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Computational and Theoretical Chemistry Group (CATCO) at
Southern Methodist University

 

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WHAT IS THEORETICAL AND COMPUTATIONAL CHEMISTRY?

Chemistry has long been known as “the central science,” because it bridges the gap between the physical and life sciences and the applied sciences like engineering, environmental science, and medicine. The Computational and Theoretical Chemistry Group (CATCO), emphasizes an interdisciplinary approach by focusing our research and teaching efforts on the intersections of chemistry with areas of current need.

On this page, you will learn about the interdisciplinary nature of chemical research, the cutting-edge research taking place on SMU’s high-performance computers, and the history of SMU’s Theoretical and Computational Chemistry Ph.D. Program. You will also learn about our expert faculty and discover what current and former students have to say about their experiences in the program.

 

THE ROLE OF CHEMISTRY IN THE MODERN WORLD

Chemistry: The Central Science

Chemistry has long been known as “the central science,” because it bridges the gap between the physical and life sciences and the applied sciences like engineering, environmental science, and medicine. It is both “the central science” and the most foundational of the sciences since every other field of science relies on chemical insights into the nature of atoms and molecules in order to understand how more complex systems operate.

Chemistry and Key Economic Sectors

Because of its centrality and its role in transformative innovation, Chemistry is at the heart of many key economic sectors. The energy, technology, health, and materials sectors all rely on chemical insight to advance, improve, and deliver high quality products that support human life and flourishing. In addition, Chemistry plays a central, if not to say leading, role in initiating, carrying out, and supporting developments that help guarantee the sustainability of our world.

The reliance of key economic sectors on Chemistry means that there is significant federal and industry investment in the development of top-notch chemists and significant opportunity for chemists to thrive in the many roles available to them in different fields.

Chemistry and The Human Experience of the World

Chemistry is ultimately about the material world which means that advances in chemical understanding have profound implications for the world that all human beings inhabit and experience.

At Southern Methodist University, Dr. Elfi Kraka, the Chair of the Department of Chemistry, has devoted much of her research to the development of anti-cancer drug design. Her work developing drugs and therapies that can treat currently incurable diseases is just one example of the ways in which Chemistry impacts the everyday lives of all people.

Here are more examples from industries where Chemistry is improving how we live and the future of our communities:
  • Energy — catalysts, biofuels, hydrogen generation, solar energy collector materials
  • Health — drugs, medical devices, and processes to clean and filter water
  • Technology — computing devices and screens, all advances in nanotechnology and biotechnology
  • Materials — recyclable packaging, earthquake safe structures, crop fertilizer

THE IMPORTANCE OF AN INTERDISCIPLINARY APPROACH TO CHEMICAL RESEARCH

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At SMU in the Computational and Theoretical Chemistry Group (CATCO), we emphasize this interdisciplinary approach by no longer offering graduate courses in the classical disciplines of chemistry (general, organic, analytical, and physical), but instead, teaching our courses on the major topics in an interdisciplinary way, focusing our research and teaching efforts on the intersections of chemistry with areas of current need.

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One major criterion of the research work at CATCO is the chemical relevance of the results obtained from our efforts for Chemistry, Pharmacy, or Nanotechnology. Therefore, the members of CATCO collaborate and continuously seek new cooperation with experimental groups in all disciplines of Chemistry, Pharmacy, and Nanotechnology.

The development and application of methods and computer programs in Computational Chemistry for the purpose of initiating, carrying out, and fostering interdisciplinary research and teaching in all areas of chemistry, materials sciences, and nanotechnology at a high level of excellence.”

— CATCO Mission Statement

THE CHALLENGES FACING CHEMISTS AND CHEMICAL ENGINEERS

Molecular design, Computational Chemistry: Learn how to design and produce new substances, materials, and molecular devices with properties that can be predicted, tailored, and tuned before production (use of chemical theory and computation)

Biochemistry: Understand the chemistry of living systems in detail (assembling of biomolecules into functional complexes, chemistry of the living cell, chemistry of the brain)

Drug Design: Develop medicines and therapies that can cure currently untreatable diseases (drug design for cancer, viral diseases, ADME)

Materials science, Nanotechnology: Develop self-assembly as a useful approach to the synthesis and manufacturing of complex systems and materials (nanotechnology)

Environmental Chemistry: Understand the complex chemistry of the earth, including land, sea, atmosphere, and biosphere so we can maintain its livability (how to deal with pollution and other threats to earth)

Energy: Develop unlimited and inexpensive energy (new ways for energy generation, storage, transportation)

Biomaterials, Materials Science: Design and develop self-optimizing chemical systems (copying the development of biological systems through evolution: medicines, catalysts)

Chemical Engineering: Revolutionize the design of chemical processes to make them safe, compact, flexible, energy efficient, environmentally benign

Public Relations: Communicate effectively to the general public the contributions that chemistry and chemical engineering make to society (use the media, give lectures)

Education: Attract the best and the brightest students into the chemical sciences

THE RELATIONSHIP BETWEEN COMPUTATIONAL CHEMISTRY AND TRADITIONAL CHEMISTRY

Among these disciplines under Theoretical Chemistry, Quantum Chemistry is by far the most popular field. There are hundreds of investigations and research projects carried out every year in this field.

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WHAT IS COMPUTATIONAL CHEMISTRY?

Although the terms Theoretical Chemistry and Computational Chemistry are very often used synonymously, the fields are not identical. Computational Chemistry takes the conceptual framework of Theoretical Chemistry and allows the insights and questions of Theoretical Chemistry to be rigorously tested, modeled, and observed by running programs on high-performance super computers. Computational Chemistry requires a strong understanding of theory, but also the ability to translate theoretical methods into suitable computer programs so that chemical problems can be solved.

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WHAT IS TRADITIONAL CHEMISTRY?

Traditional Chemistry is a way of thinking about Chemistry as separated into four or five distinct sub-disciplines: general, organic, analytical, and physical. The focus of traditional Chemistry is the study of matter in a laboratory setting where chemical reactions can be tangibly attempted, observed, and recorded. As technology and computing power improve, chemical problems that reach beyond the borders of traditional Chemistry and that involve multidisciplinary and interdisciplinary research efforts are being addressed and solved.

PARTNERSHIP BETWEEN TRADITIONAL AND COMPUTATIONAL CHEMISTRY

The primary goal of Chemistry is to control chemical reactions with the purpose of generating useful, non-toxic, and non-dangerous materials with desirable properties in an economic way.

Computational Chemistry is a discipline of chemistry that can substantially contribute to all the fields of science as well as the metamorphosis of traditional to modern Chemistry. Computational chemistry with quantum chemistry, molecular modeling, and molecular dynamics as its major tools has matured and become an important partner of experimental chemistry in the last decades. These computational tools are used to shorten and facilitate chemical discovery processes, avoid costly and/or dangerous experiments, and obtain information not amenable to experiment.

All work of the CATCO Group at SMU has as a common goal to understand the electronic structure of molecules so that reliable predictions of their properties and chemical behavior can be made. These predictions become important in all those cases where chemical experiments are not conclusive, too dangerous, too costly or not possible at all.

Computational Chemistry makes advances that are beyond the possibility of traditional chemistry, but relies on input from other branches of science to inform the relevance of its modeling efforts. This is one of the major reasons the CATCO Group at SMU emphasizes an interdisciplinary approach to teaching and research.

WHAT THEORETICAL AND COMPUTATIONAL CHEMISTRY RESEARCH LOOKS LIKE

Theoretical and Computational Chemistry

Our Theoretical and Computational Chemistry Research falls into six categories:

  1. Method development
  2. Molecular Properties
  3. Chemical Substance Classes
  4. Drug Design and Biochemically
    Relevant Topics
  5. Heuristic Models
  6. Chemical Disciplines

The leaders of the CATCO group have published more than 395 peer-refereed research papers and their research has been supported by 1.2 million dollars in grants in the last 5 years.

Innovative Research Opportunities in the Future

The CATCO Group at SMU is at the forefront of the dynamic and expanding future of Computational Chemistry. Our extensive research plan details the challenges and chemical problems that we are tackling in the next 10 years

The 3-5 Year Plan

We have special objectives that will be fulfilled within the next 3-5 years:

  1. Developing and improving quantum chemical methods to facilitate the reliable prediction of molecular properties for a broad spectrum of different chemical and physical situations and the modeling of all states of matter. View Chart
  2. Merging methods from molecular quantum chemistry and solid state physics to model matter at all degrees of condensation, facilitating computational research with regard to materials science and nanotechnology problems. View Chart
  3. Extending and improving the Cal-X methods (developed by CATCO members) that combine calculated and experimental information to gain a new level of insight into the properties of chemical compounds and their chemical reactions.
  4. Supporting the research of members of the Department of Chemistry by utilizing computational methods and programs developed, maintained, and applied by CATCO members; initiating and supporting in this way intra-departmental interdisciplinary research with the objective of strengthening research at SMU.
  5. Offering materials science, nanotechnology, surface chemistry, and catalysis courses at the graduate or undergraduate level.
  6. Providing a special training in form of workshops, intensive weekend and summer sessions to the graduate students of the CATCO group beyond the normal education that will enable them to compete with the best students on a nationwide and international basis.
  7. Reaching out beyond the borders of the Department of Chemistry, Dedman College, or even SMU to initiate and /or participate in interdisciplinary and multidisciplinary research programs in drug design, reaction mechanism, development of quantum chemical methods, materials science, nanotechnology, catalysis, and other topics.

The 10 Year Plan

CATCO’s vision for the next 10 years comprises the following goals:

  1. Modeling materials through all length scales and time scales. CATCO will make the necessary steps to fulfill this goal within the next 10 years. View Chart
  2. Reliably predicting the properties of smart materials in connection with molecular transistors, molecular switches, molecular motors to give chemists and engineers information about the best way of making nano-devices.
  3. Developing principles, rules, tools, and strategies for computer-assisted materials design (CAMaD) and computer- assisted catalyst design (CACaD) starting from knowledge in Computer-assisted Drug Design (CADD) so that CAMaD and CACaD research can be carried out on a regular basis with reliable predictions within a foreseeable timeframe.
  4. Supporting and sustaining Materials Science and Medicinal Chemistry groups at the Department of Chemistry, SMU, by interdisciplinary collaborations involving all faculty members with the objective of creating attractive, externally funded, and visible research projects.
  5. Supporting and being an important part of a Computational Sciences Center at SMU that offers to science and engineering students both at the graduate and undergraduate level educational, training and research possibilities of excellence.
  6. Offering on a regular basis workshops and summer schools in Computational Chemistry, Materials Sciences, Drug Design, Surface Chemistry, Catalysis, or Nanotechnology for high school students and/or high school teachers as well as interested students and colleagues from other departments and schools
  7. Fostering active partnerships with other computational chemistry groups from the Dallas-Fort Worth area to make them visible nationwide and beyond.

HEROES OF THEORETICAL AND COMPUTATIONAL CHEMISTRY: THEIR INNOVATIVE RESEARCH

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Dieter Cremer (1944-2017)

Dieter Cremer became a postdoctoral fellow with the Pople group at Carnegie Mellon in the fall of 1972. He worked closely with the Nobel Laureate winner, Pople, on a number of projects and learned from him about computational methods. Their productive time together resulted in the development of:

  1. The “Cremer-Pople” ring puckering coordinates and the ab initio description of the conformational energy surfaces of medium-seized ring molecules now used worldwide
  2. The explanation of the conformational features of geminal double rotors in terms of sigma- and pi-electron delocalization,
  3. The development of programs for the geometry optimization in terms of special ring coordinates,
  4. The description of the strain of small- and medium-sized ring molecules.

Dieter Cremer went on from there to his own illustrious scientific and teaching career. While at the University of Cologne, he was a founding member of the original CATCO Group, a union of theoretical and computational chemists who designed and used the quantum chemical program package, COLOGNE, as a major tool in their work.

Former members of the CATCO Group are today working in 8 different countries all over the world. 20 of these members are working as assistant, associate or full professors at well-known universities. So far, there have been more than 75 graduate students and research associates working in the CATCO group.

In 2009, Cremer moved the CATCO Group to Southern Methodist University and became the Director of SMU’s Computational and Theoretical Chemistry Group (CATCO) and Professor of Chemistry at Dedman College.

His research ranged from the development of state-of-the-art relativistic methods and computer programs, and their application to chemical problems. His recent work focused on computer design of new catalysts, the description of H-bonds in proteins, as well as chelating organic molecules that can precipitate toxic metals such as lead, cadmium and mercury from industrial wastewater.

He has published more than 360 peer-reviewed research articles in high-ranking journals, more than 50 of which he published since joining the Southern Methodist University. Dr. Dieter Cremer has presented his research at nearly 200 international conferences, and 18 of the 60 graduate and postgraduate students he has supervised to date have become professors at universities in seven different countries around the world.

The CATCO Group at SMU is proud to honor the memory of Dr. Dieter Cremer and carry on his legacy of excellence in research and teaching.

THE FIRST THEORETICAL AND COMPUTATIONAL CHEMISTRY PH.D. PROGRAM IN THE UNITED STATES

Our Program:

  1. Involves relevant, high-quality research. Graduate students are introduced to research from their very first semester in the program. A broad spectrum of modern research topics is available stretching from method and program development to modeling of H-bonding in materials and biochemical compounds, homogeneous and enzyme catalysis, computer assisted drug design. CATCO’s unique synergy of program development and application of these programs to pending chemical problems offers a unique research experience.
  2. Features the very first full 4-year curriculum (66 units) devoted to TCC: Instead of only offering a few classes in TCC like many institutions, we’ve developed the first in-depth education in TCC. Graduate students are taught courses on advanced computational chemistry, computer assisted drug design, Hartree-Fock Density Functional Theory and electron correlations methods; models and concepts in chemistry, symmetry and group theory, and an extensive training how to write a paper, prepare for presentations, interviews and your future career path.
  3. Provides entry to a promising job market: The demand for a highly trained Computational and Theoretical Chemistry workforce is increasing. ChemCensus2010 reports that the number of computational chemists with a Ph.D. degree working in industry grew from 55,200 in 1990 to 109,500 in 2010. The U.S. Bureau of Labor Statistics predicts that until 2026 that there will be a further annual increase of at least 19%. This is a faster growth than found for all other chemistry related jobs.
  4. Offers extensive mentoring and individual supervision: Our graduate students work closely with faculty, class sizes are small, and the program as a whole provides continuous feedback to students as they progress.
  5. Prepares students quickly for careers and publication: The program is a fast track bachelor’s degree to Ph.D. program. Graduate students are expected to defend their thesis in four years and will have published 5 peer-refereed papers in scientific journals by their graduation.
  6. Utilizes outstanding computational facilities: SMU’s new High Performance Computer (HPC) Center is one of the most powerful academic supercomputers in the country. Our ManeFrame computer is recognized as one of the top 500 fastest supercomputers in the world.
  7. Includes networking and professional development opportunities: The CATCO Group at SMU is also the organizer and host of The Austin Symposium on Molecular Structure and Dynamics, a major academic conference that takes place annually. Between the ASMD, other speaker series hosted by the Chemistry Department, trips to conferences, and research days organized by SMU, graduate students have many opportunities to meet experts in the field and communicate with others about their work.
  8. Gives students generous financial support: Each Ph.D. student receives a stipend of $25,000 and a full tuition waiver per annum as well as substantial health insurance support and travel allowance to national conferences.

SOUTHERN METHODIST UNIVERSITY: THE PERFECT HOME FOR THE UNITED STATES’ FIRST TCC PH.D. PROGRAM

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HIGH PERFORMANCE COMPUTING

CATCO has access to three high-performance clusters:

  1. ManeFrame
  2. SMUHPC
  3. CATCO Cluster (Scheme1a1)

The SMU HPC facility encompasses multiple compatible clusters, known as ManeFrame and SMUHPC. The resources on both clusters are freely available for research and educational use to all faculty and students. They are jointly managed by the Center for Scientific Computation, an association of faculty from across the University, and the Office of Information Technology. In 2015 the two clusters were merged for more effective resource management of more than 10,900 cores and 1.5 PB of storage.

One of the key administrators of the computational facilities at SMU is Rob Kalescky, a graduate from the CATCO group. His graduate work with the CATCO group prepared him for his current role as HPC Applications Scientist.

MANEFRAME

ManeFrame has a total of 1,104 Dell M610 compute nodes each with two Intel Xeon Nehalem 4-core 2.80GHz processors with a total compute capacity of 8,832 cores. It is supported with a 1PB high performance Lustre parallel storage system for high-speed scratch space, backed by a DDN S2A9900 storage array and controllers. Compute nodes and storage are all connected via a high speed DDR InfiniBand network at 20Gbps. Of the 1,104 compute nodes, 20 have 192GB RAM for memory intensive jobs, and the remaining nodes have 24 GB each for distributed applications.

SMU’s latest addition to the computer facilities: ManeFrame (ranked among the top 500 fastest supercomputers in the world)

Total Capacity in 2015: 10,900 cores, 120 teraflops, 1.5 PB storage

SMUHPC

The SMUHPC cluster has a total of 215 Dell compute nodes for a total of 2,080 CPU cores. SMUHPC has a mix of Intel Xeon Nehalem and Intel Xeon Westmere processors and has 6GB RAM per CPU core. In addition it has two high memory nodes with 144GB RAM on each. SMUHPC is also supported with a 500TB high performance Lustre parallel storage system for high speed scratch space backed by a NexSAN storage array and controllers. In addition, two nodes provide NVIDIA accelerator processors with 1,472 GPU cores. In combination the theoretical peak performance of ManeFrame and SMUHPC totals approximately 120 TFLOP’s.

CATCO CLUSTER

CATCO received from SMU in 2010 a 32 cpu local computing cluster (Scheme1a1) with 128 cores, 768 GB shared memory (resources of individual nodes combined via an aggregated virtual machine), and 16 TB hard drive capacity. This computer is generally used for program development and smaller benchmark tests. Large-scale production runs are performed at no cost at SMU’s High Performance Computing (HPC) Facility.

INTERDISCIPLINARY RESEARCH WORK

Because of the high quality research environment at SMU beyond the Department of Chemistry, there are exciting avenues of interdisciplinary work available to graduate students.”

For example, SMU’s Center for Drug Discovery, Design, and Delivery (CD4) in the Dedman College of the Humanities and Sciences is a novel multi-disciplinary focus for scientific research targeting medically important problems in human health. Using innovative approaches, CD4’s mission is to potentiate the development of new therapeutics, their delivery methods as well as the translation of these new therapeutics to clinical studies. Training new generations of biomedical researchers in state-of-the-art techniques completes the overall mission of the center.”

CATCO thought leaders, Dr. Dieter Cremer and Dr. Elfi Kraka have been involved in the work of CD4 and have published several investigations including their research on “A Computer Assisted Drug Design Approach to Non-toxic Enediyne Anti-tumor Drug Candidates” and “Investigation of Artemisinin – a Traditional Chinese anti-Malaria drug.”

MEET THE CATCO PROFESSORS AT SOUTHERN METHODIST UNIVERSITY

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DR. Peng Tao

Dr. Peng Tao joined the Department of Chemistry in the fall of 2013 as an Assistant Professor. He received his B.S. in Chemistry (1998) and M.S. in Physical Chemistry (2001) from the Peking University in China. He obtained his Ph.D. in Computational Chemistry from the Ohio State University in 2007. The Tao Research Group focuses on developing highly efficient and accurate computational methods to calculate free energy for chemical reactions and biological processes. They are also applying these novel free methods in combination of powerful computational tools, such as molecular dynamics (MD) and quantum mechanics (QM), to solve real world chemistry and biology problems.

Learn more about the Tao Research Group

STUDENT TESTIMONIALS

I feel proud that I could finish my Ph.D. on time with six world-class publications in such a demanding program. This was only possible due to the high-performance computer provided by SMU and due to the great effort and patience that my mentors, Dr. Cremer, and Dr. Kraka, invested in my education. It was a great honor and privilege to learn from their classes, seminars, and workshops.”

— Vytor Oliveira
Seth Yannacone

Seth Yannacone

Hometown: Denver, Colorado

Status: first year graduate student in the TCC Ph.D.

Description of research: “My first projects involved transition state (TS) theory. My latest project involves investigating the role of intra-molecular hydrogen bonds in stabilizing neutral histidine. My future project will be to investigate and help advance theory behind un-traditional non-classical agnostic bonding complexes.”

The TCC program is preparing me well for my future career by teaching me how to conduct quality research, produce professional publications, and present my work to the scientific community.”

— Seth Yannacone

ADDITIONAL RESOURCES

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