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Results tagged with molecular-structure
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user 1782
This tag should be applied to questions that deal with the particular arrangement of atoms in a molecule, the so-called molecular structure or geometry.
3
votes
Accepted
Have the shapes of synthesized anthropomorphic molecules (nanoputians) been verified experim...
I think to solve the question "seeing one of the nanoscholars, nanotexan, etc." in this particular conformation shown requests (at least) two steps:
The deposit of a single molecule on a clean, flat …
- 31.2k
5
votes
How to convert Gaussian input file .gjf to SMILES?
It is not aiming for code golf, but the following offers the conversion to intermediate .xyz which may be processed further (cf. vide infra):
import fnmatch
import os
import sys
gjf_register = []
f …
- 31.2k
1
vote
Automated Identification of Isomeric Relationship from 3D Structure?
You might become interested in OpenBabel. Written in C++, it offers bindings to Python (ref). It looks like stereochemistry is covered more in detail (here, here) than the obchiral command (here).
…
- 31.2k
4
votes
Is HC(=NH)OH a stable compound?
Compound 7 is the imidic acid of formic acid (hence formimidic acid). However as indicated by $\Delta{}G$, its tautomer formamide 8 is thermodynamically favoured. Some activation ($\Delta{}G^\#$) ha …
- 31.2k
4
votes
Transform raw atomic coordinate data into SDF file
Your work ahead requires two steps
completion of the file to be a valid .xyz file
transformation of the .xyz into a .sdf file, a task for which openbabel already is one of the tools suitable (in my e …
- 31.2k
3
votes
How to convert CAS ID to SMILES
First you should check if the CAS registry number is numerically plausible. ACS outlines this by
The CAS Registry Number may be written in a general form as:
$N_i....N_4N_3 - N_2N_1 - R $
in which $R …
- 31.2k
7
votes
Accepted
Have the STRUCTURES of synthesized anthropomorphic molecules (nanoputians) been verified exp...
The first article wikipedia's entry refers to (here) is not only a publication behind a paywall, but with freely available supporting information, too. This in principle allows to replicate the work. …
- 31.2k
27
votes
Accepted
How can you build a model of tetrahedral coordination from objects found at home?
Inflate balloons, and tie them «at their stem» like a bouquet of flowers. If you take four of them, not too much inflated, you well demonstrate a situation close to $sp^3$ hybridization. These models …
- 31.2k
5
votes
How to interpret BRICS fragments
Cutting a molecule (expressed with SMILES strings) into fragments yields sub-structures. Typically these fragments can't be considered as molecules for their open, non-bonding valencies. Derived fro …
- 31.2k
4
votes
From chemfig to .mol file/SMILES
The answer is a definitively yes there are programs to scan papers with the aim to retrieve chemical information from the illustrations. One of them is OSRA hosted by NIH (project landing page) with …
- 31.2k
6
votes
Accepted
Adding hydrogens to multiple pdb files using Openbabel GUI software
If you got an installation of openbabel's GUI, you equally have an installation of openbabel for the terminal (e.g., in Linuxes) / command line cmd.exe (in Windows). There is nothing wrong using the …
- 31.2k
1
vote
Accepted
What is "tail" in case of secondary structure of protein?
«Tail» probably is just one word to describe both N-terminus (amino/ammonium group) and C-terminus (carboxylic acid/carboxylate) of a sequence of amino acids/proteins.
The shape of a sequence of amino …
- 31.2k
8
votes
Double bond crossed lines representation
It is, for example, used by Marvin JS -- one of the editors in the GUI of Reaxys by Elsevier to query the database for structures, where you do not impose either (E)-, nor (Z)-configuration of the dou …
- 31.2k
8
votes
Why are there two infrared vibrational frequencies for the terminal CO ligands of Fe2(CO)9?
Despite the title of the publication, Fletcher et al. both present an IR spectrum of diiron nonacarbonyl in a matrix of ($\ce{Ar}$ + 10% $\ce{CO}$, recorded at $\pu{15 K}$) in the $\nu(\ce{C-O})$ regi …
- 31.2k
14
votes
Are physical space filling molecular modelling kits still available anywhere?
Note, CPK (for Corey–Pauling–Koltun) is a colour scheme, i.e., a convention to symbolize atoms of carbon in black, oxygen in red, nitrogen in blue, etc. which took inspiration on the colour scheme in …
- 31.2k