17

trb456 and Mad Scientist have raised the point that enantiomeric forms of a bioactive molecule may have markedly different activities, however there's more to it than that. A molecule that has a similar shape and surface charge distribution to another biologically important molecule is liable to bind to the same protein receptor sites, but in different ways. ...


17

One example of disastrously different effects of very similar molecules is thalidomide. There are two isomers, only differing in their stereochemistry. The (R)-isomer is responsible for the sedating effect it was initially used for. The (S)-isomer lead to horrifying birth defects in the children of woman that took that drug. It is somewhat more complicated,...


15

The $\ce{Fe}$-porphyrin complex is a vastly conjugated $\pi$-system, in which the oxidation state of the $\ce{Fe}$ plays a central role. The wavelength of light absorbed by hemoglobin exactly corresponds to the the difference in energy between the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) of the heme $\pi$-...


15

I (accidentally) stumbled upon the following statement in Atkins' "Elements of Physical Chemistry" (p378): We represent dipole moments by an arrow with a length proportional to $\pmb{\mu}$ and pointing from the negative charge to the positive charge (1). (Be careful with this convention: for historical reasons the opposite convention is still widely used.)...


10

None of the chemical file formats are typically accepted by 3D printing services. The reason is that chemical file formats are fundamentally different from those describing 3D objects. In the simplest case, a chemical file format describes a list of atoms and their positions (plus possible metadata). An example is the XYZ format, which stores exactly that. ...


9

Szilágyi and Závodszky published an article in the journal Structure which analyses a number of different structural parameters of proteins of moderately thermophilic ($45~\mathrm{^\circ C} < \vartheta_\mathrm{opt} < 80~\mathrm{^\circ C}$) and hyperthermophilic ($\vartheta_\mathrm{opt} \approx 100~\mathrm{^\circ C}$) organisms compared to homologous ...


9

There's several aspects to your question. Does quantum mechanics play a role in protein folding? Yes. The origin of the van der Waals interaction is ultimately a quantum mechanical one. (At least the induced dipole portions: how the electrons move with respect to each other and an external electrical field is driven by quantum mechanics.) Also, while part ...


8

Let's take a simple case of a positive charge $q_+$ and a negative charge $q_-$ with $q_+ + q_- = 0$ placed along the $x$-axis at $x_+$ and $x_-$, respectively. The dipole at the $x=0$ is $$\mu=q_+x_+ + q_-x_- $$ which can be rewritten as $$\mu=q_+(x_+ -x_-) $$ which is a vector pointing from $x_-$ towards $x_+$. So this is the "natural" direction based on ...


7

There is a paper on bolaamphiphiles (1) where it is stated that measured surface area corresponding to the area of a bixin molecule lying on the water surface with most methyl groups pointing outside is approx. $\pu{1.0 nm^2/molecule}$ at zero pressure. If the methyl groups were parallel to the water surface, a molecular area of approx. $\pu{1.7 nm^2/...


7

UPDATED: I wrote a first answer assuming that $t>0$ which got close to what's in the paper, but not quite the same. Thanks go to Karsten Theis for pointing out that $t<0$ in these "backward equations". Here's a corrected explanation: The scenario is that we have a system that can be in any of seven consecutive states (numbered 0 through 6). At some ...


6

Protein folding takes a very long time (relatively speaking) when thinking of quantum mechanical effect. First note that, in principle, for the time being, quantum mechanics is considered to be universally valid at all size and time scales. So, in general, it does not really matter how big a system is or how long a process takes: every system is a quantum ...


6

I'll use quotes from B. Rupp, Biomolecular Crystallography (p. 7-8) to answer. Generally the structure is similar... Comparison of many nuclear magnetic resonance (NMR) solution structure ensembles with crystallographic structure has shown that the core structure of protein molecules remains unchanged compared with the solution state during ...


6

If you got an installation of openbabel's GUI, you equally have an installation of openbabel for the terminal (e.g., in Linuxes) / command line cmd.exe (in Windows). There is nothing wrong using the GUI for an edit on one file or a few data -- your instructions set are right -- however using the CLI is closer to the engine, thus often more powerful. Enter ...


4

I did some work on interpreting neural network QSAR models - I won't claim that they explain everything and has a number of limitations (linearizes network connections, applicable only to feed forward networks). But maybe it will be useful Interpreting Computational Neural Network QSAR Models:  A Measure of Descriptor Importance Interpreting Computational ...


4

Since you are interested in Artificial Neural Networks that also explain their decisions/predictions you may be interested in transparent neural networks, although they have not been used to my knowledge on chemical information. Other interesting approaches include inductive logic programming which have among other things been applied to predicting binding ...


4

One way to do it is to perform a quantum chemistry calculation of the electrostatic field generated by the molecule. Another is to determine (or assume) partial atomic charges for each of the atoms of the system, and use a Poisson solver (as I believe APBS is) to calculate the electrostatic field generated by this point charge distribution.


4

In biochemistry branch searching for new drugs, it was common to search for new active substances using chemical similarity. It does have reasoning behind it. Most drugs acts, binding themselves to some protein site, in the place, where normal ligand of the protein will bind. However, chemical similarity is not enough to be a drug. Sure, a substance must ...


4

I was curious to see what kind of research had been done on this topic, and didn't expect to find much, but I was quite wrong. So, I'll summarize some articles that I found and give the references at the bottom. Why would we ever consider quantum mechanics in protein folding? First, an introduction to why someone would even try to come up with a quantum ...


4

There are several kinds of snake venom, and as far as I know they are all complex enzymes: it means that they are complex macromolecules, made by amminoacids (these, "small molecules") bound with peptide bonds. For enzymes and proteins, the chemical nomenclature is quite impratical: it's way easier to define the enzyme by giving the names of the amminoacid ...


4

Are all the biochemicals that our body uses enantiomerically pure or are racemic mixtures too? Many molecules exist in both forms in nature. One fun example are the enantiomeric terpenoids R-(–)-carvone and S-(+)-carvone. The R-form smells like spearmint while the S-form smells like caraway. The difference in smell shows that properties other than the ...


4

While it is true that some antiparallel beta sheets have neighboring strands that are adjacent in primary sequence, other cases do exist. As for parallel beta sheets, the polypeptide chain between strands could be connected via a loop or a helix if the two strands are close in primary sequence. The mapping of strands on the primary structure has been studied ...


4

Experimental phasing and molecular replacement provide initial phases used to start model building. Later on (refinement, validation) phases are calculated from the model. If the phases are what determine the final electron density irrespective of the amplitudes used Both amplitudes and phases are used to determine the electron density. If you calculate ...


4

[OP] ...if we don't have the phases (say for a part of a model), it just wouldn't get built even if we have the amplitudes for that part, right? Or is it that in this case (of omitting a part), there would be an electron density (because the amplitudes are still there), just that it would be featureless For each reflection, the structure factor $F_{hkl}$ ...


4

The illustration is likely taken from a later edition of Baum's Introduction to organic and biological chemistry. The first edition [1, p. 292] presents nearly identical illustration under a different number alongside with a note that the image was adapted from Bennett's Graphic Biochemistry [2]: Unfortunately, at the moment (2020-10-16) [1] is available on ...


3

Yes it is true that protein folding takes a long time compared to bond vibrations (few femtosecond) or rotations of a amino acid (picoseconds to nanoseconds) and for small proteins can take of the order of a few tens of nanoseconds. Typically proteins with many amino acid residues, say 100, this time can reach to microseconds and seconds and in fact cannot ...


3

Just browsing through this "Unanswered Question" now (in late 2014). I hope it's not too late? In protein structure validation, Ramachandran outliers are a strong, but not absolute, indicator that the backbone confirmation of your protein structure deviates from all the high resolution structures known to date, and hence need your attention during the ...


3

The data provided by @F'x are very helpful towards answering the question. But the relative stabilization of the bases when hydrogen bonded to each other is germane to the question. Because the role of stacking is still being worked out, I don't think this question has a simple answer. Since wobble pairs are observed, but I haven't seen them outside a ...


3

DNA is not a protein, as @MARamezani states. See http://www.answers.com/Q/Is_DNA_a_protein. There is a prevalence (or lack) of some amino acids in certain sources. For example, maize ("corn" in America) is deficient in tryptophan and lysine, so if your sample is short on those two, it is more likely that it is from corn. A list of some foods and amino acid ...


3

I am sure that a more definitive answer could be provided by someone more familiar with the field, but here are a couple of observations. First, I think it is a bit of an exaggeration to say that protein folding is almost entirely the result of entropy because the protein will have larger entropy in the unfolded state than in the folded state. The main ...


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