Science topic

Chemical Physics - Science topic

Chemical physics is a subdiscipline of chemistry and physics that investigates physicochemical phenomena using techniques from atomic and molecular physics and condensed matter physics; it is the branch of physics that studies chemical processes from the point of view of physics. While at the interface of physics and chemistry, chemical physics is distinct from physical chemistry in that it focuses more on the characteristic elements and theories of physics. Here we discuss the methods that will allow us to better describe and predict chemical processes.
Questions related to Chemical Physics
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Can it be published in Physical Chemistry Chemical Physics completely free of charge?
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If you don't want to make it open access, are there any indicators why that shouldn't be possible?
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Biomass can be converted into activated carbon by chemical or physical activation. The physical activation, especially using steam, produces a lot of pyrolytic oil and the yields are rather low. Using chemical activation the yields are much higher and little or no pyrolytic oil is formed.
What is removed by the physical activation but not by the chemical one? Do the ACs produced by chemical activation have more functional groups left compared to the ones produced by physical activation?
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Interesting questions Romar, I think that first of all, it is important to note that the two methods of biomass activation you mentioned each has merits and demerits. Several factors need to be considered in the choice of a surfactant or activation reagent. It is also important to note that, different activation reagents have different effects on the biomass. It is widely argued for example, that oxygenated compounds have a good activation effect on biomass. However, as I have indicated earlier, the output of the activated carbon is largely dependent on so many factors, including the chemical properties of the biomass. I have used surfactants such as H2SO4, H3PO4, KOH, HNO3, KCl, Na2CO3 etc. What I observed with KOH for example was that, there was high biomass loss in the process due to cell wall disruptions and the efficiency of the modified biomass was also low. H2SO4, H3PO4 and Na2CO3, KCl had a good activation effect on the biomass. One way to detect if new functional groups emerged on surfaces of the AC or not, is to do an FT-IR analysis on the unactivated samples and compare them with the AC among other evaluation tests. In summary, some biomaterials give good performance if they are physically activated or modified, some other materials give good results via chemical modification and some require hybrid. Hope my input is helpful. Cheers Henrik Romar
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I am going to prepare activated carbon from the waste activated sludge coming out of WWTP.
Can you please help me in understanding, which chemical/physical activating agent will be most eco-friendly and most effective for giving high BET surface area and micropore volume of the produced activated carbon?
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Hello .. Good idea .. Please take advantage of this research ... Good luck@
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Friend, can I ask you a question?
Please, can you help me with the search for these pdf files that are scientific publications made in China?
1. Fengxing, Z., Zhizhen, G., Peiheng, C., Jinhua, M., & Yunsheng, C. (1993). A Study on the Phase Diagram of the Quinary System LiCl NaCl — KCl — MgCl_2 — H_2O (25 ℃) at Iso-Lithium Chloride Content [J]. Journal of Salt Lake Research, 3.
2. Fengxing, Z., Zhizhen, G., Peiheng, C., Jinhua, M., & Yunsheng, C. (1987). Studies on the Solubility and the Isothermal Evaporation Process in the Quinary System Li, Na, K, Mg / Cl-H_2O at 25 ℃ [J]. Chemical Research In Chinese Universities, 4.
3. Zongxi, L. J. W. L. Z. (1996). Heat Capacities, Heats of Dilution and Apparent Molal Enthalpies of LiCl-NaCl-KCl-MgCl_2-H_2O Systems at 298. 15K. Chinese Journal of Chemical Physics, 1.
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A question is about positron chemistry. Does the pH of an aqueous solution affect the lifetime of positronium (Ps)? The following references reported that the interactions between Ps and MnO4- was almost the same at pH=2, 7 and 12.
Are there any other similar examples? I wonder if it is correct to assume that the lifetime of Ps is unaffected by pH. Or conversely, are there any reports that the lifetime of Ps changes with pH?
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Thanks for the multiple replies.
The probability of pick-off annihilation in positronium (Ps) is primarily due to electron density, as Rüdiger Mitdank has pointed out. It is described by the overlap of the positron and electron wave functions. However, in practical terms, it is not determined by that alone, but is also affected by various environmental factors. In this discussion, I would like to get into these factors.
For example, water and many other liquids expand as their temperature rises. Since expansion decreases the molecular density (electron density), it is assumed that the higher the temperature, the longer the Ps lifetime. However, this assumption is not true. In fact, the lifetime of Ps is shorter in warm water than in cold water.
Similarly, the relationship between Ps lifetime and pH is not easy to estimate. Therefore, we should base our decisions on experimental data.
Most of the basic Ps chemistry was done in the 1960s and 1970s. In those days, the resolution and stability of measuring instruments were not as good as they are today, and the use of computers was limited. Straight lines were drawn with a ruler on hand-drawn one-log graphs. Therefore, the environmental factors that were reported to be "independent" at that time may or may not be due to the lack of measurement accuracy. As the application of positron science to medicine has progressed, motivation to revisit some of the issues has arisen.
I hope somebody will continue to let us know if you have any information on the relationship between pH and the lifetime of Ps. Thank you very much for your time.
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I am actually intern in a pharmaceutical company and I am doing a bibliographical research to group all studys which show interest on the impact of Ethylene Oxide sterilization on the physico chemical properties of rubbers. Therefore I need your help, please reach me on RG if you have already be concerned about this subject or if you have any documents (scientific articles for example) on it.
Regards
Quentin Cojean
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It is a disadvantage of the sterilization method that ethylene oxide sterilization remains only residue rather than the physicochemical effect on rubber materials. You can do a literature search on this subject with google academic.
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What are the prevailing methods (if any software or app) to search or screen for a material with a desired chemical, physical or electrical (what not) properties?
How do scientist do this nowadays? by intuition? or knowledge from their textbooks? from literature survey? or simply through a software?
What are the tools involved?
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Several software programs are available to study the physical and chemical properties of materials. each software is implemented in a method. for example the Win2k it is implemented in the FP-LAPW method ..
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The third rotation allegedly leaves the molecule unchanged no matter how much it is rotated, but is it really okay to assume this? A response in mathematics is welcomed, but if you can explain it in words that would be good, too.
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Dear Cory Camasta, Three degrees of freedom come from free motion, one from rotational and one from vibrational & E= 5/2 KBT. The remaining rotational degree has a very small moment of inertia as some participants noted previously.
See the following external post for the full explanation regarding the separation of levels mentioned by Prof.
Gert Van der Zwan
:
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My question is about your experience of archaeological sciences (Chemical, physic, biosciences, metallurgy, archeo-geophysics, mapping (3D), DNA archaeology, etc. and, Could you explain how it has helped your project? So may we can discuss here: How archaeology will be affected by these archaeological sciences in the future? l think that there are positive correlations between archaeological sciences and archeology. When science finds a new discovery we can adopt in archaeology. For example drone technology... From the point of view how the archeology making science in the future?
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Yes, archeology is an interdisciplinary science, because both in the research methods used in excavations and when analyzing artifacts found in excavations, exhibits, etc. often originating from distant, old eras, constantly improved research instruments are used, perfected using modern technologies created and developed in various fields of knowledge, in various disciplines of science and also the results of research, scientific discoveries provide knowledge about the history of the development of civilization, man, specific old cultures, determinants of technology development, factors of development of human creativity, development of art, trends and trends in art, development of human relations in relation to nature, etc. Archaeological discoveries provide source knowledge for the development of many other fields of knowledge, update and enrich historical knowledge on almost all aspects of human activity in more than Sci., Currently, research methods and techniques in the field of archeology are being improved through the use of ICT, Internet and Industry 4.0 information technologies. Thanks to the implementation of these modern technologies for archaeological research and the use of their results, sharing archaeological knowledge databases in the open formula, online knowledge databases, the possibilities of using archeological research results also in other science disciplines are increasing.
Greetings,
Dariusz Prokopowicz
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When deriving the Hartee-Fock method, we minimize the electronic energy with respect to all molecular orbitals with the constraint of orthonormality of the molecular orbitals by using the method of Lagrange multipliers. Is there a fundamental reason why the molecular orbitals need to be orthogonal? Does it ensure a lower energy compared to any non-orthogonal set of molecular orbitals?
Thank you very much for your help
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Simply go back to the definition of Hartree-Fock. The idea is to approximate the many-body wave function with a single Slater determinant. Because of the determinant, any non-orthogonal component of the orbitals is irrelevant and only the orthogonal part survives. In other words, if you take a non-orthogonal set of orbitals and construct a Slater determinant out of those, you will get the same determinant if you would have first orthogonalised them (Gram-Schmidt, Löwdin, canonical, etc.). You still have the same volume.
Generally one prefers to work with orthogonal orbitals, since this makes it easier to work out the expectation values of the determinants (e.g. energy) via the Slater-Condon rules. Generalisations also exist for non-orthogonal orbitals, but due to the cross-terms, you get overlap matrices, cofactors and adjugates all over the place. So in this sense, orthonormal orbitals are more a convenience than a necessity. Non-orthogonal orbitals would not add anything (the determinant remains the same).
On the other hand, once you have used the Slater-Condon rules to work out the expectation value of the Hamiltonian, this energy expression is only valid for orthonormal orbitals. So you better enforce orthonormality in the optimisation, to get a physically sensible answer out. (All orbitals could become identical, so all the particles would occupy the same state. So you would get bosons out instead of fermions.)
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My system has inversion symmetry. Therefore, I'm calculating the optical transition for a material which is allowed when parities of conduction band (CB) and valence band (VB) are different (there is some finite probability for it), otherwise it is zero. I have obtained the WAVEDERF file that contains some band number (occupied and unoccupied) with specific energy, and real and imaginary part of dipole transition matrix elements. I want to plot (K-path/K-points vs. optical transition probability), but do not know how to obtain this from WAVEDERF file.
Any help would be appreciated.
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- First, let's review some basic equation:
+ From VASP source code:
CDER(k, m, n, j) = <u_m|- i d/dk_j | u_n> = - <u_m| r_j |u_n> (j = x, y, z)
(k=wave vector; m, n are band indices, u is periodic part of the wave function; for now, I ignored spin index of CDER)
CDER can be obtained from WAVEDER or WAVEDERF using this function: https://github.com/hungpham2017/mcu/blob/master/mcu/vasp/utils.py#L82
+ The square of CDER is defined as the dipole transition matrix:
dipole transition matrix (k) = CDER(k, conduction_index, valence_index)^2
+ Finally the transition probability R per unit cell is given by:
R = pre-factor * sum_k (dipole transition matrix (k) )
or R(k) ~ CDER(k, conduction_index, valence_index)^2
To know the value of pre-factor, please see the section 6.2.2 of this book:https://www.springer.com/gp/book/9783642007095
If you are not interested in the absolute value of R(k) with the correct unit, then you just need to plot the R(k) ~ CDER(k, conduction_index, valence_index)^2 as a function of k.
- In practice, the function I wrote will read the WAVEDERF file and give you:
CDER(spin, k, m, n, j). Simply, do the math:
R(k) ~ CDER[spin, k, m, n, 0]**2 + CDER[spin, k, m, n, 1]**2 + CDER[spin, k, m, n,2]**2 with m, n are indices of conduction and valence band.
I will include this R(k) calculations (with correct unit) in my code soon.
Hope this is helpful
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I'm trying to calculate the spectroscopic parameters for Mn2+ doped ZnAl2O4 such as B, Dq, etc. For this, and to solve the Tanabe Sugano matrix, I need to compute the Trees correction coefficient ( alpha). Now, the authors Y. Yu, X. Li (Materials Research Bulletin 73 (2016) 96–101 the file attached) say that the value has been determined as 76cm-1. I checked the origins of this coefficient (ANJANI K. MEHRA , The Journal of Chemical Physics 48.10 (1968): 4384-4386) and haven't been able to figure out how this value is computed.
Besides, since Yu and Li's paper is also on Mn2+ doped ZnAl2O4, I'd like to know if I can use the same value for alpha or can it vary? If it can vary, what are the steps to follow to calculate this value from the spectroscopic data that I have?
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Dear Samvit Menon, you can get the Trees parameter from the best fit of your observed tfansitions, using a ligand field program. Best suited for this is the program AOMX, developed by Heribert Adamsky and co-workers. If you are intersted we can supply you with the program.
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I'm trying to conduct a study about the effects floating pv has on chemical/physical/biologic water qualities. Has there been any studies about it that shows then significant effects? If yes please refer it to me. Thank you.
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Yes, there are articles about this and though authors categorise some effects as "good" or "bad", I honestly think it depends on each niche the floating PVs are installed.
It is known that floating PVs produce more energy than land ones because of water reflection. As to the effects cause on the water itself:
- The shading created by the panel prevents growth of algae (which, again, can be good or bad depending on the approach);
- Prevents excessive water evaporation, thus it can be used as a tool in arid and semi arid spaces;
- Inhibits the convertion of bromide into bromate;
Here's an article for you:
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Chemical, physical and biological
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Types of biosensors :
  • Electrochemical
  • Piezoelectrical
  • Thermometric
  • Optical
  • Physical
Best regards,
Marie B.
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acidification of soils is a problem for sustainable agricultural use.
Liming of soils is a propriate and for a long time used application in agricultur and forest.
Therefore new scientific work is interesting and good to understand the different singel chemical, physical and biological impacts.
Therefore I am very interested in all new results about lime, liming of soils.
Thank you for information.
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As you might observe from the earthworm dissection after the reproductive glands the calciferous glands are a major investment of earthworms.
Earthworms depend on adequate calcium for the digestive process and in addition the diagnosis of a well wormed soil is by the presence of excreted calcitic limestone granules.
The majority of earthworms are inhibited and do not do well in acid soils. soils with little organic matter, and dry soils.
The addition of lime and manure can supercharge the soil by the enrichment of the soil in earthworm castings.
If farmers can provide lime animal manure and water the worms can act as bio tillers.
A single earthworm can produce 5 kilograms of castings in a single year.
In a grass legume pasture with manure addition millions of earthworms can be produced in a single hectare.
Earthworm castings are also 30% carbon it might be possible that the resolution of global warming is global worming and that would need liming and maintaining the earthworm habitat to optimize their amazing abilities.
While the human of 76 kg resides in a hectare the mass of earthworms can reach 1000's of kgs per hectare more than any other life forms in the living soil.
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silvernano particles are produed from palnt extract various chemical and physical process can be used to produce silver nano particles
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Google (and Wikipedia) is your friend:
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Referring to this article ' Dorai, K. and Kumar, A., chemical physics letter 335 (2001) 176-182', where they have considered the influence of large CSA (chemical shift anisotropy) on NMR relaxation of nuclei like 19F. They have determined cross correlation rates from the initial slope of buildup curves of multi spin mode obtained as a result of nuclei selective inversion recovery NMR experiments. How it is possible to generate multispin mode (two spin mode in this article) using inversion recovery experiments. As per my knowledge, INEPT kind of NMR sequences are required to generate second order spin mode
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Bhanwa,
maybe my little attache scribbling helps a bit.
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For an ancient carbonate build up is it possible to measure rates of reef carbonate production and erosion, associated with different biological, chemical and physical processes,?
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Very difficult but interesting question indeed. One of the ways could be to look into experimental results of the modern day reefal growth in the near by areas and compare it with the ancient carbonate buildups. The temperature and physico-chemical conditions of the modern day sea water, calcium content, co2 content and transgressions and regression in the past need to be compared as all of these factors would have also influenced reefal growth in the past. I am sure it would be interesting study. The satellite images would also help but how far, these may not be available for distant past so analogues need to be developed to estimate various aspects. Regards
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I need values of specific heat capacities of TDA solution containing (TDA+O-dichlorobenzene) & TDI.
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The starting point of thermodynamic logic is: 1) opposing perpetual motion. 2) The irreversibility of dynamics. Let's look at how to get Carnot efficiency = 1-T1/T2.
1.1 There are many kinds of type 2 perpetual motors, each of which is a natural phenomenon.
A) Machine A: against the irreversibility of thermodynamics (diffusion, heat conduction, friction, etc) - dynamics;
B) Machine B: Utilizing the Difference of Carnot Efficiency (Reversible Thermodynamics) - Thermodynamics
1.2 A and B belong to different disciplines. There is a parallel relationship between them and there is no logical mutual inevitability.
1.3. Logic of the Second Law of Thermodynamics:
Experience induction, deny that A machine==> B machine can not be manufactured==> All material Kano efficiency: 1-T1/T2.
1.4 The logic of the second law of thermodynamics violates the physical logic that A and B cannot be inferred from each other.
1.5 The second law of thermodynamics elevates the "irreversibility", which is in fact only a kinetic experience.
📷 Detailed discussion can be found in the following figure.
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In the synthesis of nanoparticles from a solution whose color changes to dark red! This means that the product is a nanoparticle
It is important to note changes in this color in all methods, either by chemical, physical or biological methods
Why does color change in almost all methods with the same color?
In some research, nanoparticles produced by chemical method may be toxic, but the biological method may resolve this issue.
Is there a relationship between color change and the collection of all these methods?
What is evidence that nanoparticles produced by the biological methods are safer than the chemical method?
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The color is due to your nanoparticles. So it will independent on the methods.
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as I see some differences in such data from website to another specially the solubility and pKa
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You can refer to The United States Pharmacopeia (USP) or British Pharmacopoeia for reference.
There is other book called Remington practice of pharmacy can also partially solve the issue.
The best option would be the drug information provided in the USFDA Accessdata site or EMC Summary of product characteristics and PubChem site as the information provided here are supposed to be most accurate legally for any particular molecule.
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what are the chemical and physical properties of sodium trihydroxoplumbate(II) ?
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Hello Abdelwahab
Try looking at nist webbook
It has chemical and physical property data of almost all compounds
Good Luck !
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Chemical adsorption
Physical adsorption
Adsorption
Catalyst
Activated Carbon
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Physical adsorption (characteristic of weak van der Waals forces) and Chemical adsorption (characteristic of covalent bonding). Physical adsorption is very effective and occurs usually at a temperature close to the critical temperature of a given gas. Chemical adsorption occurs usually at temperatures much higher than the critical temperature.
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Are there singularities in the equations of Physical Chemistry, similar to those that appear in Classical Electromagnetism, General Relativity, Cosmology and Aerodynamics? What would be their physical implication, interpretation and consequences?
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Of course, yes. To give an example, from quantum chemistry, let z be a perturbation parameter and suppose that we computed E(z) function by using Rayleigh-Schrödinger perturbation series (n>3 order). This function involves singularity points in the complex z plane which are responsible for the convergence of the perturbation series. In terms of Schrödinger equation (and conformal mapping) these singularities manifests some changes in molecular geometry or in basis set. Such points may connect the ground state to an excited state of the molecule (generally to a low lying excited state or the one as its lowest symmetry). Some other points behave as critical points upon dissociation. MP4 and CCSD(T) type computations reveal such phenomena.
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I would like to know if anyone knows how to plot the surface ([B] vs t vs k1/k2 ) as a numerical solution of the kinetic model of the mechanism A -> B -> C, specifically for the concentration profile of the intermediate specie [B], using any MATLAB ODE solver.
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Hi Enmanuel Duarte, the ODE solver will return a solution set of data points from the universe of discourse. So I think, at most, you can only get the 3-D line plot, not the surface, unless you want to obtain the slope field.
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my question is interested in water treatment methods for agricultural uses , depending in which class of treatment methods is more important due to the final uses , Does Bio m phys, or chemical methods???
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yes
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Magnetite (Fe3O4) is being reduced in a fluidized bed at 1175 K by using CO.Total pressure is 3 atm. The iron(austenite) produced is to contain 1 wt%C.How many moles of CO need to be put in the reactor per mole of Fe3O4 reduced?
You may use the reaction 3Fe(s)+2O2(g)=Fe3O4(s),delta G nought=-1102200+307.4TJ
Cp,O2=29.96 J/Kmol
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Mr. Koyal,
The topic of your question is basic knowledge module Inorganic Chemistry I.
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We are studying the chemical, physical and mechanical properties of mushrooms.
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What is the effect of harvest time of mushrooms on physical, mechanical and chemical properties ?
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The Mechanical ,chemical, and physical properties of UMF and UF resins
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To start with, I shall give a good site that provides information about the preparation & properties of M/F resins. On the left side of the page, you can see reference to U/F resins:
Best wishes for success in your research.
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Dear Professors,
I find many researches emerging on the hybrid nanofluids wherein the nanoparticles are taken and mixed in conventional fluids. But I do not know the chemical or physical constraints to be taken into account while choosing such particles. Kindly let me know the clear micro-structural phenomenon by which two or more nanoparticles could be chosen for preparing the hybrid nanosuspensions.
Thank you.
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hi,
A simplest approach would be to test thermal conductivity of a fluid under use which is as per your need/choice and compare it with the thermal conductivity of the same fluid after adding the appropriate metal/alloy nanoparticles. Usually the addition of such metal nanoparticles enhances the thermal conductivity of the fluid.Easy said than done. You need to optimized on many levels. An arbitrary choice for fluid and type of nanoparticle may give erratic results or may even cause degradation of the device under study. Just make sure you do the thorough research before you actually start mixing things together.
Regards
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Mutational agents are chemical and physical.
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Dear samiee
I agree with Dr. Miri and also tissue culture techniques that ensure genetic stability are particularly useful for in vitro mutation induction and mutant plant regeneration. In vitro method needs lower concentration of chemical agents that could be safer incomparision of in vivo.
Best wishes
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I'm wondering if you could suggest highly viscous solvent which is non-polar or slightly polar and can't form H-bond interactions.
Most preferrably: a glass forming solvent at low temperatures to be used in UV-Vis measuremens.
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Hi Sk Imadul, Thanks but i need more viscous solvents at least > 30 cP
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Based on our previous discussion, I am wondering, can we say that nanohybrids, in nanomaterials, are mixtures of two or more components that have physical or chemical bonds or generally speaking that have physical or chemical interactions between each other.
Thank you so much for your interest and time.
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Yes you can say it. But in nano-hybrid, the physical property of the individual does not remain intact. Rather, new properties generate.
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Based on our previous discussion,
I am wondering, can we define nanocomposite as a mixture of two or more components which do not have any interaction (physical nor chemical) between each other?
Thank you so much for your effort, time, and interest.
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Dear Mostafa Y Nassar,
Nanocomposites are nanomaterials that incorporate nano-sized particles into a matrix of standard material. The result of the addition of NPs is a drastic improvement in properties that can include mechanical strength, toughness and electrical or thermal conductivity. The effectiveness of the NPs is such that the amount of material added is normally only between 0.5 and 5% by weight.
There is no ambiguity in saying this that all of the components within the Nanocomposites exhibits strong molecular interactions. For better understandings i suggest you to study the following.
In above link you would see that how we have developed the nanocomposites of Amorphous and Crystalline Nano-materials.
-ALL THE BEST-
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Modification process
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Mr. Al-Mobarak,
It is modified chemically.
Physical modification means thermonuclear rection.
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How to decide intensity of which peaks of the multiplet to be subtracted?
I have read few papers but i am not clear how to quantify this rate using initial rate approximation mentioned in these papers. How the difference has taken to create second order spin mode?
Chemical Physics Letters 489 (2010) 248–253
Chemical Physics Letters 335 (2001) 176–182
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Is it rare or common in rice that such cases appear? If so, what would be the safe botanical means other than chemical and physical (light) for its control?
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Wow. Thank you a lot. The link is very useful. Apart from control measure, I too have my concern of the situation on standing paddy crop.
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How can I perform Opt with Gaussian using CAM-b3lyp introduced by Yanai et al (Chemical Physics Letters 393 (2004) 51–57) upon explicitly set alpha, beta and mi in the route input?
for example alpha=.4 , beta=.2, mi=.3
thanks,
Matteo
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The original CAM-B3LYP with ω = 0.33, α = 0.19 ,and β = 0.46 would have the following Iop values in a gaussian input file (of course the IOp provide redundant information in this case):
# CAM-B3LYP/basis iop(3/107=0330000000) iop(3/108= 0330000000) iop(3/119=0460000000) iop(3/120=0460000000) iop(3/130=01900) iop(3/131=01900)
An input for a modified version of CAM-B3LYP with ω = 0.30, α = 0.25 ,and β = 0.40 would be
# CAM-B3LYP/basis iop(3/107=0300000000) iop(3/108=0300000000) iop(3/119=0400000000) iop(3/120=0400000000) iop(3/130=02500) iop(3/131=02500)
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The scope of environmental risk assessment has been expanded from the traditional chemical and accident assessment to the inclusion of the potential harm from artificial introduction of species, both natural and genetically modified, into an ecosystem. Thus major categories of environmental hazards include chemical, physical, biological, and/or their combinations. Environmental entities can be more complex with respect to system structure and functions, although the methodologies are largely transplanted from human health risk assessment. Environmental risk assessment processes would involve problem formulation, characterization of exposure and effects, and risk characterization. The assessment can be made retrospective or predicative, depending on the risks involved and management requirements. Thus, is it possible to implemented the dynamic system methods to risk management in order to prevent environmental damage?
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Dear Dino Rimantho
Dynamic system is relation between stimulus and responds. If we know characteristic of the system we can predict the respond, especially related with the stability of the system, stability or chaotic responds. Really if we give input reference to the system we expected the result is the same as input references, if the result is different it is mean the system has a failure. Using risk management method using ISO 31000 or ISO 14971 we can analyze failure mode of your system, effect of this failure (level of severity) , probability of this failure and how to detect.
Salam
Susanto
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They are both widely used in research references but many times misunderstood.
Interphase means between or among phases of matter. Interface means between faces or surfaces. Please go further and beyond my scope in order to make notice for others.
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Interface is the two dimensional BOUNDARY between two surfaces.  Interphase is the three dimensional REGION between two phases.  Thus, we talk of the interfacial adhesion in a fiber-matrix composite being determined by the strength of the interaction between the fiber and the matrix at the interphase. There is an intrinsic problem with this definition that has to do with length scale.  What appears as an interface at large length scales (mm) may look like an interphase at smaller length scales (nm).  I think, it is for this reason, the word interphase is not that widely used in materials science, unless interphase, an intermediate phase, is being explicitly discussed.
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My 5-y-old son has playfully done an experiment. he poured a little amount of water (50-100 ml) into a balloon followed by fully air inflating. Being left at room temperature (25-30 C) for 3 days, some unexpected results are surprisingly seen. What would you think if the water is being faded while the balloon is fully air-inflated?. What is happening chemically or physically?  
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Hi, William. 
I don't understand your mean by "..., that should have been a give away indicator". please give more explanation. Notably, as I said previously, the balloon was such one that remained air-inflated for several days after the entirely fade of the water.
Regards  
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I have some difficulties to get the natural localized molecular orbital NLMO of ruthenium complexes and I would like someone to help me handle that issue.
when I perform the calculation by entering the keywords like $NBO NLMO $END or $NBO PLOT $END or $NBO DIPOLE $END with POP=NBOread for any complex, I get the same message displayed below.
NATURAL LOCALIZED MOLECULAR ORBITAL (NLMO) ANALYSIS:
Highest occupied NBOs are not at the beginning of the NBO list;
The NLMO program is not currently set up to handle this.
I don’t understand what it means. However, when I perform the same calculation with the same complex by only replacing ruthenium by iron Fe or osmium Os that share the same periodic group with Ru, the result is successful.
therefore, what can be the problem with Ru? thank you
My best regards
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Dear Alejandro Martinez,
I actually thank you very much for your help. I've tried many times your method and I found it successful. so thank you. but when I was writing the key words, I didn't add "set bace".
besides, would you tell me were you get those informations? I want now to understand the meaning of these words.
best regards
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everybody can answer one of them or both. i really need to continue my project,
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Dear Aslamic,
The enclosed article can help you. good luck in your project.
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I want to make the solid films by using these two silicone based polymers (separately).I am not able to find out the suitable and efficient curing agents which can cross link these polymers chemically or physically  to form a film 
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I read about the moisture effect in its MSDS. I tried to make the solid films in open environment at around 25-28oC , it took around 40 hours to make a brittle film 
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The equilibrium pressure for a metal hydride during absorption process given by the Van't Hoff when modified to include slope correction and hysteresis factor is:
Peq= exp{(S/R)-(H/(R*T))+(phi + phi0)*tan(pi*(c/cf-0.5)) +beta/2 }
where c is the concentration of hydrogen at any time t whereas cf is the concentration of hydrogen in the metal bed upon saturation.
Now my problem is that at t=0 or t upto 0-100 s the concentration of hydrogen in the bed is very low. This is making my tan term infinite as it becomes tan(-pi/2). Also as t increases around 400 s to 500 s, c becomes equal to cf and again my tan term gives tan(pi/2). Therefore, my model is not working. Any ideas where I am going wrong?
phi=0.35, phi0=0.15 and beta=0.2
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You are doing nothing wrong. At x->0 your equation gives ln P  = -∞ from which we obtain P = 0.
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How to decide the cut-off distance for the Lennard-Jones potential in Molecular simulation dynamics? 
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Usually the cutoff is set to 2.5xSigma or less than half of the simulation box length. A good book to start with is by Frenkel and Smit.
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Biocontrol, chemical, physical and combination control.
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1. Biological control using PGRB/F such as bacillus and mycorrhizal antagonists
2. Drenching using copper and sulphur based fungicides
3. Cultural practices such as roguing diseased plants, solarization and non-host plant cropping
4. Using biofumogants
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If anyone is aware of a research group / lab in US where femtosecond time resolved photoluminescence can be done, please let me know.
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There are likely many labs where this occurs. Run a google scholar search of "unconverted PL" if you need sub-ps resolution. If ps resolution is good enough, a Streak camera may suffice. You may also look into studies of 2D Transition metal dichalcogenides or other material systems where the PL lifetime are quite short. That should give you an idea of the groups that are active.
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I am trying to understand the possible chemical bonding between the carboxylic group and SDBS. Is there anyone here to help me out about this matter? Thanks,
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SDBS seems effectively to be sodium dodecyl benzene sulfonate, so Saeed is correct in writing a possible H-bond between the sulfonate anion and the acidic H. This interaction is only possible with the unionized RCOOH, for example in the solid state or in some organic solvent which cannot compete for H-bonding (I may discuss this point further if necessary). The H-bond is seen as "a non-covalent bond". "Chemical bonding" is not well defined in this context, but a covalent bond is unlikely between these two molecules.
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Rice soil specially wetland rice soil is different from other upland crop soil. There are many chemical, physical and biological changes occur in rice soil. On the other hand rice plant is a semi-aquatic plant. In this regard characteristics of rice soil must be unique compared to other soil.
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Dear Dr. Islam (Aminul),
Dr. F. N. Ponnamperuma*, the celebrated Rice Soil Chemist and former Principal Soil Chemist, International Rice Research Institute (IRRI), Los Banos, Philippines listed the following following chemical characteristics of fertile wetland rice soils:
pH 5.0-6.5, ECe (mS/cm) <2, Eh (after submergence, in volt) +0.2 to -0.2, org matter (%) 2.0-3.5, total N (%) >0.2, total P (%) >0.02, Olsen P (mg/kg) >10, exch K (mmol/kg) >2, avail S (mg/kg) >10, CEC (mmol/kg) >200, clay composition >50% montmorillonite, active Fe (%) >0.5%, active Mn (%) >0.05, avail Zn (mg/kg) >1, avail B (mg/kg) <5.
(*I was privileged to conduct my Ph.D. thesis research under the guidance of Dr. F. N. Ponnamperuma at IRRI, Los Banos, Philippines during early 1980s).
Ref: Ponnamperuma FN (1981) Properties of Tropical Rice Soils. Text of a Series of Lectures Delivery to Graduate Students at the Topical Agriculture College, H. Cardenas, Tabasco, Mexico on 23-25 July 1981.
Hope you find this input useful. 
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I am going to build complete spherical copper nano particle in the size range of 1-10 nm.
but i don't know, how many copper can build complete spherical shape, which the the surface atoms are in the same situation.
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Up-vote on the response of Aras Kartouzian.
To elaborate, it sounds like you are interested in the magic clusters. Magic clusters are clusters of atoms consisting of some integer number of complete shells of atoms about a single central atom. Suppose you take a single atom and surround it with exactly one layer of atoms in a close-packed arrangement. It takes exactly 12 balls to completely surround a central ball (Try it with tennis balls, if you can find enough tennis balls.) This is smallest magic cluster. It has one central atom and 12 surface atoms for a total of 13.  If we add a second shell of atoms, it takes 42 atoms to complete the second layer. This cluster has 55 atoms total, 13 in the interior and 42 on the surface. It takes 92 atoms to make a third shell. This cluster has a total of 147 atoms. The next cluster has 309 atoms. The sequence is: 1, 13, 55, 147, 309... These are the "centered icosahedral numbers".
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Please give me the procedure to make porous graphite from solid graphite. Thanks in advance. 
Regards, 
-Jayesh
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Dear Jayesh
Interesting to your question I want to ask the result of last year experiments as "impregnation in H3PO4 (85% solution) at 550°C or in molten KOH at 800°C" or "gasification in a stream of water vapour at 850°C, or of CO2 at 900°C".
If it is possible say what happened.
Thanks a lot
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Hi,
i'm trying to calculate dipole moment function the ground state of AlCl. i'm using ACPF method, however i'm not sure if it's the best method. any one knows which method is the best for this particular calculation. second, is it necacarry to specify occupied, closed and core shells for acpf calculation(since without occ, closed and core cards , it runs a lot faster, but i'm not sure it's accurate enough). ? below is the input i'm using for this calculation. any one can please on the my input file? thank you
***,AlCl moments
r=[1.53,1.55,1.57,1.59,1.61,1.63,1.65,1.67,1.69,1.71,1.73,1.75,1.77,1.79,1.81,1.83,1.85,1.87,1.89,1.91,1.93,1.95,1.97,1.99,2.01,2.03,2.05,2.07,2.09,2.11,2.13,2.15,2.17,2.19,2.21,2.23,2.25,2.27,2.29,2.31,2.33,2.35,2.37,2.39,2.41,2.43,2.45,2.47,2.49,2.51,2.53,2.55,2.57,2.59,2.61,2.63,2.65,2.67,2.69,2.71,2.73,2.75,2.77,2.79,2.81,.83,2.85,2.87,2.89,2.91,2.93,2.95,2.97,2.99,3.01,3.03,3.05,3.07,3.09]
do l=1,#r
basis=av5z
print,orbitals,civector
geometry={Al;Cl,Al,$r(l)}
{rhf;occ,9,3,3,0;wf,30,1,0} !rhf for sigma state
$method=[multi,acpf] ! 2 methods to be used are CASSCF, then ACPF
erhf(l)=rhfenergy
t=0
t=t+1
{multi;closed,4,1,1,0 ;occ,10,4,4,0; !active space: 4sigma, 2pi, 1 delta
wf,30,1,0 } !state averaged casscf for sigma, pix, piy states
gexpec,dm !calculate dipole moments for CASSCF
dip_expect(t)=dmz*todebye !save CASSCF dmz and convert to Debye
e(t)=energy
t=t+1
{acpf;closed,4,1,1,0 ;occ,10,4,4,0;core,2,0,0,0;wf,30,1,0; !mrci for sigma
save,5000.2} !save wavefunction
e(t)=energy
gexpec,dm !calculate dipole moments for acpf
dip_expect(t)=dmz*todebye !save acpf dmz and convert to Debye
t=0
n=#method
do m=1,#method
t=t+1
energ(m)=e(t)
bond(m)=r(l)
enddo
table,method, bond,energ,dip_expect
title,AlCl results, r=$r(l), theta=0 degree, basis=$BASIS
end do
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Dear Dr.Monajjemi
i had a calculation using MRCI method. i will send the input and output files to you by email. please have a look at it and give your comments on it. 
thank you 
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Simulations, Lammps
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Yes, I had calculated it using Gaussian, considering an isolated molecule.  But, wanted to obtain an answer considering many molecules (making a system) and then find out.
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Aromatic carbon differs from aliphatic carbon.  How can we obtain the RDF of each and every carbon atom using RDF command in LAMMPS.
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No. RDFs are normally for solutions. I am suggesting you to read some sample articles that have used molecular dynamics or Monte Carlo simulations for similar compounds to yours in order to have an estimation about the required number of molecules and methods of calculations with reliable results.
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I am a PhD student from VNIT, Nagpur and I am working on rare earth containing glasses. I want suggestions for the calculation of Judd-Ofelt  parameters.
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The following (Judd-Ofelt Theory: Principles and Practices) I hope it helps you to solve your problem:
Judd-Ofelt Theory: Principles and Practices
1. Judd-Ofelt Theory: Principles and Practices Brian M. Walsh NASA Langley Research Center National Aeronautics and Erice, Italy (June 2005) Space Administration
2. Part I: Principles What is the Judd-Ofelt Theory? Based on static, free-ion and single configuration approximations: • static model - Central ion is affected by the surrounding host ions via a ‘static’ electric field. • free ion model - Host environment treated as a perturbation on the free ion Hamiltonian. • single configuration model - Interaction of electrons between configurations are neglected. The Judd-Ofelt theory describes the intensities of 4f electrons in solids and solutions. The remarkable success of this theory provides a sobering testament to simple approximations. National Aeronautics and International School of Atomic and Molecular Spectroscopy Space Administration Erice, Italy (June 2005)
3. Distribution of Citations by Year 200 B.R. Judd, Phys. Rev. 127, 750 (1962). G.S. Ofelt, J. Chem. Phys. 37, 511 (1962). 150 ~ 2000 citations (1962-2004) Number of citations 100 50 0 62 72 82 92 02 Year National Aeronautics and International School of Atomic and Molecular Spectroscopy Space Administration Erice, Italy (June 2005)
4. Referenced in 169 Journal Titles Top 20 Titles # of citations PHYSICAL REVIEW B 127 JOURNAL OF NON-CRYSTALLINE SOLIDS 108 JOURNAL OF APPLIED PHYSICS 90 JOURNAL OF CHEMICAL PHYSICS 83 JOURNAL OF ALLOYS AND COMPOUNDS 81 JOURNAL OF LUMINESCENCE 77 JOURNAL OF PHYSICS-CONDENSED MATTER 58 MOLECULAR PHYSICS 57 CHEMICAL PHYSICS LETTERS 48 OPTICAL MATERIALS 43 JOURNAL OF THE OPTICAL SOCIETY OF AMERICA B 38 JOURNAL OF PHYSICS AND CHEMISTRY OF SOLIDS 35 PHYSICA STATUS SOLIDI A-APPLIED RESEARCH 33 OPTIKA I SPEKTROSKOPIYA 30 IEEE JOURNAL OF QUANTUM ELECTRONICS 27 PHYSICS AND CHEMISTRY OF GLASSES 27 OPTICS COMMUNICATIONS 26 SPECTROCHIMICA ACTA PART A 26 INORGANIC CHEMISTRY 24 JOURNAL OF THE AMERICAN CERAMIC SOCIETY 19 National Aeronautics and International School of Atomic and Molecular Spectroscopy Space Administration Erice, Italy (June 2005)
5. Prelude “Lanthanum has only one oxidation state, the +3 state. With few exceptions, this tells the whole boring story about the other 14 lanthanides.” G.C. Pimentel & R.D. Sprately, quot;Understanding Chemistryquot;, Holden-Day, 1971, p. 862 http://www.chem.ox.ac.uk/icl/heyes/LanthAct/I1.html ( some amusing mnemonics for the Lanthanides and Actinides) So much for ‘Understanding Chemistry’… Let’s do some physics! National Aeronautics and International School of Atomic and Molecular Spectroscopy Space Administration Erice, Italy (June 2005)
6. Ions in Solids Solids • insulators (not semiconductors) • bandgaps are > 5ev (VUV photon) • produce a crystal field Ions • replace host ions substitutionally • transition metal and lanthanide series • unfilled electronic shells • Stark splitting from crystal field • optical transitions occur within bandgap Examples • Nd:Y3Al5O12 - Er:fiber - Cr:Al2O3 (Ruby) National Aeronautics and International School of Atomic and Molecular Spectroscopy Space Administration Erice, Italy (June 2005)
7. Atomic Structure of Laser Ions National Aeronautics and International School of Atomic and Molecular Spectroscopy Space Administration Erice, Italy (June 2005)
8. Atomic Interactions 4f 95d Hc >> Hso (LS-coupling) Hc << Hso (jj-coupling) Hc ≈ Hso (Intermediate coupling) !1 !2 !3 !4 5S 5I 4f10 5F 4 5I 5 5I 5I Configurations 6 Ho = central field 5I Terms 2S+1 L 7 (Electrons in field 5I Hc = Coulomb field 8 of the nucleus) (Mutual repulsion Levels 2S+1L J of electrons) Hso = spin orbit (Coupling between spin and orbital Stark Levels angular momentum) Vo = crystal field Ho >Hc , Hso >Vo (Electric field of host) Hund’s Rules*: F. Hund, Z. Phys. 33, 345 (1925) 1.) Lowest state has maximum 2S+1 2.) Of these, that with largest L will be lowest 3.) Shells < 1/2 full (smallest J is lowest), Shells > 1/2 full (largest J is lowest) *These rules apply only to the ground state, not to excited states. National Aeronautics and International School of Atomic and Molecular Spectroscopy Space Administration Erice, Italy (June 2005)
9. Transitions and Selection Rules • Not all transitions between atomic states that are energetically feasible are quot;allowed”. • Forbidden transitions are “forbidden*” to first order, which means they may occur in practice, but with low probabilities. • Selection rules for transitions depend on type of transition – Electric dipole (E1) – Electric quadrupole (E2) – Magnetic dipole (M1) • Wavefunctions must have correct parity (Laporte’s rule) • Symmetry plays a role in selection rules – Vibronics, crystal field, other perturbing effects. * This nomenclature is historically embedded, although not entirely accurate. National Aeronautics and International School of Atomic and Molecular Spectroscopy Space Administration Erice, Italy (June 2005)
10. Multipole Selection Rules ! ! Electric dipole operator (E1) P = quot;e! ri (odd operator) i ! equot; ! ! Magnetic dipole operator (M1) M =quot; ! I i + 2si 2mc i (even operator) ! ! ! ! 1 Q = $ ! k # ri quot;ri 2 i ( ) Quadrupole operator (E2) (even operator) S L J (No 0 ↔ 0) Parity Electric Dipole ΔS = 0 ΔL= 0, ±1 ΔJ = 0, ±1 opposite Magnetic dipole ΔS = 0 ΔL= 0 ΔJ = 0, ±1 same Electric quadrupole ΔS = 0 ΔL = 0, ±1, ±2 ΔJ = 0, ±1, ±2 opposite National Aeronautics and International School of Atomic and Molecular Spectroscopy Space Administration Erice, Italy (June 2005)
11. A Brief History of Parity Otto Laporte (1902-1971) empirically discovered the law of parity conservation in physics. He divided states of the iron spectrum into two classes, even and odd, and found that no radiative transitions occurred between like states: O.Laporte, Z. Physik 23 135 (1924). Eugene Paul Wigner (1902-1995) explicitly formulated the law of parity conservation and showed that Laporte’s rule is a consequence of the invariance of systems under spatial reflection. E. P. Wigner, “Gruppentheorie und Ihre Anwendung auf die Quantenmechanik der Atomspektren”. Braunschweig:F. Vieweg und Sohn, 1931. English translation by J. J. Griffin. New York: Academic Press, 1959. Wavefunctions are classified as even (+1 parity) or odd (-1 parity). By convention, the parity of a photon is given by the radiation field involved: ED ( -1), MD (+1). For mathematical reasons, the parity of any system is the product of parities of the individual components. If the initial and final wavefunction have same parity (±1): ED: ±1 = (-1)(±1) Parity is NOT conserved. Transition is forbidden! MD: ±1 = (+1)(±1) Parity IS conserved. Transition is allowed! Laporte Rule: States with even parity can be connected by ED transitions only with states of odd parity, and odd states only with even ones. National Aeronautics and International School of Atomic and Molecular Spectroscopy Space Administration Erice, Italy (June 2005)
12. Parity Selection Rules ED allowed ED forbidden MD forbidden MD allowed EQ forbidden EQ allowed s → p s → s p → d d → d d → f p → p f → g f → f s → f g → g p → g Orbital s p d f g Angular momentum ! 0 1 2 3 4 !- odd # electrons ! = ( quot;1)# i ! even odd even odd even !- even # electrons i odd even odd even odd National Aeronautics and International School of Atomic and Molecular Spectroscopy Space Administration Erice, Italy (June 2005)
13. Historical Perspective I • J.H. Van Vleck - J. Phys. Chem. 41, 67-80 (1937) (The Puzzle of Rare-Earth Spectra in Solids) – Why are spectral lines in rare earths observable? – Electric dipole(E1), magnetic dipole(M1), quadrupole(E2)? – Concludes a combination is possible. – Suggests that crystal field makes mixed parity states (E1). • L.J.F. Broer, et al., - Physica XI, 231- 250 (1945) (On the Intensities and the multipole character in the spectra of the rare earth ions) – Considers all mechanisms. – Concludes quadrupole radiation is too weak. – Considers magnetic dipole , but as a special case only. – ED transitions dominate as suggested by Van Vleck! National Aeronautics and International School of Atomic and Molecular Spectroscopy Space Administration Erice, Italy (June 2005)
14. Historical Perspective II • G. Racah - Phys. Rev. 76, 1352 (1949) (Theory of Complex Spectra IV) – Applies group theory to problems of complex spectra – Creates the tools required to make detailed spectroscopic calculations involving states of the 4f shell. – Revolutionizes the entire subject of rare earth spectroscopy. • Subsequent developments – Racah’s methods applied to crystal field theory. – Ideas of Racah applied to transition metal ions (Griffiths). – Practical calculations assisted by computer generated tables of angular momentum coupling coefficients. • By 1962 the stage was set for the next major development: The Judd-Ofelt theory of the intensities of RE transitions. National Aeronautics and International School of Atomic and Molecular Spectroscopy Space Administration Erice, Italy (June 2005)
15. The Stage is Set “I suggest that the coincidence of discovery was indicative that the time was right for the solution of the problem.” Brian G. Wybourne “The fascination of rare earths - then, now and in the future” Journal of Alloys and Compounds 380, 96-100 (2004) National Aeronautics and International School of Atomic and Molecular Spectroscopy Space Administration Erice, Italy (June 2005)
16. Judd and Ofelt Publish (1962) National Aeronautics and International School of Atomic and Molecular Spectroscopy Space Administration Erice, Italy (June 2005)
17. States of an Ion in the Crystal The Crystal field, V, is considered as a first order perturbation that ‘admixes’ in higher energy opposite parity configurations: } quot;a V quot;# ! a = quot;a + % quot;# # Ea $ E# Mixed Parity quot;# V quot;b States ! b = quot;b + % quot;# # Eb $ E# ! ! ! ( +a V +* quot; + * P +b + a P + * + * V +b % quot; ,a P,b = !' + $ * quot; & Ea ) E * Eb ) E* quot; # φa and φb have the same parity (4f N states) φβ has opposite parity (4f N-15d states) V is the crystal field (treated as a perturbation) ! P is the electric dipole operator National Aeronautics and International School of Atomic and Molecular Spectroscopy Space Administration Erice, Italy (June 2005)
18. Tensor Forms of Operators Racah defined irreducible tensors, C(k), which transform as spherical harmonics, having the components: quot; 4! % 1/2 Cq ) (k =$ # 2k + 1 ' Ykq & The position vector r is a tensor of rank 1, defined as r = rC (1) Dipole Operator Crystal Field ! ! Standard Form P = quot;e! ri V = ! ! Akq ri kYkq (quot; i , # i ) i i kq Dq = !equot; ri #Cq % D p ) = ! Atp ! rit quot;C p ) $ (1) (1) (t (t Tensor Form $ & i # % i i tp i Note: t is odd since only odd order terms contribute to parity mixing. Even order terms are responsible for energy level splitting. National Aeronautics and International School of Atomic and Molecular Spectroscopy Space Administration Erice, Italy (June 2005)
19. J-O Theory Assumptions 1&2 1.) The states of φβ are completely degenerate in J. Assume an average energy for the excited configuration above the 4fN, that is, the 4f N-15d. 2.) The energy denominators are equal ( Ea-Eβ = Eb-Eβ ) Assume that the difference of average energies, ΔE(4f-5d), is the same as the difference between the average energy of the 4f N-15d and the energy of the initial and final states of the 4fN These assumptions are only moderately met, but offer a great simplification. Otherwise, the many fold sum of perturbation expansions is not suitable for numerical applications. National Aeronautics and International School of Atomic and Molecular Spectroscopy Space Administration Erice, Italy (June 2005)
20. 4f and 4f N N-15d configurations 35 4fn configuration 30 4fn-15d1 configuration 25 Energy(×104cm-1) 20 Lanthanides in YLF: K. Ogasawara et al., 15 J. Solid State Chem. vol. 178, 412 (2005 10 5 0 Ce Pr Nd Pm Sm Eu Gd Tb Dy Ho Er Tm Yb 58 59 60 61 62 63 64 65 66 67 68 69 70 Atomic Number & Symbol National Aeronautics and International School of Atomic and Molecular Spectroscopy Space Administration Erice, Italy (June 2005)
21. Advantages of the Assumptions I.) Energy denominators can be removed from the summations II.) Closure can be used ( the excited configuration forms a complete orthonormal set of basis functions) #! quot; !quot; = 1 quot; III.) Angular parts of the electric dipole operator and crystal field Cq = ! C (1) !! U q (1) (1) and C p ) = ! C (t ) !! U p ) (t (t can be combined into an effective tensor operator %t 1 quot; ( + t 1 quot; . (quot; ) U U (1) (t ) = # (!1) 1+t + quot; +Q (2 quot; + 1) & )- 0 UQ ' ! ! !$ * , p q Q / q p quot;Q The 3j symbol ( ) is related to the coupling probability for two angular momenta. The 6j symbol { } is related to the coupling probability for three angular momenta. The Wigner 3-j and 6-j symbols are related to Clebsch-Gordon coupling coefficients. National Aeronautics and International School of Atomic and Molecular Spectroscopy Space Administration Erice, Italy (June 2005)
22. Reduced Matrix Elements Nevertheless, combining the tensors for the electric dipole and crystal field terms in a combined tensor operator, UQ! ) , ( can be simplified further by the Wigner-Eckart Theorem: Geometry Physics (transformations) (Dynamics) % J quot; J# ( N f N! JM UQquot; ) f N! # J #M # = ($1)J $ M ' ( f ! J U ( quot; ) f N! # J # & $M Q M #* ) The matrix elements on the right side have been tabulated: “Spectroscopic Coefficients of the p N, d N, and f N Configurations,” C.W. Nielson and G.F. Koster, M.I.T Press, Cambridge, MA (1963). The 3-j and 6-j symbols have also been tabulated: “The 3-j and 6-j symbols,” M. Rotenberg, R, Bivens, N. Metropolis, J.K. Wooten Jr., Technology Press, M.I.T, Cambridge, MA (1959). National Aeronautics and International School of Atomic and Molecular Spectroscopy Space Administration Erice, Italy (June 2005)
23. “Full Judd-Ofelt Theory” ! 1 * * J( $ () 1)J )M )Q (2* + 1)AtpY (t , * )' t $' J , a P , b = )e!! % %q Q quot;% quot; + a U ( * ) +b tp *Q & p quot;% ) M #& Q M (quot; # n! r nquot;!quot; nquot;!quot; r t n! &1 t ! ) Where, Y (t, ! ) = 2% ! C (1) !quot; !quot; C (t ) ! ' * n! Ea # E$ ( ! !quot; ! + This is the “Full Solution” of the Judd-Ofelt Theory. This form can be used to find electric dipole matrix elements between mixed parity states for individual Stark level to Stark level transitions. Application of “Full Judd-Ofelt Theory”: R.P. Leavitt and C.A. Morrison, “Crystal-field Analysis of triply Ionized lanthanum trifluoride. II. Intensity Calculations.” Journal Of Chemical Physics, 73, 749-757 (1980). National Aeronautics and International School of Atomic and Molecular Spectroscopy Space Administration Erice, Italy (June 2005)
24. J-O Theory Assumptions 3&4 Oscillator strength (f-number) for electric dipole transition: 2 8+ mc 2 (n + 2% 2 ! ! 2 f = n& & 3n ## )JM P ) quot;J quot;M quot; 3quot;* (2 J + 1)e 2 ' $ L.J.F. Broer, et al., - Physica XI, 231- 250 (1945) 3.) Sum over Stark split J-levels (Assumes all Stark levels equally populated) $ J ! Jquot; ' $ J !quot; J quot; ' 1 *& Q M quot; ) & #M = + + Qquot; M quot; ) 2 ! + 1 !! quot; QQ quot; M = -J, -(J-1), …, 0, …, (J-1), J MM quot; % #M (% ( 4.) Sum over dipole orientations (Assumes optically isotropic situation) quot;1 ! t % quot;1 ! t) % 1 ($ q Q p' $ q Q = * * p) ' 2t + 1 tt ) pp ) Q = 0 (π-polarized, E ⊥ c) Q # &# & Q = ±1 (σ-polarized, E || c) National Aeronautics and International School of Atomic and Molecular Spectroscopy Space Administration Erice, Italy (June 2005)
25. “Approximate Judd-Ofelt Theory” 2 2 8! mc 2 # n + 2& 2 Atp ) )) 2 (quot; ) f = n% (2 quot; + 1) Y (t, quot; ) * a U 2 *b 3hquot; (2J + 1) $ 3n ( ' quot; = 2, 4,6 p t =1, 3,5 (2t + 1) 2 Atp Defining Ωλ as: !quot; = (2 quot; + 1)# # (2t + 1)Y 2 (t, quot; ) Judd-Ofelt p t =1, 3,5 parameters 2 8! 2 mc # n2 + 2 & + 2 (quot; ) f = n% )quot; * a U *b Oscillator 3hquot; (2J + 1) $ 3n ( ' quot; = 2, 4,6 strength $ 2 (quot; ) SED = !quot; # a U #b is called the Linestrength. quot; = 2, 4,6 This is the “Approximate Solution” of the Judd-Ofelt theory. It can be used to find electric dipole matrix elements between mixed parity states for manifold to manifold transitions. National Aeronautics and International School of Atomic and Molecular Spectroscopy Space Administration Erice, Italy (June 2005)
26. Judd-Ofelt Parameters In principle, the Judd-Ofelt parameters can be calculated “ab-initio” if the crystal structure is known, and hence, Atp: 2 Atp !quot; = (2 quot; + 1)# # Y 2 (t, quot; ) p t =1, 3,5 (2t + 1) n! r nquot;!quot; nquot;!quot; r t n! &1 t ! ) Y (t, ! ) = 2% ! C !quot; !quot; C ! ' (1) (t ) * n! Ea # E$ ( ! !quot; ! + # ! 1 !! & ! C (1) !! = (quot;1)! % ( 2! + 1)1/2 ( 2!! + 1)1/2 $0 0 0( ' # !! t ! & ! C (t ) !! = (quot;1)!! % ( 2!! + 1)1/2 ( 2! + 1)1/2 $ 0 0 0( ' 3-j and 6-j symbols can be calculated for ! = 3 (4f ) and !! = 2 (5d) Radial integrals between configurations and crystal field components, Atp, are difficult to calculate. Instead, Judd-Ofelt parameters are usually treated as phenomenological parameters, determined by fitting experimental linestrength data. National Aeronautics and International School of Atomic and Molecular Spectroscopy Space Administration Erice, Italy (June 2005)
27. Intermission “The two papers of 1962 represent a paradigm that has dominated all further work on the intensities of rare earth transitions in solutions and solids up to the present time.” Brian G. Wybourne “The fascination of rare earths - then, now and in the future” Journal of Alloys and Compounds 380, 96-100 (2004). National Aeronautics and International School of Atomic and Molecular Spectroscopy Space Administration Erice, Italy (June 2005)
28. Part II: Practices The Judd-Ofelt theory, in practice, is used to determine a set of phenomenological parameters, Ωλ (λ=2,4,6), by fitting the experimental absorption or emission measurements, in a least squares difference sum, with the Judd-Ofelt expression. Absorption Least Squares Judd-Ofelt Collect Matrix Measurements Fitting Parameters Elements # ( )=0 ! quot;2 Ωλ manifold ! (quot; )d quot; |<U(λ)>|2 !# k Transition τr and β Probabilities AJ′J The Judd-Ofelt parameters can then be used to calculate the transition probabilities, AJ′J, of all excited states. From these, the radiative lifetimes, τr, and branching ratios, β, are found. National Aeronautics and International School of Atomic and Molecular Spectroscopy Space Administration Erice, Italy (June 2005)
29. Selection Rules Revisited ! j1 j2 j3 $ #1 t ! & ! j1 j2 j3 $ $ J ! Jquot; ' quot; %=0 $ ' #m =0 #! 1 !2 !3 & ! !quot; ! ( quot; 1 m2 m3 & % & #M % Q M quot;) ( % Unless: Unless: J! quot; J # $ ! = 2, 4, 6 ji ! 0 ji ! 0 t = 1, 3, 5, 7 !J quot; 6 !i ! 0 mi quot; ji ! quot;1+ t !L quot; 6 j1 quot; j2 # j3 # j1 + j2 m1 + m2 + m3 = 0 !S = 0 !! quot; ! # 1 ji , mi (1, 1/2 integer) ! 2 quot; ! 3 # j1 # ! 2 + ! 3 J = 0 : J # $ even Only d or g j1 # j2 quot; j3 quot; j1 + j2 ! 1 quot; ! 3 # j2 # ! 1 + ! 3 orbitals can J # = 0 : J $ even mix parity ! 1 quot; ! 2 # j3 New Selection Rules From Judd-Ofelt Theory S L J (No 0 ↔ 0) Parity Electric Dipole ΔS = 0 ΔL ≤ 6 ΔJ ≤ 6 opposite ΔJ = 2,4,6 (J or J′ = 0) Magnetic dipole ΔS = 0 ΔL = 0 ΔJ = 0, ±1 same Electric quadrupole ΔS = 0 ΔL = 0, ±1, ±2 ΔJ = 0, ±1, ±2 opposite National Aeronautics and International School of Atomic and Molecular Spectroscopy Space Administration Erice, Italy (June 2005)
30. Judd-Ofelt Analysis I Matrix Forms 3ch(2J + 1) # 3 & 2 Sm = 8! e quot; 3 2 n% 2 $ n + 2( ' * manifold ) (quot; )d quot; S jm Components of 1 x N matrix 3 $ S = quot; M ij !i 2 (quot; ) SED = !quot; # a U #b t j quot; = 2, 4,6 i =1 N = number of tramsitions Mij - components of N x 3 matrix for square matrix elements of U ( 2 ), U ( 4 ), U (6 ) Ωi - components of 1 x 3 matrix for Judd-Ofelt parameters Ω 2, Ω 4, Ω 6 2 N % m 3 ( ! = $ ' S j quot; $ M ij #i * 2 LEAST SQUARES DIFFERENCE j =1 & i =1 ) ( ) = $2 ! quot;2 N & m 3 ) ( !(0) = M †M ) quot;1 !# k % ' M jk ( S j $ % M ij #i + = 0 MINIMIZED * M †Sm j =1 i =1 Judd-Ofelt Parameters 1 x 3 Matrix National Aeronautics and International School of Atomic and Molecular Spectroscopy Space Administration Erice, Italy (June 2005)
31. Judd-Ofelt Fit (Ho:YLF) 6.0 Visible absorption spectrum of Ho:YLF 5.0 !ab (10-20 cm2) (! and quot; polarization) 4.0 3.0 2.0 1.0 0.0 280 330 380 430 480 530 580 630 680 Wavelength (nm) National Aeronautics and International School of Atomic and Molecular Spectroscopy Space Administration Erice, Italy (June 2005)
32. Judd-Ofelt Analysis II With the Judd-Ofelt parameters, the ED transition probability for any excited state transition (J´→ J) can be calculated 64quot; 4 e2 * $ n2 + 2 ' 2 - Transition probability A J !J = 3 ,n & SED + n SMD / 2 3h(2 J ! + 1)# , % + 3 ) ( / . (Einstein A coefficient) 1 = # AJ quot;J Radiative lifetime !r J (natural decay time) AJ quot;J Branching ratio ! J quot;J = # AJ quot;J (fraction of total photon flux) J MD transitions are normally orders of magnitude smaller than ED transitions. Since ED transitions for ions in solids occur as a result of a perturbation, some MD transitions will make significant contributions. National Aeronautics and International School of Atomic and Molecular Spectroscopy Space Administration Erice, Italy (June 2005)
33. Magnetic Dipole Contributions Magnetic dipole contributions can be easily calculated using an appropriate set of intermediate coupled wavefunctions for transitions obeying the selection rules ( ΔS = 0, ΔL= 0, ΔJ = 0, ±1). 2 ' quot; $ ! ! f n [SL]J L + 2S f n [S !L!]J ! 2 S MD =% quot; MD Linestrength & 2mc # 1/ 2 LS-coupled 2 - (J + 1) . (L . S ) * ! ! ! n '- ! 2 2 *$ f [SL]J L + 2 S f [S /L/]J / = &+(S + L + 1) . (J + 1) + matrix elements n 2 ((# !+ %, , 4(J + 1) )(! )quot; G.H. Shortley Phys. Rev. 57, 225 (1940) Intermediate coupled wavefunctions f n [SL]J = ! C ( S, L ) f n SLJ SL (linear combination of LS states) ! ! n quot; ! n f [SL]J L + 2S f [S quot;Lquot;]J quot; = n ! C (S , L )C (S , L ) f SLJ L + 2S f S quot;Lquot;J quot; n SL ,S quot;Lquot; Intermediate coupled matrix elements National Aeronautics and International School of Atomic and Molecular Spectroscopy Space Administration Erice, Italy (June 2005)
34. Judd-Ofelt Results (Ho:YLF) National Aeronautics and International School of Atomic and Molecular Spectroscopy Space Administration Erice, Italy (June 2005)
35. Testing the J-O theory Branching ratios can be measured directly from emission spectra. Use reciprocity of emission and absorption to indirectly “measure” the radiative lifetimes. Z! *$ hc ' - ! em ( quot; ) = ! ab ( quot; ) exp ,& EZL # ) kT / D.E. McCumber Zu +% quot;( . Phys. Rev. 136, A954 (1964). By comparing the measured emission cross section quot;5 3I& ( quot; ) ! (quot; ) = P. Moulton 8# cn 2 ($ r / % ) + ' 2I ! ( quot; ) + I # ( quot; ) ) quot; d quot; ( * J. Opt. Soc Am. B 3, 131 (1986). with the emission cross section derived from absorption, the quantity (τr/β) can be determined and the radiative lifetime extracted for comparison with the Judd-Ofelt theory National Aeronautics and International School of Atomic and Molecular Spectroscopy Space Administration Erice, Italy (June 2005)
36. Reciprocity of Ho:YLF (5I7 ↔ 5I8) National Aeronautics and International School of Atomic and Molecular Spectroscopy Space Administration Erice, Italy (June 2005)
37. Accuracy of J-O theory (Ho&Tm) Results are somewhat better in Ho3+ than Tm3+. Overall, the accuracy of the Judd-Ofelt theory is quite good, despite the approximations used. National Aeronautics and International School of Atomic and Molecular Spectroscopy Space Administration Erice, Italy (June 2005)
38. Special Case I: Pr3+ ion (A failure of the standard Judd-Ofelt theory?) Pr3+ ions suffer from several problems in applying Judd-Ofelt theory 1.) Large deviations between calculations and experiment observations. 2.) Negative Ω2 sometimes obtained, in opposition with definition. 3.) Ω2, Ω4, Ω6 highly dependent on transitions used in fit. These inconsistencies are usually explained by the small energy gap (~ 50,000 cm -1) between the 4f N and 4f N-15d configurations in Pr3+ Solutions: 1.) Modify the standard theory: quot;!# = quot;# &1 + ( $Eij % 2E4 f ) ( E5d % E4 f ) ( ' 0 ) E.E. Dunina, et al., Sov. Phys. Solid State 32, 920 (1990). 2.) Remove 3H4 → 3P2 from the fit, or augment fit with fluorescence β’s R.S.Quimby, et al., J. Appl. Phys. 75, 613 (1994). 2 N +% ( . 3.) Use normalized least squares fitting procedure: ! = $ -' S jm quot; $ M ij #i * ! i 0 2 j =1 , & i ) / P. Goldner, et al., J. Appl. Phys. 79, 7972 (1996). National Aeronautics and International School of Atomic and Molecular Spectroscopy Space Administration Erice, Italy (June 2005)
39. Special Case II: Eu3+ ions (Beyond the standard Judd-Ofelt theory)  The ED transitions 7F0 ↔ 5DJodd, 7FJodd ↔ 5D0 and 7F0 ↔ 5D0 in Eu3+ are “forbidden” in standard JO-theory. They violate the selection rules: • ΔS = 0 G.W. Burdick, J. Chem Phys. 91 (1989). • If J = 0 then J′ is even • If J′ = 0 then J is even M. Tanaka, Phys. Rev. B, 49, 16917 (1994). •0↔0 T. Kushida, Phys. Rev B, 65, 195118 (2002).  These transitions are primarily MD, but all three do occur as ED with low intensity in the spectra of some materials.  This implies that the standard Judd-Ofelt theory is incomplete. These ‘forbidden’ transitions provide an ideal testing ground for extensions to the standard theory.  What mechanism or mechanisms could be responsible? Are they meaningful! National Aeronautics and International School of Atomic and Molecular Spectroscopy Space Administration Erice, Italy (June 2005)
40. Europium’s Peculiar Properties (Adventures of The Atom) The Atom, Issue 2 August 1962 (DC Comics) Coincident with the publications of Judd and Ofelt, who were both also interested in Europium’s peculiar properties. National Aeronautics and International School of Atomic and Molecular Spectroscopy Space Administration Erice, Italy (June 2005)
41. Extensions I 1) J-mixing: The wavefunctions of the J ≠ 0 state are mixed into the J = 0 state by even parity terms of the crystal field. Explains the radiative transition 7F3 ↔ 5D0 in Eu3+. J.E. Lowther, J. Phys. C: Solid State Phys. 7, 4393 (1974). 2) Electron correlation: Electrostatic interaction between electrons is taken into account. Goes beyond the single configuration approximation and electron correlation within the 4f shell is incorporated by configuration interactions. Contributes to “allowing” the “forbidden” 0 ↔ 0 transitions such as 7F0 ↔ 5D0 in Eu3+. K. Jankowski, J. Phys B: At. Mol. Phys. 14, 3345 (1981). 3) Dynamic coupling: The mutual interaction of the lanthanide ion and the crystal environment are taken into account. Goes beyond the static coupling model. Explains hypersensitive transitions (transitions highly sensitive to changes in environment). M.F. Reid et al., J. Chem Phys. 79, 5735 (1983). National Aeronautics and International School of Atomic and Molecular Spectroscopy Space Administration Erice, Italy (June 2005)
42. Extensions II 4) Wybourne-Downer mechanism: Involves spin-orbit interaction among states of the excited configurations, leading to an admixing of spin states into the 4f N configuration. This accounts for the observed spin “forbidden” transitions ΔS = 1 B.G. Wybourne, J. Chem. Phys. 48, 2596 (1968). M.C. Downer et al., J. Chem. Phys 89, 1787 (1988). 5) Relativistic contributions: Relativistic treatment of f → f transitions in crystal fields. Reformulation of crystal field and operators in relativistic terms. Importance unknown. L. Smentek, B.G. Wybourne, J. Phys. B: At. Mol. Opt, Phys. 33, 3647 (2000). L. Smentek, B.G. Wybourne, J. Phys. B: At. Mol. Opt, Phys. 34, 625 (2001). Review Articles Early development: R.D. Peacock, Structure and Bonding, vol. 22, 83-122 (1975). Later developments L. Smentek, Physics Reports, vol. 297, 155-237 (1998). National Aeronautics and International School of Atomic and Molecular Spectroscopy Space Administration Erice, Italy (June 2005)
43. Summary Physical Mechanisms: (Not a complete list)  Crystal field influence based on static model. Second order in the perturbation. (This is the standard Judd-Ofelt theory).  Crystal field influence based on static and dynamic model. Second order.  Electron correlation based on static and dynamic model. Third order.  Spin-orbit interaction. Intermediate coupling and Third order effects.  Relativistic effects. Remaining Problems:  Estimating the relative importance of each mechanism is considerable. (Many competing mechanisms producing various effects. Entangled situation)  Ab-initio calculations still not entirely successful. - Theory of f - f transitions not yet complete. - Calculation of Radial integrals and knowledge of odd crystal field parameters. - Vibronics (Vibrational lattice-ion coupling)  Multitude of mechanisms and new parameters abandons simplicity. - Simple linear parametric fitting to observed spectra is lost. - Physically meaningful descriptions can be obscured. National Aeronautics and International School of Atomic and Molecular Spectroscopy Space Administration Erice, Italy (June 2005)
44. What’s next? “It has been in a very real sense the first step in the journey to an understanding of the rare earths and their much heavier cousins, the actinides, but like many journeys into the unknown, the end is not in sight.” Brian G. Wybourne “The fascination of rare earths - then, now and in the future” Journal of Alloys and Compounds 380, 96-100 (2004). National Aeronautics and International School of Atomic and Molecular Spectroscopy Space Administration Erice, Italy (June 2005)
45. Judd and Ofelt Finally Meet 40 years after publications B.R. Judd G.S. Ofelt B.G. Wybourne Ladek Zdroj,Poland - June 22, 2003 “4th International Workshop on Spectroscopy. Structure and Synthesis of Rare Earth Systems.” National Aeronautics and International School of Atomic and Molecular Spectroscopy Space Administration Erice, Italy (June 2005)
46. 2007 School of Atomic and Molecular Spectroscopy 2007 will be the 45th anniversary of the simultaneous publications of Brian Judd and George Ofelt. A special session is certainly worth considering in the next course. “The fascination of the Rare Earths - 45th Anniversary of Judd-Ofelt theory” Possible invited lecturers: Brian R. Judd - The Johns Hopkins University, Baltimore, MD 21218, USA E-mail: juddbr@eta.pha.edu George S. Ofelt - 824 Saint Clement Road, Virginia Beach, VA 23455, USA E-mail: gsofelt@pilot,infi,net Lydia Smentek - Vanderbilt University, Box 1547, Station B. Nashville, TN 37235, USA E-mail: sementek1@aol.com G.W. Burdick - Andrews University, Berrien Springs, MI 49104, USA E-mail: gburdick@andrews.edu Francois Auzel -UMR7574, CNRS, 92195 Meudon Cedux, France E-mail: francois.auzel@wanaoo.fr Sverker Edvardsson, Mid Sweden University, S-851 70, Sundsvall, Sweden E-mail: Sverker.Edvardsson@mh.se National Aeronautics and International School of Atomic and Molecular Spectroscopy Space Administration Erice, Italy (June 2005)
47. Acknowledgements Rino DiBartolo- Thank you for your years of wisdom and my first lecture on Judd-Ofelt theory in your office in ‘old’ Higgins Hall. Also for inviting me to Erice these last 10 years. Norm Barnes- Thank you for helping me see the laser side of life. The discussions we have had over the years remain with me. National Aeronautics and International School of Atomic and Molecular Spectroscopy Space Administration Erice, Italy (June 2005)
48. Dedication Brian G. Wybourne (1935-2003) Professor Brian G Wybourne Commemorative Meeting: Symmetry, Spectroscopy and Schur Institute of Physics, Nicolaus Copernicus University, Torun, Poland June 12-14, 2005. A commemorative meeting in honor of Professor Brian G. Wybourne will be held in Torun, Poland from 12-th to 14-th June 2005. The aim is to celebrate Brian's academic life and his contributions to many aspects of physics and mathematics. This meeting will bring together friends, students, collaborators of Brian as well as people interested in the results and consequences of his research. National Aeronautics and International School of Atomic and Molecular Spectroscopy Space Administration Erice, Italy (June 2005)
49. National Aeronautics and Erice, Italy (June 2005) Space Administration
50. National Aeronautics and International School of Atomic and Molecular Spectroscopy Space Administration Erice, Italy (June 2005)
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I did some energy calculations for geometry optimised compounds and the values given for the HOMO and LUMO energies are negative (e.g. -0.23066 and -0.11119 Hartrees).
I'm a little confused about this. What are these values in relation to? Can they be converted to be relative to absolute zero?
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Dear Daniel,
All bonding orbitals have negative energies, while all antibonding orbitals have positive energies. This is because the zero of energy is defined as a non-bonded state: bonding orbitals are more stable (lower energy than zero), while anti-bonding orbitals are less stable (higher energy than zero). Most non-bonding orbitals are at or close to zero in energy.
Your results indicate that the HOMO is more stable than the LUMO and the gap has a positive value, which is fine.
Regarding the negative value of the LUMO: I have seen negative LUMO values when calculated in certain methods, but other methods give positive values. It depends on the calculations method you use. It is suggested that you rerun your calculations using both time-independent and time-dependent DFT (TD-DFT). The DFT functionals may include the local spin density approximation (LSDA), (GGA) functionals, hybrid GGA functionals, hybrid meta GGA functional.
Hoping this will be helpful,
Rafik
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I want to study functional groups of fungal cell wall, but I have no idea about how to prepare fungal biomass (solid particle) to FTIR analysis. Is any chemical or physical treatment required?
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Mr. Tikendra varma
Sterilize by autoclaving, as first step seperate fungal mycelium by centrifugation. Then wash the pellet or mycelial mass thrice with double distiilled water (if required centrifuge thrice)-This is for avoiding nutrients and other secondary products in the mass. 
second step, dry in hot air oven at controlled temperature (at 313 K) till to complete removal of humidity in the biomass. Later, powdered it by trituration of the biomass (please avoid contamination and other chemicals and nutrients).
Then by Kbr pellet method you can find functional groups present on the biomass. Generally -NH2, C=O groups predominantly present on the fungal biomass.
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Except distillation, is there any other method (chemical or physical) to remove ketone and amine from their schiff bases?
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Reactive Distillation.
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I want to study the uni molecular reaction dynamics of some of the fission reactions  in the high energy regime and I don't want to use the classical master equation . In this regime, the reaction rates could be limited by the intramolecular vibrational energy redistribution so what  could be the best model to predict the dynamics and find the reaction rate in such IVR-controlled regime. furthermore, I am wandering what could be actual bottleneck that limits the rats in this case. Is there any role of localization or delocalization of the vibrational density of states?
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Hi there,
We are working on those issues here at University of Ottawa. We have developed some python codes, but still waiting for a paper to be published with all the math. We are using Boltzmann distributions for internal energy calculated from the density of states (Beyer-Swineheart), calculating rate constants using the RRKM theory on DFT potential energy surfaces.  And we use temperature values in a different way as usal.
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In an NPT simulation the most relaxed or stable conformer of a protein is the one with lowest potential energy? Or the lowest total energy? 
I know that potential energy transforms to a kinetic energy when the energy is conserved, However in NPT MD it is not. So which one is better to probe the probability of certain conformer in MD to be in a minima in real life ?
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Neither. Trying to extract a protein-only total or potential energy is meaningless; it's not a free energy, which is what really tells you what happens in the physical world. The most populated state (judged from some suitable clustering analysis of the trajectory) would be more appropriate, but even then it would be hard to definitively say that it is the most stable conformer. It's potentially biased by the force field, and MD simulations are prone to being stuck in local minima, so all you can say is it is the dominant state in that particular trajectory. Perhaps other evidence will emerge based on known experimental data that you can corroborate such a claim. Multiple, long simulations and/or use of enhanced sampling techniques should be employed here to make any defensible claim.
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Hi all,
I am looking at calculating transition state energies of triazoline degradation in the prodrugs I am synthesizing. It is the step between step 2 and step 3 (in the attached figure).
The protocol I am following at the moment is to use Avogadro to conduct a systematic rotor search (conformer search) to find the conformers at local minima and subsequently conduct a optimization and frequency calculations on Gaussian 09.
I am having issues with finding a suitable conformer. As Avogardo does not provide the same set of conformer every single time I conduct the "systematic rotor search". And also on conducting an energy minimization on the obtained local minima conformers the energy drops further leading to a totally new conformer.
Can you suggest any better way of doing this?
Thank you.
Regards,
Siddharth.
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If you are just trying to locate the TS, there are two strategies - if you can draw a reasonable TS, then do that and use opt=(ts,calcfc,noeigentest) in G09 and that should find the TS - if you can't draw what would be a reasonable looking TS, then you can use the structure of the reactant and the structure of the products in the G09 input file along with opt=(qst2,calcfc,noeigentest) and that will find a TS along a path from reactant to products - I hope this helps -
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I have been using OriginLab to plot ternary phase diagrams but I want to replace it with an open source package that may have more decent capabilities in that sense.
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for example Mn doped ZnS.
another peak correlated to Doped ion (emission wavelength: 590 nm) did not observed.
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Dear Zahra,
According to Dong Zhu et al. Mn-doped ZnS quantum dots (QDs) prepared by a conventional aqueous synthetic method usually suffer from poor crystallinity and low quantum yield due to their relatively low reaction temperature. In addition, the authors of the study you mentioned stated that Curcumin caused defect-related fluorescence quenching of the probe at 458 nm, whereas the orange transition emission of the probe at 590 nm changed only negligibly with variations in curcumin concentration.
Which means that the concentration of curcumin plays dominant role in obtaining the desired dots.
Herein the study of Dong Zhu et al. entitled " Microwave-assisted aqueous synthesis of Mn-doped ZnS quantum dots and their room-temperature phosphorescence detection of indapamide" which describes the required dots using microwave:
Paper Microwave-assisted aqueous synthesis of Mn-doped ZnS quantum dots and their room-temperature phosphorescence detection of indapamide
Dong Zhu,*a Wei Li,*a Hong-Mei Wen,a Qian Chen,a Li Maa and Yue Hua
Show Affiliations
Anal. Methods, 2014,6, 7489-7495
DOI: 10.1039/C4AY01235F
Received 23 May 2014, Accepted 08 Jul 2014
First published online 09 Jul 2014
Mn-doped ZnS quantum dots (QDs) prepared by a conventional aqueous synthetic method usually suffer from poor crystallinity and low quantum yield due to their relatively low reaction temperature. In this paper, high-quality Mn-doped ZnS QDs with long-lived emissions were prepared using a green and rapid microwave-assisted synthetic approach in an aqueous solution. The QDs were used for room-temperature phosphorescence (RTP) detection of indapamide with a detection limit of 0.89 μM, and the RTP intensity showed a good linear relationship with the concentration of indapamide in the range from 1.5 to 80 μM. The relative standard deviation for seven independent measurements of 10 μM indapamide was 3.4%, and the recovery ranged from 94% to 105%.
Hoping this will be helpful,
Rafik
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I am doing on the CBS extrapolation from the work of Helgaker et al (T. Helgaker, W. Klopper, H. Koch, J. Noga, The Journal of Chemical Physics 106 (1997) 9639). I got into some troubles with the "alpha" parameter of Hartree - Fock energies using by Feller (D. Feller, The Journal of Chemical Physics 96 (1992) 6104.), e.g. E_HF(X) = E_HF(CBS) + B exp(-alpha.X). I cannot find its value in his research, how could I obtain it if I only use two basis set for extrapolating CBS limit. I really appreciate if you give me any comments/advice!
Best wishes,
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They all are excellent answers. Here is my experience: three equations need to be solved for three variables. A good set of three basis sets is aug-cc-pVTZ, aug-cc-pVQZ, and aug-cc-pV5Z.
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I've been trying to find Sherwood number correlation for simple situation: stirred vessel filled with liquid and stagnant gas phase above, with no sucess. I would like to calculate the gas-phase mass transfer coefficient for absorption of stagnat gas into stirred liquid. I found the Sherwood number correlation for stirred vessels in
Versteeg, G. F., Blauwhoff, P. M. M., & Van Swaaij, W. P. M. (1987). The effect of diffusivity on gas-liquid mass transfer in stirred vessels. Experiments at atmospheric and elevated pressures. Chemical Engineering Science, 42(5), 1103-1119.
But the correlation is valid when both phases are being mixed. My question is, how to find kg (gas-phase mass transfer coefficient), when gas phase is stagnant, and liquid phase is being mixed.
Regards,
Marcin Stec
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Hi, Marcin
Your question is “how to find kg (gas-phase mass transfer coefficient), when gas phase is stagnant, and liquid phase is being mixed.”
My suggestion is:
1.      I have found the gas resistance cannot be neglected when the partial pressure of measured gas is very low and gas agitation is not enough, you have cited my paper in this discussion
2.      I did not measure the kg in the paper because I increased the gas stirrer numbers and agitation speed. Then the gas phase resistance is reduced and can be neglected.
3.      If you want to measure the kg at stagnant gas phase, you should do two comparison experiments:
      a.  One is measuring the -dpA/dt vs. PA at stagnant gas phase, where the gas phase resistance cannot be neglected, you can get the overall mass transfer coefficient KG, i.e. 1/KG =(1/kg + He/kL)
      b.  The other is measuring the -dpA/dt vs. PA at good gas phase agitation, where the gas phase resistance can be neglected, you also can get the overall mass transfer coefficient K’G, i.e. 1/K’G =(0 + He/kL)
      c. HE/kL in the two equations could be equal when the agitation speeds are same, then comparing the two results, you will get kyou asked.
4.      The method you can refer to my thesis (I think you have got it), page 131, equation (7.26 - 7.29) or the paper
      Industrial & Engineering Chemistry Research 52(7):2548–2559
Hope it’s useful for you :)
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Please help me in these regards. 
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Dear Chetan,
Please see the table in page 634 of the attached file.
Hoping this will be helpful,
rafik
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