Science topics: Chemistry
Science topic

Chemistry - Science topic

Chemistry is the science of matter, especially its chemical reactions, but also its composition, structure and properties. Chemistry is concerned with atoms and their interactions with other atoms, and particularly with the properties of chemical bonds.
Questions related to Chemistry
  • asked a question related to Chemistry
Question
30 answers
Which software is best for making high-quality graphs? Origin or Excel? Thank you
Relevant answer
Answer
origin
  • asked a question related to Chemistry
Question
3 answers
Mehlich-3, 20 L final volume:
0.2 M acetic acid (230 mL concentrated glacial acetic acid, ACS)
0.25 M NH4NO3 (400 g ammonium nitrate, ACS)
0.015 M NH4F (11.1 g ammonium fluoride, ACS)
0.013 N HNO3 (16.5 mL concentrated nitric acid, ACS)
0.001 M EDTA (5.85 g EDTA free acid, ACS)
Purpose: Soil nutrient extraction for boron, copper, zinc, phosphorus, iron, manganese, magnesium, potassium, calcium, and sulfur to be measured by ICP-OES.
Once all compounds are combined and dissolved, my Mehlich-3 extractant has a pH of approximately 3.2 instead of the pH 2.5 the SOP I'm following indicates the extractant should be. Should the unadjusted pH of the extractant be 2.5 and, if not, what acid would be appropriate to adjust the pH without impacting extractant performance?
Some preparation instructions suggest making a 3.75 M NH4F + 0.25 M EDTA free acid stock solution and adding a volume of that rather than adding NH4F and EDTA directly to the extractant as I'm doing above but I've never managed to get the EDTA to dissolve after dissolving the NH4F using that approach.
Thank you!
Relevant answer
Answer
Formic Acid maybe. It is used in LC-MS.
  • asked a question related to Chemistry
Question
2 answers
Good day,
If anyone can assist me, please. How do you measure ammonium and nitrogen from urine? what is the best simple method for someone who is new in chemistry if you can recommend the site where I can find the experiment of measuring ammonium and nitrogen would really appreciate it.
Thanks
Relevant answer
Answer
Hello,
in order to determine ammonium, i find that the Nessler method of determining ammonium should be suitable for you. As suggested in Paul Milham's answer, it is a colorimetric assay. It has the advantage of being easy to perform (no need to heat, for urine there should be no need to correct the pH and the reaction is fast) and sensitive. Don't hesitate to ask if you have any questions. Good luck.
  • asked a question related to Chemistry
Question
11 answers
How long does it take to a journal indexed in the "Emerging Sources Citation Index" get an Impact Factor? What is the future of journals indexed in Emerging Sources Citation Index?
Relevant answer
Answer
Clarivate announced that starting with 2023 ESCI-indexed journals will also be assigned an impact factor. See: https://clarivate.com/blog/clarivate-announces-changes-to-the-2023-journal-citation-reports-release/
  • asked a question related to Chemistry
Question
2 answers
We can test an antagonist e.g. at 10uM with varying concentrations of agonist. We can then use Schild/gaddum equation to find a KD (also known as KB) for the antagonist.
If i was to change antagonist concentration to some other concentration like 100nM, but test with same agonist, will the KD calculated for the antagonist change or not
Relevant answer
Answer
The Ki value of a ligand is normalized by the affinity of the radioligand for the protein of interest (Cheng Prusoff equation). Likewise, the functionally calculated Kb value is normalized to the EC50 of the agonist and the concentration of agonist used (described by Cheng in the Power Issue article that Tomasz referred to). In this case, it's best to run the EC50 calculation for each independent assay as a control. As long as the IC50 is well defined by complete competition, the calculated Ki or Kb value should be robust and consistent across varying concentrations of radioligand or agonist.
Ideally, though, you wouldn't want a completely saturating concentration of radioligand or agonist (stick to ~Kd/EC50) to ensure full competition.
  • asked a question related to Chemistry
Question
6 answers
Hello! What are the oldest literary sources you know that would mention pharmaceutical salts? I am aware of the first cocrystal [benzoquinone + hydroquinone] (1:1) investigated in 1844, but I could not find any mention of the first (or even the first described) pharmaceutical salt (Wohler, F. Untersuchungen über das Chinon / F. Wohler // Ann. Chem. Pharm. – 1844. – V. 51. – P. 145-163). If you know of such sources, please share them. Thanks in advance
Relevant answer
Answer
As far as I understand, at the turn of the 19th and 20th centuries, there were enough chlorides and sodium salts of the API. However, it is not yet clear when salts with organic counterions began to be used. Perhaps someone has such information?
  • asked a question related to Chemistry
Question
12 answers
If someone is granted with utility model can he/she claim it to be granted a Patent?
Is it legally acceptable?
Relevant answer
Answer
It would depend on the jurisdiction because patents are national rights as are utility models. Many countries don't have utility models and there are some which have what are called "petty patents" which are like utility models. I am only qualified to advise on UK law (and it would be a criminal offense under the UK Patent Act to mark a product so as to claim to have a UK patent if you didn't have a UK patent), but the rule of thumb for every jurisdiction must be to act honestly and reasonably. So if you have a German Utility Model then say you have a German Utility Model, if you have an Indian Patent Application, then claim you have an Indian Patent Application, etc etc
  • asked a question related to Chemistry
Question
2 answers
Data augmentation techniques drastically improved AI models while dealing with images and text, however, it is not so obvious how to translate these approaches to chemistry and materials science. What methods do you know and how legal do you think they are?
Relevant answer
Answer
When I was looking into data augmentation techniques, I came across SMILES enumeration for molecules.
  • asked a question related to Chemistry
Question
2 answers
I have some flyash and want to leach out Al2O3 and SiO2 using NaOH. IS there any additive which can help me to improve rate of leaching or dissolution .
Relevant answer
Answer
Under some circumstances there are a few organic acid ions such as oxalate, glycolate that marginally assist in silicate leaching but I am not sure if they would work in your case. However, if you find nothing else, they might be worth investigating.
  • asked a question related to Chemistry
Question
1 answer
We talk about the round oval shape objects. Grid is 15 um. We supossed some kind of drug crystals, but patient has no special medication.
Chemistry:
blood 2+
leukocytes 2+
pH 7.0
SG 1.009
Relevant answer
Answer
Fat droplets? Check with polarized light. https://www.labce.com/spg2087066_oil_or_fat_droplets.aspx
  • asked a question related to Chemistry
Question
1 answer
Hi, I need to make an optical window 0.5 - 1mm thick and 6 mm in diameter from PMMA. I would really want to master the skill of production instead of buying some slug or film sheet because later would need to modify the shape ( make a wedge instead of a plane window ) and so on.
I am planning to make a mold using a 3d printed circular part ( see the drawing attached ) wedged between two microscope slides.
We gave it a try and made a sample, but at that time we didnt have the vacuum chamber and poured the pmma into the could mold. ( see the picture attached )
The problem is that the fist sample was quite large and separated from the glass rather easily, which is not the case for smaller sample. The second problem is bubbles.
Could you please suggest the exact step by step scheme to follow ( the concentration, temperature mode, time frames and so on ) to improve our results and obtain bubble free sample which can be safely parted from the mold after the hardening.
What I have:
1. Methyl methacrylate (CAS Number: 80-62-6) from sigmaaldrich
2. Azobisisobutyronitrile (CAS Number:78-67-1) from sigmaaldrich
3. magnetic stirrer hot plate, beakers, vacuum chamber, heating chamber
Thanks a lot in advance.
Relevant answer
Answer
Hello Georgy,
the first step is to produce a prepolymer with short chains of pmma. You have to figure out your iniator yield to get reproductive bubble free polymers. There are numerous literatur about these topic. At first glance I would recommend a smaller amount of AIBN for prepolymerisation and a thorough degassing of the slightly thickening batch (stirring, vacuum, cooling, ...).
With best regards
Carsten
  • asked a question related to Chemistry
Question
2 answers
I have synthesized cerium oxide nanoparticles (CeO2 NPs) using the combustion method. My attempts to functionalize the NPs using the APTES have failed so far. After APTES functionalization, the particles are not stable; they settle rapidly. I would greatly appreciate it if someone could propose a solution and reason to the problem.
#Nanoparticles #chemistry.
Relevant answer
Answer
Nadir chami, Thank you for the response.! Please suggest any reference for that protocol.
Thank you
  • asked a question related to Chemistry
Question
3 answers
Hello Scholars,
I am an undergraduate at the University of Cross River State, Nigeria currently pursuing a microbiology program. For familiarity and enhanced understanding of the course, I wish to seek recommendations on the virtual/simulation laboratory software that would be very helpful to me and my colleagues. With my interest in research too, I will be pleased if a research simulator is recommended to help widen my understanding of Microbiological research.
Your recommendations would go a long way to significantly contribute to my academic career as well as my colleagues.
Thank you
Relevant answer
Answer
Hi Daniel,
In the following links you can find ope-source software and web-based tools for predictive microbiology and risk analysis:
Here are some of my favorites to use in teaching/demonstrating how microbes can grow in foods and lab culture media and respond to inactivation/stresses:
And these are two databases that also allows a bit of modelling:
All the best.
  • asked a question related to Chemistry
Question
2 answers
I want to apply Post-doc Chemistry in Turkey. Can anyone suggest me a University in Turkey???
Relevant answer
Answer
I hv to collect information from alumni of my college (Science college, University of Calcutta) associated with educational institutes ,mainly IIT s. Give me some time. But you can also contact with Universities there.
  • asked a question related to Chemistry
Question
2 answers
I would like to generate a *.sdf file like those posted NIST Chemistry Webbook from a *.log or *.chk Gaussian 16 file and cannot immediately find how to do this. Many thanks for helping me.
Relevant answer
Answer
To be more specific. I can use e.g.
obabel molec.log -O molec.sdf
but I want to also add to *.sdf information on vibrational frequencies and IR intensities.
  • asked a question related to Chemistry
Question
2 answers
I'm finding some cationic molecules like below.
I tried finding on www.sigmaaldrich.com , but couldn't find anything.
Where can I buy some molecules like this?
ref)Ikeda, Taichi, and Yoshitaka Matsushita. "Tetrahedral Tetra-cationic ionic liquids." Chemistry Letters 49.1 (2020): 14-16.
Relevant answer
Answer
if you got the cas you can try http://www.chemexper.com/ they search over different chemical companies, but such kind of systems can get quite expensive.
  • asked a question related to Chemistry
Question
1 answer
I will be working on a slow-release fertilizer for my undergraduate thesis, but I am confused about how other authors measure cumulative nitrogen release for a time interval (including the instruments and calculations)?
More exactly how they measure the exact nitrogen released each time.
Please provide a step-by-step process for a rapid water test.
-Thank you for helping a chemistry student.
Relevant answer
Answer
Not something I've done but the idea is to have a stirred cell which contains the fertiliser suspended in water, and continuous/timed sampling connected to an analysis system (e.g., spectrophotometer, conductivity cell ....)
  • asked a question related to Chemistry
Question
4 answers
Some Oxford Nanopore kits have Primers with 5 ' modification that provide ligation to adapters without the need for ligases (ligase-free method), as in 16S barcoding kits. Does anyone know what modification this is or the chemistry involved in the process? I'm very grateful if anyone can help me with this information. Thanks.
Relevant answer
Answer
It may be a Topoisomerase directed ligation similar to these kits from ThermoFisher: https://www.thermofisher.com/us/en/home/life-science/cloning/topo/topo-resources/the-technology-behind-topo-cloning.html
  • asked a question related to Chemistry
Question
1 answer
I wonder if the removal of pi bond and the addition of heteroatoms such as halogens would increase or decrease the energy gap between the ground state and excited state of the electrons.
Relevant answer
Answer
After the first step of an electrophilic addition reaction an intermediate (carbonium ion) is formed (with a much higher energy). There are no more pi-electons.
  • asked a question related to Chemistry
Question
27 answers
We are living in a world where recently Artificial intelligence is being used in many applications for prediction of many events and things. We all know that the amount and balance of certain Chemicals in the brain have a role in causing us think creative , feel emotional or happy etc. I would like to learn the valuable opinions of Scientists on what specific roles Chemistry would have in creating human conciousness ?
Relevant answer
Answer
Thank you Jerry, very helpful reference and information
  • asked a question related to Chemistry
Question
4 answers
Salt has an ionic bond. It's chemically bonded. So, when it dissolves in water, the ionic bond is somewhat lost. But, people argue that it is a physical change because-:
a) The mixture of salt and water can be separated by evaporation.
b) No new substance is formed.( how though? isn't salty water completely different from just water or salt alone?)
c) There is no energy produced. (but then again when we tear paper, the ripping creates some energy...so how is there no energy in a physical change?)
Thank you in advance,
B.P.
Relevant answer
Answer
Dissolution can cause hydration reaction with creation of charged and uncharged complexes. Example: gypsum dissolution
  • asked a question related to Chemistry
Question
7 answers
thanks in advance on sharing the method
Relevant answer
Answer
Please find the attached article - Determination of Chloride Content in Cementitious Materials. (It may be helpful)
  • asked a question related to Chemistry
Question
2 answers
I am evaluating the options, especially in the true open-source world, for making reliable calculations with high-accuracy using quantum correlation methods.
Relevant answer
Answer
You might want to consider ORCA or PSI4 depending on what you want to do. ORCA is very good for high accuracy correlated methods.
  • asked a question related to Chemistry
Question
4 answers
I synthesized a molecule. I want to know what are the self-assembled structures possible for it through hydrogen bonding.
If possible, please suggest me some free software available (installation-based or online)
Any relevant suggestions are highly appreciated. Thanks.
Relevant answer
Answer
Using GROMACS to perform molecular dynamics simulation is a very good choice. GROMACS is quite fast, flexible and meantime freely available.
  • asked a question related to Chemistry
Question
4 answers
Hello, I recently discovered via GC-MS that my sample contains crown ether. This was really unexpected. I would like to know how to isolate these compounds for further analysis. I appreciate any paper suggestions or personal tips!
Relevant answer
Answer
In aqueous media? I'd try solid phase extraction onto reverse phase. Wash with water, then wash with steps of increasing concentration of acetonitrile in water.
  • asked a question related to Chemistry
Question
1 answer
Who is your nominate for the chemistry and physics Nobel prize?
Relevant answer
Answer
My guess in the field of tissue engineering is Robert Langer from MIT. For the Chemistry Nobel Prize.
  • asked a question related to Chemistry
Question
3 answers
Chemistry question: I've received compounds to dissolve at 10uM. They sent MW, FW, and mg amts for each. Some cpds MW=FW, but others have "salts" added, and those have FW>MW. Should I use MW or FW to convert the mg amt to moles for calculations to achieve uM solutions?
Relevant answer
Answer
It depends on what the experiment is determining. For instance if the experiment required analyzing perchlorate (anion) and you were given sodium perchlorate salt to dissolve you would need to "subtract" the sodium to determine the uM concentration of perchlorate anion in the solution. In the above example if you were not to correct for the salt and just used the MW to determine perchlorate concentration in your solution you would be ~19% off. 0.1231g of NaClO4 is equivalent to 0.1000g of ClO4 anion. So it makes a big difference - especially if you are using the solution for an analytical standard, or for instrument calibration. We could dive into this deeper if you gave us more information. You can always calculate it both ways as well, unless the experiment requires a specific concentration - then you would need to know up front if you should prepare the solution based on the anion concentration.
regards and hope you come up with the correct solution :)
  • asked a question related to Chemistry
Question
2 answers
Please Suggest me research topic for bachelor degree of chemistry
Relevant answer
Answer
Nischal
Do you have a mentor/professor to guide you? You should!
  • asked a question related to Chemistry
Question
3 answers
self‐assembly in the crystalization process.
The origin and the first study in the field of self‐assembly
Relevant answer
Answer
Dear Mohammad,
I suggest to clearly define what you mean by "self-assembly".
The problem is that this term has been very often used in completely non-specific way, just to boost the importance of a paper or report. I call this buzz-wording. Imho this term should not be used for:
1) the assembly of ions in a crystal lattice
2) any simple bond formation of a coordinative or covalent bond
Personally, I find the term "self" misleading as in many cases, the researchers are driving the assembly clearly in just one way. Or there is only one way of aggregation of the ions or molecules.
I would use the term "selective assembly" if there are more than one possibility to form an aggregate or a crystal or a complex and one way is selective over the others.
If there is only one way how the particles (ions, ligands, molecules) can assemble, then there is no extra word like "self" needed, and we should call this specifically "coordination", "forming of H bond", "crystallisation" depending what forces finally keep the particles together.
Best
AXEL
  • asked a question related to Chemistry
Question
4 answers
Hello everyone, I have a question about COD (Chemical Oxygen Demand) electrolysis of organic compounds. When doing the COD analysis of the initial sample before treatment, why did it produce a high COD level? what factors in the COD level caused the initial COD level to be very high?
Meanwhile, after being electrolyzed (after treatment), the COD level decreased, what caused the COD level to decrease and were there any structural changes that occurred related to the reagents in the electrolysis process (organic compounds, electrolyte, additional H2O2, COD reagents) .
So, for example, the sample is acetaminophen
Before treatment (acetaminophen + aquades), why was the COD level of the acetaminophen sample so high? what causes the high value? and why after treatment, the COD level of acetaminophen decreased? what causes the COD level of acetaminophen decrease? Are there any structural changes that occur in acetaminophen related to the reagents associated with the electrolysis process after treatment? if there is a change, what kind of change and how?
Thanks in advance.
Relevant answer
Answer
to answer your question well I want to know how you do the electrolysis? is it by electrocoagulation?
  • asked a question related to Chemistry
Question
3 answers
How can a correlation be obtained from subatomic to superatomic? Why does the subatomic behave differently than the superatomic? Why does something that makes something behave differently from what it creates? Let's give an example to this first: Let's think of H2o water, hydrogen and oxygen: Here, hydrogen and oxygen atoms will behave differently from the water they form. So why is this? Is this due to the change in chemical structure? This means that the change in the chemistry of atoms under matter ensures that matter itself exists on matter. So what provides this? So what is it that changes the chemistry? How is it changing? So why does the thing that brings together this changing chemistry (structure) become matter? If the chemistry changes in the atoms under matter, what do we say if this matter is different from the substance itself, and since the submatter will normally form the above matter logically? If atomic chemistry, that is, subatomic, changes, it becomes supermaterial and they behave differently. Here we reach something: In contrast to atoms, there is something else under matter. In other words, apart from quantum, there is a structure under matter that interacts with atoms under matter and forms the upper part of matter. What should we call this:? Should we call it such a thing that it interacts with atoms and changes their structure and turns them into normal matter? So let it act in classical physics. So what makes atoms move in classical physics? Let's ask this. How do we determine whether something is in quantum or classical physics? If something moves relative to atoms, it's quantum. If there is something directly related to matter itself, it is classical physics. So what is it that differentiates atoms from what is directed directly at matter itself? Let's first explain the quantum theory: An atom could be in more than one place at the same time. So this would mean that an atom cannot be in more than one place at the same time when it interacts and changes chemistry. But what does it do? What kind of thing makes atoms lose this quality? What kind of thing in the universe loses the function of a particle being in two places at once? First of all, let's ask this: Being in two places at the same time;. It means being able to copy yourself and be able to influence at different points. So this thing, the thing that changes the chemistry, must have a function that destroys this quality. What thing in the universe reduces or eliminates influence at different points? What is the most influential thing in the universe? Matter is the answer, which occurs through this space-time warping. So as a result, Isaac Newton's m1.m2/r'2 formula gives us the output. As the distance between the objects increases; gravity (ie, space-time warping), that is, the twist by matter would decrease. In that case, as the distance between matter increases in the universe, the relationship that a substance establishes with submaterial and supermaterial brings us the existence of the supermaterial. Thank you.
Relevant answer
Answer
Hakan,
Perhaps my article `Subquantum leapfrog` will give you some thoughts on this topic
I'm talking about quantum mechanics and molecules.
  • asked a question related to Chemistry
Question
2 answers
In electrofenton, there is one method, namely electrochemical peroxidation, what are the advantages of this method so that it can degrade organic compounds? How is it different from electrocoagulation? what makes electrofenton/electrochemical peroxidation better than electrocoagulation?
Also, there are electrocoagulation and traditional coagulation, what makes electrocoagulation better than traditional coagulation? as well as the electrofenton and traditional fenton, why is the electrofenton better than the traditional fenton? What is the effect of Fe and H2O2 in degrading organic compounds? why when an electric current is applied the results are better? if there is no electricity, is it also good to degrade organic compounds?
Thanks in advance
Relevant answer
Answer
Electrochemical treatment on real wastewater or contaminated water works best, but in the water/wastewater pH band of 6 to 8 only, with or without aid.
  • asked a question related to Chemistry
Question
2 answers
What parameters play a role in the ability of amines to be protonated in water? Can the base strength of amines be a sufficient measure to compare the protonation ability of two amines? For example, is the protonation ability of n-butylamine more than morpholine?
Thank you
Relevant answer
I would say yes, but you have to remember not to extrapolate it to another solvent. pKas varies from solvent to solvent. So, one amine can be more basic in one specific solvent, and less basic in another one.
  • asked a question related to Chemistry
Question
2 answers
Hi everybody. I have a question about study kinetics. So, I did electrolysis by dissolving organic compounds with aquades as a sample under acidic conditions with Na2SO4 as electrolyte, with additional H2O2 (Fenton reaction) using iron as anode and graphite as cathode. In discussing the study of kinetics, I found that if the kinetic graph that R2 close to one or almost linear is in pseudo-second order graph, what does this pseudo-second order mean? what does pseudo-second order actually mean? i was told that "the pseudo explains that something is involved but doesn't appear in the rate law, for example the solvent or there is usually the fraction of the reactant that matters" is that true? So, if what is meant by second order is that there are two reagents that have an effect in this case, for example H2O2 and Na2SO4, but in pseudo-second order something is involved but it doesn't appear, what is it? also, if you also know, what kind of reaction mechanism that produces the pseudo?
Thanks in advance
Relevant answer
Answer
Send your email address to me, dgamble@ns.sympatico.ca. I can send my published comments about second order kinetics.
Best regards,
Donald Gamble
  • asked a question related to Chemistry
Question
4 answers
Hello everyone!
I want to simulate a premixed combustion case with Hydrogen/air (or oxygen) chemistry.
I know simulating a non-premixed combustion case with hydrogen/air detailed chemistry means injecting hydrogen as fuel and air as oxygen at a particular temperature and pressure and using any available chemical mechanism (GRI, UCSD, etc...).
But, what is meant by simulating premixed combustion with detailed chemistry?
Relevant answer
Answer
Thanks for your answer. It is very helpful
  • asked a question related to Chemistry
Question
4 answers
:I don`t understand this bold part
The mono- and bidentate bonding are formed via protonation of the surface hydroxyl group and releasing one water molecule, leading to a strong P-O-M bond.
Article title:Organic Hole Transport Layers for Efficient, Stable and Scalable Inverted Perovskite Solar Cells
doi:10.1002/adma.202203794
Relevant answer
Answer
P-O-M is simply phosphorous-oxygen-metal bond. In other words, the linkage between the metal based substrate.
  • asked a question related to Chemistry
Question
17 answers
Hello everyone. I need a little help here.
can we use essential oils to reduce chlorinous odor in a hypochlorous acid solution without decreasing free chlorine or pH value? any toughts and propositions are much appreciated
Relevant answer
Answer
There is a Japanese patent on this, they used eucalyptus and peppermint oil it seems. https://patents.google.com/patent/WO2018174136A1/en I just tried it and in small amounts dissolved in alcohol, it still has potent free chlorine. However cross the line and add too much and the HOCl is ruined. As others have mentioned, organochlorine chemicals are potentially unsafe, doesn't seem like a great idea. Hypochlorous odor will dissipate quickly, if it is not actually hypochlorite... check the pH.
  • asked a question related to Chemistry
Question
2 answers
I saw this sentence .Hydroxyl group and amino group are the both nuclephilic. So no reaction will take place
I have prepared a sample and apparent physical properties show excellent coverage, but I do not how to explain. can anyone help me?
Relevant answer
Answer
What kind of reaction?
surface Si-OH is relatively acidic.
amine is basic
so Si-OH + R3N -> Si-O- + R3N-H +
ionic forces will hold them together.
but if you wash with water they may desorb
if you wash with acidic water at a low enough pH to protonate Si-O- it will definitely desorb.
  • asked a question related to Chemistry
Question
5 answers
I am carrying out a Research on the effect of blended learning on senior secondary school students achievement and retention in Chemistry. Could someone
help me with materials?
Relevant answer
Answer
Thanks so much Mr. Faroum. Am grateful
  • asked a question related to Chemistry
Question
3 answers
Hi there,
would like to learn more about appropriate material for the application of PPE in Epidemiology.
As all the material seems to be Polyethylene/Polypropylene, would love to learn, whether it is possible to use Polyamide material instead? Are the properties sufficient?
If Polyamide does the job, are normal Snowboarding and Fishing Overalls an alternative to the ordinary Hazmats?
Cherish your feedback.
Relevant answer
Answer
The chemical nature of Polyamides, with potential reactive chemical groups, make it more susceptible to contamination than inert PE/PP in an Epidemiology environment. Physical properties are OK.
  • asked a question related to Chemistry
Question
1 answer
Defining the dilution factor is very important when we are working at the level of ppb (parts per billion) or ppt (parts per trillion). Other day, I was working on plant biomass samples to analyze available Si (Silicon) in plant biomass. I have gone through several steps of dilution and became so confused about what is DILUTION FACTOR. I did several dilutions at several steps (digestion, adding chemicals, again diluting to come up with the range of AAS) and it became so complicated. As always, I approached Dr. Rafael Santos and he solved this problem very easily, I would say just in 10 minutes when I was struggling for an hour. Finally, Dr. Santos made a good explanation with their whiteboard and step by step he came up with the solution. Again, doing a Ph.D. is not just collecting and analyzing data but also needs to understand the chemistry happening in between. If you don't know how to do it then seek help. Asking someone doesn't mean your basics are not strong, asking someone means you know what you're looking for but you don't know how to approach it. I am thankful to have Dr. Santos as my mentor, peer and guide. PS: Here's complex whiteboard solution in the picture :) #ppb #ppt #help #academia #PhD #chemistry #data #AAS
Relevant answer
Answer
Asking for guidance is the best learning method after attempting a solution.
Sounds like you have a great mentor.
  • asked a question related to Chemistry
Question
13 answers
Research chemists continue in their slow uptake of preprints. I've lately suggested one key reason for this unique behaviour of scholars in the basic sciences in two OA studies, one published by Publications:
and another by Insights:
What is your opinion on the origin of this delay? Has your team recently embraced preprint publishing? What are your favorite preprint repositories?
Thank you in advance for your insight.
Relevant answer
Dear Prof. Mario Pagliaro, Preprints are defined as an author’s version of a research manuscript prior to formal peer review at a journal, which is deposited on a public server. ResearchGate (RG) said about "Preprints": early-stage research. On the other side, RG is not a publisher and, in turn, uploaded unpublished text is not regarded as a publication. Hence, a preprint is an author's own original or draft version of their paper before any peer review has taken place and before it is published.
Before answering this valuable question, please let me give my own opinion about the preprint dilemma (مُعضلة ما قبل الطباعة):
I have a different perspective on uploading any preprint anywhere before it has been published. Why do you let others know about your insights and methodologies before publication? You should avoid telling the other researchers about the details of any one of your papers until it has been published and seeing your name by yourself. You may say that I am somewhat old-fashioned, but I have a different perspective on uploading any preprint anywhere before it has been published by your name. My advice is not to put your research anywhere until it is published. It is a security issue:
  • Your manuscript may be copied and then published by others before you can do that. This stealing of your paper might be happening. So, you must wait until the paper is accepted and then published in that journal. Then, upload that research item on any platform you wish.
  • A journal may have automated plagiarism software to check the paper before admitting it to the reviewing process. There are chances that your paper can get a rejection at any point. Thus, to avoid this problem. Publish the preprint after you got the paper as "ACCEPTED".
  • There may be a "cold war" between the professors of a given department. They do not like to discuss ideas as others will "steal" them and publish an article on them without giving credit to the one from whom they got the idea. My suggestion is to keep your work "private" and share it only with those who are really interested.
  • Academic publishing remains a competitive process. If someone else has recently published a paper very similar to mine, mine is less likely to be accepted. So although I may share my topic, I prefer to keep my methodology, findings, and discussion private, until published in a peer-reviewed journal. So. there is a high chance that someone may claim your idea as theirs!
  • Preprint gives a false feeling of security. Personally, I would always wait until the paper is accepted by the editor of a journal. After that, I can post it as a regular research item on any platform you wish.
Finally, for the coming future, do not upload any paper anywhere until it is published with your name. Even if it is a "preprint"! For the time being, If you had done something like that as a "preprint", for instance, I advise you to delete the preprint from any elsewhere and wait for two months before sending the paper to any journal.
  • asked a question related to Chemistry
Question
4 answers
Does anyone has an experience with sodium tert-butoxide? How dangerous it actually is?
Do I need to use a glovebox while weighting and handling it?
Do I have to dissolve it in THF at -30C or room temperature will also do?
How do you store it after the can is opened?
We have 100g of sodium tert-butoxide in total, the planned amount for my synthesis is ca. 1.5 g.
Relevant answer
Answer
Do not breathe dust/fume/gas/mist/vapours/spray. Avoid breathing dust/fume/gas/mist/vapours/spray. Use only outdoors or in a well- ventilated area.
  • asked a question related to Chemistry
Question
2 answers
This is a graphical abstract image from one of the paper of eminent total synthesis chemist KC Nicolaou. Can anyone tell me how I can draw such type of image?
Please comment
  • asked a question related to Chemistry
Question
6 answers
Hi everyone!
I am working on different polymers and modifying them chemically and I want to write the chemical reaction. If I want to confirm whether the proposed chemical reaction is right or wrong, is there any software or something?
Thanks for your help!
Relevant answer
Answer
You can use the :-
- ChemReaX (is a free web app for modeling and simulating basic chemical reactions)
- Molecular Workbench
Best Wishes...
  • asked a question related to Chemistry
Question
5 answers
Hi all,
To set things clearly: I am a PhD student working on the process implications of electryfing the ammonia production by replacing conventional SMR with Water Electrolysis. A part of my preliminary work is to assess the difference in theoretical minimum energy consumption. To do so, I have calculated a first approximation by summing up the reactions (SMR, Water gas shift, Haber-Bosch,...) and calculating the enthalpy of the resulting "total" reaction. I have done this for the "Water Electrolysis + Haber-Bosch scenario" and validated the minimum with values from the literature.
However, for the conventional "SMR + Haber-Bosch scenario", values from the literature are different. To be more specific, here is the energy minimum calculated in the following conference paper:
(...) the theoretical minimum of energy consumption for the process itself (represented by LHV of methane) is 22.2 GJ/t NH3 (...)
So here is my question: Why use the LHV of methane (instead the enthalpy of reactions) to calculate the energy minimum ? I feel like this is incorrect as I do not take into account the synthesis of methane.
Thanks in advance for any answers,
Antoine
Relevant answer
Answer
The paper you cited also includes the combustion of methane to provide the energy needed to account for the endothermic reaction as well as bringing the reaction temperature to that where the reaction occurs (850 C). For the combustion reaction, the LHV of methane is appropriate, where as for the SMR reaction, the heat of formation is appropriate. The reactor(s) consist of tubes packed with catalyst where the SMR, WGS, and HB reactions occur. On the outside of the tubes, CH4 is burned using either air or pure O2 to provide the energy needed for the process.
  • asked a question related to Chemistry
Question
29 answers
Dear all
Hope you are doing well!
What are the best books in Materials Science and Engineering (Basics and Advanced)? Moreover, what are the best skills (or materials topic related) that materials scientists have to develop and to acquire?
Thanks in advance
^_^
Relevant answer
Answer
Dear all, following a list of interesting books. My Regards
- Fundamentals of Materials Science and Engineering: An Integrated Approach, William D. Callister, David G. Rethwisch, 5th Edt (2015).
- Materials Science and Engineering: An Introduction, 10e WileyPLUS NextGen Card with Loose-Leaf Print Companion Set, Callister Jr., William D., Rethwisch, David G. 10th Edt (2018).
- The Science and Engineering of Materials, Donald R. Askeland, Wendelin J. Wright. 7th Edt (2014).
- Materials Science and Engineering: A First Course, V. Raghavan, (2004).
- Foundations of Materials Science and Engineering, Willaim Smith, Javed Hashemi, 6th Edt (2019).
  • asked a question related to Chemistry
Question
1 answer
This statement is claimed by
Simplistic notion of law of mass action or common ion effect cannot explain it . So what is the reason?
Please do not refer to the references on the paper
Kron I, Marshall SL,
May PM, Hefter G, and Konigsberger E (1995) The ionic product of water
in highly concentrated aqueous electrolyte solutions. Monatshefte für
Chemie 126: 819–837.
Relevant answer
Answer
At initial concentration, atoms of the salt molecules have not ionized to form part of the solution. The already auto-ionized water ions(H+ & OH- ) tend to interact with the salt molecules until complete ionization can take place.
  • asked a question related to Chemistry
Question
4 answers
Dear all,
what are the possible instruments to use to obtain the purity of a powder (NaCl sold in a pellet form) (has 99% purity or above)?
the cheapest instrument to the expensive one if possible according to your experience
Thank you in advance
Relevant answer
Answer
Purification of chemicals is a large branch of chemical technology, with a large number of non-universal methods. In the case of NaCl, it is sufficient to simply recrystallize it from an aqueous solution.
  • asked a question related to Chemistry
Question
5 answers
0.1 N concentration solution of both was taken, with HCl as titrant abd HPh as indicator. After reaching the endpoint of colourless condition, the colour reappears after continous shaking for 5 mins. even sometimes after 15 mins. How to be sure of that this much time is enough, for shaking to confirm completion of titration?
Relevant answer
Answer
in case of titration, 0.1 N sodium carbonate solution the required hcl concentration is concentrated or 0.1 N solution used.
  • asked a question related to Chemistry
Question
6 answers
Good day,
i have a general question about tissue culture.
I have found the following recipe for Epipremnum Aureum "Marble Queen":
Leaf Explant: MS Medium + 4.54 µM TDZ + 1.07 µM NAA (Thidiazuron in Micropropagation of Aroid Plants by Chen and Wei (2018), p. 105, DOI: 10.1007/978-981-10-8004-3_4)
Specifically, I have the following questions.
1) Do i only need to autoclave the agar with distilled water (I use a pressure cooker for this) and when the agar has cooled down a bit just add the MS, TDZ and NAA and mix it or do i need to autoclave the MS as well?
2) Will the TDZ dissolve in the agar water at all and how hot can the agar water be to add the MS, TDZ and NAA?
3) Is it even necessary to autoclave the water incl. agar (in the pressure cooker) if I clean all the jars with NaClO (sodium hypochlorite)?
Thank you in advance!
Relevant answer
Answer
In general, all things associated with tissue culture need to be properly sterilized. For me, I autoclave the complete media (MS, hormones(I use 2.4-D, NAA, BAP, Kinetin), and agar) along with the culture vessel (petri dish or test tube). But it is better to filter sterilize (.2 micron) the hormones and vitamins (of the media) and add them to MS media (agar mixed) when the temperature drops to about 50 degrees celcius.
  • asked a question related to Chemistry
Question
8 answers
Kindly discuss your ideas and viewpoints on the origin of life and the RNA world hypothesis.
What are the contradictory views on why researchers are still unsure about the origin of life through RNA or such analogous molecular intermediate pre-cursors preceding its existence?
"The general notion of an “RNA World” is that, in the early development of life on the Earth, genetic continuity was assured by the replication of RNA and genetically encoded proteins were not involved as catalysts. There is now strong evidence indicating that an RNA World did indeed exist before DNA- and protein-based life. However, arguments regarding whether life on Earth began with RNA are more tenuous. It might be imagined that all of the components of RNA were available in some prebiotic pool and that these components assembled into replicating, evolving polynucleotides without the prior existence of any evolved macromolecules. A thorough consideration of this “RNA-first” view of the origin of life must reconcile concerns regarding the intractable mixtures that are obtained in experiments designed to simulate the chemistry of the primitive Earth. Perhaps these concerns will eventually be resolved, and recent experimental findings provide some reason for optimism. However, the problem of the origin of the RNA World is far from being solved, and it is fruitful to consider the alternative possibility that RNA was preceded by some other replicating, evolving molecule, just as DNA and proteins were preceded by RNA." - Robertson and Joyce
[This is as per the explanation by Michael P Robertson and Gerald F Joyce in the article: "The origins of the RNA world." published in the Cold Spring Harb. Perspect. Biol. 4, a003608 (2012).]
The scientific community must resolve this contradicting conjecture through rational discussion and debate backed by strong experimental evidence on what must be the pre-cursor molecule to the Origin of Life if it is not RNA!
Relevant answer
Answer
One of the issues that is holding the concept of an RNA world back from being more scientifically useful - irrespective of whether there ever was such a thing - is that we don't use the idea in the scientific way it was intended. Just like any other prebiotic scenario, it is not (nor has it ever been) a scientific hypothesis. In fact, scenarios are usually not intended as such. Scenario authors from all niches (including RNA world) have pointed out that scenarios themselves are untestable. However, they guide thinking and allow to conceive of hypotheses that are testable. If we go through the old literature we find very explicit passages to support this fact.
For the specific authors advanced in the question, G.F. Joyce and L.E. Orgel, we have a passage from 1999 in "prospects for understanding the origins of the RNA world". (The RNA World 2nd ed. 49-77).
"The presumed RNA World should be viewed as a milestone, a plateau in the early history of life on earth. So too, the concept of an RNA World has been a milestone in the scientific study of life's origins. Although this concept does not explain how life originated, it has helped to guide scientific thinking and has served to focus experimental efforts."
You can find this point of view expressed in foundational work for all niches related to the popular scenarios today. But you can also find it for scenarios most people in origins have never heard of. E.g. the idea that celllular life started with terpenoids found in G. Ourisson and Y. Nakatomi's "the terpenoid theory of the origin of cellular life: the evolution of terpenoids to cholesterol. (1994) Chem & Biol. 1 11-23".
"The hypothesis provides an attractive way of ordering the terpenoids: like all evolutionary theories, it cannot be tested directly. The ideas summarized here do, however, suggest a multitude of experiments having some bearing on the fundamental and fascinating question: how did the first cells appear? We hope to carry out some of them."
A related line of thought - but highly influential - is the exposition by Harold J. Morowitz from 1992 in his book "Beginnings of Cellular Life: Metabolism Recapitulates Biogenesis". If we go to the conclusion, we find this explicit clarification on the distinction between a genuine scientific theory and a scenario:
"at this stage of the thought process, it is important to focus on the hypothesis that intermediary metabolism recapitulates prebiotic chemical evolution. This hypothesis is not a strictly vulnerable theory in the Popperian sense, but it does provide us with a valuable heuristic method for using modern knowledge of biochemistry to search for events that have left their trace. If the intermediary metabolism of autotrophs does not recapitulate biogenesis, then the discontinuities will have to be explained."
More than 2 decades back, many authors made a clear distinction regarding this nuance. Scenarios are here to help: they guide thinking and design experiments. They only guide thinking in a scientifically meaningful direction as long as we can easily abondon scenarios and enthusiastically continue replacing them with new, more informed scenarios. A situation where a scenario gets entrenched and where researchers treat it as a scientific hypothesis is - by construction - hard to escape.
In fact, this is exactly the situation that many researchers have described around the 80s, when criticism mounted against the prebiotic broth scenario. The passage from Wächtershäuser's 1988 "Theory of a Surface Metabolism" is telling:
"The prebiotic broth theory has received devastating criticism for being logically paradoxical (11, 135), incompatible with thermodynamics (11, 144, 160), chemically and geochemically implausible (134, 136, 144), discontinuous with biology and biochemistry (160), and experimentally refuted (135, 160). The reason for the tenacity with which it is retained as accepted dogma has been forcefully and clearly stated by Scherer (126): "If this rejection is substantiated, there will remain no scientifically valid model of the selforganization of the first living cells on earth."
Clearly, the broth scenario had overstayed its welcome. One reason for this is that its 'claims' (which for a scenario can only be speculations) were too much in contradiction with claims from fields of science that do not suffer the same restrictions when it comes to testing and refuting their theories. One example of a very controversial idea that can be found in Haldane's formulation of a broth scenario, is the purported necessity of a long, highly functional protein randomly emerging from a soup, as an extremely rare event: we expect this to be prohibitively unlikely and hence a far from parsimonious explanation.
Quite a few of the critiques voiced against the prebiotic broth scenario are equally valid critiques of some scenarios we have today, including RNA world.
The RNA world is an old and multifaceted concept. There are contrasting formulations that make different claims (to be interpreted as speculations) about history. As with the prebiotic broth scenario (and any scenario), it has raised genuine scientific objections. These have remained largely unadressed, in spite of its long dominance.
It is instructive to bear in mind that scenarios don't come from nowhere. They're fairly detailed speculations about purported historical events. To make them, each author makes assumptions. Some of these concern speculations that later became testable, e.g. about chemistry and physics. You will find different scenario authors make different assumptions and different arguments (and flaws therein). There's an inevitable bias here with respect to the fields an author is trained in. Some of the foundational assumptions in popular scenarios like RNA world are at least 50 years old, but some unchallenged assumptions date back to a literature that is more than a century old. A time before IUPAC, modern quantum mechanics, genetics, and so forth.
That has been enough time to forget that scenarios like RNA world are by construction not testable hypotheses and that they were not intended as such. Scenarios are here to guide thinking, to inspire experiments. The best thing a scenario can do for us, is generate insights that spur us to change the way we think and thereby necessitate replacing our old scenarios with new ones, and repeat the cycle. The science coming out of the community today is a lot more conducive to doing that than previously.
The same cannot be said for the rather myopic RNA-centric framing of a question in the cited passage, which attempts to elevate RNA world to more than a scenario. Rather than forcing ourselves to think about the rather narrow and outdated proposal by Joyce and Robertson, ("consider the alternative possibility that RNA was preceded by some other replicating, evolving molecule"), it is more productive to critically revisit all the things that have been assumed and argued when the concept of an RNA world was conceived and how which of these premises are considered valid or plausible today, and which ones back then. Is there a formulation of RNA world for abiogenesis that is logically sufficient? And if so is it logically necessary that abiogenesis proceeded this way?
It is also instructive to check how much of the logic was sound. e.g. the rhetorical tricks employed in RNA world introduce all sorts of hidden assumptionsm.
As an example of the latter: some still justify an RNA world by the party trick 'chicken-and-egg' question 'protein or RNA, which came first?', only to conclude with 'RNA, it encodes proteins' and hastily conclude with an even stronger 'RNA-first' for abiogenesis. 'chicken-and-egg' fallacies are nothing new in origins. In fact, they were already identified as such long ago. E.g. in chapter 8 of "Seven Clues to the Origin of Life (1985)" by Cairns-Smith, there's an illustrated passage detailing that these types of paradoxes in origins frame the question in a manner that prevent us from considering scaffolds.
"
The fact is that even the so-called simple organisms such as E. coli are very complex enterprises with all sorts of things going on together. There is plenty of scope for accidental discoveries of effective new combinations of subsystems. It seems inevitable that every so often an older way of doing things will be displaced by a newer way that depends on a new set of subsystems. It is then that seemingly paradoxical collaborations may come about.
To see how, consider this very simplified model - an arch of stones: This might seem to be a paradoxical structure if you had been told that it arose from a succession of small modifications, that it had been built one stone at a time.
scaffolds that starts like this:
This might seem to be a paradoxical structure if you had been told that it arose from a succession of small modifications, that it had been built one stone at a time. How can you build any kind of arch gradually? The answer is with a supporting scaffolding. In this case you might have used a scaffolding of stones. First you would build a wall, one stone at a time:
Then you would remove stones to leave the 'paradoxical' structure.
"
It should be noted that in 2022, even in RNA-world, very few scholars remain that find RNA-first a convincing idea. As a scenario, however, it is not useless: it is instructive to consider what the underlying ideas are that at some point in time made such a highly specific idea compelling to so many of us.
A fixed motif in scenario papers is to start explicitly and implicitly assuming a few things about what chemistry can and cannot do and some properties of abiogenesis. These sort of assumptions used to be spelled out routinely, also outside scenario papers. Let me give two examples.
The original 1953 paper for the "Frank Model" "on spontaneous asymmetric synthesis", has the passages
".. the defining property of a living entity the ability to reproduce its own kind ...
confining attention to chemical molecules, the complexity of any having this essential property of life is likely to be great enough to make it highly improbable that it has a centre of symmetry."
(*I should point out that Frank makes an important error here: the capacity for molecular reproduction is not a molecular property but a property of a reaction network. If we add an additional thermodynamic criterion this property is autocatalysis and we can then check this claim from the IUPAC definition: https://goldbook.iupac.org/terms/view/C00876. It turns out there are trivial ways to make small networks that have this property https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d67469df42226f44295/original/emergent-autocat-animation.gif.)
The point to retain here is that Frank considers it to be generally accepted that one can assume this property to be prohibitively rare in chemistry. This belief was wideheld, and we can e.g. read in "the units of selection" (1970) by Lewontin a summary on scientific views on abiogenesis
"The present view ... Since there was no autocatalysis, there was no reproduction or heredity and so no possibility of natural selection."
The coacervates in Oparins scenario were notably invoked to adress this issue.
When it comes to assumptions in scenarios, this systematically involved conjecturing that chemistry 'in the wild' intrinsically and deterministically becomes a 'mess', undergoing no meaningful complexification, and for which no reproduction and evolution can reasonably be expected. From there, it appears that no process of abiogenesis should conceivably occur naturally, and thereafter some specific sequence of exceptional events is proposed as plausible, because it appears to be the sole contender.
Let us make more explicit why this is not an innocent procedure:
We still find our understanding of 'basic chemistry' to be plagued with limitations and long-lived misinterpretations (e.g. 2 days ago we learned that methyl substitution destabilizes radicals instead of the textbook knowledge that it stabilizes them ).
Moving beyond the basics, we by and large lack a lot of formal theory, experiment, or even a simple reference frame for the things that happen then. Joyce and Robertson honor the tradition of purporting from the outset that 'chemistry in the wild' becomes an intractable mess. The issue is that we don't know at all if that's the case. We cannot assume this from the outset, we need to extensively study it. We require extensive experiments and theory and a reference frame for all the phenomenology associatied with complex systems (e.g. multiple components, compartments, multiple forms of nonequilibrium driving, length scales, time scales).
In making the routine assumption of 'messy, intractable chemistry that can neither complexify nor multiply', we have decided in advance that, once we finally understand 'chemistry in the wild' with its 'so-called intractible mixtures', it cannot have any bearing on abiogenesis. Let alone explain it.
That is a disproportionately bold conjecture about fundamental science, and a very consequential one: all historical scenarios - RNA world being one out of many - have been justified by formulating conjectures of this sort (many authors also insist on other properties, e.g. chemistry being deterministic). Clearly, it should be the first priority of everyone in the field to test this conjecture, by extensively and rigorously studying complex chemical systems as an end in itself. If the conjecture is correct, it provides an important validation for historical scenario approaches. If the conjecture turn out wrong, we are in a much better position to conceive of more scientifically informed scenarios, but potentially the approach will change entirely.
In presenting it as such, I am making it appear as if it could be an open question whether the chemical conjectures underpinning our scenarios in origins may be true or not. In fact, we have learned quite a few things in the meantime. And some clumsy mistakes were made elsewhere.
- Determinism:
When it comes to chemistry being deterministic (a key tennet of e.g. Sutherlands scenario and Wächtershäusers surface metabolism): upon critical evaluation of what is known of basic chemistry this idea becomes unacceptable, especially when considering the chemical processes on the surface of a planet, as opposed to a quick reaction in pyrex.
1) insofar as it is reproducible, modern chemistry owes much of it to big strides of standardization in glassware, methodology, synthesis protocols (e.g. usage of stirring bars).
2) lab chemistry exhibits many forms of contingency. This is particularly the case when it comes to phase behavior, e.g. habit modification, polymorphism. Aspirin purportedly has 8 reported polymorphs, phenobarbitone 13.
3) glassware is cleaned between reactions, thereby making successive reactions in the same glassware independent. In nature, this property of independence is absent. In fact, effort to make an evolutionary classification of minerals are rooted in the opposite: that certain minerals start to form conditional on the presence of certain others. (https://pubs.geoscienceworld.org/msa/ammin/article/104/6/810/570840/An-evolutionary-system-of-mineralogy-Proposal-for)
- Autocatalysis:
A first issue to get out of the way is the misconception that autocatalysis is prohibitively rare. A prominent PI in origins (RNA world, not a chemist) told me that chemists throughout history have found exactly one example. Claims about the contents of a literature one cannot realistically have read in a lifetime is a common error we can find in the origins literature. Below are some reviews.
I should stress that these reviews discuss examples from a few niches in chemistry. These reviews do at least allow to have 100s of counterexamples to dubious claims about no autocatalysis in chemistry, but it's only a small fraction. Virtually all branches of chemistry have regular reports of autocatalysis, but very few focus on autocatalysis in its own right. And hence most branches do not review their reported examples.
By critically examining the IUPAC definitions, one can show that autocatalysis is dramatially more widespread than long thought. In part, this is because the definition applies to a wealth of situations where the term is not routinely employed. By examinging the requirements of autocatalysis as an emergent network property, one can demonstrate that this property emerges particularly readily in a heterogeneous / multicompartment context. With the disclaimer that I'm an author I refer to the following:
- Messy chemistry:
Refreshing counterexamples are afforded by the literature on systems chemistry and dynamic combinatorial libraries.
In the context of origins, a recent work that is greatly aiding in fixing our misconceptions is : https://www.nature.com/articles/s41557-022-00956-7
Where a reaction of purported immense complexity is found to exhibit highly reproducible and ordered behavior as function of environmental inputs. How chemistry exactly works on this level is still poorly understood. I think I do, but it'll have to await peer review. But we cannot in good scientific conscience take for granted anymore that chemistry becomes messy and intractable. When we do the experiments, we see something very different.
in conclusion, I want to come back to the final point of the question
"The scientific community must resolve this contradicting conjecture through rational discussion and debate backed by strong experimental evidence on what must be the pre-cursor molecule to the Origin of Life if it is not RNA!"
No. The sientific community should strive to do what it can justify scientifically. Those that find it fruitful to relegate the RNA world - which is not a hypothesis - are justified in doing so. Notably because it is is founded on scientifically refuted premises and logical errors.
Those that find ways to make it fruitful to keep it are justified in doing so: it's a scenario, one can draw inspiration from it. Perhaps a thoroughly altered version can be developed that fixes previous issues.
Above all else, RNA is an amazing molecule that has been used for fundamental research that concerns everyone in origins, and will continue to do so irrespective of how serious the RNA world scenario is still taken.
What the origins of life community needs, first and foremost, however, is concern itself with more important matters.
Complex chemistry needs to be studied thoroughly on an experimental and theoretical level.
New scenarios are needed. And these scenarios should no longer require chemistry to have properties it doesn't have, and vice versa. These scenarios should also explicitly be appraciated for what they are, an for what they're not. They're here to help, to guide thinking, inspire experiments, produce testable predictions, update our beliefs. They are not scientific hypotheses in and of themselves.
  • asked a question related to Chemistry
Question
9 answers
i got my phd awarded recently in chemistry. i want to do post doctoral fellowship in abroad. i request you to suggest me a good country and at the same time a good institute with all details.
Relevant answer
Answer
Dear Sajiya,
thank you for your posting. I will try to give a quick answer on both questions.
1. Where to get a grant.
A) You can look up the DAAD portal (DAAD = German Academic Exchange Programme). In the Scholarship database you will find the most important institutional grants (including Humboldt etc):
B) You check homepages of colleagues if they have open positions. Or you send emails to them asking if they have open positions.
2. How to find suitable places/colleagues for a post-doc?
This depends on what you want to do during your post-doc.
A) You want to continue research on the topic of your PhD. Then it's simple. You know the experts in the field, you check where they are located and you write them an email.
Concerning research especially in Germany, there is an expert on any topic in Germany.
B) You want to switch from your PhD research to something different and you have a specific idea about the topic.
Then you have to find the experts in this new field and write them an email. ...
You can recognise experts in the field from reviews in important journals, from books and book chapters.
C) You want to switch from your PhD reseach to something different but you are not decided what.
No problem, start making up your mind in which direction you want to work: organic, inorganic, bio, materials, analytics, .... whatever. Then check for the hot topics. They will probably lie in the fields of "energy conversion" or "medical chemistry". Having decided what to do, it is like B).
D) You don't care about the topic of your post-doctoral work. You just want to do research in Germany (US, UK, France). Don't get me wrong, but that is a weak starting point for a post-doc application. I am getting such unselective applications very often and I always reject them. The reason is simple. You are a well-educated scientists and you have specialised skills. If you are trying to enter a completely new field, you have no skills at all and why should somebody hire you as post-doc, if he/she can have somebody with broad skills in this topic.
A very last, but important point:
Approaching my colleagues is not always easy. Sending email frequently does not help - they simply do not respond. What can you do:
1. If you tried for a specific colleague and he/she did not answer, modify your application (may it was not good enough), write in more detail why you selected him/her and try again.
2. Try others. My experience is that many of my colleagues do NEVER answer.
3. Maybe you add a sentence to your email like this: If you do not have open positions for post-docs at the moment, or my portfolio is not perfectly meeting your expectations, I would be happy to receive suggestions for other colleagues in the field.
Best wishes
AXEL
  • asked a question related to Chemistry
Question
3 answers
We are testing new chemicals for redox flow batteries. We consistently see this weird potential "x" with galvanostatic bulk electrolysis cycling experiments in an H cell, has anyone had this issue before? We have this same issue with the novel anolyte/catholyte chemicals we are testing, so we ran a bulk electrolysis experiment with Fc/Fc+ symmetric cell to see if the issue persisted (both with membrane and with fritted H cells). I see this potential crossover all the time with 100% and 80% SOC experiments, I'm going to test 50% SOC to see if the crossover remains. The reference electrode seems fine based on CV experiments, the reference electrode issues are the only thing I can think of. Isn't it theoretically impossible for the oxidation to start at a more negative potential than the reduction? I see some solvent loss over the period of the experiment. This is the first redox cycle and the crossover is consistent throughout the experiment.
Symmetric h-cell setup
0.001 M Analyte (Fc/FcPF6)
0.1M TBAPF6 in MeCN
10 mL Volume on each side
AMI-7001 selective membrane
BASI nonaqueous coralpor fritted reference electrode (0.01M AgNO3 in 0.1M TBAPF6 in MeCN)
0.27 mA for 1 h (100% SOC)
Relevant answer
Answer
Simon Gersib Hi, the resistance of the glass frit ion flows is surely an issue. Have you measured the ac impedance of your cell in the background electrolyte? With your current being 0.27 mA, it means that a resistance of 350 ohm in the glass frit will produce roughly 100 mV voltage drop (iR drop) which is high enough to cause the crossover.
However, I shall point out that in the bridge section of your H-cell, stirring is almost no effect.
  • asked a question related to Chemistry
Question
6 answers
I want to prepare 2% solution of chitosan using 0.5 M acetic acid but need to adjust pH to 4. How can I do that? I added NaOH to the chitosan solution, precipitates were formed in chitosan solution.
Relevant answer
Answer
I think you should add the conjugate base (CH3COONa) but not NaOH
  • asked a question related to Chemistry
Question
2 answers
Forgive some of my ignorance in the math for thermodynamics and heat exchange but my background is heavier in Chemistry and could use some help.
The project is to keep about 70L of water in an aquarium at 17C when the ambient temperature is 22C in the room. The original project built had the following set up:
(Top to Bottom):
1. 80x80x38mm fan running at 5700 RPMs and 76CFM
2. 80x80x20mm copper fin heatsink (0.5mm fin thickness and 40 fins with a 3.5mm bottom thickness)
3. 2-TEC1-12706 hot side towards heatsink, cold side down towards water block (Imax: 6.4A, Umax: 15.4V, Qmax: (dT=0) 63W, dTmax=68C)
4. 40x80x12mm water block centered under the heatsink (surrounded on the sides with 20mm styrofoam and 10mm styrofoam at the back)
5. ~26mm thick styrofoam
6. Wood base
• All power is supplied by an AC/DC converter (12V 20A 240W)
• Power to the system is managed by a W1209 Temperature Control Module (Relay)
• Water flow is achieved by a 4L/min water pump (slowest I can find)
This set up is only cooling the water to 18C at night and will slowly creep up to 18.7 across the day so I know this set up is not keeping up with the heat load. (also worth noting that output temp is about 1.5-2C cooler than input temp to the waterblock). My hypothesis is that the water does not have enough time in the water block for good thermal exchange or that the cooler is not creating enough of a dT in the water block to absorb the amount of heat needed to in that cycle time. The fact that the Aluminum water block has a 5x lower specific heat than water is what is making me think either more contact time or great dT is needed.
My thoughts were to swap out the water block for an 40x200x12mm water block and increase the number of peltier coolers from 2->5 and going with the TEC1-12715 (Imax: 15.6A, Umax: 15.4V, Qmax: (dT=0) 150W, dTmax=68C).
This is where is am lost in the weeds and need help. I am lacking in the intellectual horsepower for this. Will using the 5 in parallel do the trick and not max out the converter? OR Will using 5 in series still produce the needed cooling effect with the lower dT associated with the lower amperage? Or is there another setup someone can recommend? I am open to feedback and direction, thank you in advance.
Relevant answer
Answer
Have you considered evaporative cooling for your aquarium. As long as the relative humidity in the room is not pushing 100%, you can achieve cooling using this technique. This link will show your how it is done:
  • asked a question related to Chemistry
Question
1 answer
I have a chemical I dissolve in DMSO. But if I put it in the centrifuge and spin it, all the chemical 'bits' will drop out of its dissolved state and form pellet on side of eppendorf.
Relevant answer
Answer
Your suspect compound is one with mid-high molecular weight that must be of organic nature. Centrifugating over 5000 rpm will "pelletize" this kind of compounds. Assuming you're working with inorganic or low-molecular compounds it would be a contamination: of your reagents, the DMSO itself or both.
In my experience DMSO is prone to contaminate due his highly miscibility with organic compounds, even some bacterial spores could survive on 99% DMSO. I recommend you to centrifugal your DMSO alone to see if pellets form. If that happens, try using a switch to another batch of reagent, or change to another supplier. You can also try to filter your DMSO with a 0,22 um filter, but I suspect it won't help.
  • asked a question related to Chemistry
Question
1 answer
Hey, I have been looking for it a lot. Are there sigma + - constants for meta substitution?
And also I couldn't find the sigma * constants.
Relevant answer
Answer
This is where I usually look for the Hammett constants: A Survey of Hammett Substituent Constants and Resonance and Field Parameters. Chem. Rev. 1997, 91, 165-195.
  • asked a question related to Chemistry
Question
3 answers
regards
Relevant answer
Answer
Si is usually ok to add in bulk pure form. It doesn't readily oxidize. Also on an unrelated note, Si chips look very cool.
  • asked a question related to Chemistry
Question
2 answers
ethanol can change chemistry of biochar. what possible changes could occur in biochar by washing with ethanol.
Relevant answer
Answer
The washing with ethanol helps to a deep removal of organic matter. Depending on the further use of it, it could be beneficial.
  • asked a question related to Chemistry
Question
2 answers
Hello all,
I am preparing a compilation file for doing MESMER calculations but I am having an issue. I am running some g08 calculations with acetyl and it seems like the transition state from for going to the RO2 to QOOH is unstable as the difference between the target energy and the calculated energy differs by about 0.1 - 1.1. There is too big a difference in the energy barriers between the RO2 and QOOH, but all other energies for the stationary points in the channels are comparative to the expected value. The IRC from the obtained transition state gave a significantly high "jump" in the potential energy graph. Would anyone happen to know what is going on?
Relevant answer
Answer
By unstable, I mean that the SCF Done is coming out too low than the expected. The target energy is coming from a the Ethanal+OH/O2 system that has been studied in literature that we are trying to emulate. The unit of measurement is in Hartrees
  • asked a question related to Chemistry
Question
6 answers
We are planning to extract phosphorus from biochar by organic acids. If anyone has some procedure (concentration of organic acids & steps) please inform.
Relevant answer
  • asked a question related to Chemistry
Question
6 answers
The common method for phosphorus solubilization efficiency measurement of soil microbes is zone formation in agar media (generally Pikovskaya media) but this is a qualitative study. However, there is also a liquid culture method with insoluble phosphorus in liquid media. The estimation of available phosphorus by ICP-OES is quite promising and precise.
Relevant answer
Answer
Based on the following study it has been concluded that Phosphorus measurements by HP-ICP-OES showed accurate results with very small uncertainties (0.1%) can be obtained with ICP-OES on digested DNA as has been seen with single-element solutions also, it is suitable for any size of nucleic acid from nucleotides to genomic DNA.
  • asked a question related to Chemistry
Question
1 answer
Hello Community,
I am currently restarting my work on battery management systems, I plan to use Lithium Iron Phosphate cells for their better energy density and relatively better resistance to thermal behaviour than few other commonly sought after battery chemistries. I require some help with good materials or references to help me accomplish BMS for 2W EV. I see that there are Kalman filter based estimations available, but they seem complex and expensive in terms of computations such algorithms require to be implemented.
Kindly request the experienced fraternity to guide me to understand and implement SOX estimation for LiFePO4 Cells.
Thanks in advance.
Relevant answer
Answer
Hello,
Firstly I would like to give a small correction: the energy density of LFP is lower than other lithium ion batteries. This is mainly due to the lower voltage produced by this anode-cathode pair. I have made my master thesis on this subject 5 years ago so I will give you some information based on what I still remember (keep in mind that some of my references may be a bit outdated).
On the state of charge (SoC) discussion: the major difficulty with LFP is that its voltage-SoC curve is very flat over a large part of its capacity. This means that the open-circuit voltage does not change strongly as the cell is being charged-discharged. Only at the tails of the capacity (generally about < 20% SoC and > 80% SoC) will the voltage change strongly for a change in Coulombs (which can be expressed as the differential voltage, or dV/dQ). A comparison of estimation methods can be found at (Wladislaw Waag, Christian Fleischer, and Dirk Uwe Sauer. Critical review of the methods for monitoring of lithium-ion batteries in electric and hybrid vehicles. Journal of Power Sources) and another good reference is (Wen-Yeau Chang. The state of charge estimating methods for battery: A review. ISRN Applied Mathematics, 2013)
To make a simple but decent estimation of the SoC of an LFP battery, I'd propose you need 1 main piece of battery/cell-related information and one optional piece of information: mainly the voltage-SoC curve at sufficiently high resolution (which can be transformed to a dV/dQ-SoC curve) and additionally a mapping of the internal resistance of the battery over a range of temperatures & SoC. With this information, you can use a current counting algorithm which simply integrates the current (dis)charged by the battery and uses this to determine the SoC. The issue with current counting is that any measurement error is also integrated and over time this results in a large error. There are some simple fixes for this, at least if your use case allows for it. The idea is to reset the counter and SoC at specific moments: the most useful moment is to reset it when the battery is full, is empty, and/or when it is at rest. If the battery is at rest in the "flat" part of its profile you could also reset the counter, assuming your voltage measurement is sufficiently accurate. If at rest for a very high (or low) SoC, reseting becomes more accurate. If there are not many "rest moments" then it becomes more tricky, but you could use the internal resistance map to estimate the OVC of the battery while it is under load (you could even implement a higher order equivalent circuit model of a battery for a better estimation).
You could also use a simple recursive least squares method to estimate the SoC which has been widely documented in the literature (one example is here: Hongwen He, Xiaowei Zhang, Rui Xiong, Yongli Xu, and Hongqiang Guo. Online
model-based estimation of state-of-charge and open-circuit voltage of lithium-ion
batteries in electric vehicles. Energy, 39(1):310 – 318, 2012. Sustainable Energy
and Environmental Protection 2010)
Good luck!
  • asked a question related to Chemistry
Question
5 answers
Dear science community!
I need your help, please!
I`m totally disapointed and at a loss!
In 2020 (at the end of October) there were the IOP Conference Series: Materials Science and Engineering (ICoSiET 2020). Me and my colegues took part in these conference. As the result (like a result of any other conference) the thesis collection should have been published (at the 4th quarter of the 2020)). Unfortanately, these collection still haven`t publised (despite the fact that 2021 is already at its end).
So, I wonder, if there are anybody, who know something about this situation? Maby there are any of those who also waiting for their thesis?
We have wrote lots of messages to the organizators and the head of the university (in which this conference took place) but they stoped to respond us.
I think this situation shows disrespect for the conference participants. And I believe that such situations should be inlighted in our community!
Thank you, for your attention!
Relevant answer
Answer
Using the link as indicated by Shoffan Saifullah , the good news is now that your paper is finally published https://iopscience.iop.org/article/10.1088/1757-899X/1212/1/012013 The thing is that “IOP Conference Series: Materials Science and Engineering” is ' suffering' from their own success and are recently even discontinued (see enclosed file) in Scopus.
The reason is most likely the enormous increase in number of accepted and published papers over the last few years which can be seen by clicking on “Scopus content coverage” here https://www.scopus.com/sourceid/19700200831
I think that the people behind IOP now try to ‘spread’ the papers over more than one year so that the number of papers published annually goes down again towards more acceptable/realistic numbers (at least in terms of inclusion criteria for Scopus).
So, at the very best this is a desperate attempt of the publisher to correct their suspicious behavior (by publishing too many papers in a year which raises questions on how to maintain scientific standards/quality control). This victimize researchers like you who learn the hard way how a publisher is trying to get their act together (again).
Best regards.
  • asked a question related to Chemistry
Question
1 answer
We are doing a fab process involving a patterned titania layer sitting on quartz. We now want to etch a few microns of the quartz underneath the titania, in order to "release" the slab. What could be a could wet etching chemistry to etch quartz without etching (too much) titania?
Relevant answer
Answer
In principle silica is more sensitive to hot concentrated base than titania. However, a "quartz" substrate, whether silica glass or real crystalline quartz, is dense and etches very slowly, while your titania is probably deposited from the gas/plasma phase and not very dense. Selectivity may go the "wrong" way.
HF-based solutions will also attack both silica and titania, as you know. You may be able to find conditions of concentration and pH where silica will etch faster than titania, but to etch away the substrate while keeping the (presumably much thinner) deposited film is asking much.
One option I would consider is to interpose a thin Ti metal between the silica and the titania. Ti metal etches very fast in HF, even dilute HF, so you may be able to lift off the titania film without much damage. However, if the titania requires high-temperature annealing it is possible that the Ti will react with the titania to form TiO2-x.
  • asked a question related to Chemistry
Question
5 answers
Can you please suggest some *primary amine protecting group* which one do not chemically disturb by *nBuLi* reagent.
I already tried with PMBCl and Boc
In *PMBCl*, it facilitate ortho direction by itself only.
In the case of *Boc* it doesn't stable, hence it cleave during the reaction and enhance the formation of unwanted side reaction.
I'm studying the chemistry of below listed protecting compound
1) TBDMS
2) Trimethylsilyl chloride
3) MEM
4) MOM
Please give your suggestion which one is compatible protecting group for primary amine in presence of nBuLi reagent.
Relevant answer
Answer
The only N protection that is stable enough to allow typical n-BuLi chemistry of which I am aware is to attach two benzyl groups to a primary amine nitrogen, one benzyl group to a secondary amine nitrogen. Removal is by hydrogenation in the presence of one equivalent of HCl added to an ethanolic solution 0.2 M in your benzyl-protected amine derivative, where the HCl is added in the form of 1 M aqueous HCl (the ethanol can be 100% anhydrous or 95% ethanol). The typical catalyst for this is 10% Pd/C. The typical reducing agent is H2 at 60 psi. Typical times for complete removal vary depending on steric crowding around the amine group. PMB (para-methoxybenzyl) is easier to remove by both hydrogenation and by treatment with various acids.
A more thorough discussion is available if you have access to Green's book of protecting groups (Online ISBN: 9780470053485). More rugged groups each have their own problems. For example, a primary amine treated with succinaldehyde [HC(=O)CH2CH2C(=O)H] gives a pyrrole that can be cleaved back to an amine under various conditions. Converting the amine to a succinimide followed by TMSCl and a base gives an easier to remove 2,5-bis(trimethylsilyloxy)pyrrole. 1,2-bis(chlorodimethylsilyl)ethane and base protects the amine as 5-membered ring stable to base but labile to acid and TBAF.
You can mask the amine group as some other group; phenylselenyl chloride makes a phenylselenylamine; similarly phenylsulfenyl chloride makes a phenylsulfenylamine. These can be removed by mercuration or H2/Raney nickel. You can react the amine with an electron-deficient aryl chloride, displacing chloride and generating an electron-deficient aniline derivative that may lose one proton but not react further. Picryl chloride and chloropentafluorobenzene can react with amines to give anilines, and there are probably cutting-edge protecting groups based on these.
I would recommend against using MOM and MEM groups because under basic conditions these might result in a more reactive imine forming that can react with n-BuLi. These protecting groups are not suited to amines. They work well with alcohol protection, where the products are acetals of formaldehyde. If you are interested in that kind of group, think about exploring turning your primary amine into a derivative of thiamorpholine [a two-step but very clean reaction sequence avoiding the use of bis(2-chloroethyl)sulfide is treatment with 2,2'-thiodiacetic acid using a coupling reagent strong enough to form the cyclic imide, followed by reduction by borane-dimethylsulfide to the thiamorpholine group]. Removal can be the same as removing other sulfur-based groups (H2/Raney nickel, which leaves behind a diethylamino group) or oxidation (by MCPBA/bicarbonate or H2O2 etc.) in acetonitrile followed by aqueous base like 5%-10% potassium carbonate (the end product is the primary amine and 2,2'-sulfonyldiethanol, a water-soluble diol byproduct). I did the latter and it is a high-yielding, very mild protection and deprotection in which BOC-protecting group, acetals, esters, nitro groups, and conjugated C=C-C=O survive, but isolated C=C groups, carboxylic acid, aldehyde and ketones don't. I don't recall the literature references I used, off-hand, sorry. I would need access to a literature searching tool better than Google Scholar, but I don't have that. However, it's an example of "seek and you will find" that worked for my particular synthesis of a differentially protected non-natural amino acid, 2,4-diaminobutanoic acid, sometime around the late 1990's. So keep seeking. Best wishes.
  • asked a question related to Chemistry
Question
10 answers
I am looking for a topic to start my research in chemistry. something which is untouched so far or where research gap persists. A topic which has national and international importance. Completed my coursework so far.
Relevant answer
Answer
You're welcome Roma. All the best.
  • asked a question related to Chemistry
Question
9 answers
I have synthesized the metal nanoparticles and I want to know that the size of magnets used for stirring purpose has any effect on size of nanoparticles so does the speed of stirring.
Relevant answer
Answer
Dear all, the size of the stirring bar influence essentially two factors, i.e., shear degree or level and heat conduction and dissipation. These two factors are in direct influence on all NPs features : growth kinetics, shape, size and its distribution. The effect may not be monotonically scaled, but for sure it is a compromise between these factors. My Regards