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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 ...

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 ...

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: 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 ...

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 ...

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 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 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 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 ...

&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 ...

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 ...

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 ...

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: 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: 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: 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: 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: 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 ...

Synthesis Of A Ti(III) Metallocene Using Schlenk Line Technique

Source: Tamara M. Powers, Department of Chemistry, Texas A&#38;M University&#160;
Inorganic chemists often work with highly air- and water-sensitive compounds. The two most common and practical methods for air-free synthesis utilize either Schlenk lines or gloveboxes. This experiment will demonstrate how to perform simple manipulations on a Schlenk line with a focus on solvent preparation and transfer. Through the synthesis of a reactive Ti(III) metallocene complex, we will demonstrate a new, simple method to degas solvent as well as how to transfer solvent by cannula and by syringe on a Schlenk line.
The synthesis of a Ti(III) metallocene compound 3 is shown in Figure 1.1 Compound 3 is highly reactive with O2, (see oxidation of compound 3 to Ti(IV) metallocene 4 shown in Figure 1). Therefore, it is important to run the synthesis under anaerobic conditions. The synthesis of target compound 3 can be monitored visually and progresses through one additional color change before arriving at the desired product, which is blue in color. If during the experiment there is an observed color change from blue to yellow (or green = blue + yellow), this is an indication that O2 entered the flask and that undesired oxidation of compound 3 to the Ti(IV) analog (compound 4) has occurred.
<img alt="Figure 1" src="/files/ftp_upload/10428/10428fig1v2.jpg" /> 
Figure 1. Synthesis of Ti(III) metallocene compound 3 and it&#39;s reaction with O2.

Synthesis Of A TiIII Metallocene Using Schlenk Line Technique

Synthèse d'un métallocène de Ti(III) avec une ligne Schlenk

Source: Tamara M. Powers, Department of Chemistry, Texas A&#38;M University&#160;
Inorganic chemists often work with highly air- and water-sensitive ...

Glovebox and Impurity Sensors

Source: Tamara M. Powers, Department of Chemistry, Texas A&#38;M University&#160;
The glovebox provides a straightforward means to handle air- and moisture-sensitive solids and liquids. The glovebox is what it sounds like: a box with gloves attached to one or more sides, which allows the user to perform manipulations within the glovebox under an inert atmosphere.
For manipulations under inert atmospheres, chemists can choose between Schlenk or high-vacuum techniques and a glovebox. Schlenk and particularly high-vacuum techniques offer a higher degree of control of the atmosphere, and are thus suitable for reactions that are greatly air- and moisture-sensitive. The glovebox, however, provides greater access for manipulations in an inert atmosphere. Weighing out reagents, filtering reactions, preparing samples for spectroscopy, and growing crystals are all examples of routine procedures that are more readily performed in a glovebox versus a Schlenk/vacuum manifold. Advancements in glovebox design have increased its performance, such as running reactions at reduced temperatures and spectroscopy within the glovebox.
This video will demonstrate how to bring items in and out of the glovebox and how to qualitatively ensure a good working environment. Basic manipulations within a glovebox will be demonstrated through the synthesis of sodium benzophenone.

Glovebox-Operating Procedure and Use of Impurity Sensors

Boîte à gants et capteurs d'impuretés

Source: Tamara M. Powers, Department of Chemistry, Texas A&#38;M University&#160;
The glovebox provides a straightforward means to handle air- and ...

Purification of Ferrocene by Sublimation

Source: Tamara M. Powers, Department of Chemistry, Texas A&#38;M University&#160;
Sublimation, the direct phase transition of a solid into a gas without first becoming a liquid, takes place at temperatures and pressures lower than that of the compound&#39;s triple point (Figure 1).The process of sublimation can be utilized to purify both organic and inorganic solids. During the purification technique, a solid is heated directly into the gas-phase. All non-volatile impurities are left behind while the vaporized compound is then collected (deposition) as a solid on a cold surface. Here, we will use sublimation to purify ferrocene, an inorganic solid with a triple point temperature of 183 &#176;C.1
<img alt="Figure 1" src="/files/ftp_upload/10429/10429fig1v2.jpg" /> 
Figure 1. Generic phase diagram. The colored lines represent the pressure and temperature requirements for phase transitions. Distillation of a solid will occur at pressures and temperatures above the triple point, represented by the green line in the phase diagram. The blue line represents the temperature and pressure conditions where sublimation occurs.

Sublimation: Concept, Purification of Ferrocene, Applications

Purification du Ferrocène par sublimation

Source: Tamara M. Powers, Department of Chemistry, Texas A&#38;M University&#160;
Sublimation, the direct phase transition of a solid into a gas without ...

The Evans Method

Source: Tamara M. Powers, Department of Chemistry, Texas A&#38;M University&#160;
While most organic molecules are diamagnetic, wherein all their electrons are paired up in bonds, many transition metal complexes are paramagnetic, which has ground states with unpaired electrons. Recall Hund&#39;s rule, which states that for orbitals of similar energies, electrons will fill the orbitals to maximize the number of unpaired electrons before pairing up. Transition metals have partially populated d-orbitals whose energies are perturbed to varying extents by coordination of ligands to the metal. Thus, the d-orbitals are similar in energy to one another, but are not all degenerate. This allows for complexes to be diamagnetic, with all electrons paired up, or paramagnetic, with unpaired electrons.
Knowing the number of unpaired electrons in a metal complex can provide clues into the oxidation-state and geometry of the metal complex, as well as into the ligand field (crystal field) strength of the ligands. These properties greatly impact the spectroscopy and reactivity of transition metal complexes, and so are important to understand.
One way to count the number of unpaired electrons is to measure the magnetic susceptibility, &#967;, of the coordination compound. Magnetic susceptibility is the measure of magnetization of a material (or compound) when placed in an applied magnetic field. Paired electrons are slightly repelled by an applied magnetic field, and this repulsion increases linearly as the strength of the magnetic field increases. On the other hand, unpaired electrons are attracted (to a larger extent) to a magnetic field, and the attraction increases linearly with magnetic field strength. Therefore, any compound with unpaired electrons will be attracted to a magnetic field.1
When we measure the magnetic susceptibility, we obtain information on the number of unpaired electrons from the magnetic moment, &#181;. The magnetic susceptibility is related to the magnetic moment, &#181; by Equation 12:
<img alt="Equation 1" src="/files/ftp_upload/10304/10304eq1.jpg" /> (1)
The constant <img alt="Equation 2" src="/files/ftp_upload/10304/10304eq2.jpg" /> = [(3kB)/N&#946;2)], where &#946;= Bohr magneton of the electron (0.93 x 10-20 erg gauss-1), N = Avogadro&#39;s number, and kB = Boltzmann constant 
XM = molar magnetic susceptibility (cm3/mol) 
T = temperature (K) 
&#181; = magnetic moment, measured in units of Bohr magneton, &#181;B = 9.27 x 10-24 JT-1
The magnetic moment for complexes is given by Equation 21:
<img alt="Equation 3" src="/files/ftp_upload/10304/10304eq3.jpg" /> (2)
g = gyromagnetic ratio = 2.00023 &#181;B 
S = spin quantum number = &#8721;ms = [number of unpaired electrons, n]/2 
L = orbital quantum number = &#8721;ml
This equation has both orbital and spin contributions. For first-row transition metal complexes, the orbital contribution is small and hence can be omitted, so the spin-only magnetic moment is given by Equation 3:
<img alt="Equation 4" src="/files/ftp_upload/10304/10304eq4.jpg" /> (3)
The spin-only magnetic moment can thus directly give the number of unpaired electrons. This approximation can also be made for heavier metals, though orbital contributions may be significant for second and third row transition metals. This contribution may be so significant that it inflates the magnetic moment enough that the compound appears to have more unpaired electrons than it does. Therefore, additional characterization may be required for these complexes.
In this experiment, the solution magnetic moment of tris(acetylacetonato)iron(III) (Fe(acac)3) is determined experimentally using Evans method in chloroform.

The Evans Method: Calculating Unpaired Electrons and Magnetic Susceptibility

La méthode Evans

Source: Tamara M. Powers, Department of Chemistry, Texas A&#38;M University&#160;
While most organic molecules are diamagnetic, wherein all their ...

Single Crystal and Powder X-ray Diffraction

Source: Tamara M. Powers, Department of Chemistry, Texas A&#38;M University&#160;
X-ray crystallography is a technique that uses X-rays to study the structure of molecules. X-ray diffraction (XRD) experiments are routinely carried out with either single-crystal or powdered samples.
Single-crystal XRD:
Single-crystal XRD allows for absolute structure determination. With single-crystal XRD data, the exact atomic positions can be observed, and thus bond lengths and angles can be determined. This technique provides the structure within a single crystal, which does not necessarily represent the bulk of the material. Therefore, additional bulk characterization methods must be utilized to prove the identity and purity of a compound.
Powder XRD:
Unlike single-crystal XRD, powder XRD looks at a large sample of polycrystalline material and therefore is considered a bulk characterization technique. The powder pattern is considered a &#34;fingerprint&#34; for a given material; it provides information about the phase (polymorph) and crystallinity of the material. Typically, powder XRD is used to study minerals, zeolites, metal-organic frameworks (MOFs), and other extended solids. Powder XRD can also be used to establish bulk purity of molecular species.
Previously, we have seen how to grow X-ray quality crystals (see video in Essentials of Organic Chemistry series). Here we will learn the principles behind XRD. We will then collect both single-crystal and powder data on Mo2(ArNC(H)NAr)4, where Ar = p-MeOC6H5.

Diffraction par rayons X : cristal vs poudre

Source: Tamara M. Powers, Department of Chemistry, Texas A&#38;M University&#160;
X-ray crystallography is a technique that uses X-rays to study the ...

Electron Paramagnetic Resonance (EPR) Spectroscopy

Source: David C. Powers, Tamara M. Powers, Texas A&#38;M
In this video, we will learn the basic principles behind Electron Paramagnetic Resonance (EPR). We will use EPR spectroscopy to study how dibutylhydroxy toluene (BHT) behaves as an antioxidant in the autoxidation of aliphatic aldehydes.

EPR Spectroscopy, Paramagnetic Molecule and Zeeman Effect

Spectroscopie par résonance paramagnétique électronique (RPE)

Source: David C. Powers, Tamara M. Powers, Texas A&#38;M
In this video, we will learn the basic principles behind Electron Paramagnetic Resonance (EPR). ...

M&#246;ssbauer Spectroscopy

Source: Joshua Wofford,&#160;Tamara M. Powers, Department of Chemistry, Texas A&#38;M University&#160;
M&#246;ssbauer spectroscopy is a bulk characterization technique that examines the nuclear excitation of an atom by gamma rays in the solid state. The resulting M&#246;ssbauer spectrum provides information about the oxidation state, spin state, and electronic environment around the target atom, which, in combination, gives evidence about the electronic structure and ligand arrangement (geometry) of the molecule. In this video, we will learn about the basic principles of M&#246;ssbauer spectroscopy and collect a zero field 57Fe M&#246;ssbauer spectrum of ferrocene.

M&amp;#246;ssbauer Spectroscopy

Spectroscopie Mössbauer

Source: Joshua Wofford,&#160;Tamara M. Powers, Department of Chemistry, Texas A&#38;M University&#160;
M&#246;ssbauer spectroscopy is a bulk ...

Lewis Acid-Base Interaction in Ph3P-BH3

Source: Tamara M. Powers, Department of Chemistry, Texas A&#38;M University&#160;
One of the goals of chemistry is to use models that account for trends and provide insights into the properties of reactants that contribute to reactivity. Substances have been classified as acids and bases since the time of the ancient Greeks, but the definition of acids and bases has been modified and expanded over the years.1
The ancient Greeks would characterize substances by taste, and defined acids as those that were sour-tasting, such as lemon juice and vinegar. The term &#34;acid&#34; is derived from the Latin term for &#34;sour-tasting.&#34; Bases were characterized by their ability to counteract or neutralize acids. The first bases characterized were those of ashes from a fire, which were mixed with fats to make soap. In fact, the term &#34;alkaline&#34; is derived from the Arabic word for &#34;roasting.&#34; Indeed, it has been known since ancient times that acids and bases can be combined to give a salt and water.
The first widely-used description of an acid is that of the Swedish chemist, Svante Arrhenius, who in 1894 defined acids as substances which dissociate in water to give hydronium ions, and bases as substances which dissociate in water to give hydroxide ions. This definition is thus limited to aqueous acids and necessitates that an acid contribute a proton.2 For example, in water, HCl is an acid, as it dissociates to give the hydronium ion (H3O)+ and the chloride ion. Boron trichloride would not be considered an acid, as in water it hydrolyzes to give B(OH)3 and 3 HCl; the product HCl though is an Arrhenius acid.
In 1923, Johannes Nicolaus Br&#248;nsted and Martin Lowry independently defined acids and bases on their ability to donate and accept hydrogen ions, or protons. Thus came the concept of acid-base conjugate pairs, and the expansion of the definition of acids and bases in solvents other than water. For example, ammonium is an acid, as it can donate a proton and generate ammonia. Ammonia can accept a proton, to give ammonium. Thus, ammonia is the conjugate base of ammonium. This acid-base reaction can occur in water, ammonia, or other solvents.
This video deals with the acid-base definition of the American chemist, Gilbert N. Lewis, who also defined acids and bases in 1923. Indeed, this is the same Lewis from Lewis-dot structures in General Chemistry. His approach focuses not on the ability of acids and bases to donate and accept protons, but rather on their ability to accept and donate electron pairs, respectively. This encompasses the Br&#248;nsted-Lowry definition, as H+ accepts an electron pair from a Br&#248;nsted base during protonation. However, it greatly expands the definition of an acid, now encompassing metal ions and main-group compounds. Here, we compare the 31P NMR of the Lewis acid-base adduct Ph3P-BH3 to free triphenylphosphine.

Lewis Acid-Base Interaction in Ph3P-BH3

Interaction des acides et bases de Lewis au sein du complexe Ph3P-BH3

Source: Tamara M. Powers, Department of Chemistry, Texas A&#38;M University&#160;
One of the goals of chemistry is to use models that account for trends ...

Structure Of Ferrocene

Source: Tamara M. Powers, Department of Chemistry, Texas A&#38;M University&#160;
In 1951, Kealy and Pauson reported to Nature the synthesis of a new organometallic compound, ferrocene.1&#160;In their original report, Pauson suggested a structure for ferrocene in which the iron is singly bonded (sigma bonds) to one carbon atom of each cyclopentadiene ligand (Figure 1, Structure I).1,2,3&#160;This initial report led to wide-spread interest in the structure of ferrocene, and many leading scientists participated in the structure elucidation of this interesting new molecule. Wilkinson and Woodward were quick to suggest an alternative formulization where the iron is &#34;sandwiched&#34; between two cyclopentadiene ligands, with equal binding to all 10 carbon atoms (Figure 1, Structure II).4&#160;Here, we will synthesize ferrocene and decide, based on experimental data (IR and 1H NMR), which of these structures is observed. In addition, we will study the electrochemistry of ferrocene by collecting a cyclic voltammogram. In the course of this experiment, we introduce the 18-electron rule and discuss valence electron counting for transition metal complexes.
<img alt="Figure 1" src="/files/ftp_upload/10347/10347fig1v2.jpg" /> 
Figure 1. Two proposed structures of ferrocene.

Structure Determination of Ferrocene-an Organometallic Complex

Structure du ferrocène

Source: Tamara M. Powers, Department of Chemistry, Texas A&#38;M University&#160;
In 1951, Kealy and Pauson reported to Nature the synthesis of a new ...

Application of Group Theory to IR Spectroscopy

Source: Tamara M. Powers, Department of Chemistry, Texas A&#38;M University
Metal carbonyl complexes are used as metal precursors for the synthesis of organometallic complexes as well as catalysts. Infrared (IR) spectroscopy is one of the most utilized and informative characterization methods of CO containing compounds. Group theory, or the use of mathematics to describe the symmetry of a molecule, provides a method to predict the number of IR active C-O vibrational modes within a molecule. Experimentally observing the number of C-O stretches in the IR is a direct method to establish the geometry and structure of the metal carbonyl complex.
In this video, we will synthesize the molybdenum carbonyl complex Mo(CO)4[P(OPh)3]2, which can exist in the cis- and trans-forms (Figure 1). We will use group theory and IR spectroscopy to determine which isomer is isolated.
<img alt="Figure 1" src="/files/ftp_upload/10442/10442fig1.jpg" /> 
Figure 1. The cis- and trans-isomers of Mo(CO)4[P(OPh)3]2.

Symmetry Elements, Group Theory and IR-Active Vibrations

Application de la théorie des groupes à la spectroscopie IR

Source: Tamara M. Powers, Department of Chemistry, Texas A&#38;M University
Metal carbonyl complexes are used as metal precursors for the synthesis of ...

Molecular Orbital (MO) Theory

Source: Tamara M. Powers, Department of Chemistry, Texas A&#38;M University
This protocol serves as a guide in the synthesis of two metal complexes featuring the ligand 1,1&#39;-bis(diphenylphosphino)ferrocene (dppf): M(dppf)Cl2, where M = Ni or Pd. While both of these transition metal complexes are 4-coordinate, they exhibit different geometries at the metal center. Using molecular orbital (MO) theory in conjunction with 1H NMR and Evans method, we will determine the geometry of these two compounds.

Molecular Orbital MO Theory: Predicting Geometry of Transition Metal Complexes

Théorie de l’orbital moléculaire (OM)

Source: Tamara M. Powers, Department of Chemistry, Texas A&#38;M University
This protocol serves as a guide in the synthesis of two metal complexes ...

Quadruply Metal-Metal Bonded Paddlewheels

Source: Corey Burns, Tamara M. Powers, Department of Chemistry, Texas A&#38;M University
Paddlewheel complexes are a class of compounds comprised of two metal ions (1st, 2nd, or 3rd row transition metals) held in proximity by four bridging ligands (most commonly formamidinates or carboxylates) (Figure 1). Varying the identity of the metal ion and the bridging ligand provides access to large families of paddlewheel complexes. The structure of paddlewheel complexes allows for metal-metal bonding, which plays a vital role in the structure and reactivity of these complexes. Due to the diversity of electronic structures that are available to paddlewheel complexes - and the corresponding differences in M-M bonding displayed by these structures - paddlewheel complexes have found application in diverse areas, such as in homogeneous catalysis and as building blocks for metal-organic frameworks (MOFs). Understanding the electronic structure of the M-M bonds in paddlewheel complexes is critical to understanding their structures and thus to application of these complexes in coordination chemistry and catalysis.
<img alt="Figure 1" src="/files/ftp_upload/10441/10441fig1v2.jpg" /> 
Figure 1. General structure of paddlewheel complexes, where M can be a 1st, 2nd, or 3rd row transition metal.
When two transition metals are held in close proximity the d-orbitals overlap, which can result in the formation of M-M bonds. Overlapping d-orbitals can form three types of bonds - &#963;, &#960;, and &#948; - depending on the symmetry of the orbitals involved. If we assign the molecular z-axis to be coplanar with the M-M bond, a &#963; bond is formed by overlap of the dz2 orbitals and &#960; bonds are formed by overlap of the dxz and dyz orbitals. &#948; bonds are generated by overlap of d-orbitals that have two planar nodes (dxy and dx2&#8211;y2). As a result, all four lobes of the d-orbital overlap and the corresponding &#948; bond has two planar nodes (Figure 2). In theory, with the addition of &#948; bonds, paddlewheel complexes are capable of supporting quintuple bonds, or five bonds between metal atoms.1 In most complexes, the dx2&#8211;y2 forms strong metal-ligand bonds and does not meaningfully contribute to M-M bonding. Thus, quadruple bonds are the maximum bond order in many complexes.
<img alt="Figure 2" src="/files/ftp_upload/10441/10441fig2v2.jpg" /> 
Figure 2. Visual representation of &#963;, &#960;, and &#948; bonding MOs resulting from the linear combination of metal d-orbitals. The dz2 atomic orbitals have the best spatial overlap, followed by the dxz and dyz orbitals. The dxy atomic orbitals have the least amount of spatial overlap.
In this video, we will synthesize the dimolybdenum paddlewheel complex Mo2(ArNC(H)NAr)4, where Ar = p-(MeO)C6H4, which features a quadruple bond. We will characterize the compound by NMR spectroscopy and use X-ray crystallography to study the M-M bond.

Quadruples clusters métalliques

Source: Corey Burns, Tamara M. Powers, Department of Chemistry, Texas A&#38;M University
Paddlewheel complexes are a class of compounds comprised of two ...

Dye-sensitized Solar Cells

Source: Tamara M. Powers, Department of Chemistry, Texas A&#38;M University
Today&#39;s modern world requires the use of a large amount of energy. While we harness energy from fossil fuels such as coal and oil, these sources are nonrenewable and thus the supply is limited. To maintain our global lifestyle, we must extract energy from renewable sources. The most promising renewable source, in terms of abundance, is the sun, which provides us with more than enough solar energy to fully fuel our planet many times over.
So how do we extract energy from the sun? Nature was the first to figure it out: photosynthesis is the process whereby plants convert water and carbon dioxide to carbohydrates and oxygen. This process occurs in the leaves of plants, and relies on the chlorophyll pigments that color the leaves green. It is these colored molecules that absorb the energy from sunlight, and this absorbed energy which drives the chemical reactions.
In 1839, Edmond Becquerel, then a 19-year old French physicist experimenting in his father&#39;s lab, created the first photovoltaic cell. He illuminated an acidic solution of silver chloride that was connected to platinum electrodes which generated a voltage and current.1&#160;Many discoveries and advances were made in the late 19th and first half the 20th century, and it was only in 1954 that the first practical solar cell was built by Bell Laboratories. Starting in the 1950s, solar cells were used to power satellites in space.2
Solar cells are electrical devices that utilize light to create a current. This video demonstrates preparation and testing of one such type of cell, the dye-sensitized solar cell (DSSC). First invented at UC Berkeley by Brian O&#39;Regan and Michael Gr&#228;tzel, Gr&#228;tzel pursued this work at the &#201;cole Polytechnique F&#233;d&#233;rale de Lausanne in Switzerland, culminating in the first highly efficient DSSC in 1991.3&#160;These solar cells, like plants, use a dye to help harness energy from the sun.

Dye-sensitized Solar Cells: Principle, Fabrication and Performance

Capteurs solaires teintés

Source: Tamara M. Powers, Department of Chemistry, Texas A&#38;M University
Today&#39;s modern world requires the use of a large amount of energy. While ...

Synthesis of an Oxygen-Carrying Cobalt(II) Complex

Source: Deepika Das, Tamara M. Powers, Department of Chemistry, Texas A&#38;M University
Bioinorganic chemistry is the field of study that investigates the role that metals play in biology. Approximately half of all proteins contain metals and it is estimated that up to one third of all proteins rely on metal-containing active sites to function. Proteins that feature metals, called metalloproteins, play a vital role in a variety of cell functions that are necessary for life. Metalloproteins have intrigued and inspired synthetic inorganic chemists for decades, and many research groups have dedicated their programs to modeling the chemistry of metal-containing active sites in proteins through the study of coordination compounds.
The transport of O2 is a vital process for living organisms. O2-transport metalloproteins are responsible for binding, transporting, and releasing oxygen, which can then be used for life processes such as respiration. The oxygen-carrying cobalt coordination complex, [N,N&#39;-bis(salicylaldehyde)ethylenediimino]cobalt(II) [Co(salen)]2&#160;has been studied extensively to gain understanding about how metal complexes reversibly bind O2.1
In this experiment, we will synthesize [Co(salen)]2 and study its reversible reaction with O2 in the presence of dimethylsulfoxide (DMSO). First, we will quantify the amount of O2 consumed upon exposure of [Co(salen)]2 to DMSO. We will then visually observe the release of O2 from the [Co(salen)]2-O2 adduct by exposing the solid to CHCl3.

Synthesis of an Oxygen-Carrying [Cosalen]2 Complex

Synthèse d'un complexe de cobalt(II) porteur d'oxygène

Source: Deepika Das, Tamara M. Powers, Department of Chemistry, Texas A&#38;M University
Bioinorganic chemistry is the field of study that investigates ...

Photochemical Initiation Of Radical Polymerization Reactions

Source: David C. Powers, Tamara M. Powers, Texas A&#38;M
In this video, we will carry out the photochemically initiated polymerization of styrene to generate polystyrene, which is an important commodity plastic. We will learn the fundamentals of photochemistry and use simple photochemistry to initiate radical polymerization reactions. Specifically, in this module we will examine the photochemistry of benzoyl peroxide and its role as a photo-initiator of styrene polymerization reactions. In the described experiments, we will investigate the role of wavelength, photon absorption, and excited state structure on the efficiency (measured as quantum yield) of photochemical reactions.

Initiation photochimique des réactions de polymérisation radicalaire

Source: David C. Powers, Tamara M. Powers, Texas A&#38;M
In this video, we will carry out the photochemically initiated polymerization of styrene to ...

Education Inorganic Chemistry

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Education Inorganic Chemistry

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