Posts Tagged ‘chiral’

Origem da Vida: Moléculas quirais no espaço

quarta-feira, junho 15th, 2016

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A MOLECULE IN SPACE COULD HELP US UNDERSTAND THE ORIGIN OF LIFE ON EARTH

http://www.popsci.com/molecule-in-space-could-help-us-understand-life-on-earth

chiral molecules

Left and right molecules of propylene oxide

Moleculas quirais esquerda e direita de propylene oxide

Obs: Notar que a molecula ‘e separada em dois conjuntos. Um possui apenas um carbono e não tem oxigênio. O outro possui dois carbonos e tem um oxigênio. Segundo a formula da Matrix/DNA isto se explica como os dois conjuntos sendo a s duas meias-faces da formula. A face esquerda e’ a primeira, que tem as três funções. Depois a segunda face da direita, tem o oxigenio porque e’ entropica. Existe ali um jogo que necessita dois carbonos, e desconfio que ‘e para servir como catalitico, não permitindo que a face degrade rapidamente. Ver isso.

O que estava acontecendo ocultamente nas sôpas primordiais da superficie terrestre e no fundo dos oceanos enquanto a Matrix/DNA trabalhava no esforço de criar a Vida na Terra.

quarta-feira, agosto 24th, 2011

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Fonte/Artigo:

Anomeric argument

http://prospect.rsc.org/blogs/cw/2011/08/15/anomeric-argument/

 

The Anomeric Effect

Existe um fenômeno na quimica molecular denominado “efeito anomérico” ou “anômero” que parece ser muito importante para a Vida mas que ainda é desconhecido seus mecanismos e causas pela comunidade cientifica tendo fomentado muita controvérsia e debates. Ao ler o artigo abaixo e pesquisar brevemente alguns detalhes em outras fontes como Wikipedia tambem suspeitei que o fenômeno é muito importante para desenvolver a Matrix/DNA. Postei um comentário no artigo do CHEMISTRYWORLDBLOG ( o qual está copiado abaixo) e aqui registro o fato para tê-lo na memória e voltar a esta pesquisa sempre que alguma novidade relacionada aparecer.

Moléculas: Rotações Espirais e Circulares

Normalmente estas “sugar-moléculas” apresentam-se com rotação equatorial (o que penso ser meramente rotação esférica horizontal ou circular) como é mostrado na figura da direita pelo OH que está à direita do eixo horizontal. Mas tem um caso especial onde o mesmo composto molecular inverte o OH do eixo passando-o para o tôpo da base, o que deve “concavear” a mólécula tornando-a uma espiral, mais como uma cópia mais fiel e inicial da quimica do software/Matrix da fase astronomica. Existem ao menos seis tipos de açucares com esse efeito que é denominado “efeito anômero” e importante é observar que os seis tipos surgem de uma cadeia de transformções sucessivas que muito lembra o circuito do software/Matrix e indica como funciona a actividade óptica a nível de simbologia quimica (ver figura a seguir).

Molecular Circuito da MatrixDNA D Galactose

Vamos ao artigo e aos meus comentários?

CHEMISTRYWORLDBLOG
http://prospect.rsc.org/blogs/cw/2011/08/15/anomeric-argument/#more-8685
Anomeric argument

Posted by Josh on Mon 15 Aug 2011
Categories: News

Fierce debate has erupted in the Journal of the American Chemical Society (JACS) over a phenomenon known as the anomeric effect. The controversy reminds us once again that while observations are usually verifiable, interpreting results is something all scientists need to play a part in.

The anomeric effect, familiar to many chemists, is important because it influences the shape of sugar molecules, which are, of course, biologically and medicinally relevant. In essence it means that sugars prefer their C1 hydroxyl groups to be in an axial orientation, whereas other cyclohexane based systems usually have their large substituents in an equatorial orientation. The reason for the anomeric effect is normally assumed to be hyperconjugation of a lone pair of electrons on the ring oxygen to the antibonding orbital of the carbon next door. The truth is though that academic dispute over the cause of the effect still exists.

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(Matrix’s notes:
1 – ( From Wikipedia) : DNA and RNA are built up of the sugars ribose and deoxyribose. The sugar in DNA is deoxyribose, and has the formula C5H10O4.
2 – Cyclohexane is a molecular formula C6H12.
Cyclohexane conformation
The 6-vertexed ring does not conform to the shape of a perfect hexagon. The conformation of a flat 2D planar hexagon has considerable angle strain because its bonds are not 109.5 degrees; the torsional strain would also be considerable because all of the bonds would be eclipsed bonds. Therefore, to reduce torsional strain, cyclohexane adopts a three-dimensional structure known as the chair conformation. This was first proposed as early as 1890 by Hermann Sachse, but only gained widespread acceptance much later. The new conformation puts the carbons at an angle of 109.5°. Half of the hydrogens are in the plane of the ring (equatorial) while the other half are perpendicular to the plane (axial). This conformation allows for the most stable structure of cyclohexane. Another conformation of cyclohexane exists, known as boat conformation, but it interconverts to the slightly more stable chair formation. If cyclohexane is mono-substituted with a large substituent, then the substituent will most likely be found attached in an equatorial position, as this is the slightly more stable conformation.
Cyclohexane has the lowest angle and torsional strain of all the cycloalkanes, as a result cyclohexane has been deemed a 0 in total ring strain, a combination of angle and torsional strain. This also makes cyclohexane the most stable of the cycloalkanes and therefore will produce the least amount of heat (per CH2 unit) when burned compared to the other cycloalkanes.)
3 – Comparisons between cyclohexanes and axial sugars suggests that Nature was trying to change the Matrix’s formula at its closed systemshape stablished asastronomicsystems towards the shape of opened systems, as required by biologicalsystems. Being the torsional strain of cyclohexanes more stable than the other cycloalkanes, it means that cyclohexanes were the first terrestrialmolecularcompoinds and cycloalkanes were the intermediate fases of the transformation, which the finalfase should bethe sugars of RNA andDNA. These sugars should be rotational and espiraling for tobean opened system, instead achiral and equatorial circular.

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It’s difficult to study the anomeric effect, firstly because in solution it’s difficult to isolate solvent molecules’ contributions to it and secondly because there is a relative scarcity of methods which can probe the underlying parameters which give rise to the effect.

It was interesting then, when Oxford University’s Ben Davis managed to create a gas phase complex of separate anomers and resolve their electronic spectra. He did this by shining a laser on a dry carbohydrate (D-glucose) mixed with an oligopeptide receptor. This created a gas phase mixture of the two anomers complexed separately by the receptor. The complicating solvent issue was removed and the α- and β-anomers could be studied independently. The infra-red spectra of the two complexes differed in some key points – notably the frequency of the peptidic N-H bond signals. This indicates the hydrogen bonding interactions between the receptor and the sugar is different for each anomer.

The electron density on the ring oxygen should be different for each anomer due to the different degrees of hyperconjugation. In theory this would contribute to different hydrogen bonding strengths between the ring oxygen and the peptidic NHs.

Interesting stuff. Except that a shadow was about to fall over Davis’ work in the shape of US-based computational chemist Yirong Mo. Almost immediately after Davis’ work came out Mo and his colleagues published what you might call a stern rebuttal of their conclusions. What’s a little disappointing is that Mo is just one of several scientists to comment on Davis’ work but since his rebuttal is put in the strongest possible terms, it seems likely that it is this paper which will garner the most attention. Mo’s work consists of computational modelling of a very similar system to the one Davis used where the anomeric effect is disabled. Mo showed that in this case, his modelling still predicts the same spectral differences that Davis observed and, therefore, says that the changes are not caused by the anomeric effect. The abstract of Mo’s paper states that Davis’ ‘”sensor” cannot probe the anomeric effect as claimed’, essentially proposing that Davis’ experiment is flawed.

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Matrix’s notes:
1 – I don’t know the model used for computational simulations here. I am sure it is not based in the Matrix’s formula. Then, it should be a good method elaborating a computational simulation based in Matrix’s formula. Maybe the final result could be different and more likely Davis results.

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I spoke to Davis and Mo as well as computational chemistry experts Jeremy Harvey from the University of Bristol and Jonathan Goodman from Cambridge University. A very subtle argument emerged. ‘The bottom line here is that intermolecular interactions – as between the sugar and the peptide model – are complicated,’ Harvey says, ‘assigning their strength based on relatively simple concepts such as the anomeric effect is hard. Spectroscopy, and energy decomposition analysis […] provide lots of insight, but leave lots of room for ambiguity.’

Davis emphasised that his work is very much a reporting of experimental results and that he doesn’t insist upon any specific conclusions about the causes of the anomeric effect. But he says ‘it’s great to see our experimental results stimulating such a lively debate in the theoretical community’.

To the uninitiated (which, given the complexity of the arguments involved, is many people) it looks like Mo’s paper shows Davis’ to be completely wrong. That is, after all, what he says in his abstract. This could be an instance when a little post-publication peer review could make a big difference to people’s perceptions. Picking apart the arguments is complex and time consuming, so when people take the time to look at complex debates like this it would be great to see their ideas and conclusions posted alongside the articles. That would make it clear that, actually, there is a debate to be had here, and as scientists, we want to stimulate it.

Josh Howgego

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Post from

Louis Morelli says: Your comment is awaiting moderation.
Wed 24 Aug 2011 at 9:49 pm

Hay, Josh

I am researching this issue also but I have a “away off the beam” approach. It can be fuel for novelty thought.

As author of “The Matrix/DNA of Natural Systems” I am advocating and testing the idea that organic molecules were direct product from the action of the astronomical state of the world 3,7 millions years ago, and this state can be pictured as a diagram of software –the matrix formula, as showed in my website. If the hypothesis is right, the terrestrial atoms were configured like the astronomic system shape, then, we can understand a lot of new mechanisms and the whole means of the process. For instance:

1 – Why sugars prefer the axial rotation?

Matrix’s formula suggestion: “The astronomic state of the world about 4 billion years ago was based on the closed shape of natural systems, a closed door to evolution. Then, happened the entropy, the closed shape was fragmented, miniaturized and lift up as opened system = biological systems. The astronomic formula was resumed in a base par of nucleotides, the fundamental unit of information of RNA and DNA. The sugars at the DNA strains are a copy made with atoms of matrix’s formula, which is a rotating spiral, like galaxies. While equatorial rotation suggests a bias towards closed systems at biological scale, the rotating spiral suggests a bias towards opened systems. Then, the anomeric effect is a transition from closed system towards opened system. We can see this transition when “the anomers of glucopyranose are diastereomers, with the beta anomer on the right having an OH group pointing up equatorially in the lower right-hand corner of the figure, and the alpha anomer on the left having that OH group pointing down axially”. And we can see the systemic circuit of Matrix/DNA formula in the chain reaction called “Open-chain form of D-galactose” where each fase is a representation of each systemic function.”

By the way there are a lot of informations coming from the formula, which is unknown by scientific community. Since the formula is only theoretical yet and the method for getting it does not permit published peer review papers, there are no way for introducing it to scientific community beyond my website. I should be very grateful for continuing my work if my comment here will be questioned/criticized. Thanks…