidated through 1D, 2D-NMR and HR-MS(ESI) spectra and X-ray crystallography. All designed compounds were screened for cytotoxic activity against four human cancer cell lines (HepG2, LU-1, SW480 and HL-60) and one human normal kidney cell line (HEK-293). Compound 6f exhibited the most marked cytotoxicity meanwhile cytotoxicity of compounds 6e, 6h and 6l was more profound toward cancer cell lines than toward normal cell. These new derivatives were further analyzed via molecular docking studies on GSK-3β enzyme. Docking analysis shows that most of the derivatives exhibited potential inhibition activity against GSK-3β with characteristic interacting residues in the binding site. The fast pulling of ligand scheme was then employed to refine the binding affinity and mechanism between ligands and GSK-3β enzyme. The computational r...

Research paper thumbnail of Estimation of the ligand-binding free energy of checkpoint kinase 1 via non-equilibrium MD simulations

Journal of Molecular Graphics and Modelling, 2020

This is a PDF file of an article that has undergone enhancements after acceptance, such as the ad... more This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. This version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. Please note that, during the production process, errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.

Research paper thumbnail of DFT investigation of Au9M2+ nanoclusters (M = Sc-Ni): The magnetic superatomic behavior of Au9Cr2+

Chemical Physics Letters, 2022

Research paper thumbnail of Correction: The binary aluminum scandium clusters AlxScy with x + y = 13: when is the icosahedron retained?

RSC Advances, 2022

Correction for ‘The binary aluminum scandium clusters AlxScy with x + y = 13: when is the icosahe... more Correction for ‘The binary aluminum scandium clusters AlxScy 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.

Research paper thumbnail of Magnetic domain-wall motion study under an electric field in a Finemet thin film on flexible substrate

Influence of applied in-plane elastic strains on the static magnetic configuration of a 530 nm ma... more Influence of applied in-plane elastic strains on the static magnetic configuration of a 530 nm magnetostrictive FeCuNbSiB thin film. The in-plane strains are induced via the application of a voltage to a piezoelectric actuator on which the film/substrate system was glued. A quantitative characterization of the voltage dependence of the induced-strain at the surface of the film was performed using a digital image correlation technique. MFM images at remanence (H=0 Oe and U=0 V) clearly reveal the presence of weak stripe domains. The effect of the voltage-induced strain shows the existence of a threshold value above, which the break of the stripe configuration set in. For a maximum strain of exx~0.5*10-3 we succeed in destabilizing the stripes configuration helping the setting up of a complete homogeneous magnetic pattern.

Research paper thumbnail of The binary aluminum scandium clusters AlxScy with x + y = 13: when is the icosahedron retained?

RSC Advances

The icosahedral structure of the AlxScy clusters with x + y = 13.

Research paper thumbnail of Prediction of AChE-ligand affinity using the umbrella sampling simulation

Journal of Molecular Graphics and Modelling

Acetylcholinesterase (AChE) is characterized as a key target for designing inhibitors to prevent ... more Acetylcholinesterase (AChE) is characterized as a key target for designing inhibitors to prevent Alzheimer's disease (AD). The binding free energy of a ligand to the AChE enzyme is a critical factor to screen the potential inhibitor in addition to pharmacokinetics and pharmacology estimation. The biased sampling or umbrella sampling (US) method emerges as a reliable technique to estimate the AChE-inhibitor affinity. The affinity is computed as the difference between the largest and smallest values of the free energy change, obtained by using a potential of mean force (PMF) analysis. The obtained affinities overestimate the experimental ones with a value of ∼4.10 kcal/mol. However, a very good correlation coefficient (R=0.94) between the computational and experimental values is observed. Consequently, the obtained precision is high since the mean error of the free energy value is of δ=1.17 kcal/mol. The binding affinity of a new ligand can be consistently appraised via the US technique. Therefore, the absolute binding free energy of a ligand to the AChE protein can be obtained via the linear regression with the root-mean-square errors (RMSE) of 0.98 kcal/mol. The small value of RMSE implies that ligands revealing the similar binding affinities are able to be discriminated through the US simulations. In addition, the derivatives of Cordyceps were recently reported that they are able to inhibit the AChE enzyme, resulting in an improvement in learning and cognitive ability for curing AD. The active metabolites of Cordyceps were thus evaluated as the potential inhibitors for the AChE enzyme, and the 5-Carboxy-2'-deoxyuridine compound can inhibit the activity of the AChE enzyme. These compounds are also passed the testing of Lipinski's rule of five, toxicity, crossing blood-brain barrier (BBB) ability, and human intestinal absorption.

Research paper thumbnail of Insights into the magnetic origin of CunCr (n= 9÷11) clusters: A superposition of magnetic and electronic shells

Vietnam Journal of Science and Technology

Interests in Cu-Cr sub-nanometer systems have been increasing due to the recently-found icosahedr... more Interests in Cu-Cr sub-nanometer systems have been increasing due to the recently-found icosahedral Cu12Cr cluster as a superatomic molecule, where the 3d-Cr and 4s-Cu electrons can phenomenologically form the 18-e molecular shell (1S21P61D10) of Cu12Cr. In this report, we set out to investigate the energetically-preferred geometries and stabilities of CunCr (n = 9÷11) clusters using the density-functional-theory calculations. It is found that not all of 3d-Cr electrons involve in the formation of the cluster shell and the remaining localized ones cause the magnetic moment of the clusters, which is different from what was believed.

Research paper thumbnail of Magnetic domain-wall motion study under an electric field in a thin film on flexible substrate

Journal of Magnetism and Magnetic Materials, 2014

We study the influence of applied in-plane elastic strains on the static magnetic configuration o... more We study the influence of applied in-plane elastic strains on the static magnetic configuration of a 530 nm magnetostrictive FeCuNbSiB ðFinemet s Þ thin film. The in-plane strains are induced via the application of a voltage to a piezoelectric actuator on which the film/substrate system was glued. A quantitative characterization of the voltage dependence of the induced-strain at the surface of the film was performed using a digital image correlation technique. Magnetic Force Microscopy (MFM) images at remanence (H ¼0 Oe and U ¼0 V) clearly reveal the presence of weak stripe domains. The effect of the voltage-induced strain shows the existence of a voltage threshold value for the strike configuration break. For a maximum strain of ε XX $ 0:5 Â 10 À 3 we succeed in destabilizing the stripes configuration helping the setting up of a complete homogeneous magnetic pattern.