electrons, Red-Ox-states, stress and diseases (phys-chem-bio-med)

Redox state of cells (see oxidative metabolism) reflect different oxidation states* of elements and Periodic system of chemical compounds and metabolism with C-C /N-O/ O-O/S-S/O-Cl/Se-Se/Cr…Mo…, AA, proteins and NA . In living cells the less  abundant elements are replaced by the more common ones, as S(+) -> P(+5) -> C(+3+4 in AA and GenCod), K — Ca -> NH(-3). The abundance of S and K-potassium   slightly greater than sodium and chlorine (70 kg — 150 lb human body contains about 140 g).  The biogeochemical cycles and multistep biochemical transformation of carbon dioxide requires organosulfur cofactors, for Methanogenesis include S(-2/+4+6) in coenzyme M, CH3SCH2CH2SO3, the immediate precursor to methane.[3] 

Integer oxidation states*, example compound and biogeochemical cycles

state Group IV (+4/-4): carbon V (+5/-3): nitrogen cycle VI (+6/-2): Sulfur metabolism —cycle
N-8 −4 CH4 -3: NH3 ammonia -2: =O, water,   H2S -SH Cys,  thio-
N-7 −3 C2H6 -2: N2H4 hydrazine -1: -O-O-, -S-S-, FeS clusters
N-6 −2 CnH2nC2H4, CH3Cl, ROH -1: NH2OH hydroxylamine 0: O2, → S8
N-5 −1 C2H2C6H6(CH2OH)2 0: N2dinitrogen  S2Cl2
N-4 0 HCHOCH2Cl2 +1: N2O nitrous oxide thiosulfate,
N-3 +1 OCHCHOC2H2Cl4 +2: NO (nitric oxide),   tetrathionate, SCl2
N-2 +2 HCOOHCHCl3 +3: HNO2, N2O3  diN trioxide), SO2→ SO32−sulfite
N-1 +3 HOOCCOOHC2Cl6 NO2 (N dioxide), N2O4 (diNtetroxide),  polythio s
N +4 carbonateCCl4,

CO2 dioxide

N2O5 (diN/Pentoxide)

nitrate, HPO3

SO42−

These numbers of electrons descripted e.g.  Bioenergetics of coferments (like NAD+H), Biochemist Szent-Györgyi won the Nobel Prize in Physiology or Medicine in 1937 for discovering vitamin C and the components and reactions of the citric acid cycle, developed On Oxidation, Fermentation, Vitamins, Health, and Disease (1940), conceptions of Submolecular Biology (1960), Electronic Biology (1976), The living state (1972) and Bioelectronics: a study in cellular regulations, defense and cancer

(In 1938, he found that the biophysics of muscle movement contain actin, combined with myosin and the energy source ATP, in 1947,  established the Institute for Muscle Research in Woods Hole, Massachusetts, with NIH and HeartA, in 1950s using electron microscopes to study subunit level, received the Lasker Award in 1954,  developed ideas of quantum mechanics to the biochemistry (quantum biology) and cancer, began to pursue free radicals as a potential cause of cancer as an electronic problem at the molecular level, in 1974 from quantum proposed the term «syntropy» replace the term «negentropy» (See [10], «Free Radical: Albert Szent-Gyorgyi and the Battle over Vitamin C», as precursor to Linus Pauling (from the oxidation number and electronegativity of the atoms as «ions» to vit.C and cancer), Watson, JD. Type 2 diabetes as a redox disease (Lancet. 2014; 383: 841–843) and Oxidants, antioxidants and the current incurability of metastatic cancers (Open Biol. 2013), Sies H. Oxidative stress: a concept in redox biology and medicine, what is now dubbed redox signaling. Sednev Y.V. Ru-p.196 Conf.Minsk)

De Duve (1917-2013) proposed for origin of life that  thioester and peroxisomes may have been the first before DNA [63][64] in Symbiogenesis and the endosymbiotic theory that eukaryotic cell oraganelles originated as prokaryotic cells, as endosymbionts, including their ability to capture food by endocytosis and to digest it intracellularly[62] 

In biochemistry, sulfur operates as a carrier of reducing hydrogen and its electrons for cellular repair of oxidation. In plants and animals, the amino acids cysteine and methionine contain most of the sulfur, in all polypeptides, proteins, and enzymessulfite oxidase and red-ox-changes are needed for the metabolism, disulfide bonds (S-S bonds) between cysteine residues in peptide chains confer extra toughness and rigidity as in hair and feathers (chicks, the characteristic odor of rotting eggs is due to hydrogen sulfide and disagreeable odor of SO2 when burned). -SH moieties to handle reactions involving acyl-containing biochemicals as coenzyme A and alpha-lipoic acid[2], vitamins biotin and thiamine being named for its sulfur content. Reduced glutathione, a sulfur-containing tripeptide, is a reducing agent through its sulfhydryl (-SH) moiety derived from cysteine (like the thioredoxins, a class of small proteins).

The amino acids tellurocysteine, selenocysteine, cysteine and serine (S) are also considered isoelectronic (as carbonate and nitrate[42] at least valence, better — homoelectronic): SelenoCysteineSer (S).*

Inorganic sulfur forms a part of iron–sulfur clusters as well as many copper, nickel, and iron proteins. The ferrodoxins serve as electron shuttles in cells. In bacteria, the important nitrogenase enzymes contains an Fe–Mo–S cluster and is a catalyst that performs the important function of nitrogen fixation, converting atmospheric nitrogen to ammonia that can be used by microorganisms and plants to make proteins, DNA, RNA, alkaloids, and the other organic nitrogen compounds necessary for life.[4]  FdRedox.pngSulfur metabolism and Sulfur cycle, may be base of life, before Oxigen-world and chemistry. Sergei Winogradsky found inorgoxidation (oxidation of inorganic compounds as hydrogen sulfide H2S (an energy source of Beggiatoa) from 1880- to Selman Waksman until the 1950s. Sulfur oxidizers can use as energy sources reduced sulfur compounds, including sulfides, sulfur, sulfite, thiosulfate, and various polythionates (e.g., tetrathionate),[5]  depend on enzymes such as sulfur oxygenase and sulfite oxidase. Some lithotrophsbacteria and archaea use hydrogen sulfide in place of water as the electron donor in chemosynthesis similar to photosynthesis that produces sugars and utilizes oxygen as the electron acceptor. The photosynthetic green and purple sulfur bacteria and some lithotrophs use elemental oxygen to carry out such oxidization of hydrogen sulfide to produce elemental sulfur (S0), oxidation state = 0. In volcanic vents the giant tube worm uses hydrogen sulfide (via bacteria) as food to be oxidized. The so-called sulfate-reducing bacteria, by contrast, «breathe sulfate» instead of oxygen, and reduce back into sulfide partially oxidized sulfur compounds (e.g. thiosulfates, thionates, polysulfides, sulfites), with the smell of intestinal gases (flatus) and decomposition products. Sulfur is absorbed by plants roots from soil as sulfate, transported as a phosphate ester, reduced to sulfide via sulfite before it is incorporated into cysteine and other organosulfur compounds:[6] SO42− → SO32− → H2S → cysteine → methionine

Oxidation of the most reduced of a thiol group (-SH), cysteine, CoA-SH produces a disulfide bond (cystine Cys-S-S-Cys, are readily reversible; resolving mixed disulfide bonds and higher oxidation states, such as sulfinic acid (Cys-SOOH), were once considered irreversible, can reduced back to thiol, in an ATP-dependent manner, by sulfiredoxin, discovered in yeast,  conserved in all eukaryotes, including mammals (Srxn1). The glutathione metabolism by transferring the glutamyl moiety to a variety of acceptor molecules including water, certain L-amino acids, and peptides (glutamyl-peptide + an amino acid \rightleftharpoons peptide + glutamyl amino acid), leaving the cysteine product to preserve intracellular homeostasis of oxidative stress.[10][11]

It can cause toxic effects through the production of free radicalsperoxides that damage all components of the cell, including proteins, lipids, and DNA, as strand breaks in DNA. Reactive oxygen species (ROS) generated, e.g. O2 (superoxide radical), OH (hydroxyl radical) and H2O2 (hydrogen peroxide)[1] , act as cellular messengers in redox signaling,  cellular signaling.
Oxidative stress mechanisms in tissue, free radical toxicity induced by xenobiotics and the subsequent detoxification by cellular enzymes (termination).

ROS — reactive oxygen species,  can be used by the immune system as a way to attack and kill pathogens.[19] Short-term oxidative stress may also be important in prevention of aging by induction of a process named mitohormesis.[20]  But oxidative stress is thought to be involved in the development of  cancer,[4] Depression[] Parkinson’s Disease[5] Lafora disease,[6] Alzheimer’s disease,[7] atherosclerosis,[8] heart failure,[9] myocardial infarction,[10][11] fragile X syndrome,[12] Sickle Cell Disease,[13] lichen planus,[14] vitiligo,[15] autism,[16] infection, Chronic fatigue syndrome,[17] andAsperger syndrome,[2] ADHD,[3] (See: Chemical and biological effectsProduction and consumption of oxidantsDiseasesAntioxidants as supplementsMetal catalystsNon-metal redox catalystsImmune defenseSee also  References)

 

1.*Antoine Lavoisier believed that what we now call oxidation was always the result of reactions with oxygen,[19] thus the name. Oxidation states were one of the intellectual stepping stones that Mendeleev used to derive the periodic table.

The ending -ic for the higher metal oxidation state and the ending -ous for the lower (FeCl3 is ferric chloride and FeCl2 is ferrous chloride  — iron(II) chloride in Stock nomenclature (Alfred Stock, 1919) . The current concept of «oxidation state» was introduced by W. M. Latimer in 1938.[21] In 1940 IUPAC recommended that the term Stock number should be replaced by the term oxidation number. In 1947 Linus Pauling proposed that the oxidation number could be determined using the electronegativity of the atoms to determine the «ions» in the formal determination of oxidation number.[7] In 1970[10] IUPAC defined oxidation number in terms of electronegativity. «Towards a comprehensive definition of oxidation state» (project 2008-040-1-200) .. the current definition in the IUPAC Gold Book was seen to be «narrow and circular», and «inapplicable to clustersZintl phases and some organometallic complexes».[27]

The periodicity of the oxidation states led Irving Langmuir  to adopt the octet rule[97] in 1919.

Langmuir valence.png

List of oxidation states of the elements

h= mc\wave  Compton (1927 -«for his discovery of the effect named after him»), 1945 — Pauli «for the discovery of the Exclusion Principle, also called the Pauli Principle»,

*связи трех главных понятий постоянной Планка как кванта действия и энергии, квантов света Эйнштейна и квантовых чисел (КЧ) атома Бора завершают взаимодействие частиц и волн света, впервые названных фотонами, в ЭК, с принципом Паули2 и связью спина со статистикой, отличной для полу-целых и не-четных, бозе- и ферми-, поля и вещества. Обобщение длин волн Комптона для любой скорости и е- атома Бора дает формулу волн материи де Бройля, из которой развивается волновая механика Шредингера и принцип неопределенности Гейзенберга. Заряд связан с ПП  безразмерной а, не зависящей от человека, с  множеством других явлений, начиная с атома Бора. Бор рассчитал величину Ридберга, энергии ионизации атома Н, главной и в химии и в астрофизике, начиная со времени рекомбинации. Это время и температура рекомбинации (кТ ок. 3000 К) также зависит от концентрации, как в химии и звездах, по уравнению Саха. Пока это не поняли, о составе звезд судили по спектрам, как в 19 веке, думали, что больше кальция, чем водорода и гелия, на деле составивших 99% и объяснивших формирование планет СС и др.

2Кроме главного КЧ (Бальмера! – в химии определяющего и номер периода х.э.), сравнение с планетарной моделью дало орбитальное и его проекции как 3-е, магнитное КЧ. Они отвечают 3 измерениям пространства УШ и дополняются внутренним, «неклассической двузначностью» с принципом Паули… антипротоны также превращаются в нейтроны в-, как те далее в р+. Очевидно, эта триада аналогична известной тройке р+, Н и Н- (гидрид ион определяет и видимый диаметр Солнца и звезд, имея Е связи 0.75 эв, гораздо меньше 13.6 Ридберга, но порядка кТ термосфер, может определять 99% «химии» и поведения поверхности и видов звезд) с прежними «внутриядерными е-«. Гамов здесь переходит к контактным-поверхностным силам, как в его модели капельной ядра (и белков в 50-60-х).

Измерение а-через КЭХ, сопротивление Холла, показывает фундаментальную связь электро-магнетизма (Холла) через квантование уровней Ландау. Связь квантования магнитного (потока) и частиц ведет к дробному КЭХ и м.б. общей моделью, по Лафлину, и включения-«интериоризации» внешнего. 1943 — Stern «for … molecular ray method and his discovery of the magnetic moment of the proton», с 1944 — Rabi «for his resonance method for recording the magnetic properties of atomic nuclei»

2*. From 1934 Hoffmann–La Roche bought the Reichstein process to mass-produce and market synthetic vitamin C, under the brand name of Redoxon.[175]  Irwin Stone use its food preservative properties and the theory that humans possess a mutated form of the  enzyme L-gulonolactone oxidase coding gene[178], the last of the chain of four.[176][177]  In 2008 the Un.Montpellier discovered that in humans and other primates the red blood cells have evolved a mechanism to more efficiently utilize the vitamin C present in the body by recycling oxidized L-dehydroascorbic acid (DHA) back into ascorbic acid which can be reused by the body (not in mammals that synthesize their own).[67] Vitamin C content of a food can be calculated by measuring the volume of the sample required to decolorize a solution of dichlorophenolindophenol (DCPIP). See: Swiss Postage stamp of a molecule of vitamin C to International Year of Chemistry.[179] 

 

Periodic systems of small molecules…specific kinds of molecules such as alkanes (Morozov);[14] benzenoids (Dias);[15][16] functional groups containing fluorineoxygennitrogen and sulfur (Haas);[17][18] or a combination of core charge, number of shells, redox potentials, and acid-base tendencies (Gorski).[19][20] , formula enumerations (Dias), the hydrogen-displacement principle (Haas), reduced potential curves (Jenz),[21] a set of molecular descriptors (Gorski),  E. V. Babaev[22] has erected a hyperperiodic system…the total number of constituent atomic valence electrons,

*data for isoelectronic molecules …as CH, C-= N = O+ radical ion are isoelectronic because each has five electrons in the outer electronic shell. Similarly, the cations K+Ca2+,  Sc3+
…Mn+7=[Ar]=anions Cl−S2−,  P3−, Si-4 are all isoelectronic with the Ar atom. In such monatomic cases, there is a clear trend in the sizes of such species, with atomic radius decreasing as charge increases.  COCN−N2C2−2, and NO+ are isoelectronic because each has two nuclei and 10 valence electrons, with each atom considered to have 5 of them (a lone-pair and a triple-bond). Isoelectronicity does not relate to formal charge … balanced (:C≡O:+ :NN:).  CO2FCNN2ONO2+N3, and NCO are all isoelectronic.

Isoelectronicity leads to the concept of hydrogen-like atoms, ions with one electron which are thus isoelectronic with hydrogen.  The uncharged H
2C
=C=O (ethenone) and H
2N
-CN (cyanamidemolecules and the zwitterionic H
2C
=N+   =N−  (diazomethane) molecule are isoelectronic.

SelenocysteineCysteineSerine  The amino acids tellurocysteineselenocysteinecysteine and serine are also considered (at least valence) isoelectronic.

  1. IUPACCompendium of Chemical Terminology, 2nd ed. (the «Gold Book») (1997). Online corrected version:  (2006–) «isoelectronic«.Isoelectronic Configurations iun.edu

http://elements.wlonk.com/ElementsTable.htm