Serine octamer cluster

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The Serine octamer cluster in physical chemistry is an unusually stable cluster consisting of eight serine molecules (Ser) implicated in the origin of homochirality. [1] [2] This cluster was first discovered in mass spectrometry experiments. Electrospray ionization of an aerosol of serine in methanol results in a mass spectrum with a prominent ion peak of 841 corresponding to the Ser8+H+ cation. The smaller and larger clusters are virtually absent in the spectrum and therefore the number 8 is called a magic number. The same octamer ions are also produced by rapid evaporation of a serine solution on a hot (200-250 °C) metal surface or by sublimation of solid serine. After production, detection again is by mass-spectroscopic means. For the discussion of homochirality, these laboratory production methods are designed to mimic prebiotic conditions.

Physical chemistry is the study of macroscopic, atomic, subatomic, and particulate phenomena in chemical systems in terms of the principles, practices, and concepts of physics such as motion, energy, force, time, thermodynamics, quantum chemistry, statistical mechanics, analytical dynamics and chemical equilibrium.

Serine is an ɑ-amino acid that is used in the biosynthesis of proteins. It contains an α-amino group, a carboxyl group, and a side chain consisting of a hydroxymethyl group, classifying it as a polar amino acid. It can be synthesized in the human body under normal physiological circumstances, making it a nonessential amino acid. It is encoded by the codons UCU, UCC, UCA, UCG, AGU and AGC.

Molecule electrically neutral entity consisting of more than one atom (n > 1); rigorously, a molecule, in which n > 1 must correspond to a depression on the potential energy surface that is deep enough to confine at least one vibrational state

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.

The cluster is not only unusually stable but also unusual because the clusters have a strong homochiral preference. A racemic serine solution produces a minimum amount of cluster and with solutions of both enantiomers a maximum amount is formed of both homochiral D-Ser8 and L-Ser8. In another experiment cluster formation of a racemic mixture with deuterium enriched L-serine results in a product distribution with hardly any 50/50 D/L clusters but a preference for either D or L enantioenriched clusters.

Enantiomer 1 of 2 stereoisomers that are mirror images of each other that are non-superposable,not identical,much as ones left&right hands are the same except for being reversed along one axis(the hands cannot be made to appear identical simply by reorientatio

In chemistry, an enantiomer, also known as an optical isomer, is one of two stereoisomers that are mirror images of each other that are non-superposable, much as one's left and right hands are the same except for being reversed along one axis. A single chiral atom or similar structural feature in a compound causes that compound to have two possible structures which are non-superposable, each a mirror image of the other. Each member of the pair is termed an enantiomorph ; the structural property is termed enantiomerism. The presence of multiple chiral features in a given compound increases the number of geometric forms possible, though there may be some perfect-mirror-image pairs.

Deuterium isotope of hydrogen with 1 neutron

Deuterium is one of two stable isotopes of hydrogen. The nucleus of deuterium, called a deuteron, contains one proton and one neutron, whereas the far more common protium has no neutron in the nucleus. Deuterium has a natural abundance in Earth's oceans of about one atom in 6420 of hydrogen. Thus deuterium accounts for approximately 0.0156% of all the naturally occurring hydrogen in the oceans, while protium accounts for more than 99.98%. The abundance of deuterium changes slightly from one kind of natural water to another.

A model for chiral amplification is proposed whereby enantioenriched clusters are formed from a non-racemic mixture already enriched by L-serine as a result of a mirror-symmetry breaking process. Cluster formation is followed by isolation and on subsequent dissociation of the cluster a serene solution forms with a higher concentration of L-serine than in the original mixture. A cycle can be maintained in which each turn results in an incremental enrichment in L-serine. Many such cycles eventually result in enantiopure L-serine. This model has been experimentally verified.

Chiral transmission is assumed to take place through so-called substitution reactions of serine clusters. In these reactions, a serine monomer in a cluster can be replaced by another small biologically relevant molecule. For instance Ser8 reacts with glucose (Glc) to the Ser6 + Glc3 + Na+ cluster. Moreover, the cluster of synthetic L-glucose with Ser8 is less abundant than that with the biological D-glucose.

Glucose A simple form of sugar

Glucose (also called dextrose) is a simple sugar with the molecular formula C6H12O6. Glucose is the most abundant monosaccharide, a subcategory of carbohydrates. Glucose is mainly made by plants and most algae during photosynthesis from water and carbon dioxide, using energy from sunlight. There it is used to make cellulose in cell walls, which is the most abundant carbohydrate. In energy metabolism, glucose is the most important source of energy in all organisms. Glucose for metabolism is partially stored as a polymer, in plants mainly as starch and amylopectin and in animals as glycogen. Glucose circulates in the blood of animals as blood sugar. The naturally occurring form of glucose is D-glucose, while L-glucose is produced synthetically in comparably small amounts and is of lesser importance.

See also

Methane clathrate flammable solid similar to ice

Methane clathrate (CH4·5.75H2O) or (4CH4·23H2O), also called methane hydrate, hydromethane, methane ice, fire ice, natural gas hydrate, or gas hydrate, is a solid clathrate compound (more specifically, a clathrate hydrate) in which a large amount of methane is trapped within a crystal structure of water, forming a solid similar to ice. Originally thought to occur only in the outer regions of the Solar System, where temperatures are low and water ice is common, significant deposits of methane clathrate have been found under sediments on the ocean floors of the Earth.

Magic angle spinning

In nuclear magnetic resonance, magic-angle spinning (MAS) is a technique often used to perform experiments in solid-state NMR spectroscopy and, more recently, liquid Proton nuclear magnetic resonance.

A superatom is any cluster of atoms that seem to exhibit some of the properties of elemental atoms.

Related Research Articles

Phosphorylation the process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.

In chemistry, phosphorylation of a molecule is the attachment of a phosphoryl group. Together with its counterpart, dephosphorylation, it is critical for many cellular processes in biology. Phosphorylation is especially important for protein function, as this modification activates almost half of the enzymes present in yeast, thereby regulating their function. Many proteins are phosphorylated temporarily, as are many sugars, lipids, and other molecules.

In chemistry, a racemic mixture, or racemate, is one that has equal amounts of left- and right-handed enantiomers of a chiral molecule. The first known racemic mixture was racemic acid, which Louis Pasteur found to be a mixture of the two enantiomeric isomers of tartaric acid. A sample with only a single enantiomer is an enantiomerically pure or enantiopure compound.

The SN1 reaction is a substitution reaction in organic chemistry. "SN" stands for "nucleophilic substitution", and the "1" says that the rate-determining step is unimolecular. Thus, the rate equation is often shown as having first-order dependence on electrophile and zero-order dependence on nucleophile. This relationship holds for situations where the amount of nucleophile is much greater than that of the carbocation intermediate. Instead, the rate equation may be more accurately described using steady-state kinetics. The reaction involves a carbocation intermediate and is commonly seen in reactions of secondary or tertiary alkyl halides under strongly basic conditions or, under strongly acidic conditions, with secondary or tertiary alcohols. With primary and secondary alkyl halides, the alternative SN2 reaction occurs. In inorganic chemistry, the SN1 reaction is often known as the dissociative mechanism. This dissociation pathway is well-described by the cis effect. A reaction mechanism was first proposed by Christopher Ingold et al. in 1940. This reaction does not depend much on the strength of the nucleophile unlike the SN2 mechanism. This type of mechanism involves two steps. The first step is the reversible ionization of Alkyl halide in the presence of aqueous acetone or an aqueous ethyl alcohol. This step provides a carbocation as an intermediate.

A carbanion is an anion in which carbon is trivalent (forms three bonds) and bears a formal negative charge in at least one significant mesomeric contributor (resonance form). Absent π delocalization, carbanions assume a trigonal pyramidal, bent, or linear geometry when the carbanionic carbon is bound to three (e.g., methyl anion), two (e.g., phenyl anion), or one (e.g., acetylide anion) substituents, respectively. Formally, a carbanion is the conjugate base of a carbon acid:

In chemistry, racemization is the conversion of an enantiomerically pure mixture into a mixture where more than one of the enantiomers are present. If the racemization results in a mixture where the D and L enantiomers are present in equal quantities, the resulting sample is described as a racemic mixture or a racemate. Racemization can proceed through a number of different mechanisms, and it has particular significance in pharmacology as different enantiomers may have different pharmaceutical effects.

Chirality (chemistry) geometric property of some molecules and ions

Chirality is a geometric property of some molecules and ions. A chiral molecule/ion is non-superposable on its mirror image. The presence of an asymmetric carbon center is one of several structural features that induce chirality in organic and inorganic molecules. The term chirality is derived from the Ancient Greek word for hand, χεῖρ (kheir).

Homochirality is a uniformity of chirality, or handedness. Objects are chiral when they cannot be superposed on their mirror images. For example, the left and right hands of a human are approximately mirror images of each other but are not their own mirror images, so they are chiral. In biology, 19 of the 20 natural amino acids are homochiral, being L-chiral (left-handed), while sugars are D-chiral (right-handed). Homochirality can also refer to enantiomerically pure substances in which all the constituents are the same enantiomer, but some sources discourage this use of the term.

Enantiomer self-disproportionation

Enantiomer self-disproportionation is a process in stereochemistry describing the separation of a non-racemic mixture of enantiomers in an enantioenriched fraction and a more racemic fraction as a result of the formation of heterochiral or homochiral aggregates. This process is known to occur in achiral column chromatography.

In organic chemistry, kinetic resolution is a means of differentiating two enantiomers in a racemic mixture. In kinetic resolution, two enantiomers react with different reaction rates in a chemical reaction with a chiral catalyst or reagent, resulting in an enantioenriched sample of the less reactive enantiomer. As opposed to chiral resolution, kinetic resolution does not rely on different physical properties of diastereomeric products, but rather on the different chemical properties of the racemic starting materials. This enantiomeric excess (ee) of the unreacted starting material continually rises as more product is formed, reaching 100% just before full completion of the reaction. Kinetic resolution relies upon differences in reactivity between enantiomers or enantiomeric complexes. Kinetic resolution is a concept in organic chemistry and can be used for the preparation of chiral molecules in organic synthesis. Kinetic resolution reactions utilizing purely synthetic reagents and catalysts are much less common than the use of enzymatic kinetic resolution in application towards organic synthesis, although a number of useful synthetic techniques have been developed in the past 30 years.

Chiral derivatizing agent

A chiral derivatizing agent (CDA) also known as a chiral resolving reagent, is a chiral auxiliary used to convert a mixture of enantiomers into diastereomers in order to analyze the quantities of each enantiomer present within the mix. Analysis can be conducted by spectroscopy or by chromatography. The use of chiral derivatizing agents has declined with the popularization of chiral HPLC. Besides analysis, chiral derivatization is also used for chiral resolution, the actual physical separation of the enantiomers.

Chiral resolution in stereochemistry is a process for the separation of racemic compounds into their enantiomers. It is an important tool in the production of optically active drugs. Other terms with the same meaning are optical resolution and mechanical resolution.

Pirkles alcohol chemical compound

Pirkle's alcohol is an off-white, crystalline solid that is stable at room temperature when protected from light and oxygen. This chiral molecule is typically used, in nonracemic form, as a chiral shift reagent in nuclear magnetic resonance spectroscopy, in order to simultaneously determine absolute configuration and enantiomeric purity of other chiral molecules. The molecule is named after William H. Pirkle, Professor of Chemistry at the University of Illinois whose group reported its synthesis and its application as a chiral shift reagent.

Chiral Lewis acids (CLAs) are a type of Lewis acid catalyst that effects the chirality of the substrate as it reacts with it. In such reactions the synthesis favors the formation of a specific enantiomer or diastereomer. The method then is an enantioselective asymmetric synthesis reaction. Since they affect chirality, they produce optically active products from optically inactive or mixed starting materials. This type of preferential formation of one enantiomer or diastereomer over the other is formally known as an asymmetric induction. In this kind of Lewis acid. the electron-accepting atom is typically a metal, such as indium, zinc, lithium, aluminium, titanium, or boron. The chiral-altering ligands employed for synthesizing these acids most often have multiple Lewis basic sites that allow the formation of a ring structure involving the metal atom.

In chemistry, isomers are ions or molecules with identical formulas but distinct structures. Isomers do not necessarily share similar properties. Two main forms of isomerism are structural isomerism and stereoisomerism.

Base-promoted epoxide isomerization is the conversion of alkyl epoxides to ring-opened products through the action of strong base. Isomerizations of this type are most often used to synthesize allylic alcohols, although other products are possible.

Asymmetric ester hydrolysis with pig liver esterase is the enantioselective conversion of an ester to a carboxylic acid through the action of the enzyme pig liver esterase. Asymmetric ester hydrolysis involves the selective reaction of one of a pair of either enantiotopic or enantiomorphic ester groups.

In enantioselective synthesis, a non-linear effect refers to a process in which the enantiopurity of the catalyst or chiral auxiliary does not correspond with the enantiopurity of the product produced. For example: a racemic catalyst would be expected to convert a prochiral substrate into a racemic product, but this is not always the case and a chirally enriched product can be produced instead.

Thiolate-protected gold cluster

Thiolate-protected gold clusters are a type of ligand-protected metal cluster, synthesized from gold ions and thin layer compounds that play a special role in cluster physics because of their unique stability and electronic properties. They are considered to be stable compounds.

A copper nanoparticle is a copper based particle 1 to 100 nm in size. Like many other forms of nanoparticles, a copper nanoparticle can be formed by natural processes or through chemical synthesis. These nanoparticles are of particular interest due to their historical application as coloring agents and their modern-day biomedical ones.

In homogeneous catalysis, a C2-symmetric ligands usually describes bidentate ligands that are dyssymmetric but not asymmetric by virtue of their C2-symmetry. Such ligands have proven valuable in catalysis. With C2 symmetry, C2-symmetric ligands limit the number of possible reaction pathways and thereby increase enantioselectivity, at least relative to asymmetrical analogues. Most chiral ligands combine with metals to form chiral catalyst engages in a chemical reaction in which chirality is transfer to the reaction product.

References

  1. ↑ Cooks, R. G., Zhang, D., Koch, K. J. (2001). "Chiroselective Self-Directed Octamerization of Serine: Implications for Homochirogenesis". Anal. Chem. 73 (15)): 3646–3655. doi:10.1021/ac010284l. PMID   11510829.
  2. ↑ Nanita, S., Cooks, R. G. (2006). "Serine Octamers: Cluster Formation, Reactions, and Implications for Biomolecule Homochirality". Angew. Chem. Int. Ed. 45 (4): 554–569. doi:10.1002/anie.200501328. PMID   16404754.
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