Supramolecular Chemistry - Science topic

Dear all, the following documents deal with the different techniques to characterize supramolecular polymers. My Regards

Daer Rejomon, thank you for this important technical question which is certainly of significant interest to many other RG members as well. For some general information on inorganic supramolecular chemistry you can easily search the "Publications" section of RG. Just search for the term "inorganic supramolecular chemistry" and then click on "Publications". This will provide you with a long list of references on this topic which have been posted on RG, many of the even as public full texts.

For some typical freely accessible articles please see e.g. the following RG links:

Please not that this is just a small selection of useful references. There are many others. Good luck with your work and best wishes, Frank Edelmann

What exactly do you need, Dr. George! Would you please elaborate. Are you looking just for few reviews on the topic?!

Bijit Chowdhury Deconvolution of a composite peak into its individual peaks plays an important role in the interpretation of many types of graphs including XRD, XPS, FTIR, and PL etc. In this video, I have discussed how to deconvolute simple combined peaks, composite peaks and how to correct missing data in a given peak with the help of deconvolution. In the case you want to further ask about it, please do comment on the specific video, I'll respond to it shortly. I have provided the practice files (OriginLab) here. Thanks

Dear Apramita Chand , you can use diamond software for a better look of your crystal packing. It gives a nice color and shining to individual atoms. You can look from 100, 010 or 001 planes etc. Alternatively you can use Mercury also. You can see the crystal packing here in below articles.

Each approach has its advantages and dis advantages. I think your question can be a topic for aresearch project or a postgraduate thesis. It will make a weighting scale for both approaches and provide the best for the researchers according to their local environment.

Nice to hear from you, Elisabeth.

@sci-hub.tw/

Hi Ahmed, difficult question.

Are you working with multi-walled or single-walled CNT's? Do you know the CNT diameter or length? Does it affect the binding?

Fluorescence is a problem since it is not quantitative.

Can you turn the question around and immobilize your compound and see what CNTs bind to it?

Thank you Anthuan

Mr. Zhou,

Please pay attention to the attachment.

@Valery V Gorbatchuk Thank you for your valuable inputs.

1. Make a list of all possible hydrogen bonds.

2. Calculate distances and angles for all possible hydrogen bonds for each frame.

3. Determine the presence/absence of each hydrogen bond in every frame using cutoff values for the distances and angles.

4. Statistics, plots . . . 

The main (stereochemical) examples for complexes having coordination number 7 are: pentagonal bipyramidal, capped octahedral and capped trigonal prismatic. But, the energy difference between these structures is often small, and hence a priory prediction of the geometry of a particular complex tends to be unreliable; the number of counter ions and the specific stereochemcal requirements of chelating ligands can have an influence difficult to predict beforehand.

 The equations of the chemistry behind are shown in the files that I attached to my first comment.

You should use desorption data for that reason.

The direct approach is to calculate the energy of each molecule separately (after optimization) in independent calculations, and then to calculate the difference between the energy of the combined system and the sum of the two molecules on their own.  We did something similar for just amine, copper sulfate and silica here:

http://dx.doi.org/10.1039/C2CP22539E 

May be the attached article can help you

Best regards,

Pedro

Yes, you would have to take it into account!

I usually go by the inverse susceptibility. It should be proportional to the temperature (which is easily checked) and you can get the (squared) effective moment from the slope. In such a plot the paramagnetic Curie-Weiss temperature corresponds just to a horizontal displacement of the curve and not a fit parameter since that does not affect the slope. Nevertheless you can read it off directly from the intersect of the straight with the temperature axis!.

Dear Jyoti,

There are four different methods to determine the permeability of metal ions such as  Ca ⁺⁺ or Mg⁺⁺ through membranes:

A number of chelators of divalent cations have different fluorescence spectra in the bound and unbound states. Chelators for Ca²⁺ are well established, have high affinity for the cation, and low interference from other ions. Mg²⁺ chelators lag behind and the major fluorescence dye for Mg²⁺ (mag-fura 2) actually has a higher affinity for Ca²⁺.This limits the application of this dye to cell types where the resting level of Ca²⁺ is < 1 μM and does not vary with the experimental conditions under which Mg²⁺ is to be measured. Recently, Otten et al. (2001) have described work into a new class of compounds that may prove more useful, having significantly better binding affinities for Mg²⁺.The use of the fluorescent dyes is limited to measuring the free Mg²⁺. If the ion concentration is buffered by the cell by chelation or removal to subcellular compartments, the measured rate of uptake will give only minimum values of k_m and V_max.

First, ion-specific microelectrodes can be used to measure the internal free ion concentration of cells and organelles. The major advantages are that readings can be made from cells over relatively long periods of time, and that unlike dyes very little extra ion buffering capacity is added to the cells.

Second, the technique of two-electrode voltage-clamp allows the direct measurement of the ion flux across the membrane of a cell. The membrane is held at an electric potential and the responding current is measured. All ions passing across the membrane contribute to the measured current.

Third, the technique of patch-clamp uses isolated sections of natural or artificial membrane in much the same manner as voltage-clamp but without the secondary effects of a cellular system. Under ideal conditions the conductance of individual channels can be quantified. This methodology gives the most direct measurement of the action of ion channels.

Maguire, M.E.; Cowan, J. A. (2002). "Magnesium chemistry and biochemistry". BioMetals 15 (3): 203–210. 

Tevelev, A.; Cowan, J. A. (1995). J.A. Cowan, ed. Metal substitution as a probe of the biological chemistry of magnesium ion. The Biological Chemistry of Magnesium (New York: VCH).

Drakenberg, T. (1995). J. A. Cowan, ed. Physical methods for studying the biological chemistry of magnesium. The Biological Chenistry of Magnesium (New York: VCH).

Raju, B.; Murphy, E.; Levy, L. A.; Hall, R. D.; London, R. E. (1989). "A fluorescent indicator for measuring cytosolic free magnesium". Am J Physiol Cell Physiol 256: C540–548.

Grubbs, R. D. (2002). "Intracellular magnesium and magnesium buffering". BioMetals 15 (3): 251–259.

Otten, P.A.; London, R.E.; Levy, L. A. (2001). "4-Oxo-4H-quinolizine-3-carboxylic acids as Mg2+ selective, fluorescent indicators". Bioconjugate Chemistry 12 (2): 203–212. 

Gunzel, D.; Schlue, W.-R. (2002). "Determination of [Mg2+]i - an update on the use of Mg2+-selective electrodes". BioMetals 15 (3): 237–249. 

Hille, B. (1992). "2". Ionic channels of excitable membranes. Sunderland: Sinauer Associates Inc. ISBN 0-87893-322-0.

Dean, J.R. (1997). Atomic Absorption and Plasma Spectroscopy. Chichester: John Wiley & Sons. ISBN 0-471-97255-X. for descriptions of the methodology as applied to analytical chemistry.

Hoping this will be helpful,

Rafik

In the acidic conditions (HBr/HOAc) whats happening is a protonation of the Lewis basic oxygens. This opens the door to carbocation formation in order to stabilise the charge on the oxygen, which is then evidenced by the breaking of the C-O bond, both in the ethereal and in the alcoholic moieties. If you don't mind stereoinversion from alcohol to alkyl halide  you can try PPh₃/hexabromoacetone, or PPh₃/CBr₄. It's pretty well-known that PBr₃ should be able to convert your alcohol to a bromide without cleaving the ether. Maybe you're using too high a temperature.

Please refer to my publication: 

For a simple estimation I'd rather calculate diffusion coefficient from viscosity and radiuses, and then used it to calculate collisions.

Mr. Kumar,

What kind advise you neer - about the softwares, methods?

For slower reactions a fiber optic UV-vis such as the ones from Ocean Optics can be used to collect UV-vis spectra in real time as you irradiate your sample.  Depending on your settings you can collect spectra about once a second.

Dear Fatima Lucio,

Compounds with maximum atom number of  60-70 can DFT handle. Your compound is huge. Your job which was submitted to G09 crashed because of the length of your compound which needs a huge memory.  There is NO way that you can optimize this large molecule with DFT or ab initio methods.

You can optimize your compound by molecular mechanics methods (MM2 and etc), or you can try to optimize it with semi-empirical method such as AM1 or PM3.

Hoping this will be helpful,

Rafik

J-aggregates: is bathochromic shift  i.e. red-shift in absorption because of pi-pi stacking of aromatic molecules, in which molecule orient in head-to-tail fashion. Which is completely opposite to H-type aggregates (blue-shift in absorption, side-by-side stacks within the assembly. Hope it helps.

Dear Huang Xue,

D-R equation was developed 50 years ago for the determination of micropore volume and thereby surface area of micrporous carbons. This equation is based on the theory of volume filling of micropores. On the other hand, DA equation was primerily developed for zeolites. Actually, the D-A equation is equal to the D-R equation when the heterogeneity parameter, n, is equal to 2.

Attached please find a file describing the source of each of the two equations and the relationship between them.

Hoping this will be helpful,

Rafik

Dear Alireza,

To my knowledge, there is no way since to abstract a hydrogen from the alkyl chain of ether is not feasible.

rafik

I would also try the method proposed by Paramita. [Ni(DMG)2] is a very stable complex and additionally drops out of solution if a suitable pH and ionicity of the aqueous is adjusted. And please, Saikat, tell us if and how it worked!

Details?

Are you sure it's photoactive?

I know nothing on NH-Pi.

Dear Parsa,

Abstract. This paper provides an overview of the most up-to-date information available relating to chitin nanowhiskers. This paper presents aspects about chitin nanowhiskers, including methods of extraction and preparation, chemical modification and applications. Chitin nanowhiskers can be obtained by hydrochloric acid hydrolysis, TEMPO-mediated oxidation, partial deacetylation with NaOH by fibril surface cationization, ultrasonication, electrospinning, aqueous

counter collision treatment, a simple grinding treatment and gelation with 1-allyl-3- methylimidazolium bromide. An introduction into the methods used to prepare chitin nanowhiskers is given. The chitin nanowhiskers applications are used mainly as reinforcing polymer nanocomposites, but also to prepare scaffolds, hydrogels and wound dressings, as adsorbents in industry, water purification, for protein immobilization, transformation of bacteria by exogenous genes, stabilization of oil-in-water emulsion and nematic gels, formation of CaCO3 /chitin-whisker

hybrids and as carbon precursors.

Hoping this will be helpful,

Rafik

Here are a few things you can try:

Also attached are a few general hints on what may be of interest/use to you. Good luck!

That is one massive cavity you're after! None of the usual macrocycles will do. Most likely you'll have to design it and synthesize it yourself. 

Synthesis of a macrocyclic porphyrin hexamer with a nanometer-sized cavity as a model for the light-harvesting arrays of purple bacteria

Tetrahedron Letters (1999), 40, (48), 8347-8350.

Good luck!

Hi,

water:THF cluster are probably not so easy to model with TDDFT. The larger the cluster gets, the more problem you will get with spurious charge-transfer states. The RI-CC2 or RI-ADC(2) approaches might be more suitable methods for such problems.

Cheers,

Arnim

After i smoothed my XRPD data using the savitky-golay smoothing function in The Unsrambler X, i tested the correlation optimized warping algorithm (The Unscrambler X) for my XRPD data and it was able to improve my model performance so maybe this would also be an option.

Synthesis of 4-formylbenzo 15 crown 5 can be synthesized by Duff reaction using hexamine and trifluro acetic acid. You can insert CHO group directly in the benzene ring ..

THANKS

Are you sure you have a correct way of detection? Could it be that your substance absorbs insufficiently in UV? What is your HPLC column, is it the same C18?

Dear Ali

If you draw your molecule and do its study using computational chemistry software's like Gaussain , Turbomole etc it would be a gas phase calculation which may not necessarily match with the solid state structure of your compound and the calculations would not be correct for their results. However  if you have crystal structure of your compound then you can use the crystal coordinates to open the depict the structure in Gaussain and do the single point energy calculation (not full optimization) to generate   the checkpoint and output file from which all the physico chemical properties including energy and orbital contours and spectra can be obtained. From the Time Dependent Density Functional theory the transitions etc can also be worked out.

Hope it answers the question f

ya, this video is really complete about dispersion interaction , thanks a lot!!

you can do nanoindentation, see the article

I tried my best to find an article to answer your question and this is what i got . I hope you find it useful .

Hello,

there is a better way - run a CIFcheck via IUCr site (http://journals.iucr.org/b/services/authorservices.html), and at the end of listing there will be a form provided for your structure. You can just paste and copy it into your CIF file.

Based on your description, it sounds like Zn and N are drifting apart during optimization. The structure of a molecule in a crystal typically has a large contribution from interaction with neighboring unit cells. When you pluck a molecule out of that environment and do an isolated optimization, bad things could happen. Peyghan's suggestion of freezing all atoms will take care of this but that may not give you what you are after. If the goal is to compare calculated vs. experimental structure of the molecule IN the crystalline state, you may have to resort to periodic boundary condition calculations.  Alternately, you could freeze the distance between the two Zn atoms (or apply other minimal constraints of this type) and let the rest of the molecule relax. 

Zhichang, the cetyl part is enough hydrophobic for the complexation, but betaCD does not prefer the alkyl chains. AlphaCD would be better but I am almost sure that will not form (enough) insoluble complex.

 I am almost sure also, that after a tedious preparation of heparin somebody does not want to infect the sample with another ion.

 The controlled ionexchange might be the right way: wash very well the strong cationic ionexchanger (in H+ from, of course) then stir the concentrated solution of the impure heparin and check periodically the CTAB conc. Because the heparin in solution might be ionized it is not sure that the CTAB+ will attach first to the ionexchanger. I would remove first the bromide also (with e.g. Ag2O) to prevent the solution to be too acidic.

I don't follow the body of your question, but in response to the title. The interaction of a dendrimer with a drug may cause confinement of the drug within the dendrimer, forcing it into a smaller number of conformations, therefore inducing an entropic penalty. And the dendrimer is less able to move while interacting with the drug, also giving an entropic penalty.

There are also likely to be solvent effects, for example if water is displaced from the dendrimer by the drug, into the bulk solvent, this might well be entropically favourable.

Hi, Yin. To answer your question requires more information. Your experiment should be discussed in quantitative terms to make a conclusion on a cause for the observed effect. Terms like "more", "less", etc do not work here at all. Just read a good quality research paper (experimental section) to see what type of data is usually provided. In your case, it would be helpful to know experimental conditions, like concentrations of components, their spectra, instrument settings, how you conduct the experiment, etc. After this, it would be possible to conclude whether the observed effect is due to interaction between compounds or it is an artifact, error, or something else.

Dear friend, very interesting question.

However, the easiest way is searching the related document by typing the keywords into google scholar. You will find some related articles.

If yet to find the articles, do not hesitate to let me know. InsyaALLAH I will help you in detail.

Good luck. Dr Zol Bahri - Universiti Malaysia Perlis

Yes, it should work. The mesurament cell should be filled correctly for limiting errors, and the chamber should be flushed with He many times to desorb moisture (if any).

Alain

Dear Dr Oleg,

Thanks for your kind support.

'Your system is ion-pair system: two cations Me4N+, HF2-, and an anion': its correct absolutely.

Let me try with ur valuable suggestions.

Soon, I will get back to you with results.

Thanks,

Bye!

PG

Thank you for your valuable information.

I wish you a happy, healthy and prosperous new year.

Thanking you 

Dear Kamyar Khoshnevisan ,

Thank you very much for you reply. I will check the methods you suppose. By the way, Can we measure it by electrochemical way?

Q800 can be programmed to perform multiple steps: 1. Deform the shape memory material by heating while it is under a force or deformed to a desired amount. 2. Cool without removing the force or deformation. 3. Remove the force and allow the material to recover and equilibrate for a relatively long time at the low temperature. 4. Heat the material the same as for step 1, except without any imparted force or deformation. The material should recover from its locked-in shape memory deformation and the stored stress can be measured. 

I use TA Instruments DMA Q800 frequently and for many test types and combinations using the custom settings. I hope that the steps shown are consistent with what you want to do. Equilibration in step 3 will be important because you will then only measure the shape memory effect and not normal recovery with time at ambient temperature.

Thank you, Prof-Dr Abdel-Raheem. According to Hans Selye, at page 264 of his book "Thrombohemorrhagic Phenomena" (1966), Hauss, et al (1962) and Emmrich et al (1964) theorized that the universal nonspecific mesenchymal reaction was the Sanarelli-Shwartzman phenomenon. According to Selye, "[T]his response was indicative of an "acceleration of mesenchymal metabolism". Thank you for sharing the link to the 1962 article. I'm very interested in this topic. Please let me know, if you'd like to discuss this further, perhaps by email.

Hauss, W.H., Junge-Hülsing, G. and Holländer, H.J. (1962). Changes in metabolism of connective tissue associated with ageing and arterio- or atherosclerosis. Journal of atherosclerosis research, 2, 50-61.

Hauss, W.H., Gerlach, U., Junge-Hülsing, G., Themann, H. and Wirth, W. (1969). STUDIES ON THE “NONSPECIFIC MESENCHYMAL REACTION” AND THE 1TRANSIT ZONE” IN MYOCARDIAL LESIONS AND ATHEROSCLEROSIS. Annals of the New York Academy of Sciences, 156, 207-218.

You can do Absorption Correction of your crystal data directly by using software which  already installed in single crystal X-ray diffraction (SCXRD) instrument. Which company SXCRD are you using?  

i only have access to public site of rsc http://pubs.rsc.org/ and the search of your name gives no results back. could you please provide more infos? (tilel, abstract or upload the paper(s)?) thanks a lot

if you are measuring the scattering from particles then the anisotropy should be 1 ideally, that is true - I misunderstood and thought you were measuring on labelled spheres (to e.g. slow down rotational diffusion)

anisotropy loss from FRET would typically appear as an artifact one wishes to avoid due to the difficulty in extracting quantitative data from this effect. It appears quite often in over-labeled proteins for instance, so that is a good place to start. Try for instance searching for anisotropy loss and labeling ratio in proteins

one recent example: http://www.sciencedirect.com/science/article/pii/S0006349514002264

otherwise, there should be sections dealing with this (with appropriate references) in the books of both Lakowicz and Valeur

Check your structure

And remove all the keywords

put everything in default and give command to run

all the best 

Fr.Xavier

As I understand it a non-trivial problem. See IUPAC report in Pure and Applied Chemistry 2011 and the not-yet reported IUPAC project "Guidelines for Measurement of Luminescence Spectra and Quantum Yields of Inorganic Compounds, Metal Complexes and Materials"

Indeed, don't bother with chromatography; it should be easy to recrystallize. Or perhaps simple precipitation is sufficient? Did you wash with acid? did you get a solid or an oily material after removal of the solvent?

I recommend water with some trepidation, as i find it hard to gauge the stability of the pivalate ester. Often, these electron poor phenolates are somewhat reactive.

The Alerts from cif check are not always meant to be correctable or unavoidable depending on your crystal.  The Alerts are there for you to be aware of possible problems with the structure.  They are meant to be understood and addressed if possible and then to be explained when they are unavoidable.  The THETM01_ALERT_3_A alert might be that your crystals do not diffract to high angles and may never diffract to high angles no matter how many crystals you try because of extreme disorder in the lattice that causes too much deconstructive interference.  Materials such as some MOF's often have poor diffraction at high angles and so you may not have integrated to the preferred resolution of 0.83 angstroms, but instead to 1 angstrom because that is the best data you can obtain.  The PLAT029 alert is because Acta prefers that you have collected at least 95% of the data.  Here you only have 93.5% of the data.  Is it because you did not collect a full data set or because reflections are missing from the high angle data because they were too weak to be counted?  Is this situation avoidable with another data collection or is 93.5% of the possible data enough to refine a chemically relevant crystal structure for the purposes in which you intend to use it? The PLAT 043 and 051 alerts have to do with the reported formula either it is wrong or your formula is correct but not all the atoms are represented in the structure model.  This could happen because you included solvate molecule in the formula, but "squeezed" them from the structure. 

Dear Nagapradeep N.,

From my experience on TGA, the small increment of mass of your sample that you are observing at these temperatures is the Archimedes effect. When you hang an object in a fluid, the fluid tends to force the object upwards. Before you start your TGA analysis, you put your sample in the analyzer and the fluid (N2) force the sample upwards. It is when you tare your analyzer. When the analysis starts, the density of the fuild is sligthly decreased (by increasing the temperature) and consequently the hanged sample goes down. Then you record these changes as mass increment but they are produced by a small change in the density of the sourrounding fluid. You should observe the same effect with an inert sample (a piece of glass?) and same temperature program. This effect is worse at higher heating rates.

I hope this explanation could help you.

Extraction with 1 M HCl is easiest

A mystery is solved, it is (very nicely written indeed!) article of Joel Bernstein from Crystal Growth & Design's virtual special issue in honor of our great guru G. R. Desiraju :)

Hi Lucas

Thank you for your reply. I would be very much interested in starting some collaborative projects aimed to test your glass micromachined microchip on our pharma/food applications.

Could you please provide me an e-mail contact to stay in touch more directly ?

Bye for now

Claudio

VERY interesting question! IMO, the key point relates to H-bond cooperativity and quantum (phase) coherence of interfacial water. These are central tenets of the exogenous interfacial water stress (EIWS) theory of inflammation and disease. The vast majority of biological water is interfacial water. I suggest looking carefully at the experimental detail provided in the papers by Luc Montagnier and Jacques Benveniste. Water memory is no longer conjecture. The detailed mechanism of homeopathic "imprinting" is provable. Succusion is not the only way to "imprint" vicinal water, but it probably has the longest history behind it.

The stabililty constants of cyclodextrin inclusion compounds are usually low, Please make sure the inclusion compound is stable on water first.

the easiest way is mixing CuSO4 and sodium ascorbate (0.15 eq: 0.45 eq respectively) in water and adding the resultant solution to the mixture of the alkyne and azide in dichloromethane. Normally this procedure works well in most cases... but in some cases you need to use more complex ligands of Cu. Good luck

I used to take phospholipids dissolved in ether and shoot them into warm water with a syringe which gave vesicles by EM observation.

take propargyl alcohol and sodium hydride in 1:1.2 mole ratio in dry THF solventat at zero degrees Celsius. stir the reaction mixture for 1 hour. Add alkyl bromide dropwise to the mixture for half-an-hour through syringe at room temp. stir the reaction mixture for 24 hrs. add dist. water (equal amount to THF) to quench the reaction.Add diethyl ether to the reaction mixture. collect upper layer of diethyl ether and evaporate solvent. collect the product.

If your compound is water insoluble, just dissolve it in ether and wash it with water in sep funnel. Seperate the phases, dry with MgSO4, filter and remove the solvent on rotovap.

One other possibility is that your compound is so concentrated that the light is absorbed before it has a chance of reaching the observation volume. Aside from that, there are the various incarnations of self-quenching, as mentioned in the previous answers.

I agree with Conner. When running a chemistry NMR facility, the most common cause of broad lines/aggregation I saw was high sample concentration. If you're primarily interested in 1D 1H data, you can get by with much less than 1mg of sample; simply use more scans to improve your S/N.

Also, why do you need to measure your coupling constants? If you need to determine which 1H's are scalar-coupled to one another, a simple COSY will provide answers even on aggregated samples.

Please see this page:

The occupation number depends on the actual position of the N-atom. The occupation number of a position is its multiplicity divided by the multiplicity of a general position.

Saying the N atom is on a cell axis is not enough. Imagine that the coordinates are (0,0,0) : the multiplicity of that special position is 2, so you divide 2 by 12 and obtain 0.16667 for the N. If the N atom is on (1/2, 0, 0), or any combination of 0 and 1/2, the multiplicity is 6, so the occupation number would be 0.5. Any other position involving the axis would have an occupation number of 1.

One possible application for DNA origami that I was thinking about in early 2011 was to somehow utilize the self-assembling properties of DNA in those experimentally demonstrated DNA-wrapped carbon nanotubes (see here: http://www.nature.com/nature/journal/v460/n7252/full/nature08116.html) to achieve a particular arrangement of carbon nanotubes which has been theoretically predicted to store a high concentration of hydrogen (here: http://onlinelibrary.wiley.com/doi/10.1002/adma.201003669/abstract).

I do not think you can directly correlate the energetic changes measured in melting curves with H-bond strengths. There are a lot of other energetic components involved in the breaking/forming of the double-stranded DNA, which should be even more important than the H-bond (which by the way is in competition with H-bond with solvent molecules!). Hydrophobic, stacking, entropic and ionic effects (polyelectrolyte) are in fact the main contributors to the energetics of the equilibrium.

Perhaps this could help: A. N. Lane, T. C. Jenkins, Q. Rev. Biophys. 2000, 33, 255–306.

These intermolecular forces also include hydrogen bonding as HF exists as dimer, water shows an exceptional high melting and boiling point so does sulphuric acid, Or the comparison of the basic nature of ammonia and phosphine and their stability.