Physical organic chemistry

Source: Wikipedia, the free encyclopedia.

Physical organic chemistry, a term coined by

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.

Application

Physical organic chemists use

enzymology, and chemical biology, as well as to commercial enterprises involving process chemistry, chemical engineering, materials science and nanotechnology, and pharmacology in drug discovery
by design.

Scope

Physical organic chemistry is the study of the relationship between structure and reactivity of

organic molecules and provides a theoretical framework that interprets how structure influences both mechanisms and rates of organic reactions. It can be thought of as a subfield that bridges organic chemistry with physical chemistry
.

Physical organic chemists use both experimental and theoretical disciplines such as

organic reactions and the relative chemical stability of the starting materials, transition states, and products.[1][page needed] Chemists in this field work to understand the physical underpinnings of modern organic chemistry, and therefore physical organic chemistry has applications in specialized areas including polymer chemistry, supramolecular chemistry, electrochemistry, and photochemistry.[1][page needed
]

History

The term physical organic chemistry was itself coined by

Louis Hammett in 1940 when he used the phrase as a title for his textbook.[2]

Chemical structure and thermodynamics

Thermochemistry

Main articles: Thermochemistry and Chemical thermodynamics

Organic chemists use the tools of

Van 't Hoff plot
, to calculate these values.

Empirical constants such as

heats of formation. This type of analysis is often referred to as Benson group increment theory, after chemist Sidney Benson who spent a career developing the concept.[1][page needed] [3][4]

The thermochemistry of reactive intermediates—

carbanions, and radicals—is also of interest to physical organic chemists. Group increment data are available for radical systems.[1][page needed] Carbocation and carbanion stabilities can be assessed using hydride ion affinities and pKa values, respectively.[1][page needed
]

Conformational analysis

One of the primary methods for evaluating chemical stability and energetics is

A-values of various substituents
it is possible to quantitatively predict the preferred conformation of a cyclohexane derivative.

In addition to molecular stability, conformational analysis is used to predict reaction products. One commonly cited example of the use of

conformational analysis
can be used to design molecules that possess enhanced reactivity.

The physical processes which give rise to

bond rotation barriers are complex, and these barriers have been extensively studied through experimental and theoretical methods.[7][8][9] A number of recent articles have investigated the predominance of the steric, electrostatic, and hyperconjugative contributions to rotational barriers in ethane, butane, and more substituted molecules.[10]

Non-covalent interactions

Main article:
Noncovalent bonding
cation demonstrating host–guest chemistry. Cryptands are tricyclic compounds that tightly encapsulate the guest cation via electrostatic interactions
(ion-dipole interaction).

Chemists use the study of intramolecular and intermolecular

cryptands
, which can act as hosts to guest molecules.

Acid–base chemistry

Main article: Acid–base reaction
anion
) via induction and through resonance by delocalizing the negative charge.

The properties of

resonance, hybridization, aromaticity, and solvation
—to predict relative acidities and basicities.

The hard/soft acid/base principle is utilized to predict molecular interactions and reaction direction. In general, interactions between molecules of the same type are preferred. That is, hard acids will associate with hard bases, and soft acids with soft bases. The concept of hard acids and bases is often exploited in the synthesis of inorganic coordination complexes.

Kinetics

Main article: Chemical kinetics

Physical organic chemists use the mathematical foundation of chemical kinetics to study the rates of reactions and reaction mechanisms. Unlike thermodynamics, which is concerned with the relative stabilities of the products and reactants (ΔG°) and their equilibrium concentrations, the study of kinetics focuses on the

Curtin-Hammett principle, and the theory of microscopic reversibility are often applied to organic chemistry. Chemists have also used the principle of thermodynamic versus kinetic control
to influence reaction products.

Rate laws

Main article: Rate equation

The study of

spectroscopic
techniques. In most cases, the determination of rate equations is simplified by adding a large excess ("flooding") all but one of the reactants.

Catalysis

Main article: Catalysis
intermediates
.

The study of

catalyst participates in the chemical reaction but is not consumed in the process.[12][page needed] A catalyst lowers the activation energy barrier (ΔG‡), increasing the rate of a reaction by either stabilizing the transition state structure or destabilizing a key reaction intermediate, and as only a small amount of catalyst is required it can provide economic access to otherwise expensive or difficult to synthesize organic molecules. Catalysts may also influence a reaction rate by changing the mechanism of the reaction.[1][page needed
]

Kinetic isotope effect

Main article: Kinetic isotope effect

Although a rate law provides the stoichiometry of the

vibrational state of the associated molecules, shorter and stronger bonds in molecules with heavier isotopes and longer, weaker bonds in molecules with light isotopes.[6][page needed
] Because vibrational motions will often change during a course of a reaction, due to the making and breaking of bonds, the frequencies will be affected, and the substitution of an isotope can provide insight into the reaction mechanism and rate law.

Substituent effects

The study of how substituents affect the reactivity of a molecule or the rate of reactions is of significant interest to chemists. Substituents can exert an effect through both

electron-donating groups would be expected to increase the rate of the reaction.[1][page needed
]

Other

Grunwald-Winstein Plot provides quantitative insight into these effects.[1][page needed] [13]

Solvent effects

Main article: Solvent effects

Solvents can have a powerful effect on solubility, stability, and reaction rate. A change in solvent can also allow a chemist to influence the thermodynamic or kinetic control of the reaction. Reactions proceed at different rates in different solvents due to the change in charge distribution during a chemical transformation. Solvent effects may operate on the ground state and/or transition state structures.[1][page needed
]

An example of the effect of solvent on organic reactions is seen in the

example needed
]

protic solvents, the equilibrium lies towards the keto form as the intramolecular hydrogen bond competes with hydrogen bonds originating from the solvent.[15][non-primary source needed][non-primary source needed] [16][non-primary source needed][non-primary source needed] [17][non-primary source needed][non-primary source needed
]

THF
.

A modern example of the study of

asymmetric synthesis
.

Quantum chemistry

Main article: Quantum chemistry

Many aspects of the structure-reactivity relationship in organic chemistry can be rationalized through

wavefunction
through the use of mathematical operators.

Time-independent Schrödinger equation (general)

The energy associated with a particular

electrons
and are treated as point charges in practical applications of quantum chemistry.

Due to complex interactions which arise from electron-electron repulsion, algebraic solutions of the Schrödinger equation are only possible for systems with one electron such as the

molecular orbitals stretching through the entire molecule rather than two isolated double bonds as predicted by a simple Lewis structure.[citation needed
]

A complete electronic structure offers great predictive power for organic transformations and dynamics, especially in cases concerning

Diels Alder cycloadditions.[19]

Chromium's unoccupied d-orbitals mediate electron withdrawal from benzene, greatly enhancing its electrophilicity.

Quantum chemistry can also provide insight into the mechanism of an organic transformation without the collection of any experimental data. Because wavefunctions provide the total energy of a given molecular state, guessed molecular geometries can be optimized to give relaxed molecular structures very similar to those found through experimental methods.[20][page needed] Reaction coordinates can then be simulated, and transition state structures solved. Solving a complete energy surface for a given reaction is therefore possible, and such calculations have been applied to many problems in organic chemistry where kinetic data is unavailable or difficult to acquire.[1][page needed]

Spectroscopy, spectrometry, and crystallography

Physical organic chemistry often entails the identification of molecular structure, dynamics, and the concentration of reactants in the course of a reaction. The interaction of molecules with light can afford a wealth of data about such properties through nondestructive spectroscopic experiments, with light absorbed when the energy of a photon matches the difference in energy between two states in a molecule and emitted when an excited state in a molecule collapses to a lower energy state. Spectroscopic techniques are broadly classified by the type of excitation being probed, such as vibrational, rotational, electronic, nuclear magnetic resonance (NMR), and electron paramagnetic resonance spectroscopy. In addition to spectroscopic data, structure determination is often aided by complementary data collected from X-Ray diffraction and mass spectrometric experiments.[21][page needed]

NMR and EPR spectroscopy

Main articles: Nuclear magnetic resonance and Electron paramagnetic resonance
Splitting of nuclei spin states in an external magnetic field

One of the most powerful tools in physical organic chemistry is

nuclear Overhauser effect experiments, and through-bond spin-spin coupling through homonuclear correlation spectroscopy.[23] In addition to the spin excitation properties of nuclei, it is also possible to study the properties of organic radicals through the same fundamental technique. Unpaired electrons also have a net spin, and an external magnetic field allows for the extraction of similar information through electron paramagnetic resonance (EPR) spectroscopy.[1][page needed
]

Vibrational spectroscopy

Main article: Infrared spectroscopy
The first eight states in a quantum harmonic oscillator. The horizontal axis shows the position x, and the vertical axis shows the energy. Note the even spacing of the energy levels: all excitations between adjacent states require the same energy, and therefore absorb the same wavelength of light

extrasolar planetary atmospheres, and planetary surfaces
.

Electronic excitation spectroscopy

Main article:
Ultraviolet-visible spectroscopy

organic molecules color. A detailed understanding of an electronic structure is therefore helpful in explaining electronic excitations, and through careful control of molecular structure it is possible to tune the HOMO-LUMO gap to give desired colors and excited state properties.[24]

Mass spectrometry

Main article: Mass spectrometry

ionized and the resulting ionic species are accelerated by an applied electric field into a magnetic field. The deflection imparted by the magnetic field, often combined with the time it takes for the molecule to reach a detector, is then used to calculate the mass of the molecule. Often in the course of sample ionization large molecules break apart, and the resulting data show a parent mass and a number of smaller fragment masses; such fragmentation can give rich insight into the sequence of proteins and nucleic acid polymers. In addition to the mass of a molecule and its fragments, the distribution of isotopic variant masses can also be determined and the qualitative presence of certain elements identified due to their characteristic natural isotope distribution. The ratio of fragment mass population to the parent ion population can be compared against a library of empirical fragmentation data and matched to a known molecular structure.[25] Combined gas chromatography and mass spectrometry
is used to qualitatively identify molecules and quantitatively measure concentration with great precision and accuracy, and is widely used to test for small quantities of biomolecules and illicit narcotics in blood samples. For synthetic organic chemists it is a useful tool for the characterization of new compounds and reaction products.

Crystallography

Single crystal structure of a fullerene caught in molecular tweezers.
Main article: Crystallography

Unlike spectroscopic methods,

NMR active nucleus such as oxygen. Indeed, before x-ray structural determination methods were made available in the early 20th century all organic structures were entirely conjectural: tetrahedral carbon, for example, was only confirmed by the crystal structure of diamond,[26] and the delocalized structure of benzene was confirmed by the crystal structure of hexamethylbenzene.[27] While crystallography provides organic chemists with highly satisfying data, it is not an everyday technique in organic chemistry because a perfect single crystal of a target compound must be grown. Only complex molecules, for which NMR data cannot be unambiguously interpreted, require this technique. In the example below, the structure of the host–guest complex would have been quite difficult to solve without a single crystal structure: there are no protons on the fullerene, and with no covalent bonds between the two halves of the organic complex spectroscopy alone was unable to prove the hypothesized structure.[citation needed
]

See also

References

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  22. ^ James Keeler. "NMR and energy levels (Ch.2)" (PDF). Understanding NMR Spectroscopy. University of California, Irvine. Retrieved 2013-10-26.
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  24. ^ Reusch, William. "Visible and Ultraviolet Spectroscopy". Michigan State University Website. Michigan State University. Retrieved 26 October 2013.
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Further reading

General

History

Thermochemistry
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