1.
Molecule
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A molecule is an electrically neutral group of two or more atoms held together by chemical bonds. Molecules are distinguished from ions by their lack of electrical charge, however, in quantum physics, organic chemistry, and biochemistry, the term molecule is often used less strictly, also being applied to polyatomic ions. In the kinetic theory of gases, the molecule is often used for any gaseous particle regardless of its composition. According to this definition, noble gas atoms are considered molecules as they are in fact monoatomic molecules. A molecule may be homonuclear, that is, it consists of atoms of one element, as with oxygen, or it may be heteronuclear. Atoms and complexes connected by non-covalent interactions, such as hydrogen bonds or ionic bonds, are not considered single molecules. Molecules as components of matter are common in organic substances and they also make up most of the oceans and atmosphere. Also, no typical molecule can be defined for ionic crystals and covalent crystals, the theme of repeated unit-cellular-structure also holds for most condensed phases with metallic bonding, which means that solid metals are also not made of molecules. In glasses, atoms may also be together by chemical bonds with no presence of any definable molecule. The science of molecules is called molecular chemistry or molecular physics, in practice, however, this distinction is vague. In molecular sciences, a molecule consists of a system composed of two or more atoms. Polyatomic ions may sometimes be thought of as electrically charged molecules. The term unstable molecule is used for very reactive species, i. e, according to Merriam-Webster and the Online Etymology Dictionary, the word molecule derives from the Latin moles or small unit of mass. Molecule – extremely minute particle, from French molécule, from New Latin molecula, diminutive of Latin moles mass, a vague meaning at first, the vogue for the word can be traced to the philosophy of Descartes. The definition of the molecule has evolved as knowledge of the structure of molecules has increased, earlier definitions were less precise, defining molecules as the smallest particles of pure chemical substances that still retain their composition and chemical properties. Molecules are held together by covalent bonding or ionic bonding. Several types of non-metal elements exist only as molecules in the environment, for example, hydrogen only exists as hydrogen molecule. A molecule of a compound is made out of two or more elements, a covalent bond is a chemical bond that involves the sharing of electron pairs between atoms
2.
Color
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Color or colour is the characteristic of human visual perception described through color categories, with names such as red, yellow, purple, or blue. This perception of color derives from the stimulation of cells in the human eye by electromagnetic radiation in the spectrum of light. Color categories and physical specifications of color are associated with objects through the wavelength of the light that is reflected from them and this reflection is governed by the objects physical properties such as light absorption, emission spectra, etc. By defining a color space, colors can be identified numerically by coordinates, there may also be more than three color dimensions in other color spaces, such as in the CMYK color model, wherein one of the dimensions relates to a colours colorfulness). The photo-receptivity of the eyes of species also varies considerably from our own. Honeybees and bumblebees for instance have trichromatic color vision sensitive to ultraviolet but is insensitive to red, papilio butterflies possess six types of photoreceptors and may have pentachromatic vision. The most complex color vision system in the kingdom has been found in stomatopods with up to 12 spectral receptor types thought to work as multiple dichromatic units. The science of color is sometimes called chromatics, colorimetry, or simply color science and it includes the perception of color by the human eye and brain, the origin of color in materials, color theory in art, and the physics of electromagnetic radiation in the visible range. Electromagnetic radiation is characterized by its wavelength and its intensity, when the wavelength is within the visible spectrum, it is known as visible light. Most light sources emit light at different wavelengths, a sources spectrum is a distribution giving its intensity at each wavelength. Although the spectrum of light arriving at the eye from a given direction determines the color sensation in that direction, in each such class the members are called metamers of the color in question. The table at right shows approximate frequencies and wavelengths for various pure spectral colors, the wavelengths listed are as measured in air or vacuum. A common list identifies six main bands, red, orange, yellow, green, blue, Newtons conception included a seventh color, indigo, between blue and violet. It is possible that what Newton referred to as blue is nearer to what today is known as cyan, the color of an object depends on both the physics of the object in its environment and the characteristics of the perceiving eye and brain. Some objects not only light, but also transmit light or emit light themselves. This effect is known as color constancy, opaque objects that do not reflect specularly have their color determined by which wavelengths of light they scatter strongly. If objects scatter all wavelengths with roughly equal strength, they appear white, if they absorb all wavelengths, they appear black. Opaque objects that reflect light of different wavelengths with different efficiencies look like mirrors tinted with colors determined by those differences
3.
Absorption (electromagnetic radiation)
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In physics, absorption of electromagnetic radiation is the way in which the energy of a photon is taken up by matter, typically the electrons of an atom. Thus, the energy is transformed into internal energy of the absorber. The reduction in intensity of a wave propagating through a medium by absorption of a part of its photons is often called attenuation. The mass attenuation coefficient, also called mass extinction coefficient, which is the absorption coefficient divided by density, the absorption cross section and scattering cross-section are closely related to the absorption and attenuation coefficients, respectively. Extinction in astronomy is equivalent to the attenuation coefficient, absorbance and optical depth are two related measures All these quantities measure, at least to some extent, how well a medium absorbs radiation. However, practitioners of different fields and techniques tend to use different quantities drawn from the list above. The absorbance of an object quantifies how much of the incident light is absorbed by it and this may be related to other properties of the object through the Beer–Lambert law. A few examples of absorption are ultraviolet–visible spectroscopy, infrared spectroscopy, understanding and measuring the absorption of electromagnetic radiation has a variety of applications. Here are a few examples, In meteorology and climatology, global and local temperatures depend in part on the absorption of radiation by gases and land. In medicine, X-rays are absorbed to different extents by different tissues, for example, see computation of radiowave attenuation in the atmosphere used in satellite link design. In chemistry and materials science, because different materials and molecules will absorb radiation to different extents at different frequencies, in optics, sunglasses, colored filters, dyes, and other such materials are designed specifically with respect to which visible wavelengths they absorb, and in what proportions. In physics, the D-region of Earths ionosphere is known to significantly absorb radio signals that fall within the electromagnetic spectrum. Optical Propagation in Linear Media, Atmospheric Gases and Particles, Solid-State Components, physics Archive - Ask a scientist
4.
Wavelength
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In physics, the wavelength of a sinusoidal wave is the spatial period of the wave—the distance over which the waves shape repeats, and thus the inverse of the spatial frequency. Wavelength is commonly designated by the Greek letter lambda, the concept can also be applied to periodic waves of non-sinusoidal shape. The term wavelength is also applied to modulated waves. Wavelength depends on the medium that a wave travels through, examples of wave-like phenomena are sound waves, light, water waves and periodic electrical signals in a conductor. A sound wave is a variation in air pressure, while in light and other electromagnetic radiation the strength of the electric, water waves are variations in the height of a body of water. In a crystal lattice vibration, atomic positions vary, wavelength is a measure of the distance between repetitions of a shape feature such as peaks, valleys, or zero-crossings, not a measure of how far any given particle moves. For example, in waves over deep water a particle near the waters surface moves in a circle of the same diameter as the wave height. The range of wavelengths or frequencies for wave phenomena is called a spectrum, the name originated with the visible light spectrum but now can be applied to the entire electromagnetic spectrum as well as to a sound spectrum or vibration spectrum. In linear media, any pattern can be described in terms of the independent propagation of sinusoidal components. The wavelength λ of a sinusoidal waveform traveling at constant speed v is given by λ = v f, in a dispersive medium, the phase speed itself depends upon the frequency of the wave, making the relationship between wavelength and frequency nonlinear. In the case of electromagnetic radiation—such as light—in free space, the speed is the speed of light. Thus the wavelength of a 100 MHz electromagnetic wave is about, the wavelength of visible light ranges from deep red, roughly 700 nm, to violet, roughly 400 nm. For sound waves in air, the speed of sound is 343 m/s, the wavelengths of sound frequencies audible to the human ear are thus between approximately 17 m and 17 mm, respectively. Note that the wavelengths in audible sound are much longer than those in visible light, a standing wave is an undulatory motion that stays in one place. A sinusoidal standing wave includes stationary points of no motion, called nodes, the upper figure shows three standing waves in a box. The walls of the box are considered to require the wave to have nodes at the walls of the box determining which wavelengths are allowed, the stationary wave can be viewed as the sum of two traveling sinusoidal waves of oppositely directed velocities. Consequently, wavelength, period, and wave velocity are related just as for a traveling wave, for example, the speed of light can be determined from observation of standing waves in a metal box containing an ideal vacuum. In that case, the k, the magnitude of k, is still in the same relationship with wavelength as shown above
5.
Visible spectrum
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The visible spectrum is the portion of the electromagnetic spectrum that is visible to the human eye. Electromagnetic radiation in this range of wavelengths is called light or simply light. A typical human eye will respond to wavelengths from about 390 to 700 nm, in terms of frequency, this corresponds to a band in the vicinity of 430–770 THz. The spectrum does not, however, contain all the colors that the human eyes, unsaturated colors such as pink, or purple variations such as magenta, are absent, for example, because they can be made only by a mix of multiple wavelengths. Colors containing only one wavelength are called pure colors or spectral colors. Visible wavelengths pass through the window, the region of the electromagnetic spectrum that allows wavelengths to pass largely unattenuated through the Earths atmosphere. An example of this phenomenon is that clean air scatters blue light more than red wavelengths, the optical window is also referred to as the visible window because it overlaps the human visible response spectrum. The near infrared window lies just out of the vision, as well as the Medium Wavelength IR window. In the 13th century, Roger Bacon theorized that rainbows were produced by a process to the passage of light through glass or crystal. In the 17th century, Isaac Newton discovered that prisms could disassemble and reassemble white light and he was the first to use the word spectrum in this sense in print in 1671 in describing his experiments in optics. The result is red light is bent less sharply than violet as it passes through the prism. Newton divided the spectrum into seven named colors, red, orange, yellow, green, blue, indigo, the human eye is relatively insensitive to indigos frequencies, and some people who have otherwise-good vision cannot distinguish indigo from blue and violet. For this reason, some commentators, including Isaac Asimov, have suggested that indigo should not be regarded as a color in its own right. However, the evidence indicates that what Newton meant by indigo, comparing Newtons observation of prismatic colors to a color image of the visible light spectrum shows that indigo corresponds to what is today called blue, whereas blue corresponds to cyan. In the 18th century, Goethe wrote about optical spectra in his Theory of Colours, Goethe used the word spectrum to designate a ghostly optical afterimage, as did Schopenhauer in On Vision and Colors. Goethe argued that the spectrum was a compound phenomenon. Where Newton narrowed the beam of light to isolate the phenomenon, Goethe observed that a wider aperture produces not a spectrum but rather reddish-yellow, the spectrum appears only when these edges are close enough to overlap. Young was the first to measure the wavelengths of different colors of light, the connection between the visible spectrum and color vision was explored by Thomas Young and Hermann von Helmholtz in the early 19th century
6.
Molecular orbital
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In chemistry, a molecular orbital is a mathematical function describing the wave-like behavior of an electron in a molecule. This function can be used to calculate chemical and physical properties such as the probability of finding an electron in any specific region, the term orbital was introduced by Robert S. Mulliken in 1932 as an abbreviation for one-electron orbital wave function. At an elementary level, it is used to describe the region of space in which the function has a significant amplitude, Molecular orbitals are usually constructed by combining atomic orbitals or hybrid orbitals from each atom of the molecule, or other molecular orbitals from groups of atoms. They can be calculated using the Hartree–Fock or self-consistent field methods. A molecular orbital can be used to represent the regions in a molecule where an electron occupying that orbital is likely to be found, Molecular orbitals are obtained from the combination of atomic orbitals, which predict the location of an electron in an atom. A molecular orbital can specify the configuration of a molecule. Most commonly a MO is represented as a combination of atomic orbitals. They are invaluable in providing a model of bonding in molecules. Most present-day methods in computational chemistry begin by calculating the MOs of the system, a molecular orbital describes the behavior of one electron in the electric field generated by the nuclei and some average distribution of the other electrons. In the case of two electrons occupying the orbital, the Pauli principle demands that they have opposite spin. Necessarily this is an approximation, and highly accurate descriptions of the electronic wave function do not have orbitals. Molecular orbitals arise from allowed interactions between orbitals, which are allowed if the symmetries of the atomic orbitals are compatible with each other. Efficiency of atomic orbital interactions is determined from the overlap between two atomic orbitals, which is significant if the atomic orbitals are close in energy. Finally, the number of molecular orbitals that form must equal the number of orbitals in the atoms being combined to form the molecule. Here, the orbitals are expressed as linear combinations of atomic orbitals. Molecular orbitals were first introduced by Friedrich Hund and Robert S. Mulliken in 1927 and 1928, the linear combination of atomic orbitals or LCAO approximation for molecular orbitals was introduced in 1929 by Sir John Lennard-Jones. His ground-breaking paper showed how to derive the electronic structure of the fluorine and this qualitative approach to molecular orbital theory is part of the start of modern quantum chemistry. Linear combinations of atomic orbitals can be used to estimate the molecular orbitals that are formed upon bonding between the constituent atoms
7.
Electron
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The electron is a subatomic particle, symbol e− or β−, with a negative elementary electric charge. Electrons belong to the first generation of the lepton particle family, the electron has a mass that is approximately 1/1836 that of the proton. Quantum mechanical properties of the include a intrinsic angular momentum of a half-integer value, expressed in units of the reduced Planck constant. As it is a fermion, no two electrons can occupy the same state, in accordance with the Pauli exclusion principle. Like all elementary particles, electrons exhibit properties of particles and waves, they can collide with other particles and can be diffracted like light. Since an electron has charge, it has an electric field. Electromagnetic fields produced from other sources will affect the motion of an electron according to the Lorentz force law, electrons radiate or absorb energy in the form of photons when they are accelerated. Laboratory instruments are capable of trapping individual electrons as well as electron plasma by the use of electromagnetic fields, special telescopes can detect electron plasma in outer space. Electrons are involved in applications such as electronics, welding, cathode ray tubes, electron microscopes, radiation therapy, lasers, gaseous ionization detectors. Interactions involving electrons with other particles are of interest in fields such as chemistry. The Coulomb force interaction between the positive protons within atomic nuclei and the negative electrons without, allows the composition of the two known as atoms, ionization or differences in the proportions of negative electrons versus positive nuclei changes the binding energy of an atomic system. The exchange or sharing of the electrons between two or more atoms is the cause of chemical bonding. In 1838, British natural philosopher Richard Laming first hypothesized the concept of a quantity of electric charge to explain the chemical properties of atoms. Irish physicist George Johnstone Stoney named this charge electron in 1891, electrons can also participate in nuclear reactions, such as nucleosynthesis in stars, where they are known as beta particles. Electrons can be created through beta decay of isotopes and in high-energy collisions. The antiparticle of the electron is called the positron, it is identical to the electron except that it carries electrical, when an electron collides with a positron, both particles can be totally annihilated, producing gamma ray photons. The ancient Greeks noticed that amber attracted small objects when rubbed with fur, along with lightning, this phenomenon is one of humanitys earliest recorded experiences with electricity. In his 1600 treatise De Magnete, the English scientist William Gilbert coined the New Latin term electricus, both electric and electricity are derived from the Latin ēlectrum, which came from the Greek word for amber, ἤλεκτρον
8.
Ground state
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The ground state of a quantum mechanical system is its lowest-energy state, the energy of the ground state is known as the zero-point energy of the system. An excited state is any state with greater than the ground state. In the quantum theory, the ground state is usually called the vacuum state or the vacuum. If more than one ground state exists, they are said to be degenerate, many systems have degenerate ground states. Degeneracy occurs whenever there exists a unitary operator which acts non-trivially on a ground state, according to the third law of thermodynamics, a system at absolute zero temperature exists in its ground state, thus, its entropy is determined by the degeneracy of the ground state. Many systems, such as a crystal lattice, have a unique ground state. It is also possible for the highest excited state to have zero temperature for systems that exhibit negative temperature. In 1D, the state of the Schrödinger equation has no nodes. This can be proved considering the energy of a state with a node at x =0, i. e. ψ =0. Consider the average energy in this state ⟨ ψ | H | ψ ⟩ = ∫ d x where V is the potential, now consider a small interval around x =0, i. e. x ∈. Take a new wave function ψ ′ to be defined as ψ ′ = ψ, x < − ϵ and ψ ′ = − ψ, x > ϵ, if ϵ is small enough then this is always possible to do so that ψ ′ is continuous. Note that the energy density | d ψ ′ d x |2 < | d ψ d x |2 everywhere because of the normalization. For definiteness let us choose V ≥0, then it is clear that outside the interval x ∈ the potential energy density is smaller for the ψ ′ because | ψ ′ | < | ψ | there. Therefore, the energy is unchanged up to order ϵ2 if we deform the state with a node ψ into a state without a node ψ ′. We can therefore remove all nodes and reduce the energy, which implies that the wave function cannot have a node. The wave function of the state of a particle in a one-dimensional well is a half-period sine wave which goes to zero at the two edges of the well. The wave function of the state of a hydrogen atom is a spherically-symmetric distribution centred on the nucleus. The electron is most likely to be found at a distance from the equal to the Bohr radius
9.
Excited state
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In quantum mechanics, an excited state of a system is any quantum state of the system that has a higher energy than the ground state. Excitation is an elevation in energy level above a baseline energy state. In physics there is a technical definition for energy level which is often associated with an atom being raised to an excited state. The temperature of a group of particles is indicative of the level of excitation and this return to a lower energy level is often loosely described as decay and is the inverse of excitation. Long-lived excited states are called metastable. Long-lived nuclear isomers and singlet oxygen are two examples of this, a simple example of this concept comes by considering the hydrogen atom. The ground state of the hydrogen atom corresponds to having the single electron in the lowest possible orbit. By giving the additional energy, the electron is able to move into an excited state. If the photon has too much energy, the electron will cease to be bound to the atom, after excitation the atom may return to the ground state or a lower excited state, by emitting a photon with a characteristic energy. Emission of photons from atoms in excited states leads to an electromagnetic spectrum showing a series of characteristic emission lines An atom in a high excited state is termed Rydberg atom. A system of highly excited atoms can form a long-lived condensed excited state e. g. a condensed phase made completely of excited atoms, hydrogen can also be excited by heat or electricity. This phenomenon has been studied in the case of a gas in some detail. These calculations are more difficult than non-excited state calculations, a further consequence is reaction of the atom in the excited state, as in photochemistry. Excited states give rise to chemical reaction, Rydberg formula Stationary state Repulsive state NASA background information on ground and excited states
10.
Functional group
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In organic chemistry, functional groups are specific groups of atoms or bonds within molecules that are responsible for the characteristic chemical reactions of those molecules. The same functional group will undergo the same or similar chemical reaction regardless of the size of the molecule it is a part of, however, its relative reactivity can be modified by other functional groups nearby. The atoms of functional groups are linked to other and to the rest of the molecule by covalent bonds. Any subgroup of atoms of a compound also may be called a radical, and if a covalent bond is broken homolytically, Functional groups can also be charged, e. g. in carboxylate salts, which turns the molecule into a polyatomic ion or a complex ion. Complexation and solvation is also caused by interactions of functional groups. In the common rule of thumb like dissolves like, it is the shared or mutually well-interacting functional groups give rise to solubility. For example, sugar dissolves in water because both share the functional group and hydroxyls interact strongly with each other. Combining the names of groups with the names of the parent alkanes generates what is termed a systematic nomenclature for naming organic compounds. In traditional nomenclature, the first carbon atom after the carbon that attaches to the group is called the alpha carbon, the second, beta carbon. IUPAC conventions call for numeric labeling of the position, e. g. 4-aminobutanoic acid, in traditional names various qualifiers are used to label isomers, for example isopropanol is an isomer is n-propanol. The following is a list of functional groups. In the formulas, the symbols R and R usually denote an attached hydrogen, or a side chain of any length. Functional groups, called hydrocarbyl, that only carbon and hydrogen. Each one differs in type of reactivity, there are also a large number of branched or ring alkanes that have specific names, e. g. tert-butyl, bornyl, cyclohexyl, etc. Hydrocarbons may form charged structures, positively charged carbocations or negative carbanions, examples are tropylium and triphenylmethyl cations and the cyclopentadienyl anion. Haloalkanes are a class of molecule that is defined by a carbon–halogen bond and this bond can be relatively weak or quite stable. In general, with the exception of fluorinated compounds, haloalkanes readily undergo nucleophilic substitution reactions or elimination reactions, the substitution on the carbon, the acidity of an adjacent proton, the solvent conditions, etc. all can influence the outcome of the reactivity. Compounds that contain nitrogen in this category may contain C-O bonds, compounds that contain sulfur exhibit unique chemistry due to their ability to form more bonds than oxygen, their lighter analogue on the periodic table
11.
Photon
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A photon is an elementary particle, the quantum of the electromagnetic field including electromagnetic radiation such as light, and the force carrier for the electromagnetic force. The photon has zero rest mass and is moving at the speed of light. Like all elementary particles, photons are currently best explained by quantum mechanics and exhibit wave–particle duality, exhibiting properties of both waves and particles. For example, a photon may be refracted by a lens and exhibit wave interference with itself. The quanta in a light wave cannot be spatially localized, some defined physical parameters of a photon are listed. The modern concept of the photon was developed gradually by Albert Einstein in the early 20th century to explain experimental observations that did not fit the classical model of light. The benefit of the model was that it accounted for the frequency dependence of lights energy. The photon model accounted for observations, including the properties of black-body radiation. In that model, light was described by Maxwells equations, in 1926 the optical physicist Frithiof Wolfers and the chemist Gilbert N. Lewis coined the name photon for these particles. After Arthur H. Compton won the Nobel Prize in 1927 for his studies, most scientists accepted that light quanta have an independent existence. In the Standard Model of particle physics, photons and other particles are described as a necessary consequence of physical laws having a certain symmetry at every point in spacetime. The intrinsic properties of particles, such as charge, mass and it has been applied to photochemistry, high-resolution microscopy, and measurements of molecular distances. Recently, photons have been studied as elements of quantum computers, in 1900, the German physicist Max Planck was studying black-body radiation and suggested that the energy carried by electromagnetic waves could only be released in packets of energy. In his 1901 article in Annalen der Physik he called these packets energy elements, the word quanta was used before 1900 to mean particles or amounts of different quantities, including electricity. In 1905, Albert Einstein suggested that waves could only exist as discrete wave-packets. He called such a wave-packet the light quantum, the name photon derives from the Greek word for light, φῶς. Arthur Compton used photon in 1928, referring to Gilbert N. Lewis, the name was suggested initially as a unit related to the illumination of the eye and the resulting sensation of light and was used later in a physiological context. Although Wolferss and Lewiss theories were contradicted by many experiments and never accepted, in physics, a photon is usually denoted by the symbol γ
12.
Retinal
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Retinal is also known as retinaldehyde. It was originally called retinene, and renamed after it was discovered to be vitamin A aldehyde, retinal is one of the many forms of vitamin A. Retinal is a chromophore, bound to proteins called opsins. Retinal allows certain microorganisms to convert light into metabolic energy, vertebrate animals ingest retinal directly from meat, or they produce retinal from carotenoids, either from one of two carotenes or from β-cryptoxanthin, a type of xanthophyll. These carotenoids must be obtained from plants or other photosynthetic organisms, no other carotenoids can be converted by animals to retinal, and some carnivores cannot convert any carotenoids at all. The other main forms of vitamin A, retinol, and an active form, retinoic acid. Invertebrates such as insects and squid use hydroxylated forms of retinal in their visual systems, living organisms produce retinal by irreversible oxidative cleavage of carotenoids. For example, beta-carotene + O2 →2 retinal catalyzed by a beta-carotene 15, 15-monooxygenase or a beta-carotene 15, vision begins with the photoisomerization of retinal. When the 11-cis-retinal chromophore absorbs a photon it isomerizes from the 11-cis state to the all-trans state, the absorbance spectrum of the chromophore depends on its interactions with the opsin protein to which it is bound, different opsins produce different absorbance spectra. Opsins are proteins and the visual pigments found in the photoreceptor cells in the retinas of eyes. An opsin is arranged into a bundle of seven transmembrane alpha-helices connected by six loops, in rod cells the opsin molecules are embedded in the membranes of the disks which are entirely inside of the cell. The N-terminus head of the molecule extends into the interior of the disk, in cone cells the disks are defined by the cells plasma membrane so that the N-terminus head extends outside of the cell. Retinal binds covalently to a lysine on the transmembrane helix nearest the C-terminus of the protein through a Schiff base linkage, formation of the Schiff base linkage involves removing the oxygen atom from retinal and two hydrogen atoms from the free amino group of lysine, giving H2O. Retinylidene is the divalent group formed by removing the oxygen atom from retinal, opsins are prototypical G protein-coupled receptors. Bovine rhodopsin, the opsin of the rod cells of cattle, was the first GPCR to have its X-ray structure determined, bovine rhodopsin contains 348 amino acid residues. The retinal chromophore binds at Lys296, although mammals use retinal exclusively as the opsin chromophore, other groups of animals additionally use four chromophores closely related to retinal. These are 3, 4-didehydroretinal, -3-hydroxyretinal, -3-hydroxyretinal, and -4-hydroxyretinal, many fish and amphibians use 3, 4-didehydroretinal, also called dehydroretinal. With the exception of the dipteran suborder Cyclorrhapha, the higher flies
13.
Conjugated system
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Lone pairs, radicals or carbenium ions may be part of the system. The compound may be cyclic, acyclic, linear or mixed, conjugation is the overlap of one p-orbital with another across an intervening σ bond. A conjugated system has a region of overlapping p-orbitals, bridging the interjacent single bonds and they allow a delocalization of pi electrons across all the adjacent aligned p-orbitals. The pi electrons do not belong to a bond or atom. The largest conjugated systems are found in graphene, graphite, conductive polymers, conjugation is possible by means of alternating single and double bonds. As long as each contiguous atom in a chain has an available p-orbital, for example, furan is a five-membered ring with two alternating double bonds and an oxygen in position 1. Oxygen has two pairs, one of which occupies a p-orbital on that position, thereby maintaining the conjugation of that five-membered ring. The presence of a nitrogen in the ring or groups α to the ring like a group, an imine group. There are also types of conjugation. Homoconjugation is an overlap of two separated by a non-conjugating group, such as CH2. For example, the molecule CH2=CH–CH2–CH=CH2 is homoconjugated because the two C=C double bonds are separated by one CH2 group, cyclic compounds can be partly or completely conjugated. Annulenes, completely conjugated monocyclic hydrocarbons, may be aromatic, non-aromatic or anti-aromatic, conjugated, planar, cyclic compounds that follow Hückels rule are aromatic and exhibit an unusual stability. The classic example benzene has a system of 6 π-electrons, which forms the ring along the planar σ-ring with its 12 electrons. Not all compounds with alternating double and single bonds are aromatic, cyclooctatetraene, for example, possesses alternating single and double bonds. The molecule typically adopts a tub conformation, because the p-orbitals of the molecule do not align themselves well in this non-planar molecule, the electrons are not as easily shared between the carbon atoms. The molecule can be considered conjugated, but is neither aromatic. Many pigments make use of conjugated electron systems to absorb visible light, for example, the long conjugated hydrocarbon chain in beta-carotene leads to its strong orange color. When an electron in the system absorbs a photon of light of the right wavelength, in this model the lowest possible absorption energy corresponds to the energy difference between the highest occupied molecular orbital and the lowest unoccupied molecular orbital
14.
Pi bond
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In chemistry, pi bonds are covalent chemical bonds where two lobes of one involved atomic orbital overlap two lobes of the other involved atomic orbital. Each of these orbitals is zero at a shared nodal plane. The same plane is also a plane for the molecular orbital of the pi bond. The Greek letter π in their name refers to p orbitals, P orbitals often engage in this sort of bonding. D orbitals also engage in pi bonding, and form part of the basis for metal-metal multiple bonding, Pi bonds are usually weaker than sigma bonds. From the perspective of quantum mechanics, this weakness is explained by significantly less overlap between the component p-orbitals due to their parallel orientation. This is contrasted by sigma bonds which form bonding orbitals directly between the nuclei of the atoms, resulting in greater overlap and a strong sigma bond. Pi bonds result from overlap of atomic orbitals that are in contact through two areas of overlap, pi-bonds are more diffuse bonds than the sigma bonds. Electrons in pi bonds are referred to as pi electrons. Molecular fragments joined by a pi bond cannot rotate about that bond without breaking the pi bond, for homonuclear diatomic molecules, bonding π molecular orbitals have only the one nodal plane passing through the bonded atoms, and no nodal planes between the bonded atoms. The corresponding antibonding, or π* molecular orbital, is defined by the presence of a nodal plane between these two bonded atoms. A typical double bond consists of one bond and one pi bond, for example. A typical triple bond, for example in acetylene, consists of one sigma bond, two pi bonds are the maximum that can exist between a given pair of atoms. Quadruple bonds are rare and can be formed only between transition metal atoms, and consist of one sigma bond, two pi bonds and one delta bond. A pi bond is weaker than a bond, but the combination of pi. The enhanced strength of a multiple bond versus a single is indicated in many ways, for example, in organic chemistry, carbon–carbon bond lengths are about 154 pm in ethane,134 pm in ethylene and 120 pm in acetylene. More bonds make the total bond shorter and stronger, a pi bond can exist between two atoms that do not have a net sigma-bonding effect between them. In certain metal complexes, pi interactions between an atom and alkyne and alkene pi antibonding orbitals form pi-bonds
15.
Chemical bond
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A chemical bond is a lasting attraction between atoms that enables the formation of chemical compounds. The bond may result from the force of attraction between atoms with opposite charges, or through the sharing of electrons as in the covalent bonds. Since opposite charges attract via an electromagnetic force, the negatively charged electrons that are orbiting the nucleus. An electron positioned between two nuclei will be attracted to both of them, and the nuclei will be attracted toward electrons in this position and this attraction constitutes the chemical bond. This phenomenon limits the distance between nuclei and atoms in a bond, in general, strong chemical bonding is associated with the sharing or transfer of electrons between the participating atoms. All bonds can be explained by quantum theory, but, in practice, simplification rules allow chemists to predict the strength, directionality, the octet rule and VSEPR theory are two examples. Electrostatics are used to describe bond polarities and the effects they have on chemical substances, a chemical bond is an attraction between atoms. This attraction may be seen as the result of different behaviors of the outermost or valence electrons of atoms and these behaviors merge into each other seamlessly in various circumstances, so that there is no clear line to be drawn between them. However it remains useful and customary to differentiate different types of bond, which result in different properties of condensed matter. In the simplest view of a covalent bond, one or more electrons are drawn into the space between the two atomic nuclei, energy is released by bond formation. This is not as a reduction in energy, because the attraction of the two electrons to the two protons is offset by the electron-electron and proton-proton repulsions. In a polar covalent bond, one or more electrons are shared between two nuclei. Such weak intermolecular bonds give organic molecular substances, such as waxes and oils, their soft bulk character, also, the melting points of such covalent polymers and networks increase greatly. In a simplified view of a bond, the bonding electron is not shared at all. In this type of bond, the atomic orbital of one atom has a vacancy which allows the addition of one or more electrons. These newly added electrons potentially occupy a lower energy-state than they experience in a different atom, thus, one nucleus offers a more tightly bound position to an electron than does another nucleus, with the result that one atom may transfer an electron to the other. This transfer causes one atom to assume a net charge. The bond then results from electrostatic attraction between atoms and the atoms become positive or negatively charged ions, ionic bonds may be seen as extreme examples of polarization in covalent bonds
16.
Aromatic
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Aromatic molecules are very stable, and do not break apart easily to react with other substances. Organic compounds that are not aromatic are classified as aliphatic compounds—they might be cyclic, since the most common aromatic compounds are derivatives of benzene, the word “aromatic” occasionally refers informally to benzene derivatives, and so it was first defined. Nevertheless, many aromatic compounds exist. In living organisms, for example, the most common aromatic rings are the bases in RNA and DNA. An aromatic functional group or other substituent is called an aryl group, the earliest use of the term aromatic was in an article by August Wilhelm Hofmann in 1855. Hofmann used the term for a class of compounds, many of which have odors. In terms of the nature of the molecule, aromaticity describes a conjugated system often made of alternating single and double bonds in a ring. This configuration allows for the electrons in the pi system to be delocalized around the ring, increasing the molecules stability. The molecule cannot be represented by one structure, but rather a hybrid of different structures. These molecules cannot be found in one of these representations, with the longer single bonds in one location. Rather, the molecule exhibits bond lengths in between those of single and double bonds and this commonly seen model of aromatic rings, namely the idea that benzene was formed from a six-membered carbon ring with alternating single and double bonds, was developed by August Kekulé. The model for benzene consists of two forms, which corresponds to the double and single bonds superimposing to produce six one-and-a-half bonds. Benzene is a stable molecule than would be expected without accounting for charge delocalization. As is standard for resonance diagrams, the use of an arrow indicates that two structures are not distinct entities but merely hypothetical possibilities. Neither is a representation of the actual compound, which is best represented by a hybrid of these structures. A C=C bond is shorter than a C−C bond, but benzene is perfectly hexagonal—all six carbon–carbon bonds have the same length, intermediate between that of a single and that of a double bond. In a cyclic molecule with three alternating double bonds, cyclohexatriene, the length of the single bond would be 1.54 Å. However, in a molecule of benzene, the length of each of the bonds is 1.40 Å, a better representation is that of the circular π-bond, in which the electron density is evenly distributed through a π-bond above and below the ring
17.
Food coloring
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Food coloring, or color additive, is any dye, pigment or substance that imparts color when it is added to food or drink. They come in many forms consisting of liquids, powders, gels, Food coloring is used both in commercial food production and in domestic cooking. Food colorants are used in a variety of non-food applications including cosmetics, pharmaceuticals, home craft projects. People associate certain colors with certain flavors, and the color of food can influence the flavor in anything from candy to wine. During the Middle Ages, the economy in the European countries was based on agriculture, under feudalism, aesthetic aspects were not considered, at least not by the vast majority of the generally very poor population. This situation changed with urbanization at the beginning of the Modern Age, one of the very first food laws, created in Augsburg, Germany, in 1531, concerned spices or colorants and required saffron counterfeiters to be burned. With the onset of the revolution, people became dependent on foods produced by others. These new urban dwellers demanded food at low cost, analytical chemistry was still primitive and regulations few. Copper arsenite was used to recolor used tea leaves for resale and it also caused two deaths when used to color a dessert in 1860. Again his tea if mixed or green, he would not escape without the administration of a little Prussian blue. Many color additives had never tested for toxicity or other adverse effects. Historical records show that injuries, even deaths, resulted from tainted colorants, in 1851, about 200 people were poisoned in England,17 of them fatally, directly as a result of eating adulterated lozenges. Originally, these were dubbed coal-tar colors because the materials were obtained from bituminous coal. Many synthesized dyes were easier and less costly to produce and were superior in coloring properties when compared to naturally derived alternatives, some synthetic food colorants are diazo dyes. Diazo dyes are prepared by coupling of a compound with a second aromatic hydrocarbons. The resulting compounds contain conjugated systems that absorb light in the visible parts of the spectrum. The attractiveness of the synthetic dyes is that their color, lipophilicity, the color of the dyes can be controlled by selecting the number of azo-groups and various substituents. Yellow shades are often achieved by using acetoacetanilide, Red colors are often azo compounds
18.
Azo compound
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Azo compounds are compounds bearing the functional group R–N=N–R′, in which R and R′ can be either aryl or alkyl. IUPAC defines azo compounds as, Derivatives of diazene, HN=NH, the more stable derivatives contain two aryl groups. The N=N group is called an azo group, the name azo comes from azote, the French name for nitrogen that is derived from the Greek ἀ- + ζωή. Most colored textile and leather articles are treated with azo dyes, as a consequence of п-delocalization, aryl azo compounds have vivid colors, especially reds, oranges, and yellows. Therefore, they are used as dyes, and are known as azo dyes. Some azo compounds, e. g. methyl orange, are used as acid-base indicators due to the different colors of their acid, most DVD-R/+R and some CD-R discs use blue azo dye as the recording layer. The development of azo dyes was an important step in the development of the chemical industry, azo pigments consist of colorless particles colored using an azo compound. Azo pigments are important in a variety of paints including artists paints and they have excellent coloring properties, again mainly in the yellow to red range, as well as good lightfastness. The lightfastness depends not only on the properties of the azo compound. Aryl azo compounds are stable, crystalline species. Azobenzene is the prototypical aromatic azo compound and it exists mainly as the trans isomer, but upon photolysis, converts to the cis isomer. The oxidation of hydrazines also gives azo compounds, typical aniline partners are shown below. Illustrative azo compounds that are precursors to dyes Aliphatic azo compounds are commonly encountered than the aryl azo compounds. A commercially important alkyl azo compound is azobisisobutyronitrile, which is used as an initiator in free radical polymerizations. A simple dialkyl diazo compound is diethyldiazene, EtN=NEt, because of their instability, aliphatic azo compounds pose the risk of explosion. Likewise, several studies have linked azo pigments with basal cell carcinoma. Azo dyes derived from benzidine are carcinogens, exposure to them has classically been associated with bladder cancer, accordingly, the production of benzidine azo dyes was discontinued in the 1980s in the most important western industrialized countries. Certain azo dyes can break down under reductive conditions to any of a group of defined aromatic amines
19.
PH indicator
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A pH indicator is a halochromic chemical compound added in small amounts to a solution so the pH of the solution can be determined visually. Hence, a pH indicator is a detector for hydronium ions or hydrogen ions in the Arrhenius model. Normally, the causes the color of the solution to change depending on the pH. Indicators can also change in other physical properties, for example. The pH value of a solution is 7.0. Solutions with a pH value below 7.0 are considered acidic, as most naturally occurring organic compounds are weak protolytes, carboxylic acids and amines, pH indicators find many applications in biology and analytical chemistry. Moreover, pH indicators form one of the three types of indicator compounds used in chemical analysis. In and of themselves, pH indicators are frequently weak acids or weak bases. The general reaction scheme of a pH indicator can be formulated as, HInd + H 2O ⇌ H 3O+ + Ind− Here, HInd stands for the acid form, the ratio of these determines the color of the solution and connects the color to the pH value. If pH is above the pKa value, the concentration of the base is greater than the concentration of the acid. If pH is below the pKa value, the converse is true, usually, the color change is not instantaneous at the pKa value, but a pH range exists where a mixture of colors is present. This pH range varies between indicators, but as a rule of thumb, it falls between the pKa value plus or minus one and this assumes that solutions retain their color as long as at least 10% of the other species persists. For example, if the concentration of the base is 10 times greater than the concentration of the acid, their ratio is 10,1. Conversely, if a 10-fold excess of the acid occurs with respect to the base, the ratio is 1,10 and the pH is pKa −1. For optimal accuracy, the difference between the two species should be as clear as possible, and the narrower the pH range of the color change the better. In some indicators, such as phenolphthalein, one of the species is colorless, whereas in other indicators, such as methyl red, both species confer a color. While pH indicators work efficiently at their designated pH range, they are destroyed at the extreme ends of the pH scale due to undesired side reactions. PH indicators are frequently employed in titrations in analytical chemistry and biology to determine the extent of a chemical reaction, because of the subjective choice of color, pH indicators are susceptible to imprecise readings
20.
Lycopene
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Although lycopene is chemically a carotene, it has no vitamin A activity. Foods that are not red may also contain lycopene, such as asparagus, like all carotenoids, lycopene is a polyunsaturated hydrocarbon, i. e. an unsubstituted alkene. Structurally, lycopene is a tetraterpene and assembled from eight isoprene units that are composed entirely of carbon, lycopenes eleven conjugated double bonds give its deep red color and its antioxidant activity. Owing to the color, lycopene is a useful food coloring and is approved for usage in the USA, Australia and New Zealand. Lycopene is not a nutrient for humans, but is commonly found in the diet mainly from dishes prepared from tomatoes. Lycopene is a symmetrical tetraterpene assembled from eight isoprene units and it is a member of the carotenoid family of compounds, and because it consists entirely of carbon and hydrogen, is also a carotene. Isolation procedures for lycopene were first reported in 1910, and the structure of the molecule was determined by 1931, in its natural, all-trans form, the molecule is long and straight, constrained by its system of eleven conjugated double bonds. Lycopene absorbs all but the longest wavelengths of light, so it appears red. Plants and photosynthetic bacteria naturally produce all-trans lycopene, but a total of 72 geometric isomers of the molecule are sterically possible, when exposed to light or heat, lycopene can undergo isomerization to any of a number of these cis-isomers, which have a bent rather than linear shape. Different isomers were shown to have different stabilities due to their molecular energy, in the human bloodstream, various cis-isomers constitute more than 60% of the total lycopene concentration, but the biological effects of individual isomers have not been investigated. Lycopene, the pigment in tomato-containing sauces, turns plastic cookware orange and is insoluble in water and it can be dissolved only in organic solvents and oils. Because of its non-polarity, lycopene in food preparations will stain any sufficiently porous material, to remove this staining, the plastics can be soaked in a solution containing a small amount of household bleach. Carotenoids like lycopene are important pigments found in photosynthetic pigment-protein complexes in plants, photosynthetic bacteria, fungi and they are responsible for the bright colors of fruits and vegetables, perform various functions in photosynthesis, and protect photosynthetic organisms from excessive light damage. Lycopene is a key intermediate in the biosynthesis of many important carotenoids, such as beta-carotene, the unconditioned biosynthesis of lycopene in eukaryotic plants and in prokaryotic cyanobacteria is similar, as are the enzymes involved. Synthesis begins with mevalonic acid, which is converted into dimethylallyl pyrophosphate and this is then condensed with three molecules of isopentenyl pyrophosphate, to give the twenty-carbon geranylgeranyl pyrophosphate. Two molecules of this product are then condensed in a configuration to give the forty-carbon phytoene. Through several desaturation steps, phytoene is converted into lycopene, the two terminal isoprene groups of lycopene can be cyclized to produce beta-carotene, which can then be transformed into a wide variety of xanthophylls. Fruits and vegetables that are high in lycopene include autumn olive, gac, tomatoes, watermelon, pink grapefruit, pink guava, papaya, seabuckthorn, wolfberry, the lycopene content of tomatoes depends on species and increases as the fruit ripens
21.
Carotene
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The term carotene is used for many related unsaturated hydrocarbon substances having the formula C40Hx, which are synthesized by plants but in general cannot be made by animals. Carotenes are photosynthetic pigments important for photosynthesis and they absorb ultraviolet, violet, and blue light and scatter orange or red light, and yellow light. Carotenes are responsible for the colour of the carrot, for which this class of chemicals is named. Carotenes are also responsible for the colours in dry foliage. They also impart the yellow coloration to milk-fat and butter, the typical yellow-coloured fat of humans and chickens is a result of fat storage of carotenes from their diets. Carotenes contribute to photosynthesis by transmitting the energy they absorb to chlorophyll. They also protect plant tissues by helping to absorb the energy from singlet oxygen, the carotenes α-carotene and γ-carotene, due to their single retinyl group, also have some vitamin A activity, as does the xanthophyll carotenoid β-cryptoxanthin. All other carotenoids, including lycopene, have no beta-ring and thus no vitamin A activity, animal species differ greatly in their ability to convert retinyl containing carotenoids to retinals. Carnivores in general are poor converters of dietary ionone-containing carotenoids, chemically, carotenes are polyunsaturated hydrocarbons containing 40 carbon atoms per molecule, variable numbers of hydrogen atoms, and no other elements. Some carotenes are terminated by rings, on one or both ends of the molecule. All are coloured to the eye, due to extensive systems of conjugated double bonds. Structurally carotenes are tetraterpenes, meaning that they are synthesized biochemically from four 10-carbon terpene units, carotenes are found in plants in two primary forms designated by characters from the Greek alphabet, alpha-carotene and beta-carotene. Gamma-, delta-, epsilon-, and zeta-carotene also exist, since they are hydrocarbons, and therefore contain no oxygen, carotenes are fat-soluble and insoluble in water. 6 μg of dietary β-carotene supplies the equivalent of 1 μg of retinol and this is equivalent to 3⅓ IU of vitamin A. The two primary isomers of carotene, α-carotene and β-carotene, differ in the position of a bond in the cyclic group at one end. β-Carotene is the common form and can be found in yellow, orange. As a rule of thumb, the greater the intensity of the colour of the fruit or vegetable. Carotene protects plant cells against the effects of ultraviolet light
22.
Anthocyanin
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Anthocyanins are water-soluble vacuolar pigments that may appear red, purple, or blue depending on the pH. They belong to a parent class of molecules called flavonoids synthesized via the pathway, they are odorless but flavorful. Anthocyanins occur in all tissues of plants, including leaves, stems, roots, flowers. Anthoxanthins are clear, white to yellow counterparts of anthocyanins occurring in plants, anthocyanins are derived from anthocyanidins by adding sugars. Anthocyanins have an antioxidant role in plants against reactive oxygen species caused by abiotic stresses, such as overexposure to ultraviolet light, tomato plants protect against cold stress with anthocyanins countering reactive oxygen species, leading to a lower rate of cell death in leaves. Anthocyanins are considered secondary metabolites as an additive with E number E163, they are approved for use as a food additive in the EU, Australia. Although anthocyanins have antioxidant properties in vitro, this antioxidant effect is not conserved after the plant is consumed, as interpreted by the Linus Pauling Institute and European Food Safety Authority, dietary anthocyanins and other flavonoids have little or no direct antioxidant food value following digestion. The absorbance pattern responsible for the red color of anthocyanins may be complementary to that of green chlorophyll in photosynthetically active tissues such as young Quercus coccifera leaves and it may protect the leaves from attacks by plant eaters that may be attracted by green color. Anthocyanins are found in the vacuole, mostly in flowers and fruits but also in leaves, stems. In these parts, they are predominantly in outer cell layers such as the epidermis. Most frequently occurring in nature are the glycosides of cyanidin, delphinidin, malvidin, pelargonidin, peonidin, roughly 2% of all hydrocarbons fixed in photosynthesis are converted into flavonoids and their derivatives such as the anthocyanins. Not all land plants contain anthocyanin, in the Caryophyllales, they are replaced by betalains, anthocyanins and betalains have never been found in the same plant. Sometimes bred purposely for high anthocyanin quantities, ornamental plants such as sweet peppers may have unusual culinary, anthocyanins occur in the flowers of many plants, such as the famously blue poppies of some Meconopsis species and cultivars. Red-fleshed peaches and apples contain anthocyanins, anthocyanins are less abundant in banana, asparagus, pea, fennel, pear, and potato, and may be totally absent in certain cultivars of green gooseberries. The highest recorded amount appears to be specifically in the coat of black soybean containing around 2 g per 100 g, in purple corn kernels and husks. Due to critical differences in origin, preparation and extraction methods determining anthocyanin content. The variety known as Indigo Rose became commercially available to the agricultural industry, investing tomatoes with high anthocyanin content doubles their shelf-life and inhibits growth of a post-harvest mold pathogen, Botrytis cinerea. Tomatoes have also been modified with transcription factors from snapdragons to produce high levels of anthocyanins in the fruits
23.
Woodward's rules
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Inputs used in the calculation are the type of chromophores present, the substituents on the chromophores, and shifts due to the solvent. Examples are conjugated carbonyl compounds, conjugated dienes, and polyenes, one set of Woodward–Fieser rules for dienes is outlined in table 1. A diene is homoannular with both double bonds contained in one ring or heteroannular with two double bonds distributed between two rings. With the aid of rules the UV absorption maximum can be predicted. This diene group has 4 alkyl substituents and the bond in one ring is exocyclic to the other. In the compound on the right, the diene is homoannular with 4 alkyl substituents, both double bonds in the central B ring are exocyclic with respect to rings A and C. For polyenes having more than 4 conjugated double bonds one must use Fieser-Kuhn rules
24.
Ultraviolet
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Ultraviolet is an electromagnetic radiation with a wavelength from 10 nm to 400 nm, shorter than that of visible light but longer than X-rays. UV radiation constitutes about 10% of the light output of the Sun. It is also produced by electric arcs and specialized lights, such as lamps, tanning lamps. Consequently, the effects of UV are greater than simple heating effects. Suntan, freckling and sunburn are familiar effects of over-exposure, along with risk of skin cancer. Living things on dry land would be damaged by ultraviolet radiation from the Sun if most of it were not filtered out by the Earths atmosphere. More-energetic, shorter-wavelength extreme UV below 121 nm ionizes air so strongly that it is absorbed before it reaches the ground, Ultraviolet is also responsible for the formation of bone-strengthening vitamin D in most land vertebrates, including humans. The UV spectrum thus has both beneficial and harmful to human health. Ultraviolet rays are invisible to most humans, the lens in a human eye ordinarily filters out UVB frequencies or higher, and humans lack color receptor adaptations for ultraviolet rays. Under some conditions, children and young adults can see ultraviolet down to wavelengths of about 310 nm, near-UV radiation is visible to some insects, mammals, and birds. Small birds have a fourth color receptor for ultraviolet rays, this gives birds true UV vision, reindeer use near-UV radiation to see polar bears, who are poorly visible in regular light because they blend in with the snow. UV also allows mammals to see urine trails, which is helpful for animals to find food in the wild. The males and females of some species look identical to the human eye. Ultraviolet means beyond violet, violet being the color of the highest frequencies of visible light, Ultraviolet has a higher frequency than violet light. He called them oxidizing rays to emphasize chemical reactivity and to them from heat rays. The terms chemical and heat rays were eventually dropped in favour of ultraviolet and infrared radiation, in 1878 the effect of short-wavelength light on sterilizing bacteria was discovered. By 1903 it was known the most effective wavelengths were around 250 nm, in 1960, the effect of ultraviolet radiation on DNA was established. The discovery of the ultraviolet radiation below 200 nm, named vacuum ultraviolet because it is absorbed by air, was made in 1893 by the German physicist Victor Schumann
25.
Coordination complex
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Many metal-containing compounds, especially those of transition metals, are coordination complexes. A coordination complex whose centre is an atom is called a metal complex. Coordination complexes are so pervasive that their structures and reactions are described in many ways, the atom within a ligand that is bonded to the central metal atom or ion is called the donor atom. In a typical complex, an ion is bonded to several donor atoms. A polydentate ligand is a molecule or ion that bonds to the atom through several of the ligands atoms. These complexes are called chelate complexes, the formation of complexes is called chelation, complexation. The central atom or ion, together with all ligands comprise the coordination sphere, the central atoms or ion and the donor atoms comprise the first coordination sphere. Coordination refers to the covalent bonds between the ligands and the central atom. Originally, a complex implied a reversible association of molecules, atoms, as applied to coordination chemistry, this meaning has evolved. Some metal complexes are formed virtually irreversibly and many are bound together by bonds that are quite strong, the number of donor atoms attached to the central atom or ion is called the coordination number. The most common coordination numbers are 2,4 and especially 6, for example, the cobalt hexahydrate ion or the hexaaquacobalt ion 2+, is a hydrated-complex ion that consists of six water molecules attached to a metal ion Co. The oxidation state and the number reflect the number of bonds formed between the metal ion and the ligands in the complex ion. However the coordination number of Pt2+ 2is 4 since it has two ligands, which contain four donor atoms in total. Coordination complexes have been known since the beginning of modern chemistry, early well-known coordination complexes include dyes such as Prussian blue. Their properties were first well understood in the late 1800s, following the 1869 work of Christian Wilhelm Blomstrand, Blomstrand developed what has come to be known as the complex ion chain theory. The theory claimed that the reason coordination complexes form is because in solution and he compared this effect to the way that various carbohydrate chains form. Following this theory, Danish scientist Sophus Mads Jorgensen made improvements to it and it was not until 1893 that the most widely accepted version of the theory today was published by Alfred Werner. Werner’s work included two important changes to the Blomstrand theory, the first was that Werner described the two different ion possibilities in terms of location in the coordination sphere
26.
Chlorophyll
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Chlorophyll is any of several closely related green pigments found in cyanobacteria and the chloroplasts of algae and plants. Its name is derived from the Greek words χλωρός, chloros and φύλλον, chlorophyll is essential in photosynthesis, allowing plants to absorb energy from light. Chlorophyll absorbs light most strongly in the portion of the electromagnetic spectrum. Conversely, it is a poor absorber of green and near-green portions of the spectrum, chlorophyll molecules are specifically arranged in and around photosystems that are embedded in the thylakoid membranes of chloroplasts. Two types of chlorophyll exist in the photosystems of green plants, chlorophyll was first isolated and named by Joseph Bienaimé Caventou and Pierre Joseph Pelletier in 1817. Chlorophyll is vital for photosynthesis, which plants to absorb energy from light. Chlorophyll molecules are arranged in and around photosystems that are embedded in the thylakoid membranes of chloroplasts. In these complexes, chlorophyll serves two primary functions, the two currently accepted photosystem units are photosystem II and photosystem I, which have their own distinct reaction centres, named P680 and P700, respectively. These centres are named after the wavelength of their red-peak absorption maximum, the identity, function and spectral properties of the types of chlorophyll in each photosystem are distinct and determined by each other and the protein structure surrounding them. Once extracted from the protein into a solvent, these chlorophyll pigments can be separated into chlorophyll a, the function of the reaction center of chlorophyll is to absorb light energy and transfer it to other parts of the photosystem. The absorbed energy of the photon is transferred to an electron in a process called charge separation, the removal of the electron from the chlorophyll is an oxidation reaction. The chlorophyll donates the high energy electron to a series of molecular intermediates called a transport chain. The charged reaction center of chlorophyll is reduced back to its ground state by accepting an electron stripped from water. The electron that reduces P680+ ultimately comes from the oxidation of water into O2 and this reaction is how photosynthetic organisms such as plants produce O2 gas, and is the source for practically all the O2 in Earths atmosphere. Electron transfer reactions in the membranes are complex, however. NADPH is an agent used to reduce CO2 into sugars as well as other biosynthetic reactions. Thus, the other chlorophylls in the photosystem and antenna pigment proteins all cooperatively absorb, besides chlorophyll a, there are other pigments, called accessory pigments, which occur in these pigment–protein antenna complexes. Chlorophyll is a pigment, which is structurally similar to
27.
Hemoglobin
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Hemoglobin in the blood carries oxygen from the respiratory organs to the rest of the body. There it releases the oxygen to permit aerobic respiration to provide energy to power the functions of the organism in the process called metabolism, in mammals, the protein makes up about 96% of the red blood cells dry content, and around 35% of the total content. Hemoglobin has a capacity of 1.34 mL O2 per gram. The mammalian hemoglobin molecule can bind up to four oxygen molecules, Hemoglobin is involved in the transport of other gases, It carries some of the bodys respiratory carbon dioxide as carbaminohemoglobin, in which CO2 is bound to the globin protein. The molecule also carries the important regulatory molecule nitric oxide bound to a globin protein thiol group, Hemoglobin is also found outside red blood cells and their progenitor lines. Other cells that contain hemoglobin include the A9 dopaminergic neurons in the substantia nigra, macrophages, alveolar cells, in these tissues, hemoglobin has a non-oxygen-carrying function as an antioxidant and a regulator of iron metabolism. Hemoglobin and hemoglobin-like molecules are found in many invertebrates, fungi. In these organisms, hemoglobins may carry oxygen, or they may act to transport and regulate other small molecules and ions such as carbon dioxide, nitric oxide, hydrogen sulfide and sulfide. In 1825 J. F. Engelhard discovered that the ratio of Fe to protein is identical in the hemoglobins of several species, from the known atomic mass of iron he calculated the molecular mass of hemoglobin to n ×16000, the first determination of a proteins molecular mass. This hasty conclusion drew a lot of ridicule at the time from scientists who could not believe that any molecule could be that big, gilbert Smithson Adair confirmed Engelhards results in 1925 by measuring the osmotic pressure of hemoglobin solutions. The oxygen-carrying protein hemoglobin was discovered by Hünefeld in 1840, hemoglobins reversible oxygenation was described a few years later by Felix Hoppe-Seyler. In 1959, Max Perutz determined the structure of myoglobin by X-ray crystallography. This work resulted in his sharing with John Kendrew the 1962 Nobel Prize in Chemistry, the role of hemoglobin in the blood was elucidated by French physiologist Claude Bernard. The name hemoglobin is derived from the heme and globin. Each heme group contains one iron atom, that can bind one oxygen molecule through ion-induced dipole forces, the most common type of hemoglobin in mammals contains four such subunits. Hemoglobin consists of subunits, and these proteins, in turn, are folded chains of a large number of different amino acids called polypeptides. The amino acid sequence of any polypeptide created by a cell is in turn determined by the stretches of DNA called genes, in all proteins, it is the amino acid sequence that determines the proteins chemical properties and function. There is more than one gene, in humans, hemoglobin A is coded for by the genes, HBA1, HBA2
28.
Tetrapyrrole
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Tetrapyrroles are a class of chemical compounds whose molecules contain four pyrrole rings held together by direct covalent bonds or by one-carbon bridges, in either a linear or a cyclic fashion. A pyrrole ring in a molecule is a ring where four of the ring atoms are carbon. In cyclic tetrapyrroles, lone pairs on nitrogen atoms facing the center of the macrocycle ring can bond or chelate with a metal ion such as iron, cobalt. Some tetrapyrroles are the cores of some compounds with crucial biochemical roles in living systems, such as hemoglobin. Cyclic tetrapyrroles having three one-carbon bridges and one direct bond between the pyrroles include, Corrins, including the cores of cobalamins, when complexed with a cobalt ion, the tetrapyrrole portions of the molecules typically act as chromophores because of a high degree of conjugation in them. Therefore, these compounds are commonly colored
29.
Macrocycle
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A macrocycle is, as defined by IUPAC, a cyclic macromolecule or a macromolecular cyclic portion of a molecule. In the chemical literature, macrocycles varyingly include molecules containing rings of 8 or more atoms, well-known examples are the group of drugs known as macrolides. Many macrocycles are employed as macrocyclic ligands, in general, macrocycles are synthesized from smaller, usually linear, molecules. This cyclization proceeds by an organic reaction, not requiring any kind of directional influence of a metal ion. Usually involves equimolar concentration of the reagents in order to produce a 1,1 condensation reaction, some cyclizations are facilitated by the presence of metal ions, which helps organize the formation of the macrocyclic ligand. The metal ion acts as a template for the cyclization reaction, phthalocyanine was the first synthetic macrocycle produced by template reaction. The metal ion may direct the condensation preferentially to cyclic rather than polymeric products or stabilize the macrocycle once formed, cryptand, a macrocycle with multiple loops. Rotaxane, macrocycle stuck on a stick, generally freely Catenane, molecular knot, a molecule in the shape of a knot such as a trefoil knot. Cyclic compound Effective molarity Macrocyclic stereocontrol Chambron, J-C, weiss, J. Interlacing molecular threads on transition metals
30.
Heme
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Not all porphyrins contain iron, but a substantial fraction of porphyrin-containing metalloproteins have heme as their prosthetic group, these are known as hemoproteins. Hemoproteins have diverse functions including the transportation of diatomic gases, chemical catalysis, diatomic gas detection. The heme iron serves as a source or sink of electrons during electron transfer or redox chemistry, in peroxidase reactions, the porphyrin molecule also serves as an electron source. In the transportation or detection of gases, the gas binds to the heme iron. During the detection of gases, the binding of the gas ligand to the heme iron induces conformational changes in the surrounding protein. Hemoproteins achieve their remarkable diversity by modifying the environment of the heme macrocycle within the protein matrix. For example, the ability of hemoglobin to effectively deliver oxygen to tissues is due to amino acid residues located near the heme molecule. Hemoglobin reversibly binds to oxygen in the lungs when the pH is high, when the situation is reversed, hemoglobin will release oxygen into the tissues. This phenomenon, which states that hemoglobins oxygen binding affinity is inversely proportional to both acidity and concentration of carbon dioxide, is known as the Bohr effect. There are several biologically important kinds of heme, The most common type is heme B, other important types include heme A, isolated hemes are commonly designated by capital letters while hemes bound to proteins are designated by lower case letters. Cytochrome a refers to the heme A in specific combination with membrane protein forming a portion of cytochrome c oxidase, the following carbon numbering system of porphyrins is an older numbering used by biochemists and not the 1–24 numbering system recommended by IUPAC which is shown in the table above. Heme l is the derivative of heme B which is attached to the protein of lactoperoxidase, eosinophil peroxidase. The addition of peroxide with the glutamyl-375 and aspartyl-225 of lactoperoxidase forms ester bonds between amino acid residues and the heme 1- and 5-methyl groups, respectively. Similar ester bonds with two methyl groups are thought to form in eosinophil and thyroid peroxidases. Heme l is one important characteristic of animal peroxidases, plant peroxidases incorporate heme B, lactoperoxidase and eosinophil peroxidase are protective enzymes responsible for the destruction of invading bacteria and virus. Thyroid peroxidase is the enzyme catalyzing the biosynthesis of the important thyroid hormones, because lactoperoxidase destroys invading organisms in the lungs and excrement, it is thought to be an important protective enzyme. Heme m is the derivative of heme B covalently bound at the site of myeloperoxidase. Heme m contains the two ester bonds at the heme 1- and 5-methyls as in heme l found in other mammalian peroxidases, myeloperoxidase is present in mammalian neutrophils and is responsible for the destruction of invading bacteria and viruse
31.
Porphyrin
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Porphyrins are a group of heterocyclic macrocycle organic compounds, composed of four modified pyrrole subunits interconnected at their α carbon atoms via methine bridges. The parent porphyrin is porphin, and substituted porphines are called porphyrins, the porphyrin ring structure is aromatic, with a total of 26 electrons in the conjugated system. Various analyses indicate that not all atoms of the ring are involved equally in the conjugation or that the overall nature is substantially based on several smaller conjugated systems. Many porphyrins are naturally occurring, one of the best-known porphyrins is heme, the pigment in red blood cells, porphyrins are the conjugate acids of ligands that bind metals to form complexes. The metal ion usually has a charge of 2+ or 3+. A schematic equation for these syntheses is shown, H2porphyrin + 2+ → MLn−4 +4 L +2 H+ where M = metal ion, some iron-containing porphyrins are called hemes. Heme-containing proteins, or hemoproteins, are found extensively in nature, hemoglobin and myoglobin are two O2-binding proteins that contain iron porphyrins. Several other heterocycles are related to porphyrins and these include corrins, chlorins, bacteriochlorophylls, and corphins. Chlorins are more reduced, contain more hydrogen than porphyrins, and this structure occurs in a chlorophyll molecule. Replacement of two of the four subunits with pyrrolinic subunits results in either a bacteriochlorin or an isobacteriochlorin. Some porphyrin derivatives follow Hückels rule, but most do not, a benzoporphyrin is a porphyrin with a benzene ring fused to one of the pyrrole units. E. g. verteporfin is a benzoporphyrin derivative, a geoporphyrin, also known as a petroporphyrin, is a porphyrin of geologic origin. They can occur in oil, oil shale, coal. Abelsonite is possibly the only geoporphyrin mineral, as it is rare for porphyrins to occur in isolation, in plants, algae, bacteria and archaea, it is produced from glutamic acid via glutamyl-tRNA and glutamate-1-semialdehyde. The enzymes involved in this pathway are glutamyl-tRNA synthetase, glutamyl-tRNA reductase and this pathway is known as the C5 or Beale pathway. Two molecules of dALA are then combined by porphobilinogen synthase to give porphobilinogen, four PBGs are then combined through deamination into hydroxymethyl bilane, which is hydrolysed to form the circular tetrapyrrole uroporphyrinogen III. This molecule undergoes a number of further modifications, intermediates are used in different species to form particular substances, but, in humans, the main end-product protoporphyrin IX is combined with iron to form heme. Bile pigments are the products of heme
32.
Chlorin
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In organic chemistry, a chlorin is a large heterocyclic aromatic ring consisting, at the core, of three pyrroles and one pyrroline coupled through four =CH- linkages. Unlike porphin, the aromatic ring structure of porphyrins, a chlorin is therefore largely aromatic. Magnesium-containing chlorins are called chlorophylls, and are the central photosensitive pigment in chloroplasts, related compounds, with two pyrroles and two pyrrolines in the macrocycle are called bacteriochlorins and isobacteriochlorins. Because of their photosensitivity, chlorins are in use as photosensitizing agents in experimental photodynamic therapy
33.
Bilirubin
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Bilirubin is a yellow compound that occurs in the normal catabolic pathway that breaks down heme in vertebrates. This catabolism is a process in the bodys clearance of waste products that arise from the destruction of aged red blood cells. First the hemoglobin gets stripped of the molecule which thereafter passes through various processes of porphyrin catabolism. For example, the molecules excreted in the urine differ from those in the feces, the production of biliverdin from heme is the first major step in the catabolic pathway, after which the enzyme biliverdin reductase performs the second step, producing bilirubin from biliverdin. Bilirubin is excreted in bile and urine, and elevated levels may indicate certain diseases and it is responsible for the yellow color of bruises and the yellow discoloration in jaundice. Its subsequent breakdown products, such as stercobilin, cause the color of feces. A different breakdown product, urobilin, is the component of the straw-yellow color in urine. It has also found in plants. Bilirubin consists of a chain of four pyrrole-like rings. In heme, these four rings are connected into a larger ring, Bilirubin can be conjugated with a molecule of glucuronic acid which makes it soluble in water. This is an example of glucuronidation, Bilirubin is very similar to the pigment phycobilin used by certain algae to capture light energy, and to the pigment phytochrome used by plants to sense light. All of these contain a chain of four pyrrolic rings. Like these other pigments, some of the double-bonds in bilirubin isomerize when exposed to light and this allows the excretion of unconjugated bilirubin in bile. Some textbooks and research articles show the geometric isomer of bilirubin. The naturally occurring isomer is the Z, Z-isomer, Bilirubin is created by the activity of biliverdin reductase on biliverdin, a green tetrapyrrolic bile pigment that is also a product of heme catabolism. Bilirubin, when oxidized, reverts to become once again. This cycle, in addition to the demonstration of the potent antioxidant activity of bilirubin, has led to the hypothesis that bilirubins main physiologic role is as a cellular antioxidant, the measurement of indirect bilirubin depends on its reaction with diazosulfanilic acid to create azobilirubin. However, unconjugated bilirubin also reacts slowly with diazosulfanilic acid, so that the measured indirect bilirubin is an underestimate of the true unconjugated concentration
34.
PH
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In chemistry, pH is a numeric scale used to specify the acidity or basicity of an aqueous solution. It is approximately the negative of the base 10 logarithm of the concentration, measured in units of moles per liter. More precisely it is the negative of the logarithm to base 10 of the activity of the hydrogen ion, solutions with a pH less than 7 are acidic and solutions with a pH greater than 7 are basic. Pure water is neutral, at pH7, being neither an acid nor a base, contrary to popular belief, the pH value can be less than 0 or greater than 14 for very strong acids and bases respectively. The pH scale is traceable to a set of standard solutions whose pH is established by international agreement, the pH of aqueous solutions can be measured with a glass electrode and a pH meter, or an indicator. In the first papers, the notation had the H as a subscript to the p, as so. The exact meaning of the p in pH is disputed, but according to the Carlsberg Foundation and it has also been suggested that the p stands for the German Potenz, others refer to French puissance. Another suggestion is that the p stands for the Latin terms pondus hydrogenii, potentia hydrogenii and it is also suggested that Sørensen used the letters p and q simply to label the test solution and the reference solution. Currently in chemistry, the p stands for decimal cologarithm of, PH is defined as the decimal logarithm of the reciprocal of the hydrogen ion activity, aH+, in a solution. P H = − log 10 = log 10 For example and this definition was adopted because ion-selective electrodes, which are used to measure pH, respond to activity. For H+ number of electrons transferred is one and it follows that electrode potential is proportional to pH when pH is defined in terms of activity. The reference electrode may be a silver chloride electrode or a calomel electrode, the hydrogen-ion selective electrode is a standard hydrogen electrode. Reference electrode | concentrated solution of KCl || test solution | H2 | Pt Firstly, the cell is filled with a solution of hydrogen ion activity. Then the emf, EX, of the cell containing the solution of unknown pH is measured. PH = pH + E S − E X z The difference between the two measured emf values is proportional to pH and this method of calibration avoids the need to know the standard electrode potential. The proportionality constant, 1/z is ideally equal to 12.303 R T / F the Nernstian slope, to apply this process in practice, a glass electrode is used rather than the cumbersome hydrogen electrode. A combined glass electrode has a reference electrode. It is calibrated against buffer solutions of hydrogen ion activity
35.
Phenolphthalein
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Phenolphthalein is a chemical compound with the formula C20H14O4 and is often written as HIn or phph in shorthand notation. Phenolphthalein is often used as an indicator in acid–base titrations, for this application, it turns colorless in acidic solutions and pink in basic solutions. Phenolphthalein is slightly soluble in water and usually is dissolved in alcohols for use in experiments and it is a weak acid, which can lose H+ ions in solution. The phenolphthalein molecule is colorless, and the ion is pink. When a base is added to the phenolphthalein, the molecule ⇌ ions equilibrium shifts to the right and this is predicted by Le Chateliers principle. Phenolphthaleins common use is as an indicator in acid-base titrations and it also serves as a component of universal indicator, together with methyl red, bromothymol blue, and thymol blue. Phenolphthalein adopts four different states in aqueous solution, Under very strongly acidic conditions, it exists in protonated form, between strongly acidic and slightly basic conditions, the lactone form is colorless. The singly deprotonated phenolate form gives the familiar pink color, in strongly basic solutions, phenolphthaleins pink color undergoes a rather slow fading reaction and becomes completely colorless above 13.0 pH. The rather slow fading reaction that produces the colorless InOH3− ion is used in classes for the study of reaction kinetics. Phenolphthaleins pH sensitivity is exploited in other applications, Concrete has naturally high pH due to the calcium hydroxide formed when Portland cement reacts with water, as the concrete reacts with carbon dioxide in the atmosphere, pH decreases to 8. 5-9. When a 1% phenolphthalein solution is applied to concrete, it turns bright pink. However, if it remains colorless, it shows that the concrete has undergone carbonation, in a similar application, spackling used to repair holes in drywall contains phenolphthalein. When applied, the basic spackling material retains a pink coloration, when the spackling has cured by reaction with carbon dioxide. Phenolphthalein is used in toys, for example as a component of disappearing inks, in the ink, it is mixed with sodium hydroxide, which reacts with carbon dioxide in the air. The pattern will disappear again because of the reaction with carbon dioxide. Thymolphthalein is used for the purpose and in the same way. Phenolphthalein has been used for over a century as a laxative, thymolphthalein is a related laxative made from thymol. Despite concerns regarding its carcinogenicity, the use of phenolphthalein as a laxative is unlikely to cause ovarian cancer, phenolphthalein has been found to inhibit human cellular calcium influx via store-operated calcium entry
36.
Fuchsia (color)
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Fuchsia is a vivid purplish red color, named after the color of the flower of the fuchsia plant, which took its name from the 16th century German botanist Leonhart Fuchs. The color fuchsia was first introduced as the color of a new aniline dye called fuchsine, patented in 1859 by the French chemist François-Emmanuel Verguin. The dye was renamed later in the same year, to celebrate a victory of the French army at the Battle of Magenta on June 4,1859. In color printing and design, there are variations between magenta and fuchsia. Fuchsia is usually a more color, whereas magenta is more reddish. Fuchsia flowers themselves contain a variety of purples. The first recorded use of fuchsia as a name in English was in 1892. The first synthetic dye the color of fuchsia, called fuchsine, was patented in 1859 by François-Emmanuel Verguin and it was later renamed magenta, and became highly popular under that name. The name fuchsia is used on the HTML web color list for this color and they are both composed the same way, by combining an equal amount of blue and red light at full brightness, as shown in the image on the left. Displayed at right is the pale tint of fuchsia. The first recorded use of fuchsia as a color name in English was in 2014. At right is displayed the color French fuchsia, which is the tone of fuchsia called fuchsia in a color list popular in France, fashion fuchsia is a color used in fashion when a slightly less saturated color than shocking pink is desired. It also goes by the name Hollywood cerise, Fuchsia rose is the color that was chosen as the 2001 Pantone color of the year by Pantone. The source of color is the Pantone Textile Paper eXtended color list. Although red-purple is a seldom used color name in English, in Spanish it is regarded one of the tones of purple. The color fuchsia purple is displayed at right, the source of this color is the Pantone Textile Paper eXtended color list, color #18-2436 TPX—Fuchsia Purple. Deep fuchsia is the color that is called fuchsia in the List of Crayola crayon colors, displayed at right is the color fandango. The first recorded use of fandango as a name in English was in 1925
37.
Aromaticity
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Aromatic molecules are very stable, and do not break apart easily to react with other substances. Organic compounds that are not aromatic are classified as aliphatic compounds—they might be cyclic, since the most common aromatic compounds are derivatives of benzene, the word “aromatic” occasionally refers informally to benzene derivatives, and so it was first defined. Nevertheless, many aromatic compounds exist. In living organisms, for example, the most common aromatic rings are the bases in RNA and DNA. An aromatic functional group or other substituent is called an aryl group, the earliest use of the term aromatic was in an article by August Wilhelm Hofmann in 1855. Hofmann used the term for a class of compounds, many of which have odors. In terms of the nature of the molecule, aromaticity describes a conjugated system often made of alternating single and double bonds in a ring. This configuration allows for the electrons in the pi system to be delocalized around the ring, increasing the molecules stability. The molecule cannot be represented by one structure, but rather a hybrid of different structures. These molecules cannot be found in one of these representations, with the longer single bonds in one location. Rather, the molecule exhibits bond lengths in between those of single and double bonds and this commonly seen model of aromatic rings, namely the idea that benzene was formed from a six-membered carbon ring with alternating single and double bonds, was developed by August Kekulé. The model for benzene consists of two forms, which corresponds to the double and single bonds superimposing to produce six one-and-a-half bonds. Benzene is a stable molecule than would be expected without accounting for charge delocalization. As is standard for resonance diagrams, the use of an arrow indicates that two structures are not distinct entities but merely hypothetical possibilities. Neither is a representation of the actual compound, which is best represented by a hybrid of these structures. A C=C bond is shorter than a C−C bond, but benzene is perfectly hexagonal—all six carbon–carbon bonds have the same length, intermediate between that of a single and that of a double bond. In a cyclic molecule with three alternating double bonds, cyclohexatriene, the length of the single bond would be 1.54 Å. However, in a molecule of benzene, the length of each of the bonds is 1.40 Å, a better representation is that of the circular π-bond, in which the electron density is evenly distributed through a π-bond above and below the ring
38.
Tetrahedron
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In geometry, a tetrahedron, also known as a triangular pyramid, is a polyhedron composed of four triangular faces, six straight edges, and four vertex corners. The tetrahedron is the simplest of all the ordinary convex polyhedra, the tetrahedron is the three-dimensional case of the more general concept of a Euclidean simplex. The tetrahedron is one kind of pyramid, which is a polyhedron with a polygon base. In the case of a tetrahedron the base is a triangle, like all convex polyhedra, a tetrahedron can be folded from a single sheet of paper. For any tetrahedron there exists a sphere on which all four vertices lie, a regular tetrahedron is one in which all four faces are equilateral triangles. It is one of the five regular Platonic solids, which have known since antiquity. In a regular tetrahedron, not only are all its faces the same size and shape, regular tetrahedra alone do not tessellate, but if alternated with regular octahedra they form the alternated cubic honeycomb, which is a tessellation. The regular tetrahedron is self-dual, which means that its dual is another regular tetrahedron, the compound figure comprising two such dual tetrahedra form a stellated octahedron or stella octangula. This form has Coxeter diagram and Schläfli symbol h, the tetrahedron in this case has edge length 2√2. Inverting these coordinates generates the dual tetrahedron, and the together form the stellated octahedron. In other words, if C is the centroid of the base and this follows from the fact that the medians of a triangle intersect at its centroid, and this point divides each of them in two segments, one of which is twice as long as the other. The vertices of a cube can be grouped into two groups of four, each forming a regular tetrahedron, the symmetries of a regular tetrahedron correspond to half of those of a cube, those that map the tetrahedra to themselves, and not to each other. The tetrahedron is the only Platonic solid that is not mapped to itself by point inversion, the regular tetrahedron has 24 isometries, forming the symmetry group Td, isomorphic to the symmetric group, S4. The first corresponds to the A2 Coxeter plane, the two skew perpendicular opposite edges of a regular tetrahedron define a set of parallel planes. When one of these intersects the tetrahedron the resulting cross section is a rectangle. When the intersecting plane is one of the edges the rectangle is long. When halfway between the two edges the intersection is a square, the aspect ratio of the rectangle reverses as you pass this halfway point. For the midpoint square intersection the resulting boundary line traverses every face of the tetrahedron similarly, if the tetrahedron is bisected on this plane, both halves become wedges
39.
Orbital hybridisation
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In chemistry, hybridisation is the concept of mixing atomic orbitals into new hybrid orbitals suitable for the pairing of electrons to form chemical bonds in valence bond theory. Hybrid orbitals are very useful in the explanation of molecular geometry, although sometimes taught together with the valence shell electron-pair repulsion theory, valence bond and hybridisation are in fact not related to the VSEPR model. Chemist Linus Pauling first developed the theory in 1931 in order to explain the structure of simple molecules such as methane using atomic orbitals. In reality however, methane has four bonds of equivalent strength separated by the bond angle of 109. 5°. It gives a simple orbital picture equivalent to Lewis structures, hybridisation theory finds its use mainly in organic chemistry. Orbitals are a representation of the behaviour of electrons within molecules. In heavier atoms, such as carbon, nitrogen, and oxygen, hybrid orbitals are assumed to be mixtures of atomic orbitals, superimposed on each other in various proportions. For example, in methane, the C hybrid orbital which forms each carbon–hydrogen bond consists of 25% s character and 75% p character and is thus described as sp3 hybridised. Quantum mechanics describes this hybrid as an sp3 wavefunction of the form N, the ratio of coefficients is √3 in this example. Since the electron density associated with an orbital is proportional to the square of the wavefunction, the p character or the weight of the p component is N2λ2 = 3/4. The amount of p character or s character, which is decided mainly by orbital hybridisation, molecules with multiple bonds or multiple lone pairs can have orbitals represented in terms of sigma and pi symmetry or equivalent orbitals. The sigma and pi representation of Erich Hückel is the common one compared to the equivalent orbital representation of Linus Pauling. The two have mathematically equivalent total many-electron wave functions, and are related by a transformation of the set of occupied molecular orbitals. Hybridisation describes the bonding atoms from a point of view. For a tetrahedrally coordinated carbon, the carbon should have 4 orbitals with the symmetry to bond to the 4 hydrogen atoms. The carbon atom can also bond to four hydrogen atoms by an excitation of an electron from the doubly occupied 2s orbital to the empty 2p orbital, producing four singly occupied orbitals. The energy released by formation of two additional bonds more than compensates for the energy required, energetically favouring the formation of four C-H bonds. Quantum mechanically, the lowest energy is obtained if the four bonds are equivalent, a set of four equivalent orbitals can be obtained that are linear combinations of the valence-shell s and p wave functions, which are the four sp3 hybrids
40.
Carbon atom
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Carbon is a chemical element with symbol C and atomic number 6. It is nonmetallic and tetravalent—making four electrons available to form covalent chemical bonds, three isotopes occur naturally, 12C and 13C being stable, while 14C is a radioactive isotope, decaying with a half-life of about 5,730 years. Carbon is one of the few elements known since antiquity, Carbon is the 15th most abundant element in the Earths crust, and the fourth most abundant element in the universe by mass after hydrogen, helium, and oxygen. It is the second most abundant element in the body by mass after oxygen. The atoms of carbon can bond together in different ways, termed allotropes of carbon, the best known are graphite, diamond, and amorphous carbon. The physical properties of carbon vary widely with the allotropic form, for example, graphite is opaque and black while diamond is highly transparent. Graphite is soft enough to form a streak on paper, while diamond is the hardest naturally occurring material known, graphite is a good electrical conductor while diamond has a low electrical conductivity. Under normal conditions, diamond, carbon nanotubes, and graphene have the highest thermal conductivities of all known materials, all carbon allotropes are solids under normal conditions, with graphite being the most thermodynamically stable form. They are chemically resistant and require high temperature to react even with oxygen, the most common oxidation state of carbon in inorganic compounds is +4, while +2 is found in carbon monoxide and transition metal carbonyl complexes. The largest sources of carbon are limestones, dolomites and carbon dioxide, but significant quantities occur in organic deposits of coal, peat, oil. For this reason, carbon has often referred to as the king of the elements. The allotropes of carbon graphite, one of the softest known substances, and diamond. It bonds readily with other small atoms including other carbon atoms, Carbon is known to form almost ten million different compounds, a large majority of all chemical compounds. Carbon also has the highest sublimation point of all elements, although thermodynamically prone to oxidation, carbon resists oxidation more effectively than elements such as iron and copper that are weaker reducing agents at room temperature. Carbon is the element, with a ground-state electron configuration of 1s22s22p2. Its first four ionisation energies,1086.5,2352.6,4620.5 and 6222.7 kJ/mol, are higher than those of the heavier group 14 elements. Carbons covalent radii are normally taken as 77.2 pm,66.7 pm and 60.3 pm, although these may vary depending on coordination number, in general, covalent radius decreases with lower coordination number and higher bond order. Carbon compounds form the basis of all life on Earth
41.
Visual phototransduction
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Visual phototransduction is the sensory transduction of the visual system. It is a process by which light is converted into signals in the rod cells, cone cells. This cycle was elucidated by George Wald for which he received the Nobel Prize in 1967. It is so called Walds Visual Cycle after him, the visual cycle is the biological conversion of a photon into an electrical signal in the retina. This process occurs via G-protein coupled receptors called opsins which contain the chromophore 11-cis retinal, 11-cis retinal is covalently linked to the opsin receptor via Schiff base forming retinylidene protein. Following isomerization and release from the protein, all-trans retinal is reduced to all-trans retinol. It is first esterified by lecithin retinol acyltransferase and then converted to 11-cis retinol by the isomerohydrolase RPE65, the isomerase activity of RPE65 has been shown, it is still uncertain whether it also acts as hydrolase. Finally, it is oxidized to 11-cis retinal before traveling back to the rod outer segment where it is conjugated to an opsin to form new. The photoreceptor cells involved in vision are the rods and cones and these cells contain a chromophore bound to cell membrane protein, opsin. Rods deal with low level and do not mediate color vision. Cones, on the hand, can code the color of an image through comparison of the outputs of the three different types of cones. Each cone type responds best to certain wavelengths, or colors, the three types of cones are L-cones, M-cones and S-cones that respond optimally to long wavelengths, medium wavelengths, and short wavelengths respectively. Humans have a visual system consisting of three unique systems, rods, mid and long-wavelength sensitive cones and short wavelength sensitive cones. To understand the behaviour to light intensities, it is necessary to understand the roles of different currents. There is an ongoing outward potassium current through nongated K+-selective channels and this outward current tends to hyperpolarize the photoreceptor at around -70 mV. There is also an inward sodium current carried by cGMP-gated sodium channels and this so-called dark current depolarizes the cell to around -40 mV. Note that this is significantly more depolarized than most other neurons, in photopic conditions, photoreceptors hyperpolarize to a potential of -60mV. It is this switching off that activates the cell and sends an excitatory signal down the neural pathway. In the dark, cGMP levels are high and keep cGMP-gated sodium channels open allowing a steady inward current and this dark current keeps the cell depolarized at about -40 mV
42.
Chromatophore
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Chromatophores are pigment-containing and light-reflecting cells, or groups of cells, found in a wide range of animals including amphibians, fish, reptiles, crustaceans and cephalopods. Mammals and birds, in contrast, have a class of cells called melanocytes for coloration, Chromatophores are largely responsible for generating skin and eye colour in ectothermic animals and are generated in the neural crest during embryonic development. Mature chromatophores are grouped into subclasses based on their colour under white light, xanthophores, erythrophores, iridophores, leucophores, melanophores, some species can rapidly change colour through mechanisms that translocate pigment and reorient reflective plates within chromatophores. This process, often used as a type of camouflage, is called physiological colour change or metachrosis, cephalopods such as the octopus have complex chromatophore organs controlled by muscles to achieve this, whereas vertebrates such as chameleons generate a similar effect by cell signalling. Such signals can be hormones or neurotransmitters and may be initiated by changes in mood, temperature, Chromatophores are studied by scientists to understand human disease and as a tool in drug discovery. Aristotle mentioned the ability of the octopus to change colour for camouflage and signalling in his Historia animalium, The octopus. Seeks its prey by so changing its colour as to render it like the colour of the adjacent to it, it does so also when alarmed. Giosuè Sangiovanni was the first to describe invertebrate pigment-bearing cells as cromoforo in an Italian science journal in 1819 and these changes were effected in such a manner that clouds, varying in tint between a hyacinth red and a chestnut-brown, were continually passing over the body. Any part, being subjected to a shock of galvanism, became almost black, a similar effect. These clouds, or blushes as they may be called, are said to be produced by the expansion and contraction of minute vesicles containing variously coloured fluids. The term chromatophore was adopted as the name for pigment-bearing cells derived from the neural crest of cold-blooded vertebrates, the word itself comes from the Greek words khrōma meaning colour, and phoros meaning bearing. In contrast, the word chromatocyte was adopted for the responsible for colour found in birds. Only one such type, the melanocyte, has been identified in these animals. It was only in the 1960s that chromatophores were well understood to enable them to be classified based on their appearance. This classification system persists to this day, even though the biochemistry of the pigments may be useful to a scientific understanding of how the cells function. Colour-producing molecules fall into two classes, biochromes and structural colours or schemochromes. The biochromes include true pigments, such as carotenoids and pteridines and these pigments selectively absorb parts of the visible light spectrum that makes up white light while permitting other wavelengths to reach the eye of the observer. Structural colours are produced by combinations of diffraction, reflection or scattering of light from structures with a scale around a quarter of the wavelength of light
43.
Pigment
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A pigment is a material that changes the color of reflected or transmitted light as the result of wavelength-selective absorption. This physical process differs from fluorescence, phosphorescence, and other forms of luminescence, many materials selectively absorb certain wavelengths of light. Materials that humans have chosen and developed for use as pigments usually have properties that make them ideal for coloring other materials. A pigment must have a high tinting strength relative to the materials it colors and it must be stable in solid form at ambient temperatures. For industrial applications, as well as in the arts, permanence, pigments that are not permanent are called fugitive. Fugitive pigments fade over time, or with exposure to light, pigments are used for coloring paint, ink, plastic, fabric, cosmetics, food, and other materials. Most pigments used in manufacturing and the arts are dry colorants. This powder is added to a binder, a neutral or colorless material that suspends the pigment. A distinction is made between a pigment, which is insoluble in its vehicle, and a dye, which either is itself a liquid or is soluble in its vehicle. A colorant can act as either a pigment or a dye depending on the vehicle involved, in some cases, a pigment can be manufactured from a dye by precipitating a soluble dye with a metallic salt. The resulting pigment is called a lake pigment, the term biological pigment is used for all colored substances independent of their solubility. In 2006, around 7.4 million tons of inorganic, organic, asia has the highest rate on a quantity basis followed by Europe and North America. By 2020, revenues will have risen to approx, the global demand on pigments was roughly US$20.5 billion in 2009, around 1. 5-2% up from the previous year. It is predicted to increase in a growth rate in the coming years. The worldwide sales are said to increase up to US$24.5 billion in 2015, pigments appear the colors they are because they selectively reflect and absorb certain wavelengths of visible light. White light is an equal mixture of the entire spectrum of visible light with a wavelength in a range from about 375 or 400 nanometers to about 760 or 780 nm. When this light encounters a pigment, parts of the spectrum are absorbed by the molecules or ions of the pigment, in organic pigments such as diazo or phthalocyanine compounds the light is absorbed by the conjugated systems of double bonds in the molecule. Some of the inorganic pigments such as vermilion or cadmium yellow absorb light by transferring an electron from the ion to the positive ion
44.
Photophore
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A photophore is a glandular organ that appears as luminous spots on various marine animals, including fish and cephalopods. The organ can be simple, or as complex as the eye, equipped with lenses, shutters. The character of photophores is important in the identification of deep sea fishes, photophores on fish are used mainly for attracting food or confusing predators. Photophores are found on some cephalopods, including Watasenia scintillans, the sparkling enope or firefly squid, bioluminescence Biophoton Chemoluminescence Chromatophore Chromophore Photo, diagram and description of a cephalopod photophore
45.
Fluorophore
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A fluorophore is a fluorescent chemical compound that can re-emit light upon light excitation. Fluorophores typically contain several combined aromatic groups, or planar or cyclic molecules with several π bonds, fluorophores are sometimes used alone, as a tracer in fluids, as a dye for staining of certain structures, as a substrate of enzymes, or as a probe or indicator. More generally they are bonded to a macromolecule, serving as a marker for affine or bioactive reagents. Fluorophores are notably used to stain tissues, cells, or materials in a variety of methods, i. e. fluorescent imaging. Fluorescein, by its amine reactive isothiocyanate derivative FITC, has one of the most popular fluorophores. From antibody labeling, the applications have spread to nucleic acids thanks to, other historically common fluorophores are derivatives of rhodamine, coumarin, and cyanine. The fluorophore absorbs light energy of a wavelength and re-emits light at a longer wavelength. Wavelengths of maximum absorption and emission are the terms used to refer to a given fluorophore. The excitation wavelength spectrum may be a narrow or broader band. The emission spectrum is usually sharper than the spectrum, and it is of a longer wavelength. Excitation energies range from ultraviolet through the spectrum, and emission energies may continue from visible light into the near infrared region. Quantum yield, efficiency of the transferred from incident light to emitted fluorescence Lifetime. It refers to the time taken for a population of excited fluorophores to decay to 1/e of the original amount, stokes shift, difference between the maximum excitation and maximum emission wavelengths. These characteristics drive other properties, including the photobleaching or photoresistance, other parameters should be considered, as the polarity of the fluorophore molecule, the fluorophore size and shape, and other factors can change the behavior of fluorophores. Fluorophores can also be used to quench the fluorescence of other fluorescent dyes or to relay their fluorescence at longer wavelength See more on fluorescence principle. Fluorescence particles are not considered fluorophores, the size of the fluorophore might sterically hinder the tagged molecule, and affect the fluorescence polarity. Fluorophore molecules could be either utilized alone, or serve as a fluorescent motif of a functional system, fluorescent proteins GFP, YFP and RFP can be attached to other specific proteins to form a fusion protein, synthesized in cells after transfection of a suitable plasmid carrier. Oxazine derivatives, Nile red, Nile blue, cresyl violet, oxazine 170, acridine derivatives, proflavin, acridine orange, acridine yellow, etc
