SABIO-RK ( S ystem for the A nalysis of Bio chemical Pathways - R eaction K inetics) is a web-accessible database storing information about biochemical reactions and their kinetic properties.
67-426: SABIO-RK comprises a reaction-oriented representation of quantitative information on reaction dynamics based on a given selected publication. This comprises all available kinetic parameters together with their corresponding rate equations , as well as kinetic law and parameter types and experimental and environmental conditions under which the kinetic data were determined. Additionally, SABIO-RK contains information about
134-463: A closed system at constant temperature and volume, without a build-up of reaction intermediates , the reaction rate v {\displaystyle v} is defined as where ν i is the stoichiometric coefficient for chemical X i , with a negative sign for a reactant. The initial reaction rate v 0 = v t = 0 {\displaystyle v_{0}=v_{t=0}} has some functional dependence on
201-402: A fractional order , and may depend on the concentration of an intermediate species. A reaction can also have an undefined reaction order with respect to a reactant if the rate is not simply proportional to some power of the concentration of that reactant; for example, one cannot talk about reaction order in the rate equation for a bimolecular reaction between adsorbed molecules : Consider
268-454: A century earlier. In chemistry, it has been known since Proust's law of definite proportions (1794) that knowledge of the mass of each of the components in a chemical system is not sufficient to define the system. Amount of substance can be described as mass divided by Proust's "definite proportions", and contains information that is missing from the measurement of mass alone. As demonstrated by Dalton's law of partial pressures (1803),
335-517: A constant rate. In homogeneous catalysis zero order behavior can come about from reversible inhibition. For example, ring-opening metathesis polymerization using third-generation Grubbs catalyst exhibits zero order behavior in catalyst due to the reversible inhibition that occurs between pyridine and the ruthenium center. A first order reaction depends on the concentration of only one reactant (a unimolecular reaction ). Other reactants can be present, but their concentration has no effect on
402-450: A fact that greatly aided their acceptance: It was not necessary for a chemist to subscribe to atomic theory (an unproven hypothesis at the time) to make practical use of the tables. This would lead to some confusion between atomic masses (promoted by proponents of atomic theory) and equivalent weights (promoted by its opponents and which sometimes differed from relative atomic masses by an integer factor), which would last throughout much of
469-425: A graph of ln v {\displaystyle \ln v} as a function of ln [ A ] {\displaystyle \ln[{\ce {A}}]} then corresponds to the order x {\displaystyle x} with respect to reactant A {\displaystyle {\rm {A}}} . However, this method
536-414: A mass of exactly 12 g . The four different definitions were equivalent to within 1%. Because a dalton , a unit commonly used to measure atomic mass , is exactly 1/12 of the mass of a carbon-12 atom, this definition of the mole entailed that the mass of one mole of a compound or element in grams was numerically equal to the average mass of one molecule or atom of the substance in daltons, and that
603-449: A measurement of mass is not even necessary to measure the amount of substance (although in practice it is usual). There are many physical relationships between amount of substance and other physical quantities, the most notable one being the ideal gas law (where the relationship was first demonstrated in 1857). The term "mole" was first used in a textbook describing these colligative properties . Developments in mass spectrometry led to
670-541: A pseudo–first-order rate equation, which makes the treatment to obtain an integrated rate equation much easier. Mole (unit) The mole (symbol mol ) is a unit of measurement , the base unit in the International System of Units (SI) for amount of substance , a quantity proportional to the number of elementary entities of a substance. One mole contains exactly 6.022 140 76 × 10 elementary entities (approximately 602 sextillion or 602 billion times
737-460: A reaction a ·A + b ·B → c ·C with rate law v 0 = k ⋅ [ A ] x ⋅ [ B ] y , {\displaystyle v_{0}=k\cdot [{\rm {A}}]^{x}\cdot [{\rm {B}}]^{y},} the partial order x {\displaystyle x} with respect to A {\displaystyle {\rm {A}}}
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#1732914091134804-424: A single concentration squared, the time dependence of the concentration is given by The unit of k is mol dm s . The time dependence for a rate proportional to two unequal concentrations is if the concentrations are equal, they satisfy the previous equation. The second type includes nucleophilic addition-elimination reactions , such as the alkaline hydrolysis of ethyl acetate : This reaction
871-448: A special name derived from the mole is the katal , defined as one mole per second of catalytic activity . Like other SI units, the mole can also be modified by adding a metric prefix that multiplies it by a power of 10 : One femtomole is exactly 602,214,076 molecules; attomole and smaller quantities cannot be exactly realized. The yoctomole, equal to around 0.6 of an individual molecule, did make appearances in scientific journals in
938-483: A substance is equal to its relative atomic (or molecular) mass multiplied by the molar mass constant , which is almost exactly 1 g/mol. Like chemists, chemical engineers use the unit mole extensively, but different unit multiples may be more suitable for industrial use. For example, the SI unit for volume is the cubic metre, a much larger unit than the commonly used litre in the chemical laboratory. When amount of substance
1005-447: A substance was redefined as containing "exactly 6.022 140 76 × 10 elementary entities" of that substance. Since its adoption into the International System of Units in 1971, numerous criticisms of the concept of the mole as a unit like the metre or the second have arisen: October 23, denoted 10/23 in the US, is recognized by some as Mole Day . It is an informal holiday in honor of
1072-533: A trillion), which can be atoms, molecules, ions, ion pairs, or other particles . The number of particles in a mole is the Avogadro number (symbol N 0 ) and the numerical value of the Avogadro constant (symbol N A ) expressed in mol . The value was chosen on the basis of the historical definition of the mole as the amount of substance that corresponds to the number of atoms in 12 grams of C , which made
1139-420: A typical chemical reaction in which two reactants A and B combine to form a product C: This can also be written The prefactors −1, −2 and 3 (with negative signs for reactants because they are consumed) are known as stoichiometric coefficients . One molecule of A combines with two of B to form 3 of C, so if we use the symbol [X] for the molar concentration of chemical X, If the reaction takes place in
1206-400: Is mol dm s . This may occur when there is a bottleneck which limits the number of reactant molecules that can react at the same time, for example if the reaction requires contact with an enzyme or a catalytic surface. Many enzyme-catalyzed reactions are zero order, provided that the reactant concentration is much greater than the enzyme concentration which controls the rate, so that
1273-438: Is also expressed in kmol (1000 mol) in industrial-scaled processes, the numerical value of molarity remains the same, as kmol m 3 = 1000 mol 1000 L = mol L {\textstyle {\frac {\text{kmol}}{{\text{m}}^{3}}}={\frac {1000{\text{ mol}}}{1000{\text{ L}}}}={\frac {\text{mol}}{\text{L}}}} . Chemical engineers once used
1340-421: Is constant then v 0 = k [ A ] [ B ] = k ′ [ A ] , {\displaystyle v_{0}=k[{\ce {A}}][{\ce {B}}]=k'[{\ce {A}}],} where the pseudo–first-order rate constant k ′ = k [ B ] . {\displaystyle k'=k[{\ce {B}}].} The second-order rate equation has been reduced to
1407-538: Is determined using a large excess of B {\displaystyle {\rm {B}}} . In this case v 0 = k ′ ⋅ [ A ] x {\displaystyle v_{0}=k'\cdot [{\rm {A}}]^{x}} with k ′ = k ⋅ [ B ] y , {\displaystyle k'=k\cdot [{\rm {B}}]^{y},} and x {\displaystyle x} may be determined by
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#17329140911341474-444: Is first-order in each reactant and second-order overall: If the same hydrolysis reaction is catalyzed by imidazole , the rate equation becomes The rate is first-order in one reactant (ethyl acetate), and also first-order in imidazole, which as a catalyst does not appear in the overall chemical equation. Another well-known class of second-order reactions are the S N 2 (bimolecular nucleophilic substitution) reactions, such as
1541-430: Is in great excess with respect to the other reactants), its concentration can be included in the rate constant, leading to a pseudo–first-order (or occasionally pseudo–second-order) rate equation. For a typical second-order reaction with rate equation v 0 = k [ A ] [ B ] , {\displaystyle v_{0}=k[{\ce {A}}][{\ce {B}}],} if the concentration of reactant B
1608-460: Is mole per litre (mol/L). The number of entities (symbol N ) in a one-mole sample equals the Avogadro number (symbol N 0 ), a dimensionless quantity . Historically, N 0 approximates the number of nucleons ( protons or neutrons ) in one gram of ordinary matter . The Avogadro constant (symbol N A = N 0 /mol ) has numerical multiplier given by the Avogadro number with
1675-478: Is not always reliable because The tentative rate equation determined by the method of initial rates is therefore normally verified by comparing the concentrations measured over a longer time (several half-lives) with the integrated form of the rate equation; this assumes that the reaction goes to completion. For example, the integrated rate law for a first-order reaction is where [ A ] {\displaystyle [{\rm {A]}}}
1742-421: Is part of MIRIAM registry, a set of guidelines for the annotation and curation of computational models The usage of SABIO-RK is free of charge. Commercial users need a license. SABIO-RK offers several ways for data access: Result data sets can be exported in different formats including SBML , BioPAX / SBPAX , and table format. Rate equation In chemistry , the rate equation (also known as
1809-486: Is said to be second order when the overall order is two. The rate of a second-order reaction may be proportional to one concentration squared, v 0 = k [ A ] 2 , {\displaystyle v_{0}=k[{\ce {A}}]^{2},} or (more commonly) to the product of two concentrations, v 0 = k [ A ] [ B ] . {\displaystyle v_{0}=k[{\ce {A}}][{\ce {B}}].} As an example of
1876-540: Is second order and the reaction of the energized molecule which is unimolecular and first order. The rate of the overall reaction depends on the slowest step, so the overall reaction will be first order when the reaction of the energized reactant is slower than the collision step. The half-life is independent of the starting concentration and is given by t 1 / 2 = ln ( 2 ) k {\textstyle t_{1/2}={\frac {\ln {(2)}}{k}}} . The mean lifetime
1943-435: Is the concentration at time t {\displaystyle t} and [ A ] 0 {\displaystyle [{\rm {A]_{0}}}} is the initial concentration at zero time. The first-order rate law is confirmed if ln [ A ] {\displaystyle \ln {[{\ce {A}}]}} is in fact a linear function of time. In this case
2010-481: Is the overall order of reaction. In a dilute solution, an elementary reaction (one having a single step with a single transition state ) is empirically found to obey the law of mass action . This predicts that the rate depends only on the concentrations of the reactants, raised to the powers of their stoichiometric coefficients. The differential rate equation for an elementary reaction using mathematical product notation is: Where: The natural logarithm of
2077-523: Is τ = 1/k. Examples of such reactions are: In organic chemistry, the class of S N 1 (nucleophilic substitution unimolecular) reactions consists of first-order reactions. For example, in the reaction of aryldiazonium ions with nucleophiles in aqueous solution, ArN + 2 + X → ArX + N 2 , the rate equation is v 0 = k [ ArN 2 + ] , {\displaystyle v_{0}=k[{\ce {ArN2+}}],} where Ar indicates an aryl group. A reaction
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2144-428: The 2019 revision of the SI , which redefined the mole by fixing the value of the Avogadro constant, making it very nearly equivalent to but no longer exactly equal to the gram-mole), but whose name and symbol adopt the SI convention for standard multiples of metric units – thus, kmol means 1000 mol. This is equivalent to the use of kg instead of g. The use of kmol is not only for "magnitude convenience" but also makes
2211-414: The kilogram-mole (notation kg-mol ), which is defined as the number of entities in 12 kg of C, and often referred to the mole as the gram-mole (notation g-mol ), then defined as the number of entities in 12 g of C, when dealing with laboratory data. Late 20th-century chemical engineering practice came to use the kilomole (kmol), which was numerically identical to the kilogram-mole (until
2278-459: The molar concentrations of the species A {\displaystyle \mathrm {A} } and B , {\displaystyle \mathrm {B} ,} usually in moles per liter ( molarity , M {\displaystyle M} ). The exponents x {\displaystyle x} and y {\displaystyle y} are
2345-418: The rate constant k {\displaystyle k} is equal to the slope with sign reversed. The partial order with respect to a given reactant can be evaluated by the method of flooding (or of isolation) of Ostwald . In this method, the concentration of one reactant is measured with all other reactants in large excess so that their concentration remains essentially constant. For
2412-561: The rate law or empirical differential rate equation ) is an empirical differential mathematical expression for the reaction rate of a given reaction in terms of concentrations of chemical species and constant parameters (normally rate coefficients and partial orders of reaction) only. For many reactions, the initial rate is given by a power law such as where [ A ] {\displaystyle [\mathrm {A} ]} and [ B ] {\displaystyle [\mathrm {B} ]} are
2479-480: The 14th CGPM. Before the 2019 revision of the SI , the mole was defined as the amount of substance of a system that contains as many elementary entities as there are atoms in 12 grams of carbon-12 (the most common isotope of carbon ). The term gram-molecule was formerly used to mean one mole of molecules, and gram-atom for one mole of atoms. For example, 1 mole of MgBr 2 is 1 gram-molecule of MgBr 2 but 3 gram-atoms of MgBr 2 . In 2011,
2546-851: The 24th meeting of the General Conference on Weights and Measures (CGPM) agreed to a plan for a possible revision of the SI base unit definitions at an undetermined date. On 16 November 2018, after a meeting of scientists from more than 60 countries at the CGPM in Versailles, France, all SI base units were defined in terms of physical constants. This meant that each SI unit, including the mole, would not be defined in terms of any physical objects but rather they would be defined by physical constants that are, in their nature, exact. Such changes officially came into effect on 20 May 2019. Following such changes, "one mole" of
2613-420: The adoption of oxygen-16 as the standard substance, in lieu of natural oxygen. The oxygen-16 definition was replaced with one based on carbon-12 during the 1960s. The International Bureau of Weights and Measures defined the mole as "the amount of substance of a system which contains as many elementary entities as there are atoms in 0.012 kilograms of carbon-12." Thus, by that definition, one mole of pure C had
2680-400: The basic SI unit of mol/s were to be used, which would otherwise require the molar mass to be converted to kg/mol. For convenience in avoiding conversions in the imperial (or US customary units ), some engineers adopted the pound-mole (notation lb-mol or lbmol ), which is defined as the number of entities in 12 lb of C. One lb-mol is equal to 453.592 37 g‑mol , which is
2747-484: The chemical convenience of having oxygen as the primary atomic mass standard became ever more evident with advances in analytical chemistry and the need for ever more accurate atomic mass determinations. The name mole is an 1897 translation of the German unit Mol , coined by the chemist Wilhelm Ostwald in 1894 from the German word Molekül ( molecule ). The related concept of equivalent mass had been in use at least
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2814-420: The chemical equation 2 H 2 + O 2 → 2 H 2 O can be interpreted to mean that for each 2 mol molecular hydrogen (H 2 ) and 1 mol molecular oxygen (O 2 ) that react, 2 mol of water (H 2 O) form. The concentration of a solution is commonly expressed by its molar concentration , defined as the amount of dissolved substance per unit volume of solution, for which the unit typically used
2881-469: The concentrations of the reactants, and this dependence is known as the rate equation or rate law . This law generally cannot be deduced from the chemical equation and must be determined by experiment. A common form for the rate equation is a power law: The constant k {\displaystyle k} is called the rate constant . The exponents, which can be fractional, are called partial orders of reaction and their sum
2948-422: The definition of the gram was not mathematically tied to that of the dalton, the number of molecules per mole N A (the Avogadro constant) had to be determined experimentally. The experimental value adopted by CODATA in 2010 is N A = 6.022 141 29 (27) × 10 mol . In 2011 the measurement was refined to 6.022 140 78 (18) × 10 mol . The mole was made the seventh SI base unit in 1971 by
3015-436: The enzyme is saturated . For example, the biological oxidation of ethanol to acetaldehyde by the enzyme liver alcohol dehydrogenase (LADH) is zero order in ethanol. Similarly reactions with heterogeneous catalysis can be zero order if the catalytic surface is saturated. For example, the decomposition of phosphine ( PH 3 ) on a hot tungsten surface at high pressure is zero order in phosphine, which decomposes at
3082-484: The equations used for modelling chemical engineering systems coherent . For example, the conversion of a flowrate of kg/s to kmol/s only requires dividing by the molar mass in g/mol (as kg kmol = 1000 g 1000 mol = g mol {\textstyle {\frac {\text{kg}}{\text{kmol}}}={\frac {1000{\text{ g}}}{1000{\text{ mol}}}}={\frac {\text{g}}{\text{mol}}}} ) without multiplying by 1000 unless
3149-410: The experimental rate equation has been determined, it is often of use for deduction of the reaction mechanism . The rate equation of a reaction with an assumed multi-step mechanism can often be derived theoretically using quasi-steady state assumptions from the underlying elementary reactions, and compared with the experimental rate equation as a test of the assumed mechanism. The equation may involve
3216-400: The first type, the reaction NO 2 + CO → NO + CO 2 is second-order in the reactant NO 2 and zero order in the reactant CO. The observed rate is given by v 0 = k [ NO 2 ] 2 , {\displaystyle v_{0}=k[{\ce {NO2}}]^{2},} and is independent of the concentration of CO. For the rate proportional to
3283-509: The integral method. The order y {\displaystyle y} with respect to B {\displaystyle {\rm {B}}} under the same conditions (with B {\displaystyle {\rm {B}}} in excess) is determined by a series of similar experiments with a range of initial concentration [ B ] 0 {\displaystyle [{\rm {B]_{0}}}} so that
3350-448: The mass of a mole of a compound expressed in grams, numerically equal to the average molecular mass or formula mass of the compound expressed in daltons . With the 2019 revision of the SI , the numerical equivalence is now only approximate but may be assumed for all practical purposes. The mole is widely used in chemistry as a convenient way to express amounts of reactants and amounts of products of chemical reactions . For example,
3417-613: The nineteenth century. Jöns Jacob Berzelius (1779–1848) was instrumental in the determination of relative atomic masses to ever-increasing accuracy. He was also the first chemist to use oxygen as the standard to which other masses were referred. Oxygen is a useful standard, as, unlike hydrogen, it forms compounds with most other elements, especially metals . However, he chose to fix the atomic mass of oxygen as 100, which did not catch on. Charles Frédéric Gerhardt (1816–56), Henri Victor Regnault (1810–78) and Stanislao Cannizzaro (1826–1910) expanded on Berzelius' works, resolving many of
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#17329140911343484-434: The number of daltons in a gram was equal to the number of elementary entities in a mole. Because the mass of a nucleon (i.e. a proton or neutron ) is approximately 1 dalton and the nucleons in an atom's nucleus make up the overwhelming majority of its mass, this definition also entailed that the mass of one mole of a substance was roughly equivalent to the number of nucleons in one atom or molecule of that substance. Since
3551-416: The partial orders of reaction for A {\displaystyle \mathrm {A} } and B {\displaystyle \mathrm {B} } and the overall reaction order is the sum of the exponents. These are often positive integers, but they may also be zero, fractional, or negative. The order of reaction is a number which quantifies the degree to which
3618-526: The power-law rate equation is This can be used to estimate the order of reaction of each reactant. For example, the initial rate can be measured in a series of experiments at different initial concentrations of reactant A {\displaystyle {\rm {A}}} with all other concentrations [ B ] , [ C ] , … {\displaystyle [{\rm {B],[{\rm {C],\dots }}}}} kept constant, so that The slope of
3685-472: The problems of unknown stoichiometry of compounds, and the use of atomic masses attracted a large consensus by the time of the Karlsruhe Congress (1860). The convention had reverted to defining the atomic mass of hydrogen as 1, although at the level of precision of measurements at that time – relative uncertainties of around 1% – this was numerically equivalent to the later standard of oxygen = 16. However
3752-533: The rate of a chemical reaction depends on concentrations of the reactants. In other words, the order of reaction is the exponent to which the concentration of a particular reactant is raised. The constant k {\displaystyle k} is the reaction rate constant or rate coefficient and at very few places velocity constant or specific rate of reaction . Its value may depend on conditions such as temperature, ionic strength, surface area of an adsorbent , or light irradiation . If
3819-459: The rate. The rate law for a first order reaction is The unit of k is s . Although not affecting the above math, the majority of first order reactions proceed via intermolecular collisions. Such collisions, which contribute the energy to the reactant, are necessarily second order. However according to the Lindemann mechanism the reaction consists of two steps: the bimolecular collision which
3886-457: The reaction goes to completion, the rate equation for the reaction rate v = k [ A ] x [ B ] y {\displaystyle v\;=\;k[{\ce {A}}]^{x}[{\ce {B}}]^{y}} applies throughout the course of the reaction. Elementary (single-step) reactions and reaction steps have reaction orders equal to the stoichiometric coefficients for each reactant. The overall reaction order, i.e.
3953-419: The reaction of n-butyl bromide with sodium iodide in acetone : This same compound can be made to undergo a bimolecular (E2) elimination reaction , another common type of second-order reaction, if the sodium iodide and acetone are replaced with sodium tert-butoxide as the salt and tert-butanol as the solvent: If the concentration of a reactant remains constant (because it is a catalyst , or because it
4020-416: The same numerical value as the number of grams in an international avoirdupois pound . Greenhouse and growth chamber lighting for plants is sometimes expressed in micromoles per square metre per second, where 1 mol photons ≈ 6.02 × 10 photons. The obsolete unit einstein is variously defined as the energy in one mole of photons and also as simply one mole of photons. The only SI derived unit with
4087-435: The solid is composed of a certain number of moles of such entities. In yet other cases, such as diamond , where the entire crystal is essentially a single molecule, the mole is still used to express the number of atoms bound together, rather than a count of molecules. Thus, common chemical conventions apply to the definition of the constituent entities of a substance, in other cases exact definitions may be specified. The mass of
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#17329140911344154-481: The sum of stoichiometric coefficients of reactants, is always equal to the molecularity of the elementary reaction. However, complex (multi-step) reactions may or may not have reaction orders equal to their stoichiometric coefficients. This implies that the order and the rate equation of a given reaction cannot be reliably deduced from the stoichiometry and must be determined experimentally, since an unknown reaction mechanism could be either elementary or complex. When
4221-489: The two quantities having different volumes and different masses. The mole corresponds to a given count of entities. Usually, the entities counted are chemically identical and individually distinct. For example, a solution may contain a certain number of dissolved molecules that are more or less independent of each other. However, the constituent entities in a solid are fixed and bound in a lattice arrangement, yet they may be separable without losing their chemical identity. Thus,
4288-1494: The underlying biochemical reactions and pathways including their reaction participants , cellular location and detailed information about the enzymes catalysing the reactions. The data stored in SABIO-RK in a comprehensive manner is mainly extracted manually from literature. This includes reactions, their participants (substrates, products), modifiers ( inhibitors , activators, cofactors ), catalyst details (e.g. EC enzyme classification , protein complex composition , wild type / mutant information), kinetic parameters together with corresponding rate equation, biological sources ( organism , tissue , cellular location), environmental conditions ( pH , temperature, buffer) and reference details. Data are adapted, normalized and annotated to controlled vocabularies, ontologies and external data sources including KEGG , UniProt , ChEBI , PubChem , NCBI , Reactome , BRENDA , MetaCyc , BioModels , and PubMed . As of October 2021 SABIO-RK contains about 71.000 curated single entries extracted from more than 7.300 publications. Several tools, databases and workflows in Systems Biology make use of SABIO-RK biochemical reaction data by integration into their framework including SYCAMORE, MeMo-RK, CellDesigner, PeroxisomeDB, Taverna workflows or tools like KineticsWizard software for data capture and analysis. Additionally, SABIO-RK
4355-502: The unit reciprocal mole (mol ). The ratio n = N / N A is a measure of the amount of substance (with the unit mole). Depending on the nature of the substance, an elementary entity may be an atom , a molecule , an ion , an ion pair, or a subatomic particle such as a proton . For example, 10 moles of water (a chemical compound ) and 10 moles of mercury (a chemical element ) contain equal numbers of substance, with one atom of mercury for each molecule of water, despite
4422-583: The variation of k ′ {\displaystyle k'} can be measured. For zero-order reactions, the reaction rate is independent of the concentration of a reactant, so that changing its concentration has no effect on the rate of the reaction. Thus, the concentration changes linearly with time. The rate law for zero order reaction is − d [ A ] d t = k [ A ] 0 = k , {\displaystyle -{d[A] \over dt}=k[A]^{0}=k,} The unit of k
4489-459: The year the yocto- prefix was officially implemented. The history of the mole is intertwined with that of units of molecular mass , and the Avogadro constant . The first table of standard atomic weight was published by John Dalton (1766–1844) in 1805, based on a system in which the relative atomic mass of hydrogen was defined as 1. These relative atomic masses were based on the stoichiometric proportions of chemical reaction and compounds,
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