Group Publications

Department of Chemical and Biological Engineering

2016

Zhou, X., Li, W., Malbon, R., and Broadbelt, L.J. "A critical review of hemicellulose pyrolysis," Energy Technol., 2016, 5, 52-79.

Zhou, X., Broadbelt, L.J., and Vinu, R. "Chapter Two-Mechanistic understanding of thermochemical conversion of polymers and lignocellulosic biomas," Advances in Chemical Engineering, 2016, 49, 95-198.

Moura, M., Pertusi, D., Lenzini, S., Bhan, N., Broadbelt, L.J., and Tyo, K.E.J. "Characterizing and predicting carboxylic acid reductase activity for diversifying bioaldehyde production," Biotechnol. Bioeng., 2016, 113, 944-952.

Stine, A., Zhang, M., Ro, S., Clendennen, S., Shelton, M.C., Tyo, K.E.J., and Broadbelt, L.J. "Exploring De Novo metabolic pathways from pyruvate to propionic acid," Biotechnol. Prog., 2016, 32, 303-311.

Zhou, X., Mayes, H.B., Broadbelt, L.J., Nolte, M.W., and Shanks, B.H. "Fast pyrolysis of glucose-based carbohydrates with added NaCl part 1: Experiments and development of a mechanistic model," AIChE Journal, 2016, 62, 766-777.

Zhou, X., Mayes, H.B., Broadbelt, L.J., Nolte, M.W., and Shanks, B.H. "Fast pyrolysis of glucose-based carbohydrates with added NaCl part 2: Validation and evaluation of the mechanistic model," AIChE Journal, 2016, 62, 778-791.

Moura, M., Finkle, J., Stainbrook, S., Greene, J., Broadbelt, L.J., and Tyo, K.E.J. "Evaluating enzymatic synthesis of small molecule drugs," Metabolic Engineering, 2016, 33, 138-147.

2015

Gao, H., Oakley, L.H., Konstantinov, I.A., Arturo, S.G., and Broadbelt, L.J. "Acceleration of Kinetic Monte Carlo Method for the Simulation of Free Radical Copolymerization through Scaling," Ind. Eng. Chem. Res., 2015, 54, 11975-11985.

Evans, C.M., Kim, S., Roth, C.B., Priestley, R.D., Broadbelt, L.J., and Torkelson, J.M. "Role of neighboring domains in determining the magnitude and direction of Tg-confinement effects in binary, immiscible polymer systems," Polymer, 2015, 80, 180-187.

Oakley, L.H., Casadio, F., Shull, K.R., and Broadbelt, L.J. "Microkinetic modeling of the autoxidative curing of an alkyd and oil-based paint model system," Appl. Phys. A, 2015, 121, 869-878.

Jeffryes, J.G., Colastani, R.L., Elbadawi-Sidu, M., Kinda, T., Niehaus, T.D., Broadbelt, L.J., Hanson, A.D., Fiehn, O., Tyo, K.E.J., and Henry, C.S. "MINEs: open access databases of computationally predicted enzyme promiscuity products for untargeted metabolomics," J. Cheminform., 2015, 7.

Pelzer, A., Sturgeon, M.R., Yanez, A.W., Chupka, G., O'Brien, M.-K.R., Katahira, R., Cortright, R., Woods, L., Beckham, G.T., and Broadbelt, L.J. "Acidolysis of alpha-O-4 Aryl-Ether Bonds in Lignin Model Compounds: A Modeling and Experimental Study," ACS Sustainable Chem. Eng., 2015, 3, 1339-1347.

Burnham, A.K., Zhou, X., and Broadbelt, L.J. "Critical Review of the Global Chemical Kinetics of Cellulose Thermal Decomposition," Energy Fuels, 2015, 29, 2906-2918.

Ma, R., Schuette, G.F., and Broadbelt, L.J. "Towards Understanding the Activity of Cobalt Carbonic Anhydrase: A Comparative Study of Zinc- and Cobalt-Cyclen," Appl. Catal., A, 2015, 492, 151-159.

Pertusi, D.A., Stine, A.E., Broadbelt, L.J., and Tyo, K.E.J. "Efficient Searching and Annotation of Metabolic Networks Using Chemical Similarity," Bioinformatics, 2015, 31, 1016-1024.

Mayes, H.B., Nolte, M.W., Beckham, G.T., Shanks, B.H., and Broadbelt, L.J. "The Alpha-Bet(a) of Salty Glucose Pyrolysis: Computational Investigations Reveal Carbohydrate Pyrolysis Catalytic Action by Sodium Ions," ACS Catal., 2015, 5, 192-202.

2014

Bjorkman, K., Sung, C., Mondor, E., Cheng, J.C., Jan, D.-Y., and Broadbelt, L.J. "Group Additivity Determination for Enthalpies of Formation of Carbenium Ions," Ind. Eng. Chem. Res., 2014, 50(53), 19446-19452.

Zhang, G., Konstantinov, I.A., Arturo, S.G., Yu, D., and Broadbelt, L.J. "Assessment of a Cost-Effective Approach to the Calculation of Kinetic and Thermodynamic Properties of Methyl Methacrylate Homopolymerization: A Comprehensive Theoretical Study," J. Chem. Theory Comput., 2014, 10(12), 5668-5676.

Weiss, M.S., Penalver-Bernabe, B., Shin, S., Asztalos, S., Dubbury, S.J., Mui, M.D.; Bellis, A.D., Bluver, D., Tonetti, D.A., Saez-Rodriguez, J., Broadbelt, L.J., Jeruss, J.S. and Shea, L.D. . "Dynamic Transcription Factor Activity and Networks During ErbB2 Breast Oncogenesis and Targeted Therapy," Integr. Biol., 2014, 6, 1170-1182.

Regatte, V.R., Gau, H., Konstantinov, I.A., Arturo, S.G., and Broadbelt, L.J. "Design of Copolymers Based on Sequence Distribution for a Targeted Molecular Weight and Conversion," Macromol. Theory Simul., 2014, 23(9), 564-574.

Ma, R., Schuette, G.F., and Broadbelt, L.J. "Insights into the Relationship of Catalytic Activity and Structure: A Comparison Study of Three Carbonic Anhydrase Mimics," Int. J. Chem. Kinet., 2014, 46, 683-700.

Zhou, X., Nolte, M.W., Mayes, H.B., Shanks, B.H., and Broadbelt, L.J. "Experimental and Mechanistic Modeling of Fast Pyrolysis of Neat Glucose-Based Carbohydrates. 1. Experiments and Development of a Mechanistic Model," Ind. Eng. Chem. Res., 2014, 53, 13274-13289. Selected as the ACS Editors' Choice article for August 16, 2014.

Zhou, X., Nolte, M. W., Shanks, B.H., and Broadbelt, L.J. "Experimental and Mechanistic Modeling of Fast Pyrolysis of Neat Glucose-Based Carbohydrates. 2. Validation and Evaluation of the Mechanistic Model," Ind. Eng. Chem. Res., 2014, 53, 13290-13301.

Ma, R., Schuette, G.F., and Broadbelt, L.J. "Microkinetic modeling of CO2 hydrolysis over Zn-(1,4,7,10-tetraazacyclododecane) catalyst based on first principles: Revelation of rate-determining step," J. Catal., 2014, 317, 176-184.

Zhang, S., Broadbelt, L.J., Androulakis, I.P., and Ierapetritou, M.G. "Reactive Flow Simulation Based on the Integration of Automated Mechanism Generation and On-the-Fly Reduction," Energy Fuels, 2014, 28(7), 4801-4811.

Wu, D., Yue, D., You, F., and Broadbelt, L.J. "Computational evaluation of factors governing catalytic 2-keto acid decarboxylation," J. Mol. Model., 2014, 20, 2310.

Mayes, H.B., Nolte, M.W., Beckham, G.T., Shanks, B.H., and Broadbelt, L.J. "The Alpha-Bet(a) of Glucose Pyrolysis: Computational and Experimental Investigations of 5-Hydroxymethylfurfural and Levoglucosan Formation Reveal Implications for Cellulose Pyrolysis," ACS Sustainable Chem. Eng., 2014, 2(6), 1461-1473. Selected as the ACS Editors' Choice article for May 15, 2014.

Mayes, H.B., Tian, J., Nolte, M.W. Shanks, B.H., Beckham, G.T., Gnanakaran, S., and Broadbelt, L.J. "Sodium Ion Interactions with Aqueous Glucose: Insights from Quantum Mechanics, Molecular Dynamics, and Experiment," J. Phys. Chem. B, 2014, 118(8), 1990-2000. Featured on the cover of the February 27, 2014 issue.

Mayes, H.B., Broadbelt, L.J., and Beckham, G.T. "How sugars pucker: Electronic structure calculations map the kinetic landscape of five biologically paramount monosaccharides and their implications for enzymatic catalysis," J. Am. Chem. Soc., 2014, 136(3), 1008-1022.

Zamora, M.A., Pinzón, A., Zambrano, M.M., Restrepo, S., Broadbelt, L.J., Moura, M., and Barrios, A.F.G. "Analysis of Metabolic Functionality and Thermodynamic Feasibility of a Metagenomic Sample from 'El Coquito' Hot Spring," in Advances in Computational Biology, 2014, 287-293.

2013

Moura, M., Broadbelt, L., and Keith Tyo, K. "Computational Tools for Guided Discovery and Engineering of Metabolic Pathways," in Systems Metabolic Engineering., 2013, 123-147.

Bao, X., Snurr, R.Q., and Broadbelt, L.J. "Insights into the Complexity of Chiral Recognition by a Three-Point Model," Microporous Mesoporous Mater., 2013, 172, 44-50.

Skory, R.M., Penalver-Bernabe, B., Galdones, E., Broadbelt, L.J., Shea, L.D. and Woodruff, T.K. "Microarray analysis identifies COMP as the most differentially regulated transcript throughout in vitro follicle growth," Mol. Reprod. Dev., 2013, 80(2), 132-144.

Bellis, A.D., Penalver-Bernabe, B., Weiss, M.S., Shin, S., Weng, S. Broadbelt, L.J. and Shea, L.D. "Dynamic transcription factor activity profiling in 2D and 3D cell cultures," Biotechnol. Bioeng., 2013, 110(2), 563-572.

2012

Vinu, R., and Broadbelt, L.J. "A mechanistic model of fast pyrolysis of glucose-based carbohydrates to predict bio-oil composition," Energy Environ. Sci., 2012, 5, 9808-9826 (DOI: 10.1039/C2EE22784C).

Yu, X., and Broadbelt, L.J. "Kinetic Study of 1,5-Hydrogen Transfer Reactions of Methyl Acrylate and Butyl Acrylate Using Quantum Chemistry," Macromol. Theor. Simul., 2012, 21, 461-469.

Bao, X., Broadbelt, L.J. and Snurr, R.Q. "Computational screening of homochiral metal-organic frameworks for enantioselective adsorption," Micropor. Mesopor. Mat., 2012, 157, 118-123.

Bjorkman, K.R., Schoenfeldt, N.J., Notestein, J.M., and Broadbelt, L.J. "Microkinetic modeling of cis-cyclooctene oxidation on heterogeneous Mn-tmtacn complexes," J. Catalysis, 2012, 291, 17-25.

Mayes, H.B. and Broadbelt, L.J. "Unraveling the Reactions that Unravel Cellulose," J. Phys. Chem. A, 2012, 116 (26), 7098-7106.

Weiss, M.S., Penalver-Bernabe, B., Shikanov, A., Bluver, D.A., Mui, M.D., Shin, S., Broadbelt, L.J., and Shea, L.D. "The impact of adhesion peptides within hydrogels on the phenotype and signaling of normal and cancerous mammary epithelial cells," Biomaterials, 2012, 33(13), 3548-3559.

Bao, X., Sung, C.-Y., Snurr, R.Q., Broadbelt, L.J. "Rate-Determining Step in the NOx Reduction Mechanism on BaY Zeolites and the Importance of Long-Range Lattice Effects," ACS Catal., 2012, 2(3), 350-359. Cover art for the March 2, 2012 edition

Ryan, P., Konstantinov, I., Snurr, R.Q., and Broadbelt, L.J., "DFT investigation of hydroperoxide decomposition over copper and cobalt sites within metal-organic frameworks," J. Cat., 2012, 286, 95-102 (DOI: 10.1016/j.jcat.2011.10.019).

Vinu, R., Levine, S.E., Wang, L., and Broadbelt, L.J. "Detailed mechanistic modeling of poly(styrene peroxide) pyrolysis using kinetic Monte Carlo simulation," Chem. Eng. Sci., 2012, 69(1), 456-471.

Zhang, S.L., Broadbelt, L.J., Androulakis, I.P., and Ierapetritou, M.G. "Comparison of Biodiesel Performance Based on HCCI Engine Simulation Using Detailed Mechanism with On-the-fly Reduction," Energy Fuels, 2012, 26, 976-983.

Vinu, R. and Broadbelt, L.J. "Unraveling reaction pathways and specifying reaction kinetics for complex systems," Annu. Rev. Chem. Biomol. Eng. 2012, 3, 29-54.

Assary, R.S., Broadbelt, L.J., and Curtiss, L.A. "Brønsted-Evans-Polanyi relationships for C-C bond forming and C-C bond breaking reactions in thiamine-catalyzed decarboxylation of 2-keto acids using density functional theory," J. Mol. Model., 2012, 18(1), 145-150 (DOI: 10.1007/s00894-011-1062-z).

Totten, R.K., Ryan, P. Kang, B., Lee, S.J., Broadbelt, L.J., Snurr, R.Q., Hupp, J.T., and Nguyen, S.T. "Enhanced catalytic decomposition of a phosphate triester by modularly accessible bimetallic porphyrin dyads and dimers," Chem. Commun., 2012, 48, 4178-4180.

2011

Assary, R.S. and Broadbelt, L.J., "2-Keto acids to branched-chain alcohols as biofuels: Application of reaction network analysis and high-level quantum chemical methods to understand thermodynamic landscapes," Comput. Theor. Chem., 2011, 978(1-3), 160-165/

Konstantinov, I.A. and Broadbelt, L.J., "Regression Formulas for Density Functional Theory Calculated 1H and 13C NMR Chemical Shifts in Toluene-d8," J. Phys. Chem. A, 2011, 115(44), 12364-12372 (DOI: 10.1021/jp2060975).

Adamczyk, A.J. and Broadbelt, L.J., "Thermochemical Property Estimation of Hydrogenated Silicon Clusters," J. Phys. Chem. A, 2011, 115(32), 8969-8982.

Adamczyk, A.J. and Broadbelt, L.J., "The Role of Multifunctional Kinetics during Early-Stage Silicon Hydride Pyrolysis: Reactivity of Si2H2 Isomers with SiH4 and Si2H6," J. Phys. Chem. A, 2011, 115(11), 2409-2422.

Wu, D., Wang, Q., Assary, R.S., Broadbelt, L.J., and Krilov, G., "A Computational Approach to Design and Evaluate Enzymatic Reaction Pathways: Application to 1-Butanol Production from Pyruvate," J. Chem. Inf. Mod., 2011, 51(7), 1634-1647 (DOI: 10.1021/ci2000659).

Wang, L. and Broadbelt, L.J., "Model-Based Design for Preparing Styrene/Methyl Methacrylate Structural Gradient Copolymers", Macromol. Theory and Simulations, 2011, 20(3), 191-204. Cover art for March 2011 edition

Oxford, G.A.E., Dubbeldam, D., Broadbelt, L.J. and Snurr, R.Q., "Elucidating steric effects on enantioselective epoxidation catalyzed by (salen)Mn in metal-organic frameworks," J. Molecular Catal. A-Chemical, 2011, 334(1-2), 89-97.

Assary, R.S. and Broadbelt, L.J., "Computational screening of novel thiamine-catalyzed decarboxylation reactions of 2-keto acids," Bioprocess and Biosystems Engineering, 2011, 34(3), 375-388.

Wang, L. and Broadbelt, L.J., "Tracking Explicit Chain Sequence in Kinetic Monte Carlo Simulations," Macromol. Theory and Simulations, 2011, 20(1), 54-64. Featured at MaterialViews.com

Bellis, A.D., Penalver-Bernabe, B., Weiss, M.S., Yarrington, M.E., Barbolina, M.V., Pannier, A.K., Jeruss, J.S., Broadbelt, L.J. and Shea, L.D., "Cellular Arrays for Large-Scale Analysis of Transcription Factor Activity," Biotechnology and Bioengineering, 2011, 108(2), 395-403

Ryan, P., Farha, O.K., Broadbelt, L.J. and Snurr R.Q., "Computational Screening of Metal-Organic Frameworks for Xenon/Krypton Separation," AICHE J., 2011, 57(7), 1759-1766

Adamczyk, A.J., Reyniers, M.-F., Marin, G.B. and Broadbelt, L.J., "Hydrogenated Amorphous Silicon Nanostructures: Novel Structure-Reactivity Relationships for Cyclization and Ring Opening in the Gas Phase," Theor. Chem. Acc., 2011, 128(1), 91-113.

2010

Weiss, M.S., Penalver-Bernabe, B., Bellis, A.D., Broadbelt, L.J., Jeruss, J.S. and Shea, L.D., "Dynamic, Large-Scale Profiling of Transcription Factor Activity from Live Cells in 3D Culture," PLoS One, 2010, 5(10), e14026 (10.1371/journal.pone.001402).

Hidding, B., Fikri, M., Bozkurt, M., Schulz, C., Soltner, T., Kornath, A., Pfitzner, M., Lang, M., Adamczyk, A.J., Broadbelt L., Ellerbrock, H., Simone, D. and Bruno, C., "Spiking of Hydrocarbon Fuels with Silanes-based Combustion Enhancers," The ISTS Special Issue of Transactions of JSASS Aerospace Technology Japan, 2010, 8, 39-45.

Wang, L., and Broadbelt, L.J., "Kinetics of Segment Formation in Nitroxide-Mediated Controlled Radical Polymerization: Comparison with Classic Theory," Macromolecules, 2010, 43(5), 2228-2235.

Konstantinov, I.A. and Broadbelt, L.J., "Reaction Free Energies in Organic Solvents: Comparing Different Quantum Mechanical Methods," Molecular Simulation, 2010, 36(15), 1197.

Cho, A.S. and Broadbelt, L.J., "Stochastic Modeling of Gradient Copolymer Chemical Composition Distribution and Sequence Length Distribution," Molecular Simulation, 2010, 36(15), 1219.

Oxford, G.A.E., Snurr, R.Q. and Broadbelt, L.J., "Hybrid Quantum Mechanics/Molecular Mechanics Investigation of (salen)Mn for Use in Metal-Organic Frameworks," Ind. Eng. Chem. Res., 2010, 49(21), 10965-10973.

Adamczyk, A.J., Reyniers, M.-F., Marin, G.B. and Broadbelt, L.J., "Kinetic Correlations for H2 Addition and Elimination Reaction Mechanisms during Silicon Hydride Pyrolysis," Phys. Chem. Chem. Phys., 2010, 12, 12676-12696.

Adamczyk, A.J., Reyniers, M.-F., Marin, G.B. and Broadbelt, L.J., "Kinetics of Substituted Silylene Addition and Elimination in Silicon Nanocluster Growth Captured by Group Additivity," ChemPhysChem, 2010, 11(9), 1978-1994.

Konstantinov, I.A. and Broadbelt, L.J., "The Role of Oxazolidinones in L-proline-assisted Aldol-type Reactions," Topics in Catalysis, 2010, 53, 1031-1038.

Dubbeldam, D., Oxford, G.A.E., Krishna, R., Broadbelt, L.J. and Snurr, R.Q., "Distance and Angular Holonomic Constraints in Molecular Simulations," J. Chem. Phys., 2010, 133, 034114.

Cho, A.S., Wang, L., Dowuona, E., Zhou, H.Y., Nguyen, S.T., Broadbelt, L.J., "4-Acetoxystyrene Nitroxide-Mediated Controlled Radical Polymerization: Comparison with Styrene," J. Appl. Poly. Sci., 2010, 118(2), 740-750 (10.1002/app.31641)

Bao, X.Y., Broadbelt, L.J. and Snurr, R.Q. "Elucidation of consistent enantioselectivity for a homologous series of chiral compounds in homochiral metal-organic frameworks," Phys. Chem. Chem. Phys., 2010, 12(24), 6466-6473 (10.1039/c000809e)

Finley, S.D., Broadbelt, L.J. and Hatzimanikatis, V. "In Silico Feasibility Study of Novel Biodegradation Pathways for 1,2,4-Trichlorobenzene," BMC Systems Biology, 2010, 7, Article 4.

Henry, C.S., Broadbelt, L.J. and Hatzimanikatis, V. "Discovery and Analysis of Novel Biosynthesis Pathways," Biotechnology and Bioengineering, 2010, 106(3), 462-473.

2009

Adamczyk, A.J.,Reyniers, M.-F., Marin, G.B. and Broadbelt, L.J., "Exploring 1,2-Hydrogen Shift in Silicon Nanoparticles: Reaction Kinetics from Quantum Chemical Calculations and Derivation of Transition State Group Additivity (TSGA) Database," J. Phys. Chem. A, 2009, 113 (41), 10933-46.

Wang, L., and Broadbelt, L.J., "Explicit Sequence of Styrene/methyl methacrylate Gradient Copolymers Synthesized by Forced Gradient Copolymerization with Nitroxide-Mediated Controlled Radical Polymerization," Macromolecules, 2009, 42, 7961-7968.

Wang, L., and Broadbelt, L.J., "Factors Affecting the Formation of the Monomer Sequence along Styrene/Methyl Methacrylate Gradient Copolymer Chains," Macromolecules, 2009, 42, 8118-8128.

Bao, X.Y., Snurr, R.Q. and Broadbelt, L.J., "Collective Effects of Multiple Chiral Selectors on Enantioselective Adsorption," Langmuir, 2009, 25(18), 10730-10736.

Bao, X., Broadbelt, L.J. and Snurr, R.Q., "A Computational Study of Enantioselective Adsorption in a Homochiral Metal-Organic Framework," Molec. Simulation, 2009, 35(1-2), 50-59 (DOI: 10.1080/08927020802422064)

Khan, S.S., Zhang, Q. and Broadbelt, L.J., "Automated mechanism generation. Part 1: amechanism development and rate constant estimation for VOC chemistry in the atmosphere," J. Atm. Chem., 2009, 63(2), 125-156 (10.1007/s10874-010-9164-z)

Khan, S.S. and Broadbelt, L.J., "Automated mechanism generation. Part 2: application to atmospheric chemistry of alkanes and oxygenates," J. Atm. Chem., 2009, 63(2), 157-186 (DOI: 10.1007/s10874-010-9162-1)

Khan, S.S., Yu, X., Wade, J.R., Malmgren, R.D. and Broadbelt, L.J., "Thermochemistry of Radicals and Molecules Relevant to Atmospheric Chemistry: Determination of Group Additivity Values Using G3//B3LYP Theory," J. Phys. Chem. A., 2009, 113, 17, 5176-5194 (DOI: 10.1021/jp809361y)

Finley, S.D., Broadbelt, L.J. and Hatzimanikatis, V., "Computational Framework for Predictive Biodegradation," Biotechnology and Bioengineering, 2009, 104: 1086-1097.

Finley, S.D., Broadbelt, L.J., and Hatzimanikatis, V., "Thermodynamic Analysis of Biodegradation Pathways," Biotechnology and Bioengineering, 2009, 103: 532-541.

Zotova, N., Broadbelt, L.J., Armstrong, A., and Blackmond, D.G., "Kinetic and Mechanistic Studies of Proline-Mediated Direct Intermolecular Aldol Reactions," Bioorganic & Medicinal Chemistry Letters, 2009, 19, 14, 3934-3937.

Levine, S.E. and Broadbelt, L.J.; "Detailed Mechanistic Modeling of High-Density Polyethylene Pyrolysis: Low Molecular Weight Product Evolution." Polym. Deg. Stab., 2009, 10.1016/j.polymdegradstab.2009.01.031.

Oxford, G.A.E., Curet-Arana, M.C., Majumder, D., Gurney, R.W., Merlau, M.L., Nguyen, S.T., Snurr, R.Q., Broadbelt, L.J., "Microkinetic Analysis of the Epoxidation of Styrene Catalyzed by (Porphyrin)Mn Encapsulated in Molecular Squares," J.Catal., 2009, 266, 145-155.

Emberger, G.A., Bae, Y.-S., Nguyen, S.T., Hupp, J.T., Broadbelt, L.J. and Snurr, R.Q., "Post-synthesis Modification of a Metal-Organic Framework With Silver Ions," in Characterisation of Porous Solids VIII: Proceedings of the 8th International Conference on the Characterisation of Porous Solids, edited by S. Kaskel, P. Llewellyn, F. Rodriquez-Reinoso, N. A. Seaton,Royal Society of Chemistry, Cambridge, 2009, pp. 126-133.

2008

Curet-Arana, M.C., Snurr, R.Q. and Broadbelt, L.J., "Quantum Chemical Analysis of the Reaction Pathway for Styrene Epoxidation Catalyzed by Mn-Porphyrins," in Mechanisms in Homogeneous and Heterogeneous Epoxidation Catalysis, Chapter 19, edited by S.T. Oyama, Elsevier, Amsterdam, 2008.

Sung, C.-Y., Broadbelt, L.J. and Snurr, R.Q., "A DFT Study of Adsorption of Intermediates in the NOx Reduction Pathway over BaNaY Zeolites," Catalysis Today, 2008, 136, 64-75.

Curet-Arana, M.C., Emberger, G.A., Broadbelt, L.J. and Snurr, R.Q., "Quantum Chemical Determination of Stable Intermediates for Alkene Epoxidation with Mn-Porphyrin Catalysts," J. Molecular Catalysis A, 2008, 285, 120-127.

Ramachandran, C.E., Du, H., Kim, Y.J., Kung, M.C., Snurr, R.Q. and Broadbelt, L.J., "Solvent Effects in the Epoxidation Reaction of 1-Hexene with Titanium Silicalite-1 Catalyst," J. Catal., 2008, 253, 148-158.

Pfaendtner, J. and Broadbelt, L.J., "Mechanistic Modeling of Lubricant Degradation Part 2: The Autoxidation of Decane and Octane," Ind. Eng. Chem. Res., 2008, 47(9), 2897-2904.

Pfaendtner, J. and Broadbelt, L.J., "Mechanistic Modeling of Lubricant Degradation Part 1: Structure-Reactivity Relationships for Free-Radical Oxidation," Ind. Eng. Chem. Res., 2008, 47(9), 2886-2896.

Levine, S.E. and Broadbelt, L.J., "Reaction Pathways to Dimer in Polystyrene Pyrolysis: A Mechanistic Modeling Study," Polym. Deg. Stab., 2008, 93(5), 941-951.

Jankowski, M.D., Henry, C.S., Broadbelt, L.J. and Hatzimanikatis, V., "Group Contribution Method for Thermodynamic Analysis of Complex Metabolic Networks," Biophysical Journal, 2008, 95, 1487-1499.

Ryan, P., Broadbelt, L.J. and Snurr, R.Q., "Is Catenation Beneficial for Hydrogen Storage in Metal-Organic Frameworks?," Chem. Commun., 2008, 35, 4132-4134.

Bae, Y.-S., Mulfort, K.L., Frost, H., Ryan, P., Punnathanam, S., Broadbelt, L.J., Hupp, J.T. and Snurr, R.Q., "Separation of CO2 from CH4 using Mixed-Ligand Metal-Organic Frameworks," Langmuir, 2008, 24, 8592-8598.

Yu, X., Pfaendtner, J. and Broadbelt, L.J., "Ab Initio Study of Acrylate Polymerization Reactions: Methyl Methacrylate and Methyl Acrylate Propagation," J. Phys. Chem. A, 2008, 2008, 112(29), 6772-6782.

Albo, S.E., Snurr, R.Q. and Broadbelt, L.J., "Designing Nanostructured Membranes for Oxidative Dehydrogenation of Alkanes using Kinetic Modeling," Ind. Eng. Chem. Res., 2008, 47(15), 5395-5401.

Yu, X., Levine, S.E. and Broadbelt, L.J., "Kinetic Study of the Copolymerization of Methyl Methacrylate and Methyl Acrylate using Quantum Chemistry," Macromolecules, 2008, 41(21), 8242-8251.

2007

Henry, C.S., Broadbelt, L.J. and Hatzimanikatis, V., "Thermodynamics-Based Metabolic Flux Analysis," Biophysical J., 2007, 92(5), 1792-1805.

Pfaendtner, J. and Broadbelt, L.J., "Elucidation of Structure-Reactivity Relationships in Hindered Phenols Via Quantum Chemistry and Transition State Theory," Chem. Eng. Sci., 2007, 62(18-20), 5232-5239.

Pfaendtner, J., Yu, X. and Broadbelt, L.J., "The 1D Hindered Rotor Approximation," Theoretical Chemistry Accounts, 2007, 118(5-6), 881-898.

Priestley, R.D., Rittigstein, P., Broadbelt, L.J., Fukao, K. and Torkelson, J.M., "Evidence for the Molecular-Scale Origin of the Suppression of Physical Aging in Confined Polymer: Fluorescence and Dielectric Spectroscopy Studies of Polymer Silica Nanocomposites," J. of Physics: Condensed Matter, 2007, 19, 205120.

Feist, A.M., Henry, C.S., Reed, J.L., Krummenacker, M., Joyce, A.R., Karp, P.D., Broadbelt, L.J., Hatzimanikatis, V. and Palsson, B.O, "A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1261 ORFs and thermodynamic information," Nature Molecular Systems Biology, 2007, 3, Art. No. 121.

Rittigstein, P., Priestley, R.D., Broadbelt, L.J., and Torkelson, J.M., "Model Polymer Nanocomposites with Known Interlayer Spacing Provide Understanding of Confinement Effects in Real Nanocomposites," Nature Materials, 2007, 6(4), 278-282.

Priestley, R.D., Broadbelt, L.J., Torkelson, J.M., and Fukao, K., "Glass Transition and Alpha-Relaxation Dynamics of Thin Films of Labeled Polystyrene," Physical Review E, 2007, 75, 061806.

Albo, S.E., Broadbelt, L.J. and Snurr, R.Q., "Transmission Probabilities and Particle-wall Contact for Knudsen Diffusion in Pores of Variable Diameter," Chemical Engineering Science, 2007, 62, 6843-6850.

Pfaendtner, J. and Broadbelt, L.J., "Uncovering the Cause of Contrathermodynamic Behavior in Intermolecular Hydrogen Transfer of Alkylperoxy Radicals, ROO• + R'H," ChemPhysChem, 2007, 8(13), 1969-1978.

Priestley, R.D., Mundra, M.K., Barnett, N., Broadbelt, L.J. and Torkelson, J.M., "Confinement and Interfacial Effects on the Glass Transition of a Series of Poly(n-methacrylate) films," Australian Journal of Chemistry, 2007, 60, 765-771.

2006

Henry, C.S., Jankowski, M.D., Broadbelt, L.J. and Hatzimanikatis, V., "Genome-Scale Thermodynamic Analysis of Escherichia coli Metabolism," Biophysical J., 2006, 90(4), 1453-1461.

Ramachandran, C.E., Chempath, S., Broadbelt, L.J. and Snurr, R.Q., "Water Adsorption in Hydrophobic Nanopores: Monte Carlo Simulations of Water in Silicalite," Microporous and Mesoporous Materials, 2006, 90, 293-298.

Li, N., Cho, A.S., Broadbelt, L.J. and Hutchinson, R.A., "Low Conversion 4-Acetoxystyrene Free-Radical Polymerization Kinetics Determined by Pulsed-Laser and Thermal Polymerization," Macromol. Chem. Phys., 2006, 207(16), 1429-1438.

González-Lergier, J., Broadbelt, L.J. and Hatzimanikatis, V., "Analysis of the Maximum Theoretical Yield for the Synthesis of Erythromycin Precursors in Escherichia Coli," Biotechnology and Bioengineering, 2006, 95(4), 638-644.

Albo, S.E., Broadbelt, L.J. and Snurr, R.Q. "Multiscale Modeling of Transport and Residence Times in Nanostructured Membranes" AIChE J., 2006, 52(11), 3679-3687.

Ramachandran, C.E., Zhao, Q., Zikanova, A., Kocirik, M., Broadbelt, L.J. and Snurr, R.Q., "Is 1-Hexene Epoxidation in TS-1 Diffusion Limited in Different Solvents," Catalysis Communications, 2006, 7(12), 936-940.

Pfaendtner, J., Yu, X. and Broadbelt, L.J., "Quantum Chemical Investigation of Low-Temperature Intramolecular Hydrogen Transfer of Hydrocarbons," J. Phys. Chem. A, 2006, 110(37), 10863-10871.

Majumder, D. and Broadbelt, L.J., "A Multiscale Scheme for Modeling Catalytic Flow Reactors," AIChE Journal, 2006, 52(12), 4214-4228.

Bebe, S., Yu, X., Hutchinson, R.A. and Broadbelt, L.J., "Estimation of Free Radical Polymerization Rate Coefficients Using Computational Chemistry," Macromolecular Symposia, 2006, 243, 179-189.

2005

McMillan, S.A., Broadbelt, L.J., and Snurr, R.Q., "Theoretical Modeling of Zeolite Catalysis: Nitrogen Oxide Catalysis over Metal-Exchanged Zeolites," in Environmental Catalysis, Chapter 12, V.H. Grassian, ed., CRC Press, 2005, 287-306.

Majumder, D. and Broadbelt, L.J., "Development and Comparison of Solution Methods for Modeling Reaction and Diffusion in "Molecular Square" Membranes," Ind. Eng. Chem. Res., 2005, 44, 5977-5986.

Hatzimanikatis, V., Li, C., Ionita, J.A., Henry, C.S., Jankowski, M.D. and Broadbelt, L.J., "Exploring the Diversity of Complex Metabolic Networks," Bioinformatics, 2005, 21(8), 1603-1609.

Kruse, T.M., Levine, S.E., Wong, H.-W., Duoss, E., Lebovitz, A.H., Torkelson, J.M., and Broadbelt, L.J., "Binary Mixture Pyrolysis of Polypropylene and Polystyrene: A Modeling and Experimental Study," Journal of Analytical and Applied Pyrolysis, 2005, 73, 342-354.

Priestley, R.D., Broadbelt, L.J. and Torkelson, J.M., "Physical Aging of Ultrathin Polymer Films Above and Below the Bulk Glass Transition Temperature: Effects of Polymer-Substrate Interactions Measured by Fluorescence," Macromolecules, 2005, 38(3), 654-657.

Priestley, R.D., Ellison, C.J., Broadbelt, L.J. and Torkelson, J.M., "Structural Relaxation of Polymer Glasses at Surfaces, Interfaces and in Between," Science, 2005, 309(5733), 456-459.

González-Lergier, J., Broadbelt, L.J. and Hatzimanikatis, V., "Theoretical Considerations and Computational Analysis of the Complexity in Polyketide Synthesis Pathways," J. Am. Chem. Soc., 2005, 127(27), 9930-9938.

Broadbelt, L.J. and Pfaendtner, J., "Lexicography of Kinetic Modeling of Complex Systems," AIChE J., 2005, 51(8), 2112-2121.

2004

Haubein, N.C., McMillan, S.A., and Broadbelt, L.J., "Many-Body Optimization Using Quantum Mechanical Monte Carlo," Journal of Chemical Information and Computer Science, 2003, 43(1), 68-74.

Kruse, T.M., Souleimanova, R., Cho, A., Gray, M., Torkelson, J.M., and Broadbelt, L.J., "Limitations in the Synthesis of High Molecular Weight Polymers via Nitroxide-Mediated Controlled Radical Polymerization: Modeling Studies," Macromolecules, 2003, 36(20), 7812-7823.

McMillan, S.A., Snurr, R.Q., and Broadbelt, L.J., "Interaction of Divalent Metal Cations with Ferrierite," Microporous and Mesoporous Materials, 2004, 68(1-3), 45-53.

McMillan, S.A., Haubein, N.C., Snurr, R.Q., and Broadbelt, L.J., "Ab Initio Stochastic Optimization of Conformational and Many-Body Degrees of Freedom," Journal of Chemical Information and Computer Science, 2003, 43(6), 1820-1828.

Wong, H.W., Alva Nieto, J.C., Swihart, M.T., and Broadbelt, L.J., "Thermochemistry of Silicon-Hydrogen Compounds Generalized from Quantum Chemical Calculations," J. Phys. Chem. A., 2004, 108(5), 874-897.

Hatzimanikatis, V., Li, C., Ionita, J.A. and Broadbelt, L.J., "Metabolic Networks: Enzyme Function and Metabolite Structure," Current Opinion in Structural Biology, 2004, 14, 300-306.

Li, C., Henry, C.S., Jankowski, M.D., Ionita, J.A., Hatzimanikatis, V. and Broadbelt, L.J., "Computational Discovery of Biochemical Routes to Specialty Chemicals," Chem. Eng. Sci., 2004, 59(22-23), 5051-5060.

Wong, H.W., Li, X., Swihart, M.T., and Broadbelt, L.J., "Detailed Kinetic Modeling of Silicon Nanoparticle Formation Chemistry via Automated Mechanism Generation," J. Phys. Chem. A, 2004, 108(46), 10122-10132.

Khan, S.S. and Broadbelt, L.J., "A group additivity approach for the prediction of wavelength-dependent absorption cross-sections," Atmospheric Environment, 2004, 38(7), 1015-1022 (DOI: 10.1016/j.atmosenv.2003.10.054)

2003

Haubein, N.C., McMillan, S.A., and Broadbelt, L.J., "Many-Body Optimization Using Quantum Mechanical Monte Carlo," Journal of Chemical Computing and Information Science, 2003, 43(1), 68-74.

Wong, H.-W., Li, X., Swihart, M.T., and Broadbelt, L.J., "Detailed Mechanistic Modeling of Silicon Hydride Clustering Chemistry: Encoding of Complex Cyclic Molecules for Determining Species Uniqueness," Journal of Chemical Computing and Information Science, 2003, 43(3), 735-742.

Kruse, T.M., Wong, H.-W., and Broadbelt, L.J., "Modeling the Evolution of the Full Polystyrene Molecular Weight Distribution During Polystyrene Pyrolysis," Ind. Eng. Chem. Res., 2003, 42(12), 2722-2735.

Li, Q., Brown, S.E., Zheng, J.-G., Wu, N.Q., and Broadbelt, L.J., "Synthesis and Characterization of MCM-41-Supported Ba2SiO4 Base Catalyst," Mesoporous and Microporous Materials, 2003, 59(2-3), 105-111.

McMillan, S.A., Broadbelt, L.J. and Snurr, R.Q., "Effect of Local Framework Heterogeneity on NO Adsorption in Cobalt-Ferrierite," J. Catal., 2003, 219, 117-125.

Kruse, T.M., Wong, H.-W., and Broadbelt, L.J., "Mechanistic Modeling of Polymer Degradation: Polypropylene," Macromolecules, 2003, 36(25), 9594-9607.

McMillan, S.A., Snurr, R.Q., and Broadbelt, L.J., "Origin and Characteristics of Preferential Adsorption on Different Sites in Cobalt-Exchanged Ferrierite," J. Phys. Chem. B, 2003, 107(48), 13329-13335.

2002

Haubein, N.C., Mozeleski, E.J., Schlosberg, R.H., Mehnert, C., Farcasiu, D. and Broadbelt, L.J., "13C NMR Study of the Acid-Catalyzed Carbonylation of Methyl tert-Butyl Ether (MTBE)," Catal. Lett., 2002, 80(3-4), 139-145.

Klein, M.T., Hou, G., Quann, R.J., Wei, W., Liao, K.H., Yang, R.S.H., Campain, J.A., Mazurek, M.A. and Broadbelt, L.J., "BioMol: Computer-Assisted Biological Modeling of Complex Chemical Mixtures and Biological Processes at the Molecular Level," Environ. Health Persp. 2002, 110, 1025-1029.

Broadbelt, L.J. and Klinke, D.J., "Kinetics of Catalyzed Reactions - D (Heterogeneous)," Encyclopedia of Catalysis, 2002, Wiley Interscience, New York.

McMillan, S.A., Broadbelt, L.J. and Snurr, R.Q., "Density Functional Theory Investigation of Cobalt Siting in Ferrierite," J. Phys. Chem. B, 2002, 106 (42), 10864-10872.

Kruse, T.M., Woo, O.S., Wong, H.-W., Khan, S.S., and Broadbelt, L.J., "Mechanistic Modeling of Polymer Degradation: A Comprehensive Study of Polystyrene," Macromolecules, 2002, 35(20), 7830-7844.