Questions related to Supramolecular Chemistry
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?
Review publications of synthetic strategies for inorganic supermolecules and coordination polymers, molecular polygons and tubes, and molecular polyhedra.
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?
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?
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!
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...
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
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.
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?
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.
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!
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.
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)?
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?
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.....
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?
Ueff = 2.828*SQRT(Xp*(T-weiss constant)
I have tried with those brominating agents-PBR3, Br2/PPh3,HBr-acetic acid
Could not find enough information about cyclodextrine interaction with cholesterol. What are the concentrations and ratio of the components?
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
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.
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
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.
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?
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?
Excited state lifetime of sample and blank are almost similar (difference is 0.2 ns). Is it scattering?
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.
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?
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!
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).
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
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.
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
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.
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.
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.
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
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.
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.
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.
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?
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?
I want to measure the density of perylene and napthalene derivatives.
Anybody know some methods to measure the density of organic compounds?
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.
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......
As the title says, Is there a simple and efficient way to measure the potential of zero charge of a SAM coat-electrode?
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.
"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” ."
From which number there is no need for correction?
Single crystal X-ray, absorption coefficient, absorption correction.
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
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
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.
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.
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 .
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.
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.
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?
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.
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?
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?
In some instances compounds exhibit low fluorescence when concentrated. However, higher fluorescence intensity is observed when in dilute solution.
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.
A crystal with space group R-3c by Yves Journaux can be found in Chem. Commun., 2012, 48, 1015–1017.
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?
‘chemistry beyond the molecule’
‘the chemistry of the non-covalent bond’
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.