POSTER SECTION

Molecular Design of Novel Heterohelicenes for CP–OLEDs Applications: A DFT/TD–DFT Study

Loc Gia Hoang¹, Ngoc Bao Phan³, Truc Xuan Nguyen¹, Manh Duc Doan¹, Phuong Minh Nguyen¹, Hue Minh Thi Nguyen^1,2*

 ¹Faculty of Chemistry and Center for Computational Science, ²Institute of Natural Sciences, Hanoi National University of Education; ³Le Hong Phong High School for the Gifted.

Corresponding author: hue.nguyen@hnue.edu.vn

Circularly polarized organic light–emitting diodes (CP–OLEDs) synthesized from helicene frameworks are emerging as a promising technology for next–generation 3D displays and advanced optical devices. However, traditional helicene frameworks frequently encounter limitations regarding spectral broadening and low radiative efficiency. To overcome this barrier, the study systematically designs and investigates six luminescent derivatives including heteroatoms (O, S, N) and methoxy (–OMe) substituents into the azahelicene framework of the parent system H0. The results show that these additions help control and direct both the electric transition dipole moment (μ) and magnetic transition dipole moment (m) vectors. The oxygen–containing systems can uniformly distribute holes and electrons, yielding a high oscillator strength (f). Conversely, the combination of the large radius of sulfur and the electron–donating –OMe group widened the angle between the two vectors, amplifying the circularly polarized luminescence dissymmetry factor (g_lum) to a higher value. By explaining how heteroatoms and substituents work, this study highlights their trade-offs and provides a guide for designing diverse CP–OLED materials.

KEYWORDS: Heteroatom, helicenes, CPL, DFT, CP–OLEDs.

Nonconventional Hydrogen and Halogen Bonds in the Binary Complexes of Haloform with Hydrogen Cyanide and Methylidynephosphane Derivatives

Nguyen Tien Trung, ^1,2,* Le Thi Tu Quyen,^1,2 Vu Thi Ngan,^1,2,*

¹⁾Laboratory of Computational Chemistry and Modelling (LCCM), Quy Nhon University, 170 An Duong Vuong Street, Quy Nhon City 590000, Vietnam

²⁾Faculty of Natural Sciences, Quy Nhon University, 170 An Duong Vuong Street, Quy Nhon City 590000, Vietnam

Corresponding author’s email: nguyentientrung@qnu.edu.vn; vuthingan@qnu.edu.vn

This study presents a comprehensive analysis of the nature and stability of nonconventional hydrogen bonds in complexes formed between haloforms (CHX₃, X = F, Cl, Br) and hydrogen cyanide (HCN) or methylidynephosphane (HCP) derivatives, denoted as MCZ (M = H, F, Cl, Br, CH₃, C₂H, CN, CP, CAs, Li, Na; Z = N, P), with particular emphasis on the rarely investigated C-H···P and C-H···C hydrogen bonds. The complexes containing HCN derivatives are found to be more stable than their HCP counterparts. SAPT2+ analysis indicates that dispersion energy plays a key role in stabilizing the CHX₃···MCP complexes, whereas electrostatic interactions dominate the stabilization of the CHX₃···MCN systems. The CHX₃···MCN complexes are predominantly stabilized by nonconventional C-H···N hydrogen bonds, whereas both C-H···C/P/Cl hydrogen bonds and C-X···X/C/P halogen bonds contribute to the stabilization of the CHX₃···MCP complexes. The strength of the nonconventional hydrogen bonds decreases in the order: C-H···N >> C-H···C > C-H···Cl ≈ C-H···P. Remarkably, the C-H stretching frequency shifts change from blue to red as X varies from F to Br and M changes from electron-withdrawing substituents to electron-donating groups and subsequently to alkali metals. The magnitude of the frequency shifts is significantly smaller for C-H···P, C-H···C, and C-H···Cl than for C-H···N, with the blue shifts of the former being approximately 2.0–3.5 times weaker. The observed red and blue shifts in the C-H stretching frequencies in the C-H···N hydrogen bond are suggested to originate from Coulombic interactions between the H and N atoms.

Investigating the binding of agonists to the stability of µ-opioid receptor

Hien T. T. Lai ¹, Phung Anh Tue ^1,2, and Toan T. Nguyen ^1,*

Opioid agonists expressing analgesia are usually followed by adverse reactions such as heart failure, respiratory depression, constipation, etc. Agonist binding to µ-opioid receptors (µOR) can activate two intracellular signaling pathways: (i) the G protein signal is responsible for alleviating pain; (ii) β-arrestin results in unwanted side effects. Here, we utilize recent advances in computational power and molecular dynamics (MD) simulations to analyze and evaluate the influences of unbiased (Morphine – M6G) and biased (TRV130) compounds of the G protein signal, on the structural stability and functions of the µOR receptor. We have identified that M6G with hydroxyl groups, forms hydrogen bonds and electrostatic interactions with key residues in the catalytic site of the µOR receptor, whereas TRV130 prefers binding by hydrophobic and van der Waals interaction types. The binding to M6G leads to the higher flexibility of the µOR’s TM VII, which is known to activate the β-arrestin signal, while this TM VII is more stable in the TRV130-µOR complex. Additionally, the allosteric pockets of the Sodium (Na⁺) ion are different in these µOR complexes. Taken together, these studies may provide new avenues for the design of biased opioids with appropriate efficacy.

STRUCTURE–BONDING–OPTICAL PROPERTY RELATIONSHIPS IN PYRIDINE-BRIDGED 20-ELECTRON ANSA-FERROCENES

Yen Nguyen Tram Chau^1,2, Nguyen Thanh Si³, Pham Vu Nhat¹

¹ College of Natural Sciences, Can Tho University; ² College of Medicine and Pharmacy, Tra Vinh University; ³ Department of Chemistry and Biology, Faculty of Basic Sciences, Can Tho University of Medicine and Pharmacy

The ansa-ferrocenes with pyridine-bridged provide us with a new platform for exploring non-classical metal–ligand bonding. In this work, a pyridine-bridged 20-electron ansa-ferrocene was systematically investigated across charge–multiplicity configurations using DFT and TD-DFT calculations. Structural analysis reveals that the Fe···N distance and Cp–Fe–Cp geometry are strongly affected by the electronic-state variation. TD-DFT results show mixed LC, LMCT, and intraligand charge-transfer characters, while the monocationic quartet state  (Q1M4) exhibits the most pronounced nonlinear optical response. These findings highlight charge and spin modulation as an effective strategy for tuning the bonding and optoelectronic properties of 20-electron ferrocene-based systems.

Keywords: 20-electron ferrocene; pyridine-bridged ansa-ferrocene; Fe–N coordination; NBO analysis; TD-DFT; charge-transfer excitation; nonlinear optical response.

Quantum resource reduction for quantum-centric supercomputing via correlated mean-field downfolding framework

Thien Tran Ngoc,^1,2 Lan Tran Nguyen^1,2

¹Faculty of Physics and Engineering Physics, University of Science, Ho Chi Minh City 700000, Vietnam

²Vietnam National University, Ho Chi Minh City 700000, Vietnam

We present OBDF-SQD, a hybrid quantum-classical method that combines one-body downfolding (OBDF) based on one-body Møller-Plesset second-order perturbation theory (OBMP2) with sample-based quantum diagonalization (SQD) for use in quantum-centric supercomputing (QCS). In this approach, OBMP2 is executed classically to fold dynamical correlation from external orbitals into a renormalized one-body operator, yielding an effective active-space Hamiltonian that retains the same operator structure as the bare Hamiltonian and therefore requires no additional quantum circuit resources. SQD is then applied to this effective Hamiltonian, where, in this work, the quantum sampling is performed via the Qiskit Aer simulator rather than actual quantum hardware. We benchmark OBDF-SQD on dissociation curves of H6 chain, ring, and lattice systems and LiH, HF molecules in the cc-pVDZ basis, comparing against standard methods and active-space SQD (CAS-SQD). We observed that OBDF-SQD consistently improves upon CAS-SQD with the same active space. The simplicity of the one-body downfolding correction also makes the approach straightforwardly extensible to periodic solids within existing quantum embedding frameworks.

Keywords: Quantum Simulation, OBMP2, Quantum Downfolding, SQD.

BRIDGING QUANTUM CHEMISTRY AND SECONDARY EDUCATION THROUGH FRONTIER MOLECULAR ORBITAL THEORY

Anh H. Nguyen¹, Huy D. Pham², and Lam H. Nguyen³,*

¹. Faculty of Chemical Engineering, Ho Chi Minh City University of Technology (HCMUT), Ho Chi Minh City, 700000, Vietnam

². School of Medicine, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, 700000, Vietnam.

³. National Cheng Kung University, Tainan City, 701, Taiwan

Frontier Molecular Orbital (FMO) theory, grounded in quantum chemical principles, offers an intuitive framework for rationalizing organic reactivity through HOMO–LUMO interactions. Despite its theoretical rigor, FMO reasoning remains officially absent from pre-university curricula such as A-Level, IB, and specialized programs for gifted Vietnamese students, where students are often expected to reproduce S_N1 and S_N2 mechanisms through memorization rather than genuine mechanistic understanding. A survey of 138 Vietnamese high-school students from 28 schools, primarily in Ho Chi Minh City, confirmed this educational gap: approximately 70% perceived chemistry as difficult, 55% relied on rote memorization of reaction mechanisms, and nearly 60% found organic chemistry more challenging than inorganic chemistry. This study presents a five-period FMO instructional module designed to bridge this gap through a coherent progression from atomic orbitals to molecular orbitals, frontier molecular orbitals, and finally reaction mechanisms (AO → MO → FMO → Mechanism). The module enables students to rationalize nucleophilic attack through HOMO donation into the substrate LUMO, particularly the s antibonding orbital of the carbon–leaving group bond, and to distinguish between S_N1 and S_N2 pathways based on orbital interactions. Complementing this framework, we propose an interactive web-based learning tool, Chem-FMO, which allows students to visualize simplified molecular orbital diagrams and use HOMO–LUMO interactions to predict substitution pathways from simplified molecular structures. A pilot implementation involving ten Vietnamese high-school students demonstrated improved mechanistic reasoning and reduced reliance on memorization, supporting the feasibility of introducing quantum-based chemical reasoning at the pre-university level. More broadly, this work may contribute to increasing students’ awareness of quantum science and fostering early engagement with one of the most rapidly advancing scientific fields, especially Vietnamese students.

Keywords: frontier molecular orbital theory; HOMO–LUMO interaction; S_N1/S_N2 mechanisms; quantum chemistry education; web-based learning; computational modeling

Synthesis, crystal structure, DFT/TD-DFT calculations, anticancer activity, and molecular docking studies of Cu(I) and Zn(II) complexes containing 6-methoxy-4-(4-methoxyphenyl)-2-(pyridin-2-yl)quinoline

Phuc Viet Tran¹, Kim Ngoc Huynh¹, Bao The Nguyen¹, Hoai Thu Phung¹, Anh Nguyet Nguyen¹, Hai Hong Thi Le^1,2, Hue Minh Thi Nguyen^1,2,*.

 ¹Faculty of Chemistry, Hanoi National University of Education, Hanoi, Vietnam

²Institute of Natural Sciences, Hanoi National University of Education, Hanoi, Vietnam.

Corresponding author: hue.nguyen@hnue.edu.vn

 ABSTRACT

The reaction of 6-methoxy-4-(4-methoxyphenyl)-2-(pyridin-2-yl)quinoline (PQ) and O^O/PPh₃ ligands with Cu(I) and Zn(II) ions yielded three Cu(I) complexes with the formula [CuX(PQ)(PPh₃)] (X = Cl, Br, I) and two Zn(II) complexes with the formula [Zn(PQ)(O^O)]NO₃. The structures of the complexes were characterized by ESI-MS, ¹H NMR, and SC-XRD. All Cu(I) complexes exhibited potent anticancer activity, among which [CuBr(PQ)(PPh₃)] (Cu2) showed the highest efficacy against all four tested cell lines with IC₅₀ values < 7 µM, while demonstrating the best interaction energy against ERα and Cathepsin D proteins. Furthermore, complex [CuCl(PQ)(PPh₃)] (Cu1) demonstrated better inhibitory activity against KB and MCF7 cell lines compared to cisplatin, along with lower cytotoxicity toward normal cells with SI values > 2.7. DFT/TD-DFT calculations were carried out to investigate the electronic structures and photophysical properties of the compounds, yielding results in good agreement with the experimental findings. Additionally, molecular docking simulations were utilized to investigate the binding modes and interactions of the Cu(I) and Zn(II) complexes with the proteins, as well as to successfully predict the binding energies of derivatives bearing newly designed functional groups (–NEt₂, –CN, –NO₂), effectively guiding future experimental optimization.

KEYWORDS: 2-(pyridin-2-yl)quinoline, Cu(I) and Zn(II) complexes, anticancer activity, protein interaction.

Aromaticity Recovery: A Central Mechanism in the Radical Reactivity of Naphthoquinone Derivatives

Nguyen Thi My Hao^1,2, Phung Ngoc Thanh², Le Nguyen Ai Nhan¹, Ho Yen Nguyen¹, Pham Cam Nam^1,2

¹Faculty of Chemical Engineering, The University of Da Nang – University of Science and Technology, 550000 Da Nang, Viet Nam (K23KTHH2)

² Strategic Materials & Advanced Research Team – DUT (SMART-DUT), The University of Danang- University of Science and Technology, Danang 550000, Viet Nam

Email: haonguyenthi.2005@gmail.com

Abstract

This study employs density functional theory (DFT) at the M06-2X/6-311++G(d,p) level, incorporating the SMD solvation model, to elucidate the radical-scavenging mechanisms of 5-hydroxy-1,4-naphthoquinone (HXNQ) derivatives toward hydroxyl radicals (HO^•). By analyzing the competing pathways of single-electron transfer (SET), radical adduct formation (RAF), and hydrogen atom transfer (HAT), we demonstrate that environmental polarity significantly modulates the intrinsic energetics of the scaffold. In condensed media, the stabilization of ionic intermediates lowers ionization energies and enhances electron affinities, thereby favoring SET processes. Our findings reveal that RAF at the C2=C3 bond is the kinetically and thermodynamically dominant pathway. This reaction exhibits nearly barrierless activation energies and marked exothermicity, driven by the structural relaxation of the quinoid framework toward an aromatic transition state. In contrast, the HAT pathway is kinetically hindered by the stable O5–H···O4 intramolecular hydrogen bond, which locks the derivative in a cis conformation; successful abstraction requires an energetically demanding cis–trans isomerization. These mechanistic preferences are corroborated by harmonic oscillator model of aromaticity (HOMA) indices. Increased HOMA values for Ring A correlate with reduced bond-length alternation, facilitating RAF by minimizing structural distortion. Collectively, these results establish that ground-state aromaticity descriptors serve as both a reliable and computationally efficient framework for predicting the radical-scavenging reactivity of naphthoquinone-based antioxidants.

SOLVENT EFFECTS ON THE FLUORESCENCE SPECTRA OF  1,4-NAPHTHOQUINONE DERIVATIVES AND 1-STYRYLNAPHTHALENE

 Ho Nguyen Da Thao^1,2, Tran Thi Kim Nguyen^1,2, Nguyen Tran Thao Ngan^1,2, Pham Ngoc Chau^1,2, Pham Cam Nam^1,2

¹ Faculty of Chemical Engineering, The University of Da Nang – University of Science and Technology, 550000 Da Nang, Viet Nam

² Strategic Materials & Advanced Research Team – DUT (SMART-DUT), The University of Danang- University of Science and Technology, Danang 550000, Viet Nam

Email: dathaohonguyen91.1712005@gmail.com & kimnguyen11052005@gmail.com

 Abstract

 This paper investigates the effect of solvent viscosity on the molecular structure, optical properties, and electronic transitions of 1,4-naphthoquinone and 1-styrylnaphthalene derivatives, a viscosity-sensitive fluorescent substance with potential as a sensor for monitoring metal toxicity in plants. By combining chemical bonding theory, thermodynamics, and spectroscopy with DFT and TD-DFT calculations, the research group analyzed the molecular structure and UV-Vis absorption spectra and clarified the mechanism of solvent viscosity’s influence on HOMO-LUMO electronic transitions. The calculated results establish a correlation between viscosity and fluorescence performance, and guiding the design of viscosity sensors.

Keywords: 1,4-naphthoquinone, 1-styrylnaphthalein, fluorescence, viscosity, DFT, TD-DFT, sensor.

Zn@LOFs: A POTENTIALLY MULTIFUNCTIONAL PLATFORM FOR SINGLE-ATOM CATALYSIS AND CHARGE TRANSPORT

Lam H. Nguyen^1,* and Thanh N. Truong^2,*

^1.Department of Chemistry, National Cheng Kung University, Tainan, Taiwan

^2.Department of Chemistry, University of Utah, Salt Lake, Utah, USA

Abstract

Lantern Organic Frameworks (LOFs) are a recently developed class of porous organic materials computationally constructed through the covalent stacking of circulene-based building blocks, offering tunable pore architectures, structural robustness, and controllable electronic properties. Building upon the evolution of one-dimensional and three-dimensional LOF architectures, this study investigates their potential as hosts for isolated zinc atoms and zinc chains toward single-atom catalysis and molecular electronics.

Density functional theory calculations at the B3LYP-D3 level (LANL2DZ for Zn and 6-31+G(d) for nonmetal atoms) reveal a distinct structural dichotomy between sp- and sp³-bridged frameworks. While flexible sp³-LOFs preferentially stabilize endo-configurations, sp-LOFs create a kinetic trap that enables experimentally accessible exo-configurations and suppresses Zn–Zn agglomeration. Incorporation of Zn atoms further enables electronic tuning of the framework. Endo-Znₙ@sp-LOFs exhibit substantial HOMO–LUMO gap narrowing through metal–ligand p-conjugation, whereas the corresponding endo-Znₙ@sp³-LOF systems show only minor electronic perturbation. Electron transport analysis based on Yoshizawa’s orbital rules predicts that framework-confined Zn chains maintain appreciable conductance (10⁻²–10⁻³ G₀), demonstrating efficient charge transport despite confinement within the porous scaffold. In addition, adsorption calculations indicate stronger interactions with CO₂ than CO, with adsorption strength dependent on both framework topology and Zn location.

These results establish Zn@LOFs as multifunctional platforms that combine single-atom stabilization, tunable electronic properties, molecular charge transport, and selective gas adsorption, highlighting their potential for future catalytic and energy-related applications.

Keywords: Lantern Organic Frameworks (LOFs); Single-Atom Catalysts; Metal–Organic Confinement; Electronic Structure Engineering; Gas Adsorption

Investigation of free radical scavenging activity of pyridine derivatives containing hydroxyl and amino functional groups: experimental and quantum chemical approaches

Phan Nu Thao Van¹, Le Nu Ngoc Linh¹, Nguyen Hong Khanh Linh¹, Dinh Quy Huong¹

¹Department of Chemistry, University of Education, Hue University, Hue, Vietnam.
E-mail: dinhquyhuong@dhsphue.edu.vn, dqhuong@hueuni.edu.vn

Abstract

The free radical scavenging activities of three pyridine derivatives-isoniazid (ID), nicotinamide (NE), and pyridoxine (PE)-were evaluated using a combined theoretical and experimental approach. Density functional theory calculations were employed to optimize molecular geometries at the M06-2X/6-311++G(d,p) level, assess key thermodynamic parameters, and investigate antioxidant mechanisms, including hydrogen atom transfer (HAT), radical adduct formation (RAF), and single electron transfer (SET), in reactions with the hydroperoxyl radical (HOO^•). Theoretical results indicated that HAT was the dominant mechanism for ID and PE, while NE favored the RAF pathway. Among the studied compounds, ID exhibited the highest reactivity toward HOO^•, with calculated rate constants of 3.55 × 10⁵ M⁻¹ s⁻¹ in the gas phase and 6.48 × 10⁶ M⁻¹ s⁻¹ in aqueous solution. Experimental antioxidant assessments using DPPH^• and ABTS^•+ assays further supported these findings. ID demonstrated the strongest radical scavenging activity, with IC₅₀ values of 7.50 × 10⁻⁶ M (DPPH^•) and 1.60 × 10⁻⁵ M (ABTS^•+), followed by PE with moderate activity, while NE showed the weakest performance and was inactive against ABTS^•+. These results identified ID as the most potent antioxidant among the compounds studied.

High Selectivity of Dipeptidyl Peptidase 4 Receptor Towards 13 Aromatic Compounds in Cinnamomi ramulus Extract: Molecular Docking and Molecular Dynamics

Vo Van On*, Ho Anh Kiet, Nguyen Thi Thanh Thao, Nguyen Thi Lien Thuong*

Institute of Innovation in Pharmaceutical and HealthCare Food, Thu Dau Mot University, Ho Chi Minh City

Correspondence: onvv@tdmu.edu.vn

Abstract
Dipeptidyl peptidase 4 (DPP4) plays a pivotal role in the treatment of type 2 diabetes as an important glucose-regulating enzyme. We evaluated the molecular interactions between 13 major aromatic compounds from Cinnamomi ramulus and DPP4 enzyme through molecular docking simulation and molecular dynamics. The results showed that the studied compounds exhibited a wide range of docking energies with DPP4, in which benzyl benzoate was the most promising compound with a docking energy of -7.4 kcal/mol, which was comparable with that of saxagliptin and alogliptin. Detailed analysis revealed
that hydrophobic interactions (three–eight interactions/complex) and hydrogen bonds (three–five bonds in some complexes) played major roles in stabilizing the complexes. Molecular dynamics simulation results demonstrated ligand selectivity for the DPP4 receptor, with only four out of 13 tested compounds stabilizing at the interaction site. Evaluation results of the method using Lipinski’s rule showed that all compounds met four–five criteria for drug-likeness, indicating potential for drug development. These results provide the first scientific evidence of the potential molecular mechanism of cinnamon bark in the treatment of type 2 diabetes through DPP4 inhibition.

Keywords: Cinnamomi ramulus; dipeptidyl peptidase 4; molecular docking; molecular
dynamics simulation; Lipinski’s Rule of Five; diabetes mellitus type 2

Size-dependent superhalogenicity and ring currents of tantalum doped platinum clusters TaPt_n-1^-/0 (n = 2-21)

Bao-Ngan Nguyen-Ha,^1,2 Quang Huy Ho,³ My Phuong Pham-Ho,^4,5 Nguyen Minh Tam,^6,7*

¹ Laboratory for Chemical Computation and Modeling, Institute for Computational Science and Artificial Intelligence, Van Lang University, Ho Chi Minh City, Vietnam

² Faculty of Applied Technology, Van Lang School of Technology, Van Lang University, Ho Chi Minh City, Vietnam. Email: ngan.nguyenhabao@vlu.edu.vn

³ Faculty of Engineering Technology, University of Phan Thiet, 225 Nguyen Thong, Phu Thuy, Lam Dong, Vietnam

⁴ Faculty of Chemical Engineering, Ho Chi Minh City University of Technology (HCMUT), 268 Ly Thuong Kiet Street, Dien Hong Ward, Ho Chi Minh City, Vietnam

⁵ Vietnam National University Ho Chi Minh City, Linh Xuan Ward, Ho Chi Minh City, Vietnam

⁶ Faculty of Basic Sciences, University of Phan Thiet, 225 Nguyen Thong, Phu Thuy, Lam Dong, Vietnam. Email: nmtam@upt.edu.vn

⁷ Interdisciplinary Research Transfer and Innovation Center, University of Phan Thiet, 225 Nguyen Thong, Phu Thuy, Lam Dong, Vietnam

Abstract

The anionic and neutral TaPt_n-1^⁻/0 clusters, with n = 3-21, are systematically investigated using density functional theory (B3PW91/def2-TZVP). Their structural evolution is rationalized by four representative building units, TaPt₃^⁻/0, TaPt₇^⁻/0, TaPt₁₃^⁻/0 and Ta@Pt₁₈^⁻/0, corresponding to triangular, near triangular-pyramidal, basket-like and bipyramidal structures, respectively. The Ta dopant preferentially occupies a near-central site to maximize coordination and Ta–Pt bonding. An exohedral-to-endohedral transition occurs at n = 19, with full encapsulation established from Ta@Pt₁₈^⁻/0 onward. Ta doping markedly increases binding energies relative to pure Pt_n^⁻/0 clusters, with the anionic series generally being more stable. Pronounced electron affinity values in the range of ~3.0–3.4 eV, are obtained for TaPt₃, TaPt₇, TaPt₁₃ and Ta@Pt₁₈, indicating a quasi-superhalogen character of these magic sizes. Charge redistribution is strongly geometry-dependent, shifting from Ta→Pt donation in the exohedral TaPt₃^– to increasingly important Pt→Ta donation as the framework grows and Ta occupies an endohedral position in the TaPt₇^–, TaPt₁₃^– and Ta@Pt₁₈^–. Extensive multicenter electron delocalization consistent with coherent ring currents in TaPt₁₃^–, confirming active Ta participation in the coherent electronic motion.

Keywords: platinum clusters, nanoclusters, transition metal clusters, high magnetic moments, aromaticity.

Acknowledgement:

BNNH and MTN are grateful to Van Lang University. PHMP acknowledges Ho Chi Minh City University of Technology (HCMUT), VNU-HCM for supporting this study.

INVESTIGATION INTO THE ELECTRONIC ABSORPTION SPECTRAL VARIATIONS OF 5-HYDROXY-2-X-1,4-NAPHTHOQUINONE COMPLEXES: THE ROLES OF METAL IONS AND X-SUBSTITUENTS

Bui Hoang Vinh, Nguyen Van Gia Bao, Nguyen Anh Dung, Pham Cam Nam ^1,2

¹ Faculty of Chemical Engineering (23KTHH1&2), The University of Da Nang – University of Science and Technology, 550000 Da Nang, Viet Nam

² Strategic Materials & Advanced Research Team – DUT (SMART-DUT), The University of Danang- University of Science and Technology, Danang 550000, Viet Nam

Email: giabaonguyenvan102@gmail.com

Abstract

The study focuses on evaluating the variations in the electronic absorption spectra of 5-hydroxy-2-X-1,4-naphthoquinone derivatives complexed with three characteristic transition metal ions: Cu(II)), Zn(II), and Hg(II), with 1,4-naphthoquinone derivatives as a representative model, through advanced computational modeling. The computational calculations were utilized to optimize the molecular structures of the ligands and their complexes in ethanol solvent. Intrinsically, naturally derived naphthoquinone derivatives exhibit potent biological activities, including antimicrobial, anti-inflammatory, and notably antitumor capabilities via redox cycles. To overcome limitations such as poor solubility and non-specific toxicity, a strategy of diversifying the X-substituent at the C2 position combined with transition metal coordination was implemented to enhance pharmacokinetics and achieve biological synergistic effects. Simulations of UV-Vis spectra via the TD-DFT method, integrated with the analysis of electronic transitions, HOMO-LUMO energy gaps, and electron density on Frontier Molecular Orbitals (FMO), elucidate the Chelation-Enhanced Fluorescence (CHEF) effect of the Zn(II) ion as well as the fluorescence quenching phenomena in Cu(II) and Hg(II) systems. Consequently, this research provides a critical foundation for predicting the stability and optical characteristics of these complex systems in diverse environments.

Keyword: 5-hydroxy-1,4-naphthoquinone, Plumbagin, TD-DFT, CHEF, HOMO-LUMO.

Molecular Dynamics Simulation of Conformational Shifts in Human Serotonin Reuptake Transporter Induced by Venlafaxine and Its Metabolites

Thinh T. Q. Le,^1,2 Tho H. Ho,^1,2 Trang T. Nguyen,^1,2 Lam K. Huynh^1,2,*

¹ Vietnam National University, Ho Chi Minh City, Linh Xuan Ward, Ho Chi Minh City, Vietnam.

² International University, Quarter 33, Linh Xuan Ward, Ho Chi Minh City, Vietnam.

* Corresponding author: hklam@hcmiu.edu.vn

The human serotonin reuptake transporter (hSERT) is a crucial membrane-embedded protein that regulates synaptic serotonin levels by transitioning through a complex conformational cycle—moving from an outward-facing state to an occluded state, and finally to an inward-facing state. This cycle is driven primarily by structural shifts in the transmembrane 1 (TM1) and TM6 domains. Therapeutic agents such as the antidepressant venlafaxine (VLX) and its active metabolites O-desmethylvenlafaxine (ODV), N-desmethylvenlafaxine (NDV), and N,O-desmethylvenlafaxine (NNV) modulate hSERT function by inhibiting this transport mechanism. However, the precise molecular dynamics and energetic bases underlying these interactions remain poorly understood. In this study, we employed all-atom molecular dynamics (MD) simulations to investigate the time-dependent conformational changes, binding dynamics, and energetic profiles of serotonin (SRO), VLX, and its three metabolites within hSERT embedded in a POPC lipid bilayer. Following complex optimization, solvation, and ionization using the CHARMM force field, systems underwent energy minimization, equilibration, and production runs to evaluate structural fluctuations, residue-specific binding profiles, and free energy components.The simulations revealed that while the main transmembrane helices (TM1 and TM6) maintained structural stability during ligand binding, notable flexibility and fluctuations occurred within the beta-sheet region (residues 200–220), suggesting this domain plays a dynamic role in facilitating ligand-induced conformational changes. Binding free energy analysis ( ) highlighted Asp98 in TM1 as a critical, consistent anchor across all studied ligands, exhibiting profound stabilizing binding energies -51.61 kcal/mol for SRO, -46.22 kcal/mol for NDV, -34.04 kcal/mol for VLX, and -33.73 kcal/mol for ODV). Furthermore, Ser336 in TM6 contributed significantly to stabilizing the substrate (-10.44 kcal/mol for SRO), underscoring a cooperative mechanism between TM1 and TM6. Among the examined derivatives, NDV demonstrated the strongest overall binding energy (  = -26.54 ± 2.67 kcal/mol) and consistent structural stabilization effects. Together, these findings elucidate the molecular basis of hSERT inhibition by venlafaxine derivatives and emphasize the pivotal role of specific transmembrane anchors and regional flexibility in driving transporter conformational shifts.

Keywords: Human serotonin reuptake transporter; Venlafaxine; O-desmethylvenlafaxine; Molecular dynamics (MD) simulation.

New materials for Sodium-ion Battery Cathode by Generative Artificial Intelligence (GenAI) and First-principles Simulations

Do Dang Minh^a, Huu Doanh Nguyen^b, Que Chi Chau^b, Pham Tien Lam^c, Phi Long Nguyen^d,e, Kostya S. Novoselov^f, Laurent El Ghaoui^b,d,g, Phuong Nam Le Pham^b,d,*, Viet Bac T. Phung^b,d,*

^a Center for Materials Innovation and Technology (CMIT), VinUniversity, Vietnam;

^b College of Engineering and Computer Science, VinUniversity, Vietnam;        

^c Phenikaa University, Vietnam;

^d Center of Environmental Intelligence (CEI), VinUniversity, Vietnam;

^e School of Electrical and Electronic Engineering, Hanoi University of Industry, Vietnam;

^f Institute for Functional Intelligent Materials, National University of Singapore, Singapore;

^gBerkeley Artificial Intelligence Research and Department of Electrical Engineering and Computer Sciences, UC Berkeley, USA

^*Corresponding author: nam.lpp@vinuni.edu.vn, bac.ptv@vinuni.edu.vn

Abstract

Discovering new high-performance cathode materials for sodium-ion batteries (SIBs) remains challenging because conventional trial-and-error experiments are both time-consuming and costly. In this work, we present an integrated GenAI-ML-DFT workflow for the inverse design of novel Na-Cr-X-O cathodes, aiming to identify new structures with improved properties relative to NaCrO₂. Candidate crystal structures were first generated using MatterGen and then pre-relaxed with the M3GNet potential to obtain realistic, low-cost structural approximations. Candidates satisfying the energy-above-hull criterion were further screened using ChemEnv to ensure chemically plausible local coordination environments. FINDSYM analysis indicated that the screened candidates span diverse crystal frameworks beyond the conventional layered NaCrO₂-type structure. First-principles calculations confirmed that the shortlisted compounds possess negative formation energies and exhibit distinct redox behaviors associated with different structural motifs. These results demonstrate that the proposed workflow can efficiently expand the design space of SIB cathodes and provide a general strategy for accelerated materials discovery in complex inorganic systems.

Push–Pull Activation of CO₂ and C–O Bond Cleavage by Lewis Acid-Assisted [M(depe)₂] Complexes (M = Mn, Fe, and Co): A DFT Study

Phan Huynh Ngoc Anh¹, Dang Bao Ngoc¹, Nguyen Thi Hong Nhung¹,  Mai Van Bay¹, Nguyen Minh Thong^1,*

¹The University of Danang – University of Science and Education, Danang 550000, Vietnam.

*Corresponding authors: nmthong@ued.udn.vn

Abstract:

Developing efficient catalytic platforms for carbon dioxide activation remains a major challenge because of the high thermodynamic stability and kinetic inertness of CO₂. In this study, density functional theory calculations were employed to investigate the cooperative activation of CO₂ by electron-rich first-row transition-metal phosphine complexes and Lewis acids. The examined systems comprise [M(depe)₂]-CO₂-BX₃ adducts, where M = Mn, Fe, or Co; depe = 1,2-bis(diethylphosphino)ethane; and X = F, Cl, or Br. Geometry optimizations, vibrational-frequency calculations, charge analyses, frontier molecular orbital analyses, Wiberg bond indices, potential-energy profiles, transition-state searches, and intrinsic reaction coordinate calculations were used to evaluate CO₂ binding, structural distortion, electronic activation, and C-O bond cleavage.

In the absence of Lewis acids, the Mn and Fe complexes activate CO₂ more effectively than the Co analogue, as indicated by stronger CO₂ binding energies, greater O-C-O bending, and more pronounced C-O bond elongation. The addition of BX₃ induces a cooperative push-pull mechanism: the electron-rich metal center transfers electron density toward CO₂, whereas the Lewis acid interacts with one oxygen atom and enhances C-O bond polarization. The stabilization of the activated adducts increases in the order BF₃ < BCl₃ < BBr₃. Among the investigated systems, [Fe(depe)₂]-CO₂-BBr₃ exhibits the strongest weakening of the C-O bond, with a 21.2% bond elongation, a Wiberg bond index of 0.8292, and a binding energy of -72.1 kcal/mol. Meanwhile, [Mn(depe)₂]-CO₂-BBr₃ produces the largest CO₂ bending distortion and substantial charge transfer. Potential-energy and intrinsic reaction coordinate analyses further identify the Mn-BBr₃ and Fe–BBr₃ combinations as the most promising systems for promoting C-O bond cleavage. These findings provide molecular level design principles for Lewis acid-assisted activation and subsequent conversion of CO₂ using earth-abundant transition metals.

Keywords: CO₂ activation; Lewis acid; transition-metal phosphine complex; density functional theory; C–O bond cleavage; push-pull mechanism.

Design of New Fluorinated Chalcone Derivatives for the Treatment of Alzheimer’s Disease: A Combined Theoretical and Experimental Study

Tuan Chi Vu^1,2, Dang Son Mai Hoang ², Vu Bang Tran Do ³ , Hue Nguyen Van¹, Minh Luong Truong¹ and Hue Nguyen Thi Minh¹*,

¹Faculty of Chemistry, Hanoi National University of Education; ²Lam Son Gifted High School, ³British Vietnamese International School

Abstract

The inhibition of the acetylcholinesterase (AChE) enzyme is a crucial strategy in the symptomatic treatment of Alzheimer’s disease. In this study, we designed, theoretically evaluated, and synthesized 12 novel compounds based on a chalcone scaffold. For the computational investigation, the molecular structures were optimized using Gaussian software utilizing the density functional theory (DFT) method with the 6-311G(d) basis set. These optimized geometries were subsequently subjected to molecular docking and 200 ns molecular dynamics (MD) simulations using AutoDock Vina and GROMACS, respectively. The theoretical results demonstrated that all 12 compounds exhibited strong binding energies (ΔG < -9.0 kcal/mol) and maintained complex stability (RMSD < 0.3 nm), forming crucial interactions with key amino acid residues such as TRP86, TRP286, and PHE295. Experimental bioassays revealed that compounds FC3Bn, FC3, and FC3F exhibited the most potent AChE inhibitory activities, with small IC50 values of 5.12 ± 0.22 μg/mL, 7.58 ± 0.41 μg/mL, and 8.32 ± 0.26 μg/mL, respectively.

From Unstable B₇Si₃⁺ to Stable Li₃B₇Si₃: Reduced Electron Delocalization as the Key to Thermodynamic Stability

The structural and electronic properties of the B₇Si₃^3- and Li₃B₇Si₃ clusters were investigated through extensive isomer searches and quantum chemical analyses. Although B₇Si₃^3- exhibits significant σ-electron delocalization, it is thermodynamically unfavorable due to excessive electron delocalization within the cluster framework. In contrast, incorporation of three lithium atoms transforms the unstable B₇Si₃^3- cluster into a highly stable Li₃B₇Si₃ species. Detailed bonding analyses using AdNDP, ELF, and ETS–NOCV methods reveal that Li incorporation reduces excessive σ-delocalization while enhancing favorable edge-localized electron interactions. These electronic rearrangements provide the key stabilization mechanism for the Li₃B₇Si₃ cluster, highlighting the critical role of controlled electron delocalization in designing stable planar aromatic clusters.

Study on the collision-induced dissociation process of sodiated aldohexoses

Hai Thi Huynh¹, Pei-Kang Tsou², Cheng-chau Chiu^3,4 and Jer-Lai Kuo^5,6

¹Department of Engineering Physics, HCM City University of Technology and Engineering

²Department of Chemistry, The Scripps Research Institute

³Green Hydrogen Research Center, National Sun Yat-sen University

⁴Center for Theoretical and Computational Physics, National Sun Yat-sen University

⁵Institute of Atomic and Molecular Sciences, Academia Sinica

⁶Department of Chemistry, National Tsing Hua University

Understanding the dissociation pattern of saccharides is key to establishing mass spectrometry-based methods as routine methods for identifying oligosaccharides. To fully resolve this collision-induced dissociation (CID) process, a fundamental study on the CID mechanisms of monosaccharides is essential. However, exploring these mechanisms by using density functional theory (DFT) is highly challenging due to the to the high structural diversity of monosaccharides.

In this work, to systematically search for transition states (TS) across a vast conformer space, we proposed a three-step search scheme assisted by neural network potentials (NNP), to accelerate the computational process and enable an exhaustive exploration of low-lying channels. The obtained low-lying TSs were re-optimized at the MP2/6-311+G(d,p) level of theory and then utilized to set up a microkinetic model for simulating the CID mass spectrometry of sodiated aldohexoses (glucose, mannose, and galactose). By incorporating various linear temperature gradients to mimic experimental collision-mediated activation, the simulated product concentrations enable a direct comparison with experimental mass spectra, facilitating routine oligosaccharide identification.

Multifunctional Roles of Natural Aaptodine in Alzheimer’s Disease: DFT and MD Studies

Thi Chinh Ngo^1,2,*, Hoang Linh Nguyen^2,3,*, Dinh Hieu Truong^1,2, Thi Le Anh Nguyen^1,2, Thai Quoc Nguyen⁴, Mai Suan Li⁵, Duy Quang Dao^1,2

¹Institute of Research and Development, Duy Tan University, Da Nang, 550000, Viet Nam

² School of Engineering and Technology, Duy Tan University, Da Nang, 550000, Viet Nam

³ Institute of Fundamental and Applied Sciences, Duy Tan University, Ho Chi Minh City, 700000, Vietnam

⁴Dong Thap University, 783 Pham Huu Lau Street, Ward 6, Cao Lanh City, Dong Thap

⁵Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, Warsaw 02-668, Poland

Email: ngothichinh@duytan.edu.vn;  nguyenhoanglinh9@duytan.edu.vn

In this study, we investigate the multifunctional potential of aaptodine A in preventing oxidative stress and inhibiting amyloid-beta (Aβ) aggregation, two important pathological factors associated with Alzheimer’s disease (AD). We used Density Functional Theory (DFT) calculations with the M06-2X and M06 functionals to assess its radical-scavenging ability against hydroxyl radicals (HO^•) and hydroperoxyl radicals (HOO^•), as well as its chelation properties with Fe³⁺ and Cu²⁺ ions. Additionally, we performed molecular docking and Molecular Dynamics (MD) simulations to evaluate its inhibitory effects on Aβ aggregation. The results indicate that aaptodine A is highly effective at scavenging HO^• radicals, with a rate constant of 1.69 × 10¹⁰ M⁻¹ s⁻¹, although it exhibits limited activity against HOO^• radicals. The compound also exhibits strong metal-chelating properties, particularly toward Cu2+, forming stable complexes with both Cu²⁺ and Fe³⁺ ions upon coordination by two ligand molecules. These interactions may help reduce metal-induced reactive oxygen species generation and mitigate Cu²⁺-mediated neurotoxicity related to Aβ pathology in AD.

Furthermore, analyses using MM/PBSA and accelerated weight histogram (AWH) methods reveal that aaptodine A has a high binding affinity for Aβ42 fibrils, comparable to that of curcumin, a well-known inhibitor of Aβ fibril and oligomer formation. AWH simulations involving the Aβ tetramer further demonstrate that aaptodine A can effectively interact with both toxic oligomeric intermediates and mature fibrillar structures. Overall, these findings suggest that aaptodine A may serve as a promising multifunctional agent against Alzheimer’s disease by exerting antioxidant effects through secondary mechanisms and suppressing the formation and stability of toxic Aβ aggregates.

Advances in One-Body Møller–Plesset Perturbation Theory: Theory and Applications

Nhan Tri Tran,^1,2 Lan Nguyen Tran^3,4,*

¹Simulation in Materials Science Research Group, Science and Technology Advanced Institute, Van Lang University, Ho Chi Minh City, Vietnam

²Faculty of Applied Technology, Van Lang School of Technology, Van Lang University, Ho Chi Minh City, Vietnam

³University of Science, Vietnam National University, Ho Chi Minh City 700000, Vietnam

⁴Vietnam National University, Ho Chi Minh City 70000, Vietnam

Abstract

Developing accurate yet computationally efficient quantum chemical methods remains a central challenge in theoretical chemistry. We present recent advances of the self-consistent one-body Møller–Plesset perturbation theory (OBMP2) and its spin-opposite-scaled variant (O2BMP2), which overcome key limitations of conventional MP2 through self-consistency and spin-opposite scaling of doubleexcitation amplitudes. The performance of these methods is demonstrated for a wide range of challenging problems, including bond dissociation, ionization potentials, charge-transfer excited states, and inverted singlet–triplet (INVEST) molecules. O2BMP2 consistently improves upon standard MP2 and achieves accuracies comparable to high-level coupled-cluster methods. For excited states, it outperforms methods of similar computational cost, such as CC2 and ADC(2), and can approach CC3 accuracy for challenging charge-transfer excitations. Benchmark calculations on 30 INVEST molecules further show that O2BMP2 reproduces ADC(3) and EOM-CCSD results with high fidelity. Combined with a computational scaling reducible to O(N^4), O2BMP2 offers an attractive balance between accuracy and efficiency, making it a promising tool for studying complex electronic structures and screening next-generation functional materials.

Keywords: OBMP2, O2BMP2, Self-consistent perturbation theory, Electron correlation, Chargetransfer excited states, INVEST molecules, Quantum chemistry.

THE ANTIOXIDANT EFFICIENCY OF TROLOX CONJUGATED WITH Au₂ CLUSTER: A COMPUTATIONAL INVESTIGATION

Nguyen-Thi Nhu-Y^1,2*, Phan Huu Nghia¹, Pham Vu Nhat^1*

¹Can Tho University; ²Can Tho University of Technology

*Correspondence: ntny@ctuet.edu.vn; nhat@ctu.edu.vn

ABSTRACT

Density functional theory (DFT) calculations were employed to investigate the effect of gold nanoparticles (AuNPs, modeled as Au₂ cluster) on the antioxidant capacity of trolox (H₂T) and its conjugate base (HT‾) in scavenging hydroperoxyl radicals (HOO^•) via the hydrogen atom transfer (HAT) mechanism. The antioxidant efficiency was characterized by bond dissociation enthalpy (BDE) and ionization energy (IE). The computed results demonstrate that assembling these species onto nanostructured gold surfaces significantly enhances their antioxidant activity, offering a superior alternative to chemical structure modification. These insights elucidate the enhancement mechanism and guide future antioxidant design.

Key words: Antioxidant, Au₂ cluster, DFT, trolox.

Oxidation of Metazachlor Herbicide by Sulfate Radical in Gas and Water: Mechanism, Kinetics, and Toxicity Evaluation

Dinh Hieu Truong,^1,2,3 Nguyen Thi Ai Nhung,⁴ Thi Chinh Ngo,^1,2 Thi Le Anh Nguyen,^1,2 Sonia Taamalli,⁵ Abderrahman El Bakali,⁵ Nissrin Alharzali,^6· Ivan Černušák,⁶ Florent Louis⁵ Duy Quang Dao^1,2,*

¹Institute of Research and Development, Duy Tan University, Da Nang 550000, Viet Nam.

²School of Engineering and Technology, Duy Tan University, Da Nang 550000, Viet Nam.

³University of Sciences, Hue University, Hue City 530000, Viet Nam.

⁴Department of Chemistry, University of Sciences, Hue University, Hue City 530000, Viet Nam.

⁵Univ. Lille, CNRS, UMR 8522, Physico-Chimie des Processus de Combustion et de l’Atmosphère, 590000 Lille, France.

⁶Department of Physical and Theoretical Chemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 84215 Bratislava, Slovakia.

*Corresponding: daoduyquang@duytan.edu.vn

ABSTRACT

In recent years, pesticide use has increased significantly due to their effectiveness in protecting crops from pests. This leads to several serious environmental problems that negatively impact ecosystems and human health. Metazchlor (MTZ) is a widely used herbicide for controlling annual grasses and broad-leaved weeds. Therefore, MTZ pesticide residues have been detected in many regions worldwide. This study investigated oxidation of MTZ initiated by sulfate radical anion (SO₄^●-) using density functional theory at the M06-2X/6-311++G(3df,3pd)//M06-2X/6-31+G(d,p) level of theory. Three mechanisms were considered: hydrogen abstraction (Abs), radical addition (Add), and single electron transfer (SET). All oxidation reactions were examined in the gas and water phases at temperatures ranging from 253 to 323 K and 283 to 323 K, respectively. The initial products would be reacted with common oxidizing agents and then tested for ecotoxicity using the ECOSAR (Ecological Structure–Activity Relationships) model[1] for aquatic organisms. As a result, the degradation of MTZ in both gas and water phases was favourable and spontaneous, with very high rate constants of 1.51 × 10¹³ and 4.50 × 10¹⁰ M^-1 s^-1, respectively. The gas-phase degradation was determined to be a selective process that occurred primarily via an Abs reaction at the H24 hydrogen atom belonging to the methyl group (C13). On the contrary, multiple Add and Abs pathways in water significantly contributed to oxidation, thereby making the process non-selective. These findings highlight the effectiveness of SO₄^●−-based advanced oxidation processes for MTZ removal in different environmental phases.

Keyword: Metazachlor, Sulfate radical anion, Advanced oxidation processes, AOPs, Pesticides

References

1. D. H. Truong, N. T. A. Nhung, S. Taamalli, A. El Bakali, N. Alharzali, I. Černušák, F. Louis and D. Q. Dao, Chem. Pap., 2025, 79, 8679–8700.

2         EPA | ECOSAR. 2022 Ecological Structure Activity Relationships (ECOSAR) Predictive Model | US EPA. V2.2.

Deciphering molecular insights of HDAC6 inhibition through SHAP-based interpretation of optimized machine learning models

ABSTRACT

Histone deacetylase 6 (HDAC6) is an important target for cancer treatment; however creating effective and selective inhibitors remains a considerable challenge. Machine learning (ML) can speed up drug discovery, though the interpretability of these models is limited. This study aimed to create optimized ML models to predict HDAC6 inhibitory activity, using SHapley Additive exPlanations (SHAP) to enhance interpretability. Bioactivity data (IC50 values) for HDAC6 inhibitors were curated from ChEMBL and BindingDB. All inhibitors were classified as active or inactive based on comparison to SAHA. Five ML algorithms (Decision Tree, Random Forest, SVM, XGBoost, AdaBoost) were trained using five different molecular fingerprints: MACCS Keys, Morgan2, ECFP2, ECFP4, ECFP6. Hyperparameter tuning was conducted to optimize model performance. The best-performing model, ECFP6-RF, achieved high predictive performance on the test set (Accuracy: 90.20%, Precision: 91.53%, AUC-ROC: 96.25%) while maintaining minimal overfitting (train-test gap < 8%). SHAP analysis of the ECFP6-RF model identified key structural features that strongly contributed to HDAC6 inhibition. Notably, fragments associated with the hydroxamic acid zinc-binding group and specific aliphatic/aromatic linkers were highlighted as highly influential, consistent with established structure-activity relationships (SAR). This work demonstrates the successful application of optimized ML models combined with explainable AI (XAI), providing interpretable insights into the molecular determinants of activity.

Effects of potentiators on ion translocation through the CFTR channel

Cystic fibrosis (CF) is one of the most common progressive, lethal genetic diseases among the Caucasian population. This disease is caused by mutations in the gene encoding for the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) protein, which is widely expressed on the surface of epithelial cells, where it transports chloride ions to the extracellular space. Despite the protein being present at the membrane, certain mutations impair channel gating, reducing chloride ion transport. To address the gating defect, a type of CFTR modulator called ‘potentiator’ has been developed to increase the ion flux of mutant CFTR by prolonging the opening of the channel. Currently, there are two potentiators, ivacaftor (VX-770) and GLPG1837, which have been captured in high-resolution cryo-EM structures bound to CFTR in conformations with some open-state features, showing that both occupy the same transmembrane binding site. However, the molecular mechanisms by which these potentiators modulate CFTR channel dynamics remain poorly understood, particularly in membrane environments resembling the epithelial cell membrane. In this study, we use molecular dynamics simulation to investigate how ivacaftor and GLPG1837 influence ion translocation through CFTR. Insights from this study can serve as a guideline to develop future therapeutics with improved pharmacological properties to maximally rescue mutant CFTR.

Quantum Chemistry Meets Food Safety: Ag-Au Clusters vs. Aflatoxin & Ochratoxin

Van Hong Nguyen¹, Thanh Truc Huynh², Nguyen Nguyen Pham Tran³

¹Faculty of Education, An Giang University, Vietnam National University Ho Chi Minh City

²Faculty of Engineering – Technology – Environment, An Giang University, Vietnam National University Ho Chi Minh City

³Faculty of Chemistry, University of Science, Vietnam National University Ho Chi Minh City

Email: nvhong@agu.edu.vn; ptnnguyen@hcmus.edu.vn

Abstract

This study investigates the interactions between Ag_nAu_(8-n) (n = 0–8) bimetallic clusters and two mycotoxins, Aflatoxin B1 (AFB1) and Ochratoxin A (OTA), using density functional theory (DFT) at the PBE/Def2-SVP level with D3BJ dispersion correction and SMD solvation model. All structures, including isolated toxins, clusters, and their complexes, were fully optimized and verified by frequency calculations to ensure stable configurations. The results show that both AFB1 and OTA preferentially adsorb via electron-rich oxygen sites, with adsorption behavior strongly dependent on cluster composition: Au-rich clusters favor stronger binding through enhanced electronic stabilization and effective σ-donation/π-backdonation, while Ag-rich clusters induce greater electronic perturbation and facilitate easier desorption, improving sensor reusability. Frontier molecular orbital and NBO analyses confirm significant charge transfer and orbital interactions consistent with the Dewar-Chatt-Duncanson mechanism, while PDOS results reveal strong hybridization at the metal-molecule interface. In addition, simulated Raman spectra demonstrate pronounced surface-enhanced Raman scattering (SERS) effects, with Ag-rich clusters providing stronger signal enhancement and Au contributing mainly to structural stability, indicating that Ag_nAu_(8-n) clusters are promising tunable materials for SERS-based detection of AFB1 and OTA in food safety applications.

Keywords: Bimetallic clusters; AFB1; OTA; DFT; SERS.

INVESTIGATION OF ANTIOXIDANT ACTIVITY AND REACTION KINETICS WITH HYDROXYL RADICAL OF 1,4-NAPHTHOQUINONE DERIVATIVES

Le Thi Dieu Ly^1,2, Nguyen Thi My Hao^1,2, Ho Nguyen Da Thao^1,2, Tran Thi Kim Nguyen^1,2, Pham Cam Nam^1,2

¹ Faculty of Chemical Engineering (23KTHH1&2), The University of Da Nang – University of Science and Technology, 550000 Da Nang, Viet Nam

² Strategic Materials & Advanced Research Team – DUT (SMART-DUT), The University of Danang- University of Science and Technology, Danang 550000, Viet Nam

Email: ledieulyy1105@gmail.com

    Abstract:

This study evaluates the antioxidant activity of 1,4-naphthoquinone derivatives, specifically plumbagin (PBL), using advanced computational chemistry models. By employing quantum calculations, we established a comprehensive thermodynamic dataset across three distinct environments: the gas phase, non-polar solvents, and polar solvents. Our results indicate that polar solvents, such as water, play a pivotal role in stabilizing ionic intermediates and lowering reaction energy barriers, thereby significantly enhancing reaction rates. Analysis of the potential energy surface (PES) elucidated the competition between the primary radical-scavenging mechanisms. We found that while Hydrogen Atom Transfer (HAT) and Radical Adduct Formation (RAF) occur spontaneously with high regioselectivity at the hydroxyl (–OH) and C-positions of the ring, respectively, the Single Electron Transfer (SET) mechanism remains thermodynamically unfavorable. Beyond direct radical scavenging, this study demonstrates the superior preventive antioxidant potential of PBL through the formation of stable chelate complexes with Cu²⁺ ions, effectively inhibiting the Fenton reaction and the subsequent generation of toxic hydroxyl radicals. Collectively, this work provides a crucial theoretical foundation for the rational design and optimization of next-generation naphthoquinone derivatives, emphasizing both efficacy and biomedical safety.

Keywords: Plumbagin; 1,4-naphthoquinone; DFT; Hydrogen Atom Transfer; Radical Adduct Formation; Chelate complexes.

Evaluating Protein Restraint Strategies in Steered Molecular Dynamics Simulations of Ligand Unbinding

Ho Anh Kiet¹

¹Atomic Molecular and Optical Physics Research Group, Science and Technology Advanced Institute, Van Lang University, Ho Chi Minh City, Vietnam

Abstract

To ensure that an external force can break the interaction between a protein and a ligand, the steered molecular dynamics simulation requires a harmonic restrained potential applied to the protein backbone. A usual practice is that all or a certain number of protein’s heavy atoms or Cα atoms are fixed, being restrained by a small force. This present study reveals that while fixing both either all heavy atoms and or all Cα atoms is not a good approach, while fixing a too small number of few atoms sometimes cannot prevent the protein from rotating under the influence of the bulk water layer, and the pulled molecule may smack into the wall of the active site. We found that restraining the Cα atoms under certain conditions is more relevant. Thus, we would propose an alternative solution in which only the Cα atoms of the protein at a distance larger than 1.2 nm from the ligand are restrained. A more flexible, but not too flexible, protein will be expected to lead to a more natural release of the ligand.

Keywords: Ligand affinities; Ligand release; Protein flexibility; Protein–ligand complexes; Restrain modes; Steered molecular dynamics simulations.

Nonconventional Hydrogen bonds and Stability of CHX₃-H₂Z Binary Complexes (X = F, Cl, Br; Z = O, S, Se, Te)

Nguyen Tien Trung, ^1,2* Dinh Viet Thang, ¹ Nguyen Ngoc Tri, ^1,2  Le Thi Kim Vuong,¹ Vu Thi Ngan,^1,2#

¹⁾Laboratory of Computational Chemistry and Modelling (LCCM), Quy Nhon University, 170 An Duong Vuong Street, Quy Nhon City 590000, Vietnam

²⁾Faculty of Natural Sciences, Quy Nhon University, 170 An Duong Vuong Street, Quy Nhon City 590000, Vietnam

Corresponding author’s email: nguyentientrung@qnu.edu.vn; vuthingan@qnu.edu.vn

Abstracts

This study presents a systematic investigation of the nature and stability of nonconventional hydrogen bonds in binary complexes formed between haloforms, CHX₃ (X = F, Cl, Br), and hydrogen chalcogenides, H₂Z (Z = O, S, Se, Te), considering three optimized structures denoted as XZ-A, XZ-B, and XZ-C. The XZ-A and XZ-B structures contain a dominant C–H···Z hydrogen bond together with auxiliary Z–H···X contacts, whereas the XZ-C structure is stabilized only by Z–H···X interactions. The XZ-A and XZ-B complexes are consistently more stable than XZ-C, demonstrating that C–H···Z provides the principal contribution to the stabilization of the cyclic structures, while Z–H···X plays a secondary role. The strength of C–H···Z generally increases from CHF₃ to CHCl₃ and CHBr₃, in accordance with the decrease in the C–H bond dissociation energy of the isolated haloforms. According to the AIM analysis, the local strength of C–H···Z decreases in the order O >> Se > S > Te, whereas the overall complex stability follows O >> S > Se > Te. SAPT2+ analysis shows that electrostatic interactions dominate the stabilization of the O-containing XZ-A and XZ-B complexes, while the contribution of dispersion becomes increasingly important for the S-, Se-, and Te-containing systems. In contrast, the XZ-C complexes are predominantly dispersion-controlled. The C–H stretching frequency is mainly blue-shifted in CHF₃ complexes and in O-containing systems, whereas progressively larger red shifts are observed for S-, Se-, and Te-containing complexes, particularly those involving CHCl₃ and CHBr₃. These results demonstrate that the local strength of a hydrogen bond, the overall stability of the complex, and the corresponding vibrational frequency shift do not necessarily vary in parallel, but arise from the combined effects of C–H bond polarity, electrostatic attraction, dispersion, and molecular polarizability.

New insight into environmental oxidation of phosmet insecticide initiated by HO^● radicals in gas and water – a theoretical study

Thi Yen Nhi Pham, ^ab Dinh Hieu Truong, ^ab Hisham K. Al Rawas,^c Reem Al Mawla,^c Thi Le Anh Nguyen,^ab Sonia Taamalli,^c Marc Ribaucour,^c Abderrahman El Bakali,^c Ivan Černušák,^cd Duy Quang Dao,^ab Florent Louis^c

^aInstitute of Research and Development, Duy Tan University, Da Nang, 550000, Vietnam

^bSchool of Engineering and Technology, Duy Tan University, Da Nang 550000, Vietnam

^cUniv. Lille, CNRS, UMR 8522, Physico-Chimie des Processus de Combustion et de l’Atmosphère – PC2A, 59000 Lille, France

^dDepartment of Physical and Theoretical Chemistry, Faculty of Natural Sciences, Comenius University in Bratislava, IlkoviČova 6, 84215 Bratislava, Slovakia

Abstract

Phosmet, an organophosphorus insecticide banned in the EU in 2022, lacks well-defined environmental degradation pathways. Its oxidation by HO• radicals was investigated using DFT at the M06-2X/6-311++G(3df,3pd)//M06-2X/6-31+G(d,p) level, considering formal hydrogen transfer (FHT), radical adduct formation (RAF), and single electron transfer (SET) in the gas and aqueous phases.

FHT dominates in the gas phase, while RAF prevails in the aqueous phase at 298 K; SET is negligible. Hydrogen abstraction from the methyl and methylene groups is most favorable, and HO• addition preferentially occurs at the phosphorus atom of the dithiophosphate group. Rate constants range from 1.20 × 10⁹ to 1.40 × 10⁹ M⁻¹ s⁻¹ (aqueous, 283–323 K) and decrease from 6.29 × 10¹⁰ at 253 K to 1.32 × 10¹⁰ M⁻¹ s⁻¹ at 323 K in the gas phase. The atmospheric lifetime is ~6 h at 287 K, while in aqueous systems, it varies from seconds to years depending on conditions.

QSAR analysis indicates that phosmet and its degradation products are toxic to aquatic organisms; although less toxic than the parent compound, the products remain developmental toxicants and are non-mutagenic.

Mechanistic Insights into the Antioxidant and Pro-Oxidant Behaviors of Uric Acid in the Presence of Cu(II)

Authors: Phan Huu Nghia¹, Pham Vu Nhat², Dang T. Nguyen³

¹ Department of Health of Sciences, Can Tho University

² Department of Chemistry, Can Tho University

³ Faculty of Applied Sciences, Ton Duc Thang University

Abstract: Uric acid (HUA) is the main antioxidant in human plasma. However, it can also promote oxidation in the presence of Cu(II) ions. This dual behavior is known as the uric acid paradox. This study utilizes density functional theory (DFT) to clarify the structural, thermodynamic, and kinetic properties of the Cu(II)-urate system. All complexes and reaction pathways were modeled at the B3LYP/6-311++G(d,p) level in water. The results indicate that urate coordinates with Cu(II) as a monodentate ligand to form square-planar complexes. This copper coordination significantly reduces the radical-scavenging efficiency of urate. Formal hydrogen transfer (FHT) represents the dominant pathway for scavenging HOO radicals. In contrast, the single electron transfer (SET) pathway is negligible for all complexes. Additionally, the Cu(II)-urate complexes demonstrate high resistance to pro-oxidant activity compared to free hydrated Cu(II). Meanwhile, unbound urate retains the capacity to reduce aqueous Cu(II). These insights provide a clear molecular explanation for the dual roles of uric acid in biological systems.

Selectivity and sensitivity of tungsten trioxide toward the adsorption of volatile organic compounds using density functional theory

Phan Thi Hong Hoa^1,2, Do Ngoc Son^1,2,*

¹Ho Chi Minh City University of Technology (HCMUT), 268 Ly Thuong Kiet Street, Dien Hong Ward, Ho Chi Minh City, Vietnam.

²Vietnam National University Ho Chi Minh City, Linh Xuan Ward, Ho Chi Minh City, Vietnam.

*Corresponding author: dnson@hcmut.edu.vn

Abstract. Detecting breath-borne volatile organic compounds (VOCs) is vital for early, non-invasive cancer diagnosis. While tungsten trioxide is a promising sensing material, its sensitivity and selectivity toward these specific biomarkers remain unexplored. This study addresses this gap by using density functional theory and the Boltzmann transport equation to characterize the performance of tungsten trioxide during VOC adsorption.

Acknowledgement

Phan Thi Hong Hoa was funded by the PhD Scholarship Programme of Vingroup Innovation Foundation (VINIF), VinUniversity, code VINIF.2025.TS22.

Platinum Clusters Pt_n^+/0/- (n = 3-21): From Triangles to Remarkable Tubular Architectures   

Bao Ngan Nguyen-Ha,^1,2 My Phuong Pham-Ho,^3,4 Nguyen Minh Tam^5,*

¹ Laboratory for Chemical Computation and Modeling, Institute for Computational Science and Artificial Intelligence, Van Lang University, Ho Chi Minh City, Vietnam

² Faculty of Applied Technology, Van Lang School of Technology, Van Lang University, Ho Chi Minh City, Vietnam. Email: ngan.nguyenhabao@vlu.edu.vn

³ Faculty of Chemical Engineering, Ho Chi Minh City University of Technology (HCMUT), 268 Ly Thuong Kiet Street, Dien Hong Ward, Ho Chi Minh City, Vietnam

⁴ Vietnam National University Ho Chi Minh City, Linh Xuan Ward, Ho Chi Minh City, Vietnam.

⁵ Faculty of Basic Sciences, University of Phan Thiet, 225 Nguyen Thong, Phu Thuy, Lam Dong, Vietnam. Email: nmtam@upt.edu.vn

Abstract

This paper reports on a theoretical investigation of Pt_n^+/0/- clusters with n = 3-21 in three-charge states using density functional theory with the B3PW91 functional in conjunction with the aug-cc-pVTZ-PP and Def2-TZVP basis sets. Geometric structures of Pt_n^+/0/- in the small-to-medium size range are primarily derived from Pt₆^+/0/-; whereas Pt₁₀^+/0/-, Pt₁₄^+/0/- and Pt₁₈^+/0/- also emerge as building blocks. Tubular Pt structures are identified at the sizes of Pt₁₂, Pt₁₈ and Pt₂₄ clusters that can be constructed by either stacking planar Pt₆ or assembling prismatic Pt₆ units. These tubular configurations are energetically favorable and present an effective pathway for the design of more complex Pt-based nanostructures. The Pt₆ triangle features six σ bonds, six conjugated π-bonds of (2c-1e) delocalization and six (6c-1e) bonds reflecting a fully SP² hybridization. The Pt₆ prism contains three (6c-1e) bonds and nine σ-bonds from (2c-1e) delocalization, spanning its edges and faces. These delocalized bonds facilitate the structural integrity and connectivity of tubular Pt₁₂, Pt₁₈ and Pt₂₄ isomers. In these tubular clusters, increased bond coordination and redistribution of electron contributions among s, p and d orbitals enhance bonding interactions and promote stabilized structural assemblies.

Keywords: platinum clusters, nanoclusters, transition metal clusters, high magnetic moments, aromaticity.

Acknowledgement:

BNNH and MTN are grateful to Van Lang University. PHMP acknowledges Ho Chi Minh City University of Technology (HCMUT), VNU-HCM for supporting this study.

Integrating Computational Modeling and Experimental Evaluation for Herbal Products Formulation from Distichochlamys citrea and Cordyceps militaris

 Nguyen Vinh Phu¹, Nguyen Thi Thanh Hai², Phan Tu Quy³, Pham Van Vinh², Ton That Huu Dat⁴, Nguyen Dai Chau², Tran Quang Huy², Nguyen Thi Ai Nhung^2*

 ¹University of Medicine and Pharmacy, Hue University, Hue, Viet Nam

²University of Sciences, Hue University, Hue, Viet Nam

³Tay Nguyen University, Buon Ma Thuot, Viet Nam

⁴Mientrung Institute for Scientific Research, Vietnam National Museum of Nature, VAST, Hue, Viet Nam

*Correspondence to: Nguyen Thi Ai Nhung (Email: ntanhung@hueuni.edu.vn)

ABSTRACT

Type 2 diabetes mellitus (T2DM) is a rapidly increasing metabolic disorder worldwide, highlighting the need for evidence-based herbal products to support glycemic management. This study presents an integrated workflow combining phytochemical characterization, computational modeling, experimental validation, and herbal products formulation to establish a scientific basis for developing a herbal tea product from D. citrea and C. militaris.

The ethyl acetate fraction of D. citrea exhibited remarkable antioxidant activity (DPPH IC₅₀ = 90.27 μg.mL^-1) and α-glucosidase inhibitory activity (IC₅₀ = 115.75 μg.mL^-1). Computational analyses integrating molecular docking, density functional theory (DFT), Lipinski’s analysis, and ADMET identified geraniol and β-citral as the most promising inhibitors of the target enzyme oligo-1,6-glucosidase (PDB: 3AJ7), with docking scores of –11.9 and –11.8 kcal.mol^-1, respectively. For C. militaris, the ethyl acetate extract inhibited α-glucosidase (IC₅₀ = 2.580 ± 0.194 mg/mL) and α-amylase (IC₅₀ = 6.443 ± 0.364 mg.mL^-1). LC–MS identified 14 bioactive compounds and quantified cordycepin (0.11%) and adenosine (0.01%), providing the basis for computational screening. Integrated computational analyses against three diabetes-related molecular targets (PDB: 4W93, 3W37, and 4A3A) identified cordycepin, mannitol, and adenosylribose as the most promising anti-diabetic candidates, with docking scores of –12.3, –12.6, and –12.5 kcal.mol^-1, respectively. Across both medicinal species, DFT, drug-likeness properties, and ADMET analyses consistently supported the docking results by confirming favorable electronic properties, predicted biological activities, and pharmacokinetic profiles of the selected compounds.

The integration of computational modeling and experimental validation enabled the evidence-based formulation of a herbal tea combining D. citrea and C. militaris. This study highlights the role of scientific computation in guiding bioactive compound selection, formulation design, and the development of evidence-based herbal products for glycemic management.

Keywords: Distichochlamys citrea, Cordyceps militaris, computational modeling, herbal products formulation, type 2 diabetes.

Antibacterial Phytochemicals from Elsholtzia ciliata and Blumea balsamifera Against Respiratory Streptococcal Pathogens: Molecular Modeling and Profiling

 Tran Quang Huy¹, Phan Tu Quy², Nguyen Thi Thanh Hai¹, Nguyen Vinh Phu³, Ton That Huu Dat⁴, Pham Van Vinh¹, Nguyen Dai Chau¹, Nguyen Thi Ai Nhung^1*

 ¹University of Sciences, Hue University, Hue, Viet Nam

²Tay Nguyen University, Buon Ma Thuot, Viet Nam

³University of Medicine and Pharmacy, Hue University, Hue, Viet Nam

⁴Mientrung Institute for Scientific Research, Vietnam National Museum of Nature, VAST, Hue, Viet Nam

*Correspondence to: Nguyen Thi Ai Nhung (Email: ntanhung@hueuni.edu.vn)

ABSTRACT

Respiratory infections caused by Streptococcus pneumoniae and Streptococcus pyogenes remain a major public health concern, particularly in the context of increasing antimicrobial resistance. This study integrates chemical characterization, in vitro antibacterial evaluation, and computational modeling to investigate the potential of two indigenous Vietnamese medicinal plants, Elsholtzia ciliata and Blumea balsamifera, against respiratory pathogenic bacteria. GC–MS analysis identified Carvacrol (73.48%) and Thymol (15.01%) as the major constituents of E. ciliata essential oil, whereas (+)-2-Bornanone (58.00%), Caryophyllene (15.90%), and γ-Eudesmol were the predominant compounds in B. balsamifera essential oil. In vitro antibacterial assays demonstrated that E. ciliata exhibited superior antibacterial activity, with inhibition zones of 45 and 34 mm, MIC values of 0.15625 µL.mL^-1, and MBC values of 0.15625 and 0.625 µL.mL^-1 against S. pneumoniae and S. pyogenes, respectively. B. balsamifera also showed antibacterial activity, with inhibition zones of 18 ± 2 and 10 ± 2 mm, MIC values of 1.25 and 2.50 µL.mL^-1, and MBC values of 2.50 and 2.50 µL.mL^-1 against S. pneumoniae and S. pyogenes, respectively.

Computational analyses indicated favorable electronic and physicochemical characteristics for the major phytochemicals. Molecular docking against protein targets of S. pneumoniae and S. pyogenes revealed strong interactions of Carvacrol and Thymol with target proteins, with docking scores reaching −10.1 and −12.0 kcal.mol^-1, respectively, while (+)-2-Bornanone and γ-Eudesmol exhibited the highest affinities toward S. pneumoniae and S. pyogenes, with docking scores of −9.0 and −9.4 kcal.mol^-1, respectively. Most candidate compounds satisfied Lipinski’s rule of five and exhibited physicochemical and ADMET characteristics supporting their potential biological applicability.

These findings highlight E. ciliata and B. balsamifera essential oils as promising sources of natural antibacterial compounds against respiratory pathogens and provide a scientific basis for further formulation studies and respiratory-care applications derived from indigenous Vietnamese medicinal plants.

Keywords: Elsholtzia ciliata, Blumea balsamifera, Streptococcus pneumoniae, Streptococcus pyogenes, molecular docking, drug-likeness property, ADMET.

Computational and Experimental Analyses of Antidiabetic Metabolites from Cordyceps cicadae

Nguyen Dai Chau¹, Nguyen Cong Kinh^1,2, Nguyen Thi Thanh Hai¹, Tran Quang Huy¹, Phan Tu Quy³, Pham Van Vinh¹, Nguyen Vinh Phu⁴, Tran Nhat Phong Dao⁵, Ton That Huu Dat⁶, Nguyen Thi Ai Nhung¹*

¹University of Sciences, Hue University, Hue, Viet Nam

²Duy Tan University, Da Nang, Viet Nam

³Tay Nguyen University, Buon Ma Thuot, Viet Nam

⁴University of Medicine and Pharmacy, Hue University, Hue, Viet Nam

⁵Can Tho University of Medicine and Pharmacy, Can Tho, Viet Nam

⁶Mientrung Institute for Scientific Research, Vietnam National Museum of Nature, VAST, Hue, Viet Nam

*Correspondence to: Nguyen Thi Ai Nhung (Email: ntanhung@hueuni.edu.vn)

ABSTRACT

Cordyceps cicadae is a medicinal fungus with diverse pharmacological activities; however, its antidiabetic metabolites and underlying molecular mechanisms remain insufficiently understood. This study integrated experimental and computational approaches to evaluate the antidiabetic potential of C. cicadae. LC–MS/MS profiling of the ethanol extract identified sixteen metabolites belonging to amino acid derivatives, peptides, phospholipids, saccharides, alkaloids, and steroidal compounds, with compounds 1 (53.71%) and 9 (67.93%) being the predominant constituents. In vitro enzyme assays demonstrated inhibitory activity against α-amylase and α-glucosidase, with IC₅₀ values of 2.77 ± 0.09 and 7.00 ± 0.17 mg mL^-1, respectively. To elucidate the molecular basis of enzyme inhibition, all identified metabolites were subjected to molecular docking against human pancreatic α-amylase (PDB: 4W93) and α-glucosidase (PDB: 3W37). Compound 7 exhibited the strongest affinity toward α-amylase (DS –12.9 kcal mol^-1, seven hydrogen bonds), whereas compound 14 showed the highest affinity toward α-glucosidase (DS –13.0 kcal mol^-1, eight hydrogen bonds), both comparable to or stronger than the reference inhibitor acarbose. Molecular dynamics simulations over 100 ns confirmed the stability of the [7–4W93] and [14–3W37] complexes. The [7–4W93] complex was stabilized by an extensive hydrogen-bonding network and maintained lower radius of gyration (Rg) and solvent-accessible surface area (SASA) values, whereas [14–3W37] displayed greater energetic stability and lower RMSF values, indicating a more rigid binding mode. Lipinski’s analysis identified compounds 1, 4, and 8 with favorable drug-likeness properties, whereas ADMET prediction highlighted compounds 4, 5, 9, 13, and 16 as potential candidates with acceptable pharmacokinetic and toxicity profiles. These findings highlight Cordyceps cicadae as a valuable natural source of antidiabetic enzyme inhibitors and demonstrate the effectiveness of integrating LC–MS/MS, molecular docking, ADMET prediction, and molecular dynamics simulations for natural-product-based drug discovery.

Keywords: Cordyceps cicadae, Antidiabetic Activity, Molecular Docking, Molecular Dynamics Simulation, ADMET.

Role of Heteroatom Incorporation in Oxygen Reduction Reaction on CoTMP/MoS₂ Hybrid Catalysts

Tran Phuong Dung^{1, 2}, and Do Ngoc Son^{3, 4,*}

¹Department of Chemistry, University of Science, Vietnam National University, Ho Chi Minh City, Vietnam.

²Department of Chemistry, Ho Chi Minh City University of Education, Ho Chi Minh City, Vietnam.

³Ho Chi Minh City University of Technology (HCMUT), 268 Ly Thuong Kiet Street, Dien Hong Ward, Ho Chi Minh City, Vietnam

⁴Vietnam National University Ho Chi Minh City, Linh Trung Ward, Ho Chi Minh City, Vietnam

*Corresponding author: dnson@hcmut.edu.vn

Abstract

The sluggish kinetics of the oxygen reduction reaction (ORR) motivate the development of advanced electrocatalysts. Heteroatom engineering has emerged as an effective approach to tune the electronic structure and catalytic activity of porphyrin-based and M–N–C materials. Inspired by these findings, this work extends the heteroatom-doping strategy to a CoTMP/MoS₂ hybrid catalyst system (TMP = tetramethylporphyrin), for which the influence of heteroatom incorporation on ORR activity has not yet been systematically investigated. In this study, density functional theory (DFT) calculations combined with thermodynamic modelling were employed to explore the effects of selected heteroatoms on the electronic structure, charge redistribution, adsorption behavior of oxygen-containing intermediates, and reaction energetics of the CoTMP/MoS₂ catalyst.

Formation of pyramidal structures through mixing gold and platinum atoms The Au_xPt_y²⁺ clusters with x + y = 10

Bao-Ngan Nguyen-Ha,^1,3 Long Van Duong,^2,3 My-Phuong Pham-Ho,^4,5 Nguyen Minh Tam⁶*

1, Laboratory for Chemical Computation and Modeling, Institute for Computational Science and Artificial Intelligence, Van Lang University, Ho Chi Minh City, 700000 Vietnam.

2, Atomic Molecular and Optical Physics Research Group, Science and Technology Advanced Institute, Van Lang University, Ho Chi Minh City, Vietnam.

3, Faculty of Applied Technology, School of Technology, Van Lang University, Ho Chi Minh City, Vietnam.

4, Faculty of Chemical Engineering, Ho Chi Minh City University of Technology (HCMUT), 268 Ly Thuong Kiet Street, Dien Hong Ward, Ho Chi Minh City, Vietnam.

5, Vietnam National University Ho Chi Minh City, Linh Xuan Ward, Thu Duc City, Ho Chi Minh City, Vietnam.

6, Faculty of Basic Sciences, University of Phan Thiet, 225 Nguyen Thong, Phu Thuy, Lam Dong, Vietnam.

E-mail: ngan.nguyenhabao@vlu.edu.vn

Abstract

Molecular and electronic structure of a small series of mixed gold and platinum Au_xPt_y²⁺ clusters with x + y = 10 were investigated using quantum chemical methods. A consistent tetrahedral pyramid structure emerges and the magnetic moments of Au_xPt_y²⁺ are primarily located on Pt atoms, increasing steadily from 0 to 10 μB corresponding to the increase of the number of Pt atoms from 0 to 10 and significantly enhancing the magnetic moments. Admixture of both Au and Pt atoms thus emerges as an elegant way of forming small pyramidal structure with a high, and controllable, magnetic moment.          

Keywords:             nanoclusters, transition metal clusters, high magnetic moments, aromaticity.

Acknowledgement:

BNNH is grateful to Van Lang University.

The Boron-doped Scandium Clusters B@Sc_n-1^-/0/+ with n = 2-13: Uncovering the Smallest Endohedrally Doped Cages

 Phuong Anh Pham-Tran,^1,2† Bao-Ngan Nguyen-Ha,^1,2† Nguyen Minh Tam,³ My Phuong Pham-Ho,^1,2,*

 ¹ Faculty of Chemical Engineering, Ho Chi Minh City University of Technology (HCMUT), 268 Ly Thuong Kiet Street, Dien Hong ward, Ho Chi Minh City, Vietnam. Email: phmphuong@hcmut.edu.vn

² Vietnam National University Ho Chi Minh City, Linh Xuan Ward, Ho Chi Minh City, Vietnam

³ Faculty of Basic Sciences, University of Phan Thiet, 225 Nguyen Thong, Phu Thuy, Lam Dong, Vietnam

Abstract

A theoretical investigation employing the PBE/Def2-TZVP method comprehensively explores the geometric and electronic structures and properties of the pure Sc_n^+/0- and doped Sc_n-1B^+/0/- clusters with n = 1-13 in three charged states. B@Sc₆^+/0/- clusters emerge as the smallest doped cages identified so far, distinguished by their near-perfect octahedral geometry, with a boron atom encapsulated at the center of the Sc₆^+/0/- cages. Structural evolution analysis reveals size-dependent trends, with n = 6 identified as a critical cluster size corresponding to a transformation from exohedral to endohedral configuration, and a shift in the substitution-addition pattern of the boron atom within the pure scandium host. Incorporation of a boron atom induces electron redistribution, stabilizes high-spin states, and reduces energetic degeneracy. A boron-doping enhances the stability of the initial Sc_n^+/0- clusters, showing a consistent preference for cationic isomers. A molecular orbital (MO) analysis provides a detailed explanation of the observed energy degeneracy among stable spin states by examining their electronic configurations.

From Linear Chains to Ribbon–Pentagonal Frameworks: Structural Evolution of C₃(BH)_n Clusters (n = 1– 7)

Viet Tien Nguyen,^1,2† Minh Huy Nguyen-Quoc,^1,2† Bao-Ngan Nguyen-Ha,^1,2 My Phuong Pham-Ho,^1,2,*

¹ Faculty of Chemical Engineering, Ho Chi Minh City University of Technology (HCMUT), 268 Ly Thuong Kiet Street, Dien Hong ward, Ho Chi Minh City, Vietnam. Email: phmphuong@hcmut.edu.vn

² Vietnam National University Ho Chi Minh City, Linh Xuan Ward, Ho Chi Minh City, Vietnam 

Abstract

The structural evolution, stability, and chemical bonding of C₃(BH)_n clusters (n = 1– 7) were systematically investigated using Density Functional Theory (DFT) calculations at the B3LYP/6–311++G(d,p) level, followed by CCSD(T)/6–311++G(d,p) single-point energy refinements. The relative stability of the clusters was evaluated through average binding energies (E_b), dissociation energies (ΔE), second-order energy differences (Δ₂E), and HOMO–LUMO energy gaps. Two magic clusters were identified at n = 2 and n = 5, exhibiting enhanced energetic stability and large HOMO–LUMO gaps of 4.67 and 4.37 eV, respectively. The results reveal a clear structural evolution from linear and planar configurations toward compact threedimensional ribbon– pentagonal frameworks. For n = 5– 7, cluster growth proceeds through the expansion of a characteristic ribbon–pentagonal motif, indicating the emergence of a preferred structural growth pattern. Adaptive Natural Density Partitioning (AdNDP) analysis further reveals the presence of multicenter bonding interactions that play a key role in stabilizing the magic clusters. These findings provide new insights into the structural growth mechanism and bonding characteristics of boron-rich carbon-containing clusters.

Computational Study of Stability and Characteristics of Nonconventional C_sp3–H···Y Hydrogen Bonds between haloforms and dipnictogen

Nguyen Thao Thu ¹ , Nguyen Ngoc Tri ^1,2 , Pham Ngoc Thach ^1,2 and Vu Thi Ngan ^1,2 

¹⁾Laboratory of Computational Chemistry and Modelling (LCCM), Quy Nhon University, 170 An Duong Vuong Street, Quy Nhon City 590000, Vietnam

²⁾Faculty of Natural Sciences, Quy Nhon University, 170 An Duong Vuong Street, Quy Nhon City 590000, Vietnam

Corresponding author’s email:nguyenthaothu1997@gmai.com; nguyenngoctri@qnu.edu.vn; phamngocthach@qnu.edu.vn and vuthingan@qnu.edu.vn

Abstracts

This study investigates the stability and electronic nature of nonconventional C_sp³–H···Y hydrogen bonds (HBs) in CHX₃···Y₂ complexes (X = F, Cl, Br; Y = N, P, As, Sb). Complex stability generally increases from F to Br and from N to Sb, with bent structures often being more stable than linear ones. SAPT2+ analysis reveals a shift in the dominant stabilization mechanism from electrostatic interactions in N₂ complexes to induction- and dispersion-enhanced interactions in the heavier pnictogen systems. AIM and NBO analyses confirm weak closed-shell C_sp³–H···Y HBs, although hydrogen-bond strength does not always correlate with the overall interaction energy. N₂ complexes induce blue-shifting HBs, while P₂, As₂, and Sb₂ containing complexes appear to have red-shifting HBs accompanied by C–H bond elongation. These findings provide new insight into how the nature of the Group 15 proton acceptor governs hydrogen-bond strength, complex stability, and vibrational frequency shifts in CHX₃···Y₂ complexes.

BamBamMayNut – A Graphical Interface for Interactive Generation of GROMACS .mdp Files

Tho H. Ho, ^1,2 Thinh T. Q. Le, ^1,2 Lam K. Huynh ^1,2,*

1 Vietnam National University, Ho Chi Minh City, Linh Xuan Ward, Ho Chi Minh City, Vietnam.

2 International University, Quarter 33, Linh Xuan Ward, Ho Chi Minh City, Vietnam.

* Corresponding author: hklam@hcmiu.edu.vn

Abstract

Preparation of molecular dynamics input files remains a practical challenge in computational chemistry and biomolecular simulation, especially for users working with complex GROMACS parameter sets. The .mdp file determines core aspects of simulation behavior, including integration, temperature and pressure control, nonbonded treatment, constraints, and data output, yet these settings are often edited manually through dense text-based workflows. This creates unnecessary barriers for training, increases the risk of inconsistent parameterization, and slows routine simulation setup. BamBamMayNut is a browser-based tool developed to support more accessible and reproducible generation of GROMACS .mdp files. The tool provides an interactive environment in which users can inspect simulation options, adjust parameters graphically, and generate the resulting configuration text immediately. By making parameter choices easier to review and organize, the platform aims to support more reliable setup of simulations relevant to molecular biophysics, protein-ligand systems, conformational studies, and structure-guided drug discovery. The expected impact of the tool is to reduce avoidable setup errors, improve consistency across simulation campaigns, and make molecular dynamics workflows easier to teach, share, and reproduce. This poster presents the motivation, design, and scientific utility of BamBamMayNut as a practical interface for modern simulation preparation.

Keywords: GROMACS, molecular dynamics parameters, simulation setup

Comparative DFT Study of Talazoparib Interactions with B₁₂C₁₂, Al₁₂N₁₂, C₁₂N₁₂, and B₁₂N₁₂ Nanocages for Drug Delivery Applications

Doan Le Binh^a, Tran Phuong Thao^a, Nguyen Van Trang^b and Phan Thi Thuy^a

^aDepartment of Chemistry, Vinh University, 182 Le Duan, Truong Vinh, Nghean 43000, Vietnam.

^bInstitute of Materials Science, VAST, 18 Hoang Quoc Viet, Hanoi 10000, Vietnam

Talazoparib is a highly potent PARP inhibitor used in cancer therapy; however, improving its delivery efficiency and minimizing off-target toxicity remain important challenges. In this study, the adsorption behavior of Talazoparib on four fullerene-like nanocages, including B₁₂C₁₂, Al₁₂N₁₂, C₁₂N₁₂, and B₁₂N₁₂, was systematically investigated using density functional theory at the M06-2X/6-311G(d,p) level. Geometry optimizations, adsorption energies, thermodynamic analysis, frontier molecular orbital calculations, quantum theory of atoms in molecules (QTAIM), and noncovalent interaction (NCI) analyses were performed to evaluate the stability and interaction characteristics of the drug–nanocage complexes. The calculated adsorption energies were -4.961, -2.492, -1.247, and -1.217 eV for B₁₂C₁₂, Al₁₂N₁₂, C₁₂N₁₂, and B₁₂N₁₂ were, respectively, confirming favorable adsorption on all investigated nanocages. Among them, B₁₂C₁₂ exhibited the strongest adsorption, indicating excellent drug-loading capability but potentially limited drug release. In contrast, Al₁₂N₁₂, C₁₂N₁₂, and B₁₂N₁₂ showed moderate adsorption strengths that may provide a more favorable balance between drug loading and controlled release. These findings provide theoretical insights into Talazoparib–nanocage interactions and offer valuable guidance for the rational design of nanocarriers for targeted drug delivery.

EpiSurf: Mapping the Nanobody – Antigen Interfaces by the Polar and Non-polar Interaction Energies

Phuong Chu Thi Hong, Giang Kieu Nguyen

Center for Environmental Intelligence, VinUniversity, Gia Lam, Hanoi 10000, Vietnam

Nanobodies bind diverse antigens with high specificity and have emerged as promising agents for both therapeutics and molecular detection. Elucidating the antigen – binding site, the region of the antigen surface engaged by a nanobody, is central to understanding immune recognition and to the rational design of nanobodies. However, antigen – binding sites are difficult to determine, typically demanding labour intensive structural characterization, while existing computational studies of nanobody – antigen interaction rely largely on sequence – derived statistical models that offer limited physical insight into the binding interface. Resources that describe the energetic basis of nanobody – antigen recognition at residue resolution remain scarce.

Here we aim to address this gap by constructing a dedicated database of nanobody–antigen interaction binding energies. Drawing on high-resolution complexes curated from the SAbDab-nano database, we use the molecular dynamics simulation to quantify per-residue interaction energies, decomposed into polar and non-polar interaction energies; to date, energy profiles have been successfully computed for approximately 800 nanobody–antigen complexes. Moreover, we project these per-residue energies onto the antigen molecular surface and render them through an interactive web-based viewer, providing an intuitive means to explore favorable interaction hotspots across the antigen.