Quantum Chemical Studies of Intermediates and Reaction Pathways in Selected Enzymes and Catalytic Synthetic Systems (original) (raw)
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Lee Pedersen s work in theoretical and computational chemistry and biochemistry
World Journal of Biological Chemistry, 2011
Nature at the lab level in biology and chemistry can be described by the application of quantum mechanics. In many cases, a reasonable approximation to quantum mechanics is classical mechanics realized through Newton's equations of motion. Dr. Pedersen began his career using quantum mechanics to describe the properties of small molecular complexes that could serve as models for biochemical systems. To describe large molecular systems required a drop-back to classical means and this led surprisingly to a major improvement in the classical treatment of electrostatics for all molecules, not just biological molecules. Recent work has involved the application of quantum mechanics for the putative active sites of enzymes to gain greater insight into the key steps in enzyme catalysis.
International Journal of Quantum Chemistry, 2013
Jaguar is an ab initio quantum chemical program that specializes in fast electronic structure predictions for molecular systems of medium and large size. Jaguar focuses on computational methods with reasonable computational scaling with the size of the system, such as density functional theory (DFT) and local secondorder Mïller-Plesset perturbation theory. The favorable scaling of the methods and the high efficiency of the program make it possible to conduct routine computations involving several thousand molecular orbitals. This performance is achieved through a utilization of the pseudospectral approximation and several levels of parallelization. The speed advantages are beneficial for applying Jaguar in biomolecular computational modeling. Additionally, owing to its superior wave function guess for transition-metalcontaining systems, Jaguar finds applications in inorganic and bioinorganic chemistry. The emphasis on larger systems and transition metal elements paves the way toward developing Jaguar for its use in materials science modeling. The article describes the historical and new features of Jaguar, such as improved parallelization of many modules, innovations in ab initio pKa prediction, and new semiempirical corrections for nondynamic correlation errors in DFT. Jaguar applications in drug discovery, materials science, force field parameterization, and other areas of computational research are reviewed. Timing benchmarks and other results obtained from the most recent Jaguar code are provided. The article concludes with a discussion of challenges and directions for future development of the program.
Ask the experts: focus on computational chemistry
Future medicinal chemistry
Future Medicinal Chemistry invited a selection of leading researchers to express their views on the current state of computer-aided drug discovery and design, as well as speculate on future developments in the field. Their enlightening responses provide a snapshot of the many and varied contributions being made by computational methodologies to the advancement of pharmaceutical science.
Israel Journal of Chemistry, 2022
This rosarium article relates the adventure started 50 years ago of a computational chemist who was interested in molecules; what are they, what are their shape and how do they react. The story describes results, still valid today, obtained with highly simplified models of chemical reality and elementary computational methods and the gain resulting from the use of better models and more elaborate computational methods. It was necessary to select examples. In this presentation, focus is on hydride and dihydrogen complexes as well as on nucleophiles. Nucleophiles were considered as free hydrides in gas phase at the start of the rosarium while the Grignard reaction is treated with ab initio molecular mechanisms at the end of it. understood why I was poor at playing piano, could not sing a note, did not speak Russian through genetic transmission even though she never spoke Russian to me. She just forgave my total inability in the practice of sport related activities where I oscillated between the last and the last-1 ranks during my entire time at school. Education was the solution to any problem and her motto was "study, study, study" and always take the hardest route. Just a bit hard for a young child who was an addicted reader especially of adventure stories. After the baccalauréat, I had no clue of what I would do except that I was better in science and especially in physics and chemistry than in humanities. I attempted the competitive exams of the "Ecoles Normales" (essentially honor classes for high education, in partnership with universities, providing also a stipend to students) during the spring of 1968. The exams were not interrupted by the events even if reaching the exam places was a challenge with the absence of public transportation. I was not selected for the "Ecoles Normales" but my rank was such that I could enter the university at the BA level with a small fellowship. I wanted to study at "Jussieu". the University, at the center of Paris, also known as University Pierre and Marie Curie and nowadays known as Sorbonne University. It was closer from home but it was slow to reopen after the uprising in the spring of 1968. However, University of Paris-Sud, a newer university set in Orsay, south of Paris, had reopened and most of my schoolmates registered there. I applied a bit late to the Chemical Physics section and I was accepted. This was my lucky card. Outline of this rosarium I wish to describe now how I got into the field of computational chemistry and how it changed from 1970 till today. I needed to select topics for this. I am considerably helped by an article published in ACS Catalysis in 2019, with the flattering title of A Career in Catalysis: Odile Eisenstein. 1 Five former co-workers who became colleagues and friends, David Balcells, Eric Clot, Stuart A. Macgregor, Feliu Maseras and Lionel Perrin, joined efforts to write this glowing description of my scientific activities in the domain of organometallic chemistry and the relevance to homogeneous catalysis. There is no need to repeat what is so well described in this publication, which I recommend to interested readers. I thus decided to write a personal account of how I evolved as a computational chemist, mostly interested in chemistry, from the early years where only extremely simple methods could be used to the present time where highly elaborate methods and resources are available, opening the possibility to study highly complex chemical situations. I selected topics which illustrate the challenging steps of this progression and my constant interest to interpret the results in terms which could be understood by non-theoreticians. As a guide line, I focus on chemical species and reactions which involve in diverse ways nucleophilic entities that were often hydrides. This topic led me
Nobel Prize in Chemistry 2009: When Biology Turns into Chemistry
Israel Journal of Chemistry, 2010
We find it highly timely and appropriate to dedicate the first issue of Volume 50 of the Israel Journal of Chemistry to the recent Nobel Prize in Chemistry awarded to Venkatraman Ramakrishnan, Thomas A. Steitz, and Ada E. Yonath "for studies of the structure and function of the ribosome." The scientific contribution of these three researchers has yielded a detailed description of an extremely complex biological process, protein biosynthesis, at a molecular level, using ideas and concepts, which are typical of chemistry rather than biology. These studies provide fundamental knowledge and understanding of a key paradigm in biology, known as The Central Dogma (Figure 1). According to this paradigm, there is a unidirectional flow of genetic information from nucleic acids to proteins. Three years ago, in 2006, the Nobel Prize in Chemistry was awarded to Roger Kornberg for deciphering the molecular basis of transcription of the genetic code. The
Journal of Cheminformatics
The Computational Chemistry List is a mailing list, portal, and community which brings together people interested in computational chemistry, mostly practitioners. It was formed in 1991 and continues to exist as a vibrant discussion space, highly valued by its members, and serving both its original and new functions. Its duration has been unusual for online communities. We analyze some of its characteristics, the reasons for its duration, value, and resilience, the ways it embodies and preceded the affordances of online communities recognized elsewhere long after its foundations, and project some aspects into the future. We also highlight its value as a corpus for historians of science.
The State of the Art of Chemical Biology
ChemBioChem, 2009
Considering the eminent role of chemistry in helping to decipher and control life processes, a name of its own-"chemical biology"-has rightly been given to the thriving area at the interface with biology and medicine. It has become a molecule-based bridge that paves the way to a deep and logic interpenetration-on the molecular level-of structural, functional, and developmental approaches to the natural life sciences, including medicine.