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5:29 AM

Q: How to convert amino acid sequence to SMILES format

I have an amino acids string "MKGK" and I would like to convert it into SMILES format. I tried two approaches. First with PepSMI which gives me: N[C@@]([H])(CCSC)C(=O)N[C@@]([H])(CCCCN)C(=O)NCC(=O)N[C@@]([H])(CCCCN)C(=O)O Second, using ChemAxon Marvin's molconvert command /Applications/MarvinSui...

2 hours later…

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7:08 AM

Q: Modify ORCA Orbitals

I have run a HF calculation on naphthalene and I have checked the MOs that have been obtained. Now, I have to select my active and inactive orbitals for CASCF(10,10). As there are 34 occupied orbitals, ORCA by default would read 31, 32, 33, 34, 35, 36, 37, 38, 39 but I have inspected how they loo...

physical-chemistry molecular-orbital-theory software multi-reference

4 hours later…

uhoh

11:01 AM

Q: What does 3-regularity mean in the context of this diagram of a fullerene?

This answer to What is the maximum amount of carbon atoms that can comprise a fullerene? links to Mathematical aspects of fullerenes Vesna Andova, Frantisek Kardos and Riste Skrekovski Ars Mathematica Contemporanea 11, (2016) 353-379 (also here) begins Abstract Fullerene graphs are cubic, 3-conn...

general-topology geometry terminology

1 hour later…

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12:07 PM

Q: In Kohn Sham DFT, what do we know theoretically about the exchange correlation energy?

As I understand Kohn Sham theory, it is proposed that the ground state energy for a molecule can be derived from the ground state of a fictitious set of non-interacting electrons moving in a fictitious potential. This fictitious potential is conventionally written as $E_T+E_V+E_J+E_{XC}$ where we...

quantum-chemistry density-functional-theory

4 hours later…

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3:52 PM

Q: atomic structure - why only hydrogen be separately written in periodic table

The other exception is hydrogen. It has only one s-electron and hence can be placed in group 1 (alkali metals). It can also gain an electron to achieve a noble gas arrangement and hence it can behave similar to a group 17 (halogen family) elements. Because it is a special case, we shall place hy...