1
|
Gantzer P, Creton B, Nieto-Draghi C. Inverse-QSPR for de novo Design: A Review. Mol Inform 2019; 39:e1900087. [PMID: 31682079 DOI: 10.1002/minf.201900087] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 11/04/2019] [Indexed: 11/09/2022]
Abstract
The use of computer tools to solve chemistry-related problems has given rise to a large and increasing number of publications these last decades. This new field of science is now well recognized and labelled Chemoinformatics. Among all chemoinformatics techniques, the use of statistical based approaches for property predictions has been the subject of numerous research reflecting both new developments and many cases of applications. The so obtained predictive models relating a property to molecular features - descriptors - are gathered under the acronym QSPR, for Quantitative Structure Property Relationships. Apart from the obvious use of such models to predict property values for new compounds, their use to virtually synthesize new molecules - de novo design - is currently a high-interest subject. Inverse-QSPR (i-QSPR) methods have hence been developed to accelerate the discovery of new materials that meet a set of specifications. In the proposed manuscript, we review existing i-QSPR methodologies published in the open literature in a way to highlight developments, applications, improvements and limitations of each.
Collapse
Affiliation(s)
- Philippe Gantzer
- IFP Energies nouvelles, 1 et 4 avenue de Bois-Préau, 92852, Rueil-Malmaison, France
| | - Benoit Creton
- IFP Energies nouvelles, 1 et 4 avenue de Bois-Préau, 92852, Rueil-Malmaison, France
| | - Carlos Nieto-Draghi
- IFP Energies nouvelles, 1 et 4 avenue de Bois-Préau, 92852, Rueil-Malmaison, France
| |
Collapse
|
2
|
Jørgensen SB, Lind M, Jensen N. Functional Modeling View on Product and Process Engineering in Design and Operations. Ind Eng Chem Res 2019. [DOI: 10.1021/acs.iecr.8b06338] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sten Bay Jørgensen
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, DK-2800 Kgs., Lyngby, Denmark
| | - Morten Lind
- Department of Electrical Engineering, Technical University of Denmark, DK-2800 Kgs., Lyngby, Denmark
| | - Niels Jensen
- Safepark, Kannikestræde 14, DK-3550 Slangerup, Denmark
| |
Collapse
|
3
|
Liu Q, Zhang L, Liu L, Du J, Tula AK, Eden M, Gani R. OptCAMD: An optimization-based framework and tool for molecular and mixture product design. Comput Chem Eng 2019. [DOI: 10.1016/j.compchemeng.2019.01.006] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
4
|
Austin ND, Sahinidis NV, Trahan DW. Computer-aided molecular design: An introduction and review of tools, applications, and solution techniques. Chem Eng Res Des 2016. [DOI: 10.1016/j.cherd.2016.10.014] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
5
|
Abstract
Design of chemicals-based products is broadly classified into those that are process centered and those that are product centered. In this article, the designs of both classes of products are reviewed from a process systems point of view; developments related to the design of the chemical product, its corresponding process, and its integration are highlighted. Although significant advances have been made in the development of systematic model-based techniques for process design (also for optimization, operation, and control), much work is needed to reach the same level for product design. Timeline diagrams illustrating key contributions in product design, process design, and integrated product-process design are presented. The search for novel, innovative, and sustainable solutions must be matched by consideration of issues related to the multidisciplinary nature of problems, the lack of data needed for model development, solution strategies that incorporate multiscale options, and reliability versus predictive power. The need for an integrated model-experiment-based design approach is discussed together with benefits of employing a systematic computer-aided framework with built-in design templates.
Collapse
Affiliation(s)
- Lei Zhang
- PSE for SPEED Project, Department of Chemical and Biochemical Engineering, Technical University of Denmark, DK-2800, Kongens Lyngby, Denmark
| | - Deenesh K. Babi
- PSE for SPEED Project, Department of Chemical and Biochemical Engineering, Technical University of Denmark, DK-2800, Kongens Lyngby, Denmark
| | - Rafiqul Gani
- PSE for SPEED Project, Department of Chemical and Biochemical Engineering, Technical University of Denmark, DK-2800, Kongens Lyngby, Denmark
| |
Collapse
|
6
|
Gani R, Zhang L, Kalakul S, Cignitti S. Computer-Aided Molecular Design and Property Prediction. COMPUTER AIDED CHEMICAL ENGINEERING 2016. [DOI: 10.1016/b978-0-444-63683-6.00006-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
7
|
Ng LY, Chemmangattuvalappil NG, Ng DK. Robust chemical product design via fuzzy optimisation approach. Comput Chem Eng 2015. [DOI: 10.1016/j.compchemeng.2015.01.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
8
|
Ng LY, Andiappan V, Chemmangattuvalappil NG, Ng DK. A systematic methodology for optimal mixture design in an integrated biorefinery. Comput Chem Eng 2015. [DOI: 10.1016/j.compchemeng.2015.04.032] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
9
|
Ng LY, Chong FK, Chemmangattuvalappil NG. Challenges and opportunities in computer-aided molecular design. Comput Chem Eng 2015. [DOI: 10.1016/j.compchemeng.2015.03.009] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
10
|
Ng LY, Andiappan V, Chemmangattuvalappil NG, Ng DKS. Novel Methodology for the Synthesis of Optimal Biochemicals in Integrated Biorefineries via Inverse Design Techniques. Ind Eng Chem Res 2015. [DOI: 10.1021/acs.iecr.5b00217] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lik Yin Ng
- Department of Chemical and
Environmental Engineering/Centre of Sustainable Palm Oil Research
(CESPOR), The University of Nottingham Malaysia Campus, Broga Road, Semenyih, Selangor 43500, Malaysia
| | - Viknesh Andiappan
- Department of Chemical and
Environmental Engineering/Centre of Sustainable Palm Oil Research
(CESPOR), The University of Nottingham Malaysia Campus, Broga Road, Semenyih, Selangor 43500, Malaysia
| | - Nishanth G. Chemmangattuvalappil
- Department of Chemical and
Environmental Engineering/Centre of Sustainable Palm Oil Research
(CESPOR), The University of Nottingham Malaysia Campus, Broga Road, Semenyih, Selangor 43500, Malaysia
| | - Denny K. S. Ng
- Department of Chemical and
Environmental Engineering/Centre of Sustainable Palm Oil Research
(CESPOR), The University of Nottingham Malaysia Campus, Broga Road, Semenyih, Selangor 43500, Malaysia
| |
Collapse
|
11
|
Ng LY, Chemmangattuvalappil NG, Ng DKS. A Multiobjective Optimization-Based Approach for Optimal Chemical Product Design. Ind Eng Chem Res 2014. [DOI: 10.1021/ie502906a] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Lik Yin Ng
- Department of Chemical and
Environmental Engineering/Centre of Excellence for Green Technologies, The University of Nottingham, Malaysia Campus, Broga Road, 43500 Semenyih, Selangor Malaysia
| | - Nishanth G. Chemmangattuvalappil
- Department of Chemical and
Environmental Engineering/Centre of Excellence for Green Technologies, The University of Nottingham, Malaysia Campus, Broga Road, 43500 Semenyih, Selangor Malaysia
| | - Denny K. S. Ng
- Department of Chemical and
Environmental Engineering/Centre of Excellence for Green Technologies, The University of Nottingham, Malaysia Campus, Broga Road, 43500 Semenyih, Selangor Malaysia
| |
Collapse
|
12
|
Trespalacios F, Grossmann I. Review of Mixed-Integer Nonlinear and Generalized Disjunctive Programming Methods. CHEM-ING-TECH 2014. [DOI: 10.1002/cite.201400037] [Citation(s) in RCA: 118] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
13
|
Optimal Chemical Product Design via Fuzzy Optimisation based Inverse Design Techniques. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/b978-0-444-63456-6.50055-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
|
14
|
Chemmangattuvalappil NG, Eden MR. A Novel Methodology for Property-Based Molecular Design Using Multiple Topological Indices. Ind Eng Chem Res 2013. [DOI: 10.1021/ie302516v] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Nishanth G. Chemmangattuvalappil
- Department of Chemical and Environmental Engineering, University of Nottingham Malaysia, Semenyih, Selangor,
Malaysia
- Department of
Chemical Engineering, Auburn University, Auburn, Alabama, United States
| | - Mario R. Eden
- Department of
Chemical Engineering, Auburn University, Auburn, Alabama, United States
| |
Collapse
|
15
|
Martin S. Lattice enumeration for inverse molecular design using the signature descriptor. J Chem Inf Model 2012; 52:1787-97. [PMID: 22657105 DOI: 10.1021/ci3001748] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
We describe an inverse quantitative structure-activity relationship (QSAR) framework developed for the design of molecular structures with desired properties. This framework uses chemical fragments encoded with a molecular descriptor known as a signature. It solves a system of linear constrained Diophantine equations to reorganize the fragments into novel molecular structures. The method has been previously applied to problems in drug and materials design but has inherent computational limitations due to the necessity of solving the Diophantine constraints. We propose a new approach to overcome these limitations using the Fincke-Pohst algorithm for lattice enumeration. We benchmark the new approach against previous results on LFA-1/ICAM-1 inhibitory peptides, linear homopolymers, and hydrofluoroether foam blowing agents. Software implementing the new approach is available at www.cs.otago.ac.nz/homepages/smartin.
Collapse
Affiliation(s)
- Shawn Martin
- Department of Computer Science, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand.
| |
Collapse
|
16
|
Chemmangattuvalappil NG, Solvason CC, Bommareddy S, Eden MR. Reverse problem formulation approach to molecular design using property operators based on signature descriptors. Comput Chem Eng 2010. [DOI: 10.1016/j.compchemeng.2010.07.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|
17
|
Patel SJ, Ng D, Mannan MS. QSPR Flash Point Prediction of Solvents Using Topological Indices for Application in Computer Aided Molecular Design. Ind Eng Chem Res 2009. [DOI: 10.1021/ie9000794] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Suhani J. Patel
- Mary Kay O’Connor Process Safety Center, Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843-3122
| | - Dedy Ng
- Mary Kay O’Connor Process Safety Center, Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843-3122
| | - M. Sam Mannan
- Mary Kay O’Connor Process Safety Center, Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843-3122
| |
Collapse
|
18
|
Yuan H, Yang B, Yang J. Predicting Properties of Biodiesel Fuels using Mixture Topological Index. J AM OIL CHEM SOC 2009. [DOI: 10.1007/s11746-009-1354-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
19
|
Lei Z, Chen B, Li C, Liu H. Predictive Molecular Thermodynamic Models for Liquid Solvents, Solid Salts, Polymers, and Ionic Liquids. Chem Rev 2008; 108:1419-55. [DOI: 10.1021/cr068441+] [Citation(s) in RCA: 123] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
20
|
Brown WM, Martin S, Rintoul MD, Faulon JL. Designing Novel Polymers with Targeted Properties Using the Signature Molecular Descriptor. J Chem Inf Model 2006; 46:826-35. [PMID: 16563014 DOI: 10.1021/ci0504521] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A method for solving the inverse quantitative structure-property relationship (QSPR) problem is presented which facilitates the design of novel polymers with targeted properties. Here, we demonstrate the efficacy of the approach using the targeted design of polymers exhibiting a desired glass transition temperature, heat capacity, and density. We present novel QSPRs based on the signature molecular descriptor capable of predicting glass transition temperature, heat capacity, density, molar volume, and cohesive energies of linear homopolymers with cross-validation squared correlation coefficients ranging between 0.81 and 0.95. Using these QSPRs, we show how the inverse problem can be solved to design poly(N-methyl hexamethylene sebacamide) despite the fact that the polymer was used not used in the training of this model.
Collapse
Affiliation(s)
- W Michael Brown
- Department of Computational Biology, Sandia National Laboratories, P.O. Box 5800, Albuquerque, New Mexico 87185-0310, USA.
| | | | | | | |
Collapse
|
21
|
Giovanoglou A, Barlatier J, Adjiman CS, Pistikopoulos EN, Cordiner JL. Optimal solvent design for batch separation based on economic performance. AIChE J 2006. [DOI: 10.1002/aic.690491211] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
22
|
Sahinidis NV, Tawarmalani M, Yu M. Design of alternative refrigerants via global optimization. AIChE J 2006. [DOI: 10.1002/aic.690490714] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
23
|
Balaban AT. Can topological indices transmit information on properties but not on structures? J Comput Aided Mol Des 2005; 19:651-60. [PMID: 16328856 DOI: 10.1007/s10822-005-9010-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2005] [Accepted: 07/28/2005] [Indexed: 10/25/2022]
Abstract
A survey of several topological indices (TIs) is provided according to the nature (integers or real numbers) of the local vertex invariants (LOVIs) and of the resulting molecular descriptor (TI). The 1st generation TIs such as the Wiener index when both the LOVIs and the TI are integers have a very high degeneracy. This fact can become an asset for the problem under discussion: when confronted with the "inverse problem" (reverse engineering) such indices lead to a combinatorial explosion of possible solutions. On the other extreme, TIs with very low degeneracy may also offer the possibility to transmit information on properties but not on structures, because they may be too difficult to lend themselves to reverse engineering in a reasonable amount of time. Several such indices are discussed: the novel second-generation index G (derived from the average distance-based connectivity index J in order to include a dependence on graph size and cyclicity), and third-generation indices such as the triplet TI denoted by DN2S(4) or the Kier-Hall index TOTOP. The intercorrelation of these indices is discussed: G is almost linearly-correlated with DN2S(4), and shows a different type of correlation with TOTOP.
Collapse
|
24
|
Chen B, Lei Z, Li Q, Li C. Application of CAMD in separating hydrocarbons by extractive distillation. AIChE J 2005. [DOI: 10.1002/aic.10562] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
25
|
|
26
|
Lehmann A, Maranas CD. Molecular Design Using Quantum Chemical Calculations for Property Estimation. Ind Eng Chem Res 2004. [DOI: 10.1021/ie030120q] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Andreas Lehmann
- Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Costas D. Maranas
- Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802
| |
Collapse
|
27
|
Chavali S, Lin B, Miller DC, Camarda KV. Environmentally-benign transition metal catalyst design using optimization techniques. Comput Chem Eng 2004. [DOI: 10.1016/j.compchemeng.2004.02.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
28
|
|
29
|
Lei Z, Li C, Chen B. Extractive Distillation: A Review. SEPARATION AND PURIFICATION REVIEWS 2003. [DOI: 10.1081/spm-120026627] [Citation(s) in RCA: 279] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
|
30
|
Optimization Methods in CAMD – II. ACTA ACUST UNITED AC 2003. [DOI: 10.1016/s1570-7946(03)80006-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
|
31
|
Ostrovsky GM, Achenie LEK, Sinha M. On the solution of mixed-integer nonlinear programming models for computer aided molecular design. COMPUTERS & CHEMISTRY 2002; 26:645-60. [PMID: 12385479 DOI: 10.1016/s0097-8485(02)00049-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
This paper addresses the efficient solution of computer aided molecular design (CAMD) problems, which have been posed as mixed-integer nonlinear programming models. The models of interest are those in which the number of linear constraints far exceeds the number of nonlinear constraints, and with most variables participating in the nonconvex terms. As a result global optimization methods are needed. A branch-and-bound algorithm (BB) is proposed that is specifically tailored to solving such problems. In a conventional BB algorithm, branching is performed on all the search variables that appear in the nonlinear terms. This translates to a large number of node traversals. To overcome this problem, we have proposed a new strategy for branching on a set of linear branchingfunctions, which depend linearly on the search variables. This leads to a significant reduction in the dimensionality of the search space. The construction of linear underestimators for a class of functions is also presented. The CAMD problem that is considered is the design of optimal solvents to be used as cleaning agents in lithographic printing.
Collapse
Affiliation(s)
- Guennadi M Ostrovsky
- Department of Chemical Engineering, University of Connecticut, Storrs 06269, USA
| | | | | |
Collapse
|
32
|
|
33
|
An optimization approach to the design of value-added soybean oil products. ACTA ACUST UNITED AC 2001. [DOI: 10.1016/s1570-7946(01)80057-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
|
34
|
|
35
|
|
36
|
Siddhaye S, Camarda KV, Topp E, Southard M. Design of novel pharmaceutical products via combinatorial optimization. Comput Chem Eng 2000. [DOI: 10.1016/s0098-1354(00)00320-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
37
|
Camarda KV, Maranas CD. Optimization in Polymer Design Using Connectivity Indices. Ind Eng Chem Res 1999. [DOI: 10.1021/ie980682n] [Citation(s) in RCA: 81] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Kyle V. Camarda
- Department of Chemical Engineering, The Pennsylvania State University, 112A Fenske Laboratory, University Park, Pennsylvania 16802
| | - Costas D. Maranas
- Department of Chemical Engineering, The Pennsylvania State University, 112A Fenske Laboratory, University Park, Pennsylvania 16802
| |
Collapse
|