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Organometallics - Science topic

A place to discuss all topics of organometallic chemistry, pentaamminomethylcobalt nitrate to cobaltocene, iron catalyzed coupling reactions to ferrocene, so forth and so on.
Questions related to Organometallics
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Hi everyone,
can anyone suggest me a method for hplc analysis of organometall complexes based on Zeise salts complexes?
Using a ordinary C18 column results in one peak, that comes from the free ligand.
However, studying the stability in solution shows promising results.
I need a reliable method to distinguish between free ligand and complex. Maybe a specific column that can be used for charged complexes? The platinum complex is negatively charged, its counterion is potassium.
It is now the analytical issue to solve this problem.
Any suggestions?
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What about HPLC-MS coupling? This may answer your question which compound is "in your peak".
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With benzene ring as a typical aromatic structure, the uncompromising hydrogenation (ring saturation without altering the non-aromatic functionality such as the -OH and the -C=O) of benzene derivatives: phenol, benzyl alcohol, benzoyl moiety, aniline, etc. is well known.
However, little, if any, is documented about the reverse reaction. Have you come across or thought of the uncompromising dehydrogenation of the corresponding aliphatic (cyclohexane) derivatives to the benzene derivatives? If yes, please share your experiences, papers, weblinks, ideas, and so on.
Thanks in advance!
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Dear Stanislaus O. Okwundu thank you for sharing this very interesting chemical question with the RG community. As a synthetic inorganic chemistry I absolutely not an expert in this area of research. However, I at least found two literature references which at least come close to answering your question in part. Both describe the dehydrogention of cyclohexylamine under formation of aromatic amines. Please have a look at these articles:
A Ni–Mg–Al layered triple hydroxide-supported Pd catalyst for heterogeneous acceptorless dehydrogenative aromatization
and
Versatile routes for synthesis of diarylamines through acceptorless dehydrogenative aromatization catalysis over supported gold–palladium bimetallic nanoparticles
The second paper is even freely available as public full text. You can find and access other related articles by searching the "Publications" section of RG for the term "dehydrogenative aromatization":
Other articles are found when searching for terms like "acceptorless dehydrogenative aromatization". When searching for literature references, I think you should better avoid the term "uncompromising" as in your original question. This word seems to be rather unusual in this context.
I hope this helps. Good luck with your work and best wishes, Frank Edelmann
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The structure is very unusual but we came out with something like a Td with a fifth RCOO- ligand. Formula of the anion  Co(II)2(RCOO)5- each Co(II) is pentacordinated.
We know the J, Delta (small), lamda, E,  D and tau from Xi(DC) measurements.Therefore, there is s tetragonal distortion, sort of.
The EPR Spectra occurs only bellow 15 K, otherwise it is VERY broad. Near 4K is even broader. At 8K I can see the fine structure of Co2(RCOO)5- but only 11 lines emerge.This makes me think the spin-lattice is dominating relaxation.
I can see only one set of 11 lines, therefore I don't believe the distortion is not too large.
There are not many examples of pentacoordinate Co(II), except for proteins.
How can I rationalize these observations?
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mu at (4700 Gauss) does NOT decrease until 4K. It remains constant all the way up to 298K. My Japanese theoretician just asked me if it was a dipole or it was a Single Molecule Magnet? I don't know, yet. Before measuring Xi,I ran an EPR spectra up to 6000Gauss at 298K. Then I ran further spectra at 280K, 20K, 8K and 4K. Sample could have been magnetized. SMM. Sorry, I have never been good at History lessons.
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Is hydrated water act as HBD or HBA?
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In order to record classical CV, your "synthesized deep eutectic solvent" must have a high electric conductivity (low resistance). Commonly, an electrolyte is added to decrease a resistance. If your solution contain an electrochemically active species, you can see it as a CV peak. You can try whatever reference electrode, but you must calibrate it, for example, against ferrocene couple.
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my question is during the preparation of nonaqueous electrolytes the precursor materials are hydrated metallic salt and organic solvent after mixing two materials homogeneous nonaqueous electrolyte is formed. what is the reference electrode of this solution to measure Cv? the water from the salt is not removed? is that possible to use Ag/Agcl or Ag/Ag+? remember the water is still in the solution?
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I would propose to use a Pt wire and Ferrocene in the solution. Measure the potentials of your system against Fc/Fc+ Some people use Ag/AgNO3/ACN but you have to cover this reference electrode to hide it from light because it is not stable in light. Check often its potential against another reference electrode.
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Greetings,
I whould like some suggestions regarding exceptional and comprehensive books on the following topics:
  • Molecular symmetry and group theory applied to electronic and vibrational spectroscopy;
  • Molecular orbital theory applied to coordination compounds;
  • Crystal field theory;
  • atomic structure and quantum chemistry;
  • organometallics
  • Acids and bases applied to coordination compounds.
Best regards.
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Dear Lucas Almir Cavalcante Minho I think that the recommendations provided by Corentin Lefebvre are already very useful and comprehensive. In addition, I suggest that you also check the "Publications" section of RG for lectures and courses on certain topics of interest. Just search for the term "advanced inorganic chemistry". Then click on "Publications" and select from the list in the upper left corner either "Presentations" or "Books". You will find that many useful lectures, courses and books have been posted as public full texts which can be freely downloaded as pdf file.
Good luck with your work!
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What are the attributes to classify organometallic cluster compounds? How organometallic clusters are classified based on those?
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Dear Shafikul,
many thanks for your kind response and explanation. Unfortunately I have absolutely no idea what "TVEC 50 and 52" are....😳
According to the famous organometallic chemist Albert Cotton, a metal cluster is defined as "a finite group of metal atoms that are held together mainly, or at least to a significant extent, by bonds directly between metal atoms, even though some non-metal atoms may also be intimately associated with the cluster" (see attached presentation). Moreover "molecular clusters are composed of 3 or more metal atomsstabilized by small molecules acting as ligands, and characterized by metal-metal bonds, either localized or delocalized over the metal framework." I know that the term "metal cluster" is often used in a broader sense. Personally I prefer to adhere to the definition in the strict sense. Thus if you have a metal complex wich comprises three metal atoms but only one or two M-M bonds or even no M-M bond, I would better call this a "trinuclear complex" instead of a cluster.
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Usually for the complexation of porphyrins with Fe, Mn or Co, salts like Fe(II)-chloride, Mn(II)-acetate tetrahydrate, or Co(II)-acetate tetrahydrate can be used. But for the same with Ru or Ir, their organometallic salts are used, like Ru3(CO)12 and [Ir(COD)Cl]2. Why aren't Ru(III)-chloride or Ir(III)-chloride salts generally used for complexation of porphyrins?
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Dear Gourab Mukherjee many thanks for posting this very interesting technical question on RG. I assume that solubility problems are the main reason why the synthesis of iridium porphyrin complexes usually starts with organometallic iridium complexes and not with the chlorides. Iridium trichloride exists in two forms. The anhydrous IrCl3 is insoluble in water and common organic solvents. Then there is the trihydrate, IrCl3(H2O)3. This compound is well soluble only in water, but not in organic solvents. Thus both trichlorides are more or less unsuitable for the synthesis of iridium porphyrin complexes which is normally done in high-boiling organic solvents. Basically the same is true for ruthenium trichloride. In contrast, compounds like Ru3(CO)12 and [Ir(COD)Cl]2 are well soluble in a variety of organic solvents. Particularly the iridium complex [Ir(COD)Cl]2 is every easily accessible in high yields from IrCl3(H2O)3 and COD (= 1,5-cyclooctadiene). You can regard [Ir(COD)Cl]2 as a soluble form or iridium(I) chloride which is otherwise not accessible. Ru3(CO)12 is more difficult to make and should perhaps better be obtained from commercial sources, although it is very expensive. Both complexes can be used to synthesize porphyrin complexes of the mono- and trivalent metals. For a typical literature reference please have a look at the following article:
Syntheses and reactions of iridium complexes of octaethylporphyrin
Good luck with your research and best wishes, Frank Edelmann
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Hello,
I am attempting to optimize the [Fe(H2O)6]2+ cation in Gaussian by using M06/def2-TZVPP in SMD water solvent. Int=Ultrafine and Opt=VeryTight keywords are also used. However, the problem arises with the optimization step what is seen by the Link9999 error in the output file.
I tried to fix it as follows — Firstly, I deleted the SMD solvent and the VeryTight criterion. That led me to the optimized structure. Then, implicit solvent was added but Link9999 occurred again. Finally, I was able to solve this by using MaxStep=1, because I think the complex may be too little, so default 30 steps lead to jumping on the PES, never touching the minimum. That way, in fact, I have "optimized" the molecule, but another problem emerged — 4 imaginary frequencies are yielded.
Can someone who works with organometallic advice me how to solve this problem? This is just [Fe(H2O)6]2+ — what happens if I switch water with a larger ligand? One knows.
Maybe I could only continue with the MaxStep=1 or raise it marginally and then try to optimize the molecule?
======================
%Chk=Fe_6H2O.chk
#p M06/def2tzvpp
Opt=(MaxCycles=512, maxstep=1,verytight) Int=(UltraFine)
SCF=(maxcycle=512)
Freq
Pop=NBO
SCRF=(SMD,solvent=water)
geom=(check) guess=read
Fe_6H2O
2 1
======================
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Follow up my experience, your problem could be due to setting up the multiplicity of iron cluster. Your input was currently shown in 1, it seems that it is not right value, please try a other value. I have succeed to set up 5 value for Fe2+(H2O)5 and 6 value for Fe3+(H2O)6. Good luck!
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One of my colleague is trying to make standard mixture of organo-tin compounds.
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The solvent for dibutyl tin oxide you can use THF or dry ether
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I am trying to reduce an organometallic complex that has a tethered diaryl ketone functional group. Unfortunately aqueous or methanolic NaBH4 reduces the ketone functional group as well. 
Any other suggestions would be gratefully acknowledged.
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The mild reducing agent that can operate in water is sodium sulfide which will not reduce ketone.
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Hello everyone;
I am looking for free software that can simulate the structural, optical, and optoelectronic properties of organometal halide perovskites.
Your suggestions/recommendations will be highly appreciated.
Thank you!
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Dear Nasir Ali thank you very much for your interesting technical question. Please go through the following Open Access article which might help you in your analysis:
Device simulation of highly efficient eco-friendly CH3NH3SnI3 perovskite solar cell
The same software was employed in the following relevant studies:
Simulation and Analysis of Lead based Perovskite Solar Cell using SCAPS-1D
and
Simulation of Perovskite based Solar Cell and Photodetector using SCAPS Software
Unfortunately the program is not free, but you can test a free 7 days trial:
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Is it possible to characterize an organic metal complex using HRMS? I am just thinking that the conditions of such a technique might result in the breaking of the metal-ligand bonds. Your help is much appreciated.
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You can use HRMS for organometallic characterization, if elemental analysis has not done.
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For my organometallic complex of the type [RuCl2(Z)], where Z is a neutrally coordinated ligand, I am observing distinct changes in UV Visible spectrum upon hydrolysis (complex is added to water). However my time dependent NMR and mass spectrum of the same complex shows that the original complex remains intact. Is it possible? Why do we observe changes in UV-Vis spectrum then?
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Dear Srividya Swaminathan thank you again for your interesting question. If you would provide a few more details what you additional ligand Z is, I could do a SciFinder search and look for the reactivity and hydrolysis of the particular ruthenium complex. Is you starting ruthenium(II) complex a known or a new compound? It would also be interesting to know why you are carrying out this hydrolysis study. If you want to isolate the hydrolysis product, which is presumably a cationic species, you could try to isolated it by precipitation with a large anion such as tetraphenylborate,
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I had a question that popped up in my head. In case of organometallic complexes loss of an electron from the d orbitals of the central metal leads to an increase in the oxidation state. But loss of an electron also occurs incase of free radical generation. Incase of mass spectrometry also we see the electron loss resulting formation of cation radical. So what shall we consider loss of the pair of electrons leading to increase in oxidation state or just and electron?
Please help me out.
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Dear Tuna
Usually we asgin oxidation state for stable compounds not for radicals. However, if we have a radical cation such as O2+, O2 molecule which lost one electron, still we can say that the oxidation state of each O atom is +1/2.
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Hello,
I'm currently working on organometallic complexes which has Ti, Zr, Hf. After the synthesis of complex, I checked H-NMR results, I understood that my product is not pure. So, there are impurities such as ligand, other possible complexes. Do you have any purification methods that can be done in Glovebox?
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It is always preferable to crystallize using different solvents with different and lesser temperatures, and the process must be repeated several times, sometimes using a mixture of solvents, and we follow up the results and improvements, sometimes we need column chromatography.
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I was looking under what conditions gold can bind to carbon under room temperature conditions,but I have the question of what defines the stability of a link when high electric currents are applied? How to calculate a nanowire that will conduct high voltage with a carbon-gold bond in the chain
(Probing the nature of gold–carbon bonding in gold–alkynyl complexes nature)
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This article can probably help you regarding Organogold
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MOF-88, MOF-500, ZIP-8, MIL-101 AND MCM-41.
what is meaning of Fe- MOF-88 and how to calculate 88 numbers.
many example i need answer could tell me.
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Please see the following link;
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I'm not working on biomolecules, I work on Organic, Organometallic, and sometimes inorganic structures.
Do you know a simple way to apply the right calculation method? Is there any article or book that has explained how to choose the right method and basis set based on the result we seek or simply based on the structure of the compound?
thank you...
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@ Hanieh Moradi I misread your post, but I am glad it helps :)
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ammonium chloride is said to convert solid oxides on metal surface to volatile chlorides (ammonia is a gas), but what about the Oxygen that is taken out of oxide? Does the "ammonium oxide" break down to NH3 and H2O simply, or is there deeper mechanism? Zn and Cu chlorides are of quite high boiling point, so i think soldering them would require other fluxes. What would be the reaction mechanism of those fluxes with constituent metals? And How does ZnCl2 does fluxing while its oxides are not volatile?
(Fe, Al, Ti, Si, P, S, C has low boiling point chlorides but Mn, Cr, Ni have not).
When it comes to resin acids, how thay solubilize metal oxides? Do they retain these in a liquid state or boil up as organometallics? resin acids being much weaker than carboxylic acid, how do they dissolve the oxides in hot state? Do they form any organometallic complex involving their sterol/sterane moieties?
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My understanding of fluxes is that in general they acted more as a solvent and simply physically removed the oxide layer, then provided an anaerobic/reducing layer to protect the metal briefly.
The actual mode of action is surely very complex and different for different fluxes and metals.
But at least some do not vaporise the oxide layer and simply move it out of the area being soldered.
I suspect you have been given a very oversimplified mode of action and the reality is much more empirical (if it works, use it as a flux).
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I am studying the hydrolysis of an organometallic complex in water, for which I obtained a time dependent spectra as attached. The spectra at 0th min and 10th min dont match or have an isobestic point, however we see a possible one after 10th min to 60th minute. What can be the inference?
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Interpretation of this UV-Visible spectra . First find out wave length of maximum absorption.It looks above 380 nm this means that compd. absorbs in the near UV region. Usually conjugated compds. show absorption above 240 nm. As absorption is above 38o nm which indicates that it is congugated compd. conaining double bonds.
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We all are familiar that ionic liquids (ILs) posses relatively lower vapor pressure and several other fascinating properties that make them "green and sustainable chemicals and solvents" for variety of chemical transformations. I want to know that whether the synthesis of these compounds (Ionic Liquids) is also cost effective or not relative to synthesis of normal heterocyclic compounds ?? Please  
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Between heterocyclics and ionic liquids, heterocyclics are synthesized more cost-effectively .This is because ionic liquids are more polar and to get them in pure state & solubility problem spectral analysis is some what tedious .
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The sample is Diesel Exhaust Particle, it contains both organic and inorganic components. The organic components include PAH, aliphatic hydrocarbons. The inorganic components include metals and metal oxides. It may also contain organometallic complexes.
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TGA shoud be suitable. If you check under air you need to ramp the temp in a constant rate (usually 5 degrees/min is ok) to high temprature (let's say ~500C) and measure isotherm for ~30 minutes . While the organic part will evaporate or will be burnt, the inorganic part will remain as metal/metal-oxide. I must say this can be tricky because at high temperature the metal can undergo oxidation to metal oxides and then you will see some weight gain, so some optimizations should be done.
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I often have troubles obtaining adequate elemental analysis for iridium compounds when the ligand is triflate (CF3SO3), hydrogen and nitrogen work well but carbon is usually about 5% lower and sulfur values are random, even in samples from the same batch. Does anyone know if this is frequent? Are there any references to problems in the analysis when there is sulfur in the organometallic samples?
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P.S. Don't tell you boss that I suggested to you to skip the sulfur values... 😂
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Hello everyone,
Does anybody know a good review that contains reliable values for the density of dyes, photosensitizers, and organometallics in monolayers?
For example, for the N3 dye i could find STM-studies that indicate a density of ca. 0.6 nm^-2 (based on values from Ikeda et al., J. Photochem. Photobiol. A, 2009, 202, 185). For a rhenium dye I found a value of 1.3 nm^-2 (https://iopscience.iop.org/article/10.1088/1361-648X/aaddd3/meta).
I am in particular interested in pyridine-containing complexes.
Thank you all!
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Here an update:
We recently published experimental values for a variety of dye molecules with pyridine and bipyridine groups:
Here, the Ru dyes with more pyridine rings tended to have lower areal densities, compared to Re dyes with fewer pyridine rings. Probably, the diameter of the Ru dyes on the surface was larger due to the different anchoring with multiple bipyridine groups.
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I'm thinking about Na2S, but I was wondering if using any organic reagent like thiourea (it should thermally decompose at low temperatures) would be suitable too? Thanks
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To obtain thin CdS layers of 50-70 nm, I used thiourea. The SILAR reaction was carried out at room temperature.
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I use a carbon paste electrode modified with an organometalic complex. The electrolye was purified with N2 and the carbon paste were made carefuly
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All,
I wish to calculate the donor acceptor interaction parameter for my systems containing an organometallic molecule in complexation with a cation. For that, I need the molecular overlap potentials for a certain set of orbitals. Can anyone please help me in understanding what part of the output in Gaussian/ NBO analysis or both is required to do so.
Thanks,
Atiya
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Due to time and material constraints, I'm interested in using sodium hydrosulfide hydrate (NaSH . X H2O) for a reaction involving organometallic complexes sensitive to the presence of water. Would it be appropriate to dissolve the reagent in dry solvent, over activated molecular sieves, to remove the water from the hydrate? I understand that the water incorporates itself into the crystal structure of the hydrate, and generally heating it would suffice, but the low melting point/potentially toxic nature of this reagent make me question dehydration by heating. Has anyone had any success with using activated sieves to dry hydrates in this manner?
Thanks,
Richard
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Dear Richard, in theory you can use sieves 3A for removing water from hydrates, since water bonds to the sieves stronger than in many hydrates, however there are a lot of variables there...if you want to try maybe dissolve it in ether and add stabilizer and sieves 3A. But i strongly recommend to do what Anthony suggested.
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I have recently installed Gaussian 16 for dft calculations. I have no good idea about suitable basis set? How to specify basis set for heavy atom and light atoms? YouTube tutorial mainly related to organic compounds. My complex contains Mo, Ge, Si, O, C and H.
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Hi Dhungana
You should select all electron basis set for the Si, O, C, and H such as 6-311++g(d,p). Beside, effective core potential is good choice for transition metal for example LANL2DZ or LANL2TZ and so on.
You always select suitable basis set fro following site:
best regards
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I have organometallic ligands and I want to dock it in my modelled protein structure. Currently I am using GOLD but it did not dock (Please be aware that GOLD's parameterisation is optimised for organic compounds ) .
Any suggestions which software will dock the ligands having metal atoms in them?
Thanks
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You can check the attached paper. In this paper they have docked various organometallic ligands using different docking software's like
Autodock, Gold and Glide.
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I have prepared a supported catalyst, which is implied for catalyzing certain organic conversion. The catalyst along with reacting precursors are kept under stirring conditions in order to facilitate the better exposure. But in such situation, the powdered catalyst stays with the product obtained at the end. Therefore my question is, how one can separate the catalyst from the product before analyzing the conversion using GC or other techniques?
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Shubhangi, you should use some solvent that solubilize your product. If you do not use, you are going to lose your product. After filtering your reaction it is just necessary to evaporate the solvent to obtain your product. Depending on what you are working with it should be necessary to purify it.
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Often enzymes and artificial enzymes are defined as those molecules that show saturation kinetics. What is the alternative to this behaviour ? Would say an organometallic catalyst not show a saturation curve too? Can we apply the michaelis menten model to non enzyme catalysts?
Thanks!!
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Dear Rick,
If we have a "slow - fast - slow" behavior, then for a single chemical reaction I associate with autocatalysis - which does not mean that each autocatalytic process has to ran like this. Of course in nature and not only there are a number of processes and phenomena of such and more complicated course.
Regards,
PS. Now we are discussing something different than in the question.
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Hello
I want to start study about different cluster organometalic complexs containing cobalt and iron(2Fe and 2Co atoms) or iron only (4 Fe or 6 Fe atoms) ,please can you tell me What is the appropriate function and basis set in DFT to optimize and calculate selectivity and reactivity of cluster complex containing cobalt and iron simultaneously with phosphine groups?
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LANL2DZ for the metals and something like 6-31G(d,p) for the rest is the somewhat traditional method.
Alternatively, you can use Def2TZVP or Def2TZVPP for all elements.
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We are working on Light emitting complexes of europium and I got stuck to find out the radiative rate ( Arad is the radiative emission rate) required to calculate the quantum efficiency. I have gone thru many articles discussed about the quantum yield and intrinsic lifetime but do not know how to calculate the radiative rate as I have calculated the total radiative rate (rad +non rad) but not able to calculate the radiative from the total for europium complex.
Related articles are
1. Plasmonically Enhanced Optical Characteristics from Europium Organometallic Complex (IEEE)
2. Preparation and fluorescent properties of europium (III) complexes with β-diketone ligand and 2,2-dipyridine or 1,10-phenanthroline (Elsevier)
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Radiative rate constant is calculated from quantum yield and lifetime. Getting to know the radiative rate constant simply from lifetime won't be easy.
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Dear Members,
I am trying to optimize for triplet state of organometallic molecule in solvent but encounter convergence problems I didnot know how to solve. The optimization energy keeps oscillating and then terminated with l999 error due to out of step numbers. I tried almost everything like resubmit the output file, or scf=vshift, scf=conver=5, I also reduce maxstep but it didnt work. There are a vast amount of articles that optimize these systems in the solvent but none of the information of input file is out. Is there any idea how to overcome this problem? thank you
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You need to make a little change in your input structure right at the region where the oscillation occurs during the optimization procedure. It may be a dihedral angle or torsion strain.
Good luck
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I'm a M.Sc student in Chemistry, and I need some specific literature that has to do with the synthesis, isolation and characterization of salen type organometalic catalysts for homogenous catalysis, with Mg, Ca, Ba. These will be used in reactions of carboxylation and polimerization of some environmentally friendly compounds. It is important that be just for homogeneous catalysis, so that solied supported catalysis are not useful in this research.
Thank you.
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In top international Chemistry publications, I observed few are using LANL2DZ for both the metal and other atoms, few are using 6-311g type basis set for both the metal and other atoms and few are using LANL2DZ for metal only and 6-311g type basis set for other atoms except metal. Which one is appropriate and why? I guess the last one....
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LANL2DZ is a double zeta basis set, i.e. it doesn't include any polarization functions, but it does have relativistic effects through the use of pseudopotentials. The 6-31G basis is non-relativistic, and very small as well.
You don't need to mix basis sets to get good results. E.g. the Karlsruhe def2 basis sets are available for all the periodic table, contain relativistic effects and the split valence sets are quite affordable, so instead of using lanl2dz + 6-31g* you can just use def2-sv(p).
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Hello,
I'm a beginner to computational chemistry, I'm attempting to optimise [Re(OH2)(CO)3(phen))]+ using gaussian. I have tried to optimise the structure using B3LYP method in gen mode SDD for Re and 6-311(d,p) for the other atoms but I keep getting errors e.g. I get an .out file but when I open this on gaussview the phenanthroline is no longer attached to the complex, which is quite confusing I would appreciate if someone could help me please.
I have attached a screenshot as part of this post.
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From the snapshot it looks that water is attached to the complex. what is the distance of Re-OH2?
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Hello,
I tried to optimize geometry of a ligand(CHO) and metal (Rh), an organometallic complex using gaussian 09.
I used genECP command to give stuttgart ECP for metal, 6-31G* for CHO.
For reagents, a CH4 will be used as reagent and I want to increase quality of basis to 6-311G**.
In this case, what should I do to specify the basis set for each molecule ?
Is there no-way except increasing quaility of entire system ?
(for all CHO atom (including ligands), 6-311G** is burdening)
Many thanks,
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You can specify basis sets not only for each atom of any kind (like every Oxygen atom) but also for each atom in your input separately: see http://gaussian.com/gen/ . Something like, e.g.
1 0
6-31G*
2 0
6-311G**
will put the 6-31G* ont he first atom in input, while 6-311G** on the second one.
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Hello,
I have to optimise [Re(OH2)(CO)3(phen)]+, I have made the structure on gaussview, I have attempted to optimise the complex with B3LYP method in gen mode (SDD for Re and 6-31g(d,p) for the other atoms) but I keep experiencing problems. I would appreciate if someone could show me a sample input for gaussian to optimise this complex.
Thank you
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Hi. Here is an example of an input using multiple basis set:
#N B3LYP/gen pseudo=read OPT
blank line
name of the complex
blank line
1 1
z-matrix/cartesian
blank line
C O H 0 6-311+G(2d,p) **** Re 0 sdd **** blank line Re0 sdd blank line
blank line
Obviously the blank line means you leave the line empty.
I don't know why but the gaussian input of these type must have two blank lines at the end.
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Tuning luminescence of platinum complexes is well established by variation of cyclometalating ligand. The most common trend I find in literature is a red shift in the emission upon introducing more electron rich rings to the ligand (for example replacing phenyl with thiophene). I am observing the exact opposite, in which more electron rich ligands will result in blue shifted emission and was wondering what might be the possible reason ?
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There is no simple rule in tuning the emission of Pt(II) complexes. Every ligand system is different. What one should consider is whether that (electron-rich) group is placed on a moiety acting as HOMO or LUMO. Usually F is added to the phenyl ring of a cyclometalating ligand to increase the emission energy of the metal complex. But the following paper shows that addition of F to a phenyl ring can lead to red shift. The degree to which the emission is affected also depends on the substitution pattern.
Apart from this, usually we take it for granted that extending the conjugation of a ligand will lead to redshift in emission. But there are also exceptions:
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I am running TD-DFT analysis of small organometallic complexes using Gaussian. I have found that the experimentally obtained spectrum changes upon cooling, but this is not reflected in the TD-DFT analysis. I know that Gaussian doesn't allow for temperature changes in a TD-DFT analysis, but what temperature is TD-DFT experiment performed at? My input is as follows.
%chk =2a_4_TDDFT.chk
%Mem=3GB
%NProcShared=6
#B3LYP/Gen Pseudo = Read TD(NStates = 40)
atomic coordinates
C H N O Cl 0
6-31G(d)
****
Ni 0
LANL2DZ
****
Ni 0
LANL2DZ
Thank you and I hope you have a wonderful day!
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If we look at the Schrödinger equation we cannot find any temperature term in it. Then results from all ab initio methods which in some approximate way solve the electronic part of Schrödinger equation are in 0 K.
Temperature appears in methods like statistical thermodynamics which treats the collective behavior of molecules. The frequency calculations in Gaussian are based on the statistical thermodynamics but the program needs first to solve Schrödinger equation to obtain the energy term to calculate the partition function. As Thomas responded, temperature is applicable just in frequency calculations.
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For some reported metal complexes as anion sensors in the literature, the proposed mechanism is that upon binding of the anion to the metal center, the extent of ICT from ligand to metal is enhanced. My question is what are control experiments that can confirm such claim?
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A novel Cu-MOFs was synthesized and characterized by CHN, FT-IR, TGA, HSM, UV-VIS, SEM and X-ray crystallography.The X-ray crystallography revealed that the copper ion coordinate to the ligand through the oxygen to form an octahedral complex.
I want to study the fragmentation pattern of this Novel MOFs and I don't know which one will give a better result between GC-EI-MSD and HPLC-ESI-MS. I also need the chromatographic method
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Thanks Dr. Bojidarka B. Ivanova. I know Chromatography is method for separation. It does not provide structural information about fragment ions. My main interest is in the Mass Spectroscopy. The compound in question is pure but I don't have access to only MS, thanks.
Thanks Dr. Fatma Ulusal. But I dont have access to only MS. I only have access to GC-MS and LC-MS..........................
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such as a derivative of ferrocene and ferrocene salt.
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by phase extraction( adding a miscible solvent like acetone) or by adding a salt i think 
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The majority of samples are paramagnetic but some molecules are dimers which might have antiferomagnetic couplings between the transition metals.
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I'm not an expert for SQUID magnetometry, but I'm not sure if this is possible with liquids, at least I have only used solids for SQUID. As antiferromagnetic coupling should require very low temperatures, you will have a frozen solution at this point. This would not really be a solution anymore, so you could as well do measurements in solid state. Furthermore, if you have a large quantity of diamagnetic frozen solvent and dilute paramagnetic analytes, this will probably not be very helpful in SQUID measurements, depite the sensitivity. Preparing the samples in an inert gas glovebox should not be a problem.
However, if you are interested in the magnetic properties in (still liquid) solution, I can recommend using an NMR based approach which was proposed by Evans. This is fairly standard and will work with any NMR spectrometer. You can find some information in the linked publications.
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Because one of my crystals showing no interactions in solid state, when I have opened in mercury software. If there no any interaction how could one compound will crystallize, or what is the force that made the compound to be crystallized. Please suggest any reference if available.
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Remember that Mercury is a visualiser that is useful for looking at the arrangement of molecules, but it has only very basic functionality for looking at the interactions between molecules: Mercury bases this mostly on finding atom pairs that are closer than some cutoff distance, such as the sum of van der Waals radii. It is important to realise that interactions do not switch off at this distance. Most of the interactions between molecules are much longer-ranged than this - dispersion and particularly electrostatic interactions are still significant well beyond van der Waals radii. If you want to assess the interactions that are holding the crystal structure together, you need to perform some calculations using force fields or an electronic structure method.
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I am trying to calculate vapor pressure of an organometallic precuror for MOCVD applications, I want to use TG/DTA analysis for calculating vapor pressure at specific temperature with reference to sublimation rate at respective temperature. And is it possible that sublimation occurs above melting point of a meterial?
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Dear Tuqeer Nasir
I believe that these attached materials can answer your question
Best regards
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I need simple software to work docking for organometallic or coordination complexes molecules
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how about PLANTS1.2 ?
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A highly conjugated organic molecule was tried to load to HKUST-1 pores by dissolving the organic substance in ethanol and stirring with HKUST-1 for a day. After a day the sample was centrifuged and the supernatant (without solid HKUST-1) was examined by UV spectrometry and It was observed that the organic molecule has made a complex with Cu in the solution phase. What could be the reasons for Copper to leach to solution? I find the below possibilities probable and would like to know your view about them.  
01. Can HKUST-1 degrade within a day, to leach Cu ?
02. Can the highly conjugated organic molecule replace Cu atoms from the HKUST-1 structure ?
03. Can uncoordinated Copper be trapped within the framework and released in the presence of the organic molecule?
04. Can there be unreacted CuSO4 in the HKUST-1 sample? (However HKUST-1 was solvent exchanged for 10 times with fresh batches of ethanol in order to remove the unreacted Cu, prior to loading)        
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If I correctly understood the theme, Cu was not leached from solution but mainly from HKUST-1 net. This happens even without organic molecules interacting with Cu2+ ion, but merely with the presence of water media. If there are unstructured Cu2+ in the pores of the net, hence they should be displaced to the solvent phase through water/ethanol washings. But if you use adduct or chelating agents the scavenging of the metallic center from the net is driven through adduct, chelate or macrocyclic effect depending on the employed substance that interacts, with Cu in this case. Its own dissolution or coordinating assisted dissolution happens due to the fact that the HKUST-1 crystallites are surface open/labile materials containing -COOH, -COO- and -COOCu sides or functionalities directed to the interaction with the solvent. Therefore having these terminals, these components should displace to the media since Cu is efficiently solvated with water molecules. In this way the displacement of both Cu ions and trimesate or trimesic acid towards water is observed by UV-vis, therefore the loss of material is attained. Having less and larger crystals should diminish the dissolution rate, but if you have more and smaller crystals, the dissolution rate should be higher. I hope to be sufficiently clear in this explanation. If you need further details in order to understand the issue please contact me and looking forward to help in the analysis of your experiments. Best regards. Hiram
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Salam
I want dissolve TTIP in ethanol by drop wising ethanol to TTIP under stirring but sometimes I get a White milky solution and in other cases I get a clear solution.
How I proceed to get a clear solution of TTIP and ethanol? For information I tried pure ethanol and ethanol 96% and always I get a milky solution 
Thanks in advance
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Hi...,
small amount of water can form milky color solution with ethanol therefore  You need to dry (purify) your ethanol and TTIP from water as much as possible avoid any water vapors before and during  making solution,and do not pass saturation limits.
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I am working in organometallic feild, Any one tell me why exchange Hg atom in Ar- HgCl to Ar- TeBr3 when added TeBr4 .What is exchange mech. for this reaction .
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We generally say that the reaction is driven by the redox potential of the corresponding metals. The reactions could be considered as Nucleophilic Substitution
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I have synthesized Cu-BTC and ZIF-8 but it seems that there are different routs for calculating yield.
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Dear Prof. Carlos
Thank you for your response and advice.
Regards
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I have a [Ru(SO2)(NH3)4Cl]Cl2 and I want to change at least two of the ammine groups of the complex for H2O or another Cl. Any suggestions?
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You can by choosen strong  ligand more than ammine
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Ligand:Thioamide Ligands
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Thioamides are better ligands and more likely to cleave than amides. The Ru could activate the thioamide to nucleophilic attack by solvent or adventitious water if you in a non-aqueous solution. 
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Hi all,
Can someone recommend some good papers or online books on the microbial biodegradation of organometallic and organometalloid compounds?
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Thank you very much for the links, Vit.
Best Regards,
Yannick 
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We have been working with aromatic carboxylic-amidic compounds and Cu(NO3)2·xH2O salt in various solvents, e.g. water, EtOH, MeOH, DMF and mixtures of them, these in order to generate coordination polymers, and in these trials we have obtained dark residuals. Therefore, in this conditions we aware that we are obtaining redox products instead of the stable coordination polymer. Please provide further advise in order to understand chemical transformations involving amide and Cu ions.
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You're reducing the Cu, what about starting from 4-formyl benzoic acid? if you make the reaction ie 4-amino aniline, you'll have the schiff bases which can be easily reduced to the amine group, those are very stable with copper in different solutions. Be sure to protect the acid group at the beginning. 
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what is the restriction to form M-M bond through produce an organometallic  complex for S and P block elements?
and when form single or double or triple bond between M - M for S and P block elements?
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More reduced states open the door for closer distances between the metal atoms. Higher order bonds require the metals to be in very low oxidation states so they can get very close to each other. Moreover, lower oxidation states result in larger orbitals which allows them to have a much better overlap.
Additionally, we can use very bulky ligands to protect such bonds. 
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As I have used DMF for the synthesis process of HKUST-1, I had to activate it in the oven at 110 0C after solvent exchanging with ethanol, prior to applications. while it was in the oven the colour of HKUST-1 turned from light blue to dark blue. when it was cooled to room temperature dark blue turned to the lighter colour as before.
Is the change in color due to the loss of solvent molecules during the activation process ? or has the MOF dissociated during the activation step ? or are there any other reasons for the change of colour ?  
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The change of colour from light to dark is due to the removal of the axial ligand (ethanol, DMF or water) from the copper acetate lantern, then the dark to light colour change is due to atmospheric water binding onto this coordination site. I find it's a good way to visually identify whether the activated samples have been exposed to air.
At 110 degrees Celcius, HKUST-1 should not have degraded, but it is worth checking by PXRD anyway. I have never done this desolvation when the sample wasn't under vacuum, so I'm not sure whether the air interacts with HKUST-1 at these comparatively low temperatures.
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Dear Friends,
I need your help for preparing the three dimensional structure of a newly synthesized organometallic complex. I have tried many times using Gaussview, but I could not create the exact structure. I want to run some dft calculations of this molecule. As you know, the initial 3D structure is important for optimization. If anyone has previous experience in dft calculations of metallic complex, please help me.
Thanks in advance.
Regards
Dr. Renjith R.
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Some ideas:
1. Look for a 6-coordinated Mn complex in the CCDC database. Ideally with similar bonding pattern (4 O and 2 N), although 6 O or 6 N should also do. Get the 3d structure(s) and build your system based on the crystal one. Preoptimize in PM6/PM7 (perhaps start with the Mn-O and Mn-N bond distances frozen at a reasonable value) and check if the results are OK. If so, run DFT.
2. Do the same but start with a simple, ideally octahedral Mn complex (like Mn(H2O)6). Build your system based on this by replacing all atoms except for the 6 ligating O atoms. Don't worry if the bond lengths / angles are not perfect, PM6/PM7 will take care of it in preoptimization.
Be aware, though, that for such complicated systems there are many possibilities for their structures, and simple DFT optimziation of 1 of them does not really make a good proof of the structure. You'll need some experimental validation of your results to make it publishable.
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I am intending to optimize an organometallic complex with Gaussian and M06-2X functional. I am dissociating a bond (between two oxygen atoms), so the correspondent bond is frozen. However, I encountered the problem that tells "Cannot scale VSX exchange in M06-2X". I did not have any issue when proceeding with B3LYP. Hence, the problem might be due to the starting geometry and the exchange of the functional used. Nevertheless, is there anyway I could proceed with such an optimization imposing the constraint at the bond and employing the M062X funtional?
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Hello Enrique,
Thanks a lot for your reply! Actually, I have tried to perform optimization with both M06-HF and the pure functional M06-L. However, the obtained result is invariant. Therefore, the error must be due to another factor
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We made ligands (N1 position of the imidazole) with ethyl group and with out ethyl group. ethyl consisted ligand have slight high band gap compare to that of without ethyl ligand. Generally electron donating groups attachment can reduce the band gap. But here slight difference. Why it is like this and might be free NH (no alkyl group) group play any role in the case of indeactive effect. 
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The band gap will be affected if the substituent position is able to interact with the HOMO or LUMO. Since this is a pi-system, and you are substituting in the plane of the molecule (orthogonal to the pi-system), the likely mode of interaction will be through hyperconjugation.
DFT calculations or old school HMO calculations should elucidate the positions of electron density within the HOMO and LUMO
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I have worked with a tetradentate rigid ligand to coordinate nickel(II), cobalt(II) and copper(II) with coordinanting solvents (water, DMSO, acetonitrile). However I haven't got single crystals to XRD. How can I use liquid UV-Vis spectroscopy to decide if the complexes are square planar or if they have another geometry?
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Kamel Landolsi, for Co(II) and Cu(II) NMR spectroscopy is not suitable since they are paramagnetic species (7 and 9 d-electrons). 
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I am trying to detect creatinine and I wanted to understand if there has been any study regarding any organometallic compound that has specificity for creatinine and forms a complex with it.
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I have not gone through the cited references, may be they have given better answers to your question. However i will answer your question around the logic that creatinine (2-Amino-1-methyl-5H-imidazol-4-one)  in its stable tautomeric form has an amine group attached to 5 membered ring which is an excellent ligand to most transition metals especially copper(II) and cobalt(III). so a copper(II) fragment can selectively bind to the creatinine with a significant thermochemistry. Some literature references for copper complexes of creatinine are as under:
DOI: 10.1016/S0277-5387(00)83797-3
In fact the Quantification of creatinine in biological samples is also based on the pseudoenzyme activity of copper–creatinine complex see the ref.http://dx.doi.org/10.1016/j.saa.2012.02.104
The Fluorescent creatinine assay is a method of detecting creatinine in body fluids using an indicator which produces a fluorescent response when oxidized in the presence of a copperII/creatinine complex. A preferred indicator is 4-(1-methylhydrazino)-7-nitro benzooxadiazole (MNBDH) see ref.(US 6872573 B2)
Fundamentals of Urine and Body Fluid Analysis
Nancy A. Brunzel - 2013.
In summary a copper(II) based fragment either from the above cited references or a newly designed one can do the job one such designed complex in described in the reference DOI: 10.1016/j.saa.2015.10.028 .
Good luck
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I need an easily synthesized Cu(II) complex that would be benzene-soluble.
I would be particularly interested in Cu(II) centers with ligands such as substituted amines or pyridines.
Cheers
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I could not resist to appreciate Mr.Felipe de S. Vilhena  volunteer offer to do the calculations. I applaud the gesture, and wish such sweet  sense of mutual help for the overall development of science, prevails all over the scientific community.
Bravo... 
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how can i remove HCl in a reaction which was formed as byproduct in chlorination reaction Thionyl chloride Used as chlorination  Agent, Solevt was toluene , Distillation at 80°C u/vacuum , but HCl content remains as 3 to 4 % , need to nullify the HCl content, can any body help?
co-distillation is possible? or Not ?
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A few things to note: firstly, HCl is not soluble in toluene, and therefore to say "the HCl content remains as 3-4%" does not sound correct.  In fact, toluene is used as a solvent precisely for this reason (as opposed to THF / Et2O /dioxane, which dissolve HCl; commercial solutions of HCl in these solvents are available ).
2. How do you know you see "3-4% HCl?" NMR? Give some info here.
3. You are working with pyridines; it is very likely whatever you see as "HCl" is the pyridinium salt. Heating and vac distillation probably won't help your cause. You will need to use an external base to deprotonate.
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Are there any molecular chemistry design rules that make a compound pyrophoric?
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I am not sure I would say they are generally pyrophoric.  Ferrocene is certainly not and there are many, many complexes described that are not pyrophoric.  Now, with respect to many compounds such as lithium, sodium, magnesium , aluminum alkyls the polarization of the bonds make reactions with oxygen ver facile and the liberation of heat and the presence of oxygen  is sufficient to combust the organic fragment.  There are a number of organometallic texts out there that you should look up and consult.
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i have directly used sodium pentaborate tetrahydrate powder of Merck company with water as a solvent , stirred for 5 - 6 hours , no chemical reaction was done.have added some drops of HCL to dilute it properly.
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Michael's explanation seems plausible.  However, the aqueous borate system is extremely complicated, and it's impossible for us to know what you might have isolated.  See the diagrams in the attached patent.  I'm sure even more is known today.
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I want to know which is the adequate force field for an organometallic system and how I can  create this topology file. I was working in some tutorials in gromacs with proteins but now I want to work in my own system.
Thank you in advance
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thanks for  your answers!
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Transition metal complexes and its applications to Electrochemical sensors 
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The attached links and papers provided by Saeideh Hosseini is valuable.
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I have synthesized some of the Ru-aqua complexes with OTf as a counter ion but wanted to exchange the counter ion to like PF6 / ClO4 . So how can we come up with the solution that which counter ion can replace which one and at what reaction conditions.
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A common anion replacement strategy in Ru chemistry is to use an ammonium salt. As mentioned by Ian it's usual to do this exchange with the chloride salt but it may work with triflate. You always need an excess. As regards solubility common solvents in ruthenium chemistry include DMSO, MeCN and water. You'll have to do a solubility screening to find out what works for your complex. I should mention that the use of silver(I) in Ru(II) chemistry can be a problem as it may oxidize you complex. If want to be sure that the exchange has occurred Tl(I) would be better, although it is toxic. 
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From the theoretical calculation, I want to know an easiest method or software from which one can have an exact information on the bonding of metal with the ligand in an organometallic complex i.e which d-orbital of the metal, dxy or dxz or dyz or dx2-y2 or dz2 is taking part in the bonding with the ligand. I have done NBO analysis using gaussian09. From there can I get some idea?
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I personally have not carried out NBO analysis and therefore won't be able to give you much information. However I hope the web link from a previous RG discussion could be of help.
Now as for the choice of a software to visualize orbitals, I personally use Gabedit (web link attached). It works well, and gives you the extent of orbital participation in each bonding situation with appropriate coefficients. I believe Gaussview can also help you get the same info.
On how to visualize using Gaussview and other similar useful information can be gleaned from "The Hunt Research Group"s web link (attached). It is thorough and walks one through the basics of setting up calculations, visualizing orbitals, and understanding results.
Lastly, you must be able to more or less guess at the d-orbitals involved in bonding even as you look at any structure.  Any inorganic chemistry text (for e.g., by Meissler and Tarr) teaches how to employ Group theory to determine SALCs and the corresponding MO.
One word of caution: Depending on the symmetry of your complex, you will see heavy mixing of orbitals, and orbital images in this regard can be confusing.  So having the necessary background (through knowing what the SALCs are and what MO's to expect) will help in your interpretation. To that end, the book titled "Orbital interactions in Chemistry" is priceless.
Best wishes.
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i need research papers on alkaline metal nitrides ie M3N2 where m=Be,Mg,Ca be that experimental or theoretical . plus i need their structural representations ie if ball and stick model is their that would be great ????
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Dear Saba,
I'm not sure what you want, but everything I have is in the .cell file in my earlier post. The file is plain text, so you can just read the lattice vectors (in Cartesians) and fractional positions straight from it (they're the first 2 blocks after the header).
If you want to visualise the structure, you can import the .cell file into jmol directly; in case you haven't come across it before, jmol is a free 3D visualiser, which can be downloaded from http://www.jmol.org.
All the best,
Phil
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We are synthesizing poly(silylethers)s from diols and silanes but the purified products are viscous in nature rather than solids.
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It can be employed as thickeners agent, sealants, controlled release of drugs,  etc.
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I have applied DFT calculation, B3LYP level of theory.
I have done the split basis set.
The complex consists of H,C,Cl,N, and U.
I have tried to apply 6-31G to the light nuclei.
And have tried to apply SDD or MWB60 (ECP) to the U nucleus.
Yet no matter what I try, it never seems to be able to converge the fit.
Any suggestions for input or modifications would be helpful! Thanks.
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In the computational papers dealing with U I've seen, the most commonly used basis set is the Stuttgart RSC 1997 ECP for U. Try this basis set, as well as LANL2DZ and CRENBL (you can get all three at https://bse.pnl.gov), and see if you can obtain converegce and reasonable geometries. Also, you can think of upgrading the light atoms basis set to 6-31G* (or 6-31G**).
There is also a set of gaussian keywords that help when convergence is difficult to obtain; try these:
opt=z-matrix or opt=cartesian
scf = qc or scf = xqc or scf
and different comobinations of them.
If that doesn't help, you can try changing the starting geometry and think about changing the DFT functional to any other modern one (PBE, M06).
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I believe adding strong base would form the FeOH3 instead of the complex
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Dear Ahmed,
better to use anhydrous Fe salt for complexing with shiffbase ligand.
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Where does this value come from? Computational chemistry or experimental evidence?
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