Muhammad Khattab

58 Questions 92 Answers 0 Followers

Questions related from Muhammad Khattab

Where I can find tutorials for using AMBER molecular dynamics software on supercomputer?

Hi, I am wondering what are the files that should be prepared? how? commands? that enables me to perform MD simulations using AMBER on Supercomputer.

12 December 2019 6,086 5 View

What database or anything else enable me to find the pharmacological actions of certain pharmacophore?

I want to find a database in which i can draw the chemical structure of the core ring and it will give me all the published structures with their biological activity. For example, the...

06 June 2018 1,301 11 View

Any recommendations for highly viscous solvent but should be non-polar and aprotic one?

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...

05 May 2018 3,573 4 View

How can I get a list of FDA-approved drugs of certain category?

I'm wondering how i can find an updated list of FDA-approved drugs for example, proton pump inhibitors, Topoisomerase inhibitors or whatever category.

05 May 2018 5,014 5 View

Where I can find a downloadable list for Quartile (quantile) journals ranking?

I'm also wondering is this ranking standard or it differs from website to another.

03 March 2018 6,912 7 View

Some questions regarding proteins sequence and structural comparison?

I hope you can help in these matters. 1) What is the difference between sequence and structural comparison between proteins? 2) Which website or software is good to use to perform this task? 3)...

11 November 2017 9,761 5 View

What are files required to submit GROMACS job on supercomputer?

I don't know how to prepare input and script files for GROMACS. I appreciate if you could share example for a small job. I learnt that i have to convert .pdb file to .gro but I don't know how.

09 September 2017 2,674 13 View

Intermolecular H-bond bond can be converted into a covalent bond ?

From scientific point of view, if a h-bond is formed as in RN-H.....NAr The covalently bound proton can transfer to other side forming RN.....HN+Ar if it can take place, is there a reference for...

08 August 2017 10,079 6 View

How to purify BSA (Bovine Serum Albumin) for Absorption/Fluorescence spectroscopy use?

As you know, BSA is commercially available as 96% and 98% pure. It contains also fatty acids. Therefore, i'm wondering how to get BSA purified.

08 August 2017 5,084 3 View

What buffer concentration should be relative to solute concentration? Factor of 10 or 100 or 1000 of solute concentration?

For example, if I am using 1-10 uM of solute so that buffer solution should be 1mM, 100 mM or 1M (or it doesn’t matter). it seems that solutes salting out at higher buffer concentration.

07 July 2017 6,095 4 View

Understanding synchronous fluorescence spectrum?

In Synchronous spectrum, both Exc and Fl monochromators are scanned simultaneously. MY questions are; 1) How to determine delta wavelength 2) if delta wavelength is 20nm, does it mean the data...

07 July 2017 4,114 4 View

What the x-axis stands for in synchronous fluorescence spectrum?

I found in literature that authors plot x-axis as emission wavelength and sometimes as excitation wavelength. Is it dependent on spectrophotometer used?

07 July 2017 496 3 View

Can i find in literature comparison of cpu-cost and accuracy for all Gaussian used functionals and basis sets ?

I appreciate if someone could help me in this matter.Please, list or send me a reference comparing the accuracy and cpu-cost of methods and basis sets depending on 1- Number of atoms2- either...

06 June 2017 3,480 3 View

Can micromolar solution of substance form dimers or aggregates?

I am wondering, can dilute solution of single compound (uM) form dimers, trimers, polymers, aggregates due to available sites for H-bonding.

04 April 2017 5,265 4 View

Is ionic strength constant for all buffered solutions at pH range of (2-12) prepared by Britton-Robinson procedure?

I've prepared universal buffer solutions of Britton-Robinson within pH range 2 to 12. My question is, do all solutions at different pH have the same ionic strength? I believe it would change at...

04 April 2017 3,382 4 View

Should i use universal buffer pH=2:12 when i add only 1 uL of HCl or NaOH to 2 mL solution in cuvette?

if one needs to study the effect of acid or base on the absorption and fluorescence spectra, should a buffer solution be used? or it's enough to add for example 1 uL of acid or base to solution...

03 March 2017 5,712 3 View

Why acidified & re-acidified solution of chromophore gives different absorption and emission spectra?

I noticed when I adjust the pH of chromophore solution containing surfactant (triton X100) for example at pH=3 using HCl, it gave me absorption and emission spectra which are completely different...

03 March 2017 691 3 View

How to solve the problem of second order diffraction (Rayleigh scattering) during emission and excitation measurements ?

First, I'd like to ask is there a threshold for the amplitude of 2nd order scattering. I noticed i get offscale peak with increasing emission slit width, which means the scattering is more...

02 February 2017 5,044 3 View

How can I overcome atmospheric water condensation during fluorescence measurement in cuvette?

I noticed at low temperature (0-20) C, water condensation on cuvette walls takes place resulting in false results. Please advise how to solve this problem.

12 December 2016 2,408 7 View

Where I can find the updated journal style (endnote) ?

I downloaded the bioorganic and medicinal chemistry citation style from endnote website, however it's completely different. it was last updated on Jan. 2014. Even though i can't find downloadable...

07 July 2016 7,929 2 View

Imaginary frequencies problem of excited state using gaussian?

I currently trying to solve the problem of imaginary frequency. Simply, I open the log file showing one or two imag. frq. and i do manual displacemt at the higher absolute value of imag. freq. and...

06 June 2016 4,864 6 View

When one (should/should not) include "Nosymm" keyword in route section of gaussian job?

Also, I am wondering does the use of Nosymm affect the results of all gaussian jobs such as optimization, frequency calculation, absorption and fluorescence, ....etc

06 June 2016 3,067 2 View

What does it mean if studied compound shows 2 overlapping peaks (10 nm difference) in more than 20 solvents, but only one peak in water and TFA each ?

what are the suggested possibilities and how to test it.

05 May 2016 9,057 1 View

What are the best structural characterization techniques for positional isomers ?

For the best of my knowledge, 1- HPLC (time consuming and cost-ineffective) 2- NMR ( I appreciate if could guide me to the difference between NOSY, COSY, HSQC, .....etc telling me which one is...

04 April 2016 8,694 8 View

Fitting using different mathematical functions like gaussian, exponential ,.... etc?

I have no mathematics background and i appreciate if you provide me with resources to understand which function i should use to best fitting of my data points. Actually, i am using originlab...

03 March 2016 2,064 1 View

Dipole moment determination using Kawski-Chamma-Viallet model?

The slope (M2) of mu(ab)+mu(fl) is smaller than the slope (M1) of stokes shift correlation. Hence i got a negative value for GS dipole moment. How i can solve this problem ???!!!!

03 March 2016 8,284 1 View

What is the keyword for explicit water solvation?

I know "SCRF=CPM or CPCM" is the keyword for implicit solvation model. But i could not find how to perform explicit solvation.

03 March 2016 1,350 4 View

Dipole moment calculation using Bilot-Kawski polarity functions?

Dear all, the problem is m2 is negative and also m1 has bigger value than m2 (positive), therefore i got a negative dipole moment for the ground state. and i can't calculate the ES dipole moment...

02 February 2016 7,351 2 View

How to do multiple regression analysis for Kamlet-Taft equation using solver in microscoft Excel?

I appreciate if you could demonstrate in details how to establish Kamlet-Taft equation for the studied compound. (intercept and coefficient for alpha, beta and pi-star solvent parameters)....

02 February 2016 8,080 2 View

What are the alternatives for using LED light in FLIM microscope?

My compound can't be excited using the shortest available wavelength (448 nm). Its absorption spectrum is within 300-360 nm. So, i appreciate if you could advise how to resolve this problem either...

01 January 2016 7,714 5 View

What does it mean when blank (solvent) has intense peak in excitation spectrum, but weak one in emission (<10%) of sample intensity?

Also, sometimes I notice the reverse where weak excitation peak and strong emission peak. For the best of my knowledge, the solvent peak should be (

11 November 2015 2,527 7 View

3D excitation, emission and excitation-emission experiments?

I am wondering what is the importance and how to interpret these experiments. Also, i noticed that i can't have background corrected (No blank subtraction) for these experiments using perkin elmer...

11 November 2015 9,445 13 View

What is the difference between Absorption and excitation Spectra?

I am wondering about the difference between Ab and Exc spectra? what does it mean if they are 1) identical and 2) non-identical? Also, i want to ask what is the impact and importance of changing...

10 October 2015 7,924 0 View

Can anyone suggest how to have my cuvette completely sealed to prevent solvent evaporation during temperature dependence fluorescence measurements?

I have already a polyethylene lid which is not efficient. I tried to use parafilm but the solvent still evaporates. I tried to put Aluminum foil then the lid on to make it a quick fit, but the...

10 October 2015 4,736 8 View

What is and the importance of isoemissive and isosbestic point in UV-Vis scpectropy?

Could you illustrate exactly and clarify when and how i can use them in interpretation of temperature dependence.

10 October 2015 2,349 5 View

What is the difference between 1) locally excited state; 2) Twisted intramolecular charge transfer state (PICT); and 3) Planar (PICT) state?

Also, does it mean that the molecule can exist in the planar or twisted conformation in the ground state as well. I appreciate if you could clarify as possible as you can because i am totally...

10 October 2015 1,372 1 View

How do I make 2d cross section through molecular electrostatic potential (MEP) using gaussview?

I am wondering how to make cut through ESP through 2 different planes. for example one through the anilino ring and the other through benzimidazole which is at angle of 0 degree relative to...

09 September 2015 7,798 1 View

Could you please help me installing the executable version of Molden for molecular chemistry visualization?

i was advised to use Molden, but i failed to install it. could you advise how to install or where i can find tutorial for installation and usage.

09 September 2015 689 4 View

UV-Vis red edge measurement?

What is the red edge usefulness? how to measure it?

08 August 2015 4,324 0 View

What does irregular absorption peaks between 270-200 nm mean in UV-spectrum?

What is the meaning and explanation of finding irregular absorbance in UV-Vis spectrum. Actulayy i have 2 overlapping absorption bands at 330 and 340 nm, but i don't know why i got irregular...

08 August 2015 445 7 View

What is the advantage of synchronous fluorescence spectrum over conventional fluorescence one ?

is it worthy to do synchcronous fluorescence and when ?

07 July 2015 4,357 0 View

How can I establish an intramolecular H-bond network using Avogadro?

I am trying to visulaize h-bonds within my molecule of (.out) gaussian extension. i ticked "display settings" then marked hydrogen bonds, but still no H-bonds are formed. Could you please...

06 June 2015 8,579 6 View

What is the effect of having blank solvent peak in the excitation and emission spectra?

I am wondering if the solvent has excitation and/or emission peak, does it affects the experiment. BTW, i already subtract the blank solvent spectrum from my sample spectrum. but i mean is the...

06 June 2015 7,319 3 View

Should I rely on solvents with high peak in the excitation spectrum, yet very small in the emission spectra?

I notice the blank (excitation) spectra of different solvents, show high peak above 600 arbitrary units, while the emission blank spectra show very small peak, below 40 arbitrary units. My...

04 April 2015 7,458 1 View

What's the equation for a corrected AUC calculation of a fluorescence spectrum? its meaning? its importance?

I calculated AUC of emission spectrum and i was asked to calculate the corrected AUC. i don't know why and how.

03 March 2015 6,925 1 View

Is it applicable, the dipole moment of the ground state be negative? what it means?

Also, we can calculate the dipole moment of the excited state using Lippert-mataga or Bakhshiev or Kawski equations which give different values of dipole moment of excited state. but for measuring...

03 March 2015 6,475 0 View

Could you please tell me the solvent dipolarity and polarizability (SdP and SP) of Glycerol and N-methylformamide according to Catalan scale?

I already got a reference stating the values of most solvents, but not including glycerol and N-methylformamide. I'd appreciate if you could help in this matter.

03 March 2015 1,015 11 View

Why do chlorinated alkanes (DCM, CHloroform, .......) show unreliable results in UV-Vis spectroscopy ?

Are there some interactions happening, or do these solvents decompose into HCl?

03 March 2015 7,728 5 View

How to use the output of low level of theory calculation, as input for a higher level of theory, in details please?

i read that i can use the checkpoint file of low level method to save time and getting a better accuracy.

03 March 2015 5,080 7 View

What is the values and units of Planck's constant and speed of light in vacuum used to calculate the difference in dipole moment ?

What is the values and units of Planck's constant and speed of light in vacuum used to calculate the difference in dipole moment between excited and ground state of a compound using...

03 March 2015 8,074 1 View

What is the difference between intramolecular charge transfer (ICT), Planar intramolecular charge transfer (PICT), and Twisted (TICT)?

Also, is it the mechanism of fluorescence?

03 March 2015 5,870 0 View

Why does my UV-Vis blank shows an high excitation band?

I noticed most of Blank spectra of solvents used to solubilize my sample show high excitation bands (>700 arbitrary unit), but low emission band (

03 March 2015 8,623 4 View

Can you send me website link showing tutorials for most common jobs submitted by Gaussian09?

I am a beginner, and i have difficulties to either submitting input files or understanding the purpose of job and how to interpret the output log file.

03 March 2015 1,150 6 View

Would you kindly send me a reference listing CMC of SDS, CTAB and Triton-X-100 in different solvents and cosolvent mixtures?

I need to know CMC of those 3 surfactants to be used in spectroscopy studies.

02 February 2015 5,946 6 View

How to exactly classify solvents as Polar protic, Polar aprotic and non-polar?

In literature, sometimes I find Chloroform, CCl4 and DCM classified as Polar aprotic and sometimes as non-polar. I am totally confused. Is there international approved classification of solvents...

02 February 2015 7,997 4 View

Is CMC of a surfactant common for all solvents or it is related to water unless other solvent is specified?

Also what is the importance of molar fraction W0?

02 February 2015 5,230 9 View

Are there native fluorescent tyrosine kinase inhibitors ??

I appreciate if you could numerate some examples of intrinsically fluorescent tyrosine kinase inhibitor ?drug

10 October 2014 318 4 View

When can I use Bis(triphenylphosphine)palladium(II) dichloride or Palladium(0)?

Suzuki reaction.

01 January 2014 4,602 10 View