13.2 Structural elucidation using mass spectrometry
4 min read•august 9, 2024
Mass spectrometry is a powerful tool for figuring out what molecules are made of. It measures the mass of ions, helping scientists determine a compound's formula and structure. This technique is crucial for identifying unknown substances and understanding their properties.
In this section, we'll learn how to use mass spectrometry to determine molecular formulas and distinguish between isomers. We'll also explore how to identify functional groups and piece together molecular structures from fragmentation patterns.
Molecular Formula and Isomer Determination
Molecular Formula Calculation and Nitrogen Rule
Top images from around the web for Molecular Formula Calculation and Nitrogen Rule
Atomic Structure and Symbolism | General Chemistry View original
Is this image relevant?
Organic chemistry 33: Mass spectrometry View original
Is this image relevant?
Mass spectrum - Wikipedia View original
Is this image relevant?
Atomic Structure and Symbolism | General Chemistry View original
Is this image relevant?
Organic chemistry 33: Mass spectrometry View original
Is this image relevant?
1 of 3
Top images from around the web for Molecular Formula Calculation and Nitrogen Rule
Atomic Structure and Symbolism | General Chemistry View original
Is this image relevant?
Organic chemistry 33: Mass spectrometry View original
Is this image relevant?
Mass spectrum - Wikipedia View original
Is this image relevant?
Atomic Structure and Symbolism | General Chemistry View original
Is this image relevant?
Organic chemistry 33: Mass spectrometry View original
Is this image relevant?
1 of 3
- Molecular formula determination involves calculating the elemental composition of a compound from its
- Mass spectrometers measure the of ions, allowing precise molecular mass determination
- Accurate mass measurements combined with isotopic abundance patterns help deduce molecular formulas
- Nitrogen rule states even-mass molecules contain zero or an even number of nitrogen atoms, while odd-mass molecules contain an odd number of nitrogen atoms
- Applying the nitrogen rule narrows down possible molecular formulas for unknown compounds
High-Resolution Mass Spectrometry for Formula Determination
- High-resolution mass spectrometry provides precise mass measurements with accuracy up to four decimal places
- Exact mass measurements allow differentiation between compounds with similar nominal masses but different elemental compositions
- Resolving power of high-resolution instruments enables separation of closely spaced peaks (isobaric species)
- and instruments offer ultra-high resolution for complex mixture analysis
- High-resolution data combined with analysis significantly reduces the number of possible molecular formulas
Structural Isomers and Mass Spectrometry
- Structural isomers are compounds with the same molecular formula but different atomic arrangements
- Mass spectrometry can differentiate between some structural isomers based on their fragmentation patterns
- Constitutional isomers often produce distinct mass spectra due to different bond cleavages
- Stereoisomers (geometric isomers, optical isomers) may have similar mass spectra but can sometimes be distinguished by specialized techniques
- Ion mobility spectrometry coupled with mass spectrometry (IMS-MS) separates isomers based on their collision cross-sections
Functional Group and Structural Analysis
Functional Group Identification Using Mass Spectrometry
- Mass spectrometry identifies functional groups through characteristic fragmentation patterns and molecular ions
- Alcohols often show loss of water (M-18) and tend to have weak molecular ion peaks
- Carboxylic acids frequently exhibit loss of OH (M-17) and COOH (M-45) fragments
- Aldehydes and ketones display prominent M-1 peaks due to loss of hydrogen from the molecular ion
- Aromatic compounds typically have stable molecular ions and characteristic fragmentation patterns
- Halogenated compounds show distinct isotope patterns due to the natural abundance of halogen isotopes
Fragmentation Patterns and Structural Elucidation
- Fragmentation patterns provide crucial information about molecular structure and bonding
- Alpha cleavage occurs adjacent to functional groups, producing characteristic fragment ions
- McLafferty rearrangement involves hydrogen transfer and bond cleavage, common in ketones and esters
- Retro-Diels-Alder fragmentation helps identify cyclic compounds with conjugated double bonds
- Aromatic compounds often undergo stepwise loss of small neutral molecules (CO, HCN)
- Fragmentation rules and common neutral losses aid in predicting and interpreting mass spectra
Mass Spectral Libraries and Database Matching
- Mass spectral libraries contain reference spectra for thousands of compounds
- Library searching algorithms compare unknown spectra with reference spectra to identify compounds
- Probability-based matching scores help assess the reliability of spectral matches
- NIST (National Institute of Standards and Technology) and Wiley are widely used mass spectral libraries
- Specialized libraries exist for specific compound classes (metabolites, drugs, environmental contaminants)
- In-house libraries can be created for frequently analyzed compounds or custom synthesized molecules
Advanced Mass Spectrometry Techniques
Isotope Ratio Analysis and Applications
- measures the relative abundance of stable isotopes in samples
- help determine the origin of organic compounds and track carbon sources
- aids in studying food webs and nitrogen cycling in ecosystems
- Oxygen and hydrogen isotope ratios provide information about water sources and paleoclimate conditions
- assists in tracing pollution sources and studying biogeochemical cycles
- Multi-element isotope analysis combines multiple isotope systems for comprehensive sample characterization
High-Resolution Mass Spectrometry Techniques
- Fourier transform ion cyclotron resonance (FT-ICR) offers ultra-high resolution and mass accuracy
- Orbitrap mass analyzers provide high resolution and sensitivity without the need for superconducting magnets
- instruments with reflectrons achieve high resolution and fast acquisition rates
- High-resolution MS enables accurate mass measurements for elemental composition determination
- Resolving power of high-resolution instruments separates isobaric species and complex mixtures
- Applications include , , and analysis of environmental and petroleum samples
Tandem Mass Spectrometry (MS/MS) for Structural Analysis
- Tandem MS involves multiple stages of mass analysis to obtain structural information
- Precursor ion selection followed by fragmentation and analysis of product ions
- fragments ions through collisions with neutral gas molecules
- and provide complementary fragmentation patterns
- MS/MS techniques include product ion scanning, precursor ion scanning, and neutral loss scanning
- Applications in proteomics for peptide sequencing and post-translational modification analysis
- Structural elucidation of complex molecules and mixture analysis in metabolomics and environmental studies
Key Terms to Review (28)
Anion: An anion is a negatively charged ion formed when an atom or molecule gains one or more electrons. This charge occurs due to the imbalance between the number of protons, which are positively charged, and the additional electrons. Anions play crucial roles in various chemical processes and are fundamental to understanding molecular structures and reactions.
Base peak: The base peak is the most intense peak in a mass spectrum, representing the most abundant ion produced during the ionization and fragmentation of a sample. It serves as a reference point for comparing other peaks in the spectrum and can provide insights into the sample's fragmentation pattern, helping to deduce the structure of the compound being analyzed.
Carbon isotope ratios (13C/12C): Carbon isotope ratios (13C/12C) refer to the relative abundance of carbon isotopes in a sample, specifically the stable isotopes carbon-13 (13C) and carbon-12 (12C). This ratio is significant in various scientific fields, including structural elucidation, as it provides insights into the sources of carbon compounds and helps distinguish between different organic materials based on their isotopic signatures.
Cation: A cation is a positively charged ion that occurs when an atom loses one or more electrons, resulting in a net positive charge. This charge difference is crucial in various chemical reactions and interactions, particularly in forming ionic bonds and participating in mass spectrometry analysis. Cations can play a significant role in determining the structure and behavior of molecules as they can influence molecular fragmentation patterns in mass spectrometry.
Collision-induced dissociation (CID): Collision-induced dissociation (CID) is a mass spectrometry technique that involves the fragmentation of ions through collisions with neutral gas molecules. This process is crucial for structural elucidation, as it provides detailed information about the molecular structure and composition by analyzing the resulting fragment ions. CID enhances the understanding of complex molecules, allowing researchers to decipher chemical structures and identify compounds more effectively.
Electron capture dissociation (ecd): Electron capture dissociation (ECD) is a mass spectrometry technique where low-energy electrons are captured by multiply charged ions, leading to fragmentation of the ion through bond cleavage. This method is particularly useful for analyzing larger biomolecules, like proteins and peptides, as it helps provide detailed structural information while preserving labile modifications. ECD plays a significant role in the structural elucidation of complex molecules by generating unique fragmentation patterns that can be interpreted for further analysis.
Electron transfer dissociation (etd): Electron transfer dissociation (ETD) is a mass spectrometry technique that facilitates the fragmentation of ions through the transfer of an electron from a reagent anion to the ion of interest. This method is particularly valuable for analyzing large biomolecules, like proteins and peptides, as it generates specific fragmentation patterns without breaking peptide bonds, preserving critical structural information. ETD has become an essential tool for structural elucidation, allowing researchers to obtain detailed insights into molecular architecture and sequence.
Esi-ms: Electrospray ionization mass spectrometry (esi-ms) is a powerful analytical technique used to analyze biomolecules by converting them into ions in the gas phase, allowing for the determination of their mass-to-charge ratios. This method is particularly effective for studying large molecules like proteins and nucleic acids, as it preserves their structure and allows for detailed analysis of complex mixtures.
Fourier Transform Ion Cyclotron Resonance (FT-ICR): Fourier Transform Ion Cyclotron Resonance (FT-ICR) is a sophisticated mass spectrometry technique that utilizes magnetic fields to measure the mass-to-charge ratio of ions. This method involves trapping ions in a cyclotron motion within a strong magnetic field and detecting their frequency of oscillation, which is then transformed into a mass spectrum using Fourier transformation. FT-ICR provides extremely high mass resolution and accuracy, making it invaluable for structural elucidation and analyzing complex mixtures.
Fragmentation pattern: A fragmentation pattern refers to the unique set of ions produced when a molecule is ionized and subsequently breaks apart during mass spectrometry. This pattern is crucial for identifying the structural characteristics of a compound, as the specific ions generated and their relative abundances provide valuable clues about the molecular structure, functional groups, and the presence of specific atoms within the molecule.
Ion source: An ion source is a device that generates ions from neutral atoms or molecules, crucial for mass spectrometry. It plays a pivotal role in determining the mass-to-charge ratio of compounds, enabling the identification and structural elucidation of substances. By transforming analytes into charged particles, ion sources facilitate their subsequent analysis through various fragmentation patterns and detection techniques.
Isotope pattern: An isotope pattern refers to the distribution of different isotopes of an element in a sample as observed in mass spectrometry. This pattern provides insight into the molecular structure and composition of the analyzed substance, as the presence of isotopes leads to distinctive peaks in the mass spectrum. Understanding isotope patterns can help identify the molecular formula and structural features of compounds, aiding in their structural elucidation.
Isotope ratio mass spectrometry (IRMS): Isotope ratio mass spectrometry (IRMS) is a sensitive analytical technique used to measure the relative abundance of isotopes in a sample, providing valuable insights into molecular composition and origins. This technique plays a crucial role in various fields, including environmental science, archaeology, and biological studies, allowing researchers to uncover information about processes like metabolic pathways and climate change.
John B. Fenn: John B. Fenn was an American chemist who developed the electrospray ionization (ESI) technique, which revolutionized mass spectrometry by allowing for the analysis of large biomolecules like proteins and nucleic acids. His work paved the way for new methods of ionization that have significantly enhanced the capabilities of mass spectrometry, contributing to advancements in various fields such as biochemistry and pharmaceutical sciences.
Koichi Tanaka: Koichi Tanaka is a prominent Japanese chemist known for his groundbreaking work in the field of mass spectrometry, particularly for his development of techniques that have greatly improved the analysis of complex biological samples. His contributions have significantly advanced our understanding of molecular structures and dynamics, making him a key figure in the realm of analytical chemistry and structural elucidation.
Liquid chromatography: Liquid chromatography is a technique used to separate, identify, and quantify components in a mixture based on their interactions with a stationary phase and a mobile phase. This method is particularly useful in analyzing complex mixtures, such as those encountered in chemical and biological samples, and it plays a crucial role in conjunction with mass spectrometry for structural elucidation.
MALDI-TOF: MALDI-TOF, or Matrix-Assisted Laser Desorption/Ionization Time of Flight, is a mass spectrometry technique that uses a laser to ionize samples embedded in a matrix. This method is particularly useful for analyzing large biomolecules, such as proteins and polymers, because it allows for the determination of their molecular weights with high accuracy and resolution. The technique involves the desorption and ionization of analytes from a solid matrix, followed by their separation based on mass-to-charge ratios in a time-of-flight analyzer.
Mass analyzer: A mass analyzer is a crucial component of mass spectrometry that separates ions based on their mass-to-charge ratio (m/z). This process enables the identification and quantification of various chemical species, providing insight into the molecular composition and structure of compounds. The efficiency and resolution of a mass analyzer directly impact the quality of data obtained during structural elucidation, making it an essential tool for chemists and researchers.
Mass spectrum: A mass spectrum is a graphical representation of the mass-to-charge ratio (m/z) of ions produced from a sample, allowing for the identification and quantification of its molecular components. Each peak in the spectrum corresponds to an ion, with the height representing its relative abundance. This tool is crucial for understanding the composition of complex mixtures and provides valuable insights into molecular structure and weight.
Mass-to-charge ratio (m/z): The mass-to-charge ratio (m/z) is a dimensionless quantity used in mass spectrometry to describe the ratio of the mass of an ion to its charge. It is crucial for identifying and characterizing ions, as it allows scientists to differentiate between ions with similar masses but different charges, which is essential for structural elucidation and understanding molecular structures.
Metabolomics: Metabolomics is the comprehensive study of metabolites, the small molecules produced during metabolism, within a biological system. This field allows scientists to understand cellular processes and interactions by profiling metabolic changes in response to various conditions. It is closely connected to various analytical techniques that help identify and quantify these metabolites, offering insights into biological functions and disease mechanisms.
Nitrogen Isotope Analysis (15N/14N): Nitrogen isotope analysis (15N/14N) refers to the measurement of the relative abundance of nitrogen isotopes, specifically nitrogen-15 (15N) and nitrogen-14 (14N), in various samples. This technique is crucial in understanding biological processes, ecological interactions, and food web dynamics, as the ratios of these isotopes can provide insights into nitrogen sources and transformations in the environment. The analysis can also aid in the structural elucidation of organic compounds by revealing information about their nitrogen content and origins.
Orbitrap: An orbitrap is a type of mass analyzer used in mass spectrometry that traps ions in an electrostatic field and measures their oscillation frequencies to determine their mass-to-charge ratios. This technology allows for high-resolution mass measurements, making it particularly valuable for analyzing complex mixtures and conducting detailed structural elucidation.
Proteomics: Proteomics is the large-scale study of proteins, particularly their functions and structures. This field is crucial for understanding the role of proteins in biological processes, as it provides insights into protein expression, interaction, and modifications, which can be analyzed using various spectroscopic and mass spectrometric techniques.
Solid-phase extraction: Solid-phase extraction (SPE) is a sample preparation technique used to separate and concentrate analytes from a mixture by passing the sample through a solid adsorbent material. This method is widely applied in analytical chemistry to improve the sensitivity and accuracy of various spectroscopic techniques, including mass spectrometry, by removing unwanted matrix components and isolating the target compounds for further analysis.
Sulfur isotope analysis (34s/32s): Sulfur isotope analysis involves measuring the ratio of stable sulfur isotopes, specifically $$^{34}S$$ to $$^{32}S$$, to understand various biological and geological processes. This analysis provides insights into the sources and cycling of sulfur in the environment, helping to trace the origins of sulfur compounds in different contexts, including organic and inorganic systems. By analyzing these isotopic ratios, researchers can uncover important information about metabolic processes, environmental conditions, and even ancient ecological events.
Tandem mass spectrum: A tandem mass spectrum is a type of mass spectrum obtained from tandem mass spectrometry (MS/MS), where ions are sequentially fragmented and analyzed to provide detailed structural information about molecules. This technique helps in identifying and characterizing complex mixtures by breaking down larger ions into smaller fragments, which can be analyzed to deduce the structure and composition of the original molecule.
Time-of-flight (tof): Time-of-flight (tof) is a mass spectrometry technique that measures the time it takes for ions to travel a set distance, providing information about their mass-to-charge ratio. This method allows for the determination of molecular weights and structural elucidation by analyzing how long different ions take to reach a detector after being accelerated by an electric field.