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3:18 AM
0
Q: Can someone help me understand the motivation behind and visualize the dihedral potential and the Urey-Bradley potential?

megamenceI am studying statistical mechanics and force-fields, and I see a lot of this formula being thrown around with no explanation: $$U_{\mathrm{dihedral}} = \begin{cases} k(1+\cos (n\psi + \phi)),& n>0 \\ k(\psi - \phi)^2, & n=0 \\ \end{cases} $$ The only explanation I read is: this...

0
Q: Why aren't all the fluorescence transitions the same wavelength?

MarkIf all the excited molecules at higher S1 vibrational states rapidly relax to the lowest S1 vibrational state, why do the fluorescence transitions from v' = 1, v' = 2, v' = 3, and other states to v" = 0 have different wavelengths? Why don't they all relax to v' = 0 first and then all transition t...

 
 
1 hour later…
4:32 AM
0
Q: Are there any ADME predictions tools available for Python/RDKit?

LeitouranIs there any Pythonic way (a.k.a: a module, an rdkit package, etc) or an API I can use for ADME predictions? I need to prioritize some compounds for purchase/synthesis and some sort of ADME scoring might help me rule out most of them. I am aware of tools like SwissADME but given the amount of com...

 
 
4 hours later…
8:59 AM
0
Q: Spurious term in Thomas-Fermi-Hartree energy functional

TheOldJonnyI am quite a beginner in DFT and I am studying the theory behind the computational tools. I have some doubts about the Columb approximate functional term: $U[n] = \frac{1}{2} \int d^3 r \int d^3 r^\prime \frac {n(\mathbf{r}) n(\mathbf{r}^\prime)}{|\mathbf{r} -\mathbf{r}^\prime|}$ If I use the de...

 
 
8 hours later…
5:18 PM
-1
Q: Why does the voltage of a cell depend on its chemical elements?

123123123I know that the standard reduction potential of $\ce{Zn^{2+}}$ to $\ce{Zn} $ is $\pu{-0.76 V}$ and the one of $\ce{Ca^{2+}}$ to $\ce{Ca}$ is $\pu{-2.87 V}.$ But on the atomic level, why does this potential depend on the chemical element?

-1
Q: Confusion in formula of number of nucleons

user883022Mass of nucleon means mass of one proton or neutron. $$\text{No of nucleons} = \frac{\text{mass of one atom} }{\text{Mass of one nucleon}}$$ Now, I have confusion in this formula that why is it division. Mass of an atom = mass of electron + mass of proton + neutron. Now, I am not exactly sure if ...

 
 
4 hours later…
9:08 PM
1
Q: How to retrieve excited state molecular orbital coefficients in Gaussian?

aerospaceCurrently I am doing TD-DFT calculations in Gaussian and want to calculate transition dipole moment for $S_1$ transition manually. However, I do not manage to retrieve molecular orbital coefficients for the excited states in Gaussian, just the ground state with population keyword and a few hours ...

 
9:59 PM
1
Q: Physical interpreation of coulomb and exchange integral

DJAWhen trying to solve the Schrodinger equation for the electronic hamiltonian: $$H_{el} = \sum_{i=1}^{N} \bigg( - \frac{1}{2}\nabla_i^2 - \sum_A \frac{Z}{r_{i_A}} \bigg) + \sum_{i>j=1}^{N}\frac{1}{r_{ij}}$$ we note that two prominent integrals arise: These are the exchange integral: $$ K_b(1)\ch...

 

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