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PDF Hosted at the Radboud Repository of the Radboud University Nijmegen PDF hosted at the Radboud Repository of the Radboud University Nijmegen The following full text is a publisher's version. For additional information about this publication click this link. http://hdl.handle.net/2066/19078 Please be advised that this information was generated on 2021-09-23 and may be subject to change. Computational Chemistry Metho ds Applications to Racemate Resolution and Radical Cation Chemistry ISBN Computational Chemistry Metho ds Applications to Racemate Resolution and Radical Cation Chemistry een wetenschapp elijkeproeve op het gebied van de Natuurwetenschapp en Wiskunde en Informatica Pro efschrift ter verkrijging van de graad van do ctor aan de KatholiekeUniversiteit Nijmegen volgens b esluit van het College van Decanen in het op enbaar te verdedigen op dinsdag januari des namiddags om uur precies do or Gijsb ert Schaftenaar geb oren op augustus te Harderwijk Promotores Prof dr ir A van der Avoird Prof dr E Vlieg Copromotor Prof dr RJ Meier Leden manuscriptcommissie Prof dr G Vriend Prof dr RA de Gro ot Dr ir PES Wormer The research rep orted in this thesis was nancially supp orted by the Dutch Or ganization for the Advancement of Science NWO and DSM Contents Preface Intro duction Intro duction Chirality Metho ds for obtaining pure enantiomers Racemate Resolution via diastereomeric salt formation Rationalization of diastereomeric salt formation Computational metho ds for mo deling the lattice energy Molecular Mechanics Quantum Chemical Metho ds Summary of used mass sp ectrometry techniques Outline of this Thesis References and Notes Molden a pre and p ost pro cessing program for molecular and electronic structures Summary Intro duction Metho ds Molden as a prepro cessor the Zmatrix Editor Molden as a p ostpro cessor Discussion References and Notes The eect of iso density surface sampling on ESP derived charges and the eect of adding b ondcenters on DMA derived charges Summary Intro duction Metho ds The quality of DMA derived charges versus QMESP charge The eect of sampling on the quality of DMA derived charges and QMESP charges Results DMA derived charges Iso density surface sampling vs Van der Waals surface sam pling Timings Conclusions Acknowledgements References and Notes Quantum mechanical and force eld calculations on the diastere omeric salts of cyclic phosphoric acids with ephedrine Summary Intro duction Metho ds The crystal structures of cyclic phosphoric acid derivatives and ephedrine Computational metho ds Results Ab initio calculations on mo del systems Lattice energy calculations using a classical force eld Lattice energy calculations using distributed multip ole ex pansions Lattice energy minimizations using VASP Lattice energy minimizations using DMol Lattice energy minimizations using SIESTA The relative imp ortance of separate interactions studied with DMol Comparison of the absolute lattice energies Conclusions Acknowledgements References and Notes The gas phase chemistry of the methyl carbamate radical cation Summary Intro duction Exp erimental Results and discussion Energetic measurements Theoretical methods The unimolecular chemistry of methylcarbamate ions Conclusions Acknowledgements References Summary Samenvatting Dankwoord Curriculum Vitae Preface This thesis deals with the application of computational mo dels to solvereal life chemical problems Two distinct problems are tackled First the prediction of lattice energy dierences b etween a pair of diastereomeric salts and secondly the elucidation of the unimolecular chemistry of the methyl carbamate radical cation While the second problem deals with relatively small molecules atoms the rst deals with much larger molecules atoms Both systems were at the limit of the size that could b e handled with Quantum Mechanical metho ds at the time the calculations were p erformed This illustrates the evolution of b oth Quantum Mechanical metho ds and computer hardware in the ten years that lie b etween them Besides b eing dierent in size these systems also dier in complexity While the second problem deals with isolated molecules in the gas phase the rst deals with interacting molecules in the solid In addition the latter involves a whole sp ectrum of intermolecular interactions from weak van der Waals contacts ringring interactions to strong ionic interactions and hydrogen bridges The total energy dierences b etween diastereomeric salts however are very small kcalmol compared to the energy dierences found b etween the isomers and transition states of the methyl carbamate radical cation up to kcalmol Trying to repro duce such small energy dierences as kcalmol pushes even presentday computational metho ds to their limits Chapter Intro duction This chapter deals with the background of racemate resolution via the forma tion of diastereomeric salts In addition a brief overview will b e given of mass sp ectrometry techniques used for the elucidation of the unimolecular chemistry of the methyl carbamate radical cation A review of the applied computational metho ds will also b e given Intro duction Chirality Achiral molecule is a molecule that is not sup erimp osable on its mirror image These nonsup erimp osable mirror images are called enantiomers Enantiomer pairs of a particular molecule haveidentical physical prop erties except for optical rotation That is to say when planep olarized light is passed through a solu tion or crystal of one enantiomer the resulting rotation of the light p olarization plane is equal in magnitude but in opp osite direction to that of its enantiomeric counterpart For this reason enantiomers are also called optical isomers The prexes and or dextro and laevo DL which designate the di rection of the angle of rotation are used to distinguish enantiomers Another classication system the RS system designates the absolute conguration of a stereoisomer It has largely replaced the DL notation and is used for molecules other than amino acids Sometimes the number of chiral centers n presentina n molecule is more than one In this case not all of the p ossible stereoisomers are each others mirror image Two stereoisomers that are not each others mirror image are called a diastereomeric pair In addition to essentially identical physical prop erties enantiomers also have identical chemical prop erties except in a chiral environment such as biological Chapter systems where receptors enzyme systems and so forth typically havechiral prop erties themselves The interaction of a drug molecule with the receptor or the enzyme is very sp ecic due to their chemical and structural complementarity and may exhibit stereoselectivity In fact many active pharmaceutical drugs are chiral and were marketed up till the s as racemic mixtures ie as an equal mole ratio of their individual enantiomers The problem is that one enantiomeric form of a chiral drug may b e medicinally b enecial while the other enantiomeric form may b e completely useless or even toxic Table shows some examples of the distinct biological eects of the two enantiomers in a racemate An example of the latter is the drug thalidomide whichwas administered to pregnantwomen in the s curing morning sickness in early pregnancy One of the enantiomeric forms was found to b e medicinally b enecial while the other was found to b e teratogenic The result was babies b orn with severe limb deformities Since the US Fo o d and Drugs Administration FDA and the Europ ean Committee for Proprietary Medicinal Pro ducts have required manu facturers to researchandcharacterise eachenantiomer in all drugs prop osed to b e marketed as a mixture thus justifying that no safetyrisk exists for the racemate From that date pro duction of new racemates ceased to b e a rational commer cial option and instead b ecame a high risk route for pharmaceutical compagnies In addition it led to racemicswitching by pharmaceutical compagnies extend ing a patent protection on a racemic drug by later patenting its single active enantiomer When the FDAvoted in favour of single isomers it did so b ecause scientic advances had driven chiral technology to the p oint where it b ecame realistic and routinely p ossible to develop them Metho ds for obtaining pure enantiomers There are three options for intro ducing chiralityinto a synthesis the chirality p o ol where the required conguration is present in the starting materials used and is maintained throughout the remainder of anysynthesis asymmetric synthesis where the singleisomer pro duct is derived byintro ducing the asymmetry directly into a nonchiral material Intro duction Table Examples of enatiomers exhibiting dierent biological eects Comp ound Eect of S Eect of R enantiomer enantiomer Thalidomide teratogenic cures morning sickness Propanolol blo cker contraceptive Limonene lemon smell orange smell Dopa AntiParkinson toxic granulo cytop enia Asparagine tastes bitter tastes sweet
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