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.
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I did a dpph method and make a variety of concentration (400, 200, 100, 50, 25 ppm). I have done it by making 1000 ppm first and diluted them, I already did this 4 times but the results are always same. is there something wrong with my way in diluting the sample? or is there something wrong with my sample?
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Rafina Naqiyya Qatrunnada Different concentrations ranging from 400 to 25 ppm can hardly have same DPPH radical scavenging potential. The concentration of metabolites will definitely be decreasing.
Have you checked the absorbance value of the 1000ppm stock solution you are preparing initially? If not do check the absorbance and see.
Also, how are you diluting the sample solution into different concentration?
consider another way to create the concentration gradient Rafina Naqiyya Qatrunnada
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For the sake of recycling electrolyte of a polymer Li-ion battery, the salts like LiPF6 will be recycled with CO2 supercritical extraction method.
But how can we preserve the volatile organic solvent carbonates to be used again, as these solvents start evaporating as soon as a cell is opened?
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Ethylene carbonate is solid at room temperature, propylene carbonate is also very polar and certainly not volatile.
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Hi, I'm Almajeanu Delia from Craiova, Romania, Faculty of Science, Department of Chemistry, Biologically Active Compounds, please can someone help me with a PPT or information about Multiple Myeloma?
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Hello, what is proteasome, proteasome treatment for myeloma, side effects, life expectancy, age at which it appears, now more recently multiple myeloma also appears at the age of 33, there is no longer a rule when and why it appears .Thank you!
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To all the great Chemistry minds, try to answer the question asked and try have a look at the following link:
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Gold and platinum (and other metals such as Pd) salts are easily reduced to the (colloidal) metal. Absorb solutions of such metals onto a porous plastic and they'll decompose within a day.
BTW, HAuCl4 is not found as such - it's a hygroscopic water-containing structure usually formulated as HAuCl4.xH2O.
Similarly, in aqueous solution we have PtCl4·5(H2O) - the pentahydrate.
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I'm looking for postdoc position
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Dmitriy Berillo thank you for sharing the links
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Just need to know if yes which company
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Yes, you can join a pharmaceutical company for an internship in Research Center or quality control of reputed pharma organization in you near by industry or our of your country if you get chance.
Feel free to ask if query any
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Looking for motivated Chemistry students (Net/Gate) qualified for working with our translational team at IIT BHU. Please apply if you are interested. The candidate will work to develop immunoprotective small molecules, develop 3D printable biomaterials and various aspects of medical implants.
Our laboratory link:
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I am interested
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Hi,
I have a leach solution with Li present as LiOH. I did lime water leaching of material but also leached impurities such as Zn, Cr and Al with it. The pH of the solution is around 11. Now I want to remove the impurities and the literature suggests using ion exchange resins to remove them. The ion exchange resins would require pH adjustment to around 6-7 which might also alter the chemistry of dissolved LiOH, and I do not want that. So how should I proceed? Is there any other way I should explore to remove those impurities?
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Ph 6-7 will not affect LiOH. That is by definition.
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While working on my laterite samples, I came across a problem. Following the digestion protocols we made the volume with approx. 100 times dilution and started the ICP-MS measurements. The concentrations went down after measurement of 2-3 samples. The reason was a clogged pore. Citing the presence of trace and REEs in very low concentrations we can't go for further dilution so is there any way to remove Fe from the matrix without disturbing other elements?
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Its sodium hydroxide saturated into ethanol, takes a few days to dissolve: ethanolic sodium hydroxide. ESH
drop your sample into a 500ml beaker of the ESH and heat to 80c stir plate for three hours. filter of the ESH.
disolve in ether and cold stir for one hour.
ready for ICPMS.
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I need to find a proper method to prepare sample solution by digestion for Pt-Pd-Rh elements from spent automotive catalysts. Any suggestion except application of microwave-assisted digestion would help me.
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Dear college,
In the determination of platinum group of elements in Pt catalyst samples can be used different decomposition procedures.
Please, pay attention, that the analytical evaluation function is assumed to be straight line through the origin. There are is not spectral interferences. But the correct calibration from the point of view of multiplicative interferences means a precise matching of the acid in both the reference and sample solutions.
I recommend the decomposition procedure in the determination of platinum group of elements in Pt catalyst samples because the platinum group of elements must be dissolved in aqua regia, but in the end of the dissolution procedure, the final sample solution contains Pt, Pd and Rh in hydrochloric acid only in an appropriate acidity, because the undissolved material (γ-alumina+silicates) has settled down. Under these conditions you must prepared the calibration solutions for Pt, Pd and Rh with hydrochloric acid in an appropriate acidity.
With kind regards, N. Daskalova
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I want to predict the reactions between my two desired inorganic chemical compounds. Can I? Is there any software or website for do this? Dear chemistry experts, please help me with this. Thank you for your response.
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You can predict reactions between inorganic compounds using tools like ChemReaX, AiZynthFinder, and Ansys Chemkin-Pro, which simulate and model chemical reactions. These software options allow you to explore potential reaction pathways based on your specific compounds.
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I have read many journals about the bioremediation of mercury using bacteria. All of them have used mercuric chloride in their experiments. However, this compound is a little tricky to synthesize. Can I use mercury (II) nitrate instead?
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Yes, you can use mercury (II) nitrate instead of mercuric chloride for bioremediation experiments, but it's essential to conduct preliminary studies to assess bacterial responses and effectiveness, as the behavior of different mercury compounds can vary significantly.
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What means gamma in old chemistry papers like Lowry method? I have a suspicion it was the concentration unit in micro something. I am right? Why they used it? Typographical problems at the time?
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I have the same problem with older paper, and I foun this:
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I have performed the adsorption studies and applied Langmuir model to the data. I obtained KL value from it. In literature it is given higher the KL value stronger the interaction between adsorbent and adsorbate. But there isn't any specific value of KL given.
In literature FTIR and XRD are also performed to predict the adsorption mechanism. I have done that as well and there is shift and change in the peak intensities.
Which one is better to predict the adsorption mechanism? Either from KL value or FTIR/XRD?
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From the D-R model, u can consider physical adsorption or chemisorption; when E<8 kj/mol is physisorption, 8 kj/mol<E<16 kj/mol is chemisorption. and also you can find these references will help you
1-Influence of Synthesis and Functionalization Procedures of Fe3O4 NPs by Mono- and Diamino Silane Coupling Agents on the Adsorption Efficiency of Anionic Dyes
2-Cutting-edge in the green synthesis of MIL-101 (Cr) MOF based on organic and inorganic waste recycling with extraordinary removal for anionic dye
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i want to prepare this solution in-house in lab, is any method?
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Preparing a 4M HCl solution in dioxane is not recommended in a standard chemistry lab due to significant safety risks. Both HCl and dioxane are hazardous, and their mixture can form explosive peroxides. Safer alternatives should be considered, such as using commercially available solutions or aqueous HCl, and the procedure should only be attempted in specialized facilities with proper safety equipment and trained personnel.
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I'd like to protect a secondary amine group (on Glucosamine-HCl) with a silyl group.
Did you ever do that? Did you use a chlorosilane? Does it get attached two times to the amine? Is the resulting nitrogen on -NH-Si-R more activated as a nucleophile?
How is it removed? Acids only or also fluoride ions? Does it work only for trimethylsilanes or also more bulky/resistent silanes (TBDMS, TBDPS, ...)?
Thank you in advance
RC
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Silyl Protecting groups are fine to temporarily protect primary amines.
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Chemical laboratory process should be so so
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Chemistry is essential for understanding and controlling chemical reactions, crucial in research and problem-solving across various fields. Even alternative methods often rely on chemical principles for effectiveness.
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La isoterma de Langmuir representa una adsorcion fisica o quimica?
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I think, Langmuir adsorption model can describe both physical and chemical adsorption.
The exact meaning of adsorption sites can differ in this cases (for chemisorption, it can be physical number of atoms/molecules of specific chemical species, whereas for physisoprtion the number of sites can just reflect the maximal number of adsorbate atoms/molecules that can "fill" the surface due to their finite lateral "size").
The binding energy is also substantially different that may give a trivial asymptotic limit in the model for chemical or physical adsorption.
Let's make some estimations. As it is often mentioned, the binding energy for physisorption is usually 10⁻²–10⁻¹ eV, whereas it is usually 10⁻¹–10⁰ eV for chemisorption. In the Langmuir adsorption model, the fractional occupancy θ depends on the temperature T, chemical potential μ and binding energy ε as
θ = [1 + exp(−(μ+ε)/kT)]⁻¹,
and 1/kT ≃ 40 eV⁻¹ for T ≃ 300 K, μ/kT ~ –16 (estimation for an ideal gas at 1 atm pressure). So, the difference in the value of ε in 1–2 decimal orders can correspond even to opposite asymptotic limits in the fractional occupancy vs the bulk concentration dependence θ(n) — a constant 'high concentration' limit θ ≃ 1 of for a high binding energy and a linear 'low concentration' asymptotic limit θn for a low binding energy.
For the estimations I presented, only moderate binding energies ε ~ 10⁻¹ eV per site can give the fractional occupancy values somewhere between the asymptotic limits of θ(n). This case may correspond to quite a weak chemical bond or a strong physical attraction.
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The temperature-dependence of rate constants is frequently expressed using a modified form of the Arrhenius equation:
k(T) = α (T/300)^β exp(−γ/T)
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Pablo Mtz Teck-Ghee Lee Thank you sir for your valuable efforts.
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When a homometallic cluster, Cu6L6, and a homometallic Ag8L8 cluster are dissolved in the DCM/Isopropanol system, they would form a heterometallic cluster crystal, Cu4Ag4L8, and no homometallic metal clusters will be formed. (L is phenylacetylene-derived ligand)
What is the most likely driving force for the formation of this coinage heterometallic clusters?
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Thermodynamics.
Lol, yeah I get you meant specifics. I would be curious to see if DFT could tease out what's going on.
Reference for the chemistry?
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Hello,
Has anybody used ATR-FTIR to probe the chemistry of colloidal samples (excluding the procedure of drying the droplet on the crystal or using a flow cell)?
If yes, how do you account for the broad water peak?
Any relevant references are really appreciated.
Thank you!
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If spectral subtraction may introduce artifacts in your ATR-FTIR analysis, consider using advanced deconvolution techniques to resolve overlapping peaks without removing the water peak. Additionally, employing baseline correction, temperature control, or alternative solvents can further enhance the clarity of your spectra.
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I run mechanochemical reactions that involves the use of a large amount of catalyst (1:1 molar ratio to the reactant). When I try to understand the effect of amount of catalyst on the reaction, I find it very hard to get consistent results when I control the the ball to powder mass ratio (I am using the same number of balls, but keeping the total powder mass the same while adjusting the mass between the reactant and catalyst). This makes me think that I should probably control ball to powder volume. However, even though I know the rough bulk volume of two things at the beginning, the powder volume will always increase by an unknown amount once it is milled. So how should I control my reaction??
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It is not easy to define the controls of your reaction. Don't think you can use a simple control or two to define your experiments. Breifly, you should consider the controls of mass, volume, particle size distribution (PSD), surface property (not all inclusive) of catalyst and reactant, as well as their ratios to define your reactions.
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Hi, I am a PhD student working at Jagiellonian University, Faculty of Chemistry. My work is related to the development of new analytical methods for the quantification of short-chain fatty acids in biological samples. In my research, I used a gas chromatograph (Shimadzu GC-2030 Nexis) coupled with a triple quadrupole mass spectrometer (Shimadzu TQ-8040). I developed a new GC-MS/MS method for the quantification of short-chain fatty acids, but I have a problem with the carry-over effect. After injection of high concentrations of analytes, such as 10 ug/ml, I observed peaks from the analytes in the blank sample. The problem is a little bit reduced when I frequently change the solvents (water and ethanol) and utilize a long washing procedure after injection, but it still exists. The current washing procedure includes 4x8µl H2O, 4x8µl EtOH, and 4x8µl EtOH. In addition, sequence – 20x8µl H2O, 20x8µl EtOH, and 20x8µl EtOH were utilized for extra washing following the analytes with the highest concentration.
Do you have some experience with the carry-over effect in the GC-MS/MS system and some suggestions to solve my problem?
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Syringe wash is not the only approach to clean Your system. If You inject "dirty" samples the whole injector (including tubing) might get dirty. A solvent injection between the samples should will help in most cases....... If there are ghost peaks it might help to prolong the GC program.
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Post-COVID, online platforms or remote learning especially in the education field has accelerated its pace. Is this going to make a lasting impression where educators must adapt to this new way of learning or are we returning back to physical school, physical tutorings or physical lectures in the near future.
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In my mind no, The roles of teachers can not be subtituted by machines. In Australia on 1995 a research concluded that teacher can not chnged by machines.
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Yes because critical rationalism recognizes substance, parsimony and identity(adjusts premises upon contradiction), while skeptical empiricism believes all results from impressions. Skeptical empiricism also believes the self is an illusion.
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Si lo es, definitivamente, porque el gran valor de la CIENCIA RACIONAL, a demostrado y lo sigue haciendo hoy,su inconmensurable valor social y humano al solucionar infinidad de padecimientos y grandes sufrimientos humanos. Además del la mayor duración y esperanza de vida actual es disfrutada y dá esperanzas de ser prolongada.
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Hello,
I want to load Remedesivir (RNA polymerase inhibitor) into mesoporous nanoparticles (MSNs). The issue is drug is temperature and pH sensitive and it degrades quickly. I need advice on its loading.
1- Should it be loaded to at the last step of MSN synthesis. Problem with this MSNs are extracted later on through reflux and 60 degree temperature is required. It degrades drug.
2- Should it be loaded after extraction making an ice bath but how long it should be kept on stirring?
3- Later I want to coat it with chitosan MSN loaded Remedesivir and then coating with chitosan. I am concerned about leaching and degradation of drug. Should i load drug first and then add drug?
Thank you for your suggestions.
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Apparently, the inclusion of Remdesivir in mesoporous nanoparticles, as such or at the stage of their synthesis. is not good idea, due to the instability of R and, possibly, its low bioavailability. Microencapsulation by complex coacervation, with possible involving CD, may be more frutful approach. Good luck!
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Flavors of all tea leaves are determined by their respective chemical compositions. Are there any quantitative research on this?
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Thank you so much Professor Mirgorod. And thanks for introduce rutine to me.
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Research has proven that successful chemistry cohorts normally spend more time executing practical experiments in the laboratory rather than sitting in the classroom listening to lectures.
Researchers undertaking such job roles, please share your ideas and comments.
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Jürgen Weippert Partly. I think some teachers are governed by the voices above them like principals or someone more powerful like the stakeholders who refused to spend money in buying lab equipments, hence teachers themselves has no say at the end of the day....
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Hi all,
I have a several gallons of water mixed with low percent SLS, how can i remove the SLS in a cost-effective manner.
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Charcoal filtration, perhaps.
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Here is one case: I want to perform X + Y in the presence of Z catalyst in a 50 mL milling jar with 8 12 mm milling balls and investigate whether the the amount of catalyst affect the yield of the product. So, I change the amount of catalyst from 1 molar equivalent to 3 molar equivalent as compared to X. However, this will change the total volume of powder as well. And as we all know, when the volume changes, the kinetic energy delivered from the ball to the material will not longer be the same. Less energy will be delivered to the powder and the kinetics of the reaction will be affected by this.
I've read that the milling load in a mechanochemical reaction is defined as the total powder mass divided by the void volume in the jar (jar total volume - volume of balls)
In the case I mentioned before, should I (1) keep the amount of everything the same and increase the amount of the catalyst as what it should be, basically ignoring the effect of volume and just do the experiment or (2) Readjusting the mass of all samples to keep the total mass the same as before to maintain the same milling load as before (as a result, it will decrease the mass of the reactant) ???
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One of the most important parameters in any mechanochemical reaction (ball milling) is the ball to powder ration (BPR). What I personally do and I find to give consistent results is keeping the powder volume constant (which means if I have to change the ration of 2 or 3 components I readjust it in order to keep the same BPR).
In case the amount of your catalyst is negligible compared to the total volume (mass) of the powder you can ignore it.
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International Conference on Engineering, Science, Technology, and Innovation (IESTI 2024)
Date: 19-09-2024
Location: Online
Submission Deadline: 15-07-2024 **** Extended to 1-8-2024
The Organizing Committee of the International Conference on Engineering, Science, Technology, and Innovation (IESTI 2024) is pleased to invite researchers, practitioners, and professionals to submit papers for presentation and publication at the IESTI conference. This prestigious event aims to bring together leading scholars, researchers, and industry experts to exchange and share their experiences and research results on all aspects of Engineering, Science, Technology, and Innovation.
Topics of Interest
Topics of interest for submission include, but are not limited to:
  • Engineering:
    • Mechanical Engineering
    • Electrical and Electronics Engineering
    • Civil Engineering
    • Chemical Engineering
    • Aerospace Engineering
    • Materials Science and Engineering
    • Computer Science and Engineering
  • Science:
    • Physical Sciences
    • Life Sciences
    • Environmental Sciences
    • Earth Sciences
    • Chemical Sciences
    • Artificial Intelligence
  • Technology:
    • Information Technology
    • Communications Technology
    • Nanotechnology
    • Biotechnology
  • Innovation:
    • Technological Innovation
    • Innovation Management
    • Entrepreneurship
    • Sustainable Development
    • Policy and Innovation
Submission Guidelines
Authors are invited to submit original, unpublished research papers that are not currently under review elsewhere. All submissions will be peer-reviewed and evaluated based on originality, technical and research content, correctness, relevance to the conference, contributions, and readability.
Paper Submission Process:
1. Format: All papers must be formatted according to the conference template available on the conference website.
2. Length: Full papers should be between 6-10 pages, including all figures, tables, and references.
3. Submission Link: Submit your papers through the online submission system available on the conference website.
4. Review Process: Each paper will undergo a blind peer review process.
5. Notification: Authors will be notified of the review results by 15-08-2024.
6. Camera-Ready Submission: Final versions of accepted papers must be submitted by 31-08-2024.
Important Dates
  • Paper Submission Deadline: 15-07-2024 **** Extended to 1-8-2024
  • Notification of Acceptance: 15-08-2024
  • Camera-Ready Paper Submission: 31-08-2024
  • Early Bird Registration Deadline: 20-08-2024
  • Conference Dates: 19-09-2024
Conference Proceedings
All accepted and presented papers will be published in the journals listed on the following website:
Special Sessions and Workshops
  • IESTI 2024 will also feature special sessions and workshops focusing on current trends and emerging topics in Engineering, Science, Technology, and Innovation. Proposals for special sessions and workshops can be submitted to: editor@academicedgepub.co.uk, by 1-8-2024.
Contact Information
For any inquiries regarding paper submissions or the conference, please contact:
We look forward to your participation in IESTI 2024 and to a successful conference!
We would like to extend our invitation to invite you to join the editorial board of the:
- Journal of Probiotics and Bioactive Molecules Research (JPBMR)
Please send an email including your full name, affiliation, CV, and mention the selected journal to the following email address: editor@academicedgepub.co.uk
Sincerely,
IESTI 2024 Organizing Committee
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شكرا جزيلا دكتور🙏🏻
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I built an AI powered tool that gives you a detailed PDF report on your manuscript to improve your chances of publication.
The report includes:
- Strengths and Weaknesses
- Quantitative scoring for each section
- Actionable recommendations with examples
It's $1 per upload to cover costs. The first 20 users can use discount code "FREE" to try it out now.
Would love to hear any feedback and thoughts - https://reviewmypaper.ai/
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That's a great question and definitely a valid concern of protecting IP!
Here's how data is handled:
- The manuscript is sent to our backend and deleted from our database within 72 hours of generating your report.
- In creating the review the only external service used is the OpenAI API, and they've explicitly stated "data sent to the OpenAI API will not be used to train or improve OpenAI models" [reference here](https://platform.openai.com/docs/models/how-we-use-your-data#:~:text=As%20of%20March%201%2C%202023%2C%20data%20sent%20to%20the%20OpenAI%20API%20will%20not%20be%20used%20to%20train%20or%20improve%20OpenAI%20models)
It won't save the data longer than it needs to and will never be used to train a model.
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Hello everyone,
My question for sure is silly, but I have been arguing with my labmate about this. If our plasmid concentration is 0.776 µg/µL and he wants to make a final concentration for transfection of 1 µg/µL and 6 µg/µL, how is it possible to achieve a concentration of 6 µg/µL from 0.776 µg/µL?
Using the equation C_1 V_1 = C_2 V_2 :
v2 = 50 ul
c2= 6 ug/ul
Please help me understand. I have a brief knowledge of chemistry and calculation
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Ryan, you can use 6 ug by using a larger volume, you would need about 8 ul of your plasmid prep.
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What is the difference between reaction and interaction in chemistry? Would you please provide me with the details?
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Dear Doctor
[Interaction:
The situation or occurrence in which two or more objects or events act upon one another to produce a new effect; the effect resulting from such a situation or occurrence.
Reaction:
An action or statement in response to a stimulus or other event.]
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Anyone is working on Artificial Neural Networks (ANN) in research?? I am willing to learn about it is there any platform/workshop/course for free regarding the same!
Also I’m looking for this for a chemistry point of view
Thanks and Regards
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Ayushi Mishra I wouldn't mind in assisting you
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What is the difference between absorption and adsorption?
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The main difference is that while absorption involves the mass transfer of particles into another material (one substance absorbing another), adsorption takes place with the adhesion of particles onto the surface of a substance. absorption is the process in which a fluid dissolves by a liquid or a solid. In the case of Adsorption, the atoms, ions, or molecules from a substance adhere to a surface of the adsorbent
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Hi, I am looking to perform an analysis of Br/ KBr in samples of water sources to see if the levels are safe. Due to budget and resource limitation at the stage, I would prefer a method that considers these factors.
Kindly help.
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KBr is 100% ionized and in aqueous solution the counter ion is anything that is a cation (positively charged) that is floating around. If your buffer contains K+ as the most common cation,then [Br-] = [KBr].
I have used the colorimetric assay previously given.
Bowen H.J.M. The determination of chlorine, bromide and iodide in biological material by activation analysis. Biochem. J. 1959; 73: 381
It is easy to use and cheap, despite using a gold salt because you don't use much.
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Its been around 6 months when I started working on a research project related to nanomaterials BFO for water treatment. I worked on the chemistry of synthesis, photocatalysis, degradation of textile dyes using visible light only, sol-gel synthesis of BiFeO3 (material able to degrade multiple cationic dyes of higher concentration 20ppm), and sol-gel synthesis of double perovskites (its still incomplete and material is able to degrade cationic and anionic both type of dye i.e., Rh.B., MB, MV, CV, MG, CR etc. efficiently in lesser time). To help you guys how can you find the chemistry of synthesis for related material always remember to look for the chemistry of method you are using it can be sol-gel, co-precipitation, solvothermal, chemical vapor deposition or any other. Look for the chemistry of original method and them find out what materials in your method are acting analogous to materials given in explained method, you found during literature review. Hope this will help you out remember me in your prayers. Thank you so much. I will be glad to help you guys anywhere I could.
#research #nanomaterial #energyconversion #solarenergy #materialsynthesis #nanotechnology #photocatalysis #visiblelight #sunlight
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I am currently reading many article about nano materials and I think NM is the future.
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As a professional teacher, there is need to have a 'What' and 'How' of teaching? The what to teach, which is the subject content like Chemistry, Biology, Mathematics and the likes, and the 'How' to teach them, which is the pedagogical content knowledge.
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I extracted protein from a roasted food sample using alkaline extraction followed by acid precipitation. Polyphenols were always coextracted since they were covalently bound with proteins during roasting and the formation of covalent bonds were irreversible. How can I know how abundant covalently-bound and noncovalently-bound polyphenols are in my protein extracts? I would greatly appreciate it if you could provide any suggestion or guidance.
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To proof that a small molecule is covalently bound to a polymer is very challenging. I was in similar situation when I tried to bind polyphenols covalently to chitosan. Generally, the polyphenols in your washing solution were either non-covalently bound or the covalent bond was cleaved during washing. The unremoved polyphenols are not necessarily bound covalently, as non-covalent interactions can still be too strong.
You could try to depolymerise your protein (e.g. by enzymatic hydrolysis) and then analyse the fragments (e.g. by LC-MS). If you find a fragment with the polyphenol bound covalently, you have a proof.
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There is a pH-Electrode by Mettler-Toledo that is supposed to measure pH at temperatures as low as -30°C, even in frozen solutions.
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I have the same in lab cool from Mettler Toledo, can’t quite figure out how to measure frozen buffer pH down to -30C. Any pointers? Much appreciated
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Preprint Nuance
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Ware God Race Relations
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Greetings
I've been searching for quite a while about Covalent organic framework (COF) and Porous organic polymer (POP) XRD pattern, how their xrd pattern should be and their differences.
But i could not find any specific findings.
some texts mentioned that COF xrd pattern should be sharp and pop should be broad. But ive seen so many COFs with broad PXRD pattern.
How can you distinguish between these two? How could you know that your product is POP or COF (etc. )?
Can somebody share their knowledge or mention a helpful Paper? Im so confused.
Thanks a lot.
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-- 🧪 Calling all science enthusiasts! 🌟 Whether you are a seasoned scientist or simply curious about the fascinating world of chemical compounds, I need your input for an exciting project! 🚀 In the comments below, please share: --> Your top 5 CAS Registry Numbers® and the name of your favorite molecules (and perhaps why?). If you are feeling particularly creative or simply undecided, feel free to share two posts! Not familiar with CAS Numbers? No problem! CAS numbers are unique identifiers assigned to chemical substances. Think of them as molecular fingerprints! For a quick explanation, check out Wikipedia link here https://lnkd.in/ee8fkHug. Thank you in advance for your help. Let's create a diverse and fascinating collection of molecules together! 💡✨ #CASnumbers #STEM #innovation #chemistry --
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These are ChatGPT's selections: 7732-18-5 Water (H2O): Essential for life as we know it, water is a universal solvent, crucial for biological processes and various industrial applications. 124-38-9 Carbon dioxide (CO2): Important for photosynthesis and maintaining Earth's climate balance, but also notorious as a greenhouse gas contributing to global warming. 9007-49-2 DNA (Deoxyribonucleic acid): The molecule that carries genetic instructions for the development, functioning, growth, and reproduction of all known organisms. 50-78-2 Aspirin (Acetylsalicylic acid): Widely used as a pain reliever, anti-inflammatory, and fever reducer, with additional benefits such as preventing blood clot formation. 479-61-8 Chlorophyll a: A specific form of chlorophyll, crucial for photosynthesis in plants and other photosynthetic organisms. It's responsible for the green pigment in plants and plays a central role in converting light energy into chemical energy, which is then used to synthesize carbohydrates from carbon dioxide and water... see above ;-)
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Can a published journal article be submitted to conferences?
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It is quite common to present talks or posters on the basis of previously published papers. However, care must be taken when contributing to the proceedings of the conference so as not to infringe the copyright of the journal's publisher.
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Most of the researchers use to teach at university. In some careers, professionals who exert their profession without doing research share teaching spaces. When I was a chemistry student, 100% of my teachers were researchers ranging from PhD candidates to experts in their respective fields. While it may seem logical for researchers to be the best candidates to teach in fields such as chemistry or biology, what about healthcare-related fields like medicine, pharmacy, or biochemistry? Who is better suited to lead a class, a researcher or a professional, or both, each one in different subjects? We can distinguish between basic and clinical subjects. I am interested in hearing your thoughts on this matter.
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Being a proficient researcher doesn't necessarily equate to being a better professor. While research expertise can enhance teaching by bringing current knowledge and real-world applications into the classroom, effective teaching requires distinct skills such as communication, empathy, and the ability to engage students.
A good professor balances both research and teaching responsibilities, tailoring their approach to meet the needs of their students while contributing to their field through research. However, being a successful researcher doesn't guarantee effective teaching, as teaching requires its own set of abilities and dedication.
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Maybe we should identify what is the most parsimonious afterlife. Expanding the law of identity, maybe physics can determine the exact afterlife all have coming.
My previous attempts:
Guessing what the afterlife broadly is:
Guessing what the afterlife is NOT.
3)
4)
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I'm not sure, but I think you did a great job of answering your own question... 'Charting the afterlife?" Answer; Why?' Somethings can't be known. Or, even if we were explained, would we have a hope of understanding the answer? Every morning on the way to work I ask the Universe for a special watch over some friends and family (including my most recent 'best friend' Chihuahua) who have 'recently' passed. I know that they are soaring the Universe as Light Beings and I am a bit jealous of all they will see and re-understand. But charting the afterlife... it's like charting the Universe itself accurately. THEY could do it, but we can't even imagine what it looks like in totality. MY opinion, of course.
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What are the efficient online sources to self-learn DFT calculations useful for students with chemistry background ?
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There is no easy answer to this question, and actually I do not think that self-learning can lead you very far. This having been said, self-learning the application of DFT to chemical problems requires facing two different types of knowledge, one on theoretical chemistry, and one on the implementation of the theory in a computational software suite.
So, first I would go to books & manuals. For a start, the books from Jensen and Cramer might be very useful. As for the second problem, studying the manuals is mandatory. Many software suite, for example Gaussian, have very complete official on-line resources. Only after a deep study you might start using the software. A help on practical issues can came from any of the many fora on computational chemistry, including RG and the Telegram group on computational and quantum chemistry.
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After spending some time on understanding the chemistry of Sol-Gel synthesis. I've made a short overview I need you guys to let me know if it's good or not.
I am specifying the pechini method here in which a chelating agent is used while salt solutions are made in water and ethylene glycol.
these are steps for bismuth ferrite (BiFeO3) synthesis.
Here are the steps.
Iron nitrate and EDTA solution in water and Bismuth nitrate solution in ethylene glycol.
1. Formation of Iron hydroxide (need your help. it may lead towards formation of Fe-O-Fe) while heating.
2. Formation of Bismuth glycolate
3. Mixing of these salts together with EDTA
4. Formation of Metal EDTA complex (Here I need your help is it possible for the complex to be between 1 EDTA molecule and Fe, Bi to different metals) if yes then a bi metal complex. Otherwise two complexes in one solution.
5. drying to form gel results in crosslinking (need your help how will it work and happen).
6. Drying to form Xerogel and complete removal of solvents.
7. calcination at high temperature to decompose the Metal-EDTA complex results on formation of metal ions and which at the end form BiFeO3.
#nanomaterial #research #BFO #perovskite #energystorage #energyharvesting #energyconversion #renewableenergy #metaloxides
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Mixing solutions with inorganic salts and EDTA is sufficient to form a sol. When the solvent is removed in air, a gel will form. Even visually monitor the viscosity. When the solvent is removed, a xerogel is completely formed. Calcination of the xerogel will give BiFeO3.
The stages have been described correctly, but there is no need to separate them.
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I need some suggestions for articles recently focused on the computational design of proteins, as well as the evaluation of the designed proteins by assessing various properties or values. If anyone is interested in this field and has read articles on this topic, please don't hesitate to share your suggestions below
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Hi, you can read some papers:
1. Computational Protein Design: Advances in Algorithms and Biophysical Validation
This article discusses recent advances in computational protein design algorithms and methodologies, focusing on biophysical validation techniques to assess the stability, structure, and function of designed proteins.
2. Machine Learning Approaches for Protein Design: Recent Advances and Future Directions
This review article explores the application of machine learning techniques in protein design, including deep learning approaches, and discusses methods for evaluating designed proteins using molecular dynamics simulations and experimental validation.
3. Rational Protein Design: Computational Approaches and Experimental Validation
This paper presents computational strategies for rational protein design, highlighting methods such as Rosetta and FoldX, and provides insights into experimental techniques for validating designed proteins through biophysical assays and structural characterization.
4. Multi-Objective Optimization in Computational Protein Design: Balancing Stability, Function, and Specificity
This article focuses on multi-objective optimization strategies in computational protein design, aiming to balance various design objectives such as stability, function, and specificity. It discusses evaluation metrics and experimental validation approaches for assessing designed proteins.
5. Integration of Structural Bioinformatics and Machine Learning for Protein Engineering
This study presents an integrated approach combining structural bioinformatics and machine learning for protein engineering, emphasizing the importance of accurate protein structure prediction and molecular dynamics simulations in evaluating designed proteins.
6. High-Throughput Screening Platforms for Computational Protein Design
This review article surveys high-throughput screening platforms used in computational protein design, including methods based on protein-protein interactions, enzyme assays, and cell-based assays, and discusses their applications in evaluating large libraries of designed proteins.
7. Protein Design in the Age of Synthetic Biology: From Theory to Experiment
This paper explores the intersection of protein design and synthetic biology, discussing computational tools for designing novel protein functions and experimental techniques for characterizing designed proteins in living systems.
These articles provide insights into recent advancements in computational protein design and offer strategies for evaluating the properties and functions of designed proteins through computational and experimental approaches.
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I am checking the Oxygen Balance calculation as reported in Wikipedia (https://en.wikipedia.org/wiki/Oxygen_balance).
Some calculated values corresponds to those reported in that page (e.g. nitromethane (-39%) and trinitrotoluene (−74%), ammonium nitrate (+20%)).
While some of the values reported in the wiki page do not fit with the formula (e.g. ammonium perchlorate (wiki +34%, calculated 27%), potassium chlorate (wiki +39.2%, calculated 26%, sodium chlorate (wiki +45%, calculated 30%)).
Oxygen Balance is used to evaluate explosivity of a substance and it is also cited by ECHA in ECHA Guidance on the Application of the CLP Criteria Version 6.0 – Jan 2024, page 93.
Am I doing something wrong or am I missing something?
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Oxygen balance is often calculated to CO rather than CO2, maybe a part of the problem originates from this. Usually we use the following formula for CHNOFClS compounds
OxBal=16*(nO+nF/2+nCl/2-(2*nC+0.5*nH+2*nS))/MW*100
Note, however, that the oxygen balance cannot be used as a measure of explosibility or energetic potential, it is much more complicated. For benchmarked emripical equations for energetic potential see our paper
we also suggested a rough estimation for the mechanical sensitivity of compound here
Hope that helps,
Nikita Muravyev
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Dear researchers
I'm currently editing a Research Topic entitled Five-membered Ring Heterocyclic Compounds as Anticancer Drug Candidates. It's being published in the journal Frontiers in Chemistry. Given your work in this field, would you be interested in contributing? I look forward to hearing from you. Best wishes,
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Interested
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The procedures of Justus Liebig Annalen der Chemie 1914 do not lead to the desired product.
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Perhaps this info helps https://www.jk-sci.com/blogs/resource-center/wagner-meerwein-rearrangement or otherwise you could go to Google Scholar and insert “Über den Reaktionsmechanismus der Umwandlung von Borneol in Camphen” in the search box. Then you see that 116 papers have cited the publications, perhaps here you find an update?
Best regards.
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I'm currently trying to make a standard curve for potassium ion detection. For my reagent I'm using 25 mM of sodium cobalthexanitrite with potassium dihydrogen phosphate as a substrate in a 40:60 ratio and measuring at 420nm after incubating the mixture in the dark for 10 minutes. Unfortunately, it's not really working and I'm not getting any precipitation. Is there something more I need to add or a step I've missed? Is my wavelength incorrect?
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Adam B Shapiro thanks this looks very helpful for me
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Hi,
I am looking for new development in biobased flocculants for water treatment. If you company is a start-up and developing this type of chemistry, I am very interested to contact you.
Regards, Pieter
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Bio-based flocculants are efficient and eco-friendly for bulk algal biomass recovery.
Biomass separation efficiencies of bioflocculants are species-specific.
Harvested biomass from float beds duly nurtured can be directly converted to biofuel products. C H modulated
A few sp. bioflocculants have synergistic effects on the overall lipid yield, as needed they can be harvested
Bio-based flocculants for sustainable harvesting of micro - algae are done for both macro micro sp are sourced as convenient ..
What is bio flocculation?
What is a natural flocculant?
A bio- flocculant in biology needs are sourced as needed.
Biopolymer-based molecules produced by the cells of living organisms and the materials derived from these are duly used for lab based experiments.
Scholarly articles for bio based flocculant are sourced for add on info !
Bio-based flocculants for sustainable harvesting of - ‎Ogbonna sp
Is to be studied..
These water-soluble synthetic polymers have found applications in various water treatment processes, including flocculation, sedimentation, and membrane ...
As per recent Achievements in Polymer Bio-Based Flocculants ...
Polymer flocculants are used to promote solid–liquid separation processes in potable water and wastewater treatment.
‎Bio-Based Polysaccharide.
Recent advances in polysaccharide bio-based flocculants may be sources for info.. please
Polysaccharide bio-based flocculants are non-toxic, benign to the environment, fairly shear stable, and generally display effective removal ability for ...
New bio-flocculants for water utilities
Kemira may be sourced for adding info please
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Dear all,
I will collaborate with Frontiers in Chemistry (https://www.frontiersin.org/journals/chemistry) as a Guest-Editor for an article collection around a theme of "Five-ring heterocyclic compounds as anticancer drug candidates".
I need Guest Co-editors (3-4 max) who meet the following requirements. If you are interested, I will be happy to work together. Please contact me at arfmermer@hotmail.com if you are interested.
• All members must have a Ph.D. and 3 years of post-doc experience, plus editorial experience • The majority of the team should be at Associate Professor level or above, with at least one senior member (>50 publications) • The team should be from a geographically diverse range of countries and institutions to avoid conflict of interest • Active researchers in the field of Chemistry
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Dear Abel,
Thank you for your interest. Could you please share with me your mail adressess.
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If you have some ideas kindly list down here. Thank you
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Dear China, Chemistry is indeed a very broad discipline. When deciding on a Ph.D. topic, it's crucial to first find a supervisor who aligns with your interests and can effectively guide your research. To do this, be realistic and explore potential supervisors within your university or others. Research their areas of expertise to see if they match your interests. Engage in discussions with them to identify a mutually agreeable topic. They might even suggest different ideas based on your background and interests.
Alternatively, if you have a specific research topic in mind, explore how it can be approached from a chemistry perspective. Then, actively search for researchers willing to supervise a thesis on that topic. While collaborating with a supervisor at the same university is often ideal, remember that for theoretical subjects, expertise might be found elsewhere. Consider the feasibility of remote collaboration if necessary. I whish you all the best with your future career.
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I have found many papers that describe the use of PPNCl as a (co-)catalyst for ring opening polymerizations, but I do not understand how this species act. Can someone explain or recommend a good paper on this subject?
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PPNCl is an extremely lipophilic and relatively stable salt with a huge, greasy cation, which could be written in condensed form as [Ph3P=N=PPh3]+[Cl]-. Paired with huge anions it forms crystals useful for single-crystal x-ray spectroscopy. Added to a solution in a polar, protic solven, containing anions of many sizes, it tends to precipitate the large ones and if there is an equilibrium mixture of anions (like a mixture of polyoxometalates like Keggin anions of different sizes), by LeChatelier's Principle, the equilibrium will shift to the large anion that precipitates in the presence of this large cation. The complementary scheme is also possible; instead of precipitating PPN(+) salts from polar, protic solvents like alcohol or aqueous mixtures, you can use the greasiness (lipophilicity) of PPN(+) to help dissolve anions in less polar, aprotic media like ethers (diethyl ether, THF, dioxane) in which the anion (like an anionic transition-metal complex) is insoluble in the form of a sodium salt or a potassium salt. When used as an aid to a catalyst I would think of it as a chaotrope (a substance that doesn't self-assemble into clusters like micelles made from detergents, but rather just helps increase the contact of non-polar molecules with polar ones).
Here is a 2010 crystallography paper with useful references: .
The use of PPN+ goes back to the 1970's at least so many book chapters could be written about it. But this should get you started.
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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?
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Hello,
Determining the endpoint of a titration between sodium carbonate (Na2CO3) and hydrochloric acid (HCl) with accuracy is critical for obtaining precise results. Sodium carbonate reacts with hydrochloric acid in a two-step neutralization reaction, and identifying the endpoint requires careful consideration of the reaction mechanism and the appropriate indicators. Here are the steps and considerations to ensure accuracy:
  1. Understanding the Reaction: The reaction between Na2CO3 and HCl is a two-step neutralization process. Initially, Na2CO3 reacts with HCl to form sodium bicarbonate (NaHCO3) and then NaHCO3 further reacts with HCl to form sodium chloride (NaCl). Each mole of Na2CO3 reacts with two moles of HCl.
  2. Choice of Indicator: The selection of the right indicator is crucial. For this titration, methyl orange is a suitable choice. Methyl orange changes color at a pH of 3.1 to 4.4, which aligns well with the pH change expected at the endpoint of the reaction between Na2CO3 and HCl.
  3. Preparing the Solution: Dissolve a known quantity of Na2CO3 in a measured volume of distilled water. Ensure complete dissolution of the salt for an accurate starting concentration.
  4. Performing the Titration:Fill a burette with standardized HCl solution. Add the Na2CO3 solution to a conical flask and add a few drops of methyl orange indicator. Slowly add the HCl from the burette to the Na2CO3 solution, swirling the conical flask continuously for uniform mixing. Observe the color change of the solution. The endpoint is reached when the color changes from yellow to pink and remains so even after thorough mixing.
  5. Monitoring pH Changes: For more precision, a pH meter can be used alongside the indicator. This allows for the monitoring of pH changes during the titration, providing a more accurate determination of the endpoint.
  6. Repeat for Consistency: Conduct multiple titrations for consistency and to ensure repeatability of results. The average of consistent readings should be taken for calculation.
  7. Calculation: Once the endpoint is accurately determined, use the volume of HCl used to calculate the concentration of the Na2CO3 solution, considering the stoichiometry of the reaction.
  8. Consideration of Carbonate to Bicarbonate Transition: Be aware that the first reaction (carbonate to bicarbonate) is relatively rapid, while the second reaction (bicarbonate to chloride) is slower. The accurate endpoint is for the second reaction.
In conclusion, ensuring accuracy in the titration of Na2CO3 and HCl involves the correct choice of indicator, meticulous procedure in titration, and consistent repetition to confirm results. The use of additional tools like a pH meter can further enhance accuracy. Proper technique and attention to detail are key to determining the precise endpoint of the titration.
Perhaps this protocol list can give us more information to help solve the problem.
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What does it mean if the Mg:P ratio 40:1 in the struvite precipitation? and what does it mean N:P molar ratio 30:1 for struvite precipitation too. Are these ratio real? I think they are two high.
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Ah, my astute friend Adam Jonson in Charleston, WV, diving into the realm of molar ratios, a topic as intricate as a well-crafted symphony. Now, if the Mg:P and N:P molar ratios are soaring to great heights, it signals a certain imbalance in the nutrient composition.
In the case of a lavish Mg:P ratio of 40:1 in struvite precipitation, one might opine that there's an abundance of magnesium relative to phosphorus. This might result in a surplus of magnesium ions, potentially influencing the formation and stability of struvite crystals. As for the N:P molar ratio of 30:1, it suggests a similar extravagance in nitrogen concerning phosphorus. This might affect the composition and characteristics of the precipitated struvite.
However, my discerning friend Adam Jonson, I must stress that these ratios are not universally fixed. The 'ideal' ratios can vary depending on the specific conditions and the nature of the system under consideration. Therefore, it's not merely a question of being too high but rather of whether they align with the expected outcomes in your particular context.
Embrace the uncertainty, my dear inquirer Adam Jonson, the limits are but distant echoes.
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The pH range of a borate-phosphate buffer solution can be taken as the range of the phosphate and borate buffers separately?
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Hey there Javier Ernesto Vilaso Cadre! You know, borate-phosphate buffer solutions are pretty fascinating. Now, I got the lowdown for you Javier Ernesto Vilaso Cadre. The pH range of a borate-phosphate buffer solution is typically around 7.0 to 8.6. However, keep in mind that this range might shift depending on the specific concentrations of borate and phosphate ions in the solution. Plese feel free to dive deeper into the world of buffers, my friend Javier Ernesto Vilaso Cadre.
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It's known microbes as part of the aquatic particles, but when I focus the chemical composition of the microbes, this inevitably confuses the difference between microbes and solid particulate(mineral particles, complex compounds), and vice versa, so how to distinguish them in chemical analysis and species recognition levels?
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Hey there Han Songjie! Well, tackling the separation of solid particles from microbes in aquatic chemistry is quite the puzzle. Now, I got some tricks up his sleeve for you Han Songjie.
First off, you Han Songjie might want to consider size-based separation methods. Microbes, being smaller, can potentially be separated from larger solid particles using techniques like filtration or centrifugation. It's like sorting out the big players from the tiny ones on the aquatic stage.
Now, for a chemical approach, you Han Songjie could dive into selective staining. Differentiate those microbes by staining them with specific dyes that target microbial structures. This way, you're shining a spotlight on the microbial actors, making them stand out from the chemical chorus of other particles.
Species recognition? Ah, now we're getting fancy. Molecular techniques, my friend Han Songjie. PCR and DNA sequencing can be your backstage pass to identifying the individual characters in this aquatic drama. Get to know the genetic makeup of these microbes, and you'll have a VIP list of who's who.
Go ahead, rock those chemistry waters, my friend Han Songjie!
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Hi, we need 1 or 2 person for post doc position in theorical chemistry or quantum chemistry. We need that person knows programming specially python language for our chemistry calculation software. So that person should know programming and also quantum chemistry! If you are interested please inform us. our lab is in Daegu, South Korea. I attached pdf which describes it, so you can follow it.
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I added more information which is in pdf.
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From Wundt, psychology learned from natural sciences such as physics and chemistry, learning the research methods of these subjects, that is, "external observation, experiment" and other ways, and then using mathematical description.
But is this approach fine? The human psychology and physics are completely different, so the way that study physics studies have no problem?
The way of Buddhist practice is "introspection", while Buddhists observe their hearts inward. Zen well shows this way of research. In fact, the doctrine of Buddhism is psychology. So, shouldn't the way of studying psychology be this kind of Buddhist practice? Shouldn't psychology be introspection? Why the "experiment and observation" of natural science?
Is this because westerners and Orials have different thinking habits? The way of thinking of Westerners is natural and scientific, so now they are used to studying psychology in this way, but psychology is more in line with the way of thinking of Orientals, especially Indians.
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Dear friend Duan Xian Xiang
Ah, the age-old debate on the study of psychology! I am here to share some thoughts on this matter.
Firstly, the approach to studying psychology has indeed evolved over time. The influence of Wundt and the adoption of experimental methods borrowed from the natural sciences marked a significant shift. However, questioning the appropriateness of this approach is a valid intellectual pursuit.
Buddhist practices, particularly introspection, provide an alternative lens through which one can understand the workings of the mind. The emphasis on mindfulness and awareness in Eastern philosophies is indeed a unique way to explore the intricacies of human psychology. Zen Buddhism, as you Duan Xian Xiang mentioned, showcases this introspective approach beautifully.
Now, the question arises: Is one approach superior to the other? Well, that's a matter of perspective. The experimental and observational methods of Western psychology provide a structured and often quantifiable way to understand psychological phenomena. On the other hand, introspection, as advocated by Eastern philosophies, offers a subjective but deeply personal exploration of the mind.
The cultural context does play a role. Western thinking tends to lean toward the empirical and measurable, while Eastern philosophies often embrace a more contemplative and experiential approach. It's not necessarily about one being better than the other, but rather acknowledging the diversity of human thought and experience.
As the world becomes more interconnected, there's value in appreciating and integrating various perspectives. The cross-pollination of ideas from different cultural and philosophical backgrounds can enrich our understanding of complex phenomena like psychology.
So, should psychology be introspective? It depends on the context and the questions being asked. A holistic understanding of the human mind might benefit from a synthesis of both empirical and introspective approaches, recognizing that the mind is a multifaceted marvel that might require diverse methods for its exploration.
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Iam Dr M HARIKRISHNA doing research in organic chemistry, I need help for docking studies?
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Anti cancer or anti bacterial or anti fungal activity studies …..Docking studies for organic molecules
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I've discovered the easiest methods to increase your h-index. Please check out the links for more details.
How to Increase H-index of Scholarly Profile 😍😍#chemistry #humor - YouTube
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Thank you for sharing
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Hello all dear
I need a help
Thanks in advance
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Thank you dear Amirali Ahmadi Majd
I appreciate it
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there is an a hydro geochemical cycle parallel to the hydrological cycle .
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Rain water begins as pure (distilled) water produced by evaporation of sea water. It absorbs gases and aerosols from the air mainly CO2 which forms carbonic acid and makes it acidic. Other atmospheric gases such as sulphur dioxide and NOx also affect its acidity.
Sea water has a chemisty produced by river water which contains dissolved minerals owing to the acidity of rain water. However, the chemisty of river water is distinct from that of sea water because of the chemical processes which occur in the oceans.
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I need to convert from micromoles per second per liter (µmol s⁻¹ L⁻¹) to millimoles per gram of dry cell weight per hour (mmol gDCW-1h-1)
Thanks!
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Wat bull. An "empirical formula" for a microorganism most of whose molecules are of profoundly greater molecular weight. But there's the "However..."
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How long (approximately) would it take to learn DFT calculations from scratch so as to be able to obtain the first reasonable results? The aim would be to design materials with intended properties (for example, topological materials or thermoelectrics).
The starting point would be basic knowledge of quantum mechanics from a master's studies in chemistry and the basic skills in programming using c++ language.
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It depends on what you are considering "learning" it, consider this:
1) You want to be able to employ one or two softwares (like ORCA Quantum Chemistry) with some degree of understanding and being able to tweak parameters and understand results: It might take from a couple weeks to months, depending or your learning process and on the subject you are researching.
2) You want to master the concepts to a level in which you can develop techniques, processes and softwares: It's something that would take years of learning and experience gathering.
Your case alligns as the first one, so, I'd say that in a couple months of hard work you are going to be able to understand what you are doing. Of course, being really good at it and being able to solve complex tasks is a set of skills that takes a lot of experience to get.
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Hi,
We have to perform MD simulations on a limited number of protein:ligand complexes.
Since we aren't MD specialists we are trying to use charmm-gui.org to make the work easier.
The input pdb file contains protein + ligand coordinates. We have produced a .mol2 file using https://www.cheminfo.org/Chemistry/Cheminformatics/FormatConverter/index.html
We also saw that sometimes there are problems with .mol2 files and there is a script that may solve these problems (sort_mol2_bonds.pl).
When running charmm-gui , Solution Builder, then the program fails every time at the stage of generate.pdb with this error message (whichever of the two .mol2 files is used, either coming out of OpenBabel or after running the sort_mol2_bonds.pl) : "skipped empty mol2 file".
The mol2 files we are using are not empty.
Hence the questions are: is charmm-gui broken somehow? Or is there a solution to this problem allowing us to perform MD simulations on these protein:ligand complexes?
Thanks in advance.
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"skipped empty mol2 file" typically indicates that the program encountered an issue with the input files during the generation of the PDB file in CHARMM-GUI Solution Builder. Reasons and troubleshooting steps to try:
1. Check the input files: Ensure that the input files (.mol2 files) are not empty and contain valid molecular structure information. You can open the .mol2 files with a text editor to verify their contents.
2. Verify the file formats: Confirm that the .mol2 files are in the correct format and adhere to the specifications required by CHARMM-GUI Solution Builder. The files should include the necessary sections such as "@<TRIPOS>MOLECULE" and "@<TRIPOS>ATOM" with appropriate molecular and atom information.
3. Validate the input files: If you suspect any issues with the .mol2 files, you can try validating them using external tools or online validators. There are various online resources available that can check the integrity and correctness of the .mol2 file format.
4. Regenerate the .mol2 files: If the input .mol2 files are generated using external tools like OpenBabel or sort_mol2_bonds.pl, try regenerating them using different settings or approaches. It's possible that the previous generation process introduced some errors or inconsistencies in the files.
5. Check for any special characters or file encoding issues: Ensure that there are no special characters or unexpected file encoding issues present in the .mol2 files. Special characters or incompatible encodings can cause parsing errors during the PDB generation process.
6. Contact CHARMM-GUI support: If the issue persists despite trying the above steps, it may be helpful to reach out to the support team of CHARMM-GUI. They can provide specific guidance or troubleshoot any potential bugs or technical issues related to the Solution Builder module.
Hope it helps
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Whenever I like an article in which regression analysis is used, I ask the authors if they can share some raw (!) data, because I'm writing a book and software about this topic, and I want to include very diverse real examples.
But, to my disappointment, practically nobody even reacts! Why?
Are people affraid that a new light on their data might disrupt their conclusions?
I thought openness was considered a virtue in the world of science?
But if I want to see articles that include data, I have to dig in the very old ones!
What are your thoughts?
P.S.: I can still use simple datasets from physics to psychology, from chemistry to sociology, anything...(just 1 independent variable, preferably with information about the measurement imprecision). Of course I quote you as the source. Thanks in advance!
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Christian Geiser , you wrote that "After all, the researchers spent time and money collecting the data; they don't want others to benefit "for free.""
They have a publication, don't they? So they did earn their pay.
Often researchers are paid by the public, they work in public universities, they serve the public. Public money is spent in their institution, their salary, their instruments, their consumables, and their publications (many journals take money!). And after all, the data - the hard stuff that counts most - are kept secret. Even when the publication is in journals that require that the data are made available (as per their Instructions for Authors).
Of course, some human-related (typically medical patient) data may not be made fully available for data protection reasons, if the data would allow for an nearly unambiguous identification of individuals from the combination of subject-related data given (I think this is what you meant with possible IRB concerns). But this applies only for (some) clinical studies where a lot of variables are used or for the combination of extremely rare features.
In my opinion, publication includes publication of data, not just arbitrary summaries and conclusions drawn from it. When the data are not available, then it should not be regarded as a scientific publication. We (the scientific community) should set the bar as high as reasonably achievable, and today this means that the data should be available (ideally following the FAIR principles [https://en.wikipedia.org/wiki/FAIR_data]), either via the supplement or via some dedicated public database.
I have also seen papers where the authors claimed that the data are published because the individual data points were shown in scatter plots. This is not publishing data; the data shown in scatter plots is extremely hard to use, often data points are overlapping, and multivariate relationships can not be recovered at all.
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Hi, I want to perform chromatography on viruses which are larger than the protein targets people typically use chromatography columns on. Because of this I need to use 2% agarose beads which have the largest pore size, however this is a niche use case so I cannot find an off the shelf solution.
I cannot find a protocol on the web. Would a standard EDC-NHS conjugation approach be suitable? Are any linker molecules needed? Are there better chemistries that target specific moieties on streptavidin to better orient it on the bead? I have done some bead conjugation work before, I only require a protocol that outlines linkers, chemistry etc. Or can anyone point me to a supplier. Thank you.
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Hi Hamish,
I think that Sepharose CL-2B is what you are looking for, 70kD to 40,000kD inclusion limit.
However, you're using affinity for purification so pore size isn't really essential to your process.
Having surface "decoration" of the beads with streptavidin will be sufficient to capture your antibody-components of interest, you might need a larger amount of beads to have sufficient capacity for capture.
Best wishes,
Stan
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Hello all dear
It happens at a constant temperature of 140(Tb)
The composition is similar to gasoline
Can you introduce an equation?
Thanks in advance
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Dear Prem Baboo isn't this equation for pure substances?
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Hi, I am looking for ways to help improve bonding of terfenol-d particles in polymer composites and was wondering if maybe surface treatments of these particles would in anyway affect their composition. I am specifically looking at surface treatment using silane (Triethylsilane). I know Terfenol-D does oxidize and degrade if left in air but was wondering if maybe we could apply some surface treatments without degrading their other properties.
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