Science topic

Chemical Bonding - Science topic

Chemistry as a core subject or as applied science cannot be understood without having a strong grasp on chemical bonding. From our head to toe, from kitchen to a super market. from a cart to a spaceship, there is compounds, molecules, free radicals, ions all in one way or other shows bonding. At the same no bonding is 100%, a covalent specie has ionic character and an ionic specie show covalent character. So lets explore the world of chemical bonding by sharing, contributing or transferring our knowledge
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A variety of adsorption studies are being carried out globally. I want to know, if any molecule is adsorbed over the surface of any substrate will built-in electric field generation take place at the junction? The question needs to be divided further into two parts (i) when the molecule is adsorbed and it does not form any chemical bond with the substrate there is a charge difference at the interface and there should be the generation of a built-in electric field (ii) if there is any type of chemical bonding still the polarity difference is intact, shouldn't electric field be there ?
Please attach any literature that supports your answers.
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Hi Brajesh, I a not familiar to this area of research. I hope you will find someone better experienced person for the discussion. Moreover, if I cone to know someone working in this area, I will let you know the needful. Good luck.
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Dear Researchers :
I have this question and I have an hypothesis:
Why Natural HDPE, when extruded at temperatures about 100 °C (around) it has a white (but pale white), and then when the polymer cools down it color turns between white an yellow.
I understand that this phenomenon it is a general case of all LLDPE, LDPE and HDPE , and in all fabrication processes : Extrusion, injection, molding, pressing, etc.
So this is fundamentally, a chemical characteristic of the material ...
It has to do with a change in the Oxygen concentration in the material ?
Thank you all in advance,
Best Regards !
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Dear Franklin Uriel Parás Hernández, both degradation and crystallization are behind the change in color aspect. My Regards
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The phenomenon of material interlocking
· Joint interface
Chain entanglement,
Diffusion bonding
Chemical bonding
Please share your thought.
Your opinion is highly appreciated
Regards
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I think in similar welding, diffusion bonding takes place, while in dissimilar material, the weld is formed due to some shape of mechanical interlocking, unless the two materials are compatible
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I'm currently looking at the rheological properties of the polymer Xanthan Gum. focusing on its dynamic viscosity to be more specific. I'm assessing the effects of pH (ranging from 3.6 to 5.6, 0.4 increment, total of 6 pH's) on the dynamic viscosity of xanthan gum solution (dissolving xanthan gum powder into acetic buffer with equal ionic strength, concentration is kept at 0.04%).
Firstly, my viscosity data collected shows that, as pH increases from 3.6 to 4.0 then 4.4, the viscosity increases; but as I bring up the pH from 4.4 to 4.8, 4.8 to 5.2, then lastly 5.2 to 5.6, the increasing viscosity trend plateaus and the increase in viscosity is less significant compared to the 3.6-4.4 jump. At this range, does pH has an effect on the viscosity of xanthan gum based on its molecular configuration? Though some sources states that xanthan gum's viscosity remains stable and unchanged within the range of pH 3-12 at a high concentration like 1% not 0.04%, yet some suggest pH still plays an effect, though I'm not sure how on the chemical and molecular aspect.
A possible conjecture I can think of is the xanthan gum's order-disorder and helix-coil transition is affected by protonation. In figure 2, it demonstrates how electrolytes affect the structure of the polymer; in figure 3, it shows how at a state of a helical rod and no longer a random coil, it is capable to hydrogen bonds among each other. Hence, I'm wondering of pH plays an effect on it's structural transition, such that the increased intermolecular forces at the form of a helical rod would make it more viscous in solution.
Here are the resources I have used so far:
Brunchi, CE., Bercea, M., Morariu, S. et al. Some properties of xanthan gum in aqueous solutions: effect of temperature and pH. J Polym Res 23, 123 (2016). https://doi.org/10.1007/s10965-016-1015-4
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Dear Ryan Lo, you may find various stufies on this topic. Please have a look at the following free access RG fille. My Regards
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Hi,
I want to remove thiol molecules on a gold substrate. After searching, I found couple of method described below;
1. NH4OH–H2O2–H2O solution aim is to initiate the oxidation of the thiol compound
2. Thermal desorption (above 200 ◦C)
3. Ultraviolet light and ozone (O3)
Do you have any experience about these methods. If your answer is yes, can you share your experience with us? Thank you for sharing and helping,
Best Regards,
Osman
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I would recommend going for ethanol washing followed by oxygen plasma cleaning under a vacuum.
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What is the temperature at which hydrogen desorbs from In - polar InN?
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100 degrees centigrade. This is the reason why you denature DNA at 95 degrees centigrade.
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Is it possible to change or form new chemical bonding using frictional heating during high sliding operations?
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Yes, it is possible. It depends against which material the friction occures. For instence, PI against SS creats a new chemical bond, etc.
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Hello, I am doing a carbon surface modification with Gold nanoparticles.
from the FTIR below, I know the formation bond of NH3 and for COO , but I would like to know what is the range of thiol bond formation, is this FTIR good or not?
note that I know that the difference between the bare SPE and modified SPE is the increase of current which is measured by Potentiostat.
thanks in advance.
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Dear Aseel Alnaimi, the above FTIR spectrum is not appropriate given the fact that the corresponding transmission percentages of all peaks are higher than 90% signifying that the sample content in your KBr pellete has been rather too low. In such a condition, on account of low signal to noise ratio, some characteristic peaks are embedded in the noise level and cannot be detected at all. So, I suggest you either repeate the FTIR analysis once more with a well-prepared KBr pellete or use ATR-FTIR technique which can provide you with a higher S/N ratio for the surface functional groups. However, FTIR spectrum might not solely justify what you are dealing with but if it is accompanied with other surface characterizations especially XPS, it will most likely lead to a more rational conclusion. Please note, the characteristic peaks of the carbon materials are usually of low intensity, that is why it is mostly preferred to use XPS as a more reliable technique for inspecting their chemical structure.
Best,
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I see that silver mostly has a coordination number of two, and have seen to complex with two mono-dentates. Can Ag+ form complexes with di or tri or any polydentates ligands?
What kind of complex can Ag from with O- ? (when conditions are such that Ag2O does not form)
regards
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Hello Deepak,
this is in fact a very interesting technical question (or better two questions). For the first part of your question (Can Ag+ form complexes with di or tri or any polydentates ligands?) the answer is clearly YES. This is easily possible when the ligands are of the so-called tripod-type. The most prominent examples of these ligands are the tris(pyrazolyl)borate anions. The are also ferquently called scorpionate ligands. The tris(pyrazolyl)borate ligands and their coordination chemistry were developed by the Ukrainian-born chemist Swiatoslaw Trofimenko (1931–2007) in the mis 1960's and are still highly popular in coordination chemistry. The potassium salts ofc these ligands are easily prepared from KBH4 and various pyrazoles in a melt reaction. The resulting tris(pyrazolyl)borate anions for stable complexes with almost every metallic element in the Period Table including silver. Due to their special tripod-like geometry the scorpionate ligands are almost always tridentate. Thus with Ag+ they form tetracoordinate complexes. For a good overview of scorpionate complexes of copper, silver, and gold please have a look at the following useful review article:
Trispyrazolylborate coinage metals complexes: Structural features and catalytic transformations
Unfortunately this paper has not been posted as public full text on RG. However, two of the authors have RG profiles. Thus you can easily request the full text of this review directly from one of the authors via RG.
Good luck with your research work and best wishes, Frank Edelmann
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Dear all
My major is based on the experimental. I rare often go to get help from software.
I am looking for the software to simulate the possibility of chemical reaction between POLYMERS. The reaction was not reported yet in any paper. I tried to find somehow similar reaction between two polymers with similar functional groups. But, not successful. I tried to use MD simulation, but interaction parameters are completely unknown. Again, I tried to use the interaction parameters between two similar MOLECULES (and not polymers).
I am wondering if there any software to simulate the reaction properties including the possibility of the formation of the chemical bond, decomposition of the bond, equilibrium constant, the heat of reaction, is it equilibrium one or not, how the Temperature, pH, ionic strength, time …. Affect the reaction.
I don’t mind if the results come with some error since my synthesized polymer and my reaction not reported at all, although basically, it is very simple for the reaction between two functional groups. It is the reaction of –COOH with an amine (but both of them are a polymer).
It would be nice if I can design my polymers only with the 3-4 monomer (oligomer) and then try to see the results.
I don’t mind, I pay for software. The high cost is also OK. But, I am a Chemical Engineer, and my knowledge about chemistry is poor. I can get professional chemistry help.
Best regards
Rajabzadeh k. Saeid, Associate Professor
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Some software of quantum mechanics such as Gaussian, Hyperchem, Material Studio or Gamess could support you to solve well it.
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I have stadium stairs made of concrete, and i need to pick an adhesive material that give a good bonding strength and can resist some environmental factors such as hot and cold weather without peeling off. ( ceramic- polymer composite).. I can،t wait to read your esteemed answers.
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I would like to recommend Silicone Rubber Compounds - RTV 2 components which perform the ability of high thermal conductivity and adhesive. Some famous brand names which you can refer ShinEtsu, Momentive, or Dow-Corning.
References:
Best regards.
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Currently trying to bond a PDMS layer to the nickel plate with a very thin thickness (0.25 mm). I have tried several adhesives (epoxy, instant adhesive etc.) however none of it seems to work. Meanwhile, I have already looking at but haven't tried the method of PDMS bonding to glass by simply applying pressure while putting it at a certain temperature (60 - 80 Celcius). Does anyone have any experience with this ? or will this PDMS to glass bonding method also work for nickel plates?
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Dear Michael, many thanks for posting this very interesting technical question. In this context please have a look at the following potentially useful article which migth help you in your analysis:
Introduction of a Chemical-Free Metal PDMS Thermal Bonding for Fabrication of Flexible Electrode by Metal Transfer onto PDMS
Fortunately this paper has been posted by the authors as public full text on RG. Thus it can be freely downloaded as pdf file.
Good luck wth your research and best wishes, Frank Edelmann
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I think that urea-formaldehyde resin(UF) and melamine-formaldehyde resin(MF) or MUF resin have a physical bond with wood. Also, I think that phenol-formaldehyde resin and MDI are chemically and physically bonded with wood, but I would like to check if my thinking is wrong.
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Dear Bora, thank you for this very interesting technical question. For a good introduction to the bonding between wood and various adhesives please see the following instructive articles:
Wood Structure and Adhesive Bond Strength
and
Wood Adhesives and Bonding Theory
Both articles have been posted as publc full texts on RG so that they can be freely downloaded as pdf files.
For more detailed information about the use of urea–formaldehyde (UF) resins please also have a look at the following useful RG link:
Urea-formaldehyde (UF) adhesive resins of wood
Good luck with your work and best wishes!
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Hello everyone
I use a metal powder as the filler to a thermoplastic polymer matrix. Therefore, I wonder if there are any changes such as the molecular weight distribution, occurring in the structure by adding the filler metal powder?
My regards.
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Dear,
Some pigments can cause property modifications. I have tested PLA with different colors, and they have different tensile strengths.
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Is any way or method to seal agarose pad or channels fabricated agarose gel pad to glass slides as like we do plasma bonding with PDMS to glass slides?.
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Good question
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Understanding the presence of chemical bonding in a polymer is available using FTIR or Raman Spectroscopy.
Considering a chiral solid-polymer (fabricated mat); Is there anyone who can hint at finding out and plot dipole orientation?
Any help for a characterization technique to ascertain and analyze the dipole bond rotation by the quantity and/or quality is generous.
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Amirhossein Farahanii If you need to study orientation analysis, then you can carry out 2D XRD analysis and SAED using TEM. SAXS is also used for orientational studies. Hope this helps in any way.
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Hello,
I did a oxygen plasma surface treatment of a polydimethysiloxan surface. i coated it with two different materials and the bonding improved significantly with one of the materials.
the other material wasnt affected at all by the plasma treatment.
Now i want to draw conclussion about the polymer that are used in this materials. Which kind of polymer bond with a oxygen plasma treated pdms surface?
I think the material with the improved bonding is a silane-terminated polymer, but i am not sure about it.
Please let me know if you got some knowledge about this topic or any hints for me
Thank you
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I guess that the hydroxyl-terminated polymer will have a strong bond with the plasma treated PDMS. Because after the treament with oxygen plasma, PDMS surface will be covered by a lot of hydroxyl group.
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I would like to illustrate this question below.
I am studying the material, which has predominant covalent bonding at ambient conditions. Now I am changing (increasing) the temperature. Due to these changes in temperature, the predominant ionic bonding has been established now in my systems. In this present case, temperature-driven bonding transition (from covalent to ionic bonding) has been established in the material.
How do we characterize the above-mentioned bonding transition? What are the characterization techniques to understand this bonding transition?
I kindly request you to answer this question. Your answer will help my research work a lot.
Thanks,
Rajaji.V
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You have not mentioned whether the bonding changes caused by symmetry change or not.
Temperature (T) /pressure (P) dependent XRD could be one of the possible ways to probe the bonding changes. The bond length changes would be reflected in the T/P vs bond length plot. To get reliable information from XRD, you need high quality synchrotron XRD data and also you should do a careful Rietveld refinement. For high pressure case, there might be a change in bulk modulus before and after the bonding change. Since the bond strength of both covalent and ionic bonds are different, definitely there can be sharp changes in the corresponding phonon frequencies (in T/P vs frequency plot) at the transition point.
The above changes can also be possible due to various other reasons. So it is hard to say the above changes are purely due to bonding changes. For high pressure case, first principles calculations can also predict pressure induced changes in bonding character.
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Dear
I want to measure strength of polymer-to-metal adhesive bond. My final sample is produced in this way, first I insert metal into plastic injection mold and then inject plastic into mold by plastic injection machine. picture of final part is attached. now my question is that which standard is suitable for measuring strength of polymer- to-metal adhesive bond of this sample?
Many thanks in advance for any kind help
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Standard Test Methods for Rubber Property—Adhesion to Rigid Substrates (ASTM D429) is used for measuring bonding strength of polymer-metal. I have attached the standard.
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NBO analysis of a donor-acceptor interaction not showing any NBO associated with that particular interaction. Although there are no NBOs associated with the interaction we are interested in, is it still something else useful we may deduct from it. We are not interested in NBO charges.
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Natural Bond Orbital (NBO) PopulationAnalysisof1-Azanapthalene-8-ol
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I believe that in a particulate composite with elastic mismatch between the matrix (brittle) and the aggregate (ductile) the bond strength between the matrix and aggregate will have an impact on the overall elastic modulus of the overall composite. Would anyone be able to point me in the right direction please?
Thank you!
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There is a relationship between elasticity and particle composition as well as between turgidity and plasticity. A major factor is the type of particles and their compounds. As well as their size in structure and their landings. The presence of phases of the early-born type lead to a decrease in plasticity and an increase in the modulus of elasticity, ie the Yung modulus.
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How can an XRD or an FTIR Pattern help to identify their nature if it has not been reported previously?
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Is there any reference to explain the polymeric bonding mechanism of epoxy resin polymeric adhesives to carbon fiber reinforced polymer (CFRP) laminates or strips. I am a structural engineer and I would like to understand the chemistry aspect of this bonding process.
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You did not specify the resin used for CFRP. The adhesion mechanism all depends on what resin is used for making the composite. However, both thermoplastic matrix or cross-linked thermosetting polymer all exhausted the chemical reactivity by making the composite laminates. Even for a popular matrix for making a composite, epoxy resin matrix, the chances are that the epoxy does not have chemical functional groups left to form covalent bonds with the epoxy adhesive. This leaves the secondary bonding interactions, such as hydrogen bonding, van der Waals interaction and mechanical interlocking, the only bonding mechanisms. For example, an epoxy used for making CFRP will have residual hydroxyl groups to which the epoxy adhesive can hydrogen bond. In case you can heat treat the bonded system to rather high temperature, these hydroxy group can potentially form ether bond (covalent bond), but this is not a usual situation if you use room temperature or near room temperature curing conditions. In case the composite laminate surface can be roughened, then the epoxy adhesive can form some mechanical interlocking, which will further enhance the adhesion.
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ABO3 perovskites show cubic structure at high temperatures where the
A-site cation is having 12 coordination with oxygen ions and
B-site cation is having 6 coordination with oxygen ions
But whereas in low temperature stable phase of ABO3 structures (particularly in rhombohedral sodium bismuth titanate)
What is the effective A-site cation coordination (6 or 9 or any other) in NBT?
Please give me brief answer with references.
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Does anyone know about techniques used to study chemical bonding between protein(peptides) and vitamins after passing through artificial gut?
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You can use these articles:
DOI : 10.4155/tde.13.104
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I have a a question regarding surface modification of SiO2 chip. The presumption is that vapors of trimethylsilanol (CH3)3SiOH bond with the original hydroxyl terminated surface of the chip and cause wettability issues, not unlike the manufacturing process of hydrophobic sand (Magic Sand). Could someone please advise how would we go about removing these methyl terminating groups from surface and restore the original hydrophilic hydroxyl group termination?Oxygen plasma did not seem to have an effect on improved wettability. Surface is Si₃N₄, SiO₂, aluminium pads.
Thank you for ideas.
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Piranha, which is a hazardous mixture of sulfuric acid and hydrogen peroxide
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I did Electrophoretic deposition of Ni-Graphene composite on stainless steel and carbon steel as a substrate, but the problem that i am facing is that chemical bonding of above mentioned with substrate is not so good and can be easily removed, need a suggestion what to do?
Note:
During experiment i used Graphene and Ni soloution instead of graphene oxide.
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Thank you Sir Abu Bakr Nassr .
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I need the exact nature of chemical bonding of ZrB2. I think it is mainly covalent, however, is there any reference or an exact database about he percentage of covalent or ionic bondings?
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Shpend Mushkolaj Thank you very much for your comprehensive and insightful reply.
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What does complexion stands for, and how complexion is formed or mechanism of complexion. what is its importance in adsorption? Is it any way related to cation exchange?
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Uddipta Nath Don't use your own terminology, follow IUPAC recommendation.
For a "complex" see
"A molecular entity formed by loose association involving two or more component molecular entities (ionic or uncharged), or the corresponding chemical species. The bonding between the components is normally weaker than in a covalent bond. The term has also been used with a variety of shades of meaning in different contexts: it is therefore best avoided when a more explicit alternative is applicable. In inorganic chemistry the term 'coordination entity' is recommended instead of 'complex'. See also: activated complex, adduct, charge transfer complex, electron-donor-acceptor complex, encounter complex, inclusion complex, σ-adduct, π-adduct, transition state"
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Is this curvature only related to the spatial arrangement of the links in their structure.
Does this spiral state have a fundamental effect on the function of this molecule?
In particular, does it make it easy to copy genes?
Or is it only helping to occupy this long string in a smaller volume?
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Differences in strength of hydrogen bonds between Adenine (A) and Thymine (T) base pairs and Guanine (G) and Cytosine (C) base pairs seems to provide basis for these base pairs to be set at an angle of 36 degree rather than exactly above each other. This leads to a spiral structure of the double helix DNA.
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I tried to heat (oxidise) the Fe powder at 500C and it got sintered (bonded) together. The bonding is so strong that its not easy to manually grind it to get back the iron oxide powder. XRD shows that all Fe transformed into Fe2O3 and Fe3O4. What is the reason of this bonding? and How to avoid this?
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If your aim is to oxidize the Fe powder, this was achieved. The reason for the bonding is sintering.
Fine powders usually present high surface area, which is the driving-force for sintering processes via solid state diffusion. So basically, when heated at 500 ºC, your powders did sinter, meaning necks between the particles were likely formed. In addition to that, oxidation also took place. In fact, it is known that α‐Fe2O3 was found on abraded iron specimens which were oxidized at any temperature above merely 130°C (see H. R. Nelson, The Low Temperature Oxidation of Iron, The Journal of Chemical Physics 6, 606 (1938); https://doi.org/10.1063/1.1750132). Of course kinetics at such low temperatures require longer exposure times. You may monitor the reaction process by carrying out TG/DTA analysis and XRD analysis.
The fact that you observed sintering of the iron powder at 500ºC suggests that you should decrease temperature (try 300 ºC) in order to minimise this phenomenon. If that will not be feasible, you can try to dry mill the heat-treated powder, since at such low temperatures, sintering is certainly at its early stages and so it should not be hard to break the bonds between particles. For that you must use a planetary ball mill. You can control the powder particle size distribution by performing laser diffraction measurements on a CILAS or Malvern equipment. Bear in mind that that oxidation of iron is an exothermic reaction, so localized heat released may also enhance thermal diffusivitites, thereby promoting further sintering.
Kind regards,
Fernando Costa Oliveira
Lisboa, 20th September 2018
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Please discuss if the calculation of bonding energy (metallic/ionic/any others kind of bond) between two atom of a crystal structure (cubic/tetragonal/monoclinic/any kind of crystalline structure) is possible using the Rietveld refinement of the XRD data and how?
For example, how to calculate the bonding energy between A-B atom of ABX3 structure using the refinement study of the XRD data after details investigation and which parameters should be considered?
Thanks in Advanced.
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I have been thinking in organosilanes, but I am concerned if these binders will affect TiO2 photocatalytic properties. Although a physical deposition shows usually good adhesion, I am interested in creating a chemical bonding between the substrate and nanoparticles
Best regards
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No, but I'd consider dispersing the TiO2 in a thin epoxy and then treating the ceramic with an appropriate primer before applying the coating.
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Dear respected RG members,
I am doing Mulliken population analysis of Cobalt (Co) doped MgO lattice (rocksalt) using CASTEP code (ultrasoft pseudopotential). I found some strange data as follow:
for pure MgO
bond population (Mg-O) = - 0.73
for (3%) Doped MgO
bond population (Mg-O) = - 0.31
bond population (Co-O) = 0.42
Is the negative value of of Mg-O reliable?, since negative value indicate antibonding, small value close to zero indicate ionic bonding and large positive value (Co-O) indicate covalent bonding. As we know, MgO has a very strong ionic bond, therefore bond population (Mg-O) must be close to zero. All parameters that I used during optimization are correct. I also did the same calculation using ( norm-conserving ). The obtained data gave almost a good result as suggest by Segall et al. (Mg-O = 0.58) and (Co-O = 0.53).
Thanks in Advance
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The Populations analyses and their different corresponding bonds types.
best regards sincerely,
BENGHIA Ali
PhD in Physic and Chemistry of Materials,
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Chemical covalent bond investigation between phospholipids and protein??
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Thank you Steingrimur Stefansson and Ms Ivanova.
I will get back to you as I get more information
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Hello,
I want to bond PDMS on 3d-printed structure (from SLA 3d printer, Form 2). In fact, I don't know exact composition of resin of 3d printer, but I guess its main component is acrylate (maybe PEGDA).
How can I bond them? I've googled, and found that PDMS and PEGDA can be bonded with 3-(trimethoxysilyl) propyl methacrylate. If correct, with which process should I bond them with this chemical?
Thank you.
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Such 3D printed materials from SLA printers are more in the range of PMMA than PEDGA.
After cleaning, drying and curing the SLA part, have you tried plasma treating the surface?
If that doesn't work, discuss with the provider of the PDMS which primers he would recommend.
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First, I grew the ZnO films on Si(111) by RF sputtering system and then I used the Ar ion bombard on the ZnO films surface. I would like to observed not only changes on surface morphology but the chemical bonding or defects(XPS) on the ZnO films surface at various stages of bombardment. Moreover, the Ar ion will strike the Zn and O atoms and reveals the defects or Zn(metallitic) terminated surface. So when I used the oxygen gas into the chamber and react with the surface after bombardment process it would change the surface state again.
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There is a fair body of literature on the holes in ZnO, and these can be observed in XPS either directly as described by Thomas Breuer or by 'band bending' wherein you analyze the valance region for changes. The attached article shows how simply annealing ZnO can effect the band structure even when you are well bellow the sublimation temperature.
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Why does water molecule forms 4 hydrogen bonds maximum with others water molecules??
Is there any method to determine number of H bonds acceptance (for other molecules)
(see attached pic.)
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I think because it makes a tetrahedral which is favorable when you have oxygen there. With an NBO analysis in Gaussian you can get the number of H-bonds in your molecule.
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What kind of interaction does the performance resins offers for a filled elastomer? Is there any chemical bonding or only a physical interaction between these resins with the elastomer..?
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I did annealing of polyethylene of 200um(size 2x2 mm) on Silicon at 300 °C for 10 min. After the annealing process i saw the thickness of polyethylene increased to 500um approx!!!!!!
Can anyone explain why there is increase in the thickness of 200um to 500um of polyethylene????.
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Why would you have heated the polyethylene to 300 Celcius?? It has melted.
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Hi, in the last days i have been reading about nbo method and i have the next doubt:
is it always reliable the bonding description of a molecular system you obtain using the NBO method? In which cases do you consider that it is necessary to have special care when analyzing the NBO results?
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To begin with, the NBO algorithm is not unique. We tried to find NBOs for several similar systems (complexes of B12N12 with HX, X=Cl,Br,I) and found that with default thresholds for the NBO program we got different orbitals (e.g. different number of lone-pair orbitals on nitrogen). We had to switch to a lower, nondefault threshold to prevent this behavior. Now, in our case we will be able to detect the problem quite easily (number of LPs different from expected 12), but in other cases it may be not so straightforward. Additionally, we have found the the second-order energies from NBO could possibly show trends, but they do not correlate well with e.g. total interaction energies. Here is the DOI of our paper
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Hi dear all
I really need to find the EAM potential of Fe-Pt, but I don't find It in any sites.
Does anyone know how to find this EAM potential?
Please guide me
Thanks
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The content of README file for above mentioned LAMMPS's tool:
"EAM database tool
Xiaowang Zhou (Sandia), xzhou at sandia.gov
based on this paper:
X. W. Zhou, R. A. Johnson, and H. N. G. Wadley, Phys. Rev. B, 69,
144113 (2004).
This tool can be used to create an DYNAMO-formatted EAM
setfl file for alloy systems, using any combination
of the elements discussed in the paper and listed in
the EAM_code file, namely:
Cu, Ag, Au, Ni, Pd, Pt, Al, Pb, Fe, Mo, Ta, W, Mg, Co, Ti, Zr
Steps:
1) compile create.f -> a.out (e.g. gfortran create.f)
2) edit the input file EAM.input to list 2 or more desired elements to include
3) a.out < EAM.input will create an EAM *.set file
4) in DYNAMO or LAMMPS lingo, this is a setfl file
that can be used with the LAMMPS pair_style eam/alloy command
"
The procedure is simple and the resulted file for Cu-W is attached. May be you can try it with LAMMPS.
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I performed calculations on metal-metal multiple bond. For the Cr-Cr system, one electron on σ*-anti-bonding, two on σ-bonding, one electron on π*-anti-bonding, two on π-bonding, the bond order for Cr-Cr is 0. However, for the Fe-Fe system, one electron on σ*-anti-bonding, two on σ-bonding, one electron on π*-anti-bonding, two on π-bonding, the bond order for Fe-Fe is 1. Why? Who can tell me on what condition the half bond could exist, please?
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My suggestion is that you compute the bond order using a reliable method. If it is around 0.5 (or less) then you know that it is a partial bond. If it is around 1, then it is a single bond.
See the following paper for details: T. A. Manz, "Introducing DDEC6 atomic population analysis: part 3. Comprehensive method to compute bond orders," RSC Advances, 7 (2017) 45552-45581 (http://dx.doi.org/10.1039/C7RA07400J ). This algorithm for computing bond orders is more widely applicable than alternative methods.
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Dear all, Can anyone suggest few bonding gum/ adhesive solution which can use to assemble or to stick 2 layers of uncured rubber.
Thank you
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My suggestion is to use epoxy resin as an adhesive. The epoxy is usually sold as 2 components in 2 containers (one is the epoxy pre-polymer & the other is a hardener which is mostly a diamine). Some of the 2 materials are placed on a piece of glass & mixed with a glass rod. The mixture is applied by the rod to the 2 rubbers that are to be stuck together at the points of joining. 
This adhesive takes time to cure but it provides a tough and environmentally insensitive adhesion. Some experts claim that the epoxy can bond anything to anything (e.g.rubber to rubber, metal to plastic, plastic to wood...etc.). I used it to stick a plastic knob to a wooden cupboard & it worked very well.
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samples of coconut shell having specified length and width are cut. I am trying to make these samples straight/ flat as the coconut shell are curved (like an arc) in nature. Is there any way or method by which the coconut shell samples can be made straight/flat? Please provide some methods or techniques by which coconut shell shape can be modified. 
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Dear Alfa Guria,
Long time ago, as a student, I ground  a piece of coconut shell on to a piece of sandpaper to get it straight and thin, as such to be inspected under the microscope. I am  sorry I do not know what is your aim on it. Good luck
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Antibody – antigen interactions might involve all types of chemical bonding, except which one? Explain.
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It is the covalent bond. A covalent bond needs a chemical reaction, which does not happen in the case of antibody and antigen interaction. And all other bonds are affinity bonds.
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My primary motive is to heat seal the PP mesh with a Silicone structure. But if its not possible, then I need to know what are other options are available. 
Also, I want to know if any material other than Silicone will do the job better, given that the material has to be flexible and bio compatible.
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Best permanent solution would be to treat the PP with a Corona discharge then use hot melt reactive polyurethane adhesive to laminate it to the silicone sheet
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What I wonder is that assuming I have two proteins namely protein-A, protein-B and protein A is somehow modified by protein B (simply an enzyme catalyzing the addition of -OH group to certain Proline residues in protein-A), is it feasible to acquire profound insight as to how the protein-B comes closer to the certain sites in the protein-A and initiate the interaction?. More broadly can one be able to investigate how the structure of an enzyme affect what it does in a dynamic way (conformational changes along the catalysis, how the rest of the enzyme rather than the active sites contributes to its function or any important water enzyme interaction etc.). And besides that how one should think of the catalysis process in an intuitive way. What I mean by that is in biochemistry books it is just said that "This enzyme adds Oxygen from the dioxygen in the environment....." I mean how should one imagine this process in a more physical and theoretical way ?. It really bothers me the fact that I just cannot imagine the cascade of events in a more scientific and theoretical manner. Also if these questions are so trivial forgive my ignorance on the matter. Any suggestion would be much appreciated, thanks in advance. 
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Imagine protein A and protein B in aqueous solution.   Each is surrounded by water molecules, but more importantly, each has a solvation shell (in this case, hydration shell) around it.  There are several layers of these hydration shells (HS). The first HS is more tightly bound to the protein than the 2nd layer, and the 3rd layer more loosely bound than the 2nd layer, and so on, until you reach the bulk solvent which is no longer bound to the protein.  Now recall Brownian motion and Collision Theory in solution.  Protein A and protein B not only needs to encounter each other;  for them to get in direct contact with each other, they each have to overcome their respective HSs, but also be in the precise orientation with respect to each other so that their reactive centers (which are specific in both proteins) are in close proximity.  Only then can protein B do its job of adding -OH to protein A. So not all encounters between A and B are fruitful.  I hope this short scenario helps you imagine the "cascade of event" (as you said) that lead to the reaction between proteins A and B.  (NOTE:  Protein B must somehow pick up a water molecule in the vicinity and transfer its -OH to a proline residue  in protein A  -- I missed including this step in the above scenario, but you do get the point). 
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Can this be related to bond characteristic or electronic structure?
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It is all about the wave-functions mixing i.e. hybridization and the electronic configuration of the carbon atoms. The planar structure of the graphene is a result of mixing between the 2s and two 2p orbitals giving rise to the sp2 hybridization.
The third p orbital is left unchanged (its energy is also not changed). In silicon the situation is a little bit different as the hybridization in silicene is rather a sp2-like and the sp3 hybridization is more favoured for silicon.
Similar situation may be found at the surface of bulk silicon crystal for which unpaired broken bonds are responsible for formation of surface charge which is a driving force for the surface reconstruction. The surface located Si atoms are also characterized by the sp2-like hybridization.
It is also possible to obtain such buckled structure in graphene. You can induce a sp3-like character of the bond placing for example a hydrogen atom at a particular carbon atom in graphene layer. A good example of such structure is graphane.
I hope I could help.
Best regards
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I am trying to understand the possible chemical bonding between the carboxylic group and SDBS. Is there anyone here to help me out about this matter? Thanks,
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SDBS seems effectively to be sodium dodecyl benzene sulfonate, so Saeed is correct in writing a possible H-bond between the sulfonate anion and the acidic H. This interaction is only possible with the unionized RCOOH, for example in the solid state or in some organic solvent which cannot compete for H-bonding (I may discuss this point further if necessary). The H-bond is seen as "a non-covalent bond". "Chemical bonding" is not well defined in this context, but a covalent bond is unlikely between these two molecules.
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 how can be coated a Transition metal oxide on a sulfonated polymer surface ?
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I recommend to see the review
Best regrds
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Like helium 2s1 metastable state has internal energy of 20.61eV. How this quantity is determined?
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Mr. Das,
This value looks down upon internal energy one. Can you provide additional information associated with experimental conditions, for example?
Because of my fast computations of GS of He (1s2) show KE = 2.85532 and PE = -3.8820 a.u. (or -3.8820 a.u. or -105.63 eV). There is another theoretical data in the literature showing value -109 eV (GS). So, my computations are closed as order of magnitude and sign. Experimental data of the total energy of the state is -78.975 eV.
The data for 1s12s1 state are KE = 4.464997 and PE = -6.6797 a.u. (or -2.0298 a.u. or -55.23 eV).
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Respected All,
As through site-directed mutagensis, the catalytic activity of an enzyme is increase by analyzing there variants. But its time consuming and unpredictable when you are mutating the residues.I want to increase the activity of an enzyme by mutating there residues firstly through computational and bioinformatics analysis, then followed by experimentally among the best variants.
So by which principle i can chose to select among the active residue (interacting residue or nearby residue in the active site?) to mutate it ? Secondly how i can analysis through computationally that  this variants will  be have good activity as compared to wild type?. Can someone provide articles related to this work?
Thanks in advance.
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As Indu has mentioned about her paper ...that might be a starting for you....However in summary you have to first figure out what are the hotspot residues (residues which are participating in catalysis). You can start with the information available with the wild type PDB. Then you need to decide some biophysical properties which you want to concentrate, when you will carry out insilco mutation. Since, every site-directed mutation might not affect them quantitatively. For this you can use Swiss-PDBviewer, it gives option of mutation with different rotamer of each amino acids (it also shows the steric bumps or so). Then it has feature of calculating energy terms using gromos-96 frocefield. This software is totally free, you can download under free GNU license. Then you can use any autodock tool to know how effective those mutations are?
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It is well known that silicon interacts with lithium to form the Li-Si alloys, however, the nature of the atomic bonding between Si and Li atoms are unclear. Can you please share with me any theoretical/experimental or simulation findings about the nature of Li-Si bond?
Also, what is the best suitable simulation method to investigate the bond nature between Li and Si?
Thank you very much.
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Dear all.
I am working with the benzoyl chlorides with methoxy substituents. In that there exists S-cis and S-trans isomers. I wish to know which of the isomer possess minimum energy in general and what parameters can affect the energy of the isomers? Kindly help me knowing the same.
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Dear Venkatesan Ragavendran ,
The trans isomer always has less energy than cis one, due to the high dipole-dipole interaction that exist in case of cis isomer.
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There are a lot of questions here on RG how to calculate bond orders but i want to know how to interpret them.
So what does it mean when for example:
 - an sp3 carbon atom has a bond order significantly smaller than 4? say 3.8. 
-  a sulfur atom in a thio-ether Et-S-Et for example. has a bond order significantly larger than 2. say 2.3
- is an intramolecular hydrogen bond strong or soft when the bond order is around 0.05?
 etc. 
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Dear Jos,
counter-question: How you interpret the statement that "The average Belgian woman has 1.7 children"?
In physical reality, you deal with average electron densities around a set of atomic nuclei. The picture of single, double ... bonds is really an oversimplification of reality where you can gradually shift electron density between nuclei, instead of just "switching a bond on or off". Of course you can't split electrons, just like women don't give birth to 0.7 children, but if you look at their average distribution, that number emerges. So, to interpret bond orders: Do not think of it as a particle count, but rather as a charge density between atoms, expressed in elementary charges.
Also, as you have already noticed yourself, there are different ways to calculate bond orders. That is because you need to partition the overall electron density in your molecule into atom-centered and bonding contributions; but since there is no such strict distinction in reality, this partitioning is somewhat artificial, and different types of population analyses give you different results.
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I'm looking for a method to produce avenasterols. Does anybody know the process of making these compounds from other sterols or other sources of lipids? 
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Dear collegue
I'm very sorry, I can't answer you you can consult  reaction synthesis so biochemicel reaction that talk about this synthesis but you need enzymes and synthesis condition like cofactors and catalysors (catalysis) and more so you can consult specialist in eaction synthysis 
good chance 
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Or in other way, what is the role of atomic radii and bond length distance between two atoms in the formation of covalent bonds?
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Dear Muhammad,
The covalent radius, rcov, is a measure of the size of an atom that forms part of one covalent bond. It is usually measured either in picometres (pm) orangstroms (Å), with 1 Å = 100 pm. In principle, the sum of the two covalent radii should equal the covalent bond length between two atoms, R(AB) = r(A) + r(B). Moreover, different radii can be introduced for single, double and triple bonds (r1, r2 and r3 below), in a purely operational sense. These relationships are certainly not exact because the size of an atom is not constant but depends on its chemical environment. For heteroatomic A–B bonds, ionic terms may enter. Often the polar covalent bonds are shorter than would be expected on the basis of the sum of covalent radii. Tabulated values of covalent radii are either average or idealized values, which nevertheless show a certain transferability between different situations, which makes them useful.
The bond lengths R(AB) are measured by X-ray diffraction (more rarely, neutron diffraction on molecular crystals). Rotational spectroscopy can also give extremely accurate values of bond lengths. For homonuclear A–A bonds, Linus Pauling took the covalent radius to be half the single-bond length in the element, e.g. R(H–H, in H2) = 74.14 pm sorcov(H) = 37.07 pm: in practice, it is usual to obtain an average value from a variety of covalent compounds, although the difference is usually small. Sanderson has published a recent set of non-polar covalent radii for the main-group elements, but the availability of large collections of bond lengths, which are more transferable, from the Cambridge Crystallographic Database has rendered covalent radii obsolete in many situations.
References:
Sanderson, R. T. (1983). "Electronegativity and Bond Energy". Journal of the American Chemical Society 105 (8): 2259–2261. doi:10.1021/ja00346a026.
Jump up ^ Allen, F. H.; Kennard, O.; Watson, D. G.; Brammer, L.; Orpen, A. G.; Taylor, R. (1987). "Table of Bond Lengths Determined by X-Ray and Neutron Diffraction". J. Chem. Soc., Perkin Trans. 2 (12): S1–S19. doi:10.1039/P298700000S1.
Orpen, A. Guy; Brammer, Lee; Allen, Frank H.; Kennard, Olga; Watson, David G.; Taylor, Robin (1989). "Supplement. Tables of bond lengths determined by X-ray and neutron diffraction. Part 2. Organometallic compounds and co-ordination complexes of the d- and f-block metals". Journal of the Chemical Society, Dalton Transactions (12): S1. doi:10.1039/DT98900000S1.
Beatriz Cordero; Verónica Gómez; Ana E. Platero-Prats; Marc Revés; Jorge Echeverría; Eduard Cremades; Flavia Barragán; Santiago Alvarez (2008). "Covalent radii revisited". Dalton Trans. (21): 2832–2838.
Hoping this will be helpful,
Rafik
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I have  an octahedral iron complex
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Dear Sadeqh,
CAM-B3LYP  combines the hybrid qualities of B3LYP and the long-range correction presented by Tawada et al. CAM-B3LYP yields atomization energies of similar quality to those from B3LYP, while also performing well for charge transfer excitations in a dipeptide model, which B3LYP underestimates enormously. The CAM-B3LYP functional comprises of 0.19 Hartree–Fock (HF) plus 0.81 Becke 1988 (B88) exchange interaction at short-range, and 0.65 HF plus 0.35 B88 at long-range. The intermediate region is smoothly described through the standard error function with parameter 0.33.
B3LYP – probably the most successful functional so far.
it has a number of deficiencies:
polarizabilities of long chains.
excitation using TD-DFT for Rydberg states.
charge transfer (CT) excitations.
Reasons understood: long range exchange potential
behaves like −0.2r−1 instead of −r−1
.
CAM-B3LYP is meant to address these deficiencies.
Normalized alkene polarizabilities as a function of chain length.
CAM-B3LYP gets the trend right (close to HF). LDA too steep. B3LYP is
in the middle.
Model ethylene - tetrafluoroethylene system.
Fact: CT excitation energy varies like −R−1
.
CAM-B3LYP gives CT state with a correct trend.
LDA (SVN5) cannot describe nonlocal excitations properly.
GGA (BLYP) does not improve on it.
CAM-B3LYP provides much better estimation of non-local excitation energy
G2 test set (short bonds): CAM-B3LYP ≈ B3LYP
CAM-B3LYP improves long-range interactions: better
description of molecules with long bonds and reaction barriers.
CAM-B3LYP: a improvement on the long-range-corrected
(LC) exchange functional of Yanai.
provides as accurate description of charge-transfer systems
as LC. . .
. . . without sacrifying other properties (atomization energies).
For more information, please use the following link:
Hoping this will be helpful,
Rafik
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Can you any one tell how to optimize La0.5Eu0.5VO4 phosphor by using atomic coordinates(x,y,z) in GAUSSIAN software?
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Dear Mari,
LaVO4 and EuVO4 both have the zircon structure. As a result use the zircon structure (ZrSiO4) by replacing Zr by La and Eu. The same thing for Si that should be replaced by V. The bond length of the new structure should be changed to match the values for the experimental values of  La0.5Eu0.5VO4. If you are simulating the bulk of La0.5Eu0.5VO4  then you should use PBC for the periodic lattice which is available in Gaussian 09 software
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Any suggestion is good.
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Hello Aleksey E. Kuznetsov,
I am sorry that it has been so long before I saw your message. I can't get this paper. So could you send me it? My email is maxiaxia@bit.edu.cn
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I am just wondering if anyone has come across this value... thanks!
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Hi
Find in attach, 2 paper related to the O-H bond length in a carboxylic acid in solution.
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XX
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You are right Sudarsan. But Oxygen-Sodium bond has more ionic character than covalent.
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This is the first time that I try to calculate this constant. It is a very simple case in which an organometallic complex is coordinated by a donor ligand in a 1:1 stoichiometry. However, it is under fast exchange so I can only see one set of signals. I have accumulated NMR data at different concentrations of the ligand for a fixed concentration of the organometallic compound, and I can see how the signals are shifted with the concentration of ligand. Could anyone help me to start with this, please? Thanks in advance.
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I did this once as well, using NMR. You need the Benesi-Hildebrand model. With it, you can take the delta in the NMR shifts, factor in the concentrations of the ligand and complex you added at t=0, and fine the binding constant. It's fairly simple actually, and you've already done the hard part of collecting the actual data!
Look up Benesi-Hildebrand in Scifinder or Google to get the exact mathematical equation, make up an excel sheet, and get your results! If that doesn't work well, there's also the Foster-Fyfe model.
Good luck!
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I am taking cm and Columbus values. but not getting final result. So please inform. Peak under the curve in equation, where have to substitute (in which unit).
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Dear Rajamouli Boddula,
The following link contains a publication which depicts the units of the parameters in  Judd-Ofelt equations (theory):
Hoping this will be helpful,
rafik
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how to break R-S-S-R DISULFIDE BOND ?
for example : I have polyvinyl chloride I want to convert to polyvinyl thiol.
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Dear Ahlam,
The best method to obtain polyvinyl thiol is from polyvinyl alcohol. For this conversion from -PVOH to PVSH, see page 6741 in the attached file.
Hoping this will be helpful,
Rafik
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Why is triple-bond unstable when it's located at the end of molecules? What's the degradation mechanism? How can I protect triple-bond-containing molecules from degradation?
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Dear Zhang,
 This is because double and triple bonds are formed by lateral overlapping of p orbitals whereas single bonds are formed by head on collision of orbitals so single bonds are more stable and does not allow addition across them but the double and triple bonds are weak and allow additions across them and try to become stable like single bonds.The re activity of multiple carbon-carbon bonds are relatively greater than single bonded carbons like alkanes. Its because electrons on multiple carbon-carbon bonds are more exposed and unstable.  Multiple carbon-carbon bonds are characteristic carbon-carbon bonding to alkenes-with double bonds and alkynes-with triple bonds.  In the early days of organic chemistry, alkenes were described as “unsaturated” because, in contrast to the “saturated” alkanes, they were found to react readily with substances such as halogens, hydrogen halides, oxidizing agents, and so on. Therefore, the “chemical affinity” of alkenes was regarded as unsatisfied or “unsaturated.”
Why is ethyne so much less stable than ethene or ethane? First, C-C bonds are not as strong as C-H bonds. Therefore a gain in stability usually is to be expected when C-H bonds are made at the expense of C-C bonds; ethene and ethane each have more C-H bonds than ethyne has.  Second, ethyne has six electrons held between the two carbons and these electrons experience considerable mutual interelectronic repulsion. This accounts for the fact that the average C—C bond strength for the triple bond of an alkyne is 200/3 = 67 kcal, compared to 146/2 ==73 for the double bond of an alkene and 83 kcal for a normal single bond of an alkane. The relative bond strength of a multiple carbon-carbon bonds  such us alkyne and alkanes is smaller than normal single bond of an alkene thus making it less stable and reactive.
molecular antibonding orbitals for pi systems are lower in energy than sigma antibonding orbitals. this is resultant from less overlap between the interacting orbitals. A C-H bond is harder to cleave than a pi bond between two carbons. in oxidation reactions, you'll find that the more unsaturated a molecule is, the less stable it will be. carbon-carbon single and double bonds are too strong (for ethane, 140 kcal/mol BDE versus 90 kcal/mol BDE exact; for ethylene, 211 kcal/mol BDE versus 170 kcal/mol BDE exact). Carbon-hydrogen bonds are too weak (for ethane, 76 kcal/mol BDE versus 100 kcal/mol BDE exact; for ethylene, 82 kcal/mol BDE versus 113 kcal/mol BDE exact). The differences in CC and CH bond dissociation energies between ethane, and ethylene, and acetylene however are close to the exact values (with the exception of the CC triple bond energy), suggesting that the energy differences stem from a systematic bias in the energetics of CC versus CH versus radical electrons.But the Nitrogen triple bonds so stable and double bonded nitrogen’s are so unstable.,The three triple bonds you mention (N≡NN≡N, C≡NC≡N and C≡CC≡C) all have very high bond dissociation energies (from various sources such as this one they are ≈950,940 and 960kJ/mol≈950,940 and 960kJ/mol) so all of these triple bonds require a large amount of energy to break.
Regards,
Prem Baboo
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What is the solvent ?.can we use the 2-mercaptoethanol as reducing agent 
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Dear Alham,
The disulfide bonds are strong, with a typical bond dissociation energy of 60 kcal/mole (251 kJ mol−1). However, being about 40% weaker than C–C and C–H bonds, the disulfide bond is often the "weak link" in many molecules. Furthermore, reflecting the polarizability of divalent sulfur, the S–S bond is susceptible to scission by polar reagents, both electrophiles and especially nucleophiles:
RS–SR + Nu− → RS–Nu + RS−
The disulfide bond is about 2.05 Å in length, about 0.5 Å longer than a C–C bond. Rotation about the S–S axis is subject to a low barrier. Disulfides show a distinct preference fordihedral angles approaching 90°. When the angle approaches 0° or 180°, then the disulfide is a significantly better oxidant.
Disulfides can be hydrogenated  however, this reaction is not  practical:
RSSR + H2 → 2 RSH
For C-S bonds cleavage, please see the following:
1-Inorg Chem. 2007 Jul 9;46(14):5537-43. Epub 2007 Jun 5.
Cleavage of C-S bonds with the formation of a tetranuclear Cu(I) cluster.
Huang C1, Gou S, Zhu H, Huang W.
Author information
 
Abstract
The treatment of a ligand, 2,6-bis((4-(pyridin-2-yl)pyrimidin-2-ylthio)methyl)-4-chlorophenol (ClPPT2), with cuprous chloride under a weak base condition led to the formation of a neutral CuI4-centered cluster [Cu4(PPT2)4], whose X-ray diffraction analysis indicated that C-S bonds of the ligand were cleaved in the course of the reaction. To explain the C-S bond cleavage, a reasonable mechanism has been proposed. In support of it, four additional ligands, 2,6-bis((4-(pyridin-2-yl)pyrimidin-2-ylthio)methyl)-4-methylphenol (MePPT2), 2,6-bis((4-(pyridin-3-yl)pyrimidin-2-ylthio)methyl)-4-methylphenol (MePPT3), 2,6-bis((4-(pyridin-3-yl)pyrimidin-2-ylthio)methyl)-4-chlorophenol (ClPPT3), and 5-((4-(pyridin-3-yl)pyrimidin-2-ylthio)methyl)-2-hydroxybenzaldehyde (HBPPT2) were further tested to undertake the analogous reaction, and the cleaved products in these experiments were detected by electrospray ionization mass spectrometry techniques to clarify the process.
2-π-Conjugated Benzoperylenes: Sequential C–S Bond Cleavage and
Charge Distribution Patterns of the Anions
Ronnie Benshafrut,[a] Mordecai Rabinovitz,*[a] Roy E. Hoffman,[a] Naama Ben-Mergui,[a]
Klaus Müllen,[b] and Vivekanantan S. Iyer[b]
Keywords: Benzoperylenes / Reduction of PAH / Flavophen / Reductive sulfur extrusion / Sulfur heterocycle
Chemical reduction of polyaromatic hydrocarbons yielded already reduced hydrocarbon skeleton results in the stepwise solutions of long-lived polyanionic species. Reduction of a cleavage of the two C–S bonds and the extrusion of a sulfur
sulfur heterocycle afforded a stable sulfur-containing atom. Dimers of aromatic hydrocarbons such as pyrene and dianion. Sulfur extrusion from this dianion proceeded upon phenanthrene have been reduced as well. The interplay
further contact with the reducing metal. NMR and UV between coulombic repulsions and resonance energies is studies indicate a sulfur extrusion mechanism different than described that previously observed in THF. 
3-International Journal of Mass Spectrometry
Volume 263, Issue 1, 15 May 2007, Pages 71–81
 
Preferential cleavage of S S and C S bonds in electron detachment dissociation and infrared multiphoton dissociation of disulfide-linked peptide anions
Anastasia Kalli,
Kristina Håkansson, 
Abstract
Disulfide bonds generally show only limited cleavage in positive ion mode collision activated dissociation (CAD). However, it has been demonstrated that a reverse situation exists in negative ion mode in which preferential S S and C S bond cleavage occurs. Here, we show that electron detachment dissociation (EDD) and infrared multiphoton dissociation (IRMPD) of peptide anions containing disulfide linkages also result in preferential cleavage of S S and C S bonds. Resulting products are mainly radical ions in EDD whereas IRMPD produces even-electron product ions, as expected, thereby supporting different disulfide cleavage mechanisms for these two fragmentation processes. We also show that, in EDD, the presence of tryptophan can result in abundant side chain loss (129 Da), which effectively can compete with disulfide bond cleavage.
4- Palladium-Catalyzed Regioselective C–S Bond Cleavage of Thiophenes
Huanan Huang†, Jing Li†, Christophe Lescop‡, and Zheng Duan†
Department of Chemistry, Zhengzhou University, Zhengzhou 450001, P. R. China, and Sciences Chimiques de Rennes, UMR 6226 CNRS, Université de Rennes 1, Campus de Beaulieu, 35042, Rennes Cedex, France
Org. Lett., 2011, 13 (19), pp 5252–5255
DOI: 10.1021/ol2021302
Publication Date (Web): September 2, 2011
Copyright © 2011 American Chemical Society
5-Review Article Transition-metal mediated carbon–sulfur bond activation and transformations
Liandi Wang,a Wei Hea and Zhengkun Yu*ab
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Chem. Soc. Rev., 2013,42, 599-621
DOI: 10.1039/C2CS35323G
Received 09 Aug 2012, First published online 18 Oct 2012
C–S bond activation, cleavage and transformations by means of transition metal compounds have recently become more and more important in the petroleum industry and synthetic chemistry. Homogeneous transition metal compounds have been investigated in order to provide the fundamental insight into the C–S bond cleavage in problematic organosulfur compounds such as thiophene, benzo- and dibenzothiophene derivatives. Rendering transition-metal mediated reactions with organosulfur compounds catalytic may provide promising routes to deep hydrodesulfurization of petroleum feedstocks, and offer potentially useful synthetic protocols for cross-couplings and biomimetic organic synthesis. During the last few decades increasing work was documented on C–S bond activation and transformations by means of transition metal compounds. This review summarizes the recent advances in C–S bond cleavage via the insertion of transition metals into the inert C–S bonds of these problematic organosulfur compounds, and transition-metal mediated C–S bond transformations via C–S activation through cross-couplings of thioesters, ketene dithioacetals, sulfonyl chlorides, and other diverse organosulfur compounds.
Hoping this will be helpful,
Rafik
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Recently, I need to bond two layers together. Does anyone have the experience to bond between Si3N4 and SiO2, or TiO2 and SiO2? We cant use the anodic bonding method as we do not have the machine. I prefer to do the bonding process at room temperature. Could anyone help me to figure it out?
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What exactly are the dimensions you are talking about ? I would suggest you grow Silicon Nitrode over silicon oxide layer instead of performing the bonding (if your research/application allows). PECVD is usually used method to develop passivation layers of silicon nitride over silicon oxide.
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Hi! I'm working on a aC-Au interface , and I would like to determine when a C and an Au atoms are bonded, based on its electronic structure. for C-C I can determine it by means of the bonding distance, but I'm not sure if the same procedure would make sense for Au-C bonding. Does anyone has any ideas? Thanks
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Dear Sebastian,
I would suggest to do at least one or better all of the following: QTAIM, NCI and/or Natural Bond Orbitals.  The references to them you may find e.g. in our recent paper (see below, accessible also at the ResearchGate), and find that we were quite happy with these methods to qualitatively interpret a variety of bonds involving Au.  Make good pictures, get qualitative insights, and remember as Trzaskowski said above ""bond" is just a concept" - do not try to get too accurate or demanding. The bond length is of course a hint too.
"Noncovalent interactions determine the conformation of aurophilic complexes with
2-mercapto-4-methyl-5-thiazoleacetic acid ligands" DOI: 10.1039/c5dt01627d
Best of luck,
Grzegorz
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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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