Beyond the Molecular Frontier Challenges for Chemistry and Chemical Engineering (2003) / Chapter Skim
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6 Chemical Theory and Computer Modeling: From Computational Chemistry to Process Systems Engineering
6 Chemical Theory and Computer Modeling: From Computational Chemistry to Process Systems Engineering
Pages 71-94
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From page 71... ...
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From page 72... ...
This has happened in part by enhancing many existing computational procedures, providing a new impetus to quantum mechanical and molecular simulations at the atomic level, and optimizing processes and supply chain management at the macrosystem level. Furthermore, these computational tools have helped test new conceptual approaches to understanding matter and molecules.
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From page 73... ...
Advances in computing have facilitated major progress in computational chemistry and biochemistry, computational materials design, computational fluid dynamics, process synthesis, planning and scheduling, model-based process control, fault diagnosis, and real-time process optimization. This progress has been enabled by parallel advances in fundamental chemical physics theory, mathematics, operations research, and computer science including computational techniques for simulation and optimization of chemical systems.
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From page 74... ...
74 ._ _ e ~ e e ~ I I I I I I I I I ~ ~ Y _ ~ ~ e e ·_ Y lo Ct o Cal Cal o o ;^ o .~ ;^ Cal Cal ·_.
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From page 75... ...
Quantum Mechanics The chemical sciences are built on a set of fundamental mathematical theories that have increasing utility as computational hardware and software become more powerful. As the basis for calculating the electronic structure of molecules, quantum mechanics permits calculations, often based on rational approximations, of structure and properties of molecules, and of reactivity and reaction mechanisms.
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From page 76... ...
Molecular Mechanics One tool for working toward this objective is molecular mechanics. In this approach, the bonds in a molecule are treated as classical objects, with continuous interaction potentials (sometimes called force fields)
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From page 77... ...
of real time for an atomically detailed molecular simulation. Consequently, modeling phenomena on the femtosecond time scale would require about 103 time steps, which is not difficult, and modeling on the picosecond time scale (106 time steps)
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From page 78... ...
For example, reactions involve changes in the molecules, and hence are inherently quantum mechanical in nature. But a reaction taking place in a solution at finite temperature implies that the reaction is influenced by a dynamic environment more pragmatically described by classical molecular simulation methods.
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From page 79... ...
. Other hybrid methods, which treat just the environment around reactants quantum mechanically, are less accurate in principle but allow much longer time scales and much larger spatial scales to be accessed, since the vast majority of the molecules are treated by classical molecular simulation.
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From page 80... ...
Cross-fertilization between the fields has led to computational chemistry methods (e.g., simulated annealing) crossing over to the process design community, just as techniques from the process design community (e.g., mathematical programming methods)
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From page 81... ...
(iigand) 1 1 1 1 Hinge Helix-coil motions transitions Protein folding Protein aggregation ~ 1 Typical ligand binding to a protein Nonbiological, ~ Polymers Crankshaft Rouse modes Reptation motions Melt relaxation Creep, aging Phase separation Gel swelling '' r , ~ ~ ~ , 1993 2003 2013 2023 2033 onAa vans PROGRESS TO DATE Important insights have been developed using approximate methods that were not highly precise quantitatively, and excellent high-level methods for solving the Schrodinger equation have been developed, but the methods still have used approximations.
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From page 82... ...
In molecular mechanics, force fields and sampling methods used in the calculations are being improved continually, but they are not yet good enough that atomic-level refinement of protein structures is feasible on a robust and routine basis. It is unclear what the relative contribution of force field and sampling errors are to the problem.
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From page 83... ...
The last decade has also seen dramatic improvements in molecular simulation methodologies largely based on stochastic methods for overcoming the long relaxation times inherent in the equilibration of polymers and similar complex materials. A recent international comparative study of the industrial application of molecular modeling in the chemical, pharmaceutical, and materials industries in the United States, Europe, and Japan gathered information from over 75 sites; the report documents some of the remarkably diverse ways in which molecular modeling methods are successfully impacting industry today.8 Given the limitations of today's tools, the future for integrated molecularbased product design and process-level design and optimization is very bright indeed.
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From page 84... ...
The number of potential feasible process designs is in general very large, and selecting the right process structure generally determines most of the economic potential of a new or retrofitted chemical process. In recent industrial experience, energy reductions of 50% and overall cost reductions of 35% using systematic process synthesis techniques have been achieved.
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From page 85... ...
However, new mathematical techniques such as generalized disjunctive programming and global optimization, combined with the tremendous increases in available computing power made possible through large clusters of fast independent processors, give hope that this superstructure optimization approach to chemical process synthesis may be practical in the near future. Modeling and Optimization The chemical industry can largely be viewed as being composed of two major segments.
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From page 86... ...
86 BEYOND THE MOLECULAR FRONTIER enterprise level. Major difficulties in developing mathematical models that integrate the various parts of the chemical supply chain result from the huge differences in length and time scales in the supply chain and the number of chemical species considered at each level.
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From page 87... ...
The challenge is how to abstract the details and description of a complex system into a reduced dimensional space. Another important aspect in the modeling and optimization of the chemical supply chain is the description of the dynamics of the information and material flow through the chain.
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From page 88... ...
Concepts related to planning, scheduling, and control that have not been widely adopted by chemical engineers should play a prominent role in the modeling part of this problem. Concepts and tools of computer science and operations research will play an even greater role in terms of impacting the implementation of solutions for this problem.
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From page 89... ...
One specific challenge will be to derive density functional theory from fundamental theory in a way that reveals how to incorporate successive approximations for the exchange and correlation terms. Some work on high-level methods with better scaling may allow more immediate extension of high-accuracy calculations to larger systems.
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From page 90... ...
Improved force fields explicitly incorporating polarization are being developed. Until rapid ab initio molecular dynamics methods exist, such force fields are required for the simulation of chemical systems with chemical accuracy.
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From page 91... ...
Within the commodity chemicals industry major challenges that will be addressed include process intensification for novel unit operations, and design of environmentally benign processes. Areas that are likely to receive increased attention due to the growth in new industries include molecular design, synthesis of microchips, smart materials, bioprocess systems, bioinformatics, and design and analysis of metabolic networks.
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From page 92... ...
Another area of sharing leading to powerful new computational opportunities in the chemical sciences is the use of peer-to-peer computing in the form of sharing unused cycles on small computers. We can do very largescale computations on networks of personal computers, as is being done in studies of protein foldings and molecular docking.~° The potential here is to tackle computational problems of unprecedented size and complexity, with a relatively low investment in the actual computational resources.
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From page 93... ...
Nevertheless, assuming these obstacles can be overcome, grid computing offers the possibility of solving the largest scale problems confronting the computational chemistry and process engineering communities in the most cost-effective way. They can also facilitate collaboration between groups with complementary expertise that can share their capabilities while maintaining control over them.
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From page 94... ...
We need to develop new and powerful computational methods that span from the atomic and molecular level to the chemical-process and chemical-enterprise level in order to allow their effective integration for multiscale simulation and optimization. We want to synthesize energy-efficient and environmentally benign processes that are cost effective.
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