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Ionization - Science topic

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I am trying to determine the electron number density in my plasma by using the Saha Equation for degree of ionization. However I am slightly confused with how to determine the particle density (n = ni + ni+1) to solve for ne. Is there a standard value or...?
I presume as a first approximation I could determine the density of the gas with the ideal gas law and then use this number to approximate the density at my determined temperature. If I do so are there any obvious complications I may be overlooking?
Thanks in advance!!!!
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its a simple fractal, but not a perturbation. just run a column down Excel with line 1: ni, line 2: ni + 1, line 3: = line 1 + line 2, highlight line two and Control D two or three hundred lines. the last line is a "precise approximation."
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I am trying to run BFEE on my protein-ligand complex in a ionized water environment. I have all the NAMD files from my simulation; however, when I go to run BFEE with the files I get "the domain error: argument not in valid range". Does anyone know how to possibly fix this or has experience using VMD BFEE? I am using the restart files for .coor, .xsc, and .vel.
Below is the protein-ligand complex. I recognize that my ligand is just a small chain of amino acids.
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Update.
I got my protein ligand binding affinity to work with BFEE2 (not VMD BFEE plug in) through installing through anaconda. It is a great software program.
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What is dark matter? And how was the structure of the world formed?
Dark matter is still a subject of ongoing debate. It has been considered in the theoretical description of compact objects such as neutron stars with cores of very dense matter. Various candidates for dark matter have been proposed in the scientific literature. Among them, the sexaquark has been identified as a potential boson particle that can form in the neutron star material based on its mass properties. We investigate the viability of the sexquark as a candidate for dark matter, especially under certain density conditions. Addressing the challenges associated with the formation of a boson particle in a highly dense medium without compromising the stability of the neutron star. A direct linear mass change for the sexaquark in the hadronic equation of state. It was observed that including the sexaquark as a dark matter candidate in the hadronic matter equation of state, although it has a repulsive interaction with the baryonic matter, softens the equation of state. We assume that the interaction strength of dark matter with baryonic matter increases linearly with the baryon density. We observe that the increase in the effective mass of the Sexaquark as a result of the increase in its vacuum mass causes the equation of state to become stiffer compared to the constant mass state. We determine lower and upper mass limits for this bosonic dark matter based on observational limits for neutron stars in the DD2Y-T model, when a quark-matter phase-to-phase transition is used. Dark matter, neutron star, equation of state, relativistic mean field, phase transition, sexquark.
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Stam Nicolis added a reply
The particle content of dark matter is, for the moment, unknown.
Sexaquarks, as the name indicates, are composite particles made of six quarks-quarks are among the constituents of ``ordinary'' matter. The reason they don't have anything to do with dark matter is that dark matter is made of other kinds of particles. If it were made of known particles, quarks or leptons, it would have had known interactions with ordinary matter, beyond just gravitational interaction (which is how its presence has been established). It doesn't, however, have strong or electromagnetic interactions with ordinary matter (whether it has, only, weak interactions is, still, a matter of study), so it doesn't carry color or electric charge.
How the ``structure of the world was formed'' is known, after the era in which gravity decoupled from the other interactions, in general terms, though many details are, still, not clear. Cf. for instance: https://workshops.ift.uam-csic.es/uploads/charla/275/Zavala_SM_LCDM.pdf
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Dark Matter
Neutron Star
Density
Gravitation
Electromagnetic Phenomena
Alessandro Rizzo added a reply
1 day ago
Hello,
Dark matter is a substance that makes up about 27% of the universe. We can't see or detect it directly, but we know it's there because of its gravitational effects on visible matter. Scientists think that dark matter played a crucial role in forming galaxies and large-scale structures in the cosmos. It acts like an invisible scaffold, helping to clump regular matter together. Well We're still not sure what dark matter is made of. Some ideas include exotic particles like WIMPs or the sexaquark you mentioned. Researchers are trying to detect dark matter particles in labs and looking for indirect signs of it in space.As for how the world's structure formed, dark matter was undoubtely the key. After the Big Bang, it helped gravity pull matter together to form the first stars and galaxies. Over time, this process built up the complex web of galaxy clusters and filaments we see today. So Dark matter remains one of the biggest puzzles in physics. We're working on understanding it better, but for now, its true nature is still a mystery.
Javad Fardaei added a reply
3 days ago
Dear Abbas these two articles might answer your questions.
Article The Mythos of Gravity Or (Newtonian and Einsteinian Gravity is a Myth)
… Read more
Abbas Kashani added a reply
Dear Javad Fardai
From the United States of America
Thank you very much for your kindness, I was very impressed with your articles. Thank you Abbas
… Read more
Alessandro Rizzo added a reply
Hello,
Dark matter is a substance that makes up about 27% of the universe. We can't see or detect it directly, but we know it's there because of its gravitational effects on visible matter. Scientists think that dark matter played a crucial role in forming galaxies and large-scale structures in the cosmos. It acts like an invisible scaffold, helping to clump regular matter together. Well We're still not sure what dark matter is made of. Some ideas include exotic particles like WIMPs or the sexaquark you mentioned. Researchers are trying to detect dark matter particles in labs and looking for indirect signs of it in space.As for how the world's structure formed, dark matter was undoubtely the key. After the Big Bang, it helped gravity pull matter together to form the first stars and galaxies. Over time, this process built up the complex web of galaxy clusters and filaments we see today. So Dark matter remains one of the biggest puzzles in physics. We're working on understanding it better, but for now, its true nature is still a mystery.
Gurcharn Singh Sandhu added a reply
July 24
DARK MATTER
It is fundamentally wrong to assume the existence of fictitious Dark Matter for explaining the pattern of circular velocities of stellar objects in galactic spiral arms.
Let a stellar object of mass m, with circular velocity Vc and radial velocity Vr, be located within a spiral arm at a radial distance R from the galactic centre. Let Mr be the total baryonic mass within a sphere of radius R. Assuming approximate validity of the shell theorem for the galactic disc region and also assuming that the stellar object under consideration is moving solely under the influence of central force field of the galaxy, radial acceleration dVr/dt of the object will be given by,
dVr/dt = -GMr/R2 + Vc2/R
While justifying the necessity of dark matter, the radial acceleration dVr/dt is assumed to be zero and all trajectories of stellar objects are implicitly assumed to be circular, which is wrong. The circular or tangential velocities of stellar bodies are not directly produced by the radial acceleration field of the galaxy but depend on the initial angular momentum of the accreting matter with respect to the gravitating body. Conservation of angular momentum will ensure increase in circular velocity of stellar bodies as their distance from central gravitating body keeps decreasing. Let L be the angular momentum of the stellar object of mass m while entering the outer fringes of the galaxy which will remain constant through out its motion within the central gravitational field. The circular velocity Vc of this object, at any distance from the center of the gravitating mass Mr, will be given by Vc = L/(m.R) and this does not depend upon mass Mr. That is, the increase in circular velocity Vc with decreasing R does not depend on the strength of central gravitation field or magnitude of Mr, but is solely governed by the conservation of angular momentum. Hence it is fundamentally wrong to assume the existence of fictitious Dark Matter for explaining the pattern of circular velocities of stellar objects in spiral arms.
There are other reasons for explaining the flatness of rotation curve but definitely not the assumption of higher mass Mr or Dark Matter. In reality stellar objects in spiral arms do not move solely under the influence of central gravitation field of the galaxy, their motion is also influenced by the local gravitation fields within the spiral arms. There are localized gravitating bodies existing within the spiral arms, which produce their own gravitation field in addition to the gravitational field of the central gravitating body.
Article Ionic Gravitation and Ionized Solid Iron Stellar Bodies
Stam Nicolis added a reply
July 25
Asking the same question multiple times doesn't make much sense. It suffices to ask it once. Dark matter doesn't have anything to do with neutron stars, it has to do with the rotation curves of galaxies.
Sexaquarks aren't singled out among hadrons for having repulsive interactions with baryonic matter, that statement is wrong. Nor does their contribution ``soften the equation of state'' of baryonic matter.
Dark matter, once more, has been found to interact with ordinary mattr, baryonic or not, only gravitationally and it's not known whether it interacts with it through the weak interaction.
The mass limit of dark matter as a function of the energy budget of the Universe is known; its particle content isn't, yet, known.
Abdul Malek added a reply
July 25
"Dark Matter" is a crude fiction arising in spite of the scientific fact that Newton's theory of (one-sided) universal gravitational attraction is patently false, because it does not take into account the reality of the (gravitation opposing) centrifugal force and vis viva of Leibniz.
A (suggested) new quantitative form of the gravitational potential taking into account of the role of the opposing forces, in the dynamics of the celestial formations, eliminate the need for fictitious Dark/black cosmic monster of Fairy Tale cosmology of official "science"!
KEPLER -NEWTON -LEIBNIZ -HEGEL Portentous and Conflicting Legacies in Theoretical Physics, Cosmology and in Ruling https://www.rajpub.com/index.php/jap/article/view/9106
" THE CONCEPTUAL DEFECT OF THE LAW OF UNIVERSAL GRAVITATION OR ‘FREE FALL’: A DIALECTICAL REASSESSMENT OF KEPLER’S LAWS":
Article THE CONCEPTUAL DEFECT OF THE LAW OF UNIVERSAL GRAVITATION OR...
Moreover, the narrative of the "Big Bang" created universe, where the galaxies are supposedly formed by universal condensation of matter is false! On the contrary, new matter created by existing galaxies are ejected and/or dissipated, which then give rise to the formation of new galaxies in an infinite, eternal and ever-changing universe. Ambartsumian, Arp and the Breeding Galaxies: http://redshift.vif.com/JournalFiles/V12NO2PDF/V12N2MAL.pdf
Kanat Abildinov added a reply
19 hours ago
There isn't any dark matter, in the Universe. There is uniform acceleration of inertial motion defined by masses in the Universe.
There are four kinds of interactions in our Universe, their names: electromagnetic, strong, weak and gravitational. In the standard model electromagnetic and weak forces was combined and represented as unified electroweak force in the Grand Unification of three called interactions except for gravitational. The main problem of Physics is a building of Unified Theory of Everything, so-called Super Unification theory, or the theory of matter (field). It is now known that the classic mechanics and the quantum field theory, which is consistent with quantum mechanics and special relativity, cannot to unite four known interactions by single unified one. It was main aim in the 30 last years in the Einstein’s life. At present we have a crisis in particle physics [1] and problems in high energy astrophysics [2], such as unexplained energy and sources of ultrarelativistic charged particles (ultra-high-energy cosmic rays) [2, 3], the problems of the “dark matter” [4] and “dark energy” [4, 5] in the Universe, and the problem in the Cosmology, such as acceleration models of the Universe [4] which cannot be admitted by the philosophic principles, and by this cause cannot be understood by most of peoples. Trying to resolve some of these problems, we can consider new theory based on philosophic principles and on the geometric one. It is the Unified Theory of Interactions (UTI).
II. Philosophy of the Unified theory of Interactions The matter is continuous and infrangible, because nothing exists except of matter. The matter cannot to be split by absolutely different kind of objects, for example by means of “absolute emptiness”. The matter has two kinds: tenuous – field (ether, material space, physical vacuum) and compacted – energy substance. And the matter has its unified subpart. The material objects exist in the time because they are changeable and can detect other material objects and can affect them. In chime with this we have a following. III. Basic principles There are two main principles in the base of “Unified theory of interactions”: 1) The “Principle of Absolute Transitions”: The absolute transitions, is momentary transitions between absolutely differentiated conditions of the matter, and they are do not exist in the time. Or, by other words: The transitions between two physical values, that realize only stepwise (in a trice), without intermediate values, do not exist in the nature.
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The question is, do you believe our universe with billions of galaxies, where each galaxy holds billions of suns, and solar system like our as a complete well organize entity like anything else in it? If you say yes.
Then our universe is fed from outside.
This article might help your perception, that big bang is a joke that we earned from last century.
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We'll have vials in which we expect H2 generation to occur. Over the first few days, the amount of generated H2 is expected to be at ppb level.
GC (+ TCD) detector is best when your H2 level is in the ppm range.
GC-MS is difficult as the ionization energy of H2 is high and the M/Z ratio will be small (2).
FID is not reliable as hydrogen flame is used
Other fancy methods (e.g., Raman-based and optical methods) are quite expensive.
What are your suggestions?
Thanks
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Gas chromatography, ultrasonic meters, electrochemical sensors, Raman lidar, and gas-stripping methods are some of the most reliable techniques for measuring hydrogen gas concentrations at ppb levels, depending on the specific application and environmental conditions.
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I did GCMS/MS, LCMS of my sample of interest. I got Mass fragments in ionization process. Now facing issues to get the parent molecules name/formula. Due to complexity of sample (its a mixture of compounds) and fragments MS, I could not identify the parent molecules by predicting with basic knowledge of Mass fragments. Is there any free application or database that I can get to know the parent molecule name by inputting the MS fragments values?
And I would like to get experts comments on " What is the best way to predict/analyze/ identify the compounds in a sample by LCMS/MS, GCMS/MS, without using any automatic database paired with instrument."
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Thank you Dr. İsmail Emir Akyildiz
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My question is how to find system-specific ionization potential (IP) tuned value to improve the description of the excited state for a functional in the TD-DFT calculation.
Do I need to run any script for the same?
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You may try OptDFTw from http://sobereva.com/346.
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can anyone give me advise about charge transfer transition of transition metal and rare earth element?
and usually people see the FL and absorption, emission spectra of those materials in glass, and I just want to know how much energy need to ionization the transition metal and rare earth element.
Could you recommend some studying source about it?
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MALDI( Matrix Assisted Laser desorption Ionization)
Matrix use in MALDI in positive mode and negative mode
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In positive ion mode detection, if your instrument is a high resolving instrument (resolves monoisotopes) you should see the Matrix (whatever matrix is used) species detected at m/z: calculated mass + proton (1.00783).
In negative ion mode detection, the m/z: calculated mass - proton (1.00783).
Best,
Hediye.
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I have been pondering why nickel only exists as the Ni2+ ion in nature. I know that Ni+ and Ni3+ also exist, but unlike iron (Fe), Ni3+ is not nearly as common as Ni2+. So, I have investigated this and arrived at an explanation but haven't quite reached a conclusion yet.
This is how I understand it:
Nickel has an electron configuration of (Ar)4s2_3d8, and iron has (Ar)4s2_3d6.
It's easy to understand the ionization to Fe2+ and Ni2+ because the 4s2 electrons are farther from the nucleus and now easier to remove. It's also easy to comprehend that the ionization energy is higher for iron because the 3d shell in nickel has more electrons, thus shielding more against the nucleus's attractive force.
Ionizing to Fe3+ might be understandable as it might be relatively easy to remove one of iron's only paired electrons in 3d6, and I guess that 3d5 is stable because the shell is half-filled.
But why is it so challenging to ionize nickel's 3d8 to 3d7, 3d6, etc.? Is a shell with 8 electrons already stable? Or why is it so?
I hope to be able to understand this.
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I think the point is that Fe has one d-electron in excess of the half-filled d-shell and easily gives it away in order to minimize the total orbital momentum of this shell in accordance with the well-known Hund’s rule.
Ni already has three d-electrons over half and their reduction to two becomes not as beneficial for reducing the total orbital momentum as in the case of Fe.
Having a valence of 2 is equally beneficial for both Fe and Ni, since it involves s-electrons with zero orbital momentum.
Therefore, the Fe3+ state is more common than Ni3+.
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What do experts in HiPIMS sputtering think about a possible definition of HiPIMS? Definition: HiPIMS is a high-power density P-DCMS sputtering process with an amount of self-sputtering of target ions, where C < Ysetm/(Yseng+Yserg) < ∞, based on a critical ionization threshold of sputtered target atoms. To reach the critical threshold the -power density (current density multiplied by the discharge voltage) at the target within the pulse has to be about one order of magnitude higher than for conventional DCMS and P-DCMS. Yse secondary emission yields, tm means ions from the target material, ng noble gas, rg reactive gas. Classical (traditional) DCMS and P-DCMS are low-power density processes, gas-ion dominated discharges. If Ysetm is about 0 then target-materiel ionization is almost neglectable. If Ysetm/(Yseng+Yserg) goes to infinity, then self-sustained sputtering, SS-DCMS, a high-power density DCMS as a target-ion dominated discharge is ignited. C is a process and material specific value. C > 0 is describing the onset of LE-HiPIMS (low-energy HiPIMS). This C values have to be highlighted in future scientific investigations. Please study the model of A. Anders: Anders et al., J. Appl. Phys. 121, 171101 (2017). Thanks for your comments!
Take care.
J. Vetter
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Rajesh, yes indeed, it's a look at the classical pulsed process. However, it is possible to get target atom ionization also without pulsing? Yes its possible!
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Hello All
During the gromacs 2023.1 multiple ligand simulation , I have some problems and constraints in the simulation. In the experiments, I used AMBER99sb forcefield.
How to perform multiple ligand simulations
Whether i have to make different topology files for different ligands? because when trying to simulate at the ionization stage to get the ions.tpr file an error occurs as below:
Command line:
gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr
Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'ns_type'
NOTE 1 [file ions.mdp]:
With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
that with the Verlet scheme, nstlist has no effect on the accuracy of
your simulation.
Setting the LD random seed to 2095054833
Generated 3486 of the 3486 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 3486 of the 3486 1-4 parameter combinations
-------------------------------------------------------
Program: gmx grompp, version 2023.1
Source file: src/gromacs/gmxpreprocess/topio.cpp (line 577)
Fatal error:
Syntax error - File entacapone1_GMX.itp, line 3
Last line read:
'[ atomtypes ]'
Invalid order for directive atomtypes
For more information and tips for troubleshooting, please check the GROMACS
please help me to solve this problem, and I will be very grateful to you
Thankyou All
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You can ask always your gromacs -related questions (only) in the GROMACS forum and get your answer directly from gmx experts: https://gromacs.bioexcel.eu/
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CID problems and solutions in LC-MS/MS analysis.
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İsmail Emir Akyildiz Without knowing the amino acid composition, is it possible to conclude why would acetic acid work better than formic acid when we talk about protonation? Would could be the cause in this case? Maybe some physchem properties of acetic acid?
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The upper level energies (the abscissas of the Saha-Boltzmann plot) have been modified by adding to them the ionization energy of the lower ionization stages, that is, the energy scale begins in the ground state of the neutral atom. For the z ions, the correction is shown in the attached figure emphasized by red circle.
where is the ionization energy of species k for isolated systems (eV) and is the correction of this quantity for interactions in the plasma. These modifications have only effect for ion lines (z t 1) and are introduced in equation 1a in order to include the data of the different ionization stages in the Saha Boltzmann plot.
Reference Link:
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Javad Fardaei equation is used to determine an accurate temperature value of atomic species, which is known as plasma temperature when it is in Local thermodynamic equilibrium (LTE). The question is how to calculate the correction term as in equations 1-21.
EzJ is an atomic state whereas the second term is a singly ionized state of the same atomic species.
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My peptide is Cholecystokinin (CCK8), MW=1142.35 (COOH-D-Y-M-G-W-M-D-F-NH2).
Stock solution in NH4OH 0.05M and working solution in acetonitrile.
I do MS infusion at conc. 500 ng/ml in acetonitrile.
I use two LC/MS machines: Micromass - Quattro Premier XE of Waters (Tamdem Quadrupole) and Applied Biosystems - API 3200 LC/MS/MS (triple quadrupole)
I run ES + but I can not see the peak at 1+, 2+, 3+,4+,...for [M+H], [M+Na], [M+K]
I wonder whether I have missed some other adduct ions that could be created during the ionization?
Or maybe my peptide is being degraded during preparing the sample?
Please give me some advice! Thank you!
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Here are the other points, you may lean on;
If the purpose is quantification or purity check, LC-UV would be nice to use since the octapeptide you have several aromatic rings and would be highly responsive,
secondly, 500 ppb may be a low conc. to conduct a full scan..especially when the ionization efficiency is low.
Third, I would prefer combined flow scanning in place of infusion...In this mode, you are not taking benefits of the mobile phases which present donors to improve ionization...You should combine the lc flow and infusion (acid and/or DMSO additives in phases for pos ESI in this case) and retest the response...
By solving the peptide in an alkaline condition you are directing the peptide to deprotonation and this makes the peptide more amenable to neg ESI...If it is soluble in ACN directly..prepare your stock in ACN and dilute it with the same solvent, I prefer not to use aggressive pH which is not convenient for most of the peptides to the unintended H exchanges...
Last but not least, If the peptide is hydrophobic and dissolves only in organic solvents this is susceptible to be efficiently ionized in APCI, APPI rather than ESI...You may look for these alternative ionization techniques if MS analysis is the bottleneck and the abovementioned suggestions are useless...
Good Luck...
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In fuel cells hydrogen (H2) is ionized in the anode and is transformed into H+ and e-.
Then H+ moves through the electrolyte membrane towards the cathode, where O2 is flushed. In the meantime, the electrons move from the anode (where they separated from H2) towards the cathode, producing an electron flux, i.e. regenerating an electrical current. In the cathode O2 first captures the electrons and then react with H+ to produce water (and heat).
What I am asking here is: how elemental H2 is forced to separate into two H+ and two e-? I have read that this happens in the anode, but I did not understand how it happens.
Cheers,
Michele
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Ok i'll try to put this in a simpler way. So you are correct that the H2 goes to 2H, but not as two separate atoms, just like how its almost impossible to have nascent oxygen unless very high up in the atmosphere nascent H is also not present. Instead look at it like H-H and in this pair the electrons from each of the hydrogens balance each other out. Then with the addition of the catalyst this bond breaks releasing energy. Since this energy is generally heat energy ( you can see Pt mesh usually heats up and glows red). Now hydrogen as an atom can only stabilise and gain an electron in the presence of a metal atom to form a stable metal hydride, so it shuffles between two states of instability ( H+ and H), since there is a bond between the platinum and hydrogen, the H+ tends to be retained at the catalyst( probably due to the hydrogen bonding being strong to a proton?) and the electron is transferred as electricity.
This is the best and only explanation I have from material I can find on the internet. Apart from this maybe only someone who works with pt and hydrogen on a daily basis will be able to clear or correct.
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I am trying to detect citrate in LC-MS. I ran the samples in both negative and positive modes. I performed direct injection (without a column) using an ESI ionization source. Thank you very much
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I work with standard, the instrument is xevo g2-xs QTof.
I will ask my technician.
Thanks again.
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I am looking for an active researcher in the area of environmental sciences and Ionization to collaborate with. if anyone kindly indicate.
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Only collaborate if you have copywrite of the data and are the primary author. And publish ASAP to minimise the chance of co-authors stealing your data. In fact, never collaborate! Then you have total control and your research can be more creative :)
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  • The ionizations rate coefficients as a function of electron temperature by using the present calculated TICS of order 10^(-16) and Maxwell distribution law of temperature/energy.
  • What should be the order of Ionization rate coefficients?
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Hello, The ionization rate coefficients (k_ion) are typically expressed in units of cm³/s and depend on the electron temperature (T) in electron volts (eV) or Kelvin (K). Generally, ionization rate coefficients range from around 10^(-16) to 10^(-9) cm³/s for temperatures encountered in many plasmas of interest, such as in fusion devices, astrophysical plasmas, and technological plasmas.
However, the exact order of magnitude for the ionization rate coefficients depends on the specific ion and its charge state, as well as the electron temperature. For example, the ionization rate coefficients for hydrogen-like ions might be on the order of 10^(-12) cm³/s at electron temperatures of a few tens of eV, whereas those for fully stripped heavy ions might be on the order of 10^(-10) cm³/s at similar temperatures.
It's important to note that these values are rough estimates and can vary depending on the details of the specific plasma environment and ion species. To determine the exact order of magnitude for the ionization rate coefficients in a specific situation, it is best to consult published data or use well-established computational codes.
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I am trying to calculate the ionization energy of a metal atom cluster, i know the negative value of HOMO can be used as ionization energy. However, for some clusters, they will me give both alpha and beta mos, anyone can please tell me which one should i use and why? Thanks!
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Jose Alberto Guerrero Cruz, Is it correct to calculate the HOMO-LUMO energy gap in the same way for a metal complex with doublet as spin state?
i.e., LUMO-alpha (32) - HOMO-alpha (31)?
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Hello, I'm approaching an untargeted UHPLC-HRMS analysis using ESI source in positive ionization. I am tracing the area intensity of about 20 molecules, of which we do not yet have sufficient structural information and which may be very different from each other. I am having difficulty choosing the internal standard to use in order to normalize the areas. In theory, would any molecule capable of responding adequately in the positive be suitable for normalization activity? Thank you so much, Francesco
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Another useful piece of information about your analytes would also be the molecular formula. You write that you used a HRMS, I think a Q-ToF or Orbitrap system, so you can calculate a molecular formula for the analytes. With this you come a lot closer to the structure. In conjunction with the fragment spectra, possible candidates can be narrowed down.
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I have tried beta carotene detection in LCMSMS with an APCI source using different solvents. But ionization is not happening even when reproducing the previously available data. Please help me.
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Sir i have calibrated the APCI source it was fine. But i am still getting the issue.. the mass is highly detecting at 536 m/z possitive ionization.. but in possitive it should be around 537m/z .
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I would like to calculate the vertical ionization energy of a molecule using Gaussian16. And which is the best method to do it?
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By means of quantum chemical program package.
Please, concentrate on this paper (s.i. file):
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I am having difficulties visualizing signal in human astrocyte interphase and metaphase chromosomes hybridized with TelC-Cy3 and CentPB-FAM PNA probes. All I see is noise from the florescent scope (photos attached). The FISH protocol I used is described in the attached paper. So far, the biggest difference I noted was the use of de-ionized formamide for preparing the hybridization buffer.
Can anyone with more experience confirm or deny the impact of ionized formamide on hybridization efficiency?
Thanks
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PNA FISH probes hybridize to target DNA with high sensitivity and specificity mainly due to the electrical neutrality of its chemical structure. This trait enables PNA probes to be more efficient and useful in applying to FISH (fluorescent in situ hybridization) even at low concentrations. Hybridization occurs fast (within a couple of hours) and background noise is reduced significantly.
see the link below ......
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Hi all! I am using a Waters-TQS micro (LC/MS/MS) in negative ionization mode (MRM) to analyse a few compounds. When doing QC injections (i.e., repeated injections from same vial of standards at a certain concentration) the area response keeps going up with each subsequent injection. Now, my method is 20 minutes long. I do recall that negative mode can take some time to stabilize, hence this might be the reason why I see increasing area responses. But, question is how long would you wait for it to stabilize? Or.... is there something else at play?
Thanks for reading and potentially contributing!
Best!
T
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In negative ionization, Method stabilized minimum 2hrs, and what are the diluent using, if diluent using methanol: water, Diluent stabilized at least 1 hr
Other than this please check the gradient programmed in your method
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Hi everyone!
I am setting up an experiment regarding the analysis of several markers in cells exposed to ionizing radiation. I´m having some thoughts about choosing the most appropriate time, namely 24h after the last exposition to ionizing radiation, 72h or even longer etc.
What do you think is the most appropriate time point?
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It depends on medical managment inclding triage is high throughout assesment of radiation recivied should be cosidered .for more detailed read the attached ref.
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I am using SRIM code to simulate interaction of charged particle with a material of a known thickness. SRIM gives me the energy loss (ev/A) at different point along the path length (A) into the material as the "IONIZ" in the SRIM output folder. Using the table of the IONIZ file, how can I get a single value in keV/um, which will be an over all average energy loss per unit path length?
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This is not my subject area.
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Dear Experimentalists,
I have a question regarding to Work function / ionization potential measurement of a semiconductor surface where the surface states are located in the band gap. I was wondering how they are measured in this case? with or without surface states? where is the valence band edge then?
Please share me references if you have.
Thanks a lot
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Dear Amirhossein Bayani,
The following data may be helpful:
Electron work functions of several metals (Au, W, Ag, Cu, Mo, Ti, Al) and Si at atmospheric conditions have been measured by the method of the static capacitor with an ionized gap between the electrodes. Results for all samples, excluding Au, Al and Si, conform to reference data with an accuracy of +/- 1.0%. For samples Au, Al and Si, the electron work function values conform to reference data after short-time heat treatment at atmospheric conditions at 200 degrees C (for Al) and 600 degrees C (for Au, Si).
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Despite of its huge successes in total energy related applications, the Kohn-Sham scheme of density functional theory (DFT-Kohn-Sham) cannot get reliable single particle excitation energies for solids. In particular, it has not been able to calculate the ionization potential (IP), one of the most important material parameters, for semiconductors. We illustrate that an approximate exchange-only optimized effective potential (EXX-OEP), the Becke-Johnson exchange, can be used to largely solve this long-standing problem. For a group of 17 semiconductors, we have obtained the IP’s to similar accuracy as the much more sophisticated GW approximation (GWA), with the computational cost of only LDA/GGA. The EXX-OEP, therefore, is likely as useful for solids as for finite systems. For solid surfaces, the asymptotic behavior of the vxc has similar effects as for finite systems which, when neglected, typically causes the semiconductor IP’s to be underestimated by about 0.2 eV. This may partially explain why standard GWA systematically underestimates the IP’s, and why using the same GWA procedures has not been able to get accurate IP and band gap at the same time.
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As I understand it so far:
  • Gy = Joules of energy absorbed per kilogram of body tissue
  • Sievert measures the biological effect rather than the pure energy
  • Sv = Joules of energy absorbed per kilogram of body tissue, in terms of gamma radiation
  • 1 Gy of gamma = 1 Sv, but 1 Gy of alpha = approx. 20 Sv, because the biological effect of alpha is greater than gamma
What I'm uncertain about is what exactly these Joules represent, and how they differ from ionizing energy.
My (admittedly elementary) understanding of ionization, is that an electron has to absorb a certain amount of energy that allows it to escape the electron shells, and then the atom becomes an ion. This energy can be expressed in Joules (probably attojoules, but still!)
What I don't understand, is that in Greys, would the ionizing effect of the different types of radiation not already be taken into account by their different energies?
Is it because my description of ionization refers to the gamma ray method of ionization, whereas alpha and beta ionization is more physical (alpha collides and pulls electrons off cells)?
But surely there is still some sort of measure of alpha energy that could make it 'account for more Joules' in the Greys calculation?
Thank you for taking the time to read this, and please ask me to clarify if this is unclear.
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Hi Alan,
I will try to answer your question as simple as possible, avoiding any mathematical equations :)
"Gy" is not related to the tissue or body; it is the energy per mass. On the other hand, when you start talking about biological effects, first, you are supposed to multiply your "Gy" value with some quality factors to distinguish the radiation type, like alpha, beta, or gamma. Then when it comes to tissue, you are supposed to multiply your "Sv" value with the tissue weighting factor to obtain a tissue-specific dose. At this time, you can talk about biological effects.
I hope this simple explanation helps you.
Thank you!
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Can I able to give an evidence for self ionization of water using DFT ? Or any other computational tools?
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So you want to investigate
2H2O -> OH-+H3O+
This will of course only happen at elevated temperatures. If you do plain DFT, you will get 0K physics at which water is as frozen as frozen can be, so you will have to perform molecular dynamics. If you have the computational power to do DFT-MD you can do that, of course; if that's out of specs for you, you could start with a semiempiric method. The larger you choose your cell, the more complex moieties you will observe probably.
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Can you suggest any book which gives a simple picture behind the formation of this wave?
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Thank you. I shall go through the paper.
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Can anyone please share any article showing the minimum volume of sample/ protein concentration to perform a Laser ionization mass spectrometry (LIMS) or any mass spectrometry techniques in general?
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Various instruments and methods have different requirements for sample volume.
In the case of classic autosamplers there is some minimal vial volume. If you choose the right vials with special inserts, the minimal sample volume would be about 10 ul.
There are some tricks to avoid this problem, e.g. elution of the sample from solid phase as in the Evosep system, but it is not very common yet.
In techniques such as MALDI ionization there is no minimal sample volume recruitments because the sample is mixing with a specialized matrix during sample preparation.
The question about sensitivity is much more complicated - different molecules will have various detection range in the same conditions. To maximize sensitivity you should carefully choose ionization conditions and try to avoid contaminations.
By our experience, in the case of MALDI, the purity of the sample often is much more important than amount of target peptide in it. Sometimes, when our colleagues use poor quality plastic and do not work properly it is impossible to obtain a good signal even in very concentrated sample. The quality of plastics and solvents is very important for mass spectrometry.
Other example comes from ESI-ionization. Addition of TFA instead of FA to the sample significantly reduces signal strength for most peptides.
Finally, do not forget about derivatization techniques. Derivatization is aimed to perform chemical modifications which significantly increase ionization efficiency of the target molecule.
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Hi
I'm measuring my sample using LC-MS and DI-MS.
When I tried DI-MS first, I got a very low signal about 100 times lower compared to LC-MS results. Futhermore new peaks not observed in LC-MS appears.
I think it is due to the absence of proton source.
So my question is.. Can the sample be ionized if measured without 0.1% FA in ESI-positive mode in DI-MS ?
Only samples and ACN were directly injected to MS. The results show that the signal from the target molecule was measured, however the signal intensity was very low compared to the LC-MS measurement results. When measuring LCMS, flow solvent with ACN99: water 1+0.1% FA was used.
And another question is...
Sodium formate cluster that is used for mass calibration and instrument quality check has already positive charge and I think that sodium formate cluster is possible to some extent without formic acid. I want to know that I'm right.
thank you for reading and have a nice day.
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Other volatile ammonium salts have also been used (e.g., (NH4)2SO4, (NH4)CO3, and ammonium phenolate) in low concentrations. Ammonium equilibrates to volatile ammonia, donating a proton. Sulfate will equilibrate with water to form H2SO4, which will decompose to SO2 +H2O. Similar for the carbonate salt. Pyridinium salts (e.g., pyridium acetate) as additives also work, but smell really noxious once sprayed.
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I have myself tried using the basic method but including incomplete ionization to figure out the depletion width however I failed miserably because of many mathematical roadblocks. I was wondering if this had been done in the literature before and I just missed it.
If anyone can help me in this regard then I would be very grateful. Thanks.
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If you can send me a sample data file, I can have a look at it...
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What mean by the ionization degree of the plasma injected into the vacuum chamber for sputtering process? What's the relation between this degree and the number of gas ions?
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The relationship you are looking for is this one:
So, it's just the percentage of atoms/molecules in the gas phase which are ionized.
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I am working on cryogenic modeling of MOS Transistors and in that case I have to include incomplete ionization. That certainly puts E_A as a very important parameter. So I was just wondering if E_A changes as a function of temperature or only doping?
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In the commercial silicon-based microelectronics MOS structures used to be studied between approximately room and liquid nitrogen temperatures, whereas liquid helium temperature studies are rather rare. I tend to agree with the authors of the article that screening effects would change the Bohr orbits of acceptor's or donor's outer carriers. That is their ionization (activation) energy will become smaller. The second link below gives some more theoretical flavor to it.
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The Dyna-bead (M-280) protocol calls for a PBS with 0.05% Tween-20 solution to be used to wash and elute mAb labeled beads. Ultimately these beads will be used to enrich peptides out of samples for detection by mass spectrometry. Will the Tween contaminate my peptide samples and inhibit ionization? Is it necessary to use the detergent or can a different one be used?
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Thanks you for your reply. I will definitely try it out.
Regards,
Jon
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Dear all,
What is the criteria for selecting the positive mode or negative mode in LC-MS/MS analysis?
In brief, when is positive and negative mode of ionizations are used inn LC-MS analysis?
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Hi,
the best way to select the polarity in LC-MS analysis is to try to inject your compound of interest in both polarities and observe which of the two ones gives the most intense signal and the highest S/N.
There are general rules to select the polarity:
NEGATIVE POLARITY --> molecules already charged negatively, molecules containing phosphates, acidic moieties, molecules with many Oxygen atoms, molecules contaning phenolic groups ecc.
POSITIVE POLARITY --> proteins, amines, molecules already charged positively, e.g. anthocyanins...
BUT the best way to select polarity still remains to try both polarities and select the most suitable to you.
BTW, if you are interest in a specific compound, look at the literature, there will be surely information about the experimental conditions, including polarity
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The problem is that I have a UPS spectrum like the one in the attached photo. This spectrum goes to zero near E=1.5 eV without having a step near this value. the nearest step is about 5 eV. Most of the information I found in literature deals with spectra goes to zero around zero eV but I didn't find anything related to my case.
Can I calculate the work function using the width of the spectrum? If not, what is the correct procedure to follow to calculate the work function and the ionization potential energy?
Thanx in advance.
Attached an example and how I tried to analyse it.
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Dear Allaham,
I am not sure I fully answer your question but I have some general comments regarding UPS and workfunction measurements...
  1. Make sure that you know the limits of the analyser. The analyser record kinetic energies and the to make that it uses a series of electron optical elements that guide the electrons to the detector. The settings of these elements are controlled by lens tables and all lens tables can not operate at all kinetic energies. One would have to set for example a given pass energy in order to access a specific kinetic energy range. Different brands of photoelectron analyses have different ways of dealing with this and different pass energies can access different ranges.
  2. Make sure the sample is properly grounded and that sample holder and sample environment is not magnetic or that there are non-conducting parts. UPS is a technique for detecting very low kinetic energy electrons and the sample environment can play a big role for the outcome of the experiments as charged or magnetic objects can affect/alter the trajectories of the electrons.
  3. Make sure that your sample is clean down to the very monolayer of the surface. Things that look ok in XPS can be terrible in UPS (as XPS look sub-surface due to higher electron escape depth whereas UPS spectral contribution mainly come from the surface). If you for example have carbon “dirt” / advantageous carbon on your sample you might not get signal close to the Fermi level as the carbon contribution is very high in the spectrum. The carbon would then most likely not have any electronic states close to the Fermi level but could have it around 5 eV or so.
  4. Make sure the equipment is calibrated such that it gives the right energy (binding or kinetic) and that the scale is linear and the measurements are repetitive in nature. For UPS it would be good to use a metal sample and see if the Fermi level end up at Binding energy zero.
  5. A calibrated analyser UPS measurement on a clean sample would give you a spectrum with info of the occupied electronic states of your sample down to a level which usually is the first 10-15 eV below the Fermi level after that it becomes tricky… The kinetic energy of the electrons here are very low (21.2 eV photon energy minus 10-15 eV binding energy result in some 5-10 eV kinetic energy). The lower kinetic energy the more demand on your sample environment. And at some point the lens table will stop working as well (out of range). A photoelectron analyser can only detect kinetic energies above zero for a grounded sample and a grounded front end of the analyser. This means that in many cases there is no way of detecting the zero energy edge of your UPS spectrum (the once that make it in must be accelerated of some field generated between different elements of your sample environment) such as a bias between the analyser front and sample (which effectively is an additional lens element of your analyser).
  6. In order to measure the vacuum level you would like to access this cut off at zero kinetic energy and that is usually done by biasing the sample such that the kinetic energy of the electrons end up inside the lens table again. When biasing a field between the sample and the analyser is created and this accelerate the electrons. But when generating this field you can easily get artefacts as your field is not homogeneous around the sample (if you tilt your sample you can notice that the spectra differs with tilt angle). Biasing also creates artefacts in the intensity distribution of your sample.
  7. Once you biased and recorded spectra you can calculate the work function by using the cut off (zero energy) and excitation energy of your light and the Fermi level
    1. Here is a link for a Kratos analyser chrome-extension://efaidnbmnnnibpcajpcglclefindmkaj/viewer.html?pdfurl=https%3A%2F%2Fwww.kratos.com%2Fsites%2Fdefault%2Ffiles%2Fapplication-downloads%2FMO456%2528A%2529%2520XPS%2520UPS%2520of%2520PbBr%2520perovskite.pdf&clen=658783&chunk=true
    2. Here is a link to a lecture talking about work function and more chrome-extension://efaidnbmnnnibpcajpcglclefindmkaj/viewer.html?pdfurl=https%3A%2F%2Fpublic.wsu.edu%2F~pchemlab%2Fdocuments%2F571-UPS-Lecture1.pdf&clen=2341609&chunk=true
    3. Here is a paper showing what to do with the ionization energy for a semiconductor https://www.sciencedirect.com/science/article/pii/S1567173921001796
So looking at your spectrum I would interpret it as follows (not knowing the details) It is an insulator that has a gap of some 5 eV (sample or covered with carbon?) Your work function end up at 16.7 eV and you are using 21.2 eV light. So your ionization energy would be 4,5 +5 eV (see figure 4 in Jeong WonKim et al Current Applied Physics Volume 31, November 2021, Pages 52-59).
Best regards,
John
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As we increase the doping concentration in silicon, even at room temperature the dopants are not fully ionized. Mathematically it all makes sense. But what is the physical reason behind this phenomenon?
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Dear Venkatesh, I presume that it primarily relies on the doping element. I'd like to know what is the doping element you use, so that it's quite easy to seek answer for your context.
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Now LNP is the most famous star over the world thanks to ionizable lipids, like ALC-0315, SM-102 and MC3 (Onpattro, approved by FDA in 2018), which are neutral at physiological pH and trun to positve charge at a low pH. Just like other pH-sensitive materials. Although pH-sensitive liposomes encapsulating RNA have been developed for decades.
So, why these ionizable lipids and not other pH-sensitive materials? And why did it take so long to apply in clinic.
emmm....It's hard to describe my confusion excatly....
Just like a sad feeling about active targeting nanoparticles, which also have been developed for many years and have no application in clinic yet.
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Sadly, the Pfizer-BioNTech LNPs use cationic lipids, not ionizable lipids. It's quite shameful given the twenty-plus years of knowledge about the toxicity.
Unfortunately, the manufacturers of the LNP-based COVID vaccines go out of their way to avoid explaining the reality of their formulations. It took me quite a lot of detective work looking at papers and patents to find the truth.
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The electron and photon are extensively interrelated, and therefore should share many common properties, equalities and laws. According to De Broglie, one such law is the Planck-Einstein relation, stating that as wavelength (i.e. radial orbit path) decreases, energy increases. An electron at a smaller orbit (today believed to be the ground state) most assuredly has a lower wavelength, and therefore should display a higher energy, not a “lower” energy level of the so called ground state.
Bringing this question up previously, two primary responses are typically offered... the "negative energy" aspect taught in high school, and the "pay no attention to classical mechanics" response. The last I checked, negative energy does not exist. Even it if did, a "zero" electron energy believed to exist at ionization is still greater than a -13.6eV at the believed minimum radius ground state, and therefore does not answer the question. As far as the second typical response, some sort of waving of the hands is offered, stating that the electron does not obey classical mechanics. Ok, I'll bite for argument sake, but then please explain why even the Schrodinger probability wave function also states that electron energy is minimum at a smaller radius ground state, and increases with a radial distance increase away from the proton. No so-called classical mechanics here.
I propose a model of Hydrogen for consideration, and welcome any peer review comments:
1) When the electron gains photonic energy, its orbiting radius is reduced and therefore its orbiting path per cycle decreases, equating to a higher cyclic frequency, equating to a higher energy per the Planck-Einstein relationship [so far so good, nothing strange here].
2) As it’s radius (r) decreases its Coulomb attraction force to the proton increases by r squared, and therefore so does its Potential Energy (PE) by 1/r (since E=F x dist). Therefore to remain in this particular lower radius increased energy level state, its orbiting velocity must then also increase to remain in this stable orbit, thereby increasing its associated Kinetic Energy (KE). [if you’re going to wave your hands here and say that classical mechanics doesn't apply to atomics, then state WHY and give an explanation, please don’t just regurgitate something you have read. Electrons have mass, and it is orbiting another mass. A very "classical" situation].
3) This increasing orbital velocity (frequency) has two limits: a) The speed of light, and b) Ionization "escape velocity" of the electron mass.
4) Once either of these velocities occur, the electron must then, a) convert completely into a photon at the speed of light, b) completely ionize (escape) from the proton, or c) convert part of its energy into a photon plus transform itself to a lower energy (higher radius) energy level [nothing too strange here unless there is a classical hand waving fetish].
In other words, attempt to purge the incorrect visualization thinking that as an electron gets further and further away from the proton, that it is closer and closer to becoming ionized. Attempt to think about WHY and HOW the electron would want to ionize, and you’ll come up with the above postulate. In fact, attempt to think about WHY only particular wavelength photons will be absorbed by the Hydrogen electron. Perhaps it is because it has the same geometric orbital size or a harmonic of that size. I have actually derived this harmonic to be the Fine Structure Constant / 2 utilizing classical mechanics, and by doing so, believe I have also discovered why and how the quantum aspect of the electron energy levels must occur.
- J.L. Brady
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Hi.
I wanna discuss with you the difference between Solubility and Ionization in the solution.
For example,
Salicylic acid (SA) has very low solubility in water. However, it is a strong acid, which means that the H can be ionized from -COOH in the SA molecule.
Therefore, I'm confused that the difference between Solubility and Ionization in the solution environment.
Can you discuss this?
Thank you so much.
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The ionized form of an acid or base is more soluble than the free acid or free base. It might not be enough to overcome the hydrophobicity of the molecule, therefore logP (D) is more relevant to assess the solubility of the molecule. Sometimes it is needed more than one ionizable group to increase solubility as well as functional groups with hydrogen acceptor or donor capabilities (amides, esters).
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Using UV-Visible data, electronegativity and first ionization energy i have calculated the bandedge position of ZnO. Now I want to calculate the bandedge position of Al-doped ZnO. Can anybody suggest to me any method?
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Adding the mole fraction value of each component to the Mulliken equation will provide a good approximation for calculating the edges of the bands. The atomic positions need be preserved in the exponents.
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The water ionization process for HHO cell process.
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can use platinum-plated titanium electrodes as per ASTM Standard. Titanium won't dissolve in ionized water as stainless steel does.
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Does anyone know how the geiger statement is activated with nonlocal ionization coefficients for avalanche triggerring probability extraction?
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Mr.Alagealy,
Thank you very much for answering my question. It was really helpful.
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Hi!
I'm studying on the mechanism of one reaction.
I think formaldehyde is generated as byproducts during the reaction
So, Identification of formaldehyde is a strong proof for mechanism that I suggested.
The reaction is processed in solvent in septum cuvette.
Formaldehyde has a very low b.p(-19 °C), so even if it is generated, it will fly into the air.
I heard that LCMS has a problem to ionize formaldehyde molecule.
FTIR is also has a problem that one of the products has a C=O group.
So I can't know whether C=O group is from formaldehyde or one of the products.
How can I identify the presence of formaldehyde?
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Two colorimetric tests comes to my mind.
The first is "Le Rosen test" which I illustrate in one of the drawing with toluene. For your purpose, I think phenol is more adapted as soluble in water. A typical procedure should be preparing a test tube containing water, sulfuric acid and phenol. Via a canule, you bubble the gaz formed in your reaction into this solution. A red colour should appear in the presence of formaldehyde when forming the p-quinoïdal adduct as illustrated.
A second test could be the formation of a dihydropyridine compound (deep yellow and fluorescent). You can bubble your reaction into a hot vial (60-80°C) containing ammonium acetate (~ 2.5 g for 10 mL of water and 0.3 mL of glacial acetic acid and an amount of acetylacetone).
I hope this could help you !
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I read some paper, and it said that if the conductivity obtained in dc measurement is identical to that obtained in ac measurement means that a material has ionic conductivity and electrical conductivity.
So I wonder few things,
1. What is the difference btw ac measurement and dc measurement?
2. What is a normal method to get an electrical conductivity and ionic conductivity?
(ex. ionic conductivity - dc measurement ,,)
3. In my knowledge, the only difference between ionic conductivity and electrical conductivity is charge carrier. (IC-ion, EC- electron)
Then how can any materials be only ionic conductive or electric conductive?
Is it related to electronegativity or ionization tendency?)
4. If the results obtained in dc&ac measurement are similar, why does it mean that the material have ionic and electric conductivity?
Thank you for answering to my questions.
I hope you to be happy always.
Thank you,
Hansam.
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Hello Hansam,
the answer to your question is something more complex. In the following I refer to isotrop materials. We assume, we have only applied an electric field E(w) with circular frequency w; no magnetic field, no electromagnetic field. The temperature is constant. Remember - the tensor of conductivity is one of the most complex magnitudes in material science.
The conductivity sigma can be expressed by the charge density Ni and the mobility µi of every type of contributing charge:
sigma = e[Nee + Nhh + fi*Nii]
here are Ne - the electron concentration, Nh the hole concentration and Ni the ion concentration; fi are the number of ion charges; µ is the mobility of the corresponding component.
The mobility in the static case can be expressed by µj = e*tauj/mj
Here are e the elementary charge, tauj the lifetime of carrier (electron, hole or ion) and mj the effective mass of the conductive particle (electron mass ore hole mass or ion mass).
In the case of ac current/field, tau must be substituted by
tau/(1 + j*w*tau) . Here is j the imaginary unit. If w*tau > 1, the magnitude and phase shift (between field and current density) of sigma changes.
With Regard
R. Mitdank
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W, Mo, Re, Os, V, Nb- these are common refractory metals, and I know of volatile oxides of W, Re, Mo and V. What about other metals?
If this is the common trend, then why is this so? are the metal atoms are glued so strongly together inside metal lattice (Ion cores mediated by delocalized electron cloud) that intermediation of anions (like Oxide) significantly weaken the cohesion? Does that mean the "adhesive action" of anions compared to electrons is much weak when it comes to refractive metals? Why is this so?
Starting from Refractory metal block and gaseous oxygen and ending up to gaseous oxide, the two ways must consume the same amount of energy.
Volatilization of metal + disassociation of oxygen+ ionization of oxygen+ionization of refractory metal=Oxidation of bulk metal+ volatilization of oxide
But conservation of energy cannot provide further insights.
Can you please explain links between high cohesion between metallic ionic cores mediated by electrons and weak adhesion of ionic cores in presence of oxides?
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To Frank Kern ’s answer I would add that the elements in question also have relatively small ionic radii in their highest oxidation state – specifically, ionic radii around or below 0.6 A, which puts their oxides in the region of preferred stability of coordination number 4 or lower, rather than the very common 6. Once you move to larger ions such as Nb(V) and Ta(V) (radii~0.7 A), the preferred coordination number is 6 or larger; the 3D oxide lattice is relatively more stable and doesn’t allow easy evaporation or even easy melting.
To evaporate easily a compound needs to generate small molecules easily. For oxidation state ≥5 to be compatible with a coordination number of ≤4, the small volatile molecules must contain one or more double (or “double”) M=O bonds. Not coincidentally, the elements we are discussing are known for their capability to form relatively stable multiple bonds. Contrast that with Si(IV) or B(III), which rarely if ever form bonds with multiple character and have refractory (in the sense of non-volatile) oxides despite their normal coordination number of 4 (or in boron’s case – mostly 3).
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Hello,
I want to consider ionization potential for drug molecule before docking using Autodock Vina can any body tell me which tool (free) can be used to do that?
Thank you,
Sainitin
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pKa can be modulated by local environment, which may be different for different poses; so the best way is to let the docking algorithm itself assign the most suitable protonation state for each pose. Unreasonable protonation states can be always filtered out after docking (and some unreasonable ones may turn out to be reasonable). With AutoDock, one has to provide the protonation states beforehand.
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Hi,
I'm currently trying to simulate a model at low temperatures, around 20K, using Incomplete Ionization. However, I keep receiving RHS on input contains NaN results. And in the output, there is a [(dd_real::log): Non-positive argument] error. I would like to know if anyone knows what equations are used in incomplete ionization that would cause that? I've checked the sdevice's manual, no equations lead me to believe it will cause a log calculation error. The physics parameters enabled are Fermi, ConstantMobility, NoBandGapNarrowing, and Temperature. I've run the model using no incomplete ionization enabling and it works properly.
Further addendum (v.1):
I was able to run the model at 40K with the above parameters and with incomplete ionization enabled.
Many Thanks,
Leon
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Dear Leon Luo,
Thank you for asking again. The origin of such a mathematical calculation error can be detected by reading the output text files, which s a tedious job. NaN means Not a Numerical. There exist a logarithm (LOG) whose argument is zero or negative value; I presume However, with a little bit of thinking, we can resolve it. It is somewhat clear that LOG of DOPING ratios (e.g., ln(n/N+))occur when calculating several quantities, such as the built-in voltage of a junction and the voltage boundary conditions(of Poisson's equation). I don't think that the ionized concentration N+ (nor the density of electrons, n) can take negative values but may be zero, as a rounding error. Therefore, we'd increase the precision or prevent their to be < 0. As a user of Sentaurus, increase the "digits" in math section or switch on the switch extended pricision.higher . If this doesn't work, use uncoupled instead of coupled solution, which has many Jacobean calculations.
Good luck.
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1、I want to simulate a PIN photodiode (under reverse voltage), and i region is active layer (absorb)
2、I used the impact ionization model
3、When the negative voltage increases to 50V,the simulation does not converge, and it oscillates back and forth between positive and negative output currents
4、so I want to ask how to solve this convergence problem, changing method? or model?
5、need help! Thanks!
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Dear Liang,
At such relatively high reverse bias, the impact ionization rate makes the generation-recombination term significant and transport equations are highly coupled. Therefore, it is hard to achieve conversion (normal problem !) The solution is:
1- Check if it is near or almost near breakdown VBR of your PIN diode, using theoretical approximate formulas. If you do 2D use cylindrical junction formula, if you make 3D simulation use spherical junction formula
2- If you're near breakdown, use coupled (Newton) algorithm with small bias steps and refine mesh around all junctions.
3- Note that a premature breakdown (well before VBR) near junction surface. Therefore, check that the surface is passivated (in your input description file or the process simulation).
Good luck.
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I want to plot ionization spectra for Singly, doubly, and triply ionized molecule i.e. to be more specific is the x-ray spectra for singly to triply ionized atom or molecule using Gaussian or Orca ?
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XPS is in principle pretty straightforward, all you would need to do is take your orbital energies and put Lorentzian functions with the width that the setup you want to compare with has, that would be a simple Koopmans' theorem approach which was sufficient for most systems I came across so far. This, however, will require some sort of offset calculation because functionals are often optimized for bond lengths, relative energies and ionization potentials, not the deeper orbitals. For a more sophisticated approach that involves additional effects, see e.g.
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Helo everyone I'm upon developing new method for analyzing clavulanic acid using Ms/Ms with ESI in the negative mode and the problem what I have that I can't find a proper internal standard that ionized in the -ESI and match the same chromatography conditions of it Please any suggestions? and what is the possible m/z ions in the -ESI for the suggested internals?
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using metronidazole as an internal standard
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I am a beginner in Gaussian 16 and trying to learn the BEB method. I finished calculating the optimized structure using DFT (B3LYP/6-31G(d)). I have attached the equation used for BEB calculation, where t= T/B, u = U/B (T= Incoming energy of the electron, B= Binding energy, U= Orbital Kinetic energy, N= Orbital occupation number).
I am stuck with extracting ingredients i.e B, U, N from the Gaussian output file. It would be great if someone can point out what I am missing and how to proceed with it.
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the observe electron is the initial step to study.
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I am looking for publicly available computer code to calculate electron induced cross sections for the ionization / excitation of molecular targets
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You could try QUANTEMOL
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Dear colleagues,
I am conducting an experiment to identify un-targeted compounds in food using the GC-MS (TSQ 8000, Thermo Scientific). By using strong ionization energy (70eV), the precursor ions were barely detected. Therefore, it is difficult to identify chromatographic peak using identification software for LC-MS (e.g Compound Discoverer, MPP,...). Besides, the identification of the chromatographic peak is difficult to detect visually.
What software should be used to determine the chromatographic peak in the GC-MS method?
Thanks.
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Your welcome Thanh-Thien Tran-Lam, and if you need any help, don't hesitate to contact me.
I wish also all the best in your scientific career because you deserve it.
Best wishes,
Sabri
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I prepared a 1 WT% solution of sodium alginate and diluted it to 0.25 WT% with ionized water. I first tested the particle size of this 0.25 WT% sodium alginate solution and kept it stirred at room temperature for one week after the test. After one week, I found that this 0.25 WT% sodium alginate solution produced a lot of small white precipitates. I would like to know why the 0.25 WT% sodium alginate solution, which was dissolved before, has precipitated after continuous stirring.
In fact, I prepared another 0.25WT% sodium alginate solution in the same way, and this solution was left on the lab bench without stirring after I measured its particle size, and a week later I saw some white precipitates, but not as much as the stirred one. I also wonder if the polymer molecules in the solution have gathered together over time? Why did they clump together?
I would appreciate it if you could answer my question.
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Hi Weinire Tuerxun,
Alginate can precipitate if the charges that keep it solubilized are interacting with an oppositely charged ion (a cation). But biopolymer solutions are also prone to become hazy due to microbiological infections. So, first step is to find out if the precipitate is indeed alginate and not bacteria, yeast or molds that are feasting on your solution. Isolate the precipitate and run FT-IR on it, FT-IR requires a minimum of sample so this should be feasible.
After you have established the precipitate is indeed alginate, I would check the pH of the solution. In solutions with low salt content the pKa of alginate climbs to values above pH= 4.5. If you are close to the pKa the charged groups on the alginate become neutralized, aggregate and cause precipitation.
If it is not pH, then check for bivalent metal ions, as these will crosslink the alginate. You can prepare alginate solutions in tap water (with some Calcium ions in it) and you will obtain a clear solution as the calcium ions are initially spread over many different alginate molecules, however in time they will migrate and collect on the smaller alginate chains and cause precipitation. Alginate solutions should be kept in clear PE/PP/PET bottles and any contact with metal surfaces (stirrers, vessels, metallic covers etc.) is to be avoided. Also some glasses may leach bivalent metal ions, so I never stored my alginate solutions in glass.
Anyway, I do not believe in nucleophilic attacks leading to covalent bonds being formed, these are non-covalent interactions causing the neutralization of the charged groups leading to precipitation.
Kind regards, Leo
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  • In the basis of laser-induced breakdown sprctroscopy (LIBS), for calculate the plasma temperature by Saha-Boltzmann plot, where to find the ionization potential of the less ionized stage (EIP) and correction to the ionization potential for interactions in the plasma (E*) of Al and any other elements? Is there any database
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Hi all,
I'm planning to analyze for PFOA using LC/MS/MS, however, my solution is containing 0.5M Na2SO4- someone told me it can interfere with the ionization process of the instrument. Though, I don't want to use any ion exchange filter since it can also filter out the PFOA. I am also using internal standard addition in my analysis, and I think this can correct any interference from the salt. Another colleague of mine said with a small injection volume (10 uL) in my protocol, the mobile phase will be able to dilute the salt content to the point its effects will be negligible.
Thus, is it possible to inject 10 uL of 0.5M Na2SO4 solution to analyze for PFOA using LC/MS/MS without additional separation step prior to the analysis? I want to hear more opinions from other experts for this. Please let me know your thought/experience.
Thanks!
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I'm assuming you are doing a reverse-phase analytical separation? In which case you can probably expect your salts to be un-retained on the analytical column and come out in the void volume. You could divert the first minute or so (however long before your first analyte elutes) to waste instead of to the MS
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Hi everyone
I'm planning to do a potential energy surface scan over a specific bond for a doubly ionized Methyl Chloride (CH3Cl2+ over C-Cl bond) using Gaussian 16 (UNIX-based operating system), my question is, how to extract the energy at each point from the output file and how to specify the bond that we want to do the scan over, in the code,
the code I initially used is shown here: (I feel there should be a line specifying the CCl bond)
%chk=CCl.chk
%mem=9GB
%NProcShared=4
#scan td=(nstates=6) wb97xd/aug-cc-pvtz
CH3Cl neutral GS syn
2 1
C
H 1 B1
H 1 B2 2 A1
H 1 B3 3 A2 2 0.0
Cl 1 B4 4 A3 3 0.0
B1=1.07011
B2=1.19035
B3=1.19148
B4=1.72691
A1=94.56838
A2=69.00098
A3=52.79175
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Dear Tahereh,
With the scan keyword you will carry out what is called a rigid scan, this means that the program performs single-point calculations for different structures that vary ONLY the geometrical parameter you selected. This yields a very rough estimation of the potential energy surface, given that you are neglecting all possible relaxations that can take place upon modifying that coordinate. It is usually better (and, four your system, it is perfectly feasible) to perform a relaxed scan, in which the rest of the molecule is optimized at each step of the scan. This can be achieved with the opt=modredundant keyword.
To use this keyword, it is easier to work with Cartesian coordinates instead of z-matrix, just to simplify the input, which will look like this:
-----------------------------------------------
# opt=modredundant wb97xd/aug-cc-pVTZ
\blank line
title
\blank line
2 1
C coord_x coord_y coord_Z
H coord_x coord_y coord_Z
H coord_x coord_y coord_Z
H coord_x coord_y coord_Z
Cl coord_x coord_y coord_Z
\blank line
B 1 5 S 20 0.10
\blank line
-----------------------------------------------
If you take a look to the end of the input, the last written line says that for the bond (B) between atoms 1 and 5 (which correspond to C and Cl according to the Cartesian coordinates) you want to perform a scan (S) of 20 steps, with a step size of +0.10 angstrom (yes, you can do scans that reduce a distance/angle/dihedral just changing the sign of the last number).
Now, you can see that I have removed the td keyword. Given that TD-DFT excited states do not interact with the ground state (this is not CASSCF or any multireference method), the ground state PES will not be modified by them. And forcing the program to calculate the excited states at each step of the intermediate optimizations will increase the computational cost a lot. I think it is better to perform the scan just in the S0 PES, and once it is finished, carry out TD-DFT single-points at each point of the scan. While it involves submitting more calculations, the computational cost will be reduced.
You could have performed the relaxed scan optimizing the geometry not in the S0 surface, but on an excited state, of course. In that case, you need the td keyword, specifying the excited state you are interested. For instance, if you want to do the scan in the S1, the keyword should read td=(nstates=1,root=1). Again, you do not need the upper excited states, unless there are degeneracies.
Hope you find it helpful
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I'm doing my Master Thesis on a new design for the Ionization Stage for a micropropulsion System and I would like to learn how to use some open source software suitable for the analysis of Plasma Physics.
In a previous discussion PIConGPU was pointed out. Do you think it could be suitable for the analysis of the plasma physics inside an hollow cathode?
If yes, how should I start to learn it?
If no, do you have any other suggestion?
Thank you very much for your help!
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Hi. You can find the XOOPIC code in the below link:
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I am looking for information regarding pH influence for the peaks shift in the low aliphatic region of the protein NMR spectrum.
In my research, I've performed fragment-based screening of the protein with NMR titrations and I've come across a problem. I've observed shifting of the peak around 0.4 ppm which was dependent on small pH changes (in the range of approx. 0.5). At first, I've taken this as the binding of my fragment but the change was reversed just by the adjustment to the initial pH.
I am wondering why, in this not ionizable area, there is such big sensitivity for pH. I would be grateful for any hints regarding this topic.
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Thank you for your answer - could you also share with me some references where I can read more about the phenomena you’ve described?
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I found many diverse views taking about the calculation of calcium ionized depend on Albumin level and total calcium
they are so different and can not trust any
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Why do you want to estimate ionized Ca? Don't you have access to a more accurate ionspecific electrode for Ca?
Ionized calcium in serum is not only dependend on total calcium and albumin, but also on pH, globulin content and anions like phosphate / citrate. Disease state may effect the reliability of the estimation by for example the Payne equation.
Some publication that deal with this matter are:
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Hi all,
I am working on mid-IR spectroscopy of donor bound excitons in the Si host. I am using an FTIR spectrometer with InSb detector and + KBr or CaF2 beamsplitter. I apply above-bandgap excitation at 671 nm with power levels up to 40 mW. The donors are ion-implanted and consequently drive-in diffused. I need to observe a PL emission at the vicinity of 3 um, while the next highest transition is at 2.2 um, while donor ionization energy is 2.1 um. I observe a broad emission from 2.3-2.4 um to 3.2 um. This emission possesses multiple peaks but overlapping with each other. The emission at 3 um is barely recognized. There is a temperature and power dependency of emission intensity but not much change for the shape. I want to identify the originating factor for this emission. What should I do? How can I isolate and amplify the desired emission>
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@ Mурат Джан Сарихан, вы имете широкий выброс от 2,3-2,4 мкм до 3,2 мкм. Это излучение имеет несколько пиков, но перекрывает друг друга. Эмиссия на уровне 3 мкм практически не распознается. Интенсивность излучения зависит от температуры и мощности, но форма не сильно меняется. источник этого выброса Что делать? Как я могу выделить и усилить желаемое излучение?
Возможно, источник накачки должен иметь длину волны большую, чем 671 нм. На мой взгляд Вы получите смещение в желаемую область спектра.
Пики должны также переместится. С уважением, Оглуздин В.Е.
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In many textbooks about basics of semiconductor, they say dopants of extrinsic silicon are fully ionized and explain many equations based on this hypothesis.
But I still don't get why all the dopants in silicon are ionized for extrinsic silicon with shallow impurities. Especially, I wonder how one can get the fermi level of extrinsic silicon with density of dopants and effective density of states.
Also, for heavy doped silicon how we describe the energy band?
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In order to treat the heavy doping problem, one can not make the approximation that (Ed-Ef) greater than kT.
One has then to exactly solve the problem as follows:
One has to apply the neutrality equations
n0 = Nd+ + p0............1
n0 and p0 are the thermal equilibrium concentrations of the electrons and holes.
Nd+ is the ionized doping concentrations,
n0= Nc (2/sqrt pi)F1/2(Ef-Ec)/kT ,.............2
where F1/2 is the integral fermi function of the order 1.2.
Likewise,
p0= Nv (2/sqrt pi)F1/2(Ev-Ef)/kT,...........3
Ec is the conduction band edge, Ev is the valence band edge, Nc is the conduction band effective density of sates and Nv is the same for the condcution band.
Nd+ = Nd( 1-f(Ed))..................................4
Substituting 2,3,and 4 in 1 one get an equation in Ef which is then solved to get the fermi level.
After getting the fermi level one gets the Nd+ interns of the Nd.
It is so that as Ef approaches Ed the fraction of the ionized donors will be decrease and the assumption of full ionization is not valid.
More discussions will be given in the next post.
For the formulas used here please refer to the book physics of semicondcutor devices by S. M. Sze.
Abdelhalim
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I understand that there might be huge differences between LogD and LogP for ionizable compounds. Normally, logD should be lower than logP for ionizable compounds.
But can LogD value be significantly higher than LogP, say in my case LogP = 0.05 and LogD = 4.02. I am using ocatnol/DPBS pH7.4 for determining LogD and ocatnol/MilliQ for determining LogP. Please comment.
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Ijaz Durrani
thank you for your insights!
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I am assuming the resulting insertion/agglomeration in the presence of a surfactant or the agglomeration of surfactant may reduce the rate of ionization. The mobility of the ion may also be reduced in the presence of the surface-active agent. Kindly share me the exact/ probable reason / mechanism repression the mass spectra a compound in the presence of surface-active compounds. Interestingly fluorinated surfactants such as perfluorooctanoic acid (PFOA) and perfluorooctanesulfonic acid (PFOSA) could be employed for ESI-MS without a significant decrease in sensitivity!!
Kindly explain/ share your view.
Thanks
Best Kind Regards
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Thanks, 
Respected Madam, I have received it.  Best Kind regards
Dr. Raja Ghosh 
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I understand that there might be huge differences between LogD and LogP for ionizable compounds. Normally, logD should be lower than logP for ionizable compounds.
But can LogD value be significantly higher than LogP, say in my case LogP = 0.05 and LogD = 4.02. I am using ocatnol/DPBS pH7.4 for determining LogD and ocatnol/MilliQ for determining LogP. Please comment.
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SPSS and SAS can solve problems with large datasets
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Acording to my knowledge I know I should have matrix matched blanks, standard solutions and samples. It's really hard if you have large variety of digested samples. Standard addition is also time consuming. I read about a combination of techniques which may help. First of all I have radial plasma orientation, so matrix effects are smaller than in axial. This combination is internal standards + robust conditions + ionization buffer.
Anyone have experience in that kind of analysis?
It would help me with routine samples. From my experience (thanks to radial plasma, I guess) only large amounts Na, K, Ca and Mg interrupts my analysis, so ionization buffer would be usefull. Beside that results are pretty accurate.
I just wonder if reaserchers are usung matrix matched solutions or they are trying to speed things up :)
Thanks for any tips.
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Short answer: Yes, matrix match your standards with your solutions.
Long answer: Yes it is "really hard", even with a uniform sample type. ICP is a great technique to measure many elements in a single sample, but that doesn't make it easy, if anything it should be harder because you are measuring many elements at once.
If you "know I should have matrix matched blanks, standards and samples", then you should. There are countless examples of why you should, and