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Encyclopedia > Pyrimidine
Pyrimidine
Chemical name Pyrimidine
Chemical formula C4H4N2
Molecular mass 80.08796 g/mol
CAS number [289-95-2]
Density 1.016 g/cm3
Melting point 20–22 °C
Boiling point 123–124 °C
SMILES C1=NC=NC=C1
Disclaimer and references

Pyrimidine is a heterocyclic aromatic organic compound similar to benzene and pyridine, containing two nitrogen atoms at positions 1 and 3 of the six-member ring [1]. It is isomeric with two other forms of diazine. File links The following pages link to this file: Pyrimidine Categories: GFDL images ... IUPAC nomenclature is a system of naming chemical compounds and of describing the science of chemistry in general. ... A chemical formula (also called molecular formula) is a concise way of expressing information about the atoms that constitute a particular chemical compound. ... The molecular mass (abbreviated MM) of a substance, formerly also called molecular weight and abbreviated as MW, is the mass of one molecule of that substance, relative to the unified atomic mass unit u (equal to 1/12 the mass of one atom of carbon-12). ... CAS registry numbers are unique numerical identifiers for chemical compounds, polymers, biological sequences, mixtures and alloys. ... Density (symbol: ρ - Greek: rho) is a measure of mass per volume. ... The melting point of a solid is the temperature at which it changes state from solid to liquid. ... The boiling point of a substance is the temperature at which it can change its state from a liquid to a gas throughout the bulk of the liquid at a given pressure. ... The simplified molecular input line entry specification or SMILES is a specification for unambiguously describing the structure of chemical molecules using short ASCII strings. ... Heterocyclic compounds are substances which contain a ring structure as found in benzene and the aromatic compounds, or aromatic hydrocarbons, but in which other atoms than carbon, such as sulfur, oxygen or nitrogen are found as part of the ring. ... In chemistry, an aromatic molecule is one in which electrons are free to cycle around circular arrangements of atoms, which are alternately singly and doubly bonded to one another. ... Benzene An organic compound is any member of a large class of chemical compounds whose molecules contain carbon, with the exception of carbides, carbonates, carbon oxides and elementary carbon. ... Benzene, also known as benzol, is an organic chemical compound with the formula C6H6. ... Pyridine is a chemical compound with the formula C5H5N. It is a liquid with a distinctively sour odour. ... General Name, Symbol, Number nitrogen, N, 7 Chemical series nonmetals Group, Period, Block 15, 2, p Appearance colorless Atomic mass 14. ... Properties For alternative meanings see atom (disambiguation). ... In chemistry, isomers are molecules with the same chemical formula and often with the same kinds of bonds between atoms, but in which the atoms are arranged differently. ... Diazine refers to a group of organic compounds having the molecular formula C4H4N2. ...



Three nucleobases found in nucleic acids, namely cytosine, thymine, and uracil, are pyrimidine derivatives: Adenine Guanine Thymine Cytosine ... Schematic diagram of a double-stranded nucleic acid. ... Cytosine is one of the 5 main nucleobases used in storing and transporting genetic information within a cell in the nucleic acids DNA and RNA. It is a pyrimidine derivative, with a heterocyclic aromatic ring and two substituents attached (an amine group at position 4 and a keto group at... For the similarly-spelled vitamin compound, see Thiamine Thymine, also known as 5-methyluracil, is a pyrimidine nucleobase. ... Uracil is a common naturally occurring pyrimidine1. ...


Chemical structure of cytosine Chemical structure of thymine Chemical structure of uracil Download high resolution version (1014x1357, 5 KB) Wikipedia does not have an article with this exact name. ... Download high resolution version (1269x1363, 6 KB) Wikipedia does not have an article with this exact name. ... Download high resolution version (1017x1360, 5 KB) Wikipedia does not have an article with this exact name. ...


In DNA and RNA, these bases form hydrogen bonds with their complementary purines. Thus the purines adenine (A) and guanine (G) pair up with the pyrimidines thymine (T) and cytosine (C) respectively. The general structure of a section of DNA Deoxyribonucleic acid (DNA) is a nucleic acid that contains the genetic instructions for the biological development of a cellular form of life or a virus. ... Ribonucleic acid (RNA) is a nucleic acid polymer consisting of nucleotide monomers. ... Snapshot from a simulation of liquid water. ... In genetics, a double-stranded DNA or RNA strand consists of two complementary strands of base pairs, which are non-covalently connected via two or three hydrogen bonds. ... Purine is a heterocyclic aromatic organic compound, consisting of a pyrimidine ring fused to an imidazole ring. ... Adenine is one of the two purine nucleobases used in forming nucleotides of the nucleic acids DNA and RNA. In DNA, adenine binds to thymine via two hydrogen bonds to assist in stabilizing the nucleic acid structures. ... Guanine is one of the five main nucleobases found in the nucleic acids DNA and RNA; the others being adenine, cytosine, thymine, and uracil. ...


In RNA, the complement of A is U instead of T and the pairs that form are adenine:uracil and guanine and cytosine. Ribonucleic acid (RNA) is a nucleic acid polymer consisting of nucleotide monomers. ... Adenine is one of the two purine nucleobases used in forming nucleotides of the nucleic acids DNA and RNA. In DNA, adenine binds to thymine via two hydrogen bonds to assist in stabilizing the nucleic acid structures. ... Uracil is a common naturally occurring pyrimidine1. ... Guanine is one of the five main nucleobases found in the nucleic acids DNA and RNA; the others being adenine, cytosine, thymine, and uracil. ... Cytosine is one of the 5 main nucleobases used in storing and transporting genetic information within a cell in the nucleic acids DNA and RNA. It is a pyrimidine derivative, with a heterocyclic aromatic ring and two substituents attached (an amine group at position 4 and a keto group at...


These hydrogen bonding modes are for classical Watson-Crick base pairing. Other hydrogen bonding modes ("wobble pairings") are available in both DNA and RNA, although the additional 2'-hydroxyl group of RNA expands the configurations through which RNA can form hydrogen bonds. In genetics, two nucleotides on opposite complementary DNA or RNA strands that are connected via hydrogen bonds are called a base pair (often abbreviated bp). ... The general structure of a section of DNA Deoxyribonucleic acid (DNA) is a nucleic acid that contains the genetic instructions for the biological development of a cellular form of life or a virus. ... Ribonucleic acid (RNA) is a nucleic acid polymer consisting of nucleotide monomers. ... Ribonucleic acid (RNA) is a nucleic acid polymer consisting of nucleotide monomers. ...

Contents

Chemical properties

A pyrimidine has many properties in common with pyridine, as the number of nitrogen atoms in the ring increases the ring pi electrons become less energetic and electrophilic aromatic substitution gets more difficult while nucleophilic aromatic substitution gets easier. An example of the last reaction type is the displacement of the amino group in 2-aminopyrimidine by chlorine [2] and its reverse [3]. Reduction in resonance stabilization of pyrimidines may lead to addition and ring cleavage reactions rather than substitutions. One such manifestation is observed in the Dimroth rearrangement. Pyridine is a chemical compound with the formula C5H5N. It is a liquid with a distinctively sour odour. ... Geometry of the water molecule Molecules have fixed equilibrium geometries--bond lengths and angles--that are dictated by the laws of quantum mechanics. ... Electrophilic aromatic substitution or EAS is an organic reaction in which an atom, usually hydrogen, in an aromatic system is replaced by an electrophile. ... A nucleophilic substitution is a substitution reaction in organic chemistry in which the nucleophile displaces a good leaving group, such as a halide on an aromatic ring. ... In chemistry, especially in organic chemistry and biochemistry, an amino group is an ammonia-like functional group. ... Resonance in chemistry is a tool used (predominately in organic chemistry) to represent certain types of molecular structures. ...


Compared to pyridine N-alkylation and N-oxidation is more difficult and pyrimidines are also less basic: the pKa value for protonated pyrimidine is 1.23 compared to 5.30 for pyridine. The general structure of an amine Amines are organic compounds and a type of functional group that contain nitrogen as the key atom. ... An amine oxide, also known as amine-N-oxide and N-oxide, is a chemical compound that contains the functional group R3N+-O− (sometimes written as R3N=O or R3N→O). ... The common (Arrhenius) definition of a base is a chemical compound that either donates hydroxide ions or absorbs hydrogen ions when dissolved in water. ... In chemistry and biochemistry, acid dissociation constant, the acidity constant, or the acid-ionization constant () is a specific type of equilibrium constant that indicates the extent of dissociation of hydrogen ions from an acid. ...


Pyrimidine biosynthesis

New synthesis of pyrimidine

Unlike purines, pyrimidines are assembled before being attached to 5-phosphoribosyl-1-pyrophosphate (PRPP). The first step begins with formation of carbamoyl phosphate by carbamoyl phosphate synthetase II.This is the regulated step in the pyrimidine biosynthesis. The second major step is the creation carbamoyl aspartic acid formed by aspartic transcarbamolyase (aspartate carbamoyl transferase).The next reaction involves dehydration of the acid catalysed by the enzyme dihhydroorotase to form hydroorotate. Dihydroorotate then enters the mitochondria where it is oxidised through removal of hydrogens to form orotate. This is the only mitochondrial step in nucleotide rings biosynthesis. The enzyme involved is dihydroorotate dehydrogenase (the only mitochondrial enzyme). Once orotate is eventually formed, it is combined with PRPP to form orotidine 5' monophosphate OMP which is decarboxylated in a reaction catalysed by OMP decarboxylase to form uridine 5' monophosphate. UMP is then converted to UDP catalysed by nucleotide diphosphokinase which is further phosphorylated to UTP by CTp synthase. This later reaction eventually leads to the formation of cytidine 5'triphosphate and glutamine is utlized.


Pyrimidine catabolism

Pyrimidines are ultimately catabolized (degraded) to CO2, H2O, and urea. Cytosine can be broken down to uracil which can be further broken down to N-carbamoyl-β-alanine. Thymine is broken down into β-aminoisobutyrate which can be further broken down into intermediates eventually leading into the citric acid cycle. β-aminoisobutyrate acts as a rough indicator for rate of DNA turnover. Anabolism is the aspect of metabolism that contributes to growth. ... Carbon dioxide is a chemical compound composed of one carbon and two oxygen atoms. ... This article describes water from a scientific and technical perspective. ... Urea is an organic compound of carbon, nitrogen, oxygen and hydrogen, with the formula CON2H4 or (NH2)2CO. Urea is also known as carbamide, especially in the recommended International Non-proprietary Names (rINN) in use in Europe. ... Overview of the citric acid cycle The citric acid cycle (also known as the tricarboxylic acid cycle, the TCA cycle, or the Krebs cycle) is a series of chemical reactions of central importance in all living cells that utilize oxygen as part of cellular respiration. ...


Organic synthesis

Pyrimidines can also be prepared in the laboratory by organic synthesis. Many methods rely on condensation of carbonyls with amines for instance the synthesis of 2-Thio-6-methyluracil from thiourea and ethyl acetoacetate [4] or the synthesis of 4-methylpyrimidine with 4,4-dimethoxy-2-butanone and formamide [5]. Organic synthesis is the construction of organic molecules via chemical processes. ... Water vapor condensing over a cup of hot tea Condensation is the change in matter of a substance to a denser phase, such as a gas (or vapor) to a liquid. ... Carbonyl group In organic chemistry, a carbonyl group is a functional group composed of a carbon atom double-bonded to an oxygen atom. ... The general structure of an amine Amines are organic compounds and a type of functional group that contain nitrogen as the key atom. ... Thiourea is related to urea, where an oxygen atom is replaced by a sulfur atom. ... Flash point 70 °C R/S statement R: ? S: ? RTECS number AK5250000 Supplementary data page Structure and properties n, εr, etc. ... Formamide, also known as Methanamide (IUPAC) and Carbamaldehyde, formula HCONH2 is an amide derived from formic acid. ...


A novel method is by reaction of certain amides with carbonitriles under electrophilic activation of the amide with 2-chloro-pyridine and trifluoromethanesulfonic anhydride [6]: Amide functional group In chemistry, an amide is one of two kinds of compounds: - the organic functional group characterized by a carbonyl group (C=O) linked to a nitrogen atom (N), or a compound that contains this functional group (pictured to the right); or - a particular kind of nitrogen anion. ... The structure of a nitrile group A nitrile is any organic compound which has a -C≡N functional group. ... Triflate, more formally known as trifluoromethanesulfonate, is a functional group with the formula CF3SO3-. The triflate radical is often represented by -OTf, as opposed to -Tf for the trifyl radical, CF3SO2-. For example, the n-butyl triflate, CH3CH2CH2CH2OTf. ...

Pyrimidine Synthesis Movassaghi 2006

Image File history File links Download high-resolution version (1064x664, 14 KB) Pyrimidine Synth Amide Carbonitrile I, the creator of this work, hereby grant the permission to copy, distribute and/or modify this document under the terms of the GNU Free Documentation License, Version 1. ...

See also

  • Pyrazine, an analog with the nitrogen atoms in positions 1 and 4.
  • Pyridazine, an analog with the nitrogen atoms in positions 1 and 2.
  • Simple aromatic rings
  • Link page to external chemical sources.

Pyrazine is a symmetrical molecule. ... Pyridazine is a heteroaromatic organic compound with the molecular formula C4H4N2. ... Simple aromatic rings are aromatic organic compounds (also known as arenes or aromatics) that consist only of conjugated planar ring systems with delocalized pi electron clouds instead of discrete alternating single and double bonds. ...

References

  1. ^ Heterocyclic Chemistry (3rd Edition) Thomas. L. Gilchrist ISBN 0582278430
  2. ^ Organic Syntheses, Coll. Vol. 4, p.182 (1963); Vol. 35, p.34 (1955) Link
  3. ^ Organic Syntheses, Coll. Vol. 4, p.336 (1963); Vol. 35, p.58 (1955) Link
  4. ^ Organic Syntheses, Coll. Vol. 4, p.638 (1963); Vol. 35, p.80 (1955) Link
  5. ^ Organic Syntheses, Coll. Vol. 5, p.794 (1973); Vol. 43, p.77 (1963) Link
  6. ^ Single-Step Synthesis of Pyrimidine Derivatives Mohammad Movassaghi and Matthew D. Hill J. Am. Chem. Soc.; 2006; 128(44) pp 14254 - 14255; (Communication) DOI:10.1021/ja066405m


Organic Syntheses is a scientific journal that Since 1921 has provided the chemistry community with annual collections of detailed and checked procedures for the organic synthesis of organic compounds. ... Organic Syntheses is a scientific journal that Since 1921 has provided the chemistry community with annual collections of detailed and checked procedures for the organic synthesis of organic compounds. ... Organic Syntheses is a scientific journal that Since 1921 has provided the chemistry community with annual collections of detailed and checked procedures for the organic synthesis of organic compounds. ... Organic Syntheses is a scientific journal that Since 1921 has provided the chemistry community with annual collections of detailed and checked procedures for the organic synthesis of organic compounds. ... The Journal of the American Chemical Society (usually abbreviated as , or JACS), is a peer-reviewed scientific journal, published since 1879 by the American Chemical Society. ... A digital object identifier (or DOI) is a permanent identifier (permalink) given to a World Wide Web file or other Internet document so that if its Internet address changes, users will be redirected to its new address. ...

Nucleic acids and oligonucleotides edit
Nucleobases: Adenine | Thymine | Uracil | Guanine | Cytosine | Purine | Pyrimidine
Nucleosides: Adenosine | Uridine | Guanosine | Cytidine | Deoxyadenosine | Thymidine | Deoxyguanosine | Deoxycytidine
Nucleotides: AMP | UMP | GMP | CMP | ADP | UDP | GDP | CDP | ATP | UTP | GTP | CTP | cAMP | cADPR | cGMP
Deoxynucleotides: dAMP | TMP | dGMP | dCMP | dADP | TDP | dGDP | dCDP | dATP | TTP | dGTP | dCTP
Ribonucleic acids: RNA | mRNA | tRNA | rRNA | ncRNA | sgRNA | shRNA | siRNA | snRNA | miRNA | snoRNA | LNA
Deoxyribonucleic acids: DNA | mtDNA | cDNA | plasmid | Cosmid | BAC | YAC | HAC
Analogues of nucleic acids: GNA | PNA | TNA| morpholino
←Amino acids Major families of biochemicals Carbohydrates→

  Results from FactBites:
 
pyrimidine: Definition and Much More from Answers.com (859 words)
Pyrimidine compounds which are found universally in living organisms include uracil (2), cytosine (3), and thymine (4).
pyrimidine (pīrĭm'ĭdēn'), type of organic base found in certain coenzymes and in the nucleic acids of plant and animal tissue.
Pyrimidine is a heterocyclic aromatic organic compound similar to benzene and pyridine, containing two nitrogen atoms at positions 1 and 3 of the six-member ring.
  More results at FactBites »

 
 

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