Fluxional molecule

Last updated

In chemistry and molecular physics, fluxional (or non-rigid) molecules are molecules that undergo dynamics such that some or all of their atoms interchange between symmetry-equivalent positions. [1] Because virtually all molecules are fluxional in some respects, e.g. bond rotations in most organic compounds, the term fluxional depends on the context and the method used to assess the dynamics. Often, a molecule is considered fluxional if its spectroscopic signature exhibits line-broadening (beyond that dictated by the Heisenberg uncertainty principle) due to chemical exchange. [2] In some cases, where the rates are slow, fluxionality is not detected spectroscopically, but by isotopic labeling and other methods. [3]

Contents

Spectroscopic studies

Many organometallic compounds exhibit fluxionality. [4] Fluxionality is, however, pervasive.

NMR spectroscopy

Temperature dependent changes in the NMR spectra result from dynamics associated with the fluxional molecules when those dynamics proceed at rates comparable to the frequency differences observed by NMR. The experiment is called DNMR and typically involves recording spectra at various temperatures. In the ideal case, low temperature spectra can be assigned to the "slow exchange limit", whereas spectra recorded at higher temperatures correspond to molecules at "fast exchange limit". Typically, high temperature spectra are simpler than those recorded at low temperatures, since at high temperatures, equivalent sites are averaged out. Prior to the advent of DNMR, kinetics of reactions were measured on non-equilibrium mixtures, monitoring the approach to equilibrium.

Many molecular processes exhibit fluxionality that can be probed on the NMR time scale. [5] Beyond the examples highlighted below, other classic examples include the Cope rearrangement in bullvalene and the chair inversion in cyclohexane.

For processes that are too slow for traditional DNMR analysis, the technique spin saturation transfer (SST, also called EXSY for exchange spectroscopy) is applicable. This magnetization transfer technique gives rate information, provided that the rates exceed 1/T1. [6]

IR spectroscopy

Although less common, some dynamics are also observable on the time-scale of IR spectroscopy. One example is electron transfer in a mixed-valence dimer of metal clusters. Application of the equation for coalescence of two signals separated by 10 cm−1 gives the following result: [7]

Clearly, processes that induce line-broadening on the IR time-scale must be much more rapid than the cases that exchange on the NMR time scale.

Examples

Cyclohexane chair flip (ring inversion) reaction via boat conformation Cyclohexane ring flip.svg
Cyclohexane chair flip (ring inversion) reaction via boat conformation

The interconversion of equivalent chair conformers of cyclohexane (and many other cyclic compounds) is called ring flipping. Carbon–hydrogen bonds that are axial in one configuration become equatorial in the other, and vice versa. At room temperature the two chair conformations rapidly equilibrate. The proton- and carbon-13 NMR spectra of cyclohexane show each only singlets near room temperature. At low temperatures, the singlet in the 1H NMR spectrum decoalesces but the 13C NMR spectrum remains unchanged. [9]

Berry pseudorotation of pentacoordinate compounds

Iron-pentacarbonyl-Berry-mechanism Iron-pentacarbonyl-Berry-mechanism.png
Iron-pentacarbonyl-Berry-mechanism

A prototypical fluxional molecule is phosphorus pentafluoride. Its 19F NMR spectrum consists of a 31P-coupled doublet, indicating that the equatorial and axial fluorine centers interchange rapidly on the NMR timescale. Fluorine-19 NMR spectroscopy, even at temperatures as low as −100 °C, fails to distinguish the axial from the equatorial fluorine environments. The apparent equivalency arises from the low barrier for pseudorotation via the Berry mechanism, by which the axial and equatorial fluorine atoms rapidly exchange positions. [10] Iron pentacarbonyl (Fe(CO)5) follows the pattern set for PF5: only one signal is observed in the 13C NMR spectrum near room temperature) whereas at low temperatures, two signals in a 2:3 ratio can be resolved. In sulfur tetrafluoride (SF4), a similar pattern is observed even though this compound has only four ligands.

A well-studied fluxional ion is the methanium ion, CH+
5. [11] Even at absolute zero there is no rigid molecular structure; the H atoms are always in motion. More precisely, the spatial distribution of protons in CH+
5 is many times broader than its parent molecule CH4, methane. [12] [13]

Six-coordinate species

While nonrigidity is common for pentacoordinate species, six-coordinate species typically adopt a more rigid octahedral molecular geometry, featuring close-packed array of six ligating atoms surrounding a central atom. Such compounds do rearrange intramolecularly via the Ray-Dutt twist and the Bailar twist, but the barriers for these processes are typically high such that these processes do not lead to line broadening. For some compounds, dynamics occur via dissociation of a ligand, giving a pentacoordinate intermediate, which is subject to the mechanisms discussed above. Yet another mechanism, exhibited by Fe(CO)4(SiMe3)2 and related hydride complexes, is intramolecular scrambling of ligands over the faces of the tetrahedron defined by the four CO ligands. [14]

Dimethylformamide

A classic example of a fluxional molecule is dimethylformamide (DMF). [15]

DmfDNMR.png

At temperatures near 100 °C, the 500 MHz 1H NMR spectrum of DMF shows only one signal for the methyl groups. Near room temperature, however, separate signals are seen for the non-equivalent methyl groups. The rate of exchange can be calculated at the temperature where the two signals are just merged. This "coalescence temperature" depends on the measuring field. The relevant equation is

where Δν0 is the difference between the frequencies (in Hz) of the exchanging sites. These frequencies are obtained from the limiting low-temperature NMR spectrum. At these lower temperatures, the dynamics continue, of course, but the contribution of the dynamics to line broadening is negligible.

For example, if Δν0 = 1ppm @ 500 MHz,

(~0.5 millisecond half-life).

"Ring whizzing"

The compound Fe(η5-C5H5)(η1-C5H5)(CO)2 exhibits the phenomenon of "ring whizzing".

The structure of the ring whizzer Fe(e -C5H5) (e -C5H5)(CO)2 Fe Habcd.jpg
The structure of the ring whizzer Fe(η -C5H5) (η -C5H5)(CO)2

At 30 °C, the 1H NMR spectrum shows only two peaks, one typical (δ5.6) of the η5-C5H5 and the other assigned η1-C5H5. The singlet assigned to the η1-C5H5 ligand splits at low temperatures owing to the slow hopping of the Fe center from carbon to carbon in the η1-C5H5 ligand. [16] Two mechanisms have been proposed, with the consensus favoring the 1,2 shift pathway. [17]

See also

Further reading

Related Research Articles

<span class="mw-page-title-main">Inorganic chemistry</span> Field of chemistry

Inorganic chemistry deals with synthesis and behavior of inorganic and organometallic compounds. This field covers chemical compounds that are not carbon-based, which are the subjects of organic chemistry. The distinction between the two disciplines is far from absolute, as there is much overlap in the subdiscipline of organometallic chemistry. It has applications in every aspect of the chemical industry, including catalysis, materials science, pigments, surfactants, coatings, medications, fuels, and agriculture.

Ferrocene is an organometallic compound with the formula Fe(C5H5)2. The molecule is a complex consisting of two cyclopentadienyl rings sandwiching a central iron atom. It is an orange solid with a camphor-like odor that sublimes above room temperature, and is soluble in most organic solvents. It is remarkable for its stability: it is unaffected by air, water, strong bases, and can be heated to 400 °C without decomposition. In oxidizing conditions it can reversibly react with strong acids to form the ferrocenium cation Fe(C5H5)+2. Ferrocene and the ferrocenium cation are sometimes abbreviated as Fc and Fc+ respectively.

<span class="mw-page-title-main">Rotational spectroscopy</span> Spectroscopy of quantized rotational states of gases

Rotational spectroscopy is concerned with the measurement of the energies of transitions between quantized rotational states of molecules in the gas phase. The rotational spectrum of polar molecules can be measured in absorption or emission by microwave spectroscopy or by far infrared spectroscopy. The rotational spectra of non-polar molecules cannot be observed by those methods, but can be observed and measured by Raman spectroscopy. Rotational spectroscopy is sometimes referred to as pure rotational spectroscopy to distinguish it from rotational-vibrational spectroscopy where changes in rotational energy occur together with changes in vibrational energy, and also from ro-vibronic spectroscopy where rotational, vibrational and electronic energy changes occur simultaneously.

<span class="mw-page-title-main">Nuclear magnetic resonance spectroscopy</span> Laboratory technique

Nuclear magnetic resonance spectroscopy, most commonly known as NMR spectroscopy or magnetic resonance spectroscopy (MRS), is a spectroscopic technique based on re-orientation of atomic nuclei with non-zero nuclear spins in an external magnetic field. This re-orientation occurs with absorption of electromagnetic radiation in the radio frequency region from roughly 4 to 900 MHz, which depends on the isotopic nature of the nucleus and increased proportionally to the strength of the external magnetic field. Notably, the resonance frequency of each NMR-active nucleus depends on its chemical environment. As a result, NMR spectra provide information about individual functional groups present in the sample, as well as about connections between nearby nuclei in the same molecule. As the NMR spectra are unique or highly characteristic to individual compounds and functional groups, NMR spectroscopy is one of the most important methods to identify molecular structures, particularly of organic compounds.

<span class="mw-page-title-main">Carbonium ion</span> Any cation that has a pentavalent carbon atom

In chemistry, a carbonium ion is a cation that has a pentacoordinated carbon atom. They are a type of carbocation. In older literature, the name "carbonium ion" was used for what is today called carbenium. Carbonium ions charge is delocalized in three-center, two-electron bonds. The more stable members are often bi- or polycyclic.

<span class="mw-page-title-main">2-Norbornyl cation</span> Term in organic chemistry

In organic chemistry, the term 2-norbornyl cation describes a carbonium ionic derivative of norbornane. A salt of the 2-norbornyl cation was crystallized and characterized by X-ray crystallography confirmed the non-classical structure.

Bullvalene is a hydrocarbon with the chemical formula C10H10. The molecule has a cage-like structure formed by the fusion of one cyclopropane and three cyclohepta-1,4-diene rings. Bullvalene is unusual as an organic molecule due to the C−C and C=C bonds forming and breaking rapidly on the NMR timescale; this property makes it a fluxional molecule.

In chemistry, a pseudorotation is a set of intramolecular movements of attached groups on a highly symmetric molecule, leading to a molecule indistinguishable from the initial one. The International Union of Pure and Applied Chemistry (IUPAC) defines a pseudorotation as a "stereoisomerization resulting in a structure that appears to have been produced by rotation of the entire initial molecule", the result of which is a "product" that is "superposable on the initial one, unless different positions are distinguished by substitution, including isotopic substitution."

<span class="mw-page-title-main">Hapticity</span> Number of contiguous atoms in a ligand that bond to the central atom in a coordination complex

In coordination chemistry, hapticity is the coordination of a ligand to a metal center via an uninterrupted and contiguous series of atoms. The hapticity of a ligand is described with the Greek letter η ('eta'). For example, η2 describes a ligand that coordinates through 2 contiguous atoms. In general the η-notation only applies when multiple atoms are coordinated. In addition, if the ligand coordinates through multiple atoms that are not contiguous then this is considered denticity, and the κ-notation is used once again. When naming complexes care should be taken not to confuse η with μ ('mu'), which relates to bridging ligands.

Uranocene, U(C8H8)2, is an organouranium compound composed of a uranium atom sandwiched between two cyclooctatetraenide rings. It was one of the first organoactinide compounds to be synthesized. It is a green air-sensitive solid that dissolves in organic solvents. Uranocene, a member of the "actinocenes," a group of metallocenes incorporating elements from the actinide series. It is the most studied bis[8]annulene-metal system, although it has no known practical applications.

<span class="mw-page-title-main">Molecular symmetry</span> Symmetry of molecules of chemical compounds

In chemistry, molecular symmetry describes the symmetry present in molecules and the classification of these molecules according to their symmetry. Molecular symmetry is a fundamental concept in chemistry, as it can be used to predict or explain many of a molecule's chemical properties, such as whether or not it has a dipole moment, as well as its allowed spectroscopic transitions. To do this it is necessary to use group theory. This involves classifying the states of the molecule using the irreducible representations from the character table of the symmetry group of the molecule. Symmetry is useful in the study of molecular orbitals, with applications to the Hückel method, to ligand field theory, and to the Woodward-Hoffmann rules. Many university level textbooks on physical chemistry, quantum chemistry, spectroscopy and inorganic chemistry discuss symmetry. Another framework on a larger scale is the use of crystal systems to describe crystallographic symmetry in bulk materials.

Physical organic chemistry, a term coined by Louis Hammett in 1940, refers to a discipline of organic chemistry that focuses on the relationship between chemical structures and reactivity, in particular, applying experimental tools of physical chemistry to the study of organic molecules. Specific focal points of study include the rates of organic reactions, the relative chemical stabilities of the starting materials, reactive intermediates, transition states, and products of chemical reactions, and non-covalent aspects of solvation and molecular interactions that influence chemical reactivity. Such studies provide theoretical and practical frameworks to understand how changes in structure in solution or solid-state contexts impact reaction mechanism and rate for each organic reaction of interest.

Herbert Sander Gutowsky was an American chemist who was a professor of chemistry at the University of Illinois Urbana-Champaign. Gutowsky was the first to apply nuclear magnetic resonance (NMR) methods to the field of chemistry. He used nuclear magnetic resonance spectroscopy to determine the structure of molecules. His pioneering work developed experimental control of NMR as a scientific instrument, connected experimental observations with theoretical models, and made NMR one of the most effective analytical tools for analysis of molecular structure and dynamics in liquids, solids, and gases, used in chemical and medical research, His work was relevant to the solving of problems in chemistry, biochemistry, and materials science, and has influenced many of the subfields of more recent NMR spectroscopy.

<span class="mw-page-title-main">Seesaw molecular geometry</span> Structural molecular geometry

Disphenoidal or seesaw is a type of molecular geometry where there are four bonds to a central atom with overall C2v molecular symmetry. The name "seesaw" comes from the observation that it looks like a playground seesaw. Most commonly, four bonds to a central atom result in tetrahedral or, less commonly, square planar geometry.

<span class="mw-page-title-main">Rhodocene</span> Organometallic chemical compound

Rhodocene is a chemical compound with the formula [Rh(C5H5)2]. Each molecule contains an atom of rhodium bound between two planar aromatic systems of five carbon atoms known as cyclopentadienyl rings in a sandwich arrangement. It is an organometallic compound as it has (haptic) covalent rhodium–carbon bonds. The [Rh(C5H5)2] radical is found above 150 °C (302 °F) or when trapped by cooling to liquid nitrogen temperatures (−196 °C [−321 °F]). At room temperature, pairs of these radicals join via their cyclopentadienyl rings to form a dimer, a yellow solid.

Boron monofluoride or fluoroborylene is a chemical compound with the formula BF, one atom of boron and one of fluorine. It is an unstable gas, but it is a stable ligand on transition metals, in the same way as carbon monoxide. It is a subhalide, containing fewer than the normal number of fluorine atoms, compared with boron trifluoride. It can also be called a borylene, as it contains boron with two unshared electrons. BF is isoelectronic with carbon monoxide and dinitrogen; each molecule has 14 electrons.

<span class="mw-page-title-main">Cyclopentadienyliron dicarbonyl dimer</span> Chemical compound

Cyclopentadienyliron dicarbonyl dimer is an organometallic compound with the formula [(η5-C5H5)Fe(CO)2]2, often abbreviated to Cp2Fe2(CO)4, [CpFe(CO)2]2 or even Fp2, with the colloquial name "fip dimer". It is a dark reddish-purple crystalline solid, which is readily soluble in moderately polar organic solvents such as chloroform and pyridine, but less soluble in carbon tetrachloride and carbon disulfide. Cp2Fe2(CO)4 is insoluble in but stable toward water. Cp2Fe2(CO)4 is reasonably stable to storage under air and serves as a convenient starting material for accessing other Fp (CpFe(CO)2) derivatives (described below).

Vibronic spectroscopy is a branch of molecular spectroscopy concerned with vibronic transitions: the simultaneous changes in electronic and vibrational energy levels of a molecule due to the absorption or emission of a photon of the appropriate energy. In the gas phase, vibronic transitions are accompanied by changes in rotational energy also.

<span class="mw-page-title-main">Spectral line shape</span> Feature observed in spectroscopy

Spectral line shape or spectral line profile describes the form of an electromagnetic spectrum in the vicinity of a spectral line – a region of stronger or weaker intensity in the spectrum. Ideal line shapes include Lorentzian, Gaussian and Voigt functions, whose parameters are the line position, maximum height and half-width. Actual line shapes are determined principally by Doppler, collision and proximity broadening. For each system the half-width of the shape function varies with temperature, pressure and phase. A knowledge of shape function is needed for spectroscopic curve fitting and deconvolution.

Neon compounds are chemical compounds containing the element neon (Ne) with other molecules or elements from the periodic table. Compounds of the noble gas neon were believed not to exist, but there are now known to be molecular ions containing neon, as well as temporary excited neon-containing molecules called excimers. Several neutral neon molecules have also been predicted to be stable, but are yet to be discovered in nature. Neon has been shown to crystallize with other substances and form clathrates or Van der Waals solids.

References

  1. ↑ "Fluxional". IUPAC Gold Book. 2014. doi: 10.1351/goldbook.F02463 .
  2. ↑ Drago, Russell S. (1977). Physical Methods in Chemistry (2nd ed.). Philadelphia: W. B. Saunders. ISBN   0-7216-3184-3.
  3. ↑ J. Sandström (1982). Dynamic NMR Spectroscopy. Academic Press.
  4. ↑ John W. Faller "Stereochemical Nonrigidity of Organometallic Complexes" Encyclopedia of Inorganic and Bioinorganic Chemistry 2011, Wiley-VCH, Weinheim. doi : 10.1002/9781119951438.eibc0211
  5. ↑ Bryant, Robert G. (1983). "The NMR time scale". Journal of Chemical Education. 60 (11): 933. Bibcode:1983JChEd..60..933B. doi:10.1021/ed060p933.
  6. ↑ Jarek, R. L.; Flesher, R. J.; Shin, S. K. (1997). "Kinetics of Internal Rotation of N,N-Dimethylacetamide: A Spin-Saturation Transfer Experiment". Journal of Chemical Education. 74 (8): 978. Bibcode:1997JChEd..74..978J. doi:10.1021/ed074p978.
  7. ↑ Casey H. Londergan; Clifford P. Kubiak (2003). "Electron Transfer and Dynamic Infrared-Band Coalescence: It Looks Like Dynamic NMR Spectroscopy, but a Billion Times Faster". Chemistry: A European Journal. 9 (24): 5969ff. doi:10.1002/chem.200305028. PMID   14679508.
  8. ↑ J, Clayden (2003). Organic chemistry (2nd ed.). Oxford. p. 373. ISBN   9780191666216.{{cite book}}: CS1 maint: location missing publisher (link)
  9. ↑ Gill, G.; Pawar, D. M.; Noe, E. A. (2005). "Conformational Study of cis-1,4-Di-tert-butylcyclohexane by Dynamic NMR Spectroscopy and Computational Methods. Observation of Chair and Twist-Boat Conformations". J. Org. Chem. 70 (26): 10726–10731. doi:10.1021/jo051654z. PMID   16355992.
  10. ↑ Gutowsky, H. S.; McCall, D. W.; Slichter, C. P. (1953). "Nuclear Magnetic Resonance Multiplets in Liquids". J. Chem. Phys. 21 (2): 279. Bibcode:1953JChPh..21..279G. doi:10.1063/1.1698874.
  11. ↑ Asvany, O.; Kumar P, P.; Redlich, B.; Hegemann, I.; Schlemmer, S.; Marx, D. (2005). "Understanding the Infrared Spectrum of Bare CH5+". Science . 309 (5738): 1219–1222. Bibcode:2005Sci...309.1219A. doi: 10.1126/science.1113729 . PMID   15994376. S2CID   28745636.
  12. ↑ Thompson, KC; Crittenden, DL; Jordan, MJ (2005). "CH5+: Chemistry's chameleon unmasked". J. Am. Chem. Soc. 127 (13): 4954–4958. doi:10.1021/ja0482280. PMID   15796561.
  13. ↑ For an animation of the dynamics of CH5+, see http://www.theochem.ruhr-uni-bochum.de/research/marx/topic4b.en.html Archived 2007-12-24 at the Wayback Machine
  14. ↑ Vancea, L.; Bennett, M. J.; Jones, C. E.; Smith, R. A.; Graham, W. A. G. (1977). "Stereochemically Nonrigid Six-Coordinate Metal Carbonyl Complexes. 1. Polytopal Rearrangement and X-Ray Structure of Tetracarbonylbis(trimethylsilyl)iron". Inorganic Chemistry. 16 (4): 897–902. doi:10.1021/ic50170a035.
  15. ↑ H. S. Gutowsky; C. H. Holm (1956). "Rate Processes and Nuclear Magnetic Resonance Spectra. II. Hindered Internal Rotation of Amides". J. Chem. Phys. 25 (6): 1228–1234. Bibcode:1956JChPh..25.1228G. doi:10.1063/1.1743184.
  16. ↑ Bennett, Jr. M. J.; Cotton, F. A.; Davison, A.; Faller, J. W.; Lippard, S. J.; Morehouse, S. M. (1966). "Stereochemically Nonrigid Organometallic Compounds. I. π-Cyclopentadienyliron Dicarbonyl σ-Cyclopentadiene". J. Am. Chem. Soc. 1966 (88): 4371. doi:10.1021/ja00971a012.
  17. ↑ Robert B. Jordan, Reaction Mechanisms of Inorganic and Organometallic Systems (Topics in Inorganic Chemistry), 2007. ISBN   978-0195301007
This page is based on this Wikipedia article
Text is available under the CC BY-SA 4.0 license; additional terms may apply.
Images, videos and audio are available under their respective licenses.