Yong Zhang
Professor
Charles V. Schaefer, Jr. School of Engineering and Science
Department of Chemistry and Chemical Biology
Research
High Accuracy Computational Chemistry to Help Solve Experimental Problems
Our research focuses on developing and utilizing computational methods to provide accurate information for molecular and biomolecular systems, particularly those of broad impact on biomedicine and sustainable chemistry. Our high accuracy computational results with errors typically within 1-3% experimental ranges build a strong basis to provide critical missing information to help understand important experimental data, correct experimental errors, and guide future experiments with better desired properties/functions.
Our prior research has enabled 1) unprecedented mechanistic details for >100 reactions of important therapeutic agents, proteins of clinical interest, and green catalysts/biocatalysts. 2) accurate predictions of ~20 widely used spectroscopic properties with theory-versus-experiment correlation coefficient R2 around 0.99; 3) structure refinement and determination for active sites of ~20 metalloproteins with accuracy like small molecules. Among a total of 141 published/accepted papers, 53 are in top journals. The average journal impact factor of all his papers published at US tenured/tenure-track positions is 8.3. The complete list of the publications is here: https://scholar.google.com/citations?user=hDumUHUAAAAJ&hl=en
Our current research interests are mainly in the following areas:
1) Computational mechanistic studies of bioengineered catalysts with artificial functions for sustainable chemistry. One important topic to help make our earth sustainable is to develop inexpensive non-toxic catalysts to perform highly reactive and selective atom-economic chemical transformations for materials, drugs, and other useful substances, at room temperature and ambient pressure, in aqueous solution. Novel heme protein-based biocatalysts exhibit excellent catalytic performance for a wide range of non-native chemical reactions. A recent Nobel Prize was awarded to a few experimental pioneers in this field. Our group has provided some first and significant mechanistic insights into the electronic structures of heme carbenes and the origins of their reactivity, stereoselectivity, and chemoselectivity results in cyclopropanation, C-H insertion, N-H insertion, and Si-H insertion.
2) AI predictions of molecular/biomolecular properties and chemical/biochemical reactions. AI has been transforming the research field with two Nobel Prizes being recently awarded. However, AI tools in chemistry areas are mostly known for fast predictions but with significantly less accuracy than quantum chemistry predictions, especially for systems beyond normal organic molecules. Building on our previous strength in high accuracy predictions of experimental properties, we are developing new AI methods particularly deep learning approaches to improve the accuracy toward the quantum chemistry level while keeping its speedy feature.
3) Computational investigations of metalloprotein/metal mediated binding, formation, conversion, and detection of biological HNO and NO. These small molecules play vital roles in the cellular survival and signaling/regulation activities. Studies of NO’s effects in biomedicine have been awarded Nobel Prize. Our group has been providing some previously unknown critical structural and mechanistic information in this area, such as the first atomic level HNO bound protein active site structure, first heme and non-heme protein mediated HNO to NO conversion mechanistic pathway details, and first metal-based selective HNO sensor's reactivity mechanism, and first non-native one-electron reduction reactivity mechanism for NO in models of nitric oxide reductases.
4) Quantum chemical studies of accurate drug binding structures and pro-drug activation mechanisms. There are difficulties in obtaining x-ray structures of many drug-biomolecule complexes and accuracy problems of conventional x-ray crystallography. Our group provided accurate structures of important bisphosphonate-protein complexes and their associate interaction modes to help find new drug leads and understand their drug activity and selectivity. Such drugs have a billion-dollar global pharmaceutical market and exhibit excellent activities in treating bone-resorption diseases, Paget’s disease, and cancer. Our group revealed the activation mechanism of the bestseller anticancer prodrug cisplatin and studied prodrugs for HNO. We are exploring mechanisms of new types of drugs.
Current Group Members
Postdoc:
Jia-Min Chu
Graduate student:
Somayeh Tavasolikejani
Daisy Morgan
Undergraduate student:
Vrinda Modi
Ioannis Skoulidas
A total of 22 graduate and 40 undergraduate students have been trained for research in this group, including 55% from underrepresented groups (women and minorities).
After receiving the training in this lab at Stevens, all PhD students won some awards and many undergraduate students won up to 7 awards and scholarships, including national level honors such as ACS Division of Physical Chemistry Undergraduate Award, ACS Division of Inorganic Chemistry Undergraduate Award, and one of only 25 Physical Chemistry students nationwide selected to present at ACS national meetings.
Many students have publications in prestigious or even top journals, including undergraduate students.
For those who went to graduate and medical schools, each receives up to 7 offers from prominent universities such as Yale, John Hopkins, Cornell/Rochefeller/MSK, UCLA, University of Michigan, New York University, Rutgers.
In addition, a number of students become scientists and professors in academia or industry after graduation from this lab.
Undergraduate and graduate students with strong motivations are welcome to contact Professor Yong Zhang regarding the potential opportunity of joining his group's interesting and rewarding scientific endeavors.
Equipment:
This lab has a computational cluster in the university's Data Center with 436 cores, 1014 GB RAM, and 7.2 TB hard drive, with additional access to a school computational cluster of 880 cores, 4160 GB RAM, and 240 TB hard drive. Each student has a high-performance PC.
Our research focuses on developing and utilizing computational methods to provide accurate information for molecular and biomolecular systems, particularly those of broad impact on biomedicine and sustainable chemistry. Our high accuracy computational results with errors typically within 1-3% experimental ranges build a strong basis to provide critical missing information to help understand important experimental data, correct experimental errors, and guide future experiments with better desired properties/functions.
Our prior research has enabled 1) unprecedented mechanistic details for >100 reactions of important therapeutic agents, proteins of clinical interest, and green catalysts/biocatalysts. 2) accurate predictions of ~20 widely used spectroscopic properties with theory-versus-experiment correlation coefficient R2 around 0.99; 3) structure refinement and determination for active sites of ~20 metalloproteins with accuracy like small molecules. Among a total of 141 published/accepted papers, 53 are in top journals. The average journal impact factor of all his papers published at US tenured/tenure-track positions is 8.3. The complete list of the publications is here: https://scholar.google.com/citations?user=hDumUHUAAAAJ&hl=en
Our current research interests are mainly in the following areas:
1) Computational mechanistic studies of bioengineered catalysts with artificial functions for sustainable chemistry. One important topic to help make our earth sustainable is to develop inexpensive non-toxic catalysts to perform highly reactive and selective atom-economic chemical transformations for materials, drugs, and other useful substances, at room temperature and ambient pressure, in aqueous solution. Novel heme protein-based biocatalysts exhibit excellent catalytic performance for a wide range of non-native chemical reactions. A recent Nobel Prize was awarded to a few experimental pioneers in this field. Our group has provided some first and significant mechanistic insights into the electronic structures of heme carbenes and the origins of their reactivity, stereoselectivity, and chemoselectivity results in cyclopropanation, C-H insertion, N-H insertion, and Si-H insertion.
2) AI predictions of molecular/biomolecular properties and chemical/biochemical reactions. AI has been transforming the research field with two Nobel Prizes being recently awarded. However, AI tools in chemistry areas are mostly known for fast predictions but with significantly less accuracy than quantum chemistry predictions, especially for systems beyond normal organic molecules. Building on our previous strength in high accuracy predictions of experimental properties, we are developing new AI methods particularly deep learning approaches to improve the accuracy toward the quantum chemistry level while keeping its speedy feature.
3) Computational investigations of metalloprotein/metal mediated binding, formation, conversion, and detection of biological HNO and NO. These small molecules play vital roles in the cellular survival and signaling/regulation activities. Studies of NO’s effects in biomedicine have been awarded Nobel Prize. Our group has been providing some previously unknown critical structural and mechanistic information in this area, such as the first atomic level HNO bound protein active site structure, first heme and non-heme protein mediated HNO to NO conversion mechanistic pathway details, and first metal-based selective HNO sensor's reactivity mechanism, and first non-native one-electron reduction reactivity mechanism for NO in models of nitric oxide reductases.
4) Quantum chemical studies of accurate drug binding structures and pro-drug activation mechanisms. There are difficulties in obtaining x-ray structures of many drug-biomolecule complexes and accuracy problems of conventional x-ray crystallography. Our group provided accurate structures of important bisphosphonate-protein complexes and their associate interaction modes to help find new drug leads and understand their drug activity and selectivity. Such drugs have a billion-dollar global pharmaceutical market and exhibit excellent activities in treating bone-resorption diseases, Paget’s disease, and cancer. Our group revealed the activation mechanism of the bestseller anticancer prodrug cisplatin and studied prodrugs for HNO. We are exploring mechanisms of new types of drugs.
Current Group Members
Postdoc:
Jia-Min Chu
Graduate student:
Somayeh Tavasolikejani
Daisy Morgan
Undergraduate student:
Vrinda Modi
Ioannis Skoulidas
A total of 22 graduate and 40 undergraduate students have been trained for research in this group, including 55% from underrepresented groups (women and minorities).
After receiving the training in this lab at Stevens, all PhD students won some awards and many undergraduate students won up to 7 awards and scholarships, including national level honors such as ACS Division of Physical Chemistry Undergraduate Award, ACS Division of Inorganic Chemistry Undergraduate Award, and one of only 25 Physical Chemistry students nationwide selected to present at ACS national meetings.
Many students have publications in prestigious or even top journals, including undergraduate students.
For those who went to graduate and medical schools, each receives up to 7 offers from prominent universities such as Yale, John Hopkins, Cornell/Rochefeller/MSK, UCLA, University of Michigan, New York University, Rutgers.
In addition, a number of students become scientists and professors in academia or industry after graduation from this lab.
Undergraduate and graduate students with strong motivations are welcome to contact Professor Yong Zhang regarding the potential opportunity of joining his group's interesting and rewarding scientific endeavors.
Equipment:
This lab has a computational cluster in the university's Data Center with 436 cores, 1014 GB RAM, and 7.2 TB hard drive, with additional access to a school computational cluster of 880 cores, 4160 GB RAM, and 240 TB hard drive. Each student has a high-performance PC.
Institutional Service
- School of Engineering and Science Dean’s Faculty Advisory Council Member
- Internal Review Committee for the Chair of the Department of Chemistry and Chemical Biology Chair
- University Committee on Promotions and Tenure Member
- CCB Nominating Committee Chair
- School of Engineering and Science Research Committee Member
- CCB Graduate Admission Committee Member
- Undergraduate Chemistry Task Force Member
- MS in Chemistry Task Force Member
- Tenure Stream Faculty Search Committee Chair
- Tenure Stream Faculty Search Committee Chair
- CCB Undergraduate Education Committee Member
- School of Engineering and Science Advanced Computing Advisory Group Member
- School of Engineering and Science Honors and Awards Committee Member
- CCB Research and Infrastructure Committee Member
- Computational Biology Search Committee Chair
- Teaching Assistant Professor Search Committee Member
- Biology Lecturer Search Committee Member
- Academic Planning and Resources Committee Member
Appointments
2019-present Professor, Stevens Institute of Technology
2010-2019 Associate Professor, Stevens Institute of Technology (tenured in 2015)
2007-2010 Assistant Professor, University of Southern Mississippi
2005-2007 Research Scientist, University of Illinois Urbana-Champaign
2000-2005 Postdoctoral Research Associate, University of Illinois Urbana-Champaign
1999-2000 Associate Professor, Nanjing University
2010-2019 Associate Professor, Stevens Institute of Technology (tenured in 2015)
2007-2010 Assistant Professor, University of Southern Mississippi
2005-2007 Research Scientist, University of Illinois Urbana-Champaign
2000-2005 Postdoctoral Research Associate, University of Illinois Urbana-Champaign
1999-2000 Associate Professor, Nanjing University
Professional Societies
- American Chemical Society Member
- American Association for the Advancement of Science Member
- Society of Biological Inorganic Chemistry Member
- Society of Porphyrins and Phthalocyanines Member
Selected Publications
Journal Article
- Roy, S.; Wang, Y.; Zhao, X.; Dayananda, T.; Chu, J. M.; Zhang, Y.; Fasan, R. (2024). Stereodivergent Synthesis of Pyridyl Cyclopropanes via Enzymatic Activation of Pyridotriazoles. Journal of the American Chemical Society (29 ed., vol. 146, pp. 19673-19679).
https://pubs.acs.org/doi/abs/10.1021/jacs.4c06103. - Nam, D.; Bacik, J. P.; Khade, R.; Aguilera, M. C.; Wei, Y.; Villada, J. D.; Neidig, M. L.; Zhang, Y.; Ando, N.; Fasan, R. (2023). Mechanistic manifold in a hemoprotein-catalyzed cyclopropanation reaction with diazoketone. Nature Communications (1 ed., vol. 14).
https://www.nature.com/articles/s41467-023-43559-7. - Wang, J.; Sun, J.; Khade, R.; Chou, T.; An, H.; Zhang, Y.; Wang, H. (2023). Liposome-Templated Green Synthesis of Mesoporous Metal Nanostructures with Universal Composition for Biomedical Application. Small (46 ed., vol. 19).
https://onlinelibrary.wiley.com/doi/abs/10.1002/smll.202304880. - Shi, Y.; Stella, G.; Chu, J. M.; Zhang, Y. (2022). Mechanistic Origin of Favorable Substituent Effects in Excellent Cu Cyclam Based HNO Sensors. Angewandte Chemie - International Edition (45 ed., vol. 61).
https://onlinelibrary.wiley.com/doi/full/10.1002/anie.202211450. - Tian, S.; Fan, R.; Albert, T.; Khade, R. L.; Dai, H.; Harnden, K. A.; Hosseinzadeh, P.; Liu, J.; Nilges, M. J.; Zhang, Y.; Moënne-Loccoz, P.; Guo, Y.; Lu, Y. (2021). Stepwise nitrosylation of the nonheme iron site in an engineered azurin and a molecular basis for nitric oxide signaling mediated by nonheme iron proteins. Chemical Science (19 ed., vol. 12, pp. 6569-6579).
https://pubs.rsc.org/en/content/articlelanding/2021/sc/d1sc00364j. - Abucayon, E. G.; Khade, R. L.; Powell, D. R.; Zhang, Y.; Richter-Addo, G. B. (2019). Not Limited to Iron: A Cobalt Heme--NO Model Facilitates N--N Coupling with External NO in the Presence of a Lewis Acid to Generate N2O. Angewandte Chemie International Edition (51 ed., vol. 58, pp. 18598--18603). German Chemical Society.
https://onlinelibrary.wiley.com/doi/abs/10.1002/anie.201909137. - Vargas, D. A.; Khade, R. L.; Zhang, Y.; Fasan, R. (2019). Biocatalytic Strategy for Highly Diastereo- and Enantioselective Synthesis of 2,3-Dihydrobenzofuran-Based Tricyclic Scaffolds. Angewandte Chemie - International Edition (30 ed., vol. 58, pp. 10148-10152).
https://onlinelibrary.wiley.com/doi/abs/10.1002/anie.201903455. - Tinoco, A.; Wei, Y.; Bacik, J. P.; Carminati, D. M.; Moore, E. J.; Ando, N.; Zhang, Y.; Fasan, R. (2019). Origin of High Stereocontrol in Olefin Cyclopropanation Catalyzed by an Engineered Carbene Transferase. ACS Catalysis (2 ed., vol. 9, pp. 1514-1524).
https://pubs.acs.org/doi/10.1021/acscatal.8b04073. - Selvan, D.; Prasad, P.; Farquhar, E. R.; Shi, Y.; Crane, S.; Zhang, Y.; Chakraborty, S. (2019). Redesign of a Copper Storage Protein into an Artificial Hydrogenase. ACS Catalysis (pp. 5847-5859).
https://pubs.acs.org/doi/abs/10.1021/acscatal.9b00360. - Shi, Y.; Zhang, Y. (2018). Mechanisms of HNO Reactions with Ferric Heme Proteins. Angewandte Chemie - International Edition (51 ed., vol. 57, pp. 16654-16658).
https://onlinelibrary.wiley.com/doi/abs/10.1002/anie.201807699. - Malwal, S. R.; O'Dowd, B.; Feng, X.; Turhanen, P.; Shin, C.; Yao, J.; Kim, B. K.; Baig, N.; Zhou, T.; Bansal, S.; Khade, R. L.; Zhang, Y.; Oldfield, E. (2018). Bisphosphonate-Generated ATP-Analogs Inhibit Cell Signaling Pathways. Journal of the American Chemical Society (24 ed., vol. 140, pp. 7568-7578).
https://pubs.acs.org/doi/10.1021/jacs.8b02363. - Bhagi-Damodaran, A.; Reed, J. H.; Zhu, Q.; Shi, Y.; Hosseinzadeh, P.; Sandoval, B. A.; Harnden, K. A.; Wang, S.; Sponholtz, M. R.; Mirts, E. N.; Dwaraknath, S.; Zhang, Y.; Moënne-Loccoz, P.; Lu, Y. (2018). Heme redox potentials hold the key to reactivity differences between nitric oxide reductase and heme-copper oxidase. Proceedings of the National Academy of Sciences of the United States of America (24 ed., vol. 115, pp. 6195-6200).
https://www.pnas.org/content/115/24/6195.full. - Malwal, S. R.; Gao, J.; Hu, X.; Yang, Y.; Liu, W.; Huang, J. W.; Ko, T. P.; Li, L.; Chen, C. C.; O'Dowd, B.; Khade, R. L.; Zhang, Y.; Zhang, Y.; Oldfield, E.; Guo, R. T. (2018). Catalytic Role of Conserved Asparagine, Glutamine, Serine, and Tyrosine Residues in Isoprenoid Biosynthesis Enzymes. ACS Catalysis (5 ed., vol. 8, pp. 4299-4312).
https://pubs.acs.org/doi/10.1021/acscatal.8b00543. - Abucayon, E. G.; Khade, R. L.; Powell, D. R.; Zhang, Y.; Richter-Addo, G. B. (2018). Lewis Acid Activation of the Ferrous Heme-NO Fragment toward the N-N Coupling Reaction with NO to Generate N
2 O. Journal of the American Chemical Society (12 ed., vol. 140, pp. 4204-4207).
https://pubs.acs.org/doi/10.1021/jacs.7b13681. - Wei, Y.; Tinoco, A.; Steck, V.; Fasan, R.; Zhang, Y. (2018). Cyclopropanations via Heme Carbenes: Basic Mechanism and Effects of Carbene Substituent, Protein Axial Ligand, and Porphyrin Substitution. Journal of the American Chemical Society (5 ed., vol. 140, pp. 1649-1662).
https://pubs.acs.org/doi/10.1021/jacs.7b09171. - Reed, J. H.; Shi, Y.; Zhu, Q.; Chakraborty, S.; Mirts, E. N.; Petrik, I. D.; Bhagi-Damodaran, A.; Ross, M.; Moënne-Loccoz, P.; Zhang, Y.; Lu, Y. (2017). Manganese and Cobalt in the Nonheme-Metal-Binding Site of a Biosynthetic Model of Heme-Copper Oxidase Superfamily Confer Oxidase Activity through Redox-Inactive Mechanism. Journal of the American Chemical Society (35 ed., vol. 139, pp. 12209-12218).
https://pubs.acs.org/doi/10.1021/jacs.7b05800. - Bhagi-Damodaran, A.; Kahle, M.; Shi, Y.; Zhang, Y.; Ädelroth, P.; Lu, Y. (2017). Insights Into How Heme Reduction Potentials Modulate Enzymatic Activities of a Myoglobin-based Functional Oxidase. Angewandte Chemie - International Edition (23 ed., vol. 56, pp. 6622-6626).
https://onlinelibrary.wiley.com/doi/abs/10.1002/anie.201701916. - Bhagi-Damodaran, A.; Michael, M. A.; Zhu, Q.; Reed, J.; Sandoval, B. A.; Mirts, E. N.; Chakraborty, S.; Moënne-Loccoz, P.; Zhang, Y.; Lu, Y. (2017). Why copper is preferred over iron for oxygen activation and reduction in haem-copper oxidases. Nature Chemistry (3 ed., vol. 9, pp. 257-263).
https://www.nature.com/articles/nchem.2643.
Courses
CH 322 Theoretical Chemistry
CH 421 Chemical Dynamics
CH 520 Advanced Physical Chemistry
CH 669 Applied Quantum Chemistry
CH 421 Chemical Dynamics
CH 520 Advanced Physical Chemistry
CH 669 Applied Quantum Chemistry