Dalia Rokhsana

Assistant Professor (Computational and Bioinorganic Chemistry)

Hall of Science 338
(509) 527-5953 (phone) (509) 527-5904 (fax)

Bio

Dalia joined the Department of Chemistry at Whitman as a tenure-track assistant professor in Fall 2011. She came to Whitman in Fall 2010 as a visiting assistant professor from Montana State University in Bozeman, Montana where she conducted her postdoctoral work with Prof. David Dooley and Prof. Robert Szilagyi in the field of Bioinorganic Chemistry. Her doctoral work was in Inorganic/Organometallic chemistry at The University of Montana, Missoula, under the supervision of Prof. Edward Rosenberg. Prior to coming to the states, Dalia obtained her B. Sc. (honors) degree in Chemistry from Jahangirnagar University, Dhaka, Bangladesh. She was born and brought up in a small town located at the southwestern part of Bangladesh where she completed her early education. Dalia's current research interests are in biological systems that utilize metal atoms for their functions. She uses computational simulation to understand structure/function relationship of a bacterial enzyme, carbon monoxide dehydrogenase that removes toxic carbon monoxide from the environment while splitting water molecules to produce protons and electrons, and could be used to generate hydrogen as an alternative energy source. She is also interested to design, and synthesize functionally analogous biomimetic model complexes for splitting water molecules. She teaches a wide range of classes including General Chemistry, Organic Laboratory Techniques, Biochemistry, Advanced Synthesis and Computational Biochemistry.

Education

  • Ph.D in Inorganic Chemistry, The University of Montana, Missoula, Montana, 2005
  • B. Sc. (Honors) in Chemistry, Jahangirnagar University, Dhaka, Bangladesh, 1998

Awards

  • 2005: Outstanding Foreign Student Award, The University of Montana,Missoula MT
  • 2005: Diversity Student Achievement Award, The University of Montana, Missoula, MT
  • 2002: Bertha Morton Scholarship for outstanding graduate student, The University of Montana, Missoula, MT
  • 2002: Lola Walsh Anacker Scholarship for outstanding female graduate student, Department of Chemistry, The University of Montana, Missoula, MT

For more information, please see my Curriculum Vitae.

Courses in 2016-17

Fall 2016

  • Advanced General Chemistry (CHEM-140)
  • Biochemistry (BBMB-325)

Spring 2017

  • General Chemistry II (CHEM-126)
  • Advanced Synthesis (CHEM-370)

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Other Courses Taught at Whitman

  • General Chemistry I & II (CHEM-125 & 126)
  • Organic Lab Techniques I & II (CHEM-251 & 252)
  • Inorganic Chemistry (CHEM-360)
  • Advanced Synthesis (CHEM-370)
  • Biochemistry (BBMB-325)
  • Computational Biochemistry (CHEM-425)

Official Course Descriptions

General Chemistry (CHEM-125)

The first semester of a yearlong course in introductory chemistry. Topics include atomic and molecular structure; periodic properties of the elements; chemical bonding; properties of gases, liquids, and solids; stoichiometry; aqueous solution reactions; and perhaps an introduction to organic chemistry and biochemistry. Problem-solving involves the use of algebra. Three lectures per week. Prerequisite: two years of high school mathematics or consent of instructor.

General Chemistry (CHEM-126)

The second semester of a yearlong course in introductory chemistry. Topics include properties of solutions, elementary thermodynamics, introduction to chemical equilibrium, kinetics, oxidation-reduction and electrochemistry, acids and bases, environmental issues, and nuclear chemistry. Problem-solving in this course involves the use of logarithms and algebra including the quadratic formula. Three lectures per week. Prerequisite: Chemistry 125.

Organic Lab Techniques I (Chem251)

Introduction to fundamental organic laboratory techniques. Topics include recrystallization, distillation, melting point determination, chromatography, extraction, and one-step syntheses. One three-hour laboratory per week. Prerequisite: Chemistry 126 or Chemistry 140. Pre- or corequisite: Chemistry 245.

Organic Lab Techniques II (CHEM-252)

Continuation of organic laboratory techniques involving intermediate exercises. The course covers more challenging syntheses as compared to Chemistry 251, as well as multistep synthesis and spectroscopic analysis of products. One three-hour laboratory per week. Prerequisite: Chemistry 251. Pre- or corequisite: Chemistry 246.

Advanced Inorganic Chemistry (CHEM-360)

The concepts of modern inorganic chemistry at an advanced level. Selected topics are explored in depth rather than in a review of the entire field. Possible topics include transition-metal complexes and theories of metal-ligand bonding, acid-base theories and nonaqueous solvents, kinetics and mechanisms of transition-metal-complex reactions, bonding in solids, atomic structure and term symbols, symmetry and group theory. Three lectures per week. Pre- or corequisite: Chemistry 346.

Biochemistry (BBMB-325)

A detailed examination of protein structure and function, focusing on the role of proteins in molecular recognition and catalysis. Topics include: techniques used to characterize proteins; enzyme kinetics and mechanisms; signal transduction across membranes; bioenergetics; catabolism of proteins, fats, and carbohydrates; integration of metabolism and disease. Three lectures per week. Fulfills the Molecular/Cell Biology requirement for the Biology major.Prerequisites: Biology 111, Chemistry 246.

Advanced Methods in Inorganic and Organic Synthesis and Characterization  (CHEM-370)

This is an advanced laboratory course that combines both organic and inorganic synthesis with physical methods of characterization. A large portion of this course is an independent project chosen and developed by students within a specific theme. Two three- to four-hour laboratories per week. Prerequisites: Chemistry 246, 252, and 345. Prerequisite (recommended) or corequisite: Chemistry 360.

Computational Biochemistry (CHEM-425A)

The goal of this course is to develop a comprehensive understanding of the molecular principles necessary to understand the structures and functions of different chemical and biochemical systems using empirical and quantum-mechanical computational techniques. It will allow students to develop and graphically visualize the electronic wave function and its various properties of these systems and validate their findings through experimental data. Laboratory exercises will equip students with various computational tools to study different chemical and biochemical systems. The planned exercises are expected to improve the students' ability to generate chemical models as well as use them in quantitative analyses in further chemistry studies. Prerequisite: Chemistry 246.

Computational Simulations & Biomimetic Models

Biogeochemical carbon, nitrogen, water, and sulfur cycles are important in many aspects of our life. During these complex cycles, small molecules (such as CO2, CO, N2, and H2) are made more reactive at ambient temperatures and pressures. The enzymes involved generally contain complex inorganic active sites and understanding the activation of inert molecules by these sites is still one of the most challenging areas at the interface of chemistry and biology. Studying this active site should significantly enhance our understanding of how biological systems achieve high reaction rates, exquisite selectivity, and chemically challenging transformations under ambient conditions. Understanding how nature works so efficiently can have implications for developing future environmentally friendly “green” catalysts.

My research interest is to investigate the molybdenum-catalyzed transformation of CO, which is an intermediate in the carbon cycle. Aerobic and anaerobic microorganisms catalyze the conversion of toxic carbon monoxide to less-toxic carbon dioxide, and play an important role in the regulation of atmospheric CO levels by removing an estimated 108 tons of CO from the atmosphere annually. More importantly, CO transformation is unique in the sense that it utilizes acid-base and redox reactions, and also involves the splitting of a water molecule during the catalytic cycle to generate two electrons and two protons. The two protons and electrons produced in the reaction can be utilized to generate hydrogen gas, an alternative fuel source. This is an extremely challenging transformation, and many researchers are actively investigating the viability of this process. Activation of CO occurs at a binuclear Mo-Cu center in carbon monoxide dehydrogenase (shown in Figure).

CODH Mo is coordinated to the dithiolate of the molybdopterin-cytosine dinucleotide (MCD) cofactor with two oxo and sulfido ligands. The catalytically active state has been characterized structurally and is believed to be the oxidized form, MoVI-CuI. CO is proposed to bind at the active site pocket of the oxidized state between the Mo and the Cu atom, and interacts with the bridging sulfur. During the catalytic cycle, CO is oxidized while Mo is reduced from a +6 to +4 oxidation state while the Cu remains at a +1 oxidation state. Structural and spectroscopic data are in agreement as to the geometric environment around the Mo-Cu center; however, they significantly differ in regards to several key bond distances. These distance anomalies could be due to radiation damage during X-ray data collection and/or the different physical states of the enzyme. Furthermore, electronic communication between the Mo-Cu center in CODH appears to be critical because the enzyme is non-functional in the absence of Cu. A linear Cu concentration dependence on specific activities has been reported, which suggests that the redox inactive Cu center plays a critical role in enzyme functionality. Here are couple of the specific research questions that we are exploring at my laboratory:

  • How does the protein environment tune the active site in biological CO conversion?
  • What is the significance of the redox inactive yet obligatory Cu center in CODH?
  • What is the molecular mechanism of CO to CO2 conversion?
  • What are the key design parameters for creating improved synthetic models that mimic the CODH active site?

Current Projects

We are employing quantum mechanical calculation to find structurally and theoretically converged computational models for the active and intermediate states of CODH which will assist us to address the first three questions specified above. Knowledge from our computational studies will be utilized to design and synthesize model complexes of this enzyme that have potential promise in environmental and industrial applications for cleaner energy.

Computational Resources

ServersSoftware for QM and QM/MM Simulations:
Gaussian'09, ORCA, Gromacs, pDynamo

Visualization: Chemcraft, Discovery Studio, PyMoL

Servers: Total ~ 200 cores.

  1. Rokhsana, D.; Large, T.; Dienst, M.; Retegan, M., Neese, F. A realistic in silico model for structure/function studies of molybdenum-copper CO dehydrogenase, Journal of Biological Inorganic Chemistry, 2016, 21(4), 491-499 (DOI: 10.1007/s00775-016-1359-6)

  2. Schofield, J. A., Brennessel, W. W., Urnezius, E., Rokhsana, D., Boshart, M. D., Juers, D. H., Holland, P. L. and Machonkin, T. E. (2015), Metal–Halogen Secondary Bonding in a 2,5-Dichlorohydroquinonate Cobalt(II) Complex: Insight into Substrate Coordination in the Chlorohydroquinone Dioxygenase PcpA. European Journal of Inorganic Chemistry, 2015: 4643–4647.

  3. Machonkin, T. E.; Boshart, M. D.; Schofield, J. A.; Rodriguez, M. M.; Grubel, K.; Rokhsana, D.; Brennessel, W. W.; Holland, P. L. Structural and Spectroscopic Characterization of Iron(II), Cobalt(II), and Nickel(II) Ortho-Dihalophenolate Complexes: Insights into Metal-Halogen Secondary Bonding, Inorganic Chemistry, (2014), 53(18), 9837-9848.

  4. Rokhsana, D.; Howells A. E,; Dooley D.M.; Szilagyi, R. K. “The Role of the Tyr-Cys Crosslink to the active site properties of galactose oxidase” Inorganic Chemistry, 2012, 51(6), 3513-3512.

  5. Rokhsana, D.; Shepard, E. M.; Brown, D. E.; Dooley, D. M. (2011) Amine Oxidase and Galactose Oxidase, in Copper-Oxygen Chemistry (eds K. D. Karlin and S. Itoh), John Wiley & Sons, Inc., Hoboken, NJ, USA. doi: 10.1002/9781118094365.ch3

  6. Begum, N.; Hyder, M.L.; Hassan, M. R.; Kabir, S. E.; Bennett, D. W.; Haworth, D. T.; Siddiquee, T. A.; Rokhsana, D.; Sharmin, A.; Rosenberg, E. “ Facile E-E and E-C bond activation of PhEEPh (E = Te, Se, S) by ruthenium carbonyl clusters: Formation of Di- and triruthenium complexes bearing bridging dppm and phenylchalcogenide and capping chalcogenido ligands” Organometallics, 2008, 27, 1550-1560.

  7. Rokhsana, D.; Dooley, D. M.; Szilagyi, R. K . “Systematic development of computational models for the catalytic site in galactose oxidase: impact of outer-sphere residues on the geometric and electronic structures” Journal of Biological Inorganic Chemistry, 2008, 13, 371-383

  8. Rokhsana, D.; Dooley, D. M.; Szilagyi, R. K. “Structure of the oxidized active site of galactose oxidase from realistic in silico models” Journal of the American Chemical Society, 2006, 128(49), 15550-15551.

  9.  Begum, N.; Hyder, Md. I.; Kabir, S. E.; Hossain, G. M. G.; Nordlander, E.; Rokhsana, D.; Rosenberg, E. “ Dithiolate complexes of manganese and rhenium: X-ray structure and properties of an unusual mixed valence cluster Mn3(CO)6(m-h2-SCH2CH2CH2S)3Inorganic Chemistry, 2005, 44(26), 9887-9894.

  10. Mottalib, Md. A; Begum, N.; Abedin, S. M. T.; Akter, T.; Kabir, S. E.; Miah, Md. A. Rokhsana, D.; Rosenberg, E.; Hossain, G. M. G.; Hardcastle, K. I. “Reactions of electron-deficient triosmium clusters with diazomethane: electrochemical properties and computational studies of charge distribution” Organometallics, 2005, 24(20), 4747-4759.

  11. Kabir, S. E.; Miah, Md. A.; Sarker, N. C.; Hossain, G. M. G.; Hardcastle, K. I.; Rokhsana, D.; Rosenberg, E. “Reactions of the unsaturated triosmium cluster [(μ-H) Os3(CO)8 (Ph2PCH2P(Ph)C6H4)] with HX (X = Cl, Br, F, CF3CO2,CH3CO2): X ray structures of [(μ-H)Os3 (CO)71-Cl)( μ -Cl)2(μ -dppm)], [(μ-H)2Os3(CO)8(Ph2PCH2P(Ph)C6H4)]+[CF3O]-  and the two isomers of [(μ-H)Os3(CO)8(μ-Cl)(μ-dppm)]” Journal of Organometallic Chemistry, 2005, 690, 3044-3053.

  12. Begum, N.; Deeming, A.; Islam, M.; Kabir, S.; Rokhsana, D.; Rosenberg, E. “Reactions of benzothiazolide triosmium clusters with tetramethylthiourea” Journal of Organometallic Chemistry, 2004, 689(16), 2633-2640.

  13. Nervi, C.; Gobetto, R.; Milone, L.; Viale, A.; Rosenberg, E.; Spada, F.; Rokhsana, D.; Fiedler, J. “Solution properties, electrochemical behavior and protein interactions of water soluble triosmium carbonyl clusters” Journal of Organometallic Chemistry, 2004, 689(10), 1796-1805

  14. Rosenberg, E.; Rokhsana, D.; Nervi, C.; Gobetto, R.; Milone, L.; Viale, A.; Fiedler, J.; Botavina, M. A. “Synthesis, reduction chemistry, and spectroscopic and computational studies of isomeric quinoline carboxaldehyde triosmium clusters” Organometallics, 2004, 23(2), 215-223

  15. Nervi, C.; Gobetto, R.; Milone, L.; Viale, A.; Rosenberg, E.; Rokhsana, D.; Fiedler, J. “Spectroscopic and computational investigations of stable radical anions of triosmium benzoheterocycle clusters” Chemistry-A European Journal, 2003, 9(23), 5749-5756.

  16. Rosenberg, E.; Abedin, M. J.; Rokhsana, D.; Viale, A.; Dastru', W.; Gobetto, R.; Milone, L.; Hardcastle, K . “Ligand dependent structural changes in the acid-base chemistry of electron deficient benzoheterocycle triosmium clusters” Inorganic Chimica Acta, 2002, 334, 343-354

  17. Rosenberg, E.; Abedin, M. J.; Rokhsana, D.;Osella, D.; Milone, L.; Nervi, C.; Fiedler, J. “ The electrochemical behavior of electron deficient benzoheterocycle triosmium clusters” Inorganic Chimica Acta, 2000, 300-302, 769-777