Mark R. Nimlos

Mark Nimlos is a Principal Scientist and Supervisor for the Biomass Molecular Sciences group in the National Bioenergy Center at the National Renewable Energy Laboratory.

Education

Ph.D., Chemical Physics, University of Colorado at Boulder, Boulder, CO, 1986
B.S., Chemistry, University of Massachusetts, Boston, MA, 1981

Research Interests and Selected Publications

The Biomass Molecular Sciences group performs research in the following areas:

Molecular dynamics modeling of cellulases
Chemistry of biomass pretreatment
Science of thermal conversion of biomass
Molecular spectroscopy.

Details about our research and links to peer-reviewed publications are provided in the following sections.

Molecular Dynamics Modeling of Cellulases

We use molecular dynamics modeling to understand the relationship between the structure and function of cellulase enzymes and their interaction with cellulose substrates. The ultimate goal of this research is to be able to design more efficient cellulose-degrading enzymes or enzyme complexes.

Selected publications on the molecular dynamics modeling of cellulases:

Beckham, G. T.; Matthews, J. F.; Bomble, Y. J.; Bu, L. T.; Adney, W. S.; Himmel, M. E.; Nimlos, M. R.; Crowley, M. F. (2010). "Identification of Amino Acids Responsible for Processivity in a Family 1 Carbohydrate-Binding Module from a Fungal Cellulase." Journal of Physical Chemistry B (114:3); pp. 1447-1453.
Zhong, L. H.; Matthews, J. F.; Hansen, P. I.; Crowley, M. F.; Cleary, J. M.; Walker, R. C.; Nimlos, M. R.; Brooks, C. L.; Adney, W. S.; Himmel, M. E.; Brady, J. W. (2009). "Computational Simulations of the Trichoderma reesei Cellobiohydrolase I acting on Microcrystalline Cellulose I Beta: The Enzyme-Substrate Complex." Carbohydrate Research (344:15); pp. 1984-1992.
Bu, L. T.; Beckham, G. T.; Crowley, M. F.; Chang, C. H.; Matthews, J. F.; Bomble, Y. J.; Adney, W. S.; Himmel, M. E.; Nimlos, M. R. (2009). "The Energy Landscape for the Interaction of the Family 1 Carbohydrate-Binding Module and the Cellulose Surface is Altered by Hydrolyzed Glycosidic Bonds." Journal of Physical Chemistry B (113:31); pp. 10994-11002.
Zhong, L.; Matthews, J. F.; Crowley, M. F.; Rignall, T.; Talon, C.; Cleary, J. M.; Walker, R. C.; Chukkapalli, G.; McCabe, C.; Nimlos, M. R.; Brooks, C. L.; Himmel, M. E.; Brady, J. W. (2008). "Interactions of the Complete Cellobiohydrolase I from Trichoderma reesei with Microcrystalline Cellulose I Beta." Cellulose (15:2); pp. 261-273.
Nimlos, M. R.; Matthews, J. F.; Crowley, M. F.; Walker, R. C.; Chukkapalli, G.; Brady, J. V.; Adney, W. S.; Clearyl, J. M.; Zhong, L. H.; Himmel, M. E. (2007). "Molecular Modeling Suggests Induced Fit of Family I Carbohydrate-Binding Modules with a Broken-Chain Cellulose Surface." Protein Engineering Design & Selection (20:4); pp. 179-187.

Chemistry of Biomass Pretreatment

We use experiments and quantum modeling to understand the chemistry of biomass pretreatment. Our focus has been primarily on the production and loss of sugars during acid pretreatment.

Selected publications on the chemistry of biomass pretreatment:

Pilath, H. M.; Nimlos, M. R.; Mittal, A.; Himmel, M. E.; Johnson, D. K. (2009). "Glucose Reversion Reaction Kinetics." Journal of Agricultural and Food Chemistry (58:10); pp. 6131-6140.
Dong, H. T.; Nimlos, M. R.; Himmel, M. E.; Johnson, D. K.; Qian, X. H. (2009). "The Effects of Water on Beta-D-Xylose Condensation Reactions." Journal of Physical Chemistry A (113:30); pp. 8577-8585.
Nimlos, M. R.; Qian, X. H.; Davis, M.; Himmel, M. E.; Johnson, D. K. (2006). "Energetics of Xylose Decomposition as Determined using Quantum Mechanics Modeling." Journal of Physical Chemistry A (110:42); pp. 11824-11838.

The Science of Thermal Conversion of Biomass

Our research has been directed toward trying to understand the chemistry and physics of thermochemical processes for the conversion of biomass, with an eye toward making these processes more efficient and more selective. We use a variety of computational and experimental approaches.

Selected publications on the science of thermal conversion of biomass:

Carpenter, D. L.; Bain, R. L.; Davis, R. E.; Dutta, A.; Feik, C. J.; Gaston, K. R.; Jablonski, W.; Phillips, S. D.; Nimlos, M. R. (2010). "Pilot-Scale Gasification of Corn Stover, Switchgrass, Wheat Straw, and Wood: 1. Parametric Study and Comparison with Literature." Industrial & Engineering Chemistry Research (49:4); pp. 1859-1871.
Vasiliou, A.; Nimlos, M. R.; Daily, J. W.; Ellison, G. B. (2009). "Thermal Decomposition of Furan Generates Propargyl Radicals." Journal of Physical Chemistry A (113:30); pp. 8540-8547.
Jablonski, W.; Gaston, K. R.; Nimlos, M. R.; Carpenter, D. L.; Feik, C. J.; Phillips, S. D. (2009). "Pilot-Scale Gasification of Corn Stover, Switchgrass, Wheat Straw, and Wood: 2. Identification of Global Chemistry Using Multivariate Curve Resolution Techniques." Industrial & Engineering Chemistry Research (48:23); pp. 10691-10701.
Haas, T. J.; Nimlos, M. R.; Donohoe, B. S. (2009). "Real-Time and Post-Reaction Microscopic Structural Analysis of Biomass Undergoing Pyrolysis." Energy Fuels (23:7); pp. 3810-3817.
Bahng, M. K.; Mukarakate, C.; Robichaud, D. J.; Nimlos, M. R. (2009). "Current Technologies for Analysis of Biomass Thermochemical Processing: A Review." Analytica Chimica Acta (651:2); pp. 117-138.
Nimlos, M. R.; Blanksby, S. J.; Qian, X. H.; Himmel, M. E.; Johnson, D. K. (2006). "Mechanisms of Glycerol Dehydration." Journal of Physical Chemistry A (110:18); pp. 6145-6156.
Shin, E. J.; Nimlos, M. R.; Evans, R. J. (2001). "Kinetic Analysis of the Gas-Phase Pyrolysis of Carbohydrates." Fuel (80:12); pp. 1697-1709.
Shin, E. J.; Nimlos, M. R.; Evans, R. J. (2001). "A Study of the Mechanisms of Vanillin Pyrolysis by Mass Spectrometry and Multivariate Analysis." Fuel (80:12); pp. 1689-1696.
Friderichsen, A. V.; Shin, E. J.; Evans, R. J.; Nimlos, M. R.; Dayton, D. C.; Ellison, G. B. (2001). "The Pyrolysis of Anisole (C6H5OCH3) Using a Hyperthermal Nozzle." Fuel (80:12); pp. 1747-1755.
Brown, A. L.; Dayton, D. C.; Nimlos, M. R.; Daily, J. W. (2001). "Characterization of Biomass Pyrolysis Vapors with Molecular Beam, Single Photon Ionization Time-of-Flight Mass Spectrometry." Chemosphere (42:5-7); pp. 663-669.
Brown, A. L.; Dayton, D. C.; Nimlos, M. R.; Daily, J. W. (2001). "Design and Characterization of an Entrained Flow Reactor for the Study of Biomass Pyrolysis Chemistry at High Heating Rates." Energy Fuels (15:5); pp. 1276-1285.

Molecular Spectroscopy

We primarily use matrix isolation infrared spectroscopy to investigate structures and reactivity of transient molecules and radicals.

Selected publications in molecular spectroscopy:

Jochnowitz, E.; Zhang, X.; Nimlos, M. R.; Flowers, B.; Stanton, J. F.; Ellison, G. B. (2010). "Infrared Spectrum of the Propargyl Peroxyl Radical, HC≡C—CH2OO X̃ 2A′′." Journal of Physical Chemistry A (114:3); pp. 1498-1507.
Zhang, X.; Nimlos, M. R.; Ellison, G. B.; Varner, M. E.; Stanton, J. F. (2007). "Vibrational Overtone Spectrum of Matrix Isolated cis, cis-HOONO." Journal of Chemical Physics (126:17); 174308-1-5.
Zhang, X.; Maccarone, A. T.; Nimlos, M. R.; Kato, S.; Bierbaum, V. M.; Ellison, G. B.; Ruscic, B.; Simmonett, A. C.; Allen, W. D.; Schaefer III, H. F. (2007). "Unimolecular Thermal Fragmentation of ortho-Benzyne." Journal of Chemical Physics (126:4); pp. 44312-1-20.
Zhang, X.; Nimlos, M. R.; Ellison, G. B.; Varner, M. E.; Stanton, J. F. (2006). "Infrared Absorption Spectra of Matrix-Isolated cis, cis-HOONO and its ab initio CCSD(T) Anharmonic Vibrational Bands." Journal of Chemical Physics (124:8); pp. 084305-1-7.
Jochnowitz, E. B.; Zhang, X.; Nimlos, M. R.; Varner, M. E.; Stanton, J. F.; Ellison, G. B. (2005). "Propargyl Radical: Ab Initio Anharmonic Modes and the Polarized Infrared Absorption Spectra of Matrix-Isolated HCCCH2." Journal of Physical Chemistry A (109:17); pp. 3812-3821.
Zhang, X.; Friderichsen, A. V.; Nandi, S.; Ellison, G. B.; David, D. E.; McKinnon, J. T.; Lindeman, T. G.; Dayton, D. C.; Nimlos, M. R. (2003). "Intense, Hyperthermal Source of Organic Radicals for Matrix-Isolation Spectroscopy." Review of Scientific Instruments (74:6); pp. 3077-3086.
Nandi, S.; Blanksby, S. J.; Zhang, X.; Nimlos, M. R.; Dayton, D. C.; Ellison, G. B. (2002). "Polarized Infrared Absorption Spectrum of Matrix-Isolated Methylperoxyl Radicals, CH3OO (X)over-tilde 2A''." Journal of Physcial Chemistry A (106:33); pp. 7547-7556.
Nandi, S.; Arnold, P. A.; Carpenter, B. K.; Nimlos, M. R.; Dayton, D. C.; Ellison, G. B. (2001). "Polarized Infrared Absorption Spectra of Matrix-Isolated Allyl Radicals." Journal of Physical Chemistry A (105:32); pp. 7514-7524.
Friderichsen, A. V.; Radziszewski, J. G.; Nimlos, M. R.; Winter, P. R.; Dayton, D. C.; David, D. E.; Ellison, G. B. (2001). "The Infrared Spectrum of the Matrix-Isolated Phenyl Radical." Journal of the American Chemical Society (123:9); pp. 1977-1988.

Contact Information

Mark Nimlos
15013 Denver West Parkway, MS 3322
Golden, CO 80401
Phone: 303-384-7704
E-mail: Mark.Nimlos@nrel.gov

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