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Supramolecular Chemistry - Science topic

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A polymer is a substance or material consisting of a very large repeating unit of molecules, or macromolecules, composed of many repeating subunits. For traditional polymers (covalent polymers) we can calculate the number of molecules repeating unit and there is defined molecular weight ( number average and weight average ) and polydispersity which proves that you have formed a polymer. GPC is one of the well-known techniques which tells the molecular weight of the covalent polymer. So for supramolecular polymer, how are people saying this is a polymer. How can we calculate a number of repeating units, molecular weight, and polydispersity etc. what are the techniques or experiments which prove supramolecular polymer is a polymer, not an aggregate or something else?
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Dear all, the following documents deal with the different techniques to characterize supramolecular polymers. My Regards
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Review publications of synthetic strategies for inorganic supermolecules and coordination polymers, molecular polygons and tubes, and molecular polyhedra.
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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:
Supramolecular Chemistry: From Concepts to Applications
Noncovalent interactions in inorganic supramolecular chemistry based in heavy metals. Quantum chemistry point of view
Supramolecular Chemistry
Supramolecular Chemistry in the 3rd Millennium
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
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Diamondoid networks, supramolecular self-assembly caused by ionic interactions-hydrocarbyls, amides, and phosphides.
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What exactly do you need, Dr. George! Would you please elaborate. Are you looking just for few reviews on the topic?!
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Bijit Chowdhury
IACS,Kolkata,700032
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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
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I'm just learning to do packing diagrams for my cocrystal structures and I often get confused. How can I learn properly? Any resources from where I can get help?
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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.
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Now there are two tendencies in the study of soil organic matter: 1) chemical destruction of the SOM by permanganate, alkaline and acid solutions, extraction with cold and hot water, and 2) the use of supramolecular chemistry methods. Which approach is more informative for studying the influence of agrogenic factors (plowing, using organic and mineral fertilizers) on the state of SOM?
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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.
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A few chemists and I would like to study the text by Jonathan Steed on the subject, and I wasn't sure if group discussions/chapter questions would be appropriate to discuss here, or if we should instead use either Facebook or Reddit. Thank you!
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Nice to hear from you, Elisabeth.
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Can anyone suggest online site for downloading chemistry text book and presentations for free? now a days most of the site ask money for getting e book. If possible please give the link for those site...
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@sci-hub.tw/
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I'm interested in supramolecular structures of large pi-molecules on SWNT surface
I'm wonder how to evaluate the molecular presence on the tube surface quantitatively ?
In other words, how to know the number of adsorbed molecules on the tube surface ?
I've tried to measure TGA, but it wasn't reliable measurement in my system
Any other suggestions would be appreciated Thanks in advance
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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?
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I'm trying to find out the binding affinity between the host-guest complex using Mopac. I have only the complexed and uncomplexed files. It would be helpful if someone could explain me with the procedure. 
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Thank you Anthuan
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Like the headings. It is fundamental phenomena that every chemist knows. But what's the origin of it in microscopic level?
Indeed, molecules with CT states can form favourable interactions with polar solvent comparing to apolar solvent. But the solvent needs time to rearrange with the molecules to form interaction after the transition happened. Then how would the CT transition energy in polar solvent get reduced at the first place?
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Mr. Zhou,
Please pay attention to the attachment.
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I have a host-guest solution in an aprotic solvent medium. I suspect that there is a probability of existence of anion- π interaction during host-guest recognition process. What is the simple and best approach to investigate this phenomena if at all it is existing? (I have read several literature where they solve crystal structure, do some computational study and all. I didn't obtain any crystal of host-guest complex.) What may be the best way to approach towards solving this problem.
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@Valery V Gorbatchuk Thank you for your valuable inputs.
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I want to make h-bond analysis to show a formation and movement of an interface between two molecules (protein&RNA).  
The common h-bond analysis gives me only a duration of it's life. But I need time frames, a plot of their durations on the time axis with points of formation and breaking of every bond.
 How can I do this? Help me, please! 
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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 . . . 
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What is the criterion for determmination of the polyhedron for coordination number 7?
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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.
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I recently performed several experiments. The results shown a higher CO2 solubility in Aqeous DEA solution than the pure DEA . If you pleas guide me in this regard.
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 The equations of the chemistry behind are shown in the files that I attached to my first comment.
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Also in case of non-porous silica, if I want to know the pore volume, should the adsorption or desorption values be used for BJH calculation? 
How important is the NLDFT calculation for such compounds (mesoporous silica)?
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You should use desorption data for that reason.
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I have a silica cluster with a amino acid and I have optimized this system while freezing the silica cluster. I have used B3LYP method in G09. Now i need to calculate the adsorption energy between these two molecules. How can I do this?
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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:
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It is my understanding that the observed magnetic susceptibility (Xobs) of a material from SQUID magnetomtery data (MvT) is composed of several components
Xobs = Xpara + Xdia + Xtip
Where the paramagentic contribution (Xpara) is the key part to Curie/Curie Weiss law and for calculating the effective magnetic moment of a material. Thus the Diamagnetic contribution (Xdia) and Temperature independent paramagnetism contribution (Xtip) must be accounted for and subtracted from the Xobs in order to have an accurate description of the unpaired electrons.
The diamagnetic contribution (Xdia) from the electrons in the core orbitals can subtracted from the observed molar susceptibility by calculating from Pascals constants.
It my understanding plotting Xobs vs 1/T of a paramagnetic material will give Xtip as the intercept of the Y-axis i.e. X = C*1/T + Xtip, and thus one can easily subtract and get a nice curie plot and further calculate the effective magnetic moment.
However, I am unsure how to find/subtract the Xtip from an antiferromagnetic (or ferromagnetic for that matter) material without loosing the Weiss Constant (W). Surely if one subtracts the Y intercept then W=0 when we plot 1/Xp vs T.... what is the usual procedure for subtracting this so that one can accurately calculate W and more importantly the effective magnetic moment.....
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May be the attached article can help you
Best regards,
Pedro
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usually one calculates from their SQUID magnetometry MvT data
Ueff = 2.828*SQRT(Xp*T)
Where Ueff is the effective magnetic moment, Xp is the corrected paramagnetic susceptibility, and T is temperature
However do we need account for the Weiss constant also to get the correct result when considering ferro/antiferromagnetic materials?
so 
Ueff = 2.828*SQRT(Xp*(T-weiss constant)
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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!.
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liquid membrane technology
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Dear Jyoti,
There are four different methods to determine the permeability of metal ions such as  Ca ++ or Mg++ through membranes:
1-By fluorescent indicators
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 km and Vmax.
2-By electrophysiology
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.
3-By radioactive isotopes
4-By absorption spectroscopy
References:
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
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I have tried with those brominating agents-PBR3, Br2/PPh3,HBr-acetic acid
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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.
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Could not find enough information about cyclodextrine interaction with cholesterol. What are the concentrations and ratio of the components?
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Dear all,
I was wondering if  there is any software able to estimate the number of collisions of two reactants (A and B) in solution from basic parameters such as: hydrodynamic radius of A and B, the solvent viscosity, the temperature, concentration of A, concentration of B, etc.
Many thanks for your help
Best regards
Vicente
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For a simple estimation I'd rather calculate diffusion coefficient from viscosity and radiuses, and then used it to calculate collisions.
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Dear Researchers, I have done the optimization of one charge transfer complex and want to do their interaction with DNA  theoretically. Kindly help me in this regard.
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Mr. Kumar,
What kind advise you neer - about the softwares, methods?
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Dear all,
I would like to ask your advice to measure accurate reaction kinetics of as photochemical reaction using UV-Vis radiation.
My concern is to have a constant an reproducible source of UV-Vis radiation in order to compare the different kinetic studies and also to keep the temperature constant and controlled (I have used a 40W lamp for initial tests to irradiate an NMR tube and I found that the sample was slightly heated up).
I would perform these experiments preparing the reaction mixture in NMR tubes or UV-Vis cuvettes, then irradiate them with the light source and then measure the NMR or UV-Vis at different irradiation times.
There is any commercial device for this kind of experimental set-up?
Many thanks for your advice
Best regards
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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.
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Hello everybody:
I am trying to optimize a big structure (348 atoms including: N, S, O, Cl, P, C, H and Pd). I started with a crystal structure and I preoptimized it using: b3lyp/3-21g. Once I have this as input, I tried to optimize using b3lyp/ 6-31g(d) for non metallic atoms and lanl2dz (with an ECP) for the Pd. My route line is: opt b3lyp/gen geom=check pseudo=cards.
When I send the structure to g09, the program takes the structure information of the chk and then it ends with the message:
FoFCou: FMM=F IPFlag= 0 FMFlag= 100000 FMFlg1= 2001
NFxFlg= 0 DoJE=T BraDBF=F KetDBF=T FulRan=T
wScrn= 0.000000 ICntrl= 500 IOpCl= 0 I1Cent= 200000004 NGrid= 0
NMat0= 1 NMatS0= 1 NMatT0= 0 NMatD0= 1 NMtDS0= 0 NMtDT0= 0
Petite list used in FoFCou.
Requested convergence on RMS density matrix=1.00D-08 within 128 cycles.
Requested convergence on MAX density matrix=1.00D-06.
Requested convergence on energy=1.00D-06.
No special actions if energy rises.
Defaulting to unpruned grid for atomic number 46.
Defaulting to unpruned grid for atomic number 46.
Defaulting to unpruned grid for atomic number 46.
Which I do not understand because the error is not specified. Moreover, I have checked the memmory consumed and it is less than the one I asked for. Other thing that happens is that I look for the convergence criteria (the four YES or NO) in the log file and there is none.
I think one of the solutions could be trying to optimize at a higher level of theory than 3-21 but lower than 6-31g(d)/lanldz, however I do not know which one would be appropiated. 
Thank you very much for your help.
 
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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
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What is J-aggregates in the synthesizes of luminophores?
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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.
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i have used carbon dioxide to detect the micropores of material, however, the result of DR and DA equation are quite different, what causes these results?
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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
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i wan to functionalize the 12-crown-4  by hydroxyl group .how can i functionalize ??
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Dear Alireza,
To my knowledge, there is no way since to abstract a hydrogen from the alkyl chain of ether is not feasible.
rafik
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How I will get Nickel free ligand from a six coordinated Ni(II) complex ? Disodium salt of EDTA is not working sometimes and as my ligand backbone contains ester, I can not use ammonia/ DMGH2.
What to do?
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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!
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Excited state lifetime of sample and blank are almost similar (difference is 0.2 ns). Is it scattering?
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Details?
Are you sure it's photoactive?
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In fact I have tried to prepare the crystal of host-guest complex, due to the instability of guest molecule, I did not succeed to get crystal. I have sufficient information through DFT based studies related to NH-Pi interactions. However I would like to have best experimental data for further confirmations.   
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I know nothing on NH-Pi.
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Hi eyerybody here,
I'm looking for a method to stabilize chitin beads on agrose or other surfaces specifically to make chitin binding affinity columns.
Is there any published or exprienced protocol doing this?
Thank you.
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Dear Parsa,
Attached is a review entitled " Preparation, modification, and applications of chitin nanowhiskers: a review 225
Rev.Adv. Mater. Sci. 30 (2012) 225-242
Corresponding author: V. Ostafe, e-mail: vostafe@cbg.uvt.ro
PREPARATION, MODIFICATION, AND APPLICATIONS OF
CHITIN NANOWHISKERS: A REVIEW
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
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My question is about size measurement of G2-PAMAM-NH2 dendrimers. I've had problem with size measurement by MALVERN-ZetaSizer (Nano ZS). The PDI value is always unacceptable. Could you help me on this matter. What is your method for the characterization of PAMAM dendrimers? I'll be waiting for your suggestions. Thank you in advance!
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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!
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I was wondering if anyone can suggest a supra-molecular compound with a cavity size more than 40 Angstrom. I can only find some of them with no more than 10 Angstrom which is much smaller than the size that I am after. Thanks in advance. Remark: Please do me a favor and support your answer with the molecular formula of the proposed candidate (if any). 
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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!
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I want determine the absorption and emission at different composition of water:THf mixture, is it possible with turbomole.
Please suggest the method
thank you in advance  
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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
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I have recognized some systematic peak shifts in my X-ray powder diffractograms. Therefore i am looking for an algorithm or software routine which automatically corrects a set of diffactograms so that all peaks are at the same position. The samples can not be measured again. Can Panalyticals Highscore software correct those shifts? The positions along 2Theta have to be similar in all investigated samples as i use the signal intensities to construct PLS models.
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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.
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Has anyone had any experience with the synthesis of the title crown ether?
I am trying to follow the work of Ungaro et al (JACS 1976) but I fail to get product formation. I might be missing something small so any advice would be greatly appreciated.
Thank you for your time
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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 ..
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I want to attach PEG chain with my aromatic amine which is not nucleophillic enough. I've tosylated the PEG to make it a good leaving group. Iv tried it with different bases like triethylamine, DMAP in different apolar protic solvents like DMF and DMSO as well as CH3CN, THF but reaction is not successful. Kindly suggest me the appropriate way to couple the tosylated-PEG with my aromatic diamine.
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THANKS
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I tried to purify a highly water soluble compound using RP-HPLC. Unfortunately, no UV peak was detected, however, when a same compound was run on a normal C18 column, there were three different bands with better separation was achieved. In a normal C18 column the mobile was chosen as 5:95 CH3OH: H20 mixture. The same or higher polarity was employed for HPLC. But I was failed to detect any peak in the HPLC chromatograph.
Kindly help me with your suggestions.
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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?
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I synthesized a Keggin based supramolecule using an N-donor organic ligand. I want to study its physical properties by a software. Please guide me.
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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
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I work about Frustrated Lewis Pais, there are the combinaison of  Lewis acid and bulky lewis base, both very bulky. There isn't a covalent bond between them because of the congested but a dispersion interaction. I know Dispersion interaction is created by the electron which move creating  instantaneous dipole , so this dispersion is between an instantaneous dipole and induced dipole. This is in the Van der Waals bonds, weak, no directional, and on 1/R6 so long rang. For FLPs this interaction leads to the cohesion of them. 
Have you any complements for me, or perhaps easier explanation? I think it's a little vague. Thanks a lot, Anaëlle
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ya, this video is really complete about dispersion interaction , thanks a lot!!
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I need to test the mechanical behavior of single crystals 
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you can do nanoindentation, see the article
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i  want to synthesized Silanetetramine in lab but i could not find the proper process for it.
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I tried my best to find an article to answer your question and this is what i got . I hope you find it useful .
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How to add validation response form (vrf) in the cif files? Can anyone provide a sample cif file?
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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.
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I have optimized crystal structure of Zn bisporphyrin containing nitrogen coordinating bidentate axial ligand using b3lyp basis functional and 6-31G+ (d,p) basis set for C,H,N and LANL2DZ for Zinc metal.but after optimization Zn-N distance is increasing from 2.18, 2.17 to 2.27, 2.26 (as there is two Zn in bisporphyrin and Two Nitrogen binding sites in ligand). So I am not able to compare theoretical and crystal structure parameters.
Is there is something wrong with optimization. Please suggest me something.
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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. 
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I want to ask question regarding betacyclodextrin/CTAB inclusion complexes.
I prepared a complex of low molecular weight heparin with CTAB and i want to dissociate that complex, i tried to add different concentrations of beta cyclodextrin to complex with CTAB and free the heparin but no dissociation happened. 
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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.
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Entropy depicts distribution or partitioning of a localized surface energy noted as potential energy partitioned in different patterns within the giant molecules like intramolecular hydrogen bonding. Energy partition is calculated using Boltzmann energy concept as S = kB ln W, S entropy, kb Boltzmann constant, W partitioning factor.
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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.
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I mixed HSA with a compound. I found that after addition of the compound, the absorptivity of tryptophan (HSA) decreases. What can be reflected by this phenomenon?
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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.
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Few macrocycles can bind to anions and thereby change color when they recognize. A competitor to macrocycle can revert the color change. Can anyone suggest a competitor?
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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
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I want to measure the density of perylene and napthalene derivatives.
Anybody know some methods to measure the density of organic compounds?
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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
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I am performing a calculation in ORCA 2.7.0. Geometry optimization successfully converged, but OUT file generation shows lambda error. I have the txt file with me, if anyone is interested then I can send.
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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
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we know the position and orientation order in smectic phases and only positional order of the mesogens in nematic. Is these  orders differences causes different pattern of the textures. But why these are giving focal conic and threaded ........ is there any basic information giving these type of textures...... 
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Thank you for your valuable information.
I wish you a happy, healthy and prosperous new year.
Thanking you 
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As the title says, Is there a simple and efficient way to measure the potential of zero charge of a SAM coat-electrode?
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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?
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Though i have read some articles on triple-shape memory polymers but how to implement a method on DMA Q800 to check the polymer for triple-shape memory effect?? which cantilever will be more helpful? Detail Please.
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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.
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"Mucopolysaccharides, also known as glycosaminoglycans (GAGs), contribute to the inflammatory state of the Shwartzman phenomenon [233–236]. Upon exposure to systemic stress, increases in sulfomucopolysaccharide incorporation occur throughout the body, and this is designated as the “universal nonspecific mesenchymal reaction” [3]."
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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.
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From which number there is no need for correction?
Single crystal X-ray, absorption coefficient, absorption correction.
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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?  
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I need instrumental technique as well as a process.
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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
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Hi, I am currently trying to follow a self-assembly process of peptides by fluorescence anisotropy. However I keep getting the opposite of what I expect. When I do a self-assembly the anisotropy decrease, when I force a disassembly the anisotropy increase. I use a T-shaped set-up, that I calibrated myself. I have gone over the set-up and data many times but cannot find any explanation. Does anyone have a suggestions?
Thanks for taking the time to answer
/Morten
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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
otherwise, there should be sections dealing with this (with appropriate references) in the books of both Lakowicz and Valeur
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I am performing a gaussian calculation of a molecule having 45 atoms by B3LYP6-31gd set but each time my calculation stops it gives an error message of 'linked died--convergence termination'. please assist me to run the program 
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Check your structure
And remove all the keywords
put everything in default and give command to run
all the best 
Fr.Xavier
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As i am trying to find the quantum yield (Φ) at 77 K for the ruthenium complexes. I couldn't find the quantum yield standard value (Φstd at 77 K in CH3CN) for [Ru(bpy)3]2+. Kindly suggest any papers or give the value and source in which it is reported.
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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"
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I synthesised [3,5 -bis(tolyl carbamoyl)phenyl pivalate] by reaction of 5-acetoxyisophthalic acid with p-aminotoluene and i used DMAP and DIC as a catalyst.
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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.
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Alert level A THETM01_ALERT_3_A The value of sine(theta_max)/wavelength is less than 0.550.
Calculated sin(theta_max)/wavelength = 0.4980 PLAT029_ALERT_3_A _diffrn_measured_fraction_theta_full Low ....... 0.935 Note PLAT043_ALERT_1_A Calculated and Reported Mol. Weight Differ by .. 51.94 Check PLAT051_ALERT_1_A Mu(calc) and Mu(CIF) Ratio Differs from 1.0 by . 45.30 % PLAT122_ALERT_1_A No _symmetry_space_group_name_H-M Given .
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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. 
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During TGA of my compound (in N2 atm), I am observing an unexpected mass increase between 70 Celsius and 140 Celsius. What are the general reasons behind it? I repeated the experiment several times but result is same.
Sample details: A coordination polymer composed of an organic ligand (having carboxylate group in the appendage) and Li (I) ions.
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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.
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I synthesised [3,5 -bis(tolyl carbamoyl)phenyl pivalate] by reaction of 5-acetoxyisophthalic acid with para amino toluene and according TLC i have an exess of Para amino toluene. Moreover, i used DMAP and DIC as a catalyst. 
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Extraction with 1 M HCl is easiest
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Shortly before my travelling to the conference a week ago I read some article where some weak interactions, possibly of CH...X type, were discussed. The article contained a phrase that the simple answer to the question if these interactions exist is something like "No, they don't." I forgot bookmark this article and I am unable to find it. Can you anybody help me to find this article?
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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 :)
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I would like to start a collaboration with laboratories interested in developing new microfluidic approaches for the preparation of micro and nano particles for drug delivery, nutraceuticals and agrochemicals.
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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
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I've been doing molecular imprinting experiment. It is a core-shell structure, i.e.surface imprinting. But UV-vis cannot see any difference before and after adsorption. Does the cavity of molecule easy to adsorb template molecule in dynamic aspect? And what method can I use to investigate the details?
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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.
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Typical supramolecular host β-cyclodextrin (β-CD) has well-known host-guest interactions with a vast array of hydrophobic compounds, such as azobenzene (Az), adamantane (AD), and cholesterol. What about the stability in the blood condition?
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The stabililty constants of cyclodextrin inclusion compounds are usually low, Please make sure the inclusion compound is stable on water first.
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Alkyl azides and terminal alkynes react to form trioazole ring mostly by using Cu derivatives as catalyst.
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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
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Procedure for making micelles with phospholipid or PEGYlated phospholipid?
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I used to take phospholipids dissolved in ether and shoot them into warm water with a syringe which gave vesicles by EM observation.
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The above mentioned compounds should react to give a product with an ether linkage i.e. alkyl- oxygen-alkyl
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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.
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.
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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.
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In some instances compounds exhibit low fluorescence when concentrated. However, higher fluorescence intensity is observed when in dilute solution.
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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.
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How can I avoid signal peak broadening in H-NMR spectra due to self-aggregation of molecules in deuterated low-polar solvents (such CDCl3 or THF-d8)? This self-aggregation is due to H-Bond formed between analyte molecules. Partially the problem is solved by heating the sample NMR to a limit imposed by very volatile low-polar solvents such THF and CDCL3 but still the J cuppling constants cannot be resolved.
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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.
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A crystal with space group R-3c by Yves Journaux can be found in Chem. Commun., 2012, 48, 1015–1017.
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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.
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I'm asking after reading this article http://www.nature.com/news/2010/100310/full/464158a.html
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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).
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I run a "Tm" (melting point DNA) experiment which consists in heating a sample of DNA double strand in buffer solution from 20°C to 85°C with a constant heat rate. Simultaneously, I monitor the change in UV-VIS absorbance at 260 nm and I get a sigmoid curve called "Tm curve". I want to know how can i calculate energy of H-bonds breaking over the temperature from Tm curve. In other words, how I can correlate the hyperchromic effect in UV-Vis with hydrogen bonds destruction in the terms of energy?
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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.
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‘chemistry beyond the molecule’
‘the chemistry of the non-covalent bond’
‘non-molecular chemistry’
NON-COVALENT intermolecular forces include electrostatic interactions, ion-dipole interaction, dipole-dipole interaction including vander Waal’s forces etc. This means beyond molecular chemistry which is based on covalent bond there lays a field of supramolecular chemistry, which uses intermolecular bonding through non-covalent interactions. This allow individual molecules to held together with non-covalent intermolecular forces to form a bigger unit called SUPRAMOLCULE, where individuals having its own organization, their stability and tendency to associate or isolate.
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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.