Computational Techniques for Analytical Chemistry and Bioanalysis PDF
Preview Computational Techniques for Analytical Chemistry and Bioanalysis
Computational Techniques for Analytical Chemistry and Bioanalysis Theoretical and Computational Chemistry Series Editor-in-chief: Jonathan Hirst, University of Nottingham, Nottingham, UK Advisory board: Dongqing Wei, Shanghai Jiao Tong University, China Jeremy Smith, Oakridge National Laboratory, USA Titles in the series: 1: Knowledge-based Expert Systems in Chemistry: Not Counting on Computers 2: Non-Covalent Interactions: Theory and Experiment 3: Single-Ion Solvation: Experimental and Theoretical Approaches to Elusive Thermodynamic Quantities 4: Computational Nanoscience 5: Computational Quantum Chemistry: Molecular Structure and Properties in Silico 6: Reaction Rate Constant Computations: Theories and Applications 7: Theory of Molecular Collisions 8: In Silico Medicinal Chemistry: Computational Methods to Support Drug Design 9: Simulating Enzyme Reactivity: Computational Methods in Enzyme Catalysis 10: Computational Biophysics of Membrane Proteins 11:ColdChemistry: Molecular Scattering andReactivity Near Absolute Zero 12: Theoretical Chemistry for Electronic Excited States 13: Attosecond Molecular Dynamics 14: Self-organized Motion: Physicochemical Design based on Nonlinear Dynamics 15: Knowledge-based Expert Systems in Chemistry: Artificial Intelligence in Decision Making 16:LondonDispersionForcesinMolecules,SolidsandNano-structures: An Introduction to Physical Models and Computational Methods 17: Machine Learning in Chemistry: The Impact of Artificial Intelligence 18: Tunnelling in Molecules: Nuclear Quantum Effects from Bio to Physical Chemistry 19: Understanding Hydrogen Bonds: Theoretical and Experimental Views 20: Computational Techniques for Analytical Chemistry and Bioanalysis How to obtain future titles on publication: Astandingorderplanisavailableforthisseries.Astandingorderwillbring delivery of each new volume immediately on publication. For further information please contact: BookSalesDepartment,RoyalSocietyofChemistry,ThomasGrahamHouse, Science Park, Milton Road, Cambridge, CB4 0WF, UK Telephone: þ44 (0)1223 420066, Fax: þ44 (0)1223 420247, Email: [email protected] Visit our website at www.rsc.org/books Computational Techniques for Analytical Chemistry and Bioanalysis Edited by Philippe B. Wilson Nottingham Trent University, UK Email: [email protected] and Martin Grootveld De Montfort University, UK Email: [email protected] TheoreticalandComputationalChemistrySeriesNo.20 PrintISBN:978-1-78801-461-8 PDFISBN:978-1-78801-588-2 EPUBISBN:978-1-78801-985-9 PrintISSN:2041-3181 ElectronicISSN:2041-319X AcataloguerecordforthisbookisavailablefromtheBritishLibrary rTheRoyalSocietyofChemistry2021 Allrightsreserved Apartfromfairdealingforthepurposesofresearchfornon-commercialpurposesorfor privatestudy,criticismorreview,aspermittedundertheCopyright,DesignsandPatents Act1988andtheCopyrightandRelatedRightsRegulations2003,thispublicationmaynot bereproduced,storedortransmitted,inanyformorbyanymeans,withouttheprior permissioninwritingofTheRoyalSocietyofChemistryorthecopyrightowner,orinthe caseofreproductioninaccordancewiththetermsoflicencesissuedbytheCopyright LicensingAgencyintheUK,orinaccordancewiththetermsofthelicencesissuedbythe appropriateReproductionRightsOrganizationoutsidetheUK.Enquiriesconcerning reproductionoutsidethetermsstatedhereshouldbesenttoTheRoyalSocietyof Chemistryattheaddressprintedonthispage. Whilstthismaterialhasbeenproducedwithallduecare,TheRoyalSocietyofChemistry cannotbeheldresponsibleorliableforitsaccuracyandcompleteness,norforany consequencesarisingfromanyerrorsortheuseoftheinformationcontainedinthis publication.Thepublicationofadvertisementsdoesnotconstituteanyendorsementby TheRoyalSocietyofChemistryorAuthorsofanyproductsadvertised.Theviewsand opinionsadvancedbycontributorsdonotnecessarilyreflectthoseofTheRoyalSocietyof Chemistrywhichshallnotbeliableforanyresultinglossordamagearisingasaresultof relianceuponthismaterial. TheRoyalSocietyofChemistryisacharity,registeredinEnglandandWales, Number207890,andacompanyincorporatedinEnglandbyRoyalCharter (RegisteredNo.RC000524),registeredoffice:BurlingtonHouse,Piccadilly, LondonW1J0BA,UK,Telephone:þ44(0)2074378656. Forfurtherinformationseeourwebsiteatwww.rsc.org PrintedintheUnitedKingdombyCPIGroup(UK)Ltd,Croydon,CR04YY,UK Dedication PBW wishes to dedicate this monograph to his supportive family, in par- ticular Florence and Penelope, the two new additions who bring light to each day. TheoreticalandComputationalChemistrySeriesNo.20 ComputationalTechniquesforAnalyticalChemistryandBioanalysis EditedbyPhilippeB.WilsonandMartinGrootveld rTheRoyalSocietyofChemistry2021 PublishedbytheRoyalSocietyofChemistry,www.rsc.org vii Preface Withtheadvancesintechnologyandthevastdatastreamsnowproducedby modern analytical instrumentation, computational models, systems and routines have been developed to better treat the information obtained. In- deed, we have seen such advances in applications of AI techniques to chemical data science that certainly the relevant chapter required updating multiple times throughout the publication process. Wehaverecruitedacomprehensivegroupofcolleaguesinternationallyto develop this monograph. With chapters ranging from fundamental simu- lations of nuclear quantum effects, through to overviews of the various spectroscopic methods available andthe computational techniques applied therein, this volume should appeal to colleagues both in the chemical and biosciencesas a broad and comprehensive overview ofin silico applications in analytical methodologies. We begin in Chapter 1 with an overview of computational techniques as applied to metabolomic data analysis. Therein, Percival, Grootveld, and colleagues describe the significant advances over the past decade in data treatment,curationandavailability,whilstdescribingwell-knowntoolssuch as Wishart’s Metaboanalyst packages. Chapter2,co-authoredbyCastroandSwart,consistsofabroadandtimely review of computational NMR spectroscopy for predictive purposes. The reproduction of NMR experiments in simulations is considered, as well as the numerous parameters contributing to spectral similarity with experiment. In Chapter 3, Dario Estrin and colleagues from Universidad de Buenos Aires provide a comprehensive and contemporary perspective on compu- tationalvibrationalspectroscopy.Indeed,theydescribethestateoftheart within the field, covering the most recent developments in the context of TheoreticalandComputationalChemistrySeriesNo.20 ComputationalTechniquesforAnalyticalChemistryandBioanalysis EditedbyPhilippeB.WilsonandMartinGrootveld rTheRoyalSocietyofChemistry2021 PublishedbytheRoyalSocietyofChemistry,www.rsc.org viii Preface ix the levels of theory available and applied. Discussions of (an)harmonicity complement the narrative which covers classical to fully QM approaches. Paneth and Dybala-Defratyka consider the use of isotope effects, nuclear quantum effects and analytical probes in Chapter 4. They provide an overview of predicting isotope effects (both kinetic and equilibrium), and the information obtained which can be employed to consider the behaviour of a variety of chemical and biological systems. Applications of theoretical estimations of isotope effects are described, such as through reactions in solution, and the employment of a range of QM/MM procedures are considered in the context of enzyme-catalysed reactions. Applications of artificial intelligence techniques in chemical and bio- chemical analysis are discussed in Chapter 5, where Gibson, Kamerlin, Wilsonandcolleaguesfirstprovideaholisticoverviewoftheoryandhistory in the field, prior to covering a snapshot of advances, particularly over the last 5 years. The developments by groups such as those of Aspuru-Guzik, Cronin and others in bringing AI techniques to the forefront of con- temporary chemical analysis are described, whilst a perspective for future applications is offered. Monari, Franc´es-Monerris, and co-workers explain the development of computational spectroscopic approaches for complex biological systems in Chapter 6. First offering a short review of hybrid QM/MM techniques, they continue to provide vital guidance in the simulation of photobiological phenomena, including the adequate sampling of chromophore conformations. The narrative develops the theory and application of computational techniques in circular dichroism spectra, and a discussion on modern methods for understanding the evolution of excited states. In Chapter 7, Lucie Delemotte from KTH Stockholm considers bridging the gap between atomistic MD simulations and laboratory experiments for investigations of membrane proteins. The link between experimental char- acterisation and simulation is established, as alongside a consideration of the theoretical models developed for MD and recent advances. Moreover, a useful discussion is developed, considering the degree of automation of such studies, as well as the necessary comparability to interpretable experimental data. Chapter 8, by Molinari and colleagues, provides a perspective of compu- tational chemical analysis as applied to solid state chemistry, in particular, materials science. The methodologies and protocols applied to materials analysis are surveyed, considering surfaces and their interactions with the environment. Comparative assessments of computational methods and ex- perimental techniques are offered, suggesting the substantial advantages combinatorial approaches have on contemporary studies. We conclude by considering the computational approaches inherent in the analysis of ESR spectral data in Chapter 9, where Mart´ın, Mather, Wilsonandco-workersapproachthetopicpedagogicallythroughareviewof
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