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Computational Chemistry Research Group

1. Introduction

Computational chemistry (CC) is a discipline in which we use computations to obtain chemical information. Computations are based on the laws of physics, the theories and formalisms of either quantum or classical mechanics. Theoretical formalisms are thus implemented into computer codes using well established mathematical techniques. Computational science has made tremendous progresses thanks to spectacular advances in computer hardware. At the time of high performance computers (HPC) attaining the petaflops (1015 flops) speed (and approaching the speed of exaflops, 1018 flops), CC becomes another cornerstone of chemical science, complementing theory and experiment to explore and uncover novel chemistry. A large number of chemical information determined now by quantum chemical computations attain a high accuracy comparable to that of the best experimental techniques. For thermochemical parameters, the ‘chemical accuracy’ of ± 1 kcal/mol (± 4 kJ/mol) can be achieved for small and medium-size molecules in the gas phase. In addition, computed results allow us to understand in depth the inherent chemical phenomena.

Nowadays, CC software implemented in HPC provides chemists with a multi-purpose spectrometer for their daily investigations. CC is thus applied in all branches of chemistry. It allows chemists to collect all kind of chemical information through computations rather than by experiments. CC is still facing many challenges in the accurate computations on large-size molecules, molecules in solution and materials in solid states.

Within the limits of our resources, the Computational Chemistry Research Group at Ton Duc Thang University endeavors to use quantum chemical computations to discover new chemical compounds and phenomena, and thereby to contribute to the studies of a few fundamental problems of modern chemistry. When possible our theoretical work will be carried out in concert with experimental studies.

2. Mission and vision

- Predict the thermodynamic and kinetic parameters and spectroscopic constants of different classes of molecules with high accuracy;

- Support the design of new materials and catalysts for various chemical processes;

- Provide theoretical support for different experimental groups;

- Minimize thus expensive or dangerous experimental efforts by aiding experimental design with critical chemical data;

- Discover new chemical compounds and uncover new reactions;

- Propose chemical concepts to interpret novel chemical phenomena.

3. Research topics

- High accuracy thermochemistry

- Structure and properties of doped clusters of the elements, with applications in semiconductors, catalysis…

- Prebiotic chemistry and atmospheric chemistry

- CO2 sequestration

- Materials for new energies

- Properties of conjugated polymers (with applications in OLED)

- Properties of natural products in Vietnam

- New concepts for chemical structures and reactivities

4. Current members

COMCHEM_Nguyen_Minh_Tho.jpg

Dr. Nguyen Minh Tho

Positions:

• Adjunct professor at Ton Duc Thang University, Ho Chi Minh City, Vietnam

• Advisor of Computational Chemistry Research Group, Ton Duc Thang University, Ho Chi Minh City, Vietnam

• Full Professor of Chemistry, Department of Chemistry, University of Leuven, Leuven, Belgium

Areas of expertise: Quantum chemistry, Computational chemistry

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Dr. Truong Ba Tai

Positions:

• Member of Computational Chemistry Research Group, Ton Duc Thang University, Ho Chi Minh City, Vietnam

• FWO postdoctoral fellow, Department of Chemistry, KU Leuven, Belgium

Areas of expertise: Molecular Modelling of Organic Semiconductor and Nanomaterials

Research track record (until October of 2015):

• ISI papers: 47

• Total ISI Citations: 535

• ISI H-index: 16

• Top ISI journals (at most 5):

1. Angewandte Chemie International Edition (Impact factor: 11.261)

2. Nanoscale (Impact factor: 7.394)

3. Chemical Communications (Impact factor: 6.834)

4. Chemistry – A European Journal (Impact factor: 5.731)

5. Journal of Chemical Theory and Computation (Impact factor: 5.498)

COMCHEM_Nguyen_Minh_Tam.jpg

Dr. Nguyen Minh Tam

Positions:

• Assistant Professor in Chemistry

• Member of Computational Chemistry Research Group, Ton Duc Thang University, Ho Chi Minh City, Vietnam

• Postdoctoral Fellow, Department of Chemistry, KU Leuven, Belgium

Areas of expertise: Computational chemistry

COMCHEM_Le_Minh_Hung.jpg

Dr. Le Minh Hung

Position: Member of Computational Chemistry Research Group, Ton Duc Thang University, Ho Chi Minh City, Vietnam

Areas of expertise: Materials Modeling and Theoretical Reaction Dynamics

COMCHEM_Nguyen_Thi_Huyen.jpg

Dr. Nguyen Thi Huyen

Positions:

• Member of Computational Chemistry Research Group, Ton Duc Thang University, Ho Chi Minh City, Vietnam

• Postdoctoral Fellow, Department of Chemistry, KU Leuven, Belgium

Areas of expertise: Computational quantum chemistry

COMCHEM_Duong_Van_Long.jpg

Duong Van Long, MSc

Position: Member of Computational Chemistry Research Group, Ton Duc Thang University, Ho Chi Minh City, Vietnam

Areas of expertise: Computational chemistry

COMCHEM_Pham_Tan_Hung.jpg

Pham Tan Hung, BSc

Position: Member of Computational Chemistry Research Group, Ton Duc Thang University, Ho Chi Minh City, Vietnam

Areas of expertise: Computational chemistry

COMCHEM_Nguyen_Van_Hung.jpg

Nguyen Van Hung, BSc

Position: Member of Computational Chemistry Research Group, Ton Duc Thang University, Ho Chi Minh City, Vietnam

Areas of expertise: Biophysics and Biochemistry

5. Former members (name, title, picture)

COMCHEM_Truong_Duc_Toan.jpg

Truong Duc Toan, Bsc

Position: Former of Computational Chemistry Research Group, Ton Duc Thang University, Ho Chi Minh City, Vietnam

COMCHEM_Ngo_Son_Tung.jpg

Dr. Ngo Son Tung

Position: Former of Computational Chemistry Research Group, Ton Duc Thang University, Ho Chi Minh City, Vietnam

COMCHEM_Tran_Thi_Thuy_Linh.jpg

Dr. Tran Thi Thuy Linh

Position: Former of Computational Chemistry Research Group, Ton Duc Thang University, Ho Chi Minh City, Vietnam

COMCHEM_Nguyen_Thi_Mai.JPG

Nguyen Thi Mai, MSc

Position: Former of Computational Chemistry Research Group, Ton Duc Thang University, Ho Chi Minh City, Vietnam

6. Publications (ISI or Scopus only)

52. Son Tung Ngo, Xuan-Cuong Luu, Nguyen Thanh Nguyen, Van Van Vu, Huong Thi Thu Phung (2018); Etersalate prevents the formations of 6Aβ16-22 oligomer: An in silico study; Plos One (ISI).

51. Piero Ferrari, Jan Vanbuel, Dr. Nguyen Minh Tam, Prof. Dr. Minh Tho Nguyen, Sandy Gewinner, Dr. Wieland Schöllkopf, Dr. André Fielicke, Prof. Dr. Ewald Janssens (2018); Effects of Charge Transfer on the Adsorption of CO on Small Molybdenum‐Doped Platinum Clusters; Chemistry (ISI).

50. Hung Tan Pham, Ngo Tuan Cuong, Nguyen Minh Tam, Nguyen Thanh Tung (2018); A Systematic Investigation on CrCun Clusters with n = 9–16: Noble Gas and Tunable Magnetic Property; The Journal of Physical Chemistry A (ISI).

49. Pham Vu Nhat, Truong BaTai (2018); Electronic structure of coinage metal clusters M20 (M = Cu, Ag, Au) from density functional calculations and the phenomenological shell model; Chemical Physics Letters (ISI).

48. Yohandys A. Zulueta, Minh Tho Nguyen (2018); Lithium Hexastannate: A Potential Material for Energy Storage; Physica Status Solidi (B): Basic Research (ISI).

47. Hung Tan Pham, Thi Tuyet Mai Dang, Long Van Duong, Nguyen Minh Tam, Minh Tho Nguyen (2018); B3@Si12+: strong stabilizing effects of a triatomic cyclic boron unit on tubular silicon clusters; Physical Chemistry Chemical Physics (ISI).

46. Huyen Thi Nguyen, Jyh-Chiang Jiang, Minh Tho Nguyen (2018); A theoretical design of some silole-based dibenzothiophene-S,S-dioxide semiconducting compounds for red phosphorescence; Organic Electronics (ISI).

45. Long Van Duong, Minh Tho Nguyen (2017); On the role of different types of electron in double ring tubular clusters; Chemical Physics Letters (ISI).

44. Van V. Vu, Son Tung Ngo (2018); Copper active site in polysaccharide monooxygenases; Coordination Chemistry Reviews (ISI).

43. Nguyen Minh Tam, Khanh B. Vu, Van V. Vu, Son Tung Ngo (2018); Influence of various force fields in estimating the binding affinity of acetylcholinesterase inhibitors using fast pulling of ligand scheme; Chemical Physics Letters (ISI).

41. Hung Tan Pham, Minh Tho Nguyen (2018); Aromaticity of Some Metal Clusters: A Different View from Magnetic Ring Current; Journal of Physical Chemistry A (ISI).

40. Linh Tran, Son Tung Ngo, Minh Tho Nguyen (2018); Propafenone effects on the stable structures of Aβ16-22 system; Chemical Physics Letters (ISI).

39. Nguyen Minh Tam, Ngo Tuan Cuong, Hung Tan Pham, Nguyen Thanh Tung (2017); Au19M (M=Cr, Mn, and Fe) as magnetic copies of the golden pyramid; Scientific Reports (ISI).

38. Thi H. Ho, Viet Q. Bui, Thang Bach Phan, Yoshiyuki Kawazoe, Hung M. Le (2017); Atomistic observation of the collision and migration of Li on MoSe2 and WS2 surfaces through ab initio molecular dynamics; Physical Chemistry Chemical Physics (ISI).

37. Nguyen Minh Tam, Minh Tho Nguyen, Son Tung Ngo (2017); Evaluation of the absolute affinity of neuraminidase inhibitor using steered molecular dynamics simulations; Journal of Molecular Graphics and Modelling, Vol. 77, pp. 137-142 (ISI).

36. Son Tung Ngo, Minh Tung Nguyen, Nguyen Thanh Nguyen, Van V. Vu (2017); The Effects of A21G Mutation on Transmembrane Amyloid Beta (11–40) Trimer: An In Silico Study; Journal of Physical Chemistry B, Vol.e 121 (36), pp. 8467–8474 (ISI).

35. Hung Tan Pham, Huyen Thi Nguyen, Minh Tho Nguyen (2017); Mn@B3N3Si8+: a stable singlet manganese-doped hetero-atom-mixed silicon fullerene; Structural Chemistry, Vol. 28 (6), pp. 1887–1893 (ISI).

34. Son Tung Ngo, Xuan-Cuong Luu, Minh Tung Nguyen, Chinh N. Le,  Van V. Vu (2017); In silico studies of solvated F19W amyloid β (11–40) trimer; RSC Advances, Vol. 7 (67), pp. 42379-42386 (ISI).

33. Pham Vu Nhat, Nguyen Thanh Si, Jerzy Leszczynski, Minh Tho Nguyen (2017); Another look at structure of gold clusters Aun from perspective of phenomenological shell model; Chemical Physics, Vol. 493, pp. 140-148 (ISI).

32. Hung Tan Pham, Minh Tho Nguyen (2017); Theoretical Investigation of Metallic Heterofullerenes of Silicon and Germanium Mixed with Phosphorus and Arsenic Atoms M-A8E6, A = Si, Ge; E = P, As; and M = Cr, Mo, W; Journal of Physical Chemistry A, Vol. 121 (26), pp. 5056–5066 (ISI).

31. Pham Vu Nhat, Nguyen Thanh Si, Jerzy Leszczynski, Minh Tho Nguyen (2017); Another look at structure of gold clusters Aun from perspective of phenomenological shell model; Chemical Physics, Vol. 493, pp. 140-148 (ISI).

30. Hung M Le, Tan-Tien Pham, Vo Duy Dat, Yoshiyuki Kawazoe (2017); First-principles modeling of metal (ii) ferrocyanide: electronic property, magnetism, bulk moduli, and the role of C  ≡  N− defect; Journal of Physics D: Applied Physics, Vol. 50 (3), Article number 035004 (ISI).

29. Thi H. Ho, Hieu C. Dong, Yoshiyuki Kawazoe, Hung M. Le (2017); Effect of Elasticity of the MoS2 Surface on Li Atom Bouncing and Migration: Mechanism from Ab Initio Molecular Dynamic Investigations; Journal of Physical Chemistry C, Vol. 121 (2), pp. 1329-1338 (ISI).

28. Hung M. Le, Viet Q. Bui, Phuong Hoang Tran, Nguyen-Nguyen Pham-Tran, Yoshiyuki Kawazoe, Duc Nguyen-Manh (2017); The prospect of sensitizing organic dyes attached to the MoS2 surface: Physical insights from density functional theory investigations; Chemical Physics Letters, Vol. 667, pp. 290–295 (ISI).

27. Son Tung Ngo, Duc Toan Truong, Nguyen Minh Tam, Minh Tho Nguyen (2017); EGCG inhibits the oligomerization of amyloid beta (16-22) hexamer: Theoretical studies; Journal of Molecular Graphics and Modelling, Vol. 76, pp. 1–10 (ISI).

26. Hung Tan Pham, Nguyen Minh Tam, Yassin A. Jeilani, Minh Tho Nguyen; Structural evolution and bonding of phosphorus-doped silicon clusters SinPm−/0/+ with n = 1–10, m = 1, 2; Computational and Theoretical Chemistry, Vol. 1107 (2017), pp. 115–126 (ISI).

25. Huyen Thi Nguyen, Tran Dieu Hang, Minh Tho Nguyen; Theoretical Study of Silicon Monoxide Reactions with Ammonia and Methane; Journal of Physical Chemistry A, Vol 121 (5) (2017), pp. 1032–1040 (ISI).

24. Truong Ba Tai, Minh Tho Nguyen; Aromatic cage-like B46: existence of the largest decagonal holes in stable atomic clusters; RSC Advances, Vol. 7 (36) (2017), pp. 22243-22247 (ISI).

23. Son Tung Ngo, Minh Tung Nguyen, Minh Tho Nguyen; Determination of the absolute binding free energies of HIV-1 protease inhibitors using non-equilibrium molecular dynamics simulations; Chemical Physics Letters, Vol. 676 (2017), pp. 12–17 (ISI).

22. Le Nhan Pham, Minh Tho Nguyen; Titanium Digermanium: Theoretical Assignment of Electronic Transitions Underlying Its Anion Photoelectron Spectrum; Journal of Physical Chemistry A, Vol. 121 (9) (2017), pp. 1940–1949 (ISI).

21. Hung Tan Pham, Devashis Majumdar, Jerzy Leszczynski, Minh Tho Nguyen; 4d and 5d bimetal doped tubular silicon clusters Si12M2 with M = Nb, Ta, Mo and W: a bimetallic configuration model; Physical Chemistry Chemical Physics, Vol. 19 (2017), pp. 3115-3124 (ISI).

20. Son Tung Ngo, Huynh Minh Hung, Khoa Nhat Tran, Minh Tho Nguyen; Replica exchange molecular dynamics study of the amyloid beta (11–40) trimer penetrating a membrane; RSC Advances, Vol. 7 (2017), pp. 7346-7357 (ISI).

19. Duc Toan Truong, Minh Tung Nguyen, Van V. Vu, Son Tung Ngo; Fast pulling of ligand approach for the design of β-secretase 1 inhibitors; Chemical Physics Letters, Vol. 671 (2017), pp. 142–146 (ISI)

18. Hung Tan Pham, Devashis Majumdar, Jerzy Leszczynski, Minh Tho Nguyen; 4d and 5d bimetal doped tubular silicon clusters Si12M2 with M = Nb, Ta, Mo and W: a bimetallic configuration model; Physical Chemistry Chemical Physics, Vol. 19 (2017), pp. 3115-3124 (ISI).

17. Son Tung Ngo, Huynh Minh Hung, Duc Toan Truong, Minh Tho Nguyen; Replica exchange molecular dynamics study of the truncated amyloid beta (11–40) trimer in solution; Physical Chemistry Chemical Physics, Vol. 19 (2017), pp. 1909-1919 (ISI).

16. Le Nhan Pham, Minh Tho Nguyen; Electronic Structure of Neutral and Anionic Scandium Disilicon ScSi2–/0 Clusters and the Related Anion Photoelectron Spectrum; The Journal of Physical Chemistry A, Vol. 120 (2016), pp. 9401–9410 (ISI).

15. Son Tung Ngo, Huynh Minh Hung, Minh Tho Nguyen; Fast and Accurate Determination of the Relative Binding Affinities of Small Compounds to HIV-1 Protease Using Non-Equilibrium Work; Journal of Computational Chemistry, Vol. 37 (2016), pp. 2734–2742 (ISI).

14. Hung Tan Pham, Ngo Tuan Cuong, Nguyen Minh Tam, Nguyen Thanh Tung; A Systematic Investigation on CrCun Clusters with n = 9–16: Noble Gas and Tunable Magnetic Property; The Journal of Physical Chemistry A, Vol. 120 (2016), pp. 7335–7343 (ISI).

13. Long Van Duong, Minh Tho Nguyen; Electronic structure of the boron fullerene B-14 and its silicon derivatives B13Si+, B13Si- and B12Si2: a rationalization using a cylinder model; Physical Chemistry Chemical Physics, Vol. 18 (2016), pp. 17619-17626 (ISI).

12. Huyen Thi Nguyen, Minh Tho Nguyen; Silole-Based Nickel Bisdithiolene Complexes: A Theoretical Design for Optoelectronic Applications; The Journal of Physical Chemistry C, Vol. 120 (2016), pp. 16418–16426 (ISI).

11. Huynh Minh Hung, Vanessa P. Nguyen, Son Tung Ngo, Minh Tho Nguyen; Theoretical study of the interactions between the first transmembrane segment of NS2 protein and a POPC lipid bilayer; Biophysical Chemistry, Vol. 217 (2016), pp. 1–7 (ISI).

10. Nguyen Minh Tam, Minh Tho Nguyen; Theoretical Study of the SinMgm Clusters and Their Cations: Toward Silicon Nanowires with Magnesium Linkers; The Journal of Physical Chemistry C, Vol. 120 (2016), pp. 15514–15526 (ISI).

9. Hung Tan Pham, Nguyen Minh Tam, My Phuong Pham-Ho and Minh Tho Nguyen; Stability and bonding of the multiply coordinated bimetallic boron cycles: B8M22−, B7NM2 and B6C2M2 with M = Sc and Ti; RSC Advances, Vol. 6 (2016), pp. 51503-51512 (ISI).

8. Hung Tan Pham, Kie Zen Lim, Remco W. A. Havenith, Minh Tho Nguyen; Aromatic character of planar boron-based clusters revisited by ring current calculations; Physical Chemistry Chemical Physics, Vol. 18 (2016), pp. 11919-11931 (ISI).

7. Truong Ba Tai, Sang Uck Lee, Minh Tho Nguyen; Correction: Aromatic cages B420/+: unprecedented existence of octagonal holes in boron clusters; Physical Chemistry Chemical Physics, Vol. 18 (2016), pp. 11558-11558 (ISI).

6. Truong Ba Tai, Sang Uck Lee, Minh Tho Nguyen; Aromatic cages B0/+42: unprecedented existence of octagonal holes in boron clusters; Physical Chemistry Chemical Physics, Vol. 18 (2016), pp. 11620-11623 (ISI).

5. Ho TH, Pham-Tran NN, Kawazoe Y, Le HM; Ab Initio Investigation of O-H Dissociation from the Al-OH2 Complex Using Molecular Dynamics and Neural Network Fitting; Journal of Physical Chemistry A, Vol. 120 (2016), pp. 346-355 (ISI).

4. Truong Ba Tai, Minh Tho Nguyen; A new chiral boron cluster B44 containing nonagonal holes; Chemical Communications, Vol. 52 (2016), pp. 1653-1656 (ISI).

3. Minh Tho Nguyen, Tran Dieu Hang, Nina P. Gritsan, Vitaly G. Kiselev; Comment on "Computational Study on the Vinyl Azide Decomposition"; Journal of Physical Chemistry A, Vol. 119 (2015), pp. 12906–12907 (ISI).

2. Bui VQ, Pham TT, Le DA, Thi CM, Le HM; A first-principles investigation of various gas (CO, H2O, NO, and O2) absorptions on a WS2 monolayer: stability and electronic properties; Journal of Physics: Condensed Matter, Vol. 27 (2015), Article number 305005 (ISI).

1. Pham HT, Nguyen MT; Effects of bimetallic doping on small cyclic and tubular boron clusters: B7M2 and B14M2 structures with M = Fe, Co; Physical Chemistry Chemical Physics, Vol. 17 (2015), pp. 17335 – 17345 (ISI).

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