Computational chemistry is a branch of chemistry that uses principles of computer science to assist in solving chemical problems. It uses the results of theoretical chemistry, incorporated into efficient computer programs, to calculate the structures and properties of molecules and solids. Its necessity arises from the well-known fact that apart from relatively recent results concerning the Hydrogen molecular ion (see references therein for more details), the quantum n-body problem cannot be solved analytically, much less in closed form. While its results normally complement the information obtained by chemical experiments, it can in some cases predict hitherto unobserved chemical phenomena. It is widely used in the design of new drugs and materials.
Examples of such properties are structure (i.e. the expected positions of the constituent atoms), absolute and relative (interaction) energies, electronic charge distributions, dipoles and higher multipole moments, vibrational frequencies, reactivity or other spectroscopic quantities, and cross sections for collision with other particles.
The methods employed cover both static and dynamic situations. In all cases the computer time and other resources (such as memory and disk space) increase rapidly with the size of the system being studied. That system can be a single molecule, a group of molecules, or a solid. Computational chemistry methods range from highly accurate to very approximate; highly accurate methods are typically feasible only for small systems. Ab initio methods are based entirely on theory from first principles. Other (typically less accurate) methods are called empirical or semi-empirical because they employ experimental results, often from acceptable models of atoms or related molecules, to approximate some elements of the underlying theory.
Both ab initio and semi-empirical approaches involve approximations. These range from simplified forms of the first-principles equations that are easier or faster to solve, to approximations limiting the size of the system (for example, periodic boundary conditions), to fundamental approximations to the underlying equations that are required to achieve any solution to them at all. For example, most ab initio calculations make the Born–Oppenheimer approximation, which greatly simplifies the underlying Schrödinger equation by freezing the nuclei in place during the calculation. In principle, ab initio methods eventually converge to the exact solution of the underlying equations as the number of approximations is reduced. In practice, however, it is impossible to eliminate all approximations, and residual error inevitably remains. The goal of computational chemistry is to minimize this residual error while keeping the calculations tractable.
In some cases, the details of electronic structure are less important than the long-time phase space behavior of molecules. This is the case in conformational studies of proteins and protein-ligand binding thermodynamics. Classical approximations to the potential energy surface are employed, as they are computationally less intensive than electronic calculations, to enable longer simulations of molecular dynamics. Furthermore, cheminformatics uses even more empirical (and computationally cheaper) methods like machine learning based on physicochemical properties. One typical problem in cheminformatics is to predict the binding affinity of drug molecules to a given target.
History
Building on the founding discoveries and theories in the history of quantum mechanics, the first theoretical calculations in chemistry were those of Walter Heitler and Fritz London in 1927. The books that were influential in the early development of computational quantum chemistry include Linus Pauling and E. Bright Wilson's 1935 Introduction to Quantum Mechanics – with Applications to Chemistry, Eyring, Walter and Kimball's 1944 Quantum Chemistry, Heitler's 1945 Elementary Wave Mechanics – with Applications to Quantum Chemistry, and later Coulson's 1952 textbook Valence, each of which served as primary references for chemists in the decades to follow.
With the development of efficient computer technology in the 1940s, the solutions of elaborate wave equations for complex atomic systems began to be a realizable objective. In the early 1950s, the first semi-empirical atomic orbital calculations were carried out. Theoretical chemists became extensive users of the early digital computers. A very detailed account of such use in the United Kingdom is given by Smith and Sutcliffe. The first ab initio Hartree–Fock calculations on diatomic molecules were carried out in 1956 at MIT, using a basis set of Slater orbitals. For diatomic molecules, a systematic study using a minimum basis set and the first calculation with a larger basis set were published by Ransil and Nesbet respectively in 1960.The first polyatomic calculations using Gaussian orbitals were carried out in the late 1950s. The first configuration interaction calculations were carried out in Cambridge on the EDSAC computer in the 1950s using Gaussian orbitals by Boys and coworkers. By 1971, when a bibliography of ab initio calculations was published, the largest molecules included were naphthalene and azulene. Abstracts of many earlier developments in ab initio theory have been published by Schaefer.
In 1964, Hückel method calculations (using a simple linear combination of atomic orbitals (LCAO) method for the determination of electron energies of molecular orbitals of π electrons in conjugated hydrocarbon systems) of molecules ranging in complexity from butadiene and benzene to ovalene, were generated on computers at Berkeley and Oxford. These empirical methods were replaced in the 1960s by semi-empirical methods such as CNDO.
In the early 1970s, efficient ab initio computer programs such as ATMOL, GAUSSIAN, IBMOL, and POLYAYTOM, began to be used to speed up ab initio calculations of molecular orbitals. Of these four programs, only GAUSSIAN, now massively expanded, is still in use, but many other programs are now in use. At the same time, the methods of molecular mechanics, such as MM2, were developed, primarily by Norman Allinger.
One of the first mentions of the term "computational chemistry" can be found in the 1970 book Computers and Their Role in the Physical Sciences by Sidney Fernbach and Abraham Haskell Taub, where they state "It seems, therefore, that 'computational chemistry' can finally be more and more of a reality." During the 1970s, widely different methods began to be seen as part of a new emerging discipline of computational chemistry. The Journal of Computational Chemistry was first published in 1980.
Concepts
The term theoretical chemistry may be defined as a mathematical description of chemistry, whereas computational chemistry is usually used when a mathematical method is sufficiently well developed that it can be automated for implementation on a computer. Note that the words exact and perfect do not appear here, as very few aspects of chemistry can be computed exactly. However, almost every aspect of chemistry can be described in a qualitative or approximate quantitative computational scheme.
Molecules consist of nuclei and electrons, so the methods of quantum mechanics apply. Computational chemists often attempt to solve the non-relativistic Schrödinger equation, with relativistic corrections added, although some progress has been made in solving the fully relativistic Dirac equation. In principle, it is possible to solve the Schrödinger equation in either its time-dependent or time-independent form, as appropriate for the problem in hand; in practice, this is not possible except for very small systems. Therefore, a great number of approximate methods strive to achieve the best trade-off between accuracy and computational cost. Accuracy can always be improved with greater computational cost. Significant errors can present themselves in ab initio models comprising many electrons, due to the computational expense of full relativistic-inclusive methods. This complicates the study of molecules interacting with high atomic mass unit atoms, such as transitional metals and their catalytic properties. Present algorithms in computational chemistry can routinely calculate the properties of molecules that contain up to about 40 electrons with sufficient accuracy. Errors for energies can be less than a few kJ/mol. For geometries, bond lengths can be predicted within a few picometres and bond angles within 0.5 degrees. The treatment of larger molecules that contain a few dozen electrons is computationally tractable by approximate methods such as density functional theory (DFT). There is some dispute within the field whether or not the latter methods are sufficient to describe complex chemical reactions, such as those in biochemistry. Large molecules can be studied by semi-empirical approximate methods. Even larger molecules are treated by classical mechanics methods that employ what are called molecular mechanics. In QM/MM methods, small portions of large complexes are treated quantum mechanically (QM), and the remainder is treated approximately (MM).
In theoretical chemistry, chemists, physicists and mathematicians develop algorithms and computer programs to predict atomic and molecular properties and reaction paths for chemical reactions. Computational chemists, in contrast, may simply apply existing computer programs and methodologies to specific chemical questions. There are two different aspects to computational chemistry:
* Computational studies can be carried out to find a starting point for a laboratory synthesis, or to assist in understanding experimental data, such as the position and source of spectroscopic peaks.
* Computational studies can be used to predict the possibility of so far entirely unknown molecules or to explore reaction mechanisms that are not readily studied by experimental means.
Thus, computational chemistry can assist the experimental chemist or it can challenge the experimental chemist to find entirely new chemical objects.
Several major areas may be distinguished within computational chemistry:
* The prediction of the molecular structure of molecules by the use of the simulation of forces, or more accurate quantum chemical methods, to find stationary points on the energy surface as the position of the nuclei is varied.
* Storing and searching for data on chemical entities (see chemical databases).
* Identifying correlations between chemical structures and properties (see QSPR and QSAR).
* Computational approaches to help in the efficient synthesis of compounds.
* Computational approaches to design molecules that interact in specific ways with other molecules (e.g. drug design and catalysis).
Methods
A single molecular formula can represent a number of molecular isomers. Each isomer is a local minimum on the energy surface (called the potential energy surface) created from the total energy (i.e., the electronic energy, plus the repulsion energy between the nuclei) as a function of the coordinates of all the nuclei. A stationary point is a geometry such that the derivative of the energy with respect to all displacements of the nuclei is zero. A local (energy) minimum is a stationary point where all such displacements lead to an increase in energy. The local minimum that is lowest is called the global minimum and corresponds to the most stable isomer. If there is one particular coordinate change that leads to a decrease in the total energy in both directions, the stationary point is a transition structure and the coordinate is the reaction coordinate. This process of determining stationary points is called geometry optimization.
The determination of molecular structure by geometry optimization became routine only after efficient methods for calculating the first derivatives of the energy with respect to all atomic coordinates became available. Evaluation of the related second derivatives allows the prediction of vibrational frequencies if harmonic motion is estimated. More importantly, it allows for the characterization of stationary points. The frequencies are related to the eigenvalues of the Hessian matrix, which contains second derivatives. If the eigenvalues are all positive, then the frequencies are all real and the stationary point is a local minimum. If one eigenvalue is negative (i.e., an imaginary frequency), then the stationary point is a transition structure. If more than one eigenvalue is negative, then the stationary point is a more complex one, and is usually of little interest. When one of these is found, it is necessary to move the search away from it if the experimenter is looking solely for local minima and transition structures.
The total energy is determined by approximate solutions of the time-dependent Schrödinger equation, usually with no relativistic terms included, and by making use of the Born–Oppenheimer approximation, which allows for the separation of electronic and nuclear motions, thereby simplifying the Schrödinger equation. This leads to the evaluation of the total energy as a sum of the electronic energy at fixed nuclei positions and the repulsion energy of the nuclei. A notable exception are certain approaches called direct quantum chemistry, which treat electrons and nuclei on a common footing. Density functional methods and semi-empirical methods are variants on the major theme. For very large systems, the relative total energies can be compared using molecular mechanics. The ways of determining the total energy to predict molecular structures are:
Ab initio methods
The programs used in computational chemistry are based on many different quantum-chemical methods that solve the molecular Schrödinger equation associated with the molecular Hamiltonian. Methods that do not include any empirical or semi-empirical parameters in their equations – being derived directly from theoretical principles, with no inclusion of experimental data – are called ab initio methods. This does not imply that the solution is an exact one; they are all approximate quantum mechanical calculations. It means that a particular approximation is rigorously defined on first principles (quantum theory) and then solved within an error margin that is qualitatively known beforehand. If numerical iterative methods have to be employed, the aim is to iterate until full machine accuracy is obtained (the best that is possible with a finite word length on the computer, and within the mathematical and/or physical approximations made).
The simplest type of ab initio electronic structure calculation is the Hartree–Fock (HF) scheme, an extension of molecular orbital theory, in which the correlated electron–electron repulsion is not specifically taken into account; only its average effect is included in the calculation. As the basis set size is increased, the energy and wave function tend towards a limit called the Hartree–Fock limit. Many types of calculations (known as post-Hartree–Fock methods) begin with a Hartree–Fock calculation and subsequently correct for electron–electron repulsion, referred to also as electronic correlation. As these methods are pushed to the limit, they approach the exact solution of the non-relativistic Schrödinger equation. In order to obtain exact agreement with experiment, it is necessary to include relativistic and spin orbit terms, both of which are only really important for heavy atoms. In all of these approaches, in addition to the choice of method, it is necessary to choose a basis set. This is a set of functions, usually centered on the different atoms in the molecule, which are used to expand the molecular orbitals with the LCAO ansatz. Ab initio methods need to define a level of theory (the method) and a basis set.
The Hartree–Fock wave function is a single configuration or determinant. In some cases, particularly for bond breaking processes, this is quite inadequate, and several configurations need to be used. Here, the coefficients of the configurations and the coefficients of the basis functions are optimized together.
The total molecular energy can be evaluated as a function of the molecular geometry; in other words, the potential energy surface. Such a surface can be used for reaction dynamics. The stationary points of the surface lead to predictions of different isomers and the transition structures for conversion between isomers, but these can be determined without a full knowledge of the complete surface.
A particularly important objective, called computational thermochemistry, is to calculate thermochemical quantities such as the enthalpy of formation to chemical accuracy. Chemical accuracy is the accuracy required to make realistic chemical predictions and is generally considered to be 1 kcal/mol or 4 kJ/mol. To reach that accuracy in an economic way it is necessary to use a series of post-Hartree–Fock methods and combine the results. These methods are called quantum chemistry composite methods.
Density functional methods
Density functional theory (DFT) methods are often considered to be ab initio methods for determining the molecular electronic structure, even though many of the most common functionals use parameters derived from empirical data, or from more complex calculations. In DFT, the total energy is expressed in terms of the total one-electron density rather than the wave function. In this type of calculation, there is an approximate Hamiltonian and an approximate expression for the total electron density. DFT methods can be very accurate for little computational cost. Some methods combine the density functional exchange functional with the Hartree–Fock exchange term and are known as hybrid functional methods.
Semi-empirical and empirical methods
Semi-empirical quantum chemistry methods are based on the Hartree–Fock formalism, but make many approximations and obtain some parameters from empirical data. They are very important in computational chemistry for treating large molecules where the full Hartree–Fock method without the approximations is too expensive. The use of empirical parameters appears to allow some inclusion of correlation effects into the methods.
Semi-empirical methods follow what are often called empirical methods, where the two-electron part of the Hamiltonian is not explicitly included. For π-electron systems, this was the Hückel method proposed by Erich Hückel, and for all valence electron systems, the extended Hückel method proposed by Roald Hoffmann.
Molecular mechanics
In many cases, large molecular systems can be modeled successfully while avoiding quantum mechanical calculations entirely. Molecular mechanics simulations, for example, use a single classical expression for the energy of a compound, for instance the harmonic oscillator. All constants appearing in the equations must be obtained beforehand from experimental data or ab initio calculations.
The database of compounds used for parameterization, i.e., the resulting set of parameters and functions is called the force field, is crucial to the success of molecular mechanics calculations. A force field parameterized against a specific class of molecules, for instance proteins, would be expected to only have any relevance when describing other molecules of the same class.
These methods can be applied to proteins and other large biological molecules, and allow studies of the approach and interaction (docking) of potential drug molecules
Methods for solids
Computational chemical methods can be applied to solid state physics problems. The electronic structure of a crystal is in general described by a band structure, which defines the energies of electron orbitals for each point in the Brillouin zone. Ab initio and semi-empirical calculations yield orbital energies; therefore, they can be applied to band structure calculations. Since it is time-consuming to calculate the energy for a molecule, it is even more time-consuming to calculate them for the entire list of points in the Brillouin zone.
Chemical dynamics
Once the electronic and nuclear variables are separated (within the Born–Oppenheimer representation), in the time-dependent approach, the wave packet corresponding to the nuclear degrees of freedom is propagated via the time evolution operator (physics) associated to the time-dependent Schrödinger equation (for the full molecular Hamiltonian). In the complementary energy-dependent approach, the time-independent Schrödinger equation is solved using the scattering theory formalism. The potential representing the interatomic interaction is given by the potential energy surfaces. In general, the potential energy surfaces are coupled via the vibronic coupling terms.
The most popular methods for propagating the wave packet associated to the molecular geometry are:
* the split operator technique,
* the Chebyshev (real) polynomial,
* the multi-configuration time-dependent Hartree method (MCTDH),
* the semiclassical method.
Molecular dynamics
Molecular dynamics (MD) uses Newton's laws of motion to examine the time-dependent behavior of systems, including vibrations or Brownian motion, using a classical mechanical description. MD combined with density functional theory leads to the Car–Parrinello method.
Interpreting molecular wave functions
The atoms in molecules model developed by Richard Bader was developed in order to effectively link the quantum mechanical picture of a molecule, as an electronic wavefunction, to chemically useful older models such as the theory of Lewis pairs and the valence bond model. Bader has demonstrated that these empirically useful models are connected with the topology of the quantum charge density. This method improves on the use of Mulliken population analysis.
Software packages
There are many self-sufficient software packages used by computational chemists. Some include many methods covering a wide range, while others concentrating on a very specific range or even a single method. Details of most of them can be found in:
* Biomolecular modelling programs: proteins, nucleic acid.
* Molecular mechanics programs.
* Quantum chemistry and solid state physics software supporting several methods.
* Molecular design software
* Semi-empirical programs.
* Valence bond programs.
Saturday, October 2, 2010
Biochemistry
Biochemistry is the study of chemical processes in living organisms. It deals with the structures and functions of cellular components such as proteins, carbohydrates, lipids, nucleic acids and other biomolecules. Over the last 40 years biochemistry has become so successful at explaining living processes that now almost all areas of the life sciences from botany to medicine are engaged in biochemical research. Today the main focus of pure biochemistry is in understanding how biological molecules give rise to the processes that occur within living cells which in turn relates greatly to the study and understanding of whole organisms.
Among the vast number of different biomolecules, many are complex and large molecules (called polymers), which are composed of similar repeating subunits (called monomers). Each class of polymeric biomolecule has a different set of subunit types.For example, a protein is a polymer whose subunits are selected from a set of 20 or more amino acids. Biochemistry studies the chemical properties of important biological molecules, like proteins, and in particular the chemistry of enzyme-catalyzed reactions.
The biochemistry of cell metabolism and the endocrine system has been extensively described. Other areas of biochemistry include the genetic code (DNA, RNA), protein synthesis, cell membrane transport, and signal transduction.
History
Originally, it was generally believed that life was not subject to the laws of science the way non-life was. It was thought that only living beings could produce the molecules of life (from other, previously existing biomolecules). Then, in 1828, Friedrich Wöhler published a paper on the synthesis of urea, proving that organic compounds can be created artificially.
The dawn of biochemistry may have been the discovery of the first enzyme, diastase (today called amylase), in 1833 by Anselme Payen. Eduard Buchner contributed the first demonstration of a complex biochemical process outside of a cell in 1896: alcoholic fermentation in cell extracts of yeast. Although the term “biochemistry” seems to have been first used in 1882, it is generally accepted that the formal coinage of biochemistry occurred in 1903 by Carl Neuberg, a German chemist. Previously, this area would have been referred to as physiological chemistry. Since then, biochemistry has advanced, especially since the mid-20th century, with the development of new techniques such as chromatography, X-ray diffraction, dual polarisation interferometry, NMR spectroscopy, radioisotopic labeling, electron microscopy and molecular dynamics simulations. These techniques allowed for the discovery and detailed analysis of many molecules and metabolic pathways of the cell, such as glycolysis and the Krebs cycle (citric acid cycle).
Another significant historic event in biochemistry is the discovery of the gene and its role in the transfer of information in the cell. This part of biochemistry is often called molecular biology. In the 1950s, James D. Watson, Francis Crick, Rosalind Franklin, and Maurice Wilkins were instrumental in solving DNA structure and suggesting its relationship with genetic transfer of information. In 1958, George Beadle and Edward Tatum received the Nobel Prize for work in fungi showing that one gene produces one enzyme. In 1988, Colin Pitchfork was the first person convicted of murder with DNA evidence, which led to growth of forensic science. More recently, Andrew Z. Fire and Craig C. Mello received the 2006 Nobel Prize for discovering the role of RNA interference (RNAi), in the silencing of gene expression
Today, there are three main types of biochemistry. Plant biochemistry involves the study of the biochemistry of autotrophic organisms such as photosynthesis and other plant specific biochemical processes. General biochemistry encompasses both plant and animal biochemistry. Human/medical/medicinal biochemistry focuses on the biochemistry of humans and medical illnesses.
Monomers and polymers
The four main classes of molecules in biochemistry are carbohydrates, lipids, proteins, and nucleic acids. Many biological molecules are polymers: in this terminology, monomers are relatively small micromolecules that are linked together to create large macromolecules, which are known as polymers. When monomers are linked together to synthesize a biological polymer, they undergo a process called dehydration synthesis.
Carbohydrates
A molecule of sucrose (glucose + fructose), a disaccharide.
Carbohydrates are made from monomers called monosaccharides. Some of these monosaccharides include glucose (C6H12O6), fructose (C6H12O6), and deoxyribose (C5H10O4). When two monosaccharides undergo dehydration synthesis, water is produced, as two hydrogen atoms and one oxygen atom are lost from the two monosaccharides' hydroxyl group.
Lipids
A triglyceride with a glycerol molecule on the left and three fatty acids coming off it.
Lipids are usually made from one molecule of glycerol combined with other molecules. In triglycerides, the main group of bulk lipids, there is one molecule of glycerol and three fatty acids. Fatty acids are considered the monomer in that case, and may be saturated (no double bonds in the carbon chain) or unsaturated (one or more double bonds in the carbon chain).
Lipids, especially phospholipids, are also used in various pharmaceutical products, either as co-solubilisers (e.g. in parenteral infusions) or else as drug carrier components (e.g. in a liposome or transfersome).
Proteins
The general structure of an α-amino acid, with the amino group on the left and the carboxyl group on the right.
Proteins are very large molecules – macro-biopolymers – made from monomers called amino acids. There are 20 standard amino acids, each containing a carboxyl group, an amino group, and a side chain (known as an "R" group). The "R" group is what makes each amino acid different, and the properties of the side chains greatly influence the overall three-dimensional conformation of a protein. When amino acids combine, they form a special bond called a peptide bond through dehydration synthesis, and become a polypeptide, or protein.
Nucleic acids
The structure of deoxyribonucleic acid (DNA), the picture shows the monomers being put together.
Nucleic acids are the molecules that make up DNA, an extremely important substance which all cellular organisms use to store their genetic information. The most common nucleic acids are deoxyribonucleic acid and ribonucleic acid. Their monomers are called nucleotides. The most common nucleotides are adenine, cytosine, guanine, thymine, and uracil. Adenine binds with thymine and uracil; thymine only binds with adenine; and cytosine and guanine can only bind with each other.
Carbohydrates
The function of carbohydrates includes energy storage and providing structure. Sugars are carbohydrates, but not all carbohydrates are sugars. There are more carbohydrates on Earth than any other known type of biomolecule; they are used to store energy and genetic information, as well as play important roles in cell to cell interactions and communications.
Monosaccharides
Glucose
The simplest type of carbohydrate is a monosaccharide, which among other properties contains carbon, hydrogen, and oxygen, mostly in a ratio of 1:2:1 (generalized formula CnH2nOn, where n is at least 3). Glucose, one of the most important carbohydrates, is an example of a monosaccharide. So is fructose, the sugar commonly associated with the sweet taste of fruits. Some carbohydrates (especially after condensation to oligo- and polysaccharides) contain less carbon relative to H and O, which still are present in 2:1 (H:O) ratio. Monosaccharides can be grouped into aldoses (having an aldehyde group at the end of the chain, e. g. glucose) and ketoses (having a keto group in their chain; e. g. fructose). Both aldoses and ketoses occur in an equilibrium (starting with chain lengths of C4) cyclic forms. These are generated by bond formation between one of the hydroxyl groups of the sugar chain with the carbon of the aldehyde or keto group to form a hemiacetal bond. This leads to saturated five-membered (in furanoses) or six-membered (in pyranoses) heterocyclic rings containing one O as heteroatom.
Disaccharides
Sucrose: ordinary table sugar and probably the most familiar carbohydrate.
Two monosaccharides can be joined together using dehydration synthesis, in which a hydrogen atom is removed from the end of one molecule and a hydroxyl group (—OH) is removed from the other; the remaining residues are then attached at the sites from which the atoms were removed. The H—OH or H2O is then released as a molecule of water, hence the term dehydration. The new molecule, consisting of two monosaccharides, is called a disaccharide and is conjoined together by a glycosidic or ether bond. The reverse reaction can also occur, using a molecule of water to split up a disaccharide and break the glycosidic bond; this is termed hydrolysis. The most well-known disaccharide is sucrose, ordinary sugar (in scientific contexts, called table sugar or cane sugar to differentiate it from other sugars). Sucrose consists of a glucose molecule and a fructose molecule joined together. Another important disaccharide is lactose, consisting of a glucose molecule and a galactose molecule. As most humans age, the production of lactase, the enzyme that hydrolyzes lactose back into glucose and galactose, typically decreases. This results in lactase deficiency, also called lactose intolerance.
Sugar polymers are characterised by having reducing or non-reducing ends. A reducing end of a carbohydrate is a carbon atom which can be in equilibrium with the open-chain aldehyde or keto form. If the joining of monomers takes place at such a carbon atom, the free hydroxy group of the pyranose or furanose form is exchanged with an OH-side chain of another sugar, yielding a full acetal. This prevents opening of the chain to the aldehyde or keto form and renders the modified residue non-reducing. Lactose contains a reducing end at its glucose moiety, whereas the galactose moiety form a full acetal with the C4-OH group of glucose. Saccharose does not have a reducing end because of full acetal formation between the aldehyde carbon of glucose (C1) and the keto carbon of fructose (C2).
Oligosaccharides and polysaccharides
Cellulose as polymer of β-D-glucose
When a few (around three to six) monosaccharides are joined together, it is called an oligosaccharide (oligo- meaning "few"). These molecules tend to be used as markers and signals, as well as having some other uses. Many monosaccharides joined together make a polysaccharide. They can be joined together in one long linear chain, or they may be branched. Two of the most common polysaccharides are cellulose and glycogen, both consisting of repeating glucose monomers.
* Cellulose is made by plants and is an important structural component of their cell walls. Humans can neither manufacture nor digest it.
* Glycogen, on the other hand, is an animal carbohydrate; humans and other animals use it as a form of energy storage.
Use of carbohydrates as an energy source
Glucose is the major energy source in most life forms. For instance, polysaccharides are broken down into their monomers (glycogen phosphorylase removes glucose residues from glycogen). Disaccharides like lactose or sucrose are cleaved into their two component monosaccharides.
Glycolysis (anaerobic)
Glucose is mainly metabolized by a very important ten-step pathway called glycolysis, the net result of which is to break down one molecule of glucose into two molecules of pyruvate; this also produces a net two molecules of ATP, the energy currency of cells, along with two reducing equivalents in the form of converting NAD+ to NADH. This does not require oxygen; if no oxygen is available (or the cell cannot use oxygen), the NAD is restored by converting the pyruvate to lactate (lactic acid) (e. g. in humans) or to ethanol plus carbon dioxide (e. g. in yeast). Other monosaccharides like galactose and fructose can be converted into intermediates of the glycolytic pathway.
Aerobic
In aerobic cells with sufficient oxygen, like most human cells, the pyruvate is further metabolized. It is irreversibly converted to acetyl-CoA, giving off one carbon atom as the waste product carbon dioxide, generating another reducing equivalent as NADH. The two molecules acetyl-CoA (from one molecule of glucose) then enter the citric acid cycle, producing two more molecules of ATP, six more NADH molecules and two reduced (ubi)quinones (via FADH2 as enzyme-bound cofactor), and releasing the remaining carbon atoms as carbon dioxide. The produced NADH and quinol molecules then feed into the enzyme complexes of the respiratory chain, an electron transport system transferring the electrons ultimately to oxygen and conserving the released energy in the form of a proton gradient over a membrane (inner mitochondrial membrane in eukaryotes). Thereby, oxygen is reduced to water and the original electron acceptors NAD+ and quinone are regenerated. This is why humans breathe in oxygen and breathe out carbon dioxide. The energy released from transferring the electrons from high-energy states in NADH and quinol is conserved first as proton gradient and converted to ATP via ATP synthase. This generates an additional 28 molecules of ATP (24 from the 8 NADH + 4 from the 2 quinols), totaling to 32 molecules of ATP conserved per degraded glucose (two from glycolysis + two from the citrate cycle). It is clear that using oxygen to completely oxidize glucose provides an organism with far more energy than any oxygen-independent metabolic feature, and this is thought to be the reason why complex life appeared only after Earth's atmosphere accumulated large amounts of oxygen.
Gluconeogenesis
In vertebrates, vigorously contracting skeletal muscles (during weightlifting or sprinting, for example) do not receive enough oxygen to meet the energy demand, and so they shift to anaerobic metabolism, converting glucose to lactate. The liver regenerates the glucose, using a process called gluconeogenesis. This process is not quite the opposite of glycolysis, and actually requires three times the amount of energy gained from glycolysis (six molecules of ATP are used, compared to the two gained in glycolysis). Analogous to the above reactions, the glucose produced can then undergo glycolysis in tissues that need energy, be stored as glycogen (or starch in plants), or be converted to other monosaccharides or joined into di- or oligosaccharides. The combined pathways of glycolysis during exercise, lactate's crossing via the bloodstream to the liver, subsequent gluconeogenesis and release of glucose into the bloodstream is called the Cori cycle.
Proteins
A schematic of hemoglobin. The red and blue ribbons represent the protein globin; the green structures are the heme groups.
Like carbohydrates, some proteins perform largely structural roles. For instance, movements of the proteins actin and myosin ultimately are responsible for the contraction of skeletal muscle. One property many proteins have is that they specifically bind to a certain molecule or class of molecules—they may be extremely selective in what they bind. Antibodies are an example of proteins that attach to one specific type of molecule. In fact, the enzyme-linked immunosorbent assay (ELISA), which uses antibodies, is currently one of the most sensitive tests modern medicine uses to detect various biomolecules. Probably the most important proteins, however, are the enzymes. These molecules recognize specific reactant molecules called substrates; they then catalyze the reation between them. By lowering the activation energy, the enzyme speeds up that reaction by a rate of 1011 or more: a reaction that would normally take over 3,000 years to complete spontaneously might take less than a second with an enzyme. The enzyme itself is not used up in the process, and is free to catalyze the same reaction with a new set of substrates. Using various modifiers, the activity of the enzyme can be regulated, enabling control of the biochemistry of the cell as a whole.
In essence, proteins are chains of amino acids. An amino acid consists of a carbon atom bound to four groups. One is an amino group, —NH2, and one is a carboxylic acid group, —COOH (although these exist as —NH3+ and —COO− under physiologic conditions). The third is a simple hydrogen atom. The fourth is commonly denoted "—R" and is different for each amino acid. There are twenty standard amino acids. Some of these have functions by themselves or in a modified form; for instance, glutamate functions as an important neurotransmitter.
Generic amino acids (1) in neutral form, (2) as they exist physiologically, and (3) joined together as a dipeptide.
Amino acids can be joined together via a peptide bond. In this dehydration synthesis, a water molecule is removed and the peptide bond connects the nitrogen of one amino acid's amino group to the carbon of the other's carboxylic acid group. The resulting molecule is called a dipeptide, and short stretches of amino acids (usually, fewer than around thirty) are called peptides or polypeptides. Longer stretches merit the title proteins. As an example, the important blood serum protein albumin contains 585 amino acid residues.
The structure of proteins is traditionally described in a hierarchy of four levels. The primary structure of a protein simply consists of its linear sequence of amino acids; for instance, "alanine-glycine-tryptophan-serine-glutamate-asparagine-glycine-lysine-…". Secondary structure is concerned with local morphology (morphology being the study of structure). Some combinations of amino acids will tend to curl up in a coil called an α-helix or into a sheet called a β-sheet; some α-helixes can be seen in the hemoglobin schematic above. Tertiary structure is the entire three-dimensional shape of the protein. This shape is determined by the sequence of amino acids. In fact, a single change can change the entire structure. The alpha chain of hemoglobin contains 146 amino acid residues; substitution of the glutamate residue at position 6 with a valine residue changes the behavior of hemoglobin so much that it results in sickle-cell disease. Finally quaternary structure is concerned with the structure of a protein with multiple peptide subunits, like hemoglobin with its four subunits. Not all proteins have more than one subunit.
Ingested proteins are usually broken up into single amino acids or dipeptides in the small intestine, and then absorbed. They can then be joined together to make new proteins. Intermediate products of glycolysis, the citric acid cycle, and the pentose phosphate pathway can be used to make all twenty amino acids, and most bacteria and plants possess all the necessary enzymes to synthesize them. Humans and other mammals, however, can only synthesize half of them. They cannot synthesize isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine. These are the essential amino acids, since it is essential to ingest them. Mammals do possess the enzymes to synthesize alanine, asparagine, aspartate, cysteine, glutamate, glutamine, glycine, proline, serine, and tyrosine, the nonessential amino acids. While they can synthesize arginine and histidine, they cannot produce it in sufficient amounts for young, growing animals, and so these are often considered essential amino acids.
If the amino group is removed from an amino acid, it leaves behind a carbon skeleton called an α-keto acid. Enzymes called transaminases can easily transfer the amino group from one amino acid (making it an α-keto acid) to another α-keto acid (making it an amino acid). This is important in the biosynthesis of amino acids, as for many of the pathways, intermediates from other biochemical pathways are converted to the α-keto acid skeleton, and then an amino group is added, often via transamination. The amino acids may then be linked together to make a protein.
A similar process is used to break down proteins. It is first hydrolyzed into its component amino acids. Free ammonia (NH3), existing as the ammonium ion (NH4+) in blood, is toxic to life forms. A suitable method for excreting it must therefore exist. Different strategies have evolved in different animals, depending on the animals' needs. Unicellular organisms, of course, simply release the ammonia into the environment. Similarly, bony fish can release the ammonia into the water where it is quickly diluted. In general, mammals convert the ammonia into urea, via the urea cycle.
Lipids
The term lipid comprises a diverse range of molecules and to some extent is a catchall for relatively water-insoluble or nonpolar compounds of biological origin, including waxes, fatty acids, fatty-acid derived phospholipids, sphingolipids, glycolipids and terpenoids (e.g. retinoids and steroids). Some lipids are linear aliphatic molecules, while others have ring structures. Some are aromatic, while others are not. Some are flexible, while others are rigid.
Most lipids have some polar character in addition to being largely nonpolar. Generally, the bulk of their structure is nonpolar or hydrophobic ("water-fearing"), meaning that it does not interact well with polar solvents like water. Another part of their structure is polar or hydrophilic ("water-loving") and will tend to associate with polar solvents like water. This makes them amphiphilic molecules (having both hydrophobic and hydrophilic portions). In the case of cholesterol, the polar group is a mere -OH (hydroxyl or alcohol). In the case of phospholipids, the polar groups are considerably larger and more polar, as described below.
Lipids are an integral part of our daily diet. Most oils and milk products that we use for cooking and eating like butter, cheese, ghee etc., are composed of fats. Vegetable oils are rich in various polyunsaturated fatty acids (PUFA). Lipid-containing foods undergo digestion within the body and are broken into fatty acids and glycerol, which are the final degradation products of fats and lipids.
Nucleic acids
A nucleic acid is a complex, high-molecular-weight biochemical macromolecule composed of nucleotide chains that convey genetic information. The most common nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). Nucleic acids are found in all living cells and viruses. Aside from the genetic material of the cell, nucleic acids often play a role as second messengers, as well as forming the base molecule for adenosine triphosphate, the primary energy-carrier molecule found in all living organisms.
Nucleic acid, so called because of its prevalence in cellular nuclei, is the generic name of the family of biopolymers. The monomers are called nucleotides, and each consists of three components: a nitrogenous heterocyclic base (either a purine or a pyrimidine), a pentose sugar, and a phosphate group. Different nucleic acid types differ in the specific sugar found in their chain (e.g. DNA or deoxyribonucleic acid contains 2-deoxyriboses). Also, the nitrogenous bases possible in the two nucleic acids are different: adenine, cytosine, and guanine occur in both RNA and DNA, while thymine occurs only in DNA and uracil occurs in RNA.
Relationship to other "molecular-scale" biological sciences
Schematic relationship between biochemistry, genetics and molecular biology
Researchers in biochemistry use specific techniques native to biochemistry, but increasingly combine these with techniques and ideas from genetics, molecular biology and biophysics. There has never been a hard-line between these disciplines in terms of content and technique. Today the terms molecular biology and biochemistry are nearly interchangeable. The following figure is a schematic that depicts one possible view of the relationship between the fields:
Simplistic overview of the chemical basis of love, one of many applications that may be described in terms of biochemistry.
* Biochemistry is the study of the chemical substances and vital processes occurring in living organisms. Biochemists focus heavily on the role, function, and structure of biomolecules. The study of the chemistry behind biological processes and the synthesis of biologically active molecules are examples of biochemistry.
* Genetics is the study of the effect of genetic differences on organisms. Often this can be inferred by the absence of a normal component (e.g. one gene). The study of "mutants" – organisms which lack one or more functional components with respect to the so-called "wild type" or normal phenotype. Genetic interactions (epistasis) can often confound simple interpretations of such "knock-out" studies.
* Molecular biology is the study of molecular underpinnings of the process of replication, transcription and translation of the genetic material. The central dogma of molecular biology where genetic material is transcribed into RNA and then translated into protein, despite being an oversimplified picture of molecular biology, still provides a good starting point for understanding the field. This picture, however, is undergoing revision in light of emerging novel roles for RNA.
* Chemical Biology seeks to develop new tools based on small molecules that allow minimal perturbation of biological systems while providing detailed information about their function. Further, chemical biology employs biological systems to create non-natural hybrids between biomolecules and synthetic devices (for example emptied viral capsids that can deliver gene therapy or drug molecules).
Among the vast number of different biomolecules, many are complex and large molecules (called polymers), which are composed of similar repeating subunits (called monomers). Each class of polymeric biomolecule has a different set of subunit types.For example, a protein is a polymer whose subunits are selected from a set of 20 or more amino acids. Biochemistry studies the chemical properties of important biological molecules, like proteins, and in particular the chemistry of enzyme-catalyzed reactions.
The biochemistry of cell metabolism and the endocrine system has been extensively described. Other areas of biochemistry include the genetic code (DNA, RNA), protein synthesis, cell membrane transport, and signal transduction.
History
Originally, it was generally believed that life was not subject to the laws of science the way non-life was. It was thought that only living beings could produce the molecules of life (from other, previously existing biomolecules). Then, in 1828, Friedrich Wöhler published a paper on the synthesis of urea, proving that organic compounds can be created artificially.
The dawn of biochemistry may have been the discovery of the first enzyme, diastase (today called amylase), in 1833 by Anselme Payen. Eduard Buchner contributed the first demonstration of a complex biochemical process outside of a cell in 1896: alcoholic fermentation in cell extracts of yeast. Although the term “biochemistry” seems to have been first used in 1882, it is generally accepted that the formal coinage of biochemistry occurred in 1903 by Carl Neuberg, a German chemist. Previously, this area would have been referred to as physiological chemistry. Since then, biochemistry has advanced, especially since the mid-20th century, with the development of new techniques such as chromatography, X-ray diffraction, dual polarisation interferometry, NMR spectroscopy, radioisotopic labeling, electron microscopy and molecular dynamics simulations. These techniques allowed for the discovery and detailed analysis of many molecules and metabolic pathways of the cell, such as glycolysis and the Krebs cycle (citric acid cycle).
Another significant historic event in biochemistry is the discovery of the gene and its role in the transfer of information in the cell. This part of biochemistry is often called molecular biology. In the 1950s, James D. Watson, Francis Crick, Rosalind Franklin, and Maurice Wilkins were instrumental in solving DNA structure and suggesting its relationship with genetic transfer of information. In 1958, George Beadle and Edward Tatum received the Nobel Prize for work in fungi showing that one gene produces one enzyme. In 1988, Colin Pitchfork was the first person convicted of murder with DNA evidence, which led to growth of forensic science. More recently, Andrew Z. Fire and Craig C. Mello received the 2006 Nobel Prize for discovering the role of RNA interference (RNAi), in the silencing of gene expression
Today, there are three main types of biochemistry. Plant biochemistry involves the study of the biochemistry of autotrophic organisms such as photosynthesis and other plant specific biochemical processes. General biochemistry encompasses both plant and animal biochemistry. Human/medical/medicinal biochemistry focuses on the biochemistry of humans and medical illnesses.
Monomers and polymers
The four main classes of molecules in biochemistry are carbohydrates, lipids, proteins, and nucleic acids. Many biological molecules are polymers: in this terminology, monomers are relatively small micromolecules that are linked together to create large macromolecules, which are known as polymers. When monomers are linked together to synthesize a biological polymer, they undergo a process called dehydration synthesis.
Carbohydrates
A molecule of sucrose (glucose + fructose), a disaccharide.
Carbohydrates are made from monomers called monosaccharides. Some of these monosaccharides include glucose (C6H12O6), fructose (C6H12O6), and deoxyribose (C5H10O4). When two monosaccharides undergo dehydration synthesis, water is produced, as two hydrogen atoms and one oxygen atom are lost from the two monosaccharides' hydroxyl group.
Lipids
A triglyceride with a glycerol molecule on the left and three fatty acids coming off it.
Lipids are usually made from one molecule of glycerol combined with other molecules. In triglycerides, the main group of bulk lipids, there is one molecule of glycerol and three fatty acids. Fatty acids are considered the monomer in that case, and may be saturated (no double bonds in the carbon chain) or unsaturated (one or more double bonds in the carbon chain).
Lipids, especially phospholipids, are also used in various pharmaceutical products, either as co-solubilisers (e.g. in parenteral infusions) or else as drug carrier components (e.g. in a liposome or transfersome).
Proteins
The general structure of an α-amino acid, with the amino group on the left and the carboxyl group on the right.
Proteins are very large molecules – macro-biopolymers – made from monomers called amino acids. There are 20 standard amino acids, each containing a carboxyl group, an amino group, and a side chain (known as an "R" group). The "R" group is what makes each amino acid different, and the properties of the side chains greatly influence the overall three-dimensional conformation of a protein. When amino acids combine, they form a special bond called a peptide bond through dehydration synthesis, and become a polypeptide, or protein.
Nucleic acids
The structure of deoxyribonucleic acid (DNA), the picture shows the monomers being put together.
Nucleic acids are the molecules that make up DNA, an extremely important substance which all cellular organisms use to store their genetic information. The most common nucleic acids are deoxyribonucleic acid and ribonucleic acid. Their monomers are called nucleotides. The most common nucleotides are adenine, cytosine, guanine, thymine, and uracil. Adenine binds with thymine and uracil; thymine only binds with adenine; and cytosine and guanine can only bind with each other.
Carbohydrates
The function of carbohydrates includes energy storage and providing structure. Sugars are carbohydrates, but not all carbohydrates are sugars. There are more carbohydrates on Earth than any other known type of biomolecule; they are used to store energy and genetic information, as well as play important roles in cell to cell interactions and communications.
Monosaccharides
Glucose
The simplest type of carbohydrate is a monosaccharide, which among other properties contains carbon, hydrogen, and oxygen, mostly in a ratio of 1:2:1 (generalized formula CnH2nOn, where n is at least 3). Glucose, one of the most important carbohydrates, is an example of a monosaccharide. So is fructose, the sugar commonly associated with the sweet taste of fruits. Some carbohydrates (especially after condensation to oligo- and polysaccharides) contain less carbon relative to H and O, which still are present in 2:1 (H:O) ratio. Monosaccharides can be grouped into aldoses (having an aldehyde group at the end of the chain, e. g. glucose) and ketoses (having a keto group in their chain; e. g. fructose). Both aldoses and ketoses occur in an equilibrium (starting with chain lengths of C4) cyclic forms. These are generated by bond formation between one of the hydroxyl groups of the sugar chain with the carbon of the aldehyde or keto group to form a hemiacetal bond. This leads to saturated five-membered (in furanoses) or six-membered (in pyranoses) heterocyclic rings containing one O as heteroatom.
Disaccharides
Sucrose: ordinary table sugar and probably the most familiar carbohydrate.
Two monosaccharides can be joined together using dehydration synthesis, in which a hydrogen atom is removed from the end of one molecule and a hydroxyl group (—OH) is removed from the other; the remaining residues are then attached at the sites from which the atoms were removed. The H—OH or H2O is then released as a molecule of water, hence the term dehydration. The new molecule, consisting of two monosaccharides, is called a disaccharide and is conjoined together by a glycosidic or ether bond. The reverse reaction can also occur, using a molecule of water to split up a disaccharide and break the glycosidic bond; this is termed hydrolysis. The most well-known disaccharide is sucrose, ordinary sugar (in scientific contexts, called table sugar or cane sugar to differentiate it from other sugars). Sucrose consists of a glucose molecule and a fructose molecule joined together. Another important disaccharide is lactose, consisting of a glucose molecule and a galactose molecule. As most humans age, the production of lactase, the enzyme that hydrolyzes lactose back into glucose and galactose, typically decreases. This results in lactase deficiency, also called lactose intolerance.
Sugar polymers are characterised by having reducing or non-reducing ends. A reducing end of a carbohydrate is a carbon atom which can be in equilibrium with the open-chain aldehyde or keto form. If the joining of monomers takes place at such a carbon atom, the free hydroxy group of the pyranose or furanose form is exchanged with an OH-side chain of another sugar, yielding a full acetal. This prevents opening of the chain to the aldehyde or keto form and renders the modified residue non-reducing. Lactose contains a reducing end at its glucose moiety, whereas the galactose moiety form a full acetal with the C4-OH group of glucose. Saccharose does not have a reducing end because of full acetal formation between the aldehyde carbon of glucose (C1) and the keto carbon of fructose (C2).
Oligosaccharides and polysaccharides
Cellulose as polymer of β-D-glucose
When a few (around three to six) monosaccharides are joined together, it is called an oligosaccharide (oligo- meaning "few"). These molecules tend to be used as markers and signals, as well as having some other uses. Many monosaccharides joined together make a polysaccharide. They can be joined together in one long linear chain, or they may be branched. Two of the most common polysaccharides are cellulose and glycogen, both consisting of repeating glucose monomers.
* Cellulose is made by plants and is an important structural component of their cell walls. Humans can neither manufacture nor digest it.
* Glycogen, on the other hand, is an animal carbohydrate; humans and other animals use it as a form of energy storage.
Use of carbohydrates as an energy source
Glucose is the major energy source in most life forms. For instance, polysaccharides are broken down into their monomers (glycogen phosphorylase removes glucose residues from glycogen). Disaccharides like lactose or sucrose are cleaved into their two component monosaccharides.
Glycolysis (anaerobic)
Glucose is mainly metabolized by a very important ten-step pathway called glycolysis, the net result of which is to break down one molecule of glucose into two molecules of pyruvate; this also produces a net two molecules of ATP, the energy currency of cells, along with two reducing equivalents in the form of converting NAD+ to NADH. This does not require oxygen; if no oxygen is available (or the cell cannot use oxygen), the NAD is restored by converting the pyruvate to lactate (lactic acid) (e. g. in humans) or to ethanol plus carbon dioxide (e. g. in yeast). Other monosaccharides like galactose and fructose can be converted into intermediates of the glycolytic pathway.
Aerobic
In aerobic cells with sufficient oxygen, like most human cells, the pyruvate is further metabolized. It is irreversibly converted to acetyl-CoA, giving off one carbon atom as the waste product carbon dioxide, generating another reducing equivalent as NADH. The two molecules acetyl-CoA (from one molecule of glucose) then enter the citric acid cycle, producing two more molecules of ATP, six more NADH molecules and two reduced (ubi)quinones (via FADH2 as enzyme-bound cofactor), and releasing the remaining carbon atoms as carbon dioxide. The produced NADH and quinol molecules then feed into the enzyme complexes of the respiratory chain, an electron transport system transferring the electrons ultimately to oxygen and conserving the released energy in the form of a proton gradient over a membrane (inner mitochondrial membrane in eukaryotes). Thereby, oxygen is reduced to water and the original electron acceptors NAD+ and quinone are regenerated. This is why humans breathe in oxygen and breathe out carbon dioxide. The energy released from transferring the electrons from high-energy states in NADH and quinol is conserved first as proton gradient and converted to ATP via ATP synthase. This generates an additional 28 molecules of ATP (24 from the 8 NADH + 4 from the 2 quinols), totaling to 32 molecules of ATP conserved per degraded glucose (two from glycolysis + two from the citrate cycle). It is clear that using oxygen to completely oxidize glucose provides an organism with far more energy than any oxygen-independent metabolic feature, and this is thought to be the reason why complex life appeared only after Earth's atmosphere accumulated large amounts of oxygen.
Gluconeogenesis
In vertebrates, vigorously contracting skeletal muscles (during weightlifting or sprinting, for example) do not receive enough oxygen to meet the energy demand, and so they shift to anaerobic metabolism, converting glucose to lactate. The liver regenerates the glucose, using a process called gluconeogenesis. This process is not quite the opposite of glycolysis, and actually requires three times the amount of energy gained from glycolysis (six molecules of ATP are used, compared to the two gained in glycolysis). Analogous to the above reactions, the glucose produced can then undergo glycolysis in tissues that need energy, be stored as glycogen (or starch in plants), or be converted to other monosaccharides or joined into di- or oligosaccharides. The combined pathways of glycolysis during exercise, lactate's crossing via the bloodstream to the liver, subsequent gluconeogenesis and release of glucose into the bloodstream is called the Cori cycle.
Proteins
A schematic of hemoglobin. The red and blue ribbons represent the protein globin; the green structures are the heme groups.
Like carbohydrates, some proteins perform largely structural roles. For instance, movements of the proteins actin and myosin ultimately are responsible for the contraction of skeletal muscle. One property many proteins have is that they specifically bind to a certain molecule or class of molecules—they may be extremely selective in what they bind. Antibodies are an example of proteins that attach to one specific type of molecule. In fact, the enzyme-linked immunosorbent assay (ELISA), which uses antibodies, is currently one of the most sensitive tests modern medicine uses to detect various biomolecules. Probably the most important proteins, however, are the enzymes. These molecules recognize specific reactant molecules called substrates; they then catalyze the reation between them. By lowering the activation energy, the enzyme speeds up that reaction by a rate of 1011 or more: a reaction that would normally take over 3,000 years to complete spontaneously might take less than a second with an enzyme. The enzyme itself is not used up in the process, and is free to catalyze the same reaction with a new set of substrates. Using various modifiers, the activity of the enzyme can be regulated, enabling control of the biochemistry of the cell as a whole.
In essence, proteins are chains of amino acids. An amino acid consists of a carbon atom bound to four groups. One is an amino group, —NH2, and one is a carboxylic acid group, —COOH (although these exist as —NH3+ and —COO− under physiologic conditions). The third is a simple hydrogen atom. The fourth is commonly denoted "—R" and is different for each amino acid. There are twenty standard amino acids. Some of these have functions by themselves or in a modified form; for instance, glutamate functions as an important neurotransmitter.
Generic amino acids (1) in neutral form, (2) as they exist physiologically, and (3) joined together as a dipeptide.
Amino acids can be joined together via a peptide bond. In this dehydration synthesis, a water molecule is removed and the peptide bond connects the nitrogen of one amino acid's amino group to the carbon of the other's carboxylic acid group. The resulting molecule is called a dipeptide, and short stretches of amino acids (usually, fewer than around thirty) are called peptides or polypeptides. Longer stretches merit the title proteins. As an example, the important blood serum protein albumin contains 585 amino acid residues.
The structure of proteins is traditionally described in a hierarchy of four levels. The primary structure of a protein simply consists of its linear sequence of amino acids; for instance, "alanine-glycine-tryptophan-serine-glutamate-asparagine-glycine-lysine-…". Secondary structure is concerned with local morphology (morphology being the study of structure). Some combinations of amino acids will tend to curl up in a coil called an α-helix or into a sheet called a β-sheet; some α-helixes can be seen in the hemoglobin schematic above. Tertiary structure is the entire three-dimensional shape of the protein. This shape is determined by the sequence of amino acids. In fact, a single change can change the entire structure. The alpha chain of hemoglobin contains 146 amino acid residues; substitution of the glutamate residue at position 6 with a valine residue changes the behavior of hemoglobin so much that it results in sickle-cell disease. Finally quaternary structure is concerned with the structure of a protein with multiple peptide subunits, like hemoglobin with its four subunits. Not all proteins have more than one subunit.
Ingested proteins are usually broken up into single amino acids or dipeptides in the small intestine, and then absorbed. They can then be joined together to make new proteins. Intermediate products of glycolysis, the citric acid cycle, and the pentose phosphate pathway can be used to make all twenty amino acids, and most bacteria and plants possess all the necessary enzymes to synthesize them. Humans and other mammals, however, can only synthesize half of them. They cannot synthesize isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine. These are the essential amino acids, since it is essential to ingest them. Mammals do possess the enzymes to synthesize alanine, asparagine, aspartate, cysteine, glutamate, glutamine, glycine, proline, serine, and tyrosine, the nonessential amino acids. While they can synthesize arginine and histidine, they cannot produce it in sufficient amounts for young, growing animals, and so these are often considered essential amino acids.
If the amino group is removed from an amino acid, it leaves behind a carbon skeleton called an α-keto acid. Enzymes called transaminases can easily transfer the amino group from one amino acid (making it an α-keto acid) to another α-keto acid (making it an amino acid). This is important in the biosynthesis of amino acids, as for many of the pathways, intermediates from other biochemical pathways are converted to the α-keto acid skeleton, and then an amino group is added, often via transamination. The amino acids may then be linked together to make a protein.
A similar process is used to break down proteins. It is first hydrolyzed into its component amino acids. Free ammonia (NH3), existing as the ammonium ion (NH4+) in blood, is toxic to life forms. A suitable method for excreting it must therefore exist. Different strategies have evolved in different animals, depending on the animals' needs. Unicellular organisms, of course, simply release the ammonia into the environment. Similarly, bony fish can release the ammonia into the water where it is quickly diluted. In general, mammals convert the ammonia into urea, via the urea cycle.
Lipids
The term lipid comprises a diverse range of molecules and to some extent is a catchall for relatively water-insoluble or nonpolar compounds of biological origin, including waxes, fatty acids, fatty-acid derived phospholipids, sphingolipids, glycolipids and terpenoids (e.g. retinoids and steroids). Some lipids are linear aliphatic molecules, while others have ring structures. Some are aromatic, while others are not. Some are flexible, while others are rigid.
Most lipids have some polar character in addition to being largely nonpolar. Generally, the bulk of their structure is nonpolar or hydrophobic ("water-fearing"), meaning that it does not interact well with polar solvents like water. Another part of their structure is polar or hydrophilic ("water-loving") and will tend to associate with polar solvents like water. This makes them amphiphilic molecules (having both hydrophobic and hydrophilic portions). In the case of cholesterol, the polar group is a mere -OH (hydroxyl or alcohol). In the case of phospholipids, the polar groups are considerably larger and more polar, as described below.
Lipids are an integral part of our daily diet. Most oils and milk products that we use for cooking and eating like butter, cheese, ghee etc., are composed of fats. Vegetable oils are rich in various polyunsaturated fatty acids (PUFA). Lipid-containing foods undergo digestion within the body and are broken into fatty acids and glycerol, which are the final degradation products of fats and lipids.
Nucleic acids
A nucleic acid is a complex, high-molecular-weight biochemical macromolecule composed of nucleotide chains that convey genetic information. The most common nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). Nucleic acids are found in all living cells and viruses. Aside from the genetic material of the cell, nucleic acids often play a role as second messengers, as well as forming the base molecule for adenosine triphosphate, the primary energy-carrier molecule found in all living organisms.
Nucleic acid, so called because of its prevalence in cellular nuclei, is the generic name of the family of biopolymers. The monomers are called nucleotides, and each consists of three components: a nitrogenous heterocyclic base (either a purine or a pyrimidine), a pentose sugar, and a phosphate group. Different nucleic acid types differ in the specific sugar found in their chain (e.g. DNA or deoxyribonucleic acid contains 2-deoxyriboses). Also, the nitrogenous bases possible in the two nucleic acids are different: adenine, cytosine, and guanine occur in both RNA and DNA, while thymine occurs only in DNA and uracil occurs in RNA.
Relationship to other "molecular-scale" biological sciences
Schematic relationship between biochemistry, genetics and molecular biology
Researchers in biochemistry use specific techniques native to biochemistry, but increasingly combine these with techniques and ideas from genetics, molecular biology and biophysics. There has never been a hard-line between these disciplines in terms of content and technique. Today the terms molecular biology and biochemistry are nearly interchangeable. The following figure is a schematic that depicts one possible view of the relationship between the fields:
Simplistic overview of the chemical basis of love, one of many applications that may be described in terms of biochemistry.
* Biochemistry is the study of the chemical substances and vital processes occurring in living organisms. Biochemists focus heavily on the role, function, and structure of biomolecules. The study of the chemistry behind biological processes and the synthesis of biologically active molecules are examples of biochemistry.
* Genetics is the study of the effect of genetic differences on organisms. Often this can be inferred by the absence of a normal component (e.g. one gene). The study of "mutants" – organisms which lack one or more functional components with respect to the so-called "wild type" or normal phenotype. Genetic interactions (epistasis) can often confound simple interpretations of such "knock-out" studies.
* Molecular biology is the study of molecular underpinnings of the process of replication, transcription and translation of the genetic material. The central dogma of molecular biology where genetic material is transcribed into RNA and then translated into protein, despite being an oversimplified picture of molecular biology, still provides a good starting point for understanding the field. This picture, however, is undergoing revision in light of emerging novel roles for RNA.
* Chemical Biology seeks to develop new tools based on small molecules that allow minimal perturbation of biological systems while providing detailed information about their function. Further, chemical biology employs biological systems to create non-natural hybrids between biomolecules and synthetic devices (for example emptied viral capsids that can deliver gene therapy or drug molecules).
Analytical chemistry
Analytical chemistry is the study of the separation, identification, and quantification of the chemical components of natural and artificial materials. Qualitative analysis gives an indication of the identity of the chemical species in the sample and quantitative analysis determines the amount of one or more of these components. The separation of components is often performed prior to analysis.
Analytical methods can be separated into classical and instrumental. Classical methods (also known as wet chemistry methods) use separations such as precipitation, extraction, and distillation and qualitative analysis by color, odor, or melting point. Quantitative analysis is achieved by measurement of weight or volume. Instrumental methods use an apparatus to measure physical quantities of the analyte such as light absorption, fluorescence, or conductivity. The separation of materials is accomplished using chromatography or electrophoresis methods.
Analytical chemistry is also focused on improvements in experimental design, chemometrics, and the creation of new measurement tools to provide better chemical information. Analytical chemistry has applications in forensics, bioanalysis, clinical analysis, environmental analysis, and materials analysis.
History
Gustav Kirchhoff and Robert Bunsen
Analytical chemistry has been important since the early days of chemistry, providing methods for determining which elements and chemicals are present in the world around us. During this period significant analytical contributions to chemistry include the development of systematic elemental analysis by Justus von Liebig and systematized organic analysis based on the specific reactions of functional groups.
The first instrumental analysis was flame emissive spectrometry developed by Robert Bunsen and Gustav Kirchhoff who discovered rubidium (Rb) and caesium (Cs) in 1860.
Most of the major developments in analytical chemistry take place after 1900. During this period instrumental analysis becomes progressively dominant in the field. In particular many of the basic spectroscopic and spectrometric techniques were discovered in the early 20th century and refined in the late 20th century.
The separation sciences follow a similar time line of development and also become increasingly transformed into high performance instruments. In the 1970s many of these techniques began to be used together to achieve a complete characterization of samples.
Starting in approximately the 1970s into the present day analytical chemistry has progressively become more inclusive of biological questions (bioanalytical chemistry), whereas it had previously been largely focused on inorganic or small organic molecules. Lasers have been increasingly used in chemistry as probes and even to start and influence a wide variety of reactions. The late 20th century also saw an expansion of the application of analytical chemistry from somewhat academic chemical questions to forensic, environmental, industrial and medical questions, such as in histology.
Modern analytical chemistry is dominated by instrumental analysis. Many analytical chemists focus on a single type of instrument. Academics tend to either focus on new applications and discoveries or on new methods of analysis. The discovery of a chemical present in blood that increases the risk of cancer would be a discovery that an analytical chemist might be involved in. An effort to develop a new method might involve the use of a tunable laser to increase the specificity and sensitivity of a spectrometric method. Many methods, once developed, are kept purposely static so that data can be compared over long periods of time. This is particularly true in industrial quality assurance (QA), forensic and environmental applications. Analytical chemistry plays an increasingly important role in the pharmaceutical industry where, aside from QA, it is used in discovery of new drug candidates and in clinical applications where understanding the interactions between the drug and the patient are critical.
Classical methods
The presence of copper in this qualitative analysis is indicated by the bluish-green color of the flame.
Although modern analytical chemistry is dominated by sophisticated instrumentation, the roots of analytical chemistry and some of the principles used in modern instruments are from traditional techniques many of which are still used today. These techniques also tend to form the backbone of most undergraduate analytical chemistry educational labs.
Qualitative analysis
A qualitative analysis determines the presence or absence of a particular compound, but not the mass or concentration. That is it is not related to quantity.
Chemical tests
For more details on this topic, see Chemical test.
There are numerous qualitative chemical tests, for example, the acid test for gold and the Kastle-Meyer test for the presence of blood.
Flame test
Inorganic qualitative analysis generally refers to a systematic scheme to confirm the presence of certain, usually aqueous, ions or elements by performing a series of reactions that eliminate ranges of possibilities and then confirms suspected ions with a confirming test. Sometimes small carbon containing ions are included in such schemes. With modern instrumentation these tests are rarely used but can be useful for educational purposes and in field work or other situations where access to state-of-the-art instruments are not available or expedient.
Gravimetric analysis
For more details on this topic, see Gravimetric analysis.
Gravimetric analysis involves determining the amount of material present by weighing the sample before and/or after some transformation. A common example used in undergraduate education is the determination of the amount of water in a hydrate by heating the sample to remove the water such that the difference in weight is due to the water loss of water.
Volumetric analysis
Titration involves the addition of a reactant to a solution being analyzed until some equivalence point is reached. Often the amount of material in the solution being analyzed may be determined. Most familiar to those who have taken college chemistry is the acid-base titration involving a color changing indicator. There are many other types of titrations, for example potentiometric titrations. These titrations may use different types of indicators to reach some equivalence point.
Instrumental methods
Block diagram of an analytical instrument showing the stimulus and measurement of response
Spectroscopy
Spectroscopy measures the interaction of the molecules with electromagnetic radiation. Spectroscopy consists of many different applications such as atomic absorption spectroscopy, atomic emission spectroscopy, ultraviolet-visible spectroscopy, x-ray fluorescence spectroscopy, infrared spectroscopy, Raman spectroscopy, dual polarisation interferometry, nuclear magnetic resonance spectroscopy, photoemission spectroscopy, Mössbauer spectroscopy and so on.
Mass spectrometry
An accelerator mass spectrometer used for radiocarbon dating and other analysis.
Mass spectrometry measures mass-to-charge ratio of molecules using electric and magnetic fields. There are several ionization methods: electron impact, chemical ionization, electrospray, fast atom bombardment, matrix assisted laser desorption ionization, and others. Also, mass spectrometry is categorized by approaches of mass analyzers: magnetic-sector, quadrupole mass analyzer, quadrupole ion trap, time-of-flight, Fourier transform ion cyclotron resonance, and so on.
Crystallography
Crystallography is a technique that characterizes the chemical structure of materials at the atomic level by analyzing the diffraction patterns of usually x-rays that have been deflected by atoms in the material. From the raw data the relative placement of atoms in space may be determined.
Electrochemical analysis
Electroanalytical methods measure the potential (volts) and/or current (amps) in an electrochemical cell containing the analyte. These methods can be categorized according to which aspects of the cell are controlled and which are measured. The three main categories are potentiometry (the difference in electrode potentials is measured), coulometry (the cell's current is measured over time), and voltammetry (the cell's current is measured while actively altering the cell's potential).
Thermal analysis
Calorimetry and thermogravimetric analysis measure the interaction of a material and heat.
Separation
Separation of black ink on a thin layer chromatography plate.
Further information: Separation process, Chromatography, electrophoresis
Separation processes are used to decrease the complexity of material mixtures. Chromatography and electrophoresis are representative of this field.
Hybrid techniques
Combinations of the above techniques produce a "hybrid" or "hyphenated" technique. Several examples are in popular use today and new hybrid techniques are under development. For example, gas chromatography-mass spectrometry, gas chromatography-infrared spectroscopy, liquid chromatography-mass spectrometry, liquid chromatography-NMR spectroscopy. liquid chromagraphy-infrared spectroscopy and capillary electrophoresis-mass spectrometry.
Hyphenated separation techniques refers to a combination of two (or more) techniques to detect and separate chemicals from solutions. Most often the other technique is some form of chromatography. Hyphenated techniques are widely used in chemistry and biochemistry. A slash is sometimes used instead of hyphen, especially if the name of one of the methods contains a hyphen itself.
Microscopy
The visualization of single molecules, single cells, biological tissues and nanomaterials is an important and attractive approach in analytical science. Also, hybridization with other traditional analytical tools is revolutionizing analytical science. Microscopy can be categorized into three different fields: optical microscopy, electron microscopy, and scanning probe microscopy. Recently, this field is rapidly progressing because of the rapid development of the computer and camera industries.
Lab-on-a-chip
A glass microreactor
Further information: microfluidics, lab-on-a-chip
Devices that integrate (multiple) laboratory functions on a single chip of only millimeters to a few square centimeters in size and that are capable of handling extremely small fluid volumes down to less than pico liters.
Standards
Standard curve
A calibration curve plot showing limit of detection (LOD), limit of quantification (LOQ), dynamic range, and limit of linearity (LOL).
A general method for analysis of concentration involves the creation of a calibration curve. This allows for determination of the amount of a chemical in a material by comparing the results of unknown sample to those of a series known standards. If the concentration of element or compound in a sample is too high for the detection range of the technique, it can simply be diluted in a pure solvent. If the amount in the sample is below an instrument's range of measurement, the method of addition can be used. In this method a known quantity of the element or compound under study is added, and the difference between the concentration added, and the concentration observed is the amount actually in the sample.
Internal standards
Sometimes an internal standard is added at a known concentration directly to an analytical sample to aid in quantitation. The amount of analyte present is then determined relative to the internal standard as a calibrant.
Standard addition
The method of standard addition is used in instrumental analysis to determine concentration of a substance (analyte) in an unknown sample by comparison to a set of samples of known concentration, similar to using a calibration curve. Standard addition can be applied to most analytical techniques and is used instead of a calibration curve to solve the matrix effect problem.
Signals and noise
One of the most important components of analytical chemistry is maximizing the desired signal while minimizing the associated noise. The analytical figure of merit is known as the signal-to-noise ratio (S/N or SNR).
Noise can arise from environmental factors as well as from fundamental physical processes.
Thermal noise
Thermal noise results from the motion of charge carriers (usually electrons) in an electrical circuit generated by their thermal motion. Thermal noise is white noise meaning that the power spectral density is constant throughout the frequency spectrum.
The root mean square value of the thermal noise in a resistor is given by
v_{{RMS}} = \sqrt { 4 k_B T R \Delta f },
where kB is Boltzmann's constant, T is the temperature, R is the resistance, and Δf is the bandwidth of the frequency f.
Shot noise
Shot noise is a type of electronic noise that occurs when the finite number of particles (such as electrons in an electronic circuit or photons in an optical device) is small enough to give rise to statistical fluctuations in a signal.
Shot noise is a Poisson process and the charge carriers that make up the current follow a Poisson distribution. The root mean square current fluctuation is given by
i_{{RMS}}=\sqrt{2\,e\,I\,\Delta f}
where e is the elementary charge and I is the average current. Shot noise is white noise.
Flicker noise
Flicker noise is electronic noise with a 1/ƒ frequency spectrum; as f increases, the noise decreases. Flicker noise arises from a variety of sources, such as impurities in a conductive channel, generation and recombination noise in a transistor due to base current, and so on. This noise can be avoided by modulation of the signal at a higher frequency, for example through the use of a lock-in amplifier.
Environmental noise
Noise in a thermogravimetric analysis; lower noise in the middle of the plot results from less human activity (and environmental noise) at night.
Environmental noise arises from the surroundings of the analytical instrument. Sources of electromagnetic noise are power lines, radio and television stations, wireless devices and electric motors. Many of these noise sources are narrow bandwidth and therefore can be avoided. Temperature and vibration isolation may be required for some instruments.
Noise reduction
Noise reduction can be accomplished either in hardware or software. Examples of hardware noise reduction are the use of shielded cable, analog filtering, and signal modulation. Examples of software noise reduction are digital filtering, ensemble average, boxcar average, and correlation methods.
Applications
Analytical chemistry research is largely driven by performance (sensitivity, selectivity, robustness, linear range, accuracy, precision, and speed), and cost (purchase, operation, training, time, and space). Among the main branches of contemporary analytical atomic spectrometry, the most widespread and universal are optical and mass spectrometry.In the direct elemental analysis of solid samples, the new leaders are laser-induced breakdown and laser ablation mass spectrometry, and the related techniques with transfer of the laser ablation products into inductively coupled plasma. Advances in design of diode lasers and optical parametric oscillators promote developments in fluorescence and ionization spectrometry and also in absorption techniques where uses of optical cavities for increased effective absorption pathlength are expected to expand. Steady progress and growth in applications of plasma- and laser-based methods are noticeable. An interest towards the absolute (standardless) analysis has revived, particularly in the emission spectrometry.
A lot of effort is put in shrinking the analysis techniques to chip size. Although there are few examples of such systems competitive with traditional analysis techniques, potential advantages include size/portability, speed, and cost. (micro Total Analysis System (µTAS) or Lab-on-a-chip). Microscale chemistry reduces the amounts of chemicals used.
Much effort is also put into analyzing biological systems. Examples of rapidly expanding fields in this area are:
* Genomics - DNA sequencing and its related research. Genetic fingerprinting and DNA microarray are very popular tools and research fields.
* Proteomics - the analysis of protein concentrations and modifications, especially in response to various stressors, at various developmental stages, or in various parts of the body.
* Metabolomics - similar to proteomics, but dealing with metabolites.
* Transcriptomics - mRNA and its associated field
* Lipidomics - lipids and its associated field
* Peptidomics - peptides and its associated field
* Metalomics - similar to proteomics and metabolomics, but dealing with metal concentrations and especially with their binding to proteins and other molecules.
Analytical chemistry has played critical roles in the understanding of basic science to a variety of practical applications, such as biomedical applications, environmental monitoring, quality control of industrial manufacturing, forensic science and so on.
The recent developments of computer automation and information technologies have innervated analytical chemistry to initiate a number of new biological fields. For example, automated DNA sequencing machines were the basis to complete human genome projects leading to the birth of genomics. Protein identification and peptide sequencing by mass spectrometry opened a new field of proteomics. Furthermore, a number of ~omics based on analytical chemistry have become important areas in modern biology.
Also, analytical chemistry has been an indispensable area in the development of nanotechnology. Surface characterization instruments, electron microscopes and scanning probe microscopes enables scientists to visualize atomic structures with chemical characterizations.
Among active contemporary analytical chemistry research fields, micro total analysis system is considered as a great promise of revolutionary technology. In this approach, integrated and miniaturized analytical systems are being developed to control and analyze single cells and single molecules. This cutting-edge technology has a promising potential of leading a new revolution in science as integrated circuits did in computer developments.
Analytical methods can be separated into classical and instrumental. Classical methods (also known as wet chemistry methods) use separations such as precipitation, extraction, and distillation and qualitative analysis by color, odor, or melting point. Quantitative analysis is achieved by measurement of weight or volume. Instrumental methods use an apparatus to measure physical quantities of the analyte such as light absorption, fluorescence, or conductivity. The separation of materials is accomplished using chromatography or electrophoresis methods.
Analytical chemistry is also focused on improvements in experimental design, chemometrics, and the creation of new measurement tools to provide better chemical information. Analytical chemistry has applications in forensics, bioanalysis, clinical analysis, environmental analysis, and materials analysis.
History
Gustav Kirchhoff and Robert Bunsen
Analytical chemistry has been important since the early days of chemistry, providing methods for determining which elements and chemicals are present in the world around us. During this period significant analytical contributions to chemistry include the development of systematic elemental analysis by Justus von Liebig and systematized organic analysis based on the specific reactions of functional groups.
The first instrumental analysis was flame emissive spectrometry developed by Robert Bunsen and Gustav Kirchhoff who discovered rubidium (Rb) and caesium (Cs) in 1860.
Most of the major developments in analytical chemistry take place after 1900. During this period instrumental analysis becomes progressively dominant in the field. In particular many of the basic spectroscopic and spectrometric techniques were discovered in the early 20th century and refined in the late 20th century.
The separation sciences follow a similar time line of development and also become increasingly transformed into high performance instruments. In the 1970s many of these techniques began to be used together to achieve a complete characterization of samples.
Starting in approximately the 1970s into the present day analytical chemistry has progressively become more inclusive of biological questions (bioanalytical chemistry), whereas it had previously been largely focused on inorganic or small organic molecules. Lasers have been increasingly used in chemistry as probes and even to start and influence a wide variety of reactions. The late 20th century also saw an expansion of the application of analytical chemistry from somewhat academic chemical questions to forensic, environmental, industrial and medical questions, such as in histology.
Modern analytical chemistry is dominated by instrumental analysis. Many analytical chemists focus on a single type of instrument. Academics tend to either focus on new applications and discoveries or on new methods of analysis. The discovery of a chemical present in blood that increases the risk of cancer would be a discovery that an analytical chemist might be involved in. An effort to develop a new method might involve the use of a tunable laser to increase the specificity and sensitivity of a spectrometric method. Many methods, once developed, are kept purposely static so that data can be compared over long periods of time. This is particularly true in industrial quality assurance (QA), forensic and environmental applications. Analytical chemistry plays an increasingly important role in the pharmaceutical industry where, aside from QA, it is used in discovery of new drug candidates and in clinical applications where understanding the interactions between the drug and the patient are critical.
Classical methods
The presence of copper in this qualitative analysis is indicated by the bluish-green color of the flame.
Although modern analytical chemistry is dominated by sophisticated instrumentation, the roots of analytical chemistry and some of the principles used in modern instruments are from traditional techniques many of which are still used today. These techniques also tend to form the backbone of most undergraduate analytical chemistry educational labs.
Qualitative analysis
A qualitative analysis determines the presence or absence of a particular compound, but not the mass or concentration. That is it is not related to quantity.
Chemical tests
For more details on this topic, see Chemical test.
There are numerous qualitative chemical tests, for example, the acid test for gold and the Kastle-Meyer test for the presence of blood.
Flame test
Inorganic qualitative analysis generally refers to a systematic scheme to confirm the presence of certain, usually aqueous, ions or elements by performing a series of reactions that eliminate ranges of possibilities and then confirms suspected ions with a confirming test. Sometimes small carbon containing ions are included in such schemes. With modern instrumentation these tests are rarely used but can be useful for educational purposes and in field work or other situations where access to state-of-the-art instruments are not available or expedient.
Gravimetric analysis
For more details on this topic, see Gravimetric analysis.
Gravimetric analysis involves determining the amount of material present by weighing the sample before and/or after some transformation. A common example used in undergraduate education is the determination of the amount of water in a hydrate by heating the sample to remove the water such that the difference in weight is due to the water loss of water.
Volumetric analysis
Titration involves the addition of a reactant to a solution being analyzed until some equivalence point is reached. Often the amount of material in the solution being analyzed may be determined. Most familiar to those who have taken college chemistry is the acid-base titration involving a color changing indicator. There are many other types of titrations, for example potentiometric titrations. These titrations may use different types of indicators to reach some equivalence point.
Instrumental methods
Block diagram of an analytical instrument showing the stimulus and measurement of response
Spectroscopy
Spectroscopy measures the interaction of the molecules with electromagnetic radiation. Spectroscopy consists of many different applications such as atomic absorption spectroscopy, atomic emission spectroscopy, ultraviolet-visible spectroscopy, x-ray fluorescence spectroscopy, infrared spectroscopy, Raman spectroscopy, dual polarisation interferometry, nuclear magnetic resonance spectroscopy, photoemission spectroscopy, Mössbauer spectroscopy and so on.
Mass spectrometry
An accelerator mass spectrometer used for radiocarbon dating and other analysis.
Mass spectrometry measures mass-to-charge ratio of molecules using electric and magnetic fields. There are several ionization methods: electron impact, chemical ionization, electrospray, fast atom bombardment, matrix assisted laser desorption ionization, and others. Also, mass spectrometry is categorized by approaches of mass analyzers: magnetic-sector, quadrupole mass analyzer, quadrupole ion trap, time-of-flight, Fourier transform ion cyclotron resonance, and so on.
Crystallography
Crystallography is a technique that characterizes the chemical structure of materials at the atomic level by analyzing the diffraction patterns of usually x-rays that have been deflected by atoms in the material. From the raw data the relative placement of atoms in space may be determined.
Electrochemical analysis
Electroanalytical methods measure the potential (volts) and/or current (amps) in an electrochemical cell containing the analyte. These methods can be categorized according to which aspects of the cell are controlled and which are measured. The three main categories are potentiometry (the difference in electrode potentials is measured), coulometry (the cell's current is measured over time), and voltammetry (the cell's current is measured while actively altering the cell's potential).
Thermal analysis
Calorimetry and thermogravimetric analysis measure the interaction of a material and heat.
Separation
Separation of black ink on a thin layer chromatography plate.
Further information: Separation process, Chromatography, electrophoresis
Separation processes are used to decrease the complexity of material mixtures. Chromatography and electrophoresis are representative of this field.
Hybrid techniques
Combinations of the above techniques produce a "hybrid" or "hyphenated" technique. Several examples are in popular use today and new hybrid techniques are under development. For example, gas chromatography-mass spectrometry, gas chromatography-infrared spectroscopy, liquid chromatography-mass spectrometry, liquid chromatography-NMR spectroscopy. liquid chromagraphy-infrared spectroscopy and capillary electrophoresis-mass spectrometry.
Hyphenated separation techniques refers to a combination of two (or more) techniques to detect and separate chemicals from solutions. Most often the other technique is some form of chromatography. Hyphenated techniques are widely used in chemistry and biochemistry. A slash is sometimes used instead of hyphen, especially if the name of one of the methods contains a hyphen itself.
Microscopy
The visualization of single molecules, single cells, biological tissues and nanomaterials is an important and attractive approach in analytical science. Also, hybridization with other traditional analytical tools is revolutionizing analytical science. Microscopy can be categorized into three different fields: optical microscopy, electron microscopy, and scanning probe microscopy. Recently, this field is rapidly progressing because of the rapid development of the computer and camera industries.
Lab-on-a-chip
A glass microreactor
Further information: microfluidics, lab-on-a-chip
Devices that integrate (multiple) laboratory functions on a single chip of only millimeters to a few square centimeters in size and that are capable of handling extremely small fluid volumes down to less than pico liters.
Standards
Standard curve
A calibration curve plot showing limit of detection (LOD), limit of quantification (LOQ), dynamic range, and limit of linearity (LOL).
A general method for analysis of concentration involves the creation of a calibration curve. This allows for determination of the amount of a chemical in a material by comparing the results of unknown sample to those of a series known standards. If the concentration of element or compound in a sample is too high for the detection range of the technique, it can simply be diluted in a pure solvent. If the amount in the sample is below an instrument's range of measurement, the method of addition can be used. In this method a known quantity of the element or compound under study is added, and the difference between the concentration added, and the concentration observed is the amount actually in the sample.
Internal standards
Sometimes an internal standard is added at a known concentration directly to an analytical sample to aid in quantitation. The amount of analyte present is then determined relative to the internal standard as a calibrant.
Standard addition
The method of standard addition is used in instrumental analysis to determine concentration of a substance (analyte) in an unknown sample by comparison to a set of samples of known concentration, similar to using a calibration curve. Standard addition can be applied to most analytical techniques and is used instead of a calibration curve to solve the matrix effect problem.
Signals and noise
One of the most important components of analytical chemistry is maximizing the desired signal while minimizing the associated noise. The analytical figure of merit is known as the signal-to-noise ratio (S/N or SNR).
Noise can arise from environmental factors as well as from fundamental physical processes.
Thermal noise
Thermal noise results from the motion of charge carriers (usually electrons) in an electrical circuit generated by their thermal motion. Thermal noise is white noise meaning that the power spectral density is constant throughout the frequency spectrum.
The root mean square value of the thermal noise in a resistor is given by
v_{{RMS}} = \sqrt { 4 k_B T R \Delta f },
where kB is Boltzmann's constant, T is the temperature, R is the resistance, and Δf is the bandwidth of the frequency f.
Shot noise
Shot noise is a type of electronic noise that occurs when the finite number of particles (such as electrons in an electronic circuit or photons in an optical device) is small enough to give rise to statistical fluctuations in a signal.
Shot noise is a Poisson process and the charge carriers that make up the current follow a Poisson distribution. The root mean square current fluctuation is given by
i_{{RMS}}=\sqrt{2\,e\,I\,\Delta f}
where e is the elementary charge and I is the average current. Shot noise is white noise.
Flicker noise
Flicker noise is electronic noise with a 1/ƒ frequency spectrum; as f increases, the noise decreases. Flicker noise arises from a variety of sources, such as impurities in a conductive channel, generation and recombination noise in a transistor due to base current, and so on. This noise can be avoided by modulation of the signal at a higher frequency, for example through the use of a lock-in amplifier.
Environmental noise
Noise in a thermogravimetric analysis; lower noise in the middle of the plot results from less human activity (and environmental noise) at night.
Environmental noise arises from the surroundings of the analytical instrument. Sources of electromagnetic noise are power lines, radio and television stations, wireless devices and electric motors. Many of these noise sources are narrow bandwidth and therefore can be avoided. Temperature and vibration isolation may be required for some instruments.
Noise reduction
Noise reduction can be accomplished either in hardware or software. Examples of hardware noise reduction are the use of shielded cable, analog filtering, and signal modulation. Examples of software noise reduction are digital filtering, ensemble average, boxcar average, and correlation methods.
Applications
Analytical chemistry research is largely driven by performance (sensitivity, selectivity, robustness, linear range, accuracy, precision, and speed), and cost (purchase, operation, training, time, and space). Among the main branches of contemporary analytical atomic spectrometry, the most widespread and universal are optical and mass spectrometry.In the direct elemental analysis of solid samples, the new leaders are laser-induced breakdown and laser ablation mass spectrometry, and the related techniques with transfer of the laser ablation products into inductively coupled plasma. Advances in design of diode lasers and optical parametric oscillators promote developments in fluorescence and ionization spectrometry and also in absorption techniques where uses of optical cavities for increased effective absorption pathlength are expected to expand. Steady progress and growth in applications of plasma- and laser-based methods are noticeable. An interest towards the absolute (standardless) analysis has revived, particularly in the emission spectrometry.
A lot of effort is put in shrinking the analysis techniques to chip size. Although there are few examples of such systems competitive with traditional analysis techniques, potential advantages include size/portability, speed, and cost. (micro Total Analysis System (µTAS) or Lab-on-a-chip). Microscale chemistry reduces the amounts of chemicals used.
Much effort is also put into analyzing biological systems. Examples of rapidly expanding fields in this area are:
* Genomics - DNA sequencing and its related research. Genetic fingerprinting and DNA microarray are very popular tools and research fields.
* Proteomics - the analysis of protein concentrations and modifications, especially in response to various stressors, at various developmental stages, or in various parts of the body.
* Metabolomics - similar to proteomics, but dealing with metabolites.
* Transcriptomics - mRNA and its associated field
* Lipidomics - lipids and its associated field
* Peptidomics - peptides and its associated field
* Metalomics - similar to proteomics and metabolomics, but dealing with metal concentrations and especially with their binding to proteins and other molecules.
Analytical chemistry has played critical roles in the understanding of basic science to a variety of practical applications, such as biomedical applications, environmental monitoring, quality control of industrial manufacturing, forensic science and so on.
The recent developments of computer automation and information technologies have innervated analytical chemistry to initiate a number of new biological fields. For example, automated DNA sequencing machines were the basis to complete human genome projects leading to the birth of genomics. Protein identification and peptide sequencing by mass spectrometry opened a new field of proteomics. Furthermore, a number of ~omics based on analytical chemistry have become important areas in modern biology.
Also, analytical chemistry has been an indispensable area in the development of nanotechnology. Surface characterization instruments, electron microscopes and scanning probe microscopes enables scientists to visualize atomic structures with chemical characterizations.
Among active contemporary analytical chemistry research fields, micro total analysis system is considered as a great promise of revolutionary technology. In this approach, integrated and miniaturized analytical systems are being developed to control and analyze single cells and single molecules. This cutting-edge technology has a promising potential of leading a new revolution in science as integrated circuits did in computer developments.
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