1
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Rabitz H, Russell B, Ho TS. The Surprising Ease of Finding Optimal Solutions for Controlling Nonlinear Phenomena in Quantum and Classical Complex Systems. J Phys Chem A 2023; 127:4224-4236. [PMID: 37142303 DOI: 10.1021/acs.jpca.3c01896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
This Perspective addresses the often observed surprising ease of achieving optimal control of nonlinear phenomena in quantum and classical complex systems. The circumstances involved are wide-ranging, with scenarios including manipulation of atomic scale processes, maximization of chemical and material properties or synthesis yields, Nature's optimization of species' populations by natural selection, and directed evolution. Natural evolution will mainly be discussed in terms of laboratory experiments with microorganisms, and the field is also distinct from the other domains where a scientist specifies the goal(s) and oversees the control process. We use the word "control" in reference to all of the available variables, regardless of the circumstance. The empirical observations on the ease of achieving at least good, if not excellent, control in diverse domains of science raise the question of why this occurs despite the generally inherent complexity of the systems in each scenario. The key to addressing the question lies in examining the associated control landscape, which is defined as the optimization objective as a function of the control variables that can be as diverse as the phenomena under consideration. Controls may range from laser pulses, chemical reagents, chemical processing conditions, out to nucleic acids in the genome and more. This Perspective presents a conjecture, based on present findings, that the systematics of readily finding good outcomes from controlled phenomena may be unified through consideration of control landscapes with the same common set of three underlying assumptions─the existence of an optimal solution, the ability for local movement on the landscape, and the availability of sufficient control resources─whose validity needs assessment in each scenario. In practice, many cases permit using myopic gradient-like algorithms while other circumstances utilize algorithms having some elements of stochasticity or introduced noise, depending on whether the landscape is locally smooth or rough. The overarching observation is that only relatively short searches are required despite the common high dimensionality of the available controls in typical scenarios.
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Affiliation(s)
- Herschel Rabitz
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Benjamin Russell
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Tak-San Ho
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
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2
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Rinderspacher BC. Heuristic Global Optimization in Chemical Compound Space. J Phys Chem A 2020; 124:9044-9060. [DOI: 10.1021/acs.jpca.0c05941] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- B. Christopher Rinderspacher
- Materials Discovery and Technology Branch, US Army Research Laboratory, Aberdeen Proving Ground, Maryland 21005, United States
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3
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Fujinami M, Maekawara H, Isshiki R, Seino J, Yamaguchi J, Nakai H. Solvent Selection Scheme Using Machine Learning Based on Physicochemical Description of Solvent Molecules: Application to Cyclic Organometallic Reaction. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2020. [DOI: 10.1246/bcsj.20200045] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Mikito Fujinami
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Hiroki Maekawara
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Ryota Isshiki
- Department of Applied Chemistry, School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Junji Seino
- Waseda Research Institute for Science and Engineering (WISE), Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
- PRESTO, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Junichiro Yamaguchi
- Department of Applied Chemistry, School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Hiromi Nakai
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
- Waseda Research Institute for Science and Engineering (WISE), Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
- Elements Strategy Initiative for Catalysts and Batteries (ESICB), Kyoto University, Katsura, Kyoto 615-8520, Japan
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4
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Nutschel C, Fulton A, Zimmermann O, Schwaneberg U, Jaeger KE, Gohlke H. Systematically Scrutinizing the Impact of Substitution Sites on Thermostability and Detergent Tolerance for Bacillus subtilis Lipase A. J Chem Inf Model 2020; 60:1568-1584. [PMID: 31905288 DOI: 10.1021/acs.jcim.9b00954] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Improving an enzyme's (thermo-)stability or tolerance against solvents and detergents is highly relevant in protein engineering and biotechnology. Recent developments have tended toward data-driven approaches, where available knowledge about the protein is used to identify substitution sites with high potential to yield protein variants with improved stability, and subsequently, substitutions are engineered by site-directed or site-saturation (SSM) mutagenesis. However, the development and validation of algorithms for data-driven approaches have been hampered by the lack of availability of large-scale data measured in a uniform way and being unbiased with respect to substitution types and locations. Here, we extend our knowledge on guidelines for protein engineering following a data-driven approach by scrutinizing the impact of substitution sites on thermostability or/and detergent tolerance for Bacillus subtilis lipase A (BsLipA) at very large scale. We systematically analyze a complete experimental SSM library of BsLipA containing all 3439 possible single variants, which was evaluated as to thermostability and tolerances against four detergents under respectively uniform conditions. Our results provide systematic and unbiased reference data at unprecedented scale for a biotechnologically important protein, identify consistently defined hot spot types for evaluating the performance of data-driven protein-engineering approaches, and show that the rigidity theory and ensemble-based approach Constraint Network Analysis yields hot spot predictions with an up to ninefold gain in precision over random classification.
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Affiliation(s)
- Christina Nutschel
- John von Neumann Institute for Computing (NIC) and Institute for Complex Systems-Structural Biochemistry (ICS-6), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany.,Jülich Supercomputing Centre (JSC), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Alexander Fulton
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, 52425 Jülich, Germany
| | - Olav Zimmermann
- Jülich Supercomputing Centre (JSC), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Ulrich Schwaneberg
- Institute of Biotechnology, RWTH Aachen University, 52074 Aachen, Germany.,DWI-Leibniz-Institute for Interactive Materials, 52056 Aachen, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, 52425 Jülich, Germany.,Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Holger Gohlke
- John von Neumann Institute for Computing (NIC) and Institute for Complex Systems-Structural Biochemistry (ICS-6), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany.,Jülich Supercomputing Centre (JSC), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany.,Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
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5
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Voznyuk O, Jochim B, Zohrabi M, Broin A, Averin R, Carnes KD, Ben-Itzhak I, Wells E. Adaptive strong-field control of vibrational population in NO 2+. J Chem Phys 2019; 151:124310. [DOI: 10.1063/1.5115504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- O. Voznyuk
- Department of Physics, Augustana University, Sioux Falls, South Dakota 57197, USA
| | - Bethany Jochim
- Department of Physics, Augustana University, Sioux Falls, South Dakota 57197, USA
- J.R. Macdonald Laboratory, Department of Physics, Kansas State University, Manhattan, Kansas 66506, USA
| | - M. Zohrabi
- J.R. Macdonald Laboratory, Department of Physics, Kansas State University, Manhattan, Kansas 66506, USA
| | - Adam Broin
- Department of Physics, Augustana University, Sioux Falls, South Dakota 57197, USA
| | - R. Averin
- Department of Physics, Augustana University, Sioux Falls, South Dakota 57197, USA
| | - K. D. Carnes
- J.R. Macdonald Laboratory, Department of Physics, Kansas State University, Manhattan, Kansas 66506, USA
| | - I. Ben-Itzhak
- J.R. Macdonald Laboratory, Department of Physics, Kansas State University, Manhattan, Kansas 66506, USA
| | - E. Wells
- Department of Physics, Augustana University, Sioux Falls, South Dakota 57197, USA
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6
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Fujinami M, Seino J, Nukazawa T, Ishida S, Iwamoto T, Nakai H. Virtual Reaction Condition Optimization based on Machine Learning for a Small Number of Experiments in High-dimensional Continuous and Discrete Variables. CHEM LETT 2019. [DOI: 10.1246/cl.190267] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Mikito Fujinami
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Junji Seino
- Waseda Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
- PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Takumi Nukazawa
- Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - Shintaro Ishida
- Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - Takeaki Iwamoto
- Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - Hiromi Nakai
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
- Waseda Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
- Element Strategy Initiative for Catalysts and Batteries (ESICB), Kyoto University, Katsura, Kyoto 615-8520, Japan
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7
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Freeze JG, Kelly HR, Batista VS. Search for Catalysts by Inverse Design: Artificial Intelligence, Mountain Climbers, and Alchemists. Chem Rev 2019; 119:6595-6612. [PMID: 31059236 DOI: 10.1021/acs.chemrev.8b00759] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In silico catalyst design is a grand challenge of chemistry. Traditional computational approaches have been limited by the need to compute properties for an intractably large number of possible catalysts. Recently, inverse design methods have emerged, starting from a desired property and optimizing a corresponding chemical structure. Techniques used for exploring chemical space include gradient-based optimization, alchemical transformations, and machine learning. Though the application of these methods to catalysis is in its early stages, further development will allow for robust computational catalyst design. This review provides an overview of the evolution of inverse design approaches and their relevance to catalysis. The strengths and limitations of existing techniques are highlighted, and suggestions for future research are provided.
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Affiliation(s)
- Jessica G Freeze
- Department of Chemistry , Yale University , New Haven , Connecticut 06520 , United States.,Energy Sciences Institute , Yale University , West Haven , Connecticut 06516 , United States
| | - H Ray Kelly
- Department of Chemistry , Yale University , New Haven , Connecticut 06520 , United States.,Energy Sciences Institute , Yale University , West Haven , Connecticut 06516 , United States
| | - Victor S Batista
- Energy Sciences Institute , Yale University , West Haven , Connecticut 06516 , United States.,Department of Chemistry , Yale University , P.O. Box 208107 , New Haven , Connecticut 06520 , United States
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8
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Baumgartner LM, Coley CW, Reizman BJ, Gao KW, Jensen KF. Optimum catalyst selection over continuous and discrete process variables with a single droplet microfluidic reaction platform. REACT CHEM ENG 2018. [DOI: 10.1039/c8re00032h] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
A mixed-integer nonlinear program (MINLP) algorithm to optimize catalyst turnover number (TON) and product yield by simultaneously modulating discrete variables—catalyst types—and continuous variables—temperature, residence time, and catalyst loading—was implemented and validated.
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Affiliation(s)
| | - Connor W. Coley
- Department of Chemical Engineering
- Massachusetts Institute of Technology
- Cambridge
- USA
| | - Brandon J. Reizman
- Department of Chemical Engineering
- Massachusetts Institute of Technology
- Cambridge
- USA
| | - Kevin W. Gao
- Department of Chemical Engineering
- Massachusetts Institute of Technology
- Cambridge
- USA
- Department of Chemical and Biomolecular Engineering
| | - Klavs F. Jensen
- Department of Chemical Engineering
- Massachusetts Institute of Technology
- Cambridge
- USA
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9
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Winkler DA. Biomimetic molecular design tools that learn, evolve, and adapt. Beilstein J Org Chem 2017; 13:1288-1302. [PMID: 28694872 PMCID: PMC5496546 DOI: 10.3762/bjoc.13.125] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 06/09/2017] [Indexed: 12/17/2022] Open
Abstract
A dominant hallmark of living systems is their ability to adapt to changes in the environment by learning and evolving. Nature does this so superbly that intensive research efforts are now attempting to mimic biological processes. Initially this biomimicry involved developing synthetic methods to generate complex bioactive natural products. Recent work is attempting to understand how molecular machines operate so their principles can be copied, and learning how to employ biomimetic evolution and learning methods to solve complex problems in science, medicine and engineering. Automation, robotics, artificial intelligence, and evolutionary algorithms are now converging to generate what might broadly be called in silico-based adaptive evolution of materials. These methods are being applied to organic chemistry to systematize reactions, create synthesis robots to carry out unit operations, and to devise closed loop flow self-optimizing chemical synthesis systems. Most scientific innovations and technologies pass through the well-known "S curve", with slow beginning, an almost exponential growth in capability, and a stable applications period. Adaptive, evolving, machine learning-based molecular design and optimization methods are approaching the period of very rapid growth and their impact is already being described as potentially disruptive. This paper describes new developments in biomimetic adaptive, evolving, learning computational molecular design methods and their potential impacts in chemistry, engineering, and medicine.
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Affiliation(s)
- David A Winkler
- CSIRO Manufacturing, Bayview Avenue, Clayton 3168, Australia
- Monash Institute of Pharmaceutical Sciences, 392 Royal Parade, Parkville 3052, Australia
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Kingsbury Drive, Melbourne, Victoria 3086, Australia
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10
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Russell B, Rabitz H. Common foundations of optimal control across the sciences: evidence of a free lunch. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2017; 375:rsta.2016.0210. [PMID: 28115607 PMCID: PMC5311431 DOI: 10.1098/rsta.2016.0210] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/20/2016] [Indexed: 05/22/2023]
Abstract
A common goal in the sciences is optimization of an objective function by selecting control variables such that a desired outcome is achieved. This scenario can be expressed in terms of a control landscape of an objective considered as a function of the control variables. At the most basic level, it is known that the vast majority of quantum control landscapes possess no traps, whose presence would hinder reaching the objective. This paper reviews and extends the quantum control landscape assessment, presenting evidence that the same highly favourable landscape features exist in many other domains of science. The implications of this broader evidence are discussed. Specifically, control landscape examples from quantum mechanics, chemistry and evolutionary biology are presented. Despite the obvious differences, commonalities between these areas are highlighted within a unified mathematical framework. This mathematical framework is driven by the wide-ranging experimental evidence on the ease of finding optimal controls (in terms of the required algorithmic search effort beyond the laboratory set-up overhead). The full scope and implications of this observed common control behaviour pose an open question for assessment in further work.This article is part of the themed issue 'Horizons of cybernetical physics'.
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Affiliation(s)
- Benjamin Russell
- Department of Chemistry, Princeton University, Princeton, NJ 08540, USA
| | - Herschel Rabitz
- Department of Chemistry, Princeton University, Princeton, NJ 08540, USA
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11
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Tibbetts KM, Feng XJ, Rabitz H. Exploring experimental fitness landscapes for chemical synthesis and property optimization. Phys Chem Chem Phys 2017; 19:4266-4287. [DOI: 10.1039/c6cp06187g] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The topology of experimental fitness landscapes for chemical optimization objectives is assessed through svr-based HDMR modeling.
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12
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Abstract
Materials science is undergoing a revolution, generating valuable new materials such as flexible solar panels, biomaterials and printable tissues, new catalysts, polymers, and porous materials with unprecedented properties. However, the number of potentially accessible materials is immense. Artificial evolutionary methods such as genetic algorithms, which explore large, complex search spaces very efficiently, can be applied to the identification and optimization of novel materials more rapidly than by physical experiments alone. Machine learning models can augment experimental measurements of materials fitness to accelerate identification of useful and novel materials in vast materials composition or property spaces. This review discusses the problems of large materials spaces, the types of evolutionary algorithms employed to identify or optimize materials, and how materials can be represented mathematically as genomes, describes fitness landscapes and mutation operators commonly employed in materials evolution, and provides a comprehensive summary of published research on the use of evolutionary methods to generate new catalysts, phosphors, and a range of other materials. The review identifies the potential for evolutionary methods to revolutionize a wide range of manufacturing, medical, and materials based industries.
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Affiliation(s)
- Tu C Le
- CSIRO Manufacturing, Bag 10, Clayton South MDC, Victoria 3169, Australia
| | - David A Winkler
- CSIRO Manufacturing, Bag 10, Clayton South MDC, Victoria 3169, Australia.,Monash Institute of Pharmaceutical Sciences , 381 Royal Parade, Parkville 3052, Australia.,Latrobe Institute for Molecular Science, La Trobe University , Bundoora 3046, Australia.,School of Chemical and Physical Sciences, Flinders University , Bedford Park 5042, Australia
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13
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Sans V, Cronin L. Towards dial-a-molecule by integrating continuous flow, analytics and self-optimisation. Chem Soc Rev 2016; 45:2032-43. [PMID: 26815081 PMCID: PMC6057606 DOI: 10.1039/c5cs00793c] [Citation(s) in RCA: 125] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The employment of continuous-flow platforms for synthetic chemistry is becoming increasingly popular in research and industrial environments. Integrating analytics in-line enables obtaining a large amount of information in real-time about the reaction progress, catalytic activity and stability, etc. Furthermore, it is possible to influence the reaction progress and selectivity via manual or automated feedback optimisation, thus constituting a dial-a-molecule approach employing digital synthesis. This contribution gives an overview of the most significant contributions in the field to date.
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Affiliation(s)
- Victor Sans
- Department of Chemical and Environmental Engineering, University of Nottingham, NG7 2RD, UK.
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14
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Fournier R, Mohareb A. Optimizing molecular properties using a relative index of thermodynamic stability and global optimization techniques. J Chem Phys 2016; 144:024114. [PMID: 26772561 DOI: 10.1063/1.4939530] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We devised a global optimization (GO) strategy for optimizing molecular properties with respect to both geometry and chemical composition. A relative index of thermodynamic stability (RITS) is introduced to allow meaningful energy comparisons between different chemical species. We use the RITS by itself, or in combination with another calculated property, to create an objective function F to be minimized. Including the RITS in the definition of F ensures that the solutions have some degree of thermodynamic stability. We illustrate how the GO strategy works with three test applications, with F calculated in the framework of Kohn-Sham Density Functional Theory (KS-DFT) with the Perdew-Burke-Ernzerhof exchange-correlation. First, we searched the composition and configuration space of CmHnNpOq (m = 0-4, n = 0-10, p = 0-2, q = 0-2, and 2 ≤ m + n + p + q ≤ 12) for stable molecules. The GO discovered familiar molecules like N2, CO2, acetic acid, acetonitrile, ethane, and many others, after a small number (5000) of KS-DFT energy evaluations. Second, we carried out a GO of the geometry of CumSnn (+) (m = 1, 2 and n = 9-12). A single GO run produced the same low-energy structures found in an earlier study where each CumSnn (+) species had been optimized separately. Finally, we searched bimetallic clusters AmBn (3 ≤ m + n ≤ 6, A,B= Li, Na, Al, Cu, Ag, In, Sn, Pb) for species and configurations having a low RITS and large highest occupied Molecular Orbital (MO) to lowest unoccupied MO energy gap (Eg). We found seven bimetallic clusters with Eg > 1.5 eV.
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Affiliation(s)
- René Fournier
- Department of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada
| | - Amir Mohareb
- Department of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada
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15
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16
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Solá IR, González-Vázquez J, de Nalda R, Bañares L. Strong field laser control of photochemistry. Phys Chem Chem Phys 2015; 17:13183-200. [PMID: 25835746 DOI: 10.1039/c5cp00627a] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Strong ultrashort laser pulses have opened new avenues for the manipulation of photochemical processes like photoisomerization or photodissociation. The presence of light intense enough to reshape the potential energy surfaces may steer the dynamics of both electrons and nuclei in new directions. A controlled laser pulse, precisely defined in terms of spectrum, time and intensity, is the essential tool in this type of approach to control chemical dynamics at a microscopic level. In this Perspective we examine the current strategies developed to achieve control of chemical processes with strong laser fields, as well as recent experimental advances that demonstrate that properties like the molecular absorption spectrum, the state lifetimes, the quantum yields and the velocity distributions in photodissociation processes can be controlled by the introduction of carefully designed strong laser fields.
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Affiliation(s)
- Ignacio R Solá
- Departamento de Química Física I (Unidad Asociada de I+D+i al CSIC), Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain.
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17
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Elward JM, Rinderspacher BC. Smooth heuristic optimization on a complex chemical subspace. Phys Chem Chem Phys 2015; 17:24322-35. [DOI: 10.1039/c5cp02177d] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In the present work, several heuristic reordering algorithms for deterministic optimization on a combinatorial chemical compound space are evaluated for performance and efficiency.
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18
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Schilling LH, Niekiel F, Stock N, Hartke B. Computer-Assisted Synthesis Optimisation of Inorganic-Organic Hybrid Compounds Using the Local Optimisation Algorithm BOBYQA. Chempluschem 2014. [DOI: 10.1002/cplu.201300407] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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19
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Moore Tibbetts K, Xing X, Rabitz H. Exploring control landscapes for laser-driven molecular fragmentation. J Chem Phys 2013; 139:144201. [DOI: 10.1063/1.4824153] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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20
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Moore Tibbetts K, Xing X, Rabitz H. Systematic Trends in Photonic Reagent Induced Reactions in a Homologous Chemical Family. J Phys Chem A 2013; 117:8205-15. [DOI: 10.1021/jp403824h] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Xi Xing
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544,
United States
| | - Herschel Rabitz
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544,
United States
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21
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Moore Tibbetts KW, Li R, Pelczer I, Rabitz H. Discovering predictive rules of chemistry from property landscapes. Chem Phys Lett 2013. [DOI: 10.1016/j.cplett.2013.03.040] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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22
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Moore Tibbetts K, Xing X, Rabitz H. Optimal control of molecular fragmentation with homologous families of photonic reagents and chemical substrates. Phys Chem Chem Phys 2013; 15:18012-22. [DOI: 10.1039/c3cp52664j] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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23
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Moore KW, Li R, Pelczer I, Rabitz H. NMR landscapes for chemical shift prediction. J Phys Chem A 2012; 116:9142-57. [PMID: 22900681 DOI: 10.1021/jp306353b] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The ability to reliably predict NMR chemical shifts plays an important role in elucidating the structure of organic molecules. Additionally, an intriguing question is how the multitude of variable factors (structural, electronic, and environmental) correlate with the actual electromagnetic shielding effect that determines the chemical shift value. This work presents NMRscape as a new tool for understanding these correlations by constructing the landscape that describes the relationship between the chemical shift value and the moieties bonded to a molecular scaffold. The scaffold may be as small as a single atom probed by NMR or a larger molecular framework containing the probed atom. NMRscape operates with only a list of the chemical moieties bonded to the scaffold, without utilizing any potentially biasing chemometric descriptors. The corresponding chemical shift landscape is constructed based on fundamental physical principles, which makes NMRscape a credible chemical shift prediction and analysis tool. As an illustration, we demonstrate that NMRscape can predict (13)C chemical shifts with an accuracy exceeding the substituent chemical shift (SCS) increment, hierarchical organization of spherical environments (HOSE), and neural networks (NN), methods for three distinct families of molecules sharing a common scaffold structure with moieties placed at two variable sites. The constructed NMR landscapes confirmed known empirical rules relating chemical shift values to the variation of chemical moieties on a scaffold, as well as uncovered hitherto hidden relationships. The practical importance of NMRscape is discussed.
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Affiliation(s)
- Katharine W Moore
- Department of Chemistry, Princeton University , Princeton, New Jersey 08544, United States
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Beltrani V, Rabitz H. Exploiting time-independent Hamiltonian structure as controls for manipulating quantum dynamics. J Chem Phys 2012; 137:094109. [PMID: 22957557 DOI: 10.1063/1.4743954] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The opportunities offered by utilizing time-independent Hamiltonian structure as controls are explored for manipulating quantum dynamics. Two scenarios are investigated using different manifestations of Hamiltonian structure to illustrate the generality of the concept. In scenario I, optimally shaped electrostatic potentials are generated to flexibly control electron scattering in a two-dimensional subsurface plane of a semiconductor. A simulation is performed showing the utility of optimally setting the individual voltages applied to a multi-pixel surface gate array in order to produce a spatially inhomogeneous potential within the subsurface scattering plane. The coherent constructive and destructive electron wave interferences are manipulated by optimally adjusting the potential shapes to alter the scattering patterns. In scenario II, molecular vibrational wave packets are controlled by means of optimally selecting the Hamiltonian structure in cooperation with an applied field. As an illustration of the concept, a collection (i.e., a level set) of dipole functions is identified where each member serves with the same applied electric field to produce the desired final transition probability. The level set algorithm additionally found Hamiltonian structure controls exhibiting desirable physical properties. The prospects of utilizing the applied field and Hamiltonian structure simultaneously as controls is also explored. The control scenarios I and II indicate the gains offered by algorithmically guided molecular or material discovery for manipulating quantum dynamics phenomenon.
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Affiliation(s)
- Vincent Beltrani
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
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Abstract
Controlling dynamical processes at the atomic and molecular scales with laser radiation has been a long-standing dream. The Faraday Discussion presented a cross section of the current experimental and theoretical advances as well as the challenges for the field. This paper summarizes the current status of controlling quantum dynamics phenomena and provides a perspective on the future.
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Affiliation(s)
- Herschel Rabitz
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
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26
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Feng X, Sanchis J, Reetz MT, Rabitz H. Enhancing the efficiency of directed evolution in focused enzyme libraries by the adaptive substituent reordering algorithm. Chemistry 2012; 18:5646-54. [PMID: 22434591 DOI: 10.1002/chem.201103811] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Indexed: 11/11/2022]
Abstract
Directed evolution is a broadly successful strategy for protein engineering in the quest to enhance the stereoselectivity, activity, and thermostability of enzymes. To increase the efficiency of directed evolution based on iterative saturation mutagenesis, the adaptive substituent reordering algorithm (ASRA) is introduced here as an alternative to traditional quantitative structure-activity relationship (QSAR) methods for identifying potential protein mutants with desired properties from minimal sampling of focused libraries. The operation of ASRA depends on identifying the underlying regularity of the protein property landscape, allowing it to make predictions without explicit knowledge of the structure-property relationships. In a proof-of-principle study, ASRA identified all or most of the best enantioselective mutants among the synthesized epoxide hydrolase from Aspergillus niger, in the absence of peptide seeds with high E-values. ASRA even revealed a laboratory error from irregularities of the reordered E-value landscape alone.
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Affiliation(s)
- Xiaojiang Feng
- Department of Chemistry, Princeton University, New Jersey 08544, USA
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27
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Feng X, Pechen A, Jha A, Wu R, Rabitz H. Global optimality of fitness landscapes in evolution. Chem Sci 2012. [DOI: 10.1039/c1sc00648g] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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28
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Soh S, Wei Y, Kowalczyk B, Gothard CM, Baytekin B, Gothard N, Grzybowski BA. Estimating chemical reactivity and cross-influence from collective chemical knowledge. Chem Sci 2012. [DOI: 10.1039/c2sc00011c] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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