Bioinorganic Chemistry - Science topic

Simple UV-Vis spectrum recording should be enough as clusters show different absorbance. Then EPR is the method of choice

May be you can useful from the following article

I trapped nitric oxide and I've got many remarks and observations.

thank you Bruce, I'm not crazy

The behavior of highly charged polymers in aqueous solutions is a complicated business. I think the problem here is probably over-protonation by too-strong and/or too-concentrated acids. (See the attached link.) You want the polymer chains to be extended, not balled up, and this is dependent on the charge and also on the counterion(s). There is probably some optimum level of protonation that provides maximum solubility and minimizes agglomeration. A buffer might be helpful in maintaining the optimum pH, but thermodynamics (i.e. the solubility product) is always a limiting factor.

Dear Dr. Melanie Pilkington,

may i suggest the use Fe(ClO4)2 instead of chloride salt?and then u can use a stichiometric  amount of cyanide salt instead of excess amount?

Hi Sara Sheykhi

I wish you good luck

Sugar phosphates and phosphate esters are ubiquitous in biology and are certainly stable at near-neutral pH. Examples include DNA, RNA, ATP and other nucleotides, the phosphosugars involved in glycolysis, etc.

see this review

dx.doi.org/10.1021/cr400135x |

Chem. Rev. 2014, 114, 815−862

One can also form imine with e.g. benzaldehyde on the primary amine, protect the secondary, and then hydrolyze the imine to regenerate the -NH2.

Determining X-Ray structure is very common in India. Try to contact any inorganic chemistry department in an established institute (IIT and IISERs) in the country. Chances are they have multiple diffractometers. This is true for most national labs and universities. If you have good single crystals, it does not matter if they are organo metallic or co-ordination complexes. Most of them allow access to external users. At the Indian association for the cultivation of science (Kolkata) you can drop an email to the HOD at ictkp@iacs.res.in.

Not sure why you (or someone else) presented me with a negative rating, given the accuracy of the answer I volunteered and the vagueness of your question. But, in any case, regarding the 'fine structure' of the emission from hydrogen:

Short answer - The orbitals you quoted as being equal in energy are not equal in energy => additional structure

Longer answer - The energy of electrons in orbitals of a particular principal quantum number, but different angular momentum, are affected by 'relativistic effects' and 'spin-orbit coupling' and the like. (These effects are very small, about 10^-4 - 10^-5 the energies in the simple answer I gave earlier)

Or you could have a look at the more comprehensive answer here:

Dear Sameh,

Among the 4 diastereoisomers depicted in your Word file I  expect that 2ii and 3ii will be the most reactive. Since the orientation of H and OH is similar in both 2ii and 3 ii I believe that their reactivity will be very close, or similar.

The principle here is to look at the orientation of H and OH; the best reactivity will be when both  are in the anti conformation each to other.

Hoping this will be helpful,

Rafik

Hello Gülşah,

Some inorganic compounds do not emit light after absorption of radiation therefore molecules do not have an excitation spectrum. Usually the absorbed energy can scatter in the molecule without emitting light. Moreover, the molecules absorb light at different excited states. The emission usually occurs from the lowest of these excited states known as S₁. During the excitation to a higher state from ground state (S₀) it often ends up in the lowest excited state S₁ and then emits radiation.  In such case the excitation spectrum is same as the absorption spectrum. Nevertheless from a higher excited state a molecule does not have to undergo to the lowest excited state but directly reaches the ground state in that case it does not emit radiation.

Hope that explains your question.

Thermodynamics occurring inside the synthesis chamber decide the percentage of synthesis of nanoparticles.

however, you will never get 100% conversion in any methods.

see also refs therein

Hydrolysis of the zinc(II) ion in sodium nitrate, chloride and perchlorate medium: the effect of the anionic medium

Nikola B. Milić and Ratomir M. Jelić

Journal Article J. Chem. Soc., Dalton Trans., 1995, 3597-3600

DOI: 10.1039/DT9950003597,

The Chemistry of Aqua Ions: Synthesis, Structure and Reactivity: ATour Through the Periodic Table of the Elements 

by David T. Richens

What about my suggestion to use a borohydride reducing agent? There is literature precedent for the use of Sodium Borohydride to reduce metalloproteins in EPR studies:  http://onlinelibrary.wiley.com/doi/10.1111/j.1432-1033.1991.tb15731.x/epdf

ammonium acetate

Thanks Priola half part of your answer i have already done by calculating free energies in two oxidation states. yes these  systems have electron delocalization or charge transfer from metal to phen ligand point is how to probe that and how to quantify that the degree of charge transfer is different in two oxidation states.  

Dear Behroos

If your extracted mucus have yellow color, it means that you have a mixture of mucus with some coelomic fluid( yellow) ,so you must check the coelomic fluid reactions( oxidation and ...) during this period too.

(Based on results that i saw in laboratory, always we have a mixture of mucus and coelomic fluid...)

sometimes, structure of the metal complex may play a role. Generally the decrease in the hypochromicity is directly proportional to kb values as you have said. In complexes' UV spectra,you can see the variation in absrbance and lambda max tooo . For example, phenanthroline containing complex gives higher percentage hypochromicity than bipyridine one. 

I hope these are the probable reasons, as I don't have any idea of your structures.

not cluster but thiol complex (Au³⁺(HS-Et-OH)₃). Plz, add reducing agent such as ascorbic acid, borohydride, hydrazine, ...)

It becomes oxidized rapidly to silver oxide in contact with air and light. So perform the reaction in dark and use gloves while handling other wise your hands will have dark stains of the oxide which is long lasting. 

Are you need explain for lambert beer law O.D/min =e.c.l

e extention coefficient,  c  conc,  l  path length for cuvette

may u can reduce N=C then prepare a complex and compare with once in present of double bond

Dear Mohammed,

the "Tanabe mechanism" was introduced by Tanabe in articles from 1965 (Tanabe, Moriya, Sugano, MAGNON-INDUCED ELECTRIC DIPOLE TRANSITION MOMENT, Phys. Rev. Lett, 1965, 15, 1023 and Ferguson, Guggenheim, Tanabe, Absorption of Light by Pairs of Like and Unlike Transition-Metal Ions, Phys. Rev. Lett. 1965, 14, 737). Especially the former article has been heavily cited in the literature, so that you may find a wealth of explanations, definitions, and applications in the citing papers.

Best regards

Gerald

I am not sure how to use the software you have mentioned, but adding hydrogen to heme-proteins is quite easy with AutoDock. It is a freeware, and if you can use it you can follow these simple steps to add hydrogen:

1. Open Auto Dock Tools

2. Read your protein.pdb file using the read option

3. Go to Edit, select 'Hydrogens', then 'Add' and finally 'Polar hydrogen only'

You can further add Kollman charges and then save them as '*.pdb' file for your further analysis.

Hope it helps.

I agree with the use of Dean-Stark apparatus and on the fact that the aniline would be better if freshly distilled. I did several imines and an alternative way is to stir an equimolar amount of aniline and aldehyde (with ketones is not really efficient) in dry dichloromethane in the presence of dry Na2SO4.

You should try to do this using "real" spectroelectrochemistry. This means you record the spectral changes while scanning the potential. In your case I would suggest two experiments:

A) Use the native enzyme, not reduced with dithionite. Scan from 0 to -2 V and record the changes in the UVvis absorption spectrum every 10 or 20 mV (equilibrate the solution before measurement for 10 s). If you draw the spectral changes (intensity of a arising band or vanishing of a parent band) over the applied potential you will get some tritration-like curve. The point of return (highest slope) is the potential.

B) Reduce the enzym with dithionite (no excess!) and do the oxidative scan, collect the absorption spectra etc. ...

This method has been frequently used for enzyme e.g. by A. L. Crumbliss. Alternatively EPR or IR spectroscopy can be used.

3d metals are typically more reluctant towards oxidative addition reactions. This is due to the fact that the 3d orbitals are nodeless and thus particularly small compared to the 4d or even 5d orbitals (the latter additionally experience an expansion due to relativistic effects). Hence, 3d orbitals generally overlap less efficiently with ligand orbitals and typically form  less stable bonds. This is the reason why Ni does not reach the +IV oxidation state that easily and why Ni-H bonds are less stable.

I hope this helps; All the best

Viktoria

Hi Yehia, 

The article you referred to describes a BMD method and the recommended medium to use for that particular organism. It has nothing to do with determining ECV.

This should be very straightforward to see by UV-vis spectroscopy or EPR as the heme has distinctly different spectra in different oxidation states (this is true for both types of spectroscopies) 

We do it regularly in our lab. So if you tell me what you need, I can have my person provide you the information.

In my experience the most important point is to obtain metal-free protein in the first place. Lot of proteins bind metal ions during expression and keep them tightly bound during purification even in buffers containing chelating agents such as EDTA;  some proteins require the metal ion for correct folding. If your protein has metal ions already bound, you will not obtain any valid information from your experiment.

Please follow the links below to read publications where MST (MicroScale Thermophoresis) has been used to investigate protein binding to Ca2+. MST is an easy, fast and precise method to quantify interactions between and (bio)molecules over a broad range of binding affinities.

Dear one,

I hope you will get some information about your search , in the file attached.

Good luck

I may not have the answer to your question, but maybe you want to check the CRC Handbook of Chemistry and Physics. Its older editions are available free of charge on the internet. Just look for "Physical Constants of Inorganic Compounds", this will lead you to the corresponding chapter of this book. There you should find a large list with all kinds of inorganic compounds, including various zinc salts. Solubility (in organic solvents) is listed in the last column.

Hope this helps!

Hi Elena, I will try to discuss this further with you privately. Thanks alot for your answer....

Thank you Prof. Saeideh Hosseini, but I want to dissolve water-insoluble Schiff's bases; so any suggestion will be welcome.

If you want to determine the binding constants by spectroscopic titration, it is not necessary to have the same concentration of each complex species. For determination of DNA-complex binding constant, it is important to keep constant concentration of tested complex in the way that successive adding of μL volumes of DNA solution does not change the volume of tested complex.

Once leaf samples are removed from the plant, the elements in them won't leave the tissue unless leaf sap is coming out, or something degrades the tissue (fungus, insects etc). If frozen at -80C, the leaf samples are fine untill defrosted. If oven dried at +80C they will be suitable once they reach constant weight (ie no more water left in tissue).

To prepare samples for flame photometry, I would suggest oven drying (+80C), grinding to a homogenous powder and acid digesting (or at least dissolving/leaching in acid eg 4% HNO3). As well as calibration solutions (ie. more than one), prepare blanks and a solution of known concentration and if possible, a reference material of known Na and K concentration as well. Test the known concentration solution regularly through the run. A colleague of mine once spent months working with a flame photometer that had drift issues of 10-20% over several hours of use, and a distinctly non-linear response. Eventually he got it working well, but it had provided much data for many previous studies that we have severe doubts about now.

Cisplatin causes intrastrand as well as interstrand linkages and cause bends in DNA. In the same vein, I would assume that it is possible to form intrastrand linkages as well as interstrand linkages with your compound. I am curious as to how big your molecule is and if its dimensions exceed the width of the DNA molecule.

Send me the structure of your complex and then I will work on it.

Yours

Taibi

I hope this link "http://www.mdpi.com/2073-4360/3/4/1575/xml" will be useful for you.

The short answer is that 'oxidation states' are simply a formalism that do not really describe reality very well. They are just the numbers you get by adding up the charges you predict for an atom if:

1) you consider only the electronegativities of the individual atoms

2) all bonding is only ionic

Both of these assumptions miss significant effects. For (1) the electron density on an atom certainly is affected by what its bound to. For (2) it is pretty clear that chemical bonds are never only ionic in character (even Cs-F has some small amount of covalency)

Essentially, oxidation states are just used as an accounting tool to keep track of electrons and should not be taken too seriously as descriptions of reality.

If you do wish to have a good understanding of the bonding in molecules then MO theory is really what you need to use.

Yes it is related to solvent. Assuming your buffer is in water which may rinse out the deposited metal complex on the paper ( as it is also water soluble ) one has to use metal complexes which are not soluble in water. This can be done by changing the peripheral core of the ligand used by introducing hydrophobic groups or if the complex is ionic then one can use bulky cation ( or anion ) to precipitate out the desired complex. Introduction of such counter ion would lead the complex soluble in organic solvent but will not be soluble in water. Once this is achieved, one can get the desired solution of the complex in organic solvent and can strip of Whatman filter may be dipped into it and then dried. Now in aqueous buffer the deposited complex will not be leached out.

However, there should be some ability of the complex to interact in aqeous solvent so as to respond in a reaction once deeped into buffer. Knowing the nature of the complex and  what for it is to be used as strip in buffer a better suggestion may be provided.

If you want to determine if the complex structure in solution is roughly the same as in the solid state you could maybe do mass spectroscopy to check what complexes you have in solution. Also, assuming you have Cu(II) complexes, you could do EPR in solid powdered samples and solution. If you have approximately the same EPR parameters in both cases the structure is probably maintained. Keep in mind that in the solid state inter molecular magnetic interactions cause a series of broadenings AND narrowings of signals making it harder to extract the isolated complexes EPR parameters.

You need to measure the temperature dependence of your Mn2-spectra.  Collect the same spectra at temperatures ranging from 2-50K.  It depends on how your Mn-dimer is bridged, but coupling energies > ~3 cm-1 will result in resolved spin-manifolds and thus temperature dependent features.  Weak couplings (J < 1 cm-1) are difficult to resolve, but given the EPR spectra shown, I suspect your couplings are larger.  As the temperature changes, the Boltzmann population distribution for each spin-manifold (S=0, 1, 2, 3, 4 and 5) will change.  The exchange coupling can be determined by fitting the temperature-normalized signal intensity (SxT) versus temperature (T) to a the appropriate Boltzmann distribution function.  

The best way to do it:

P U R I F I C A T I O N  O F  L A B O R A T O R Y  C H E M I C A L S.

Fourth Edition. Armarego and Perrin.

Page:347

Dried with CaS04, 4A molecular sieves, CaH2, KOH, or K2C03, then distd, either alone or from BaO, sodium, P2O5 or CaH2.

Thank you Kyle.. it would help me a lot

Not very likely according to a very recent, high quality study (see below).

The opposite NMR signal shifts seem common in coordination compounds because of the electron density shifts from one atom to another upon complexation. Let's take platinum-dach-tu complex as an example where dach = 1,2-diaminocyclohexan and tu =  thiourea [(NH₂)₂-C=S]. After the formation of the Pt-S coordinate covalent bond, there will be an electron density shift from sulfur to platinum, so the bond strength of the sulfur-carbon double bond (S=C) is weakened. Concomitantly, the electron density shifts from nitrogen to carbon. Therefore, the electron density on the nitrogen atom decreases while the electron density on the carbon atom increases. The 1H signals shift downfield from free tu's 7.12 & 6.91 ppm to 8.30 & 7.90 ppm while the 13C signal shifts upfield from 184 ppm to 176 ppm. For the dach ligand, due to the formation of platinum-sulfur (Pt-S) bond, the stronger trans-labilizing effect of the S atom weakens the platinum-nitrogen (Pt-N) bond. That is, the electron density now shifts from the platinum-nitrogen (Pt-N) bond to the amino nitrogen, leading to an increase in electron density on this nitrogen. Therefore, protons’ signals on this nitrogen are shifted upfield from 7.12 & 6.91 ppm to 5.84 & 4.89 ppm. I do not know the details of your complexes. However, if you consider the electron density shift in the bond(s), you should be able to explain the opposite NMR signal shifts.

Cu is a common contaminant in HNO3 and H2O2 that you are likely to use for protein digestion so the correct choice of reagents is critical. For example, Fluka Trace Select H2O2 is both relatively inexpensive and very low in Cu (<0.05ppb). Cleanness of the instrument before analysis will also play an important role. It should be possible to achieve the limits of qunatification for Cu at 0.02-0.05 ppb using trace analysis grade chemical in a typical chemical laboratory (without clean air facility). Typical interferences will be from Na and Mg in the matrix and collision cell will reduce those, however, looking at both 63 and 65 Cu and monitoring Na and Mg is recommended.

When participating (successfully) in ring analyses for interlaboratory tests on metals in PA containing waste material we used an aqua regia digestion. On the one side a total metal extraction can be achieved. On the other side, PA is partially disintegrated under these conditions and organics are transferred to the extract also, at least in traces. Organics will change the characteristics of the plasma totally, and your extract is not comparable to the standard solution; you will not get reliable results.

Procedure: The material was shredded as fine as possible and treated with a.r. in covered (watch glass) quartz crucibles for about 12 hours at about 90 º C. In order to destroy the organics, we added HNO3 (1 N) to the nearly evaporated a.r. digest and, after filtering, HNO3 (65 %; 7 mL) and HClO4 (100 %) 2 mL) were added. The solution was slowly evaporated on a heating plate to dryness, starting with about 90 º C, ending with about 200 º C (quartz crucibles). Evaporation after adding HNO3 and HClO4 was repeated and finally the digest was taken up in HNO3 (1 N) for analysis. Blinds were included.

If you think, your lab furnace is not too sensitive on fumes and smokes and you do not consider volatile elements, the proposal of C. Harrington is a viable alternative.

In any case, to be on the safe side I would recommend to check the digest solution on possible matrix interferences by the standard addition method (at least partially) when analyzing by ICP-MS.

I used Chromic acid for most of my oxidative processes.The colour change from orange to green helped me recognize the completion of degradation .Opening of benzene ring /hetrocyclic rings etc. were conveniently done leaving carboxylic acid group groups as terminal

One of the most common method to prepare CT-DNA stock solution is as follow:

1.- dissolve the lyophilized sodium CT-DNA salt in Tris-buffer (NaCl 50 mM, Tris-HCl 5 mM, pH adjusted about 7-7.4 with NaOH 0.5 M).

2.- keep it overnight in fridge

3.- standardize spectrophotometrically the CT-DNA solution by using its known molar absorption coefficient at 260 nm (6600 M-1•cm-1). Is important that the ratio of UV absorbance at 260 and 280 nm, A260/A280, be > 1.8 since it is indicative that the CT-DNA solution is sufficiently free of protein.

4. finally the solution of the CT-DNA can be stored at 4 ºC and used in no more than four days or it can keep frozen until the day of the experiment.

DNA has got a lot of functional groups, which all might act as chelating ligands (basic nitrogens ons the adenine and guanine rings, oxygens on the phosphates and riboses etc.). Their amount is further increased if the DNA is single-stranded. Than again the complex building consants depend on the coordinating atom and the particular metal. If you have for instance Ag+ and Cysteine (an S-ligand) you would have certainly higher affinity than the DNA. If you have something like an alcohol, in the same case (Ag+) your affinity would be way lover. You have to take all the factors under consideration.

I don't think you would be able to obtain guanine-N3 oxide without side products. You might have to use some enzymatic reactions (with such selectivities as Xanthine-Oxidase or the opposite ones).

The red-brown colour you had to start with is clearly the iron(III) complex. The green colour, depending on its intensity may be Fe(II), - but this is very unlikely. If the geen colour is intense, then C0(III) co-ordinated to some form of beta-hydroxy carboxylate ligand(cf the intense green colour obsevever when a trace of cobalt chloride is added to a hot mixture of hydogen peroxide and Rochelle's salt solutions) is a strong candidate bearing in mind the traces of bleaches and tartarates which are often present in some grades of both writing and filter paper.

In this case, the difference in size of Cd and Zn, the difference between the effective charges (the screening are different in Cd2+ and Zn2+), and the differences betwen the energy between d-shells of Zn and Cd can play role in this different behaviour toward the same ligand. But only the nature knows the chemistry well, we can find out only some main reasons for this behaviour.

Completely agree

Try a variety of gums

The selective bio-polymer should be compatible with the miscroscopic surface characterstics of the soil to be treated

I am wondering more about things like protein or DNA-nanomaterial complexes and where these might be useful. We have for example used DNA-Nanogold complexes to examine the DNA damage responses to mismatched DNA (DNA conformations in mismatch repair probed in solution by X-ray scattering from gold nanocrystals. Hura GL, et al. Proc Natl Acad Sci U S A. 2013 Oct 22;110(43):17308-13. doi: 10.1073/pnas.1308595110 ), but I'm sure there must be lots of this and of differing uses that would be of general interest. I would like to hear what others are doing and where this is making novel and useful materials.

Cu ion sites are usually held by folded domains with histidines and cysteines being common ligands. Cu ions usually have 4 to 6 ligands with geometries such as distorted tetrahedical, square planer, and octahedral. You can check for copper proteins in the Protein data bank - http://www.rcsb.org/pdb/home/home.do - or web sites such as MetLigDB ((http://silver.sejong.ac.kr/MetLigDB). Search copper on the Protein Databank bring up over 1500 solutions with beta structure proteins being most common structure and oxidoreductases being the most common activity class.

I've just meant that you should put less reagent into a constant volume of solvent befor e cooling. Or you should cool on a smaller number of degrees. You can't completely avoid getting polycrystals but you can decrease number of them. Also if you need to get big monocrystals you could try using crystallizing dish. But it always depends on crystals which you are going to get.

It might be a little late to answer this question. But here goes. Yes, it can be done and I have done it. The difficulty being with the number different metal centres (in the different complexes), type and number of ligands and also the kinetic and thermodynamic stability.

I agree with comment Toka Swa.

The results of most studies show that the antimicrobial activity of the complexes is higher than related ligand. The increased activity of the metal complexes can be explained on the basis of chelation theory. Chelation reduces the polarity of the metal ion, because positive charges of the metal are partially shared with the donor atoms present in the ligands and there may be π-electron delocalization over the whole chelation. This phenomenon increases the lipophilic character of the

metal chelate and favors its permeation more efficiently through the lipoid layer of the microorganism, thus destroying them more forcefully. The other factors like solubility, conductivity and bond length between the metal and ligand also increase the activity.

Any amino-function (H2N-R) can be protonated forming a cation H3N(+)-R. As mentioned by Edward Sandy, amino acids or proteins are very abundant and many of the amino functions in these molecules are protonated and can thus serve as cations. To tell the full truth: an amino acid H2N-CR2-COOH under normal pH conditions will be in part present as zwitter ion: H3N(+)-CR2-COO(-) only under very acidic conditions (which are not very relevant for real biological systems) amino acids will be protonated: NH3(+)-CR2-COOH. However, already the zwitter ionic forms provide a huge amount of cations (and anions at the same time - of course).

The role of these cations lies mainly in the formation of H-bonds and thus contributing to the structure of enzymes (which determines their function!)

I think it is for the 3 hydrogen bond forming centre as well as the ability to form the square planar structure(guanine tetrad) via Hoogsten base pair formation .Which give stability to the system

For fixing carbon dioxide nature adopts non transitionmetals first like zinc in bacteriochlorohyll but considering the pH of the reaction condition laterit has been replaced by magnesium. It is the photo excitation of the chlorophyll moiety with the reasy release of electron to be used for regeneration of NADPH etc and the chlrophyl radical should be stable enough to receive electron from say PSII for the regeneration of PSI . It is the non -transition metal like Zn or Mg which do not have own redox property and so these are used only to tune the light absorption property. Any transition mretal in this case would have participated to react with the radical cation leading to structural modification of the macromolecule.. For hemoglobin to carry oxygen which is paramagentic and only high spin Fe(II) with four unpaired electron fits well to create diamagnetic oxygenated hemoglobin ready for delivering the oxygen to the tissue via myoglobin ( similar chemistry). No other 3d transition metal ion in bivalent state can interact with molecular oxygen on complexation with heme group to behave in such reversible manner with the least involvement of oxidation of the Fe(II) to Fe(III). The 4d or 5d metals are large to fit in heme group to get very stable metal -heme complex which in turn with globin made even more stable Fe-hemoglobin. This could be a preliminary answer to your queris.

S. Sarkar

Chemistry,

IIT Kanpur