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Research

2D NMR: Overview of Heteronuclear Correlation Techniques

Heteronuclear correlation spectroscopy is an analytical technique that investigates the coupling between different types of nuclei, often a proton and an X-nucleus, such as carbon-13 or nitrogen-15. This method is commonly used in nuclear magnetic resonance (NMR) spectroscopy to gain insights into complex chemical compounds&#39; structural and compositional aspects. A typical heteronuclear correlation spectrum displays X-nucleus chemical shifts on one axis and a proton spectrum on the other axis. Cross-peaks reveal the connection between specific protons and X-nuclei.
The main heteronuclear correlation experiments include HETCOR, HSQC, HMQC, and HMBC. HSQC, HMQC, and HMBC record the proton spectrum, whereas the X-nucleus spectrum is recorded by standard heteronuclear correlation spectroscopy or HETCOR. The HETCOR-HMQC-HSQC group of experiments cannot detect X-nuclei without an attached proton. HETCOR is used when ultrahigh peak resolution is required along the X-nucleus axis.
The heteronuclear single quantum correlation technique, or HSQC, investigates proton-to-X-nucleus single bond correlations. In an HSQC experiment, polarization is transferred from a proton nucleus to a neighboring X-nucleus and then back to the proton nucleus. The signal from the proton nuclei is then recorded. HSQC generates a spectrum like that of heteronuclear multiple-quantum correlation spectroscopy or HMQC but uses a different suppression method, providing better X-nucleus resolution along the axis.
Heteronuclear multiple-bond correlation, or HMBC, is a proton-detected experiment, like HMQC but with a longer initial delay time. This experiment is used to observe long-range proton to X-nucleus connectivity separated by 2-3 bonds, with some experiments going out to 4 or 5 bonds. In an HMBC experiment, direct one-bond correlations are suppressed as part of the sequence. The spectra of HMBC give rise to cross peaks that correlate which protons are coupled to what other specific X-nucleus is more than one bond away. The gradient HMBC (gHMBC) pulse sequence offers better suppression of interfering signals, making it particularly useful for analyzing complex molecules with overlapping signals.

Heteronuclear correlation spectroscopy is an analytical technique that investigates the coupling between different types of nuclei, often a proton and an ...

2D NMR: Heteronuclear Single-Quantum Correlation Spectroscopy (HSQC)

Heteronuclear single-quantum correlation spectroscopy (HSQC) is a 2D NMR technique that reveals one-bond correlations between hydrogen and a heteronucleus. The HSQC experiment is similar to the heteronuclear correlation experiment (HETCOR) but is more sensitive. In the HSQC spectrum, the proton chemical shift is plotted on the horizontal F2 axis, while the 13C chemical shift is plotted on the vertical F1 axis. The corresponding proton and 13C spectra are also shown. The HSQC contour plot does not have any diagonal peaks. All the cross-peaks indicate the protons directly attached to each carbon in a molecule. Similar to the COSY spectrum, imaginary lines are drawn in horizontal and vertical directions to identify the correlated peaks.
For example, the HSQC spectrum of 2-chlorobutane has a carbon signal at 11 ppm that can be assigned to the shielded methyl group and correlated to the proton multiplet at 1.01 ppm. The carbon signal at 24.8 ppm arises from the deshielded methyl group, which correlates to the proton multiplet at 1.52 ppm. Similarly, the methylene carbon signal at 33.3 ppm and methine carbon signal at 60.4 ppm correlate to the multiplets at 1.72 and 3.96 ppm, respectively.&#160; HSQC is a very useful technique for structurally elucidating complex molecules and is routinely used in protein NMR studies.

Heteronuclear single-quantum correlation spectroscopy (HSQC) is a 2D NMR technique that reveals one-bond correlations between hydrogen and a ...

Double Resonance Techniques: Overview

Double resonance techniques in Nuclear Magnetic Resonance (NMR) spectroscopy involve the simultaneous application of two different frequencies or radiofrequency pulses to manipulate and observe two distinct nuclear spins. One important application of double resonance is spin decoupling, which selectively suppresses coupling with one type of nucleus while observing the NMR signal from another nucleus, simplifying the spectrum and enhancing resolution.
Spin decoupling is usually achieved by irradiating the sample atoms with a suitable radio frequency (rf) pulse sequence, effectively eliminating all the coupling with one nuclide. This simplifies the observed spectrum, making it easier to analyze and understand the relationships between different nuclei.
Double resonance experiments can be classified as heteronuclear or homonuclear, depending on whether the two sets of nuclei are of different isotopes or the same isotope, respectively. They can also be selective or nonselective, depending on whether the irradiating frequency covers only a portion or all of the resonance frequencies.
In nonselective heteronuclear decoupling, samples are exposed to an appropriate radiofrequency range to remove all coupling with one nuclide. However, increased external field strengths necessitate more powerful irradiation across broader frequency ranges. In certain instruments, continuous irradiation creates enough heat to cause damage to thermally sensitive samples.
To overcome these problems, modern methods using a series of pulses and exact timing delays, like J-modulated spin echo pulse sequences, can be employed to eliminate or adjust coupling effects within the spectrum.
For example, the attached proton transfer (APT) experiment applies a J-modulated spin echo pulse sequence to focus on the phase of detected carbon signals. Carbon atoms attached to an even number of protons exhibit positive signals in the spectrum, while those bonded to an odd number of protons appear as negative signals.
It utilizes a combination of a 180&#176; proton pulse and broadband decoupling to simplify spectral interpretation and assign multiplicities. The 180&#176; pulse is applied to the protons during the APT experiment. Its role is to refocus the spin coupling evolution that naturally occurs due to interactions between protons and carbons.
Specifically, after the 90&#176; pulse creates transverse magnetization, the 180&#176; pulse ensures that the effects of coupling are frozen during the initial period where the decoupler is turned off. This means the chemical shifts evolve only during the time 1/J&#8203; (the coupling constant period) after the first 180&#176; pulse.
By carefully timing this pulse sequence, the experiment isolates carbon multiplicities by utilizing the J-coupling between carbons and their attached protons. After the coupling evolution period (1/J&#8203;), broadband decoupling is turned on. This removes the J-coupling signals, collapsing multiplets into single peaks for each carbon resonance.
The decoupling ensures that carbon signals are free of splitting, allowing for a clear differentiation of signals based on phase (positive or negative) rather than splitting patterns.
The APT technique selectively enhances carbon signals, providing valuable information about carbon-proton connectivity, the number of attached hydrogen atoms, and the overall molecular structure.

Double resonance techniques in Nuclear Magnetic Resonance (NMR) spectroscopy involve the simultaneous application of two different frequencies or ...

Insensitive Nuclei Enhanced by Polarization Transfer (INEPT)

Insensitive Nuclei Enhanced by Polarization Transfer (INEPT) is an advanced Nuclear Magnetic Resonance (NMR) technique specifically designed to detect and enhance the signals of low-abundance nuclei, such as carbon-13 and nitrogen-15, in small molecules. The fundamental principle behind INEPT is the transfer of polarization from a more abundant and highly polarizable nucleus, typically hydrogen-1, to the low-abundance nucleus of interest. This process effectively boosts the NMR signal of the low-abundance nuclei, making them more easily detectable.
The INEPT technique involves a series of carefully timed radiofrequency (RF) pulses applied to the sample. These RF pulses excite the more abundant nuclei, causing them to align their spins in a specific manner. Through the process of spin coupling, the polarization of the more abundant nuclei is then transferred to the low-abundance nuclei. As a result, the NMR signal of these low-abundance nuclei is significantly enhanced, allowing for a more detailed analysis of the molecular structure.
Various pulse sequences have been developed to improve the observability of these low-abundance nuclei when coupled to a high-receptivity nucleus. The INEPT pulse sequence combines a spin echo and selective population inversion, which includes 90&#176; and 180&#176; pulses on the high-sensitivity (the I spins) and low-sensitivity nuclei (the S spins), respectively. Coupling-constant-based delays between pulses facilitate magnetization transfer through space or bond interactions. Additional RF pulses and delays invert the low-gamma magnetization, producing an observable NMR signal. The net result is an enhanced NMR signal from low-gamma nuclei that would otherwise be challenging to detect.
Various pulse sequences have been developed to improve the detection of low-abundance nuclei when coupled with high-receptivity nuclei such as protons. The INEPT sequence yields enhanced signals for insensitive nuclei, with half of the CH group producing negative peaks and the other half positive peaks. This pattern allows for discrimination between different types of carbon-hydrogen bonds within the molecule.
Decoupling methods can be employed to enhance sensitivity and resolution in distinguishing various carbon-hydrogen bonds, making INEPT an invaluable tool in the chemical and pharmaceutical industries.

Insensitive Nuclei Enhanced by Polarization Transfer (INEPT) is an advanced Nuclear Magnetic Resonance (NMR) technique specifically designed to detect and ...

Two-Dimensional (2D) NMR: Overview

The 1D NMR spectrum of large and complex molecules like natural products has complicated splitting patterns and overlapping signals, which can be easily interpreted using 2-dimensional (2D) NMR. Unlike 1D NMR, 2D NMR has two frequency axes that provide the coupling information between the nucleus A and nucleus B in a molecule. The process from which 2D spectra are obtained has four steps.
The first step is the preparation period, during which nucleus A is excited with a radiofrequency pulse. The second step is the evolution or wait period t1, which is incremented systematically, and no data is observed during this period. The next step is the mixing period, in which a second radiofrequency pulse is introduced, which transfers the magnetization to the spins of nucleus B. In the last step, the magnetization of nuclear spins from B is detected during the acquisition time t2 for each t1. Time domains t1 and t2 are Fourier transformed into frequency domains f1 and f2, and these correspond to two dimensions of 2D spectra, while the third dimension is the intensity. In 2D experiments, coupling between the same kind of nucleus is called homonuclear 2D experiments, whereas coupling between two types of nucleus is called heteronuclear 2D experiments. 2D spectra can be displayed as stacked or contour plots. When presented as stacked plots, 2D spectra are difficult to interpret. The contour plot is the horizontal cross-section of a stacked plot where the size of the circles shows the signal intensity. Its interpretation is straightforward and it is preferred for data analysis.

The 1D NMR spectrum of large and complex molecules like natural products has complicated splitting patterns and overlapping signals, which can be easily ...

2D NMR: Overview of Homonuclear Correlation Techniques

Homonuclear correlation spectroscopy (COSY) is a powerful technique used in Nuclear Magnetic Resonance (NMR) spectroscopy to study the correlations between nuclei of the same type within a molecule. It provides information about scalar couplings between adjacent nuclei, which helps determine connectivity and structural information. There are several COSY variants, each with its unique strengths and experimental parameters.
COSY90 is the standard two-dimensional (2D) COSY experiment that utilizes a second 90-degree pulse to achieve high sensitivity and resolution. It excels in analyzing small to medium-sized molecules and provides information on directly coupled protons. COSY45, similar to COSY90, uses 45-degree pulses instead of 90-degree pulses. This results in reduced sensitivity but improved resolution.
Long-range COSY (LR-COSY) extends the COSY experiment to detect scalar couplings between nuclei further apart in the molecule. It achieves this by combining multiple pulse sequences and magnetization transfers.
Relayed COSY is a variant of COSY that adds extra pulses to the standard pulse sequence to produce cross-peaks between cross-peaks, showing specific molecular connections hidden by overlapping signals.
TOCSY (Total Correlation Spectroscopy), also known as HOHAHA (Homonuclear Hartmann-Hahn Spectroscopy), reveals all through-bond connectivity between all coupled nuclei. TOCSY is especially useful for analyzing molecules with overlapping signals and complex coupling patterns.
NOESY (Nuclear Overhauser Effect Spectroscopy) measures the nuclear overhauser effect, which arises from dipole-dipole interactions between nuclei. It provides information about spatial proximity and can be used to determine the three-dimensional structure of a molecule.
ROESY (Rotating-frame Overhauser Enhancement Spectroscopy) is similar to NOESY but employs a different mechanism to obtain through-space correlations. It provides information about spatial proximity and is particularly useful for studying molecules with weak NOE signals.
In conclusion, choosing a COSY variant depends on the molecule or reaction under investigation and the desired information. The right COSY variant can be determined based on molecular size, coupling complexity, and the need for spatial or long-range connectivity data.

Homonuclear correlation spectroscopy (COSY) is a powerful technique used in Nuclear Magnetic Resonance (NMR) spectroscopy to study the correlations ...

2D NMR: Homonuclear Correlation Spectroscopy (COSY)

Homonuclear correlation spectroscopy, or COSY, is a 2-dimensional NMR technique that provides information about coupled protons. Typically, the geminal and vicinal coupling are observed. For example, consider the COSY spectrum of ethyl acetate, where its 1D proton NMR spectrum is plotted along the vertical and horizontal axes with their corresponding chemical shift scale. Three spots on the diagonal corresponding to the three peaks in the 1D proton spectrum are called diagonal peaks. The COSY spectrum is symmetric about the diagonal, with signals above and below the diagonal called cross-peaks or off-diagonal peaks. An imaginary line is drawn from diagonal peaks parallel to the horizontal axis, leading to a cross peak. A vertical line is then drawn from the same cross peak towards the diagonal peak to correlate the peaks. The off-diagonal peaks correlating the multiplets at 1.25 and 4.2 ppm indicate that the methyl protons are coupled to the methylene protons. The signal at 2 ppm is not associated with cross-peaks because the protons are not involved in homonuclear coupling. A COSY spectrum is useful when overlapping multiplets complicate the corresponding 1D spectrum.

Homonuclear correlation spectroscopy, or COSY, is a 2-dimensional NMR technique that provides information about coupled protons. Typically, the geminal ...

&sup1;H NMR of Labile Protons:  Deuterium (&sup2;H) Substitution

This lesson illustrates the role of deuterium substitution in simplifying the NMR spectrum of compounds comprising labile protons. One method employed is the use of deuterium. Amongst the three isotopes of hydrogen, deuterium (2H) has a nucleus composed of one proton and one neutron. When the D2O solvent is added to a pure dry ethanol solution, its labile proton is substituted with deuterium.
<img alt="Figure1" src="/files/ftp_upload/12280/12280-PT_Figure_1.svg" style="text-align: center; height: 700px;" />
Figure 1. The comparison of the proton NMR spectra of pure dry ethanol and the same in D2O solvent.
The signals from deuterium are not observed in a proton NMR spectrum, as deuterium&#8211;proton coupling is negligible, and no spin-spin splitting occurs between them. As shown in Figure 1, the NMR spectra of pure ethanol and ethanol in deuterium, the disappearance of the triplet in the latter, confirms that it corresponds to the labile &#8211;OH proton. Furthermore, the methylene protons that initially showed up as a multiplet transform to a quartet, proving that the multiplet is due to the coupling with the &#8211;OH proton and the methyl protons.

This lesson illustrates the role of deuterium substitution in simplifying the NMR spectrum of compounds comprising labile protons. One method employed is ...

&sup1;H NMR of Labile Protons: Temporal Resolution

Protons bonded to heteroatoms such as nitrogen and oxygen exhibit a range of chemical shift values. This is due to the varying degree of hydrogen bonding between the proton and the heteroatom in other molecules. The extent of hydrogen bonding affects the electron density around the proton, thereby giving different chemical shift values for the protons in the proton NMR spectrum.
The &#8211;OH proton in alcohols typically appears in the range of &#948; 2 to 5 ppm but can vary depending on the specific alcohol and conditions. This &#8211;OH proton undergoes rapid proton exchange with other molecules and is referred to as a labile proton. So, the exact &#948; value of the &#8211;OH proton and the spin-spin coupling involving the &#8211;OH proton and the other protons in the alcohol depends on the rate of the &#8211;OH proton exchange. The proton exchange rate, in turn, depends on multiple factors, including the purity of the alcohol sample, temperature, and solvent.
<img alt="Figure1" src="/files/ftp_upload/12279/12279-PT_Figure_1.svg" style="text-align: center; height: 350px;" />
Figure 1. The triplet of a &#8211;OH proton in the proton NMR spectrum of neat ethanol.
For example, the &#8211;OH proton exchange in a pure dry ethanol sample is very slow on the NMR time scale, giving enough time for the spin-spin coupling. Consequently, as depicted in Figure 1, the proton NMR spectrum of pure dry ethanol shows a triplet for the &#8211;OH proton due to the spin-spin coupling with adjacent methylene protons. The methylene protons are seen as a multiplet due to the coupling with the &#8211;OH proton and the methyl protons.
The presence of trace amounts of an acid or base increases the proton exchange rate. The proton exchange becomes rapid, and the NMR spectrometer only records an average of all the possible environments for the &#8211;OH proton.
<img alt="Figure2" src="/files/ftp_upload/12279/12279-PT_Figure_2.svg" style="text-align: center; height: 325px;" />
Figure 2. The broad singlet of a &#8211;OH proton in the proton NMR spectrum of neat ethanol.
As a result, as recorded in Figure 2, the &#8211;OH proton exhibits a broad singlet. The protons from the adjacent methylene group present a quartet where the splitting is caused only by the adjoining methyl group.

Protons bonded to heteroatoms such as nitrogen and oxygen exhibit a range of chemical shift values. This is due to the varying degree of hydrogen bonding ...

Nuclear Overhauser Enhancement (NOE)

Irradiation of a spin-active nucleus causes an increase or decrease in the signal intensity of neighboring nuclei that are not necessarily chemically bonded or involved in J-coupling. &#160;This phenomenon, called the Nuclear Overhauser Enhancement (NOE), results from through-space interactions between the nuclear spins. The NOE effect decreases with increasing internuclear distance and is generally not observed beyond 4 angstroms. In NOE, dipole-dipole interactions between neighboring spin-active nuclei result in the transfer of nuclear spin polarization. These interactions can cause an increase or decrease in the signal intensity, which results in a positive or negative NOE, respectively.
NOE can be applied to improve the signal intensity of less sensitive nuclei such as carbon-13. Proton-decoupled carbon-13 spectra show a positive NOE effect, where the carbon signal intensities are substantially increased compared to those in proton-coupled spectra.
Targeted irradiation of specific nuclei can also reveal through-space proximity, which helps confirm stereochemistry and verify spectral peak assignments. The NOE effect is also applied in 2D NMR experiments, such as Nuclear Overhauser Effect Spectroscopy (NOESY), to determine the 3D structure of proteins.

Irradiation of a spin-active nucleus causes an increase or decrease in the signal intensity of neighboring nuclei that are not necessarily chemically ...

&sup1;H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR

The axial and equatorial protons in cyclohexane can be distinguished by performing a variable-temperature NMR experiment. In this process, except for one proton, the remaining eleven protons are replaced by deuterium. The deuterium substitution avoids the possible peak splitting caused by the spin-spin coupling between the adjacent protons. The remaining proton flips between the axial and equatorial positions.
<img alt="Figure1" src="/files/ftp_upload/13016/13016-PT_Figure_1.svg" style="text-align: center; height: 480px;" />
Figure 1. The temperature-dependent proton NMR spectra of cyclohexane.
Figure 1 depicts the proton NMR spectrum of the deuterium substituted sample, recorded at various temperatures. At room temperature, the rapid ring flipping of cyclohexane results in a single sharp peak. As the temperature is lowered to &#8722;60&#176;C, the rate of chair-chair interconversion reduces, resulting in the broadening of the peak.
Further lowering of the temperature broadens the peak, forming a saddle that splits into two peaks. On reaching a temperature lower than &#8722;89&#176;C, two sharp, well-resolved peaks corresponding to the equatorial and axial protons are formed. The peaks corresponding to the equatorial and axial protons occur at &#948; 1.62 and 1.14, respectively. At such low temperatures, the rate of chair-chair interconversion is reduced significantly, enabling the detection of the two distinct sets of protons on the NMR time scale.

The axial and equatorial protons in cyclohexane can be distinguished by performing a variable-temperature NMR experiment. In this process, except for one ...

&sup1;H NMR of Conformationally Flexible Molecules: Temporal Resolution

At room temperature, the chair conformer of cyclohexane undergoes rapid ring flipping between two equivalent chair conformers at a rate of approximately 105 times per second. These two chair conformers are in equilibrium. The rapid ring flipping results in the interconversion of the axial proton to an equatorial proton and an equatorial to the axial proton. Such interconversions are too rapid and cannot be detected on the NMR timescale. Hence, the NMR spectrometer cannot distinguish between the axial and equatorial protons, resulting in a single peak at &#948; 1.4.
Similarly, NMR averages all the conformations of any molecule with rapid conformational equilibria. For example, the CH3 protons in bromoethane have a single resonance and coupling constant for splitting by the CH2 protons due to the rapid internal rotation of the carbon-carbon bond. Lastly, besides conformational equilibria, the time-averaging effect of NMR spectroscopy is also observed in some chemical reactions.

At room temperature, the chair conformer of cyclohexane undergoes rapid ring flipping between two equivalent chair conformers at a rate of approximately ...

Chemical Ionization (CI) Mass Spectrometry

The molecular ion peak of a molecule in the mass spectrum provides vital information for molecular identification. However, conventional electron impact ionization can lead to the rapid dissociation of some molecular ions before they reach the detector. A milder ionization method is required to increase the lifetime of such ionized analyte molecules. Chemical ionization (CI) is a gas-phase protonation reaction useful for mass-analyzing analyte molecules that are easily protonated to yield the corresponding conjugate acid. In this process, the sample is mixed with an excess reagent gas, which ensures the electron impact occurs primarily on the reagent gas. The charged species formed from the reagent protonates the analyte molecule, producing a relatively stable protonated analyte (conjugate acid) compared to the molecular ion. This results in an M+1 peak in the mass spectrum. The conjugate acid may then undergo fragmentation that generates additional signals.
For example, the CI of di-sec-butyl ether in methane gas illustrates this process. When the ether is mixed with excess methane gas as a reagent, electron impact occurs on methane rather than the ether. The resulting methane radical cation can react with another methane molecule to generate a methane radical and a methanium ion. The methanium ion is a source of gas-phase protons, which can protonate the ether to form its conjugate acid. The sequential reactions during the chemical ionization of di-sec-butyl ether are depicted in Figure 1.
<img alt="Figure1" src="/files/ftp_upload/12300/12300_PT_Figure_1.svg" style="text-align: center; height: 175px;" />
Figure 1: Chemical ionization of di-sec-butyl ether methane mixture.
This conjugate acid of the ether (m/z = 131) is relatively more stable than the molecular ion (m/z = 130) of ether formed via the conventional electron impact ionization. In the traditional route, the molecular ion undergoes fragmentation via &#945; cleavage, giving a signal at m/z = 101. Figure 2 illustrates the reactions that occur during electron impact ionization directly on di-sec-butyl ether.
<img alt="Figure2" src="/files/ftp_upload/12300/12300_PT_Figure_2.svg" style="text-align: center; height: 175px;" />
Figure 2: Electron impact ionization of di-sec-butyl ether and fragmentation of the molecular ion.
So, the mass spectra of di-sec-butyl ether ionized via CI feature an M+1 peak at m/z = 131. On the other hand, mass spectra of di-sec-butyl ether ionized via electron impact ionization do not show any peak at the m/z value of its molecular weight. Figures 3a and 3b show the mass spectra of di-sec-butyl ether ionized via the electron impact and chemical ionization methods, respectively.
<img alt="Figure3" src="/files/ftp_upload/12300/12300_PT_Figure_3.svg" style="text-align: center; height: 225px;" />
Figure 3:&#160;a) No m/z = 130 peak is visible in the mass spectrum obtained via electron impact ionization of di-sec-butyl ether. b) The m/z = 131 peak is clearly visible in the mass spectrum obtained via chemical ionization of di-sec-butyl ether.

The molecular ion peak of a molecule in the mass spectrum provides vital information for molecular identification. However, conventional electron impact ...

Electrospray Ionization (ESI) Mass Spectrometry

Higher molecular weight biomolecules are nonvolatile compounds that may decompose before ionizing or vaporizing during mass analysis with conventional electron impact ionization methods. Accordingly, electrospray ionization (ESI) is the favored method for vaporizing and ionizing biomolecules as it circumvents rapid fragmentation and enables the recording of mass signals for the entire biomolecule.
ESI utilizes electrical energy to transfer ions from the liquid phase of the sample into the gaseous phase. The analyte biomolecule is premixed with an ionic liquid&#8212;a nonmolecular compound serving as the ionization source. The solution is sprayed through a high-voltage capillary to generate a fine aerosol. The voltage difference applied between the capillary and the entrance of the analysis chamber causes the movement of charged droplets toward the analysis chamber. The ionic liquid from the aerosol evaporates during this movement, leaving behind a variably protonated or ionized analyte molecule. These charged species are detected in the mass spectrum at an m/z value equivalent to the sum of the analyte molecule&#39;s molecular mass and the ions&#39; molecular weight from the ionic liquid associated with the analyte molecule.
The position of mass signals varies depending on the type of cations present in the ionic liquid. For example, the presence of sodium ions in the ionic liquid leads to an (M+23) peak in the mass spectra, while the presence of a proton results in an (M+1) peak.

Higher molecular weight biomolecules are nonvolatile compounds that may decompose before ionizing or vaporizing during mass analysis with conventional ...

Mass Spectrometry: Aldehyde and Ketone Fragmentation

In mass spectrometry, the fragmentation of aliphatic aldehydes and ketones generally occurs through three key mechanisms: &#945;-cleavage, inductive cleavage, and the McLafferty rearrangement.
<ol>
	<li>&#945;-Cleavage 
	&#945;-Cleavage is a common fragmentation in carbonyl compounds where the bond adjacent to the carbonyl group is broken. This process produces an alkyl radical and an acylium cation, which is often detected in the mass spectrum due to its stability.</li>
	<li>Inductive Cleavage 
	In inductive cleavage, fragmentation yields an acyl radical and an alkyl cation. This occurs when electrons are drawn toward the carbonyl, weakening adjacent bonds and resulting in a distinctive fragmentation pattern. For example, in the mass spectrum of 5-methyl-2-hexanone, inductive cleavage produces an alkyl cation at a mass-to-charge (m/z) ratio of 71.</li>
	<li>McLafferty Rearrangement 
	The McLafferty rearrangement is a specific fragmentation pattern for carbonyl compounds with &#947;-hydrogen (hydrogen on the third carbon from the carbonyl group). The molecule undergoes a six-membered cyclic transition in this rearrangement, yielding a radical cation and a neutral alkene. For 5-methyl-2-hexanone, this rearrangement results in a peak at m/z 58.</li>
</ol>
Example: Fragmentation of 5-methyl-2-hexanone 
In the mass spectrum of 5-methyl-2-hexanone, the molecular ion undergoes these fragmentation patterns:
<ol style="list-style-type: circle;">
	<li>Inductive cleavage produces an alkyl cation at m/z 71.</li>
	<li>&#945;-Cleavage results in the base peak at m/z 43.</li>
	<li>McLafferty rearrangement creates a distinct peak at m/z 58.</li>
</ol>
An additional diagnostic feature in aldehydes is the M&#8722;1 peak, which arises due to the &#945;-cleavage of the aldehyde proton. In mass spectrometric analysis, this peak can help identify aldehydes, specifically among other carbonyl compounds.
Understanding these fragmentation pathways is crucial for interpreting mass spectra, particularly in identifying functional groups and distinguishing between similar compounds.

In mass spectrometry, the fragmentation of aliphatic aldehydes and ketones generally occurs through three key mechanisms: &#945;-cleavage, inductive ...

Mass Spectrometry: Alkyl Halide Fragmentation

Chlorine isotopes exist as 35Cl and 37Cl in a 3:1 ratio, while bromine isotopes exist as 79Br and 81Br in a 1:1 ratio. The mass spectrum of alkyl halides typically produces two distinct molecular ion peaks, the molecular ion peak, [M], and the molecular ion plus two, [M + 2] peak. The relative heights of these two peaks are proportional to the isotopic abundance ratios of the halide. For example, 2&#8208;chloropropane and 1&#8208;bromopropane display two peaks with relative peak heights in a 3:1 and 1:1 ratio, respectively.
Alkyl halides typically lose a non-bonding electron from the halogen to form molecular ions. The base peak results from the heterolytic cleavage of the carbon&#8211;halogen bond, where the bonding electrons go to the most electronegative atom, forming a cation and halogen atom. Interestingly, the &#9082;-cleavage is observed only in alkyl chlorides, not alkyl bromides. In alkyl chlorides, the&#160; C&#8211;Cl and C&#8211;C bonds exhibit similar strengths, while in alkyl bromides, the C&#8211;Br bond is weaker than the C&#8211;C bond. Consequently, the alkyl chlorides form a stable cation, where the positive charge is shared between the two atoms.
While less commonly discussed, fluoroalkanes and iodoalkanes exhibit unique fragmentation behavior. Fluoroalkanes, due to the strength of the C&#8211;F bond and the presence of only one isotope (19F), show limited fragmentation and lack isotopic peaks. Iodoalkanes, with their weak C&#8211;I bond and a single isotope (127I), predominantly fragment by losing iodine, resulting in simpler spectra with less isotopic splitting.

Chlorine isotopes exist as 35Cl and 37Cl in a 3:1 ratio, while bromine isotopes exist as 79Br and 81Br in a 1:1 ratio. The mass spectrum of alkyl halides ...

Matrix-Assisted Laser Desorption Ionization (MALDI)

Matrix-assisted laser desorption ionization (MALDI) is a powerful analytical technique used in mass spectrometry. It enables the identification and characterization of various biomolecules, including proteins, peptides, nucleic acids, and carbohydrates. MALDI spectrometry is widely employed in biological and medical research, as well as in fields like pharmacology and biochemistry.
The analyte of interest, a biomolecule or a mixture of biomolecules, is mixed with a suitable matrix material. The matrix is usually an organic compound, such as a small organic acid or a crystalline substance, that facilitates ionization. This analyte-matrix mixture is then deposited onto a target surface, inserted into the mass spectrometer, and dried. During drying, the matrix forms small crystals that incorporate the analyte molecules within their structure.
Once the sample is prepared, a pulsed laser is directed onto the target surface. The matrix molecules absorb the laser beam energy, causing them to heat up and vaporize rapidly. This process is known as laser desorption. As the matrix molecules vaporize, they carry the embedded analyte molecules. The vaporized analyte molecules become ionized through a process called proton transfer. The proton transfer occurs between the matrix and the analyte molecule. The matrix molecule donates a proton to the analyte molecule, resulting in the formation of protonated ions. The analyte ions are then accelerated by an electric field and further separated based on their mass-to-charge ratio in a time-of-flight mass analyzer.
The mass spectrum obtained from MALDI spectrometry provides valuable information about the mass and relative abundance of the analyzed biomolecules.

Matrix-assisted laser desorption ionization (MALDI) is a powerful analytical technique used in mass spectrometry. It enables the identification and ...

Mass Spectrometry: Carboxylic Acid, Ester, and Amide Fragmentation

The fragmentation patterns observed for compounds such as carboxylic acids, esters, and amides in the mass spectra include &#9082;-cleavage and McLafferty rearrangement. Fragmentation by &#9082;-cleavage preferentially occurs at the carbon-carbon bond at the &#9082;-position next to the carboxylic group to generate a neutral radical and a cation. Long chain compounds with hydrogen at their &#947;-carbon undergo McLafferty rearrangement to give a radical cation and a neutral alkene.
For example, the fragmentation of butyramide is demonstrated in Figure 1. The molecular ion peak of butyramide, which contains one nitrogen atom, shows an odd mass-to-charge ratio of 87. Fragmentation of butyramide molecular ion by &#9082;-cleavage produces a cation at a mass-to-charge ratio 44. In addition to &#9082;-cleavage, butyramide molecular ion also undergoes fragmentation via McLafferty rearrangement. The base peak at the mass-to-charge ratio 59 arises due to McLafferty rearrangement.
<img alt="Figure1" src="/files/ftp_upload/13051/13051_PT_Figure_1.svg" style="text-align: center; height: 250px;" />

The fragmentation patterns observed for compounds such as carboxylic acids, esters, and amides in the mass spectra include &#9082;-cleavage and McLafferty ...

Mass Spectrometry: Aromatic Compound Fragmentation

Upon ionization, aromatic compounds generate a molecular ion that is observed as a prominent peak in their mass spectra. For example, the molecular ion peak for benzene appears at a mass-to-charge ratio of 78, while toluene is observed at a mass-to-charge ratio of 92. The molecular ion benzene is highly stable and does not readily undergo further fragmentation due to the significant amount of energy required to disrupt the aromatic stability of the benzene ring. In contrast, the molecular ion of alkyl&#8208;substituted benzenes, such as toluene, can undergo fragmentation by losing a hydrogen atom, forming a benzylic carbocation. This carbocation can rearrange to form the resonance-stabilized tropylium cation, which appears in the mass spectra as a strong peak. In the case of toluene, this strong peak is observed at a mass-to-charge ratio of 91.

Upon ionization, aromatic compounds generate a molecular ion that is observed as a prominent peak in their mass spectra. For example, the molecular ion ...

Mass Spectrometry: Alcohol Fragmentation

Alcohols (R-OH) ionize to lose one non-bonded electron from the oxygen atom, forming molecular ions. Due to their tendency to fragment rapidly, the intensity of the molecular ion peak in the mass spectrum is weak or sometimes absent. The fragmentation patterns for alcohols occur in two ways, i.e. &#9082;-cleavage and dehydration. During &#9082;-cleavage, the bond at the &#9082;-position adjacent to the hydroxyl group cleaves to give a resonance-stabilized cation and a radical. However, intramolecular dehydration involves losing a water molecule from an alcohol, forming an alkene cation, which shows a peak at M&#8722;18. Consider the fragmentation of butanol as shown below. &#9082;-cleavage produces a base peak at a mass-to-charge ratio of 31. In the case of dehydration, the fragmentation forms an alkene radical cation at a mass-to-charge ratio of 56.
<img alt="Figure1" src="/files/ftp_upload/13046/13046-PT_Figure_1.svg" style="text-align: center; height: 175px;" />

Alcohols (R-OH) ionize to lose one non-bonded electron from the oxygen atom, forming molecular ions. Due to their tendency to fragment rapidly, the ...

Mass Spectrometry: Amine Fragmentation

Amines can be identified using mass spectroscopy based on their characteristic fragmentation patterns. The molecular ions of amines undergo fragmentation via &#9082;-cleavage. The &#9082;-cleavage of the carbon-carbon bonds in amines generates an alkyl radical and resonance-stabilized nitrogen-containing cation.
In amines, the number of nitrogen atoms affects the mass of the molecular ion, which is described by the nitrogen rule of mass spectrometry. This rule states that a compound containing a single or an odd number of nitrogen atoms produces a molecular ion with an odd molecular weight, while a compound with no or an even number of nitrogen atoms generates a molecular ion with an even molecular weight.
For example, the mass spectrum of 3-methyl-1-butanamine, which contains one nitrogen atom, displays a molecular ion having an odd mass-to-charge ratio of 87. Fragmentation of this molecular ion via &#9082;-cleavage produces a base peak, which features a mass signal at a mass-to-charge ratio of 30, corresponding with the loss of the 2-methyl propyl radical.
Similarly, the fragmentation of triethylamine via &#9082;-cleavage generates a cation at a mass-to-charge ratio of 86. The molecular ion peak shows an odd mass-to-charge ratio of 101, as shown below.
<img alt="Figure1" src="/files/ftp_upload/13048/13048_PT_Figure_1.svg" style="text-align: center; height: 105px;" />

Amines can be identified using mass spectroscopy based on their characteristic fragmentation patterns. The molecular ions of amines undergo fragmentation ...

Mass Spectrometry: Cycloalkene Fragmentation

The molecular ions of cycloalkenes undergo fragmentation via a retro-Diels&#8211;Alder reaction.

The reaction proceeds via the cleavage of two carbon-carbon bonds in the cycloalkene to yield ethene. The remaining part of the cycloalkene structure is a dienyl radical cation with a molecular weight of 28 u lower than the molecular ion. This fragmentation pathway is similar to the fragmentation of cycloalkanes releasing ethene, differing only in the resultant radical cation. An alkyl species forms from the cycloalkane, whereas a dienyl species originates from the cycloalkene.

Retro-Diels&#8211;Alder reactions of cycloalkenes are also similar to the McLafferty-rearrangement-type fragmentation observed in acyclic alkenes with hydrogen on the &#947; carbon. In both cases, cleavage occurs at two positions, yielding an ethene molecule and an alkenyl species. In acyclic alkenes, the cleavage occurs at one carbon-carbon bond and a carbon-hydrogen bond, along with rearranging hydrogen from one carbon to another. In cyclic alkenes, cleavage occurs at two carbon&#8211;carbon bonds without any atomic rearrangement. Figure 1 depicts the fragmentation of cyclohexene via a retro-Diels&#8211;Alder reaction.
<img alt="Figure1" src="/files/ftp_upload/13044/13044-PT_Figure_1.svg" style="text-align: center; height: 90px;" />
Figure 1: Fragmentation of cyclohexene via a retro-Diels&#8211;Alder reaction.
In addition to the retro-Diels&#8211;Alder reaction, branched cycloalkenes exhibit fragmentation via cleavage of the side chain to form a cycloalkene cation. For example, the fragmentation of 1-methyl-1-cyclohexene via a retro-Diels&#8211;Alder reaction and side-chain cleavage are shown in Figure 2.
<img alt="Figure2" src="/files/ftp_upload/13044/13044-PT_Figure_2.svg" style="text-align: center; height: 225px;" />
Figure 2: Fragmentation of 1-methyl-1-cyclohexene via (top) a retro-Diels&#8211;Alder reaction; (bottom) side-chain cleavage.
The corresponding signals of the isoprenyl radical cation and the cyclohexenyl cation are evident in the mass spectrum of 1-methyl-1-cyclohexene shown in Figure 3.
<img alt="Figure3" src="/files/ftp_upload/13044/13044-PT_Figure_3.svg" style="text-align: center; height: 250px;" />
Figure 3: Mass spectrum of 1-methyl-1-cyclohexene.

The molecular ions of cycloalkenes undergo fragmentation via a retro-Diels&#8211;Alder reaction.

The reaction proceeds via the cleavage of two ...

Mass Spectrometry: Alkyne Fragmentation

The fragmentation of alkynes preferentially occurs at the carbon&#8211;carbon bond between the &#945; and &#946; carbon of the alkyne bond to generate a 3-propynyl cation (or propargyl cation). In terminal alkynes, there is the only type of fragmentation that yields the 3-propynyl cation. The unsubstituted 3-propynyl cation exhibits a peak at a mass-to-charge ratio of 39. In internal alkynes, the 3-propynyl cation is substituted. For example, 2-pentyne fragments into methyl-substituted 3-propynyl cation, which subsequently features as a mass signal at the mass-to-charge ratio of 56. The 3-propynyl cation is resonance-stabilized, and the corresponding mass signal is intense in the mass spectrum of alkynes. Figure 1 shows the fragmentation of 1-pentyne into an ethyl radical and a resonance stabilized 3-propynyl cation.
<img alt="Figure1" src="/files/ftp_upload/13045/13045-PT_Figure_1.svg" style="text-align: center; height: 115px;" />
Figure 1: Fragmentation of 1-pentyne molecular ion to yield the 3-propynyl cation.
Another fragmentation pathway observed in terminal alkynes is the loss of hydrogen from the terminal sp carbon. This results in a mass signal with a mass-to-charge ratio of one unit less than the molecular ion. This M&#8211;1 peak is very intense and becomes the base peak in the mass spectra of many alkynes, so it can be used to identify alkynes.
<img alt="Figure2" src="/files/ftp_upload/13045/13045-PT_Figure_2.svg" style="text-align: center; height: 275px;" />
Figure 2: The mass spectrum of 1-pentyne.

The fragmentation of alkynes preferentially occurs at the carbon&#8211;carbon bond between the &#945; and &#946; carbon of the alkyne bond to generate a ...

Mass Spectrometry: Branched Alkane Fragmentation

This lesson delves into the mass spectrometry of branched alkane fragmentation. Branched alkanes possess secondary or tertiary carbon atoms, which generate relatively stable carbocations if the cleavage occurs at the branching point. The high stability of carbocations drives the instant fragmentation of branched alkanes. Accordingly, the branched alkane&#39;s molecular ion peak is very weak or invisible in the mass spectra, especially in comparison to a linear alkane.
<img alt="Figure1" src="/files/ftp_upload/13041/13041-PT_Figure_1.svg" style="text-align: center; height: 275px;" />
Figure 1. Fragmentation pathway of 2-methylbutane (top), neopentane (middle), and n-pentane (bottom) molecular ions.
Figure 1 shows the most feasible fragmentation pathway observed in 2-methyl butane, neopentane, and n-pentane molecular ions. 2-methyl butane and neopentane fragment to yield secondary and tertiary carbocations, respectively. The stability of these carbocations drives the fragmentation reaction, even though the co-produced methyl radical is relatively unstable. In contrast, the cleavage of n-pentane leading to the methyl radical is difficult since the stability of a primary carbocation is low.
<img alt="Figure2" src="/files/ftp_upload/13041/13041-PT_Figure_2.svg" style="text-align: center; height: 105px;" />
Figure 2. Fragmentation of 2,2-dimethylpentane.
As shown in Figure 2, the fragmentation of 2,2-dimethyl pentane involves the loss of either methyl or propyl radical, resulting in a tertiary carbocation. Here, the stability of the co-produced radical determines the cleaving bond. So, the cleavage that produces a propyl radical is favored, and the signal from the 2-methyl propyl carbocation becomes the base peak.

This lesson delves into the mass spectrometry of branched alkane fragmentation. Branched alkanes possess secondary or tertiary carbon atoms, which ...

Tree Identification: How To Use a Dichotomous Key

Source: Laboratories of Margaret Workman and Kimberly Frye - Depaul University
A dichotomous key is a tool that identifies items in nature, such as leaves. This method is based on the idea of choosing between two characteristics. The word dichotomous comes from two Greek words that mean &#8220;to divide into two parts.&#8221; In a dichotomous key for leaf identification, each pair of phrases describes different features of the leaf. Only one of the phrases correctly applies to the leaf being keyed out. The correct phrase leads to the next pair of phrases, or states the name of the tree from which the leaf came. Using a field guide to trees and the iTree National Tree Benefits Calculator helps to identify trees in a field investigation, which shows the significance of trees in terms of their environmental benefits, such as storm water management, increasing property value, energy efficiency, air quality, and carbon sequestration.

Identificação de árvores: como usar uma chave dicotômica

Source: Laboratories of Margaret Workman and Kimberly Frye - Depaul University
A dichotomous key is a tool that identifies items in nature, such as ...

Tree Survey: Point-Centered Quarter Sampling Method

A number of methods are available for sampling forest communities. Point-centered quarter is one such method. It is used to gather information on the density, frequency, and coverage of tree species found in a forest. This information provides the ability to estimate the number of individual trees encountered, how often a certain tree occurs, how common the tree is compared to other trees, and the size of the tree. Compared to the standard plot analysis, the point-centered quarter method is more efficient, which is a major advantage. In a fixed-area plot sampling, a small portion of the total area of the forest is examined. In this small subsample, the density is determined directly by counting and identifying each tree. The ratio between size of the subplot and the overall forest size is used to determine the density for the entire forest.

Levantamento de Árvores: Método de Amostragem Trimestral Centrada em Pontos

A number of methods are available for sampling forest communities. Point-centered quarter is one such method. It is used to gather information on the ...

Using GIS to Investigate Urban Forestry

Source: Laboratories of Margaret Workman and Kimberly Frye - Depaul University
Urban forests broadly include urban parks, street trees, landscaped boulevards, public gardens, river and coastal promenades, greenways, river corridors, wetlands, nature preserves, natural areas, shelterbelts of trees, and working trees at industrial brownfield sites. The history of urban trees begins with trees as landscape embellishment. Today, urban trees are seen as essential components of city infrastructure and critical to human life as food, housing, and other public utilities. Urban trees are now valued for the ecosystem services they provide (e.g., preventing erosion, air pollutant removal, oxygen, shade, etc.). Yet, to efficiently make use of these benefits, trees must reach maturity, as leaf number and size directly affect a tree&#8217;s ability to provide ecosystem services. Urban forestry has had to develop its own forestry methods to address the needs and challenges unique to urban trees as compared to their woodland counterparts.
The following excerpt from the USDA Forest Service illustrates the urban tree perspective and policies of federal government:

<blockquote>Urban forests are dynamic ecosystems that provide needed environmental services by cleaning air and water, helping to control storm water, and conserving energy. They add form, structure, beauty and breathing room to urban design, reduce noise, separate incompatible uses, provide places to recreate, strengthen social cohesion, leverage community revitalization, and add economic value to our communities... This natural life support system sustains clean air and water, biodiversity, habitat, nesting and travel corridors for wildlife, and connects people to nature.</blockquote>

The management of urban trees is an interdisciplinary practice involving architecture, landscaping, planning, development, horticulture, etc. One particular discipline involved in forestry is geography, especially through the use of geographical information systems (GIS). GIS is a broad name encompassing any type of database containing geographical or spatial data that can be used to create computer-generated visual representations (e.g., maps). GIS allows for extensive data collection and management through ever-improving user interfaces, increasing the user-friendly quality of very large sets of information that can be accessed by many users. GIS applications range from free software and open access protocols, such as Google Earth, to proprietary systems, like ESRI ArcGIS. Using GIS to create and store geographical information also allows for easy data maintenance, because maps can be quickly updated by adding new information to the database and regenerating the visual output.

Uso de SIG para Investigar Florestas Urbanas

Source: Laboratories of Margaret Workman and Kimberly Frye - Depaul University
Urban forests broadly include urban parks, street trees, landscaped ...

Proton Exchange Membrane Fuel Cells

Source: Laboratories of Margaret Workman and Kimberly Frye - Depaul University
The United States consumes a large amount of energy &#8211; the current rate is around 97.5 quadrillion BTUs annually. The vast majority (90%) of this energy comes from non-renewable fuel sources. This energy is used for electricity (39%), transportation (28%), industry (22%), and residential/commercial use (11%). As the world has a limited supply of these non-renewable sources, the United States (among others) is expanding the use of renewable energy sources to meet future energy needs. One of these sources is hydrogen.
Hydrogen is considered a potential renewable fuel source, because it meets many important criteria: it&#8217;s available domestically, it has few harmful pollutants, it&#8217;s energy efficient, and it&#8217;s easy to harness. While hydrogen is the most abundant element in the universe, it is only found in compound form on Earth. For example, it is combined with oxygen in water as H2O. To be useful as a fuel, it needs to be in the form of H2 gas. Therefore, if hydrogen is to be used as a fuel for cars or other electronics, H2 needs to be made first. Thusly, hydrogen is often called an &#8220;energy carrier&#8221; rather than a &#8220;fuel.&#8221;
Currently, the most popular way to make H2 gas is from fossil fuels, through steam reforming of hydrocarbons or coal gasification. This does not reduce dependence on fossil fuels and is energy intensive. A less-used method is by electrolysis of water. This also requires an energy source, but it can be a renewable source, like wind or solar power. In electrolysis, water (H2O) is split into its component parts, hydrogen gas (H2) and oxygen gas (O2), through an electrochemical reaction. The hydrogen gas made through the process of electrolysis can then be used in a Proton Exchange Membrane (PEM) fuel cell, generating an electric current. This electric current can be used to power motors, lights, and other electrical devices.

Células de combustível de membrana de troca de prótons

Source: Laboratories of Margaret Workman and Kimberly Frye - Depaul University
The United States consumes a large amount of energy &#8211; the current ...

Biofuels: Producing Ethanol from Cellulosic Material

Source: Laboratories of Margaret Workman and Kimberly Frye - Depaul University
In this experiment, cellulosic material (such as corn stalks, leaves, grasses, etc.) will be used as a feedstock for the production of ethanol.&#160;The cellulosic material is first pretreated (ground and heated), digested with enzymes, and then fermented with yeast.&#160;Ethanol production is monitored using an ethanol probe.&#160;The experiment can be extended to optimize ethanol production by varying the feedstock used, pretreatment conditions, enzyme variation, yeast variation, etc.&#160;An alternative method of monitoring the reaction is to measure the carbon dioxide produced (using a gas sensor) instead of the ethanol.&#160;As a low-tech alternative, glucose meters (found in any drug store) can be used to monitor the glucose during the process, if an ethanol probe or carbon dioxide gas sensor is not available.
With an increased emphasis on &#8216;inquiry-based learning&#8221;, scientific probes are becoming more popular.&#160;Handheld devices like the Vernier Lab Quest used in conjunction with a variety of probes (such as those for conductivity, dissolved oxygen, voltage, and more) allow for less focus on collecting data and/or making graphs and more on analyzing the data and making predictions.&#160;Another advantage is that these are small and lightweight and can be taken into the field for measurements.

Biocombustíveis: Produzindo Etanol a partir de Material Celulósico

Source: Laboratories of Margaret Workman and Kimberly Frye - Depaul University
In this experiment, cellulosic material (such as corn stalks, leaves, ...

Testing For Genetically Modified Foods

Source: Laboratories of Margaret Workman and Kimberly Frye - Depaul University
Genetic modification of foods has been a controversial issue due to debated concerns over health and environmental safety. This experiment demonstrates technical understanding of how food DNA is genetically identified, allowing for educated decision making about the safety and potential dangers of using genetically modified organisms (GMOs) in food supplies.
Polymerase Chain Reaction (PCR) is used to amplify food DNA to test for the presence of genetically modified DNA in food products. Presence of specific DNA bands is detected by using gel electrophoresis to pull extracted food DNA through a 3% agarose gel, a concentration dense enough to separate the bands of DNA containing the genetically modified DNA. Several controls are used in the electrophoresis procedure to ensure DNA is successfully extracted from test foods (plant primer), and to provide known examples of both genetically modified DNA (purchased genetically modified DNA) and non-genetically modified DNA (purchased certified non-GMO food control).

Identifying Genetically Modified Foods Using PCR

Testes para alimentos geneticamente modificados

Source: Laboratories of Margaret Workman and Kimberly Frye - Depaul University
Genetic modification of foods has been a controversial issue due to debated ...

Turbidity and Total Solids in Surface Water

Source: Laboratories of Margaret Workman and Kimberly Frye - Depaul University
Turbidity and total solids are related measurements addressing clarity of surface waters. Turbidity is an indirect measure of water clarity that determines the amount of light that can pass through the water. Total solids is a direct measurement of solid particles suspended in water determined by weight.
High levels of turbidity and total solids are caused by soil erosion, waste discharge, runoff, or changes in ecological communities including algal growth or abundance of benthic organisms that can disrupt sediments up into the water. Higher levels of turbidity and suspended solids can lower water quality by absorbing heat causing an increase in water temperature and a decrease in oxygen levels (warm water holds less oxygen). These conditions can also cause a decrease in photosynthesis as less sunlight penetrates the water, making the water unable to support some aquatic life. Suspended solids can also clog gills, smother eggs, reduce growth rates, and disrupt microhabitats of many aquatic organisms.
One method of measuring turbidity includes using a Secchi disk. A Secchi disk is a metal disk with alternate black and white quarters (Figure 1). It is attached to a rope that has one-foot markings along it. The disk is dropped into water until it can no longer be seen (Figure 2). The drawback of this method is that it must be done in the field and ideal protocol requires sunny conditions and that the testing area be shaded. In addition, if there is a large distance between the riverbank and the water level, it is difficult to use the Secchi disk. By using turbidity tubes, one can collect water and then perform the turbidity measurements back in the laboratory.
<img alt="Figure 1" src="/files/ftp_upload/10015/10015fig1.jpg" /> 
Figure 1. The modified Secchi disk design used in freshwater.
<img alt="Figure 2" src="/files/ftp_upload/10015/10015fig2.jpg" /> 
Figure 2. Different kinds of Secchi disk. A marine style one on the left and the freshwater version on the right

Turbidez e Sólidos Totais em Águas Superficiais

Source: Laboratories of Margaret Workman and Kimberly Frye - Depaul University
Turbidity and total solids are related measurements addressing clarity of ...

Dissolved Oxygen in Surface Water

Source: Laboratories of Margaret Workman and Kimberly Frye - Depaul University
Dissolved oxygen (DO) measurements calculate the amount of gaseous oxygen dissolved in surface water, which is important to all oxygen-breathing life in river ecosystems, including fish species preferred for human consumption (e.g. bluegill and bass), as well as decomposer species critical to the recycling of biogeochemical materials in the system.
The oxygen dissolved in lakes, rivers, and oceans is crucial for the organisms and creatures living in it. As the amount of dissolved oxygen drops below normal levels in water bodies, the water quality is harmed and creatures begin to die. In a process called eutrophication, a body of water can become hypoxic and will no longer be able to support living organisms, essentially becoming a &#8220;dead zone.&#8221;
Eutrophication occurs when excess nutrients cause algae populations to grow rapidly in an algal bloom. The algal bloom forms dense mats at the surface of the water blocking out two essential inputs of oxygen for water: gas exchange from the atmosphere and photosynthesis in the water due to the lack of light below the mats. As dissolved oxygen levels decline below the surface, oxygen-breathing organisms die-off in large amounts, creating an increase in organic matter. The excess organic matter causes an increase in the oxygen-breathing decomposer populations in the benthic zone, which further depletes the remaining dissolved oxygen levels during the metabolic decomposition activity. Once the oxygen levels become this low, mobile oxygen-breathing species (e.g. fish) will move away, leaving no aerobic life in the water and creating a dead zone.
The Azide-Winkler titration method uses titration to determine the concentration of an unknown in a sample. Specifically, sodium thiosulfate is used to titrate iodine, which can be stoichiometrically related to the amount of dissolved oxygen in a sample.

Measuring Dissolved Oxygen in Water by Azide-Winkler Method

Oxigênio dissolvido em Águas Superficiais

Source: Laboratories of Margaret Workman and Kimberly Frye - Depaul University
Dissolved oxygen (DO) measurements calculate the amount of gaseous oxygen ...

Nutrients in Aquatic Ecosystems

Source: Laboratories of Margaret Workman and Kimberly Frye - Depaul University
Nitrogen and phosphorus are essential plant nutrients found in aquatic ecosystems and both are monitored as a part of water quality testing because in excess amounts they can cause significant water quality problems.&#160;
Nitrogen in water is measured as the common form nitrate (NO3-) that is dissolved in water and readily absorbed by photosynthesizers such as algae. The common form of phosphorus measured is phosphate (PO43-), which is strongly attracted to sediment particles as well as dissolved in water. In excess amounts, both nutrients can cause an increase in aquatic plant growth (algal bloom, Figure 1) that can disrupt the light, temperature, and oxygen levels in the water below and lead to eutrophication and hypoxia (low dissolved oxygen in water) forming a &#8220;dead zone&#8221; of no biological activity. Sources of nitrates and phosphorus include wastewater treatment plants, runoff from fertilized lawns and agricultural lands, faulty septic systems, animal manure runoff, and industrial waste discharge.
<img alt="Figure 1" src="/files/ftp_upload/10023/10023fig1.jpg" /> 
Figure 1. Algal bloom 
Taken in 2011, the green scum shown in this image was the worst algae bloom Lake Erie has experienced in decades. Record torrential spring rains washed fertilizer into the lake, promoting the growth of microcystin producing cyanobacteria blooms. Vibrant green filaments extend out from the northern shore.

Eutrophication, Measuring Nitrate and Phosphate in Water

Nutrientes em Ecossistemas Aquáticos

Source: Laboratories of Margaret Workman and Kimberly Frye - Depaul University
Nitrogen and phosphorus are essential plant nutrients found in aquatic ...

Measuring Tropospheric Ozone

Source: Laboratories of Margaret Workman and Kimberly Frye - Depaul University
Ozone is a form of elemental oxygen (O3), a molecule of three oxygen atoms bonded in a structure that is highly reactive as an oxidizing agent. Ozone occurs in both the stratosphere and the troposphere levels of the atmosphere. When in the stratosphere (located approximately 10-50 km from the earth&#8217;s surface), ozone molecules form to the ozone layer and help prevent harmful UV rays from reaching Earth&#8217;s surface. In lower altitudes of the troposphere (surface - approximately 17 km), ozone is harmful to human health and is considered an air pollutant contributing to photochemical smog (Figure 1). Ozone molecules can cause damage directly by harming respiratory tissue when inhaled or indirectly by harming plant tissues (Figure 2) and softer materials including tires on automobiles.
Outdoor tropospheric ozone is formed at ground level when nitrogen oxides (NOx) and volatile organic compounds (VOCs) from automobile emissions are exposed to sunlight. Consequently, health concerns over ozone concentrations escalate in sunny conditions or when and where automobile use is increased.
Reaction: NO2 + VOC + sunlight &#8594;&#160;O3 (+ other products)
Indoor tropospheric ozone is formed when electrical discharges from equipment using high voltages (e.g. ionic air purifiers, laser printers, photocopiers) break down the chemical bonds of the atmospheric oxygen (O2) in the air surrounding the equipment:
O2 &#8594; 2 O
The free radicals of oxygen in and around electrical discharge recombine to create ozone (O3).
2 O + 2 O2&#8594; 2 O3
<img alt="Figure 1" src="/files/ftp_upload/10024/10024fig1.jpg" /> 
Figure 1: Golden Gate Bridge panorama
Characteristic coloration for smog in California in the beige cloud bank behind the Golden Gate Bridge. The brown coloration is due to the NOx in the photochemical smog.
<img alt="Figure 2" src="/files/ftp_upload/10024/10024fig2.jpg" /> 
Figure 2: Plants damaged by ozone. Top row is normal, bottom row has been exposed to ozone.

Medição de Ozônio Troposférico

Source: Laboratories of Margaret Workman and Kimberly Frye - Depaul University
Ozone is a form of elemental oxygen (O3), a molecule of three oxygen atoms ...

Determination Of NOx in Automobile Exhaust Using UV-VIS Spectroscopy

Source: Laboratories of Margaret Workman and Kimberly Frye - Depaul University
In the troposphere, ozone is naturally formed when sunlight splits nitrogen dioxide (NO2):
NO2 + sunlight &#8594; NO + O
O + O2 &#8594; O3
Ozone (O3) can go on to react with nitric oxide (NO) to form nitrogen dioxide (NO2) and oxygen:
NO + O3 &#8594; NO2 + O2
This results in no net gain of ozone (O3). However, with the anthropogenic production of ozone forming precursors (NO, NO2, and volatile organic compounds) through the combustion of fossil fuels, elevated levels of ozone in the troposphere have been found. Motor vehicle exhaust is a significant source of these ozone forming precursors: NO, NO2, and volatile organic compounds (VOCs). For example, mobile sources make up nearly 60% of NO + NO2 emissions.
At the high temperatures found in a car&#8217;s combustion chamber, nitrogen and oxygen from the air react to form nitric oxide (NO) and nitrogen dioxide (NO2):
N2(g) + O2 (g)&#8594; 2 NO(g)
2 NO(g) + O2(g)&#8594; 2 NO2(g)
The nitric oxide (NO) emitted in the car exhaust is gradually oxidized to nitrogen dioxide (NO2) in ambient air. This mixture of NO and NO2 is often referred to as NOx. When NOx reacts with volatile organic compounds in the atmosphere in the presence of sunlight, tropospheric ozone forms, as seen in this simplified chemical reaction:
NOx + VOCs + sunlight &#8594; O3 + other products
This noxious mixture of air pollution, which can include aldehydes, peroxyacetyl nitrates, ozone, VOCs, and NOx, is called photochemical smog. Ozone is the largest component of photochemical smog. This smog is found in all modern cities, but it&#8217;s found especially in cities with sunny, warm, dry climates and large numbers of motor vehicles. The yellow-brown color of smog in the air is due in part to the nitrogen dioxide present, since this gas absorbs visible light near 400 nm (Figure 1).
Short-term NO2 exposure (30 min to 1 day) leads to adverse respiratory effects in healthy people and increased respiratory symptoms in people with asthma. NOx reacts with ammonia and other compounds to form particulates. These small particles can penetrate the lungs and cause respiratory problems, including emphysema and bronchitis. Individuals who spend a lot of time on the road or who live near a roadway experience considerably higher exposure to NO2.
Due to the impact it has on human health and the environment, the U.S. Environmental Protection Agency (EPA) has classified NO2 as a criteria pollutant and has set the primary standard at 100 ppb (98th percentile of 1-h daily maximum concentrations, averaged over 3 years) and 53 ppb (annual mean). Considering that on-road vehicles account for approximately 1/3 of NOx emissions in the U.S., automobile emissions are therefore regulated through the Clean Air Act. The U.S. EPA established emission standards that automobile manufacturers must follow when producing cars. Currently, Tier 2 emission standards set that manufacturers must have fleet average NOx emissions of no more than 0.07 g/mile.
One way manufacturers meet this standard is by using catalytic converters on their cars. This device is placed between the engine and the tailpipe. The exhaust stream passes through the catalytic converter and is exposed to a catalyst. A reduction catalyst of platinum and rhodium is used to reduce the NOx concentration in the exhaust. When an NO or NO2 molecule in the exhaust contacts the catalyst, the nitrogen atom is grabbed off the molecule and held onto by the catalyst. The oxygen is freed and forms O2. The nitrogen atom on the catalyst binds with another nitrogen atom held on the catalyst to form N2.
Catalytic converters have greatly reduced the emissions of NOx from car exhaust &#8211; up to 80% reduction, when performing properly. However, they only work when they have reached a fairly high temperature. Therefore, when doing a cold start of a car, the catalytic converter is removing virtually no NOx. It isn&#8217;t until the catalytic converter reaches higher temperatures that it effectively removes the NOx from the exhaust stream. Catalytic converters do not work on diesel passenger cars due to the lean conditions under which they operate. In addition, the sulfur in diesel fuel also deactivates the catalyst. The NOx in diesel engines are reduced mainly through the exhaust gas recirculation (EGR) valve, which cools the temperature of the combustion gases. As a result, diesel cars generally emit more NOx than gasoline cars.
<img alt="Figure 1" src="/files/ftp_upload/10076/10076fig1.jpg" /> 
Figure 1. Characteristic coloration for smog in California in the beige cloud bank behind the Golden Gate Bridge. The brown coloration is due to the NOx in the photochemical smog.

Determination Of NOx in Automobile Exhaust Using UV-VIS Spectroscopy

Determinação de NOx no escapamento do automóvel usando espectroscopia UV-VIS

Source: Laboratories of Margaret Workman and Kimberly Frye - Depaul University
In the troposphere, ozone is naturally formed when sunlight splits nitrogen ...

Lead Analysis of Soil Using Atomic Absorption Spectroscopy

Source: Laboratories of Margaret Workman and Kimberly Frye - Depaul University
Lead occurs naturally in soil, in levels ranging from 10-50 ppm. However, with the widespread use of lead in paint and gasoline in addition to contamination by industry, urban soils often have concentrations of lead significantly greater than background levels &#8211; up to 10,000 ppm in some places. Ongoing problems arise from the fact that lead does not biodegrade, and instead remains in the soil.
Serious health risks are associated with lead poisoning, where children are particularly at risk. Millions of children in the U.S. are exposed to soil containing lead. This exposure can cause developmental and behavioral problems in children. These problems include learning disabilities, inattention, delayed growth, and brain damage. The Environmental Protection Agency has set a standard for lead in soil at 400 ppm for play areas and 1,200 ppm for non-play areas.
Lead is also of concern in soil, when it&#8217;s used for gardening. Plants take up lead from the soil. Therefore, vegetables or herbs grown in contaminated soil can lead to lead poisoning. In addition, contaminated soil particles can be breathed in while gardening or brought into the house on clothing and footwear. It is recommended that soils with lead levels greater than 400 ppm should not be used for gardening. It is further recommended that soil with lead levels between 100 and 400 ppm not be used for leafy vegetables or herbs, because lead can be stored in the leaves. On a similar note, root vegetables should not be grown in this soil, because lead can also accumulate in plant roots.

Análise de chumbo do solo usando espectroscopia de absorção atômica

Source: Laboratories of Margaret Workman and Kimberly Frye - Depaul University
Lead occurs naturally in soil, in levels ranging from 10-50 ppm. However, ...

Carbon and Nitrogen Analysis of Environmental Samples

Source: Laboratories of Margaret Workman and Kimberly Frye - Depaul University
Elemental Analysis is a method used to determine elemental composition of a material. In environmental samples such as soils, scientists are particularly interested in the amounts of two ecologically important elements, nitrogen and carbon. Elemental analysis by the flash combustion technique works by oxidizing the sample with a catalyst through combustion in a high-temperature chamber. The products of combustion are then reduced to N2 and CO2 and detected with a thermal conductivity detector.
Unlike other methods for total nitrogen determination (Kjeldahl method) and total carbon determination (Walkley-Black, Heanes or Leco methods), the flash combustion technique does not use toxic chemicals and is therefore much safer to use.
This video will demonstrate combustion-based elemental analysis using the Flash EA 1112 instrument from Thermo Fisher Scientific.

Análise de Carbono e Nitrogênio de Amostras Ambientais

Source: Laboratories of Margaret Workman and Kimberly Frye - Depaul University
Elemental Analysis is a method used to determine elemental composition of a ...

Soil Nutrient Analysis: Nitrogen, Phosphorus, and Potassium

Source: Laboratories of Margaret Workman and Kimberly Frye - Depaul University
In this experiment, three soil macronutrients are chemically extracted, combined with color-based reagents, then analyzed using color to determine the nutrient concentration present in the soil sample.
Nitrogen, phosphorus, and potassium are the main components of soil fertilizer. These methods isolate each nutrient from the soil into a solution that can be analyzed using turbidity and color to determine the concentration of nutrients present in the soil sample. Knowing present concentration informs environmental scientists of a nutrient deficiency or surplus in soils used to support plant production, and also provides general insight into basic biogeochemical cycles of an ecosystem.

Análise de Nutrientes do Solo: Nitrogênio, Fósforo e Potássio

Source: Laboratories of Margaret Workman and Kimberly Frye - Depaul University
In this experiment, three soil macronutrients are chemically extracted, ...

Analysis of Earthworm Populations in Soil

Source: Laboratories of Margaret Workman and Kimberly Frye - Depaul University
Using mustard, Lumbricus terrestris earthworm populations can be sampled directly from soil depths without landscape disturbance or toxicity. Earthworms can then be counted for data and statistical analysis using a bar graph and student&#8217;s t-test.
Monitoring earthworm populations is a vital technique for environmental scientists, as multiple species of earthworms (most notably those from the suborder Lumbricina) have been invasively spreading throughout North America and South America. Exotic earthworms can be found on nearly every land mass and in nearly every ecosystem on the planet, and where and when these species become invasive has been a focus of international environmental research.1
Ecological invasion typically lowers biodiversity of an ecosystem by directly outcompeting, endangering, or otherwise contributing to the extirpation of native species. As ecosystem engineers, invasive earthworm species alter the cycling of nutrients through decomposition rates of organic matter on the upper horizons of soil, where plant roots mine for nutrients. Invasive Lumbricus species have both extirpated native earthworm species and have been shown to increase the available nitrogen concentration and rates of nitrogen in invaded soils.2 In a positive feedback loop, accelerated levels of nitrogen in turn make the system more hospitable to invasive plant species that are adapted to high levels of nitrogen compared to native plant species, and will outcompete natives in a phenomenon known as &#8220;invasion meltdown.&#8221; An invasion meltdown relationship has been proposed for invasive earthworm species Lumbricus terrestris (European earthworm) and an invasive plant species Rhamnus cathartica (European Buckthorn).3

Quadrat Sampling and Earthworm Population Analysis in Soil

Análise de Populações de Minhocas no Solo

Source: Laboratories of Margaret Workman and Kimberly Frye - Depaul University
Using mustard, Lumbricus terrestris earthworm populations can be sampled ...

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