Computational and theoretical chemistry is an interdisciplinary field across the traditional fields of science such as chemistry, physics, mathematics, computer science and engineering and the venture by the leading research centres in the world.Research groups across the world especially in Europe and the United States have been used computational and simulation techniques for years to study molecular and biomolecular systems and their physicochemical properties and mechanisms to understand and strengthen their fundamental knowledge. As computational chemistry is considered as a fundamental science field of research, it will have a great impact on key researches in future, particularly in protein science and medicineand it can likely provide some important results which can then be used in policy decisions.
Distinguished computational chemistry presents contemporary developments in both theory and methodologies, and state-of-the-art applications. Computational and theoretical chemistry research programme in the Department of Chemistry UPM has conducted several studies. Current research topics include protein structure prediction; protein folding/unfolding; in silico modification of biocatalysts and metalloenzymes; self-assembly process of palm-oil based esters; drug nano-delivery systems, and chiral ionic liquids using different computational molecular simulation techniques such as Quantum Mechanics (QM), Molecular Dynamics (MD) & Monte Carlo (MC) methods. It is aimed in the ever-expanding area of this field and its applications to broad scientific fields spanning chemistry, physics, mathematics, computer science, materials and life sciences. Findings have been published in local and international journals. A number of awards have been obtained by our reputable team members. This knowledge has also been shared with society through disclosure in a form of seminars, conferences and exhibitions.
Computational chemistry research is among the research area being explored by members of Department of Chemistry UPM. The application ofcomputationaland simulation techniques can reduce the cost of the initial research and testing, as well as a synergy to the data obtained by experiments. Today, the synergy of experimental data and simulation has become a great trend in publishing high-impact journals.Malaysia still lacks enough experts in computational and theoretical chemistry. This research programme is expected to attract more local students and researchers to participate in the research field. On the other hand, most of the related research in this field is interconnected and it is done by a team of experts locally or globally. Thus, it can help create a network of overseas experts with our local scientist. Given all these developments and the current situation we also need to move forward in training and developing the knowledge and skills in the field of computational chemistry and theoretical science to ensure that we can also be part of the future.
Experience researchers in the following research field;
a)Prof. Dr. Mohd Basyaruddin Abdul Rahman (Catalysis Chemistry, Molecular Modelling)
b)Prof. Dr. Mahiran Basri (Biocatalysis, Enzyme Technology)
d)Dr. Mohamed Ibrahim Mohamed Tahir (Inorganic Chemistry, Molecular Modelling)
More than 10 journal papers published in the international journals & 15 proceedings published nationally & internationally.
More than 5 MSc students graduated or on-going studies
4 PhD students graduated or on-going studies
More than 4 awards have been obtained at national and international level
i.Lim Sen Ven, Mohd Basyaruddin Abdul Rahman and Bimo Ario Tejo (2011). Virtual Screening of New Potential Inhibitors Against Methyltransferase of DengueVirus Using the Program EDULISS and LIDAEUS. BMC Bioinformatics, 2011, 12 (Suppl 13):S24.
ii.Cheong Kok Whye, Leow Thean Chor, Raja Noor Zaliha Abdul Rahman, Mahiran Basri, Mohd Basyaruddin Abdul Rahman and Abu Bakar Salleh (2011).Reductive Alkylation Causes the Formation of a Molten Globule-Like IntermediateStructure in Geobacillus zalihae Strain T1 Thermostable Lipase. Applied Biochemistry and Biotechnology 2011 Jun; 164(3):362-75. Epub 2010 Dec 14.
iii.Lam Kok Wai, Tham Chau Ling, Liew Choi Yi, Syahida Ahmad, Mohd Basyaruddin Abdul Rahman, Daud Israf Ali and Nordin Lajis (2011). Synthesis and Evaluation of DPPH and Anti-Inflammatory Activities of 2,6-Bisbenzylidenecyclohexanone and Pyrazoline Derivatives. Medicinal Chemistry Research2011, (6 January 2011), pp. 1-12.
iv.Mohd Basyaruddin Abdul Rahman, Naimah Haron, Bimo Ario Tejo, Roghayeh Abedi karjiban, Nuno Micaelo, Mahiran Basri and Abu Bakar Salleh (2011). Molecular Dynamics Simulation of New Tetraethylammonium-based Amino Acid Ionic Liquids. Journal of Molecular Modeling (in press).
v.Lam Kok Wai, Syahida Ahmad, Zaheer-ul-Haq Qasmi, Mohd Basyaruddin Abdul Rahman and Nordin Lajis. Synthesis and Biological Activity of Oxadiazole and Triazolothiadiazole Derivatives as Tyrosinase Inhibitors. Bioorganic & Medicinal Chemistry Letters 2010, 20, 3755–3759
vi.Mohd Basyaruddin Abdul Rahman, Muhammad Aliff Mohd Latif, Mahiran Basri, Abu Bakar Salleh and Raja Noor Zaliha Abdul Rahman. Molecular Dynamics Simulation of Oleyl Oleate Swollen Micelles System. Molecular Simulation 2010 1029-0435, Volume 36, Issue 5, Pages 403 – 407.
vii.Roghayeh Abedi karjiban, Mohd Basyaruddin Abdul Rahman, Abu Bakar Salleh, Mahiran Basri, Raja Noor Zaliha Abdul Rahman and Adam Leow Thean Chor. On the Importance of the Small Domain in the Thermostability of Thermoalkalophilic Lipases from L1 and T1: Insights from Molecular Dynamics Simulation, Peptide and Protein Letters 2010 Volume 17, Number 6, June 2010 , pp. 699-707(9).
viii.Mohd Basyaruddin Abdul Rahman, Huan Qiu Yi, Bimo Ario Tejo, Muhammad Aliff Mohd Latif, Mahiran Basri, Raja Noor Zaliha Abdul Rahman and Abu Bakar Salleh. Self-Assembly Formation of Palm-Based Esters Nano-Emulsion: A Molecular Dynamics Study. Chemical Physics Letters, 2009, 480(4-6), 220-224.
ix.Mohd Basyaruddin Abdul Rahman, Roghayeh Abedi karjiban, Adam Leow Thean Chor, Mahiran Basri, Raja Noor Zaliha Abdul Rahman, Abu Bakar Salleh, Habibah Abdul Wahab and Donald Jacobs. Dechipiring the Flexibility and Dynamics of Geobacillus zalihae Strain T1 Lipase at High Temperatures by Molecular Dynamics Simulation. Peptide and Protein Letters, 2009, 16(11), 1360-1370(11).
x.Roghayeh Abedi karjiban, Mohd Basyaruddin Abdul Rahman, Mahiran Basri, Abu Bakar Salleh, Habibah Abdul Wahab and Donald Jacobs. Molecular Dynamics Study of the Structure, Flexibility and Dynamics of Thermostable L1 Lipase at High Temperatures. The Protein Journal, 2009, 28(1), 14-23.
xi.Mohd. Basyaruddin Abdul Rahman, Ahmad Haniff Jaafar, Mahiran Basri, Raja Noor Zaliha Raja Abdul Rahman, Abu Bakar Salleh and Habibah Abdul Wahab. Design of Novel Semisynthetic Metalloenzyme from Thermolysin. BMC Systems Biology, 2007, 1(Suppl 1):P68 (8 May 2007).
xii.Mohd Basyaruddin Abdul Rahman, Azizah Misran, Ahmad Haniff Jaafar, Habibah Abdul Wahab, Raja Noor Zaliha Abdul Rahman, Abu Bakar Salleh and Mahiran Basri. Screening and Docking of Chemical Ligands onto Pocket Cavities of Protease for Desinging a Biocatalyst. Biocatalysis and Biotransformation, 2005, 23, 211-216.
Molecular Dynamics of Palm-Based Swollen Micelles in Nano-emulsion System for Transdermal Non-steroidal Anti-inflammatory Drugs (NSAIDs)
Development & Theoretical Elucidation of Nanodelivery System for Anti-neurodegenerative Drug
Science Fund Special Allocation, MOSTI (Co-researcher)
Postgenomic Discovery of Small Hypothetical Proteins from Bacillus lehensis G1 Alkaliphile
Elucidating Protein Flexibility and Dynamics Using Distance Constraint Model for in silico Protein Design
All of these grants are also supported by computational & simulation work:
a)Peptides Design and Synthesis Based on Enzyme Mimic for Industrial Needs
a.Grant: Science Fund Special Allocation, MOSTI
b.RM 500,000.00 – 2011 (on-going)
b)Designer Biocatalyts for Sustainable Processes in the Conversion of Renewable Raw Materials to Platform Chemicals
a.Grant: Genetics and Molecular Biology Iniatives, BIOTEK, MOSTI
b.RM 4,853,400.00 – 2009 (on-going)
c)Structural Prediction of Anti-Freeze Protein from Leucosporidium antarctica
a.Grant: Genetics and Molecular Biology Iniatives, BIOTEK, MOSTI