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Questions tagged [organic-chemistry]

Questions about or related to organic chemistry.

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3 votes
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Compare transition matrix elements in molecules and solids

Is there a general trend such that transition matrix elements for electronic/excitonic transitions are larger/smaller in molecules than in inorganic solids or vice versa?
11 votes
1 answer

How reactivity of a organic molecule depends upon HOMO and LUMO

I am studying the dehydrogenation of an organic molecule. I see the HUMO-LUMO gap remains nearly the same for many dehydrogenated steps (for some steps, it is exactly the same) while the position of ...
2 votes
0 answers

What is meant by "quinoid character"? [closed]

While reading about push-pull systems in papers, I came across the term quinoid character. I looked for it in google here is what I've found: In polyphenylene the ground state is a whole lot of ...
2 votes
0 answers

Program for distance matrix using Rdkit [duplicate]

How to find the matrix of Bond lengths between atoms in an hydrogen depleted molecule given the smiles with explicit hydrogen=true. Also how to find the geometric distance between atoms in an ...
6 votes
2 answers

How are diffusion coefficients calculated?

To support my laboratory result, I'm searching for an MD/statistical mechanics approach to predict translational diffusion coefficients in the liquid phase. I'm aiming to describe small peptides and ...
6 votes
1 answer

Accurate electron-hole localization for charge-transfer transitions

I'm studying the nature of electronic excitation in conjugated organic dyes. To define the donor and acceptor part I've run TDDFT and CIS calculation, they both gave similar set of configurations for ...
8 votes
1 answer

Where to find organic molecules atomic coordinates

I have found many organic molecule databases, such as PubChem or chEMBL. But they don't provide the atomic coordinates of each atom on the structure. I'm especially interested in organic molecules ...
7 votes
1 answer

Can the dehydrogenation energy be negative?

I am studying the dehydrogenation of a cyclohexane ring containing $\ce{B-N}$ on the adjacent position. or simply we can think about $\ce{H3N-BH3}$. If we release one $\ce{H2}$ molecule from it then ...