In thermodynamics and physical chemistry, thermochemistry is the study of the energy evolved or absorbed in chemical reactions and any physical transformations, such as melting and boiling. Thermochemistry, generally, is concerned with the energy exchange accompanying transformations, such as mixing, phase transitions, chemical reactions, and including calculations of such quantities as the heat capacity, heat of combustion, heat of formation, enthalpy, and free energy.
History
Thermochemistry rests on two generalizations. Stated in modern terms, they are as follows:
1. Lavoisier and Laplace’s law (1780): The energy change accompanying any transformation is equal and opposite to energy change accompanying the reverse process.
2. Hess's law (1840): The energy change accompanying any transformation is the same whether the process occurs in one step or many.
These statements preceded the first law of thermodynamics (1845) and helped in its formulation.
Edward Diaz and Hess also investigated specific heat and latent heat, although it was Joseph Black who made the most important contributions to the development of latent energy changes.
Gustav Kirchhoff showed in 1858 that the variation of the heat of reaction is given by the difference in heat capacity between products and reactants: dΔH / dT = ΔCp. Integration of this equation permits the evaluation of the heat of reaction at one temperature from measurements at another temperature.
Calorimetry
The measurement of heat changes is performed using calorimetry, usually an enclosed chamber within which the change to be examined occurs. The temperature of the chamber is monitored either using a thermometer or thermocouple, and the temperature plotted against time to give a graph from which fundamental quantities can be calculated. Modern calorimeters are frequently supplied with automatic devices to provide a quick read-out of information, one example being the DSC or differential scanning calorimeter.
Systems
Several thermodynamic definitions are very useful in thermochemistry. A system is the specific portion of the universe that is being studied. Everything outside the system is considered the surrounding or environment. A system may be: an isolated system — when it cannot exchange energy or matter with the surroundings, as with an insulated bomb reactor; a closed system — when it can exchange energy but not matter with the surroundings, as with a steam radiator; an open system — when it can exchange both matter and energy with the surroundings, as with a pot of boiling water.
Processes
A system undergoes a process when one or more of its properties changes. A process relates to the change of state. An isothermal (same temperature) process occurs when temperature of the system remains constant. An isobaric (same pressure) process occurs when the pressure of the system remains constant. An adiabatic (no heat exchange) process occurs when no heat exchange occurs.
Saturday, October 9, 2010
Stereochemistry
Stereochemistry, a subdiscipline of chemistry, involves the study of the relative spatial arrangement of atoms within molecules. An important branch of stereochemistry is the study of chiral molecules.
Stereochemistry is also known as 3D chemistry because the prefix "stereo-" means "three-dimensionality"
Stereochemistry is a hugely important facet of chemistry and the study of stereochemical problems spans the entire range of organic, inorganic, biological, physical and supramolecular chemistries.
Stereochemistry includes methods for determining and describing these relationships; the effect on the physical or biological properties these relationships impart upon the molecules in question, and the manner in which these relationships influence the reactivity of the molecules in question (dynamic stereochemistry).
Louis Pasteur could rightly be described as the first stereochemist, having observed in 1849 that salts of tartaric acid collected from wine production vessels could rotate plane polarized light, but that salts from other sources did not. This property, the only physical property in which the two types of tartrate salts differed, is due to optical isomerism. In 1874, Jacobus Henricus van 't Hoff and Joseph Le Bel explained optical activity in terms of the tetrahedral arrangement of the atoms bound to carbon.
One of the most infamous demonstrations of the significance of stereochemistry was the thalidomide disaster. Thalidomide is a drug, first prepared in 1957 in Germany, prescribed for treating morning sickness in pregnant women. The drug however was discovered to cause deformation in babies. It was discovered that one optical isomer of the drug was safe while the other had teratogenic effects, causing serious genetic damage to early embryonic growth and development. In the human body, thalidomide undergoes racemization: even if only one of the two stereoisomers is ingested, the other one is produced. Thalidomide is currently used as a treatment for leprosy and must be used with contraceptives in women to prevent pregnancy-related deformations. This disaster was a driving force behind requiring strict testing of drugs before making them available to the public.
Cahn-Ingold-Prelog priority rules are part of a system for describing a molecule's stereochemistry. They rank the atoms around a stereocenter in a standard way, allowing the relative position of these atoms in the molecule to be described unambiguously. A Fischer projection is a simplified way to depict the stereochemistry around a stereocenter.
Types of stereoisomerism are:
* Atropisomerism
* Cis-trans isomerism
* Conformational isomerism
* Diastereomers
* Enantiomers
* Rotamers
Stereochemistry is also known as 3D chemistry because the prefix "stereo-" means "three-dimensionality"
Stereochemistry is a hugely important facet of chemistry and the study of stereochemical problems spans the entire range of organic, inorganic, biological, physical and supramolecular chemistries.
Stereochemistry includes methods for determining and describing these relationships; the effect on the physical or biological properties these relationships impart upon the molecules in question, and the manner in which these relationships influence the reactivity of the molecules in question (dynamic stereochemistry).
Louis Pasteur could rightly be described as the first stereochemist, having observed in 1849 that salts of tartaric acid collected from wine production vessels could rotate plane polarized light, but that salts from other sources did not. This property, the only physical property in which the two types of tartrate salts differed, is due to optical isomerism. In 1874, Jacobus Henricus van 't Hoff and Joseph Le Bel explained optical activity in terms of the tetrahedral arrangement of the atoms bound to carbon.
One of the most infamous demonstrations of the significance of stereochemistry was the thalidomide disaster. Thalidomide is a drug, first prepared in 1957 in Germany, prescribed for treating morning sickness in pregnant women. The drug however was discovered to cause deformation in babies. It was discovered that one optical isomer of the drug was safe while the other had teratogenic effects, causing serious genetic damage to early embryonic growth and development. In the human body, thalidomide undergoes racemization: even if only one of the two stereoisomers is ingested, the other one is produced. Thalidomide is currently used as a treatment for leprosy and must be used with contraceptives in women to prevent pregnancy-related deformations. This disaster was a driving force behind requiring strict testing of drugs before making them available to the public.
Cahn-Ingold-Prelog priority rules are part of a system for describing a molecule's stereochemistry. They rank the atoms around a stereocenter in a standard way, allowing the relative position of these atoms in the molecule to be described unambiguously. A Fischer projection is a simplified way to depict the stereochemistry around a stereocenter.
Types of stereoisomerism are:
* Atropisomerism
* Cis-trans isomerism
* Conformational isomerism
* Diastereomers
* Enantiomers
* Rotamers
Spectroscopy
Spectroscopy was originally the study of the interaction between radiation and matter as a function of wavelength (λ). Historically, spectroscopy referred to the use of visible light dispersed according to its wavelength, e.g. by a prism. Later the concept was expanded greatly to comprise any measurement of a quantity as a function of either wavelength or frequency. Thus, it also can refer to a response to an alternating field or varying frequency (ν). A further extension of the scope of the definition added energy (E) as a variable, once the very close relationship E = hν for photons was realized (h is the Planck constant). A plot of the response as a function of wavelength—or more commonly frequency—is referred to as a spectrum; see also spectral linewidth.
Spectrometry is the spectroscopic technique used to assess the concentration or amount of a given chemical (atomic, molecular, or ionic) species. In this case, the instrument that performs such measurements is a spectrometer, spectrophotometer, or spectrograph.
Spectroscopy/spectrometry is often used in physical and analytical chemistry for the identification of substances through the spectrum emitted from or absorbed by them.
Spectroscopy/spectrometry is also heavily used in astronomy and remote sensing. Most large telescopes have spectrometers, which are used either to measure the chemical composition and physical properties of astronomical objects or to measure their velocities from the Doppler shift of their spectral lines.
Classification of methods
Nature of excitation measured
The type of spectroscopy depends on the physical quantity measured. Normally, the quantity that is measured is an intensity, of energy either absorbed or produced.
- Electromagnetic spectroscopy involves interactions of matter with electromagnetic radiation, such as light.
- Electron spectroscopy involves interactions with electron beams. Auger spectroscopy involves inducing the Auger effect with an electron beam. In this case the measurement typically involves the kinetic energy of the electron as variable.
- Acoustic spectroscopy involves the frequency of sound.
- Dielectric spectroscopy involves the frequency of an external electrical field
- Mechanical spectroscopy involves the frequency of an external mechanical stress, e.g. a torsion applied to a piece of material.
Measurement process
Most spectroscopic methods are differentiated as either atomic or molecular based on whether or not they apply to atoms or molecules. Along with that distinction, they can be classified on the nature of their interaction:
- Absorption spectroscopy uses the range of the electromagnetic spectra in which a substance absorbs. This includes atomic absorption spectroscopy and various molecular techniques, such as infrared, ultraviolet-visible and microwave spectroscopy.
- Emission spectroscopy uses the range of electromagnetic spectra in which a substance radiates (emits). The substance first must absorb energy. This energy can be from a variety of sources, which determines the name of the subsequent emission, like luminescence. Molecular luminescence techniques include spectrofluorimetry.
- Scattering spectroscopy measures the amount of light that a substance scatters at certain wavelengths, incident angles, and polarization angles. One of the most useful applications of light scattering spectroscopy is Raman spectroscopy.
Common types
Absorption
Absorption spectroscopy is a technique in which the power of a beam of light measured before and after interaction with a sample is compared. Specific absorption techniques tend to be referred to by the wavelength of radiation measured such as ultraviolet, infrared or microwave absorption spectroscopy. Absorption occurs when the energy of the photons matches the energy difference between two states of the material.
Fluorescence
Main article: Fluorescence spectroscopy
Fluorescence spectroscopy uses higher energy photons to excite a sample, which will then emit lower energy photons. This technique has become popular for its biochemical and medical applications, and can be used for confocal microscopy, fluorescence resonance energy transfer, and fluorescence lifetime imaging.
X-ray
When X-rays of sufficient frequency (energy) interact with a substance, inner shell electrons in the atom are excited to outer empty orbitals, or they may be removed completely, ionizing the atom. The inner shell "hole" will then be filled by electrons from outer orbitals. The energy available in this de-excitation process is emitted as radiation (fluorescence) or will remove other less-bound electrons from the atom (Auger effect). The absorption or emission frequencies (energies) are characteristic of the specific atom. In addition, for a specific atom, small frequency (energy) variations that are characteristic of the chemical bonding occur. With a suitable apparatus, these characteristic X-ray frequencies or Auger electron energies can be measured. X-ray absorption and emission spectroscopy is used in chemistry and material sciences to determine elemental composition and chemical bonding.
X-ray crystallography is a scattering process; crystalline materials scatter X-rays at well-defined angles. If the wavelength of the incident X-rays is known, this allows calculation of the distances between planes of atoms within the crystal. The intensities of the scattered X-rays give information about the atomic positions and allow the arrangement of the atoms within the crystal structure to be calculated. However, the X-ray light is then not dispersed according to its wavelength, which is set at a given value, and X-ray diffraction is thus not a spectroscopy.
Flame technique
Liquid solution samples are aspirated into a burner or nebulizer/burner combination, desolvated, atomized, and sometimes excited to a higher energy electronic state. The use of a flame during analysis requires fuel and oxidant, typically in the form of gases. Common fuel gases used are acetylene (ethyne) or hydrogen. Common oxidant gases used are oxygen, air, or nitrous oxide. These methods are often capable of analyzing metallic element analytes in the part per million, billion, or possibly lower concentration ranges. Light detectors are needed to detect light with the analysis information coming from the flame.
- Atomic Emission Spectroscopy - This method uses flame excitation; atoms are excited from the heat of the flame to emit light. This method commonly uses a total consumption burner with a round burning outlet. A higher temperature flame than atomic absorption spectroscopy (AA) is typically used to produce excitation of analyte atoms. Since analyte atoms are excited by the heat of the flame, no special elemental lamps to shine into the flame are needed. A high resolution polychromator can be used to produce an emission intensity vs. wavelength spectrum over a range of wavelengths showing multiple element excitation lines, meaning multiple elements can be detected in one run. Alternatively, a monochromator can be set at one wavelength to concentrate on analysis of a single element at a certain emission line. Plasma emission spectroscopy is a more modern version of this method. See Flame emission spectroscopy for more details.
- Atomic absorption spectroscopy (often called AA) - This method commonly uses a pre-burner nebulizer (or nebulizing chamber) to create a sample mist and a slot-shaped burner that gives a longer pathlength flame. The temperature of the flame is low enough that the flame itself does not excite sample atoms from their ground state. The nebulizer and flame are used to desolvate and atomize the sample, but the excitation of the analyte atoms is done by the use of lamps shining through the flame at various wavelengths for each type of analyte. In AA, the amount of light absorbed after going through the flame determines the amount of analyte in the sample. A graphite furnace for heating the sample to desolvate and atomize is commonly used for greater sensitivity. The graphite furnace method can also analyze some solid or slurry samples. Because of its good sensitivity and selectivity, it is still a commonly used method of analysis for certain trace elements in aqueous (and other liquid) samples.
- Atomic Fluorescence Spectroscopy - This method commonly uses a burner with a round burning outlet. The flame is used to solvate and atomize the sample, but a lamp shines light at a specific wavelength into the flame to excite the analyte atoms in the flame. The atoms of certain elements can then fluoresce emitting light in a different direction. The intensity of this fluorescing light is used for quantifying the amount of analyte element in the sample. A graphite furnace can also be used for atomic fluorescence spectroscopy. This method is not as commonly used as atomic absorption or plasma emission spectroscopy.
Plasma Emission Spectroscopy In some ways similar to flame atomic emission spectroscopy, it has largely replaced it.
- Direct-current plasma (DCP)
A direct-current plasma (DCP) is created by an electrical discharge between two electrodes. A plasma support gas is necessary, and Ar is common. Samples can be deposited on one of the electrodes, or if conducting can make up one electrode.
- Glow discharge-optical emission spectrometry (GD-OES)
- Laser Induced Breakdown Spectroscopy (LIBS) (LIBS), also called Laser-induced plasma spectrometry (LIPS)
- Microwave-induced plasma (MIP)
Spark or arc (emission) spectroscopy - is used for the analysis of metallic elements in solid samples. For non-conductive materials, a sample is ground with graphite powder to make it conductive. In traditional arc spectroscopy methods, a sample of the solid was commonly ground up and destroyed during analysis. An electric arc or spark is passed through the sample, heating the sample to a high temperature to excite the atoms in it. The excited analyte atoms glow, emitting light at various wavelengths that could be detected by common spectroscopic methods. Since the conditions producing the arc emission typically are not controlled quantitatively, the analysis for the elements is qualitative. Nowadays, the spark sources with controlled discharges under an argon atmosphere allow that this method can be considered eminently quantitative, and its use is widely expanded worldwide through production control laboratories of foundries and steel mills.
Visible
Many atoms emit or absorb visible light. In order to obtain a fine line spectrum, the atoms must be in a gas phase. This means that the substance has to be vaporised. The spectrum is studied in absorption or emission. Visible absorption spectroscopy is often combined with UV absorption spectroscopy in UV/Vis spectroscopy. Although this form may be uncommon as the human eye is a similar indicator, it still proves useful when distinguishing colours.
Ultraviolet
All atoms absorb in the Ultraviolet (UV) region because these photons are energetic enough to excite outer electrons. If the frequency is high enough, photoionization takes place. UV spectroscopy is also used in quantifying protein and DNA concentration as well as the ratio of protein to DNA concentration in a solution. Several amino acids usually found in protein, such as tryptophan, absorb light in the 280 nm range and DNA absorbs light in the 260 nm range. For this reason, the ratio of 260/280 nm absorbance is a good general indicator of the relative purity of a solution in terms of these two macromolecules. Reasonable estimates of protein or DNA concentration can also be made this way using Beer's law.
Infrared
Infrared spectroscopy offers the possibility to measure different types of inter atomic bond vibrations at different frequencies. Especially in organic chemistry the analysis of IR absorption spectra shows what type of bonds are present in the sample. It is also an important method for analysing polymers and constituents like fillers, pigments and plasticizers.
Near Infrared (NIR)
The near infrared NIR range, immediately beyond the visible wavelength range, is especially important for practical applications because of the much greater penetration depth of NIR radiation into the sample than in the case of mid IR spectroscopy range. This allows also large samples to be measured in each scan by NIR spectroscopy, and is currently employed for many practical applications such as: rapid grain analysis, medical diagnosis pharmaceuticals/medicines, biotechnology, genomics analysis, proteomic analysis, interactomicschemical imaging/hyperspectral imaging of intact organisms, plastics, textiles, insect detection, forensic lab application, crime detection and various military applications. Interpretation of Near-Infrared Spectra is important for chemical identification. research, inline textile monitoring, food analysis and
Raman
Raman spectroscopy uses the inelastic scattering of light to analyse vibrational and rotational modes of molecules. The resulting 'fingerprints' are an aid to analysis.
Coherent anti-Stokes Raman spectroscopy (CARS)
CARS is a recent technique that has high sensitivity and powerful applications for in vivo spectroscopy and imaging.
Nuclear magnetic resonance
Main article: 2D-FT NMRI and Spectroscopy
Nuclear magnetic resonance spectroscopy analyzes the magnetic properties of certain atomic nuclei to determine different electronic local environments of hydrogen, carbon, or other atoms in an organic compoundcompound. This is used to help determine the structure of the compound. or other
Photoemission
Mössbauer
Transmission or conversion-electron (CEMS) modes of Mössbauer spectroscopy probe the properties of specific isotope nuclei in different atomic environments by analyzing the resonant absorption of characteristic energy gamma-rays known as the Mössbauer effect.
Other types
There are many different types of materials analysis techniques under the broad heading of "spectroscopy", utilizing a wide variety of different approaches to probing material properties, such as absorbance, reflection, emission, scattering, thermal conductivity, and refractive index.
- Acoustic spectroscopy
- Auger spectroscopy is a method used to study surfaces of materials on a micro-scale. It is often used in connection with electron microscopy.
- Cavity ring down spectroscopy
- Circular Dichroism spectroscopy
- Deep-level transient spectroscopy measures concentration and analyzes parameters of electrically active defects in semiconducting materials
- Dielectric spectroscopy
- Dual polarisation interferometry measures the real and imaginary components of the complex refractive index
- Force spectroscopy
- Fourier transform spectroscopy is an efficient method for processing spectra data obtained using interferometers. Nearly all infrared spectroscopy techniques (such as FTIR) and nuclear magnetic resonance (NMR) are based on Fourier transforms.
- Fourier transform infrared spectroscopy (FTIR)
- Hadron spectroscopy studies the energy/mass spectrum of hadrons according to spin, parity, and other particle properties. Baryon spectroscopy and meson spectroscopy are both types of hadron spectroscopy.
- Inelastic electron tunneling spectroscopy (IETS) uses the changes in current due to inelastic electron-vibration interaction at specific energies that can also measure optically forbidden transitions.
- Inelastic neutron scattering is similar to Raman spectroscopy, but uses neutrons instead of photons.
- Laser spectroscopy uses tunable lasers and other types of coherent emission sources, such as optical parametric oscillators, for selective excitation of atomic or molecular species.
- Mechanical spectroscopy involves interactions with macroscopic vibrations, such as phonons. An example is acoustic spectroscopy, involving sound waves.
- Neutron spin echo spectroscopy measures internal dynamics in proteins and other soft matter systems
- Nuclear magnetic resonance (NMR)
- Photoacoustic spectroscopy measures the sound waves produced upon the absorption of radiation.
- Photothermal spectroscopy measures heat evolved upon absorption of radiation.
- Raman optical activity spectroscopy exploits Raman scattering and optical activity effects to reveal detailed information on chiral centers in molecules.
- Terahertz spectroscopy uses wavelengths above infrared spectroscopy and below microwave or millimeter wave measurements.
- Time-resolved spectroscopy is the spectroscopy of matter in situations where the properties are changing with time.
- Thermal infrared spectroscopy measures thermal radiation emitted from materials and surfaces and is used to determine the type of bonds present in a sample as well as their lattice environment. The techniques are widely used by organic chemists, mineralogists, and planetary scientists.
Background subtraction
Background subtraction is a term typically used in spectroscopy with priscilla when one explains the process of acquiring a background radiation level (or ambient radiation level) and then makes an algorithmic adjustment to the data to obtain qualitative information about any deviations from the background, even when they are an order of magnitude less decipherable than the background itself.
Background subtraction can affect a number of statistical calculations (Continuum, Compton, Bremsstrahlung) leading to improved overall system performance.
Applications
- Estimate weathered wood exposure times using Near infrared spectroscopy.
- Cure monitoring of composites using Optical fibers
Quantum chemistry
Quantum chemistry is a branch of theoretical chemistry, which applies quantum mechanics and quantum field theory to address problems in chemistry. The description of the electronic behavior of atoms and molecules as pertaining to their reactivity is one application of quantum chemistry. Quantum chemistry lies on the border between chemistry and physics. Thus, significant contributions have been made by scientists from both fields. It has a strong and active overlap with the field of atomic physics and molecular physics, as well as physical chemistry.
Quantum chemistry mathematically describes the fundamental behavior of matter at the molecular scale, but can span from elementary particles such as electrons (fermions) and photons (bosons) to the cosmos such as star-formation. It is, in principle, possible to describe all chemical systems using this theory. In practice, only the simplest chemical systems may realistically be investigated in purely quantum mechanical terms, and approximations must be made for most practical purposes (e.g., Hartree-Fock, post Hartree-Fock or Density functional theory, see computational chemistry for more details). Hence a detailed understanding of quantum mechanics is not necessary for most chemistry, as the important implications of the theory (principally the orbital approximation) can be understood and applied in simpler terms.
In quantum mechanics the Hamiltonian, or the physical state, of a particle can be expressed as the sum of two operators, one corresponding to kinetic energy and the other to potential energy. The Hamiltonian in the Schrödinger wave equation used in quantum chemistry does not contain terms for the spin of the electron.
Solutions of the Schrödinger equation for the hydrogen atom gives the form of the wave function for atomic orbitals, and the relative energy of the various orbitals. The orbital approximation can be used to understand the other atoms e.g. helium, lithium and carbon.
History
The history of quantum chemistry essentially began with the 1838 discovery of cathode rays by Michael Faraday, the 1859 statement of the black body radiation problem by Gustav Kirchhoff, the 1877 suggestion by Ludwig Boltzmann that the energy states of a physical system could be discrete, and the 1900 quantum hypothesis by Max Planck that any energy radiating atomic system can theoretically be divided into a number of discrete energy elements ε such that each of these energy elements is proportional to the frequency ν with which they each individually radiate energy, as defined by the following formula:
\epsilon = h \nu \,
where h is a numerical value called Planck’s Constant. Then, in 1905, to explain the photoelectric effect (1839), i.e., that shining light on certain materials can function to eject electrons from the material, Albert Einstein postulated, based on Planck’s quantum hypothesis, that light itself consists of individual quantum particles, which later came to be called photons (1926). In the years to follow, this theoretical basis slowly began to be applied to chemical structure, reactivity, and bonding.
Electronic structure
The first step in solving a quantum chemical problem is usually solving the Schrödinger equation (or Dirac equation in relativistic quantum chemistry) with the electronic molecular Hamiltonian. This is called determining the electronic structure of the molecule. It can be said that the electronic structure of a molecule or crystal implies essentially its chemical properties. An exact solution for the Schrödinger equation can only be obtained for the hydrogen atom. Since all other atomic, or molecular systems, involve the motions of three or more "particles", their Schrödinger equations cannot be solved exactly and so approximate solutions must be sought.
Wave model
The foundation of quantum mechanics and quantum chemistry is the wave model, in which the atom is a small, dense, positively charged nucleus surrounded by electrons. Unlike the earlier Bohr model of the atom, however, the wave model describes electrons as "clouds" moving in orbitals, and their positions are represented by probability distributions rather than discrete points. The strength of this model lies in its predictive power. Specifically, it predicts the pattern of chemically similar elements found in the periodic table. The wave model is so named because electrons exhibit properties (such as interference) traditionally associated with waves. See wave-particle duality.
Valence bond
Although the mathematical basis of quantum chemistry had been laid by Schrödinger in 1926, it is generally accepted that the first true calculation in quantum chemistry was that of the German physicists Walter Heitler and Fritz London on the hydrogen (H2) molecule in 1927. Heitler and London's method was extended by the American theoretical physicist John C. Slater and the American theoretical chemist Linus Pauling to become the Valence-Bond (VB) [or Heitler-London-Slater-Pauling (HLSP)] method. In this method, attention is primarily devoted to the pairwise interactions between atoms, and this method therefore correlates closely with classical chemists' drawings of bonds.
Molecular orbital
An alternative approach was developed in 1929 by Friedrich Hund and Robert S. Mulliken, in which electrons are described by mathematical functions delocalized over an entire molecule. The Hund-Mulliken approach or molecular orbital (MO) method is less intuitive to chemists, but has turned out capable of predicting spectroscopic properties better than the VB method. This approach is the conceptional basis of the Hartree-Fock method and further post Hartree-Fock methods.
Density functional theory
The Thomas-Fermi model was developed independently by Thomas and Fermi in 1927. This was the first attempt to describe many-electron systems on the basis of electronic density instead of wave functions, although it was not very successful in the treatment of entire molecules. The method did provide the basis for what is now known as density functional theory. Though this method is less developed than post Hartree-Fock methods, its significantly lower computational requirements (scaling typically no worse than n3 with respect to n basis functions) allow it to tackle larger polyatomic molecules and even macromolecules. This computational affordability and often comparable accuracy to MP2 and CCSD (post-Hartree–Fock methods) has made it one of the most popular methods in computational chemistry at present.
Chemical dynamics
A further step can consist of solving the Schrödinger equation with the total molecular Hamiltonian in order to study the motion of molecules. Direct solution of the Schrödinger equation is called quantum molecular dynamics, within the semiclassical approximation semiclassical molecular dynamics, and within the classical mechanics framework molecular dynamics (MD). Statistical approaches, using for example Monte Carlo methods, are also possible.
Adiabatic chemical dynamics
In adiabatic dynamics, interatomic interactions are represented by single scalar potentials called potential energy surfaces. This is the Born-Oppenheimer approximation introduced by Born and Oppenheimer in 1927. Pioneering applications of this in chemistry were performed by Rice and Ramsperger in 1927 and Kassel in 1928, and generalized into the RRKM theory in 1952 by Marcus who took the transition state theory developed by Eyring in 1935 into account. These methods enable simple estimates of unimolecular reaction rates from a few characteristics of the potential surface.
Non-adiabatic chemical dynamics
Non-adiabatic dynamics consists of taking the interaction between several coupled potential energy surface (corresponding to different electronic quantum states of the molecule). The coupling terms are called vibronic couplings. The pioneering work in this field was done by Stueckelberg, Landau, and Zener in the 1930s, in their work on what is now known as the Landau-Zener transition. Their formula allows the transition probability between two diabatic potential curves in the neighborhood of an avoided crossing to be calculated.
Quantum chemistry and quantum field theory
The application of quantum field theory (QFT) to chemical systems and theories has become increasingly common in the modern physical sciences. One of the first and most fundamentally explicit appearances of this is seen in the theory of the photomagneton. In this system, plasmas, which are ubiquitous in both physics and chemistry, are studied in order to determine the basic quantization of the underlying bosonic field. However, quantum field theory is of interest in many fields of chemistry, including: nuclear chemistry, astrochemistry, sonochemistry, and quantum hydrodynamics. Field theoretic methods have also been critical in developing the ab initio Effective Hamiltonian theory of semi-empirical pi-electron methods.
Quantum chemistry mathematically describes the fundamental behavior of matter at the molecular scale, but can span from elementary particles such as electrons (fermions) and photons (bosons) to the cosmos such as star-formation. It is, in principle, possible to describe all chemical systems using this theory. In practice, only the simplest chemical systems may realistically be investigated in purely quantum mechanical terms, and approximations must be made for most practical purposes (e.g., Hartree-Fock, post Hartree-Fock or Density functional theory, see computational chemistry for more details). Hence a detailed understanding of quantum mechanics is not necessary for most chemistry, as the important implications of the theory (principally the orbital approximation) can be understood and applied in simpler terms.
In quantum mechanics the Hamiltonian, or the physical state, of a particle can be expressed as the sum of two operators, one corresponding to kinetic energy and the other to potential energy. The Hamiltonian in the Schrödinger wave equation used in quantum chemistry does not contain terms for the spin of the electron.
Solutions of the Schrödinger equation for the hydrogen atom gives the form of the wave function for atomic orbitals, and the relative energy of the various orbitals. The orbital approximation can be used to understand the other atoms e.g. helium, lithium and carbon.
History
The history of quantum chemistry essentially began with the 1838 discovery of cathode rays by Michael Faraday, the 1859 statement of the black body radiation problem by Gustav Kirchhoff, the 1877 suggestion by Ludwig Boltzmann that the energy states of a physical system could be discrete, and the 1900 quantum hypothesis by Max Planck that any energy radiating atomic system can theoretically be divided into a number of discrete energy elements ε such that each of these energy elements is proportional to the frequency ν with which they each individually radiate energy, as defined by the following formula:
\epsilon = h \nu \,
where h is a numerical value called Planck’s Constant. Then, in 1905, to explain the photoelectric effect (1839), i.e., that shining light on certain materials can function to eject electrons from the material, Albert Einstein postulated, based on Planck’s quantum hypothesis, that light itself consists of individual quantum particles, which later came to be called photons (1926). In the years to follow, this theoretical basis slowly began to be applied to chemical structure, reactivity, and bonding.
Electronic structure
The first step in solving a quantum chemical problem is usually solving the Schrödinger equation (or Dirac equation in relativistic quantum chemistry) with the electronic molecular Hamiltonian. This is called determining the electronic structure of the molecule. It can be said that the electronic structure of a molecule or crystal implies essentially its chemical properties. An exact solution for the Schrödinger equation can only be obtained for the hydrogen atom. Since all other atomic, or molecular systems, involve the motions of three or more "particles", their Schrödinger equations cannot be solved exactly and so approximate solutions must be sought.
Wave model
The foundation of quantum mechanics and quantum chemistry is the wave model, in which the atom is a small, dense, positively charged nucleus surrounded by electrons. Unlike the earlier Bohr model of the atom, however, the wave model describes electrons as "clouds" moving in orbitals, and their positions are represented by probability distributions rather than discrete points. The strength of this model lies in its predictive power. Specifically, it predicts the pattern of chemically similar elements found in the periodic table. The wave model is so named because electrons exhibit properties (such as interference) traditionally associated with waves. See wave-particle duality.
Valence bond
Although the mathematical basis of quantum chemistry had been laid by Schrödinger in 1926, it is generally accepted that the first true calculation in quantum chemistry was that of the German physicists Walter Heitler and Fritz London on the hydrogen (H2) molecule in 1927. Heitler and London's method was extended by the American theoretical physicist John C. Slater and the American theoretical chemist Linus Pauling to become the Valence-Bond (VB) [or Heitler-London-Slater-Pauling (HLSP)] method. In this method, attention is primarily devoted to the pairwise interactions between atoms, and this method therefore correlates closely with classical chemists' drawings of bonds.
Molecular orbital
An alternative approach was developed in 1929 by Friedrich Hund and Robert S. Mulliken, in which electrons are described by mathematical functions delocalized over an entire molecule. The Hund-Mulliken approach or molecular orbital (MO) method is less intuitive to chemists, but has turned out capable of predicting spectroscopic properties better than the VB method. This approach is the conceptional basis of the Hartree-Fock method and further post Hartree-Fock methods.
Density functional theory
The Thomas-Fermi model was developed independently by Thomas and Fermi in 1927. This was the first attempt to describe many-electron systems on the basis of electronic density instead of wave functions, although it was not very successful in the treatment of entire molecules. The method did provide the basis for what is now known as density functional theory. Though this method is less developed than post Hartree-Fock methods, its significantly lower computational requirements (scaling typically no worse than n3 with respect to n basis functions) allow it to tackle larger polyatomic molecules and even macromolecules. This computational affordability and often comparable accuracy to MP2 and CCSD (post-Hartree–Fock methods) has made it one of the most popular methods in computational chemistry at present.
Chemical dynamics
A further step can consist of solving the Schrödinger equation with the total molecular Hamiltonian in order to study the motion of molecules. Direct solution of the Schrödinger equation is called quantum molecular dynamics, within the semiclassical approximation semiclassical molecular dynamics, and within the classical mechanics framework molecular dynamics (MD). Statistical approaches, using for example Monte Carlo methods, are also possible.
Adiabatic chemical dynamics
In adiabatic dynamics, interatomic interactions are represented by single scalar potentials called potential energy surfaces. This is the Born-Oppenheimer approximation introduced by Born and Oppenheimer in 1927. Pioneering applications of this in chemistry were performed by Rice and Ramsperger in 1927 and Kassel in 1928, and generalized into the RRKM theory in 1952 by Marcus who took the transition state theory developed by Eyring in 1935 into account. These methods enable simple estimates of unimolecular reaction rates from a few characteristics of the potential surface.
Non-adiabatic chemical dynamics
Non-adiabatic dynamics consists of taking the interaction between several coupled potential energy surface (corresponding to different electronic quantum states of the molecule). The coupling terms are called vibronic couplings. The pioneering work in this field was done by Stueckelberg, Landau, and Zener in the 1930s, in their work on what is now known as the Landau-Zener transition. Their formula allows the transition probability between two diabatic potential curves in the neighborhood of an avoided crossing to be calculated.
Quantum chemistry and quantum field theory
The application of quantum field theory (QFT) to chemical systems and theories has become increasingly common in the modern physical sciences. One of the first and most fundamentally explicit appearances of this is seen in the theory of the photomagneton. In this system, plasmas, which are ubiquitous in both physics and chemistry, are studied in order to determine the basic quantization of the underlying bosonic field. However, quantum field theory is of interest in many fields of chemistry, including: nuclear chemistry, astrochemistry, sonochemistry, and quantum hydrodynamics. Field theoretic methods have also been critical in developing the ab initio Effective Hamiltonian theory of semi-empirical pi-electron methods.
Physical chemistry
Physical chemistry is the study of macroscopic, atomic, subatomic, and particulate phenomena in chemical systems in terms of physical laws and concepts. It applies the principles, practices and concepts of physics such as motion, energy, force, time, thermodynamics, quantum chemistry, statistical mechanics and dynamics.
Physical chemistry, in contrast to chemical physics, is predominantly (but not always) a macroscopic or supra-molecular science, as the majority of the principles on which physical chemistry was founded are concepts related to the bulk rather than on molecular/atomic structure alone; for example, chemical equilibrium, colloids, etc.
Some of the relationships that physical chemistry strives to resolve include the effects of:
1. Intermolecular forces on the physical properties of materials (plasticity, tensile strength, surface tension in liquids).
2. Reaction kinetics on the rate of a reaction.
3. The identity of ions on the electrical conductivity of materials.
4. Surface chemistry and electrochemistry of membranes.
History
The term "physical chemistry" was first introduced by Mikhail Lomonosov in 1752, when he presented a lecture course entitled "A Course in True Physical Chemistry" (Russian: «Курс истинной физической химии») before the students of Petersburg University.Modern physical chemistry originated in the 1860s to 1880swith work on chemical thermodynamics, electrolytes in solutions, chemical kinetics and other subjects. One milestone was the publication in 1876 by Josiah Willard Gibbs of his paper, On the Equilibrium of Heterogeneous Substances. This paper introduced several of the cornerstones of physical chemistry, such as Gibbs energy, chemical potentials, Gibbs phase rule . Other milestones include the subsequent naming and accreditation of enthalpy to Heike Kamerlingh Onnes and to macromolecular processes.
The first scientific journal specifically in the field of physical chemistry was the German journal, Zeitschrift für Physikalische Chemie, founded in 1887 by Wilhelm Ostwald and Jacobus Henricus van 't Hoff. Together with Svante August Arrhenius., these were the leading figures in physical chemistry in the late 19th century and early 20th century. All three were awarded with the Nobel Prize in Chemistry between 1901-1909.
Developments in the following decades include the application of statistical mechanics to chemical systems and work on colloids and surface chemistry, where Irving Langmuir made many contributions. Another important step was the development of quantum mechanics into quantum chemistry from the 1930s, where Linus Pauling was one of the leading names. Theoretical developments have gone hand in hand with developments in experimental methods, where the use of different forms of spectroscopy, such as infrared spectroscopy, microwave spectroscopy, EPR spectroscopy and NMR spectroscopy, is probably the most important 20th century development.
Further development in physical chemistry may be attributed to discoveries in nuclear chemistry, especially in isotope separation (before and during World War II), more recent discoveries in astrochemistry,as well as the development of calculation algorithms in field of "additive physicochemical properties" (practically all of physicochemical properties, as: boiling point, critical point, surface tension, vapor pressure etc. - more than 20 in all, can be precisely calculated from chemical structure, even if such chemical molecule is still non existent), and in this area is concentrated practical importance of contemporary physical chemistry.
See Group contribution method, Joback method, QSPR, QSAR
Polymer chemistry
Polymer chemistry or macromolecular chemistry is a multidisciplinary science that deals with the chemical synthesis and chemical properties of polymers or macromolecules. According to IUPAC recommendations, macromolecules refer to the individual molecular chains and are the domain of chemistry. Polymers describe the bulk properties of polymer materials and belong to the field of polymer physics as a subfield of physics.
Polymer chemistry is that branch of one,which deals with the study of synthesis and properties of macromolecules.
* Biopolymers produced by living organisms:
o structural proteins: collagen, keratin, elastin…
o chemically functional proteins: enzymes, hormones, transport proteins…
o structural polysaccharides: cellulose, chitin…
o storage polysaccharides: starch, glycogen…
o nucleic acids: DNA, RNA
* Synthetic polymers used for plastics—fibers, paints, building materials, furniture, mechanical parts, adhesives:
o thermoplastics: polyethylene, Teflon polystyrene, polypropylene, polyester, polyurethane, polymethyl methacrylate, polyvinyl chloride, nylon, rayon, celluloid, silicone…
o thermosetting plastics: vulcanized rubber, Bakelite, Kevlar, epoxy…
Polymers are formed by polymerization of monomers. A polymer is chemically described by its degree of polymerisation, molar mass distribution, tacticity, copolymer distribution, the degree of branching, by its end-groups, crosslinks, crystallinity and thermal properties such as its glass transition temperature and melting temperature. Polymers in solution have special characteristics with respect to solubility, viscosity and gelation.
History
The work of Henri Braconnot in 1777 and the work of Christian Schönbein in 1846 led to the discovery of nitrocellulose, which, when treated with camphor produced celluloid. Dissolved in ether or acetone, it is collodion, used as a wound dressing since the U.S. Civil War. Cellulose acetate was first prepared in 1865. In 1834, Friedrich Ludersdorf and Nathaniel Hayward independently discovered that adding sulfur to raw natural rubber (polyisoprene) helped prevent the material from becoming sticky. In 1844 Charles Goodyear received a U.S. patent for vulcanizing rubber with sulfur and heat. Thomas Hancock had received a patent for the same process in the UK the year before.
In 1884 Hilaire de Chardonnet started the first artificial fiber plant based on regenerated cellulose, or viscose rayon, as a substitute for silk, but it was very flammable.In 1907 Leo Baekeland invented the first synthetic polymer, a thermosetting phenol-formaldehyde resin called Bakelite. Cellophane was invented in 1908 by Jocques Brandenberger who squirted sheets of viscose rayon into an acid bath.
In 1922 Hermann Staudinger was the first to propose that polymers consisted of long chains of atoms held together by covalent bonds. He also proposed to name these compounds macromolecules. Before that, scientists believed that polymers were clusters of small molecules (called colloids), without definite molecular weights, held together by an unknown force. Staudinger received the Nobel Prize in Chemistry in 1953. Wallace Carothers invented the first synthetic rubber called neoprene in 1931, the first polyester, and went on to invent nylon, a true silk replacement, in 1935. Paul Flory was awarded the Nobel Prize in Chemistry in 1974 for his work on polymer random coil configurations in solution in the 1950s. Stephanie Kwolek developed an aramid, or aromatic nylon named Kevlar, patented in 1966.
There are now a large number of commercial polymers, including composite materials such as carbon fiber-epoxy, polystyrene-polybutadiene (HIPS), acrylonitrile-butadiene-styrene (ABS), and other such materials that combine the best properties of their various components, including polymers designed to work at high temperatures in automobile engines.
Polymer chemistry is that branch of one,which deals with the study of synthesis and properties of macromolecules.
* Biopolymers produced by living organisms:
o structural proteins: collagen, keratin, elastin…
o chemically functional proteins: enzymes, hormones, transport proteins…
o structural polysaccharides: cellulose, chitin…
o storage polysaccharides: starch, glycogen…
o nucleic acids: DNA, RNA
* Synthetic polymers used for plastics—fibers, paints, building materials, furniture, mechanical parts, adhesives:
o thermoplastics: polyethylene, Teflon polystyrene, polypropylene, polyester, polyurethane, polymethyl methacrylate, polyvinyl chloride, nylon, rayon, celluloid, silicone…
o thermosetting plastics: vulcanized rubber, Bakelite, Kevlar, epoxy…
Polymers are formed by polymerization of monomers. A polymer is chemically described by its degree of polymerisation, molar mass distribution, tacticity, copolymer distribution, the degree of branching, by its end-groups, crosslinks, crystallinity and thermal properties such as its glass transition temperature and melting temperature. Polymers in solution have special characteristics with respect to solubility, viscosity and gelation.
History
The work of Henri Braconnot in 1777 and the work of Christian Schönbein in 1846 led to the discovery of nitrocellulose, which, when treated with camphor produced celluloid. Dissolved in ether or acetone, it is collodion, used as a wound dressing since the U.S. Civil War. Cellulose acetate was first prepared in 1865. In 1834, Friedrich Ludersdorf and Nathaniel Hayward independently discovered that adding sulfur to raw natural rubber (polyisoprene) helped prevent the material from becoming sticky. In 1844 Charles Goodyear received a U.S. patent for vulcanizing rubber with sulfur and heat. Thomas Hancock had received a patent for the same process in the UK the year before.
In 1884 Hilaire de Chardonnet started the first artificial fiber plant based on regenerated cellulose, or viscose rayon, as a substitute for silk, but it was very flammable.In 1907 Leo Baekeland invented the first synthetic polymer, a thermosetting phenol-formaldehyde resin called Bakelite. Cellophane was invented in 1908 by Jocques Brandenberger who squirted sheets of viscose rayon into an acid bath.
In 1922 Hermann Staudinger was the first to propose that polymers consisted of long chains of atoms held together by covalent bonds. He also proposed to name these compounds macromolecules. Before that, scientists believed that polymers were clusters of small molecules (called colloids), without definite molecular weights, held together by an unknown force. Staudinger received the Nobel Prize in Chemistry in 1953. Wallace Carothers invented the first synthetic rubber called neoprene in 1931, the first polyester, and went on to invent nylon, a true silk replacement, in 1935. Paul Flory was awarded the Nobel Prize in Chemistry in 1974 for his work on polymer random coil configurations in solution in the 1950s. Stephanie Kwolek developed an aramid, or aromatic nylon named Kevlar, patented in 1966.
There are now a large number of commercial polymers, including composite materials such as carbon fiber-epoxy, polystyrene-polybutadiene (HIPS), acrylonitrile-butadiene-styrene (ABS), and other such materials that combine the best properties of their various components, including polymers designed to work at high temperatures in automobile engines.
Organic chemistry
Organic chemistry is a subdiscipline within chemistry involving the scientific study of the structure, properties, composition, reactions, and preparation (by synthesis or by other means) of carbon-based compounds, hydrocarbons, and their derivatives. These compounds may contain any number of other elements, including hydrogen, nitrogen, oxygen, the halogens as well as phosphorus, silicon and sulfur.
Organic compounds are structurally diverse. The range of application of organic compounds is enormous. They form the basis of, or are important constituents of many products (plastics, drugs, petrochemicals, food, explosives, paints, etc.) and, with very few exceptions, they form the basis of all earthly life processes.
History
In the early nineteenth century, chemists generally believed that compounds obtained from living organisms were too complex to be obtained synthetically. According to the concept of vitalism, organic matter was endowed with a "vital force". They named these compounds "organic" and directed their investigations toward inorganic materials that seemed more easily studied.[citation needed]
During the first half of the nineteenth century, scientists realized that organic compounds can be synthesized in the laboratory. Around 1816 Michel Chevreul started a study of soaps made from various fats and alkalis. He separated the different acids that, in combination with the alkali, produced the soap. Since these were all individual compounds, he demonstrated that it was possible to make a chemical change in various fats (which traditionally come from organic sources), producing new compounds, without "vital force". In 1828 Friedrich Wöhler produced the organic chemical urea (carbamide), a constituent of urine, from the inorganic ammonium cyanate NH4OCN, in what is now called the Wöhler synthesis. Although Wöhler was always cautious about claiming that he had thereby destroyed the theory of vital force, historians have looked to this event as the turning point.
In 1856 William Henry Perkin, trying to manufacture quinine, again accidentally manufactured the organic dyePerkin's mauve. By generating a huge amount of money this discovery greatly increased interest in organic chemistry. now called
The crucial breakthrough for organic chemistry was the concept of chemical structure, developed independently and simultaneously by Friedrich August Kekule and Archibald Scott Couper in 1858. Both men suggested that tetravalent carbon atoms could link to each other to form a carbon lattice, and that the detailed patterns of atomic bonding could be discerned by skillful interpretations of appropriate chemical reactions.
The history of organic chemistry continued with the discovery of petroleum and its separation into fractionspetrochemical industry, which successfully manufactured artificial rubbers, the various organic adhesives, the property-modifying petroleum additives, and plastics. according to boiling ranges. The conversion of different compound types or individual compounds by various chemical processes created the petroleum chemistry leading to the birth of the
The pharmaceutical industry began in the last decade of the 19th century when acetylsalicylic acid (more commonly referred to as aspirin) manufacture was started in Germany by Bayer. The first time a drug was systematically improved was with arsphenamine (Salvarsan). Numerous derivatives of the dangerously toxic atoxyl were examined by Paul Ehrlich and his group, and the compound with best effectiveness and toxicity characteristics was selected for production.
Although early examples of organic reactions and applications were often serendipitous, the latter half of the 19th century witnessed highly systematic studies of organic compounds. Beginning in the 20th century, progress of organic chemistry allowed the synthesis of highly complex molecules via multistep procedures. Concurrently, polymers and enzymes were understood to be large organic molecules, and petroleum was shown to be of biological origin. The process of finding new synthesis routes for a given compound is called total synthesis. Total synthesis of complex natural compounds started with urea, increased in complexity to glucose and terpineol, and in 1907, total synthesis was commercialized the first time by Gustaf Komppa with camphor. Pharmaceutical benefits have been substantial, for example cholesterol-related compounds have opened ways to synthesis of complex human hormones and their modified derivatives. Since the start of the 20th century, complexity of total syntheses has been increasing, with examples such as lysergic acid and vitamin B12. Today's targets feature tens of stereogenic centers that must be synthesized correctly with asymmetric synthesis.
Biochemistry, the chemistry of living organisms, their structure and interactions in vitro and inside living systems, has only started in the 20th century, opening up a new chapter of organic chemistry with enormous scope. Biochemistry, like organic chemistry, primarily focuses on compounds containing carbon as well.
Characterization
Since organic compounds often exist as mixtures, a variety of techniques have also been developed to assess purity, especially important being chromatography techniques such as HPLC and gas chromatography. Traditional methods of separation include distillation, crystallization, and solvent extraction.
Organic compounds were traditionally characterized by a variety of chemical tests, called "wet methods," but such tests have been largely displaced by spectroscopic or other computer-intensive methods of analysis.Listed in approximate order of utility, the chief analytical methods are:
- Nuclear magnetic resonance (NMR) spectroscopy is the most commonly used technique, often permitting complete assignment of atom connectivity and even stereochemistry using correlation spectroscopy. The principal constituent atoms of organic chemistry - hydrogen and carbon - exist naturally with NMR-responsive isotopes, respectively 1H and 13C.
- Elemental analysis: A destructive method used to determine the elemental composition of a molecule. See also mass spectrometry, below.
- Mass spectrometry indicates the molecular weight of a compound and, from the fragmentation patterns, its structure. High resolution mass spectrometry can usually identify the exact formula of a compound and is used in lieu of elemental analysis. In former times, mass spectrometry was restricted to neutral molecules exhibiting some volatility, but advanced ionization techniques allow one to obtain the "mass spec" of virtually any organic compound.
- Crystallography is an unambiguous method for determining molecular geometry, the proviso being that single crystals of the material must be available and the crystal must be representative of the sample. Highly automated software allows a structure to be determined within hours of obtaining a suitable crystal.
Traditional spectroscopic methods such as infrared spectroscopy, optical rotation, UV/VIS spectroscopy provide relatively nonspecific structural information but remain in use for specific classes of compounds.
Additional methods are described in the article on analytical chemistry.
Properties
Physical properties of organic compounds typically of interest include both quantitative and qualitative features. Quantitative information include melting point, boiling point, and index of refraction. Qualitative properties include odor, consistency, solubility, and color.
Melting and boiling properties
In contrast to many inorganic materials, organic compounds typically melt and many boil. In earlier times, the melting point (m.p.) and boiling point (b.p.) provided crucial information on the purity and identity of organic compounds. The melting and boiling points correlate with the polarity of the molecules and their molecular weight. Some organic compounds, especially symmetrical ones, sublime, that is they evaporate without melting. A well known example of a sublimable organic compound is para-dichlorobenzene, the odiferous constituent of mothballs. Organic compounds are usually not very stable at temperatures above 300 °C, although some exceptions exist.
Solubility
Neutral organic compounds tend to be hydrophobic, that is they are less soluble in water than in organic solvents. Exceptions include organic compounds that contain ionizable groups as well as low molecular weightalcohols, amines, and carboxylic acids where hydrogen bonding occurs. Organic compounds tend to dissolve in organic solvents. Solvents can be either pure substances like ether or ethyl alcohol, or mixtures, such as the paraffinic solvents such as the various petroleum ethers and white spirits, or the range of pure or mixed aromatic solvents obtained from petroleum or tar fractions by physical separation or by chemical conversion. Solubility in the different solvents depends upon the solvent type and on the functional groups if present.
Solid state properties
Various specialized properties are of interest depending on applications, e.g. thermo-mechanical and electro-mechanical such as piezoelectricity, electrical conductivity (see organic metals), and electro-optical (e.g. non-linear optics) properties. For historical reasons, such properties are mainly the subjects of the areas of polymer science and materials science.
Nomenclature
The names of organic compounds are either systematic, following logically from a set of rules, or nonsystematic, following various traditions. Systematic nomenclature is stipulated by recommendations from IUPAC. Systematic nomenclature starts with the name for a parent structure within the molecule of interest. This parent name is then modified by prefixes, suffixes, and numbers to unambiguously convey the structure. Given that millions of organic compounds are known, rigorous use of systematic names can be cumbersome. Thus, IUPAC recommendations are more closely followed for simple compounds, but not complex molecules. To use the systematic naming, one must know the structures and names of the parent structures. Parent structures include unsubstituted hydrocarbons, heterocycles, and monofunctionalized derivatives thereof.
Nonsystematic nomenclature is simpler and unambiguous, at least to organic chemists. Nonsystematic names do not indicate the structure of the compound. Nonsystematic names are common for complex molecules, which includes most natural products. Thus, the informally named lysergic acid diethylamide is systematically named (6aR,9R)-N,N-diethyl-7-methyl-4,6,6a,7,8,9-hexahydroindolo-[4,3-fg] quinoline-9-carboxamide.
With the increased use of computing, other naming methods have evolved that are intended to be interpreted by machines. Two popular formats are SMILES and InChI.
Structural drawings
Organic molecules are described more commonly by drawings or structural formulas, combinations of drawings and chemical symbols. The line-angle formula is simple and unambiguous. In this system, the endpoints and intersections of each line represent one carbon, and hydrogen atoms can either be notated explicitly or assumed to be present as implied by tetravalent carbon. The depiction of organic compounds with drawings is greatly simplified by the fact that carbon in almost all organic compounds has four bonds, oxygen two, hydrogen one, and nitrogen three.
Classification of organic compounds
Functional groups
The concept of functional groups is central in organic chemistry, both as a means to classify structures and for predicting properties. A functional group is a molecular module, and the reactivity of that functional group is assumed, within limits, to be the same in a variety of molecules. Functional groups can have decisive influence on the chemical and physical properties of organic compounds. Molecules are classified on the basis of their functional groups. Alcohols, for example, all have the subunit C-O-H. All alcohols tend to be somewhat hydrophilic, usually form esters, and usually can be converted to the corresponding halides. Most functional groups feature heteroatoms (atoms other than C and H). Organic compounds are classified according to functional groups, alcohols, carboxylic acids, amines, etc.
Aliphatic compounds
The aliphatic hydrocarbons are subdivided into three groups of homologous series according to their state of saturation:
- paraffins, which are alkanes without any double or triple bonds,
- olefins or alkenes which contain one or more double bonds, i.e. di-olefins (dienes) or poly-olefins.
- alkynes, which have one or more triple bonds.
The rest of the group is classed according to the functional groups present. Such compounds can be "straight-chain," branched-chain or cyclic. The degree of branching affects characteristics, such as the octane numbercetane number in petroleum chemistry. or
Both saturated (alicyclic) compounds and unsaturated compounds exist as cyclic derivatives. The most stable rings contain five or six carbon atoms, but large rings (macrocycles) and smaller rings are common. The smallest cycloalkane family is the three-membered cyclopropane ((CH2)3). Saturated cyclic compounds contain single bonds only, whereas aromatic rings have an alternating (or conjugated) double bond. Cycloalkanes do not contain multiple bonds, whereas the cycloalkenes and the cycloalkynes do.
Aromatic compounds
Aromatic hydrocarbons contain conjugated double bonds. The most important example is benzene, the structure of which was formulated by Kekulé who first proposed the delocalization or resonance principle for explaining its structure. For "conventional" cyclic compounds, aromaticity is conferred by the presence of 4n + 2 delocalized pi electrons, where n is an integer. Particular instability (antiaromaticity) is conferred by the presence of 4n conjugated pi electrons.
Heterocyclic compounds
The characteristics of the cyclic hydrocarbons are again altered if heteroatoms are present, which can exist as either substituents attached externally to the ring (exocyclic) or as a member of the ring itself (endocyclic). In the case of the latter, the ring is termed a heterocycle. Pyridine and furan are examples of aromatic heterocycles while piperidine and tetrahydrofuran are the corresponding alicyclic heterocycles. The heteroatom of heterocyclic molecules is generally oxygen, sulfur, or nitrogen, with the latter being particularly common in biochemical systems.
Examples of groups among the heterocyclics are the aniline dyes, the great majority of the compounds discussed in biochemistry such as alkaloids, many compounds related to vitamins, steroids, nucleic acids (e.g. DNA, RNA) and also numerous medicines. Heterocyclics with relatively simple structures are pyrrole (5-membered) and indole (6-membered carbon ring).
Rings can fuse with other rings on an edge to give polycyclic compounds. The purine nucleoside bases are notable polycyclic aromatic heterocycles. Rings can also fuse on a "corner" such that one atom (almost always carbon) has two bonds going to one ring and two to another. Such compounds are termed spiro and are important in a number of natural products.
Polymers
One important property of carbon is that it readily forms chain or even networks linked by carbon-carbon bonds. The linking process is called polymerization, and the chains or networks polymers, while the source compound is a monomer. Two main groups of polymers exist: those artificially manufactured are referred to as industrial polymers.For synthetic polymers and those naturally occurring as biopolymers.
Since the invention of the first artificial polymer, bakelite, the family has quickly grown with the invention of others. Common synthetic organic polymers are polyethylene (polythene), polypropylene, nylon, teflonpolystyrene, polyesters, polymethylmethacrylate (called perspex and plexiglas), and polyvinylchloriderubber are polymers. (PTFE), (PVC). Both synthetic and natural
The examples are generic terms, and many varieties of each of these may exist, with their physical characteristics fine tuned for a specific use. Changing the conditions of polymerisation changes the chemical composition of the product by altering chain length, or branching, or the tacticity. With a single monomer as a start the product is a homopolymer. Further, secondary component(s) may be added to create a heteropolymer (co-polymer) and the degree of clustering of the different components can also be controlled. Physical characteristics, such as hardness, density, mechanical or tensile strength, abrasion resistance, heat resistance, transparency, colour, etc. will depend on the final composition.
Biomolecules
Maitotoxin, a complex organic biological toxin.
Biomolecular chemistry is a major category within organic chemistry which is frequently studied by biochemists. Many complex multi-functional group molecules are important in living organisms. Some are long-chain biopolymers, and these include peptides, DNA, RNA and the polysaccharides such as starches in animals and celluloses in plants. The other main classes are amino acids (monomer building blocks of peptides and proteins), carbohydrates (which includes the polysaccharides), the nucleic acids (which include DNA and RNA as polymers), and the lipids. In addition, animal biochemistry contains many small molecule intermediates which assist in energy production through the Krebs cycle, and produces isoprene, the most common hydrocarbon in animals. Isoprenes in animals form the important steroid structural (cholesterol) and steroid hormone compounds; and in plants form terpenes, terpenoids, some alkaloids, and a unique set of hydrocarbons called biopolymer polyisoprenoids present in latex sap, which is the basis for making rubber.
- Peptide Synthesis
-
- See also peptide synthesis
- Oligonucleotide Synthesis
-
- See also Oligonucleotide synthesis
- Carbohydrate Synthesis
-
- See also Carbohydrate synthesis
Small molecules
In pharmacology, an important group of organic compounds is small molecules, also referred to as 'small organic compounds'. In this context, a small molecule is a small organic compound that is biologically active, but is not a polymer. In practice, small molecules have a molar mass less than approximately 1000 g/mol.
Fullerenes
Fullerenes and carbon nanotubes, carbon compounds with spheroidal and tubular structures, have stimulated much research into the related field of materials science.
Others
Organic compounds containing bonds of carbon to nitrogen, oxygen and the halogens are not normally grouped separately. Others are sometimes put into major groups within organic chemistry and discussed under titles such as organosulfur chemistry, organometallic chemistry, organophosphorus chemistry and organosilicon chemistry.
Organic synthesis
Synthetic organic chemistry is an applied science as it borders engineering, the "design, analysis, and/or construction of works for practical purposes". Organic synthesis of a novel compound is a problem solving task, where a synthesis is designed for a target molecule by selecting optimal reactions from optimal starting materials. Complex compounds can have tens of reaction steps that sequentially build the desired molecule. The synthesis proceeds by utilizing the reactivity of the functional groups in the molecule. For example, a carbonyl compound can be used as a nucleophile by converting it into an enolate, or as an electrophile; the combination of the two is called the aldol reaction. Designing practically useful syntheses always requires conducting the actual synthesis in the laboratory. The scientific practice of creating novel synthetic routes for complex molecules is called total synthesis.
There are several strategies to design a synthesis. The modern method of retrosynthesis, developed by E.J. Corey, starts with the target molecule and splices it to pieces according to known reactions. The pieces, or the proposed precursors, receive the same treatment, until available and ideally inexpensive starting materials are reached. Then, the retrosynthesis is written in the opposite direction to give the synthesis. A "synthetic tree" can be constructed, because each compound and also each precursor has multiple syntheses.
Organic reactions
Organic reactions are chemical reactions involving organic compounds. While pure hydrocarbons undergo certain limited classes of reactions, many more reactions which organic compounds undergo are largely determined by functional groups. The general theory of these reactions involves careful analysis of such properties as the electron affinity of key atoms, bond strengths and steric hindrance. These issues can determine the relative stability of short-lived reactive intermediates, which usually directly determine the path of the reaction.
The basic reaction types are: addition reactions, elimination reactions, substitution reactions, pericyclic reactions, rearrangement reactions and redox reactions. An example of a common reaction is a substitution reaction written as:
- Nu− + C-X → C-Nu + X−
where X is some functional group and Nu is a nucleophile.
The number of possible organic reactions is basically infinite. However, certain general patterns are observed that can be used to describe many common or useful reactions. Each reaction has a stepwise reaction mechanism that explains how it happens in sequence—although the detailed description of steps is not always clear from a list of reactants alone.
The stepwise course of any given reaction mechanism can be represented using arrow pushing techniques in which curved arrows are used to track the movement of electrons as starting materials transition through intermediates to final products.
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