40

I was wondering what the wavy and the dotted line represent? A dashed line indicates that the bond is extending behind the plane of the drawing surface A bold-wedged line indicates that the bond is protruding out from the plane of the drawing surface A solid line indicates that the bond exists in the plane of the drawing surface. A wavy line indicates that ...


21

Final update, all earlier edits incorporated. Groundrules: Considering compounds with: only carbon and hydrogen only 4 bonds to carbon There are 37 isomers without considering trans isomers; 49 when trans isomers are included. Also, many of these compounds seem extremely unstable and therefore unlikely to exist. Note to self: check back in 20 years and ...


21

The compounds you are referring to are called catenanes (see also rotaxanes, as they are a close relative). (image source) one molecule chain of one benzene molecule, go through the center of another, before closing back up as a ring While catenanes involving larger rings can be prepared, having one benzene ring threaded through a second benzene ring ...


20

Here is the Walsh diagram depicting all the valence molecular orbitals (a diagram showing how individual molecular orbitals change in energy due to bending around the central atom). Oxygen has 6 valence electrons, so ozone has 18 electrons in total. If we start on the right where ozone would be linear, we can see that all the orbitals up to the $2\pi_\mathrm ...


20

In chemical structure diagrams, carbon atoms that are bonded to at least two other atoms are usually left unlabeled. The carbon atom is indicated by the angle in the bonds. However, according to the Graphical Representation Standards for Chemical Structure Diagrams (IUPAC Recommendations 2008), a carbon atom with two double bonds should be explicitly ...


19

General Rule #1: Most elements use only s and p orbitals to form bonds, only transition elements and heavier elements use d, f, etc. orbitals in bonding. General Rule #2: The more s-character in a bond the shorter the bond (reference). For example a $\ce{C(sp^3)-C(sp^3)}$ single bond length is ~ 1.54 $\mathrm{\mathring{A}}$ a $\ce{C(sp^2)-C(sp^3)}$ ...


18

In the hexagonal graphite structure the carbon atoms are $\ce{sp^2}$ hybridized, just like in benzene. In graphite, this p-orbital is used for bonding just as it is in benzene, resulting in an extended pi system in the graphite structure. Graphite is really just a large number of benzene rings annelated together to form a continuous, ring structure. Just ...


18

According to the website, Open Babel should do the trick: Documentation - SMILES, Sourceforge. For example, the following code will give you a neat SVG file of the molecule benzene: obabel -:"c1ccccc1" -O benzen.svg If you experience problems using it, you are welcome to ask more specifically. Alternatively, you can use a web-query from the national ...


18

Try to imagine it in a 3D fashion. You can look it at molcalc.org. The molecule rotates around the $\ce{C-C}$ bond converting one structure into the other. These rotations are very fast. Another point is, that the representations you chose are 2D, so the could still represent the same molecule:


18

Yes, this graphical representation of a substituted benzene is in accordance with Graphical Representation Standards for Chemical Structure Diagrams (IUPAC Recommendations 2008). GR-9.4 Variable attachment location In addition to allowing the type of attachment to vary, it may also be convenient to indicate that the attachment’s location is variable ...


17

trb456 and Mad Scientist have raised the point that enantiomeric forms of a bioactive molecule may have markedly different activities, however there's more to it than that. A molecule that has a similar shape and surface charge distribution to another biologically important molecule is liable to bind to the same protein receptor sites, but in different ways. ...


17

One example of disastrously different effects of very similar molecules is thalidomide. There are two isomers, only differing in their stereochemistry. The (R)-isomer is responsible for the sedating effect it was initially used for. The (S)-isomer lead to horrifying birth defects in the children of woman that took that drug. It is somewhat more complicated,...


17

Just as a side note, I think it is easier to use ChemDraw to make the graphics then import them into your LaTeX file, rather than using the chemfig package which (I find) is cumbersome. Obviously it's entirely your choice. I don't think there is an established convention per se. If you wrote $\ce{R}$, nearly everybody would understand it, especially if you ...


17

According to the Graphical Representation Standards for Chemical Structure Diagrams (IUPAC Recommendations 2008), in the structure diagram of the parent structure, variable substituents should be indicated by an unambiguous label. This label should be chosen so that it cannot easily be confused with other valid element symbols or fragment abbreviations. ...


16

$\ce{C20H18}$, 246 characters InChI=1S/C20H18/c1-2-13(1)5-15(13)7-17(15)9-19(17)11-12(19)20(11)10-18(20)8-16(18)6-14(16)3-4-14/h1-4,11-12H,5-10H2/t11-,12+,15-,16-,17-,18-,19-,20-/m1/s1 PIN: (1'R,1''R,1'''R,1''''R,1'''''R,1''''''R,2''''R,3''''S)-octaspiro[tetrakis(cyclopropane)-1,2':1',2'':1'',2''':1''',4''''-bicyclo[1.1.0]butane-2'''',2''''':1''''',2'''''':...


15

A lot of non-systematic chemical names don't describe the composition of the compound, they describe what the compound is synthesised from. That is the case here since EDTA is derived from ethylene by adding two units of the diamine. It isn't that uncommon in chemical names. Polyethylene, for example, is (simplifying only slightly) a long chain of carbons ...


15

The molecule seen in the tattoo is a protein-based mammalian hormone called oxytocin, commonly called "the love hormone" because it is involved in several aspects of sexual reproduction. Image Source


15

They mean the same thing. If the OH group on the left were written as OH, it would look like there was a carbon-hydrogen bond. By inverting the order, it makes it clear that the oxygen is bonded to the carbon and the hydrogen is bonded to the oxygen. $\ce{NH2}$ might also be written as $\ce{H2N}$ in a structure drawing if a bond was coming from the right, ...


15

$\ce{C20H18}$, 153 characters (1'S,2'S,3'R,6'S,8'S)-3'-(cycloprop-2-en-1-yl)-11'-[(cycloprop-2-en-1-yl)methylidene]spiro[cyclopropane-1,7'-tricyclo[6.3.0.02,6]undecane]-2,4',9'-triene P. S. I guess someone should just start, so I simply used the slightly modified structure from the example. I'm pretty sure this one is going to be criticized a lot by ...


14

There are often shortcuts taken in drawing complicated molecules, particularly if there's not any interesting chemistry going on at those functional groups. The $\ce{-CH3}$ is implied at the end of the "stick," just like how the carbon atoms aren't explicitly labeled in the benzene ring. Hydrogens are rarely explicitly drawn for the same reasons, given ...


14

When you see a line coming out of an aromatic ring as shown, it is meant to suggest that the substituent (in this case chlorine) could be at any position. The notation is often used when a reaction on an aromatic rings afford a mixture of products (ortho, meta, para etc), but in all cases the substituent is bonded to a specific carbon, not to the ring as a ...


13

Generally, you wouldn't describe the bonds in an ammonium ion as dative bonds. They are usually considered to be proper covalent bonds. The term "dative bond" is typically used for bonds in (transition) metal complexes between ligands and a metal center. But for those complexes Lewis structures have lots of weaknesses and are rarely a good ...


13

You might want to have a look at Open Babel. It is licensed under GNU GPLv2 It has bindings for Python It has bindings for PHP It has bindings for Ruby It can read (and write) SMILES It can read (and write) InChI It can write SVG It can write a list of painter commands


12

Noradrenaline/norepinephrine is an aromatic organic compound containing a benzene ring (the hexagon). Essentially, the vertices in the diagram are carbon atoms and the number of lines represents the covalent bond order; 1 line (eg connecting an OH to the benzene ring) means a single covalent bond. Any 'spare' bonds are where a C-H bond is. So it can be ...


12

While I do not think that cocaine is a particularly interesting molecule, the crystal structure has been reported in Ronald J. Hrynchuk, Richard J. Barton, and Beverley E. Robertson, Can. J. Chem., 1983, 61, 481. There is also an open access paper of the XII IUCr Congress available, R. D. Hrynchuk, R. J. Barton and B. E. Robertson, Acta Cryst A, 1981, A37, ...


12

Each carbon atom (you seem to have identified them) needs four of those stick-like thingies (the lines, sometimes called "bonds"). These include the dashed lines and thick triangles as well as the "double bond" you see at the lower oxygen which looks like this ($=$). That one counts twice. Every time you only see 3 or even 2 for one carbon atom, that means 1 ...


12

$\ce{C18H20}$ : 145 characters I was curious as to the isomer with the longest name that had actually been reported in the literature rather than hypothetically proposed (so we at least know it exists). The IUPAC name, whilst not quite as long as some of the examples, is a respectable 145 characters, largely due to the representation of stereochemistry and ...


12

I use ChemDraw Professional 19.1.1.32. If you follow File>Open Templates>Advanced BioDraw, you will find the black helix that I have reoriented from horizontal to vertical. The red helix was enlarged and colored red. I hope this is of help.


11

It is much easier to explain it on simpler example – $\ce{O3}$ molecule. It has structure of resonance hybrid of $\ce{O=O+-O-}$ and its mirror. And of course, central atom has hybridization state $sp^2$. One bond here is normal covalent bond and another bond is dative: an electron pair is donated onto vacant orbital of $\ce{O}$ atom with all electrons paired....


11

Well, that is simple. A Carbon (C) makes 4 bonds, a Hydrogen (H) or a halogen (X) makes 1 bond and Nitrogen (N) makes three bonds. So in a molecule with $c$ Carbons, $h$ Hydrogens, $x$ halogens and $n$ Nitrogens, we will have $4c+h+x+3n$ "bonding capacity". Assuming there are no rings, no double/triple bonds, we must have $c+h+x+n-1$ bonds in between ...


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