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Anthropic Awareness
The Human Aspects of Scientific Thinking in NMR Spectroscopy and Mass Spectrometry
1st Edition - June 22, 2015
Author: Csaba Szantay Jr.
Language: English
Hardback ISBN:9780124199637
9 7 8 - 0 - 1 2 - 4 1 9 9 6 3 - 7
eBook ISBN:9780124199798
9 7 8 - 0 - 1 2 - 4 1 9 9 7 9 - 8
Anthropic Awareness: The Human Aspects of Scientific Thinking in NMR Spectroscopy and Mass Spectrometry blends psychology, philosophy, physics, mathematics, and chemistry…Read more
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Anthropic Awareness: The Human Aspects of Scientific Thinking in NMR Spectroscopy and Mass Spectrometry
blends psychology, philosophy, physics, mathematics, and chemistry, describing a human-centered philosophy of the essence of scientific thinking in the natural sciences and in everyday life.
It addresses the reasons why we are prone to make errors in our conclusions and how to avoid such mistakes, also exploring a number of the "mental traps" that can lead to both individual mistakes and mass misconceptions.
The book advocates that by understanding the nature of these mental traps we can adopt tactics to safely evade them. It includes Illustrative examples of common scientific misunderstandings and mental traps in both the theory and real-life application of NMR spectroscopy and mass spectrometry.
Provides strategies on how to deal with molecular challenges and instrument limitations
Presents multiple applications of small molecule structure elucidation using NMR, MS, IR, and UV
Explores critical topics, including anthropic awareness (AA), NMR Spectroscopy, mass spectrometry, scientific thinking, and more
Includes tactics on how to Improve quality control and data interpretation skills while minimizing data analysis time and increasing confidence in results
Presents coverage on tactics to optimize experimental NMR parameters and enhance NMR vocabulary
Scientists working in industry and academia in the areas of drug discovery and natural product research, consumer products, food science, forensics, and cosmetics (including but not limited to analytical, organic and medicinal chemists), and graduate-level students in chemistry.
Preface
Editor’s Personal Acknowledgments
Part I: “Anthropic Awareness (AA)” (Mind Your Mind!)
Chapter 1: The Philosophy of “Anthropic Awareness” in Scientific Thinking
Abstract
Acknowledgments
1.1 Introduction
1.2 The Pillars
1.3 Mental Traps (Mind Your Mind!)
1.4 Summary
Part II: AA in Why-Science: Examples from NMR Theory (If you Think you Know NMR, Think Again…)
Chapter 2: An “Anthropically” Flavored Look at Some Basic Aspects of NMR Spin Physics Using a Classical Description
Abstract
Acknowledgments
2.1 Introduction
2.2 Introductory Thoughts on the Characteristics of NMR Theory
2.3 Classical Portrayal of an Individual Spin
2.4 Classical Portrayal of the Macroscopic Magnetization
2.5 Preliminary Comments on the Quantum-Mechanical Description of Magnetic Resonance
2.6 Summary
Chapter 3: The Ups and Downs of Classical and Quantum Formulations of Magnetic Resonance
Abstract
Acknowledgments
3.1 Introduction
3.2 Quantum Mechanics in General
3.3 Misconceptions in NMR Introductions
3.4 Where Did It Go Wrong?
3.5 A Limited Introduction to Classical and Quantum Mechanics
3.6 Indeterminism vs. Uncertainty and the Role of Measurement
3.7 The Role of Eigenstates in Single-Particle Measurements
3.8 Entanglement
3.9 Superpositions
3.10 The Missing Role of Eigenstates in Ensemble Measurements
3.11 The Role of Eigenstates in Mathematical Descriptions
3.12 Visualization of Spin Distributions
3.13 Thermal Equilibrium
3.14 Classical Eigenstates, Resonance, and Couplings
3.15 The Eigenmode Structure for Nuclear Excitation
3.16 J-Coupling
3.17 The Aftermath
Chapter 4: The RF Pulse and the Uncertainty Principle
Abstract
Acknowledgment
4.1 Introduction
4.2 Nomenclature
4.3 “Enhanced” Fourier Transform Equations
4.4 Uncertainty Principle(s)
4.5 Summary
Chapter 5: On the Nature of the RF Driving Field in NMR (with a Lookout on Optical Rotation)
Abstract
Acknowledgments
5.1 Introduction
5.2 Analysis of the “Decompositional Argument” for the NMR RF Field
5.3 Analysis of the “Decompositional Argument” for Optical Rotation
5.4 Summary
Part III: AA in What-Science: Small-Molecule Structure Elucidation by NMR and MS (Are you Sure you have Found the Correct Structure and not an Apparently Correct Structure?)
Chapter 6: An “Anthropic” Modus Operandi of Structure Elucidation by NMR and MS
Abstract
Acknowledgments
6.1 Introduction
6.2 An “Anthropic” Look at Structure Elucidation
6.3 “Anthropic” Structure Elucidation in Practice
6.4 Summary
Chapter 7: NMR Methodological Overview
Abstract
Acknowledgments
7.1 Introduction
7.2 One-Dimensional (1D) NMR Measurements
7.3 Two-Dimensional (2D) Methods
7.4 An NMR-Based Strategy for the Structure Elucidation of Small Molecules
7.5 Diffusion-Ordered Spectroscopy (DOSY)
7.6 Summary
Chapter 8: MS Methodological Overview
Abstract
Acknowledgments
8.1 Introduction
8.2 MS Basics
8.3 The Evolution of MS Instrumentation in Structure Elucidation
8.4 Principles and Pitfalls of Mass Spectrum Interpretation
8.5 MS-Based Structure Investigation Approaches Applied for Small Molecules
8.6 Conclusions
Chapter 9: Computer-Assisted Structure Elucidation in NMR
Abstract
Acknowledgments
9.1 Introduction
9.2 Introduction to CASE Systems
9.3 Structure Elucidation Strategy Used by CASE Software
9.4 Motivation for Developing CASE Systems
9.5 Examples
9.6 Conclusions
Chapter 10: Structure Elucidation of a Mysterious Trace Component of Ulipristal Acetate
Abstract
Acknowledgments
10.1 Introduction
10.2 The Winding Road to Identifying d-ULIPA
10.3 Conclusions
Chapter 11: The Adventurous Discovery of the Structure of a Novel Vincristine Impurity
Abstract
Acknowledgments
11.1 Introduction
11.2 Structure Elucidation of a Novel Vincristine Impurity
11.3 Conclusions
Chapter 12: An Elusive Degradation Product of Ziprasidone
Abstract
Acknowledgments
12.1 Introduction
12.2 The Path Toward the Structural Hypotheses
12.3 The Hunt for That Elusive 13C NMR Line
12.4 Acidic Decomposition as an Additional Proof of the Proposed Structure
12.5 Conclusions
Chapter 13: The Case of an Emotion- and Emotycs-Laden Structure Determination of a Small Synthetic Molecule with an Unexpected Structure
Abstract
Acknowledgments
13.1 Introduction
13.2 Our Surprising Encounter with Compound 13.1
13.3 Conclusions
Chapter 14: Self-Induced Recognition of Enantiomers (SIRE) in NMR Spectroscopy
Abstract
Acknowledgments
14.1 Introduction
14.2 A Puzzling Structural Problem
14.3 Understanding SIRE
14.4 Conclusions
Chapter 15: Believe It or Not: Carbon Protonation of the Pyrimidine Ring
Abstract
Acknowledgments
15.1 Introduction
15.2 The Chemical Background and a False Structural Hypothesis
15.3 Stage 1: A Hunch
15.4 Stage 2: Molecular and Spectral Symmetry
15.5 Stage 3: Believe It or Not: Carbon Protonation
15.6 Stage 4: The “Geminal” Structure
15.7 Stage 5: Assignment of the E and Z Isomer
15.8 Stage 6: Rationalization of the Carbon-Protonated Pyrimidine Structure
15.9 Aftermath
15.10 Conclusions and Summary
Epilogue
Index
No. of pages: 464
Language: English
Edition: 1
Published: June 22, 2015
Imprint: Elsevier
Hardback ISBN: 9780124199637
eBook ISBN: 9780124199798
CS
Csaba Szantay Jr.
Csaba Szántay, Jr. was born in Budapest, Hungary, but partly attended elementary school in Bufffalo, NY, USA. He obtained an MSc degree in organic chemistry from the Budapest University of Technology and Economics in 1982 with his final thesis involving the methodology and use of NMR spectroscopy. Subsequently, he became a PhD research fellow in Prof. Gábor Tóth’s NMR laboratory at the Department of Analytical Chemistry, Budapest University of Technology and Economics, and obtained his PhD in 1986 in NMR. After that, he worked as a postdoctoral fellow in the NMR laboratory of the University of Leeds, UK. Having returned to Hungary in 1989, he became a member of the NMR team of the Spectroscopic Research Division of the Hungarian pharmaceutical company Gedeon Richter Plc. He was promoted as head of the Division in 1994 and has been in this position since then. He has also maintained a teaching position at the Budapest University of Technology and Economics. He received a “Candidatura” degree in 1991 and a “Doctor of Sciences” degree in 2000 from the Hungarian Academy of Sciences for his work in NMR spectroscopy. In 2003, he was became a Private Professor at the Budapest University of Technology and Economics. Besides holding several positions in various scientific committees, he is on the Editorial Board of the journal Concepts in Magnetic Resonance and is currently the president of the Hungarian NMR Discussion Group of the Hungarian Academy of Sciences. Along with his managerial duties, his main fields of research interests are the structure elucidation of organic molecules and the theoretical aspects of NMR. He is the author/co-author of more than 100 papers published in international scientific journals.