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I'm just starting to study chemistry so sorry for the probably obvious question to you, guys. According to the definition of molecule in Wikipedia:

A molecule is an electrically neutral group of two or more atoms held together by chemical bonds.

According to that definition, I assume that parts of the molecule could be theoretically connected just with the h-bonds. As far as I understand the example of that case is DNA two strands of which are connected by only h-bonds (though many and many ones).

According to Khan Academy:

When atoms combine by forming covalent bonds, the resulting collection of atoms is called a molecule.

And now, as a newbie, I'm a little bit confused with all of that. So, could you help me with the following questions:

  1. Is that true that two strands of DNA do not have covalent bonds to each other and connected only with h-bonds?
  2. If the p. 1 is true could parts of molecule be connected only by h-bonds by definition?
  3. If the p. 3 is true then why DNA is a molecule but two water compounds (H2-O***H-O-H) are not?
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  • $\begingroup$ In short: (1) Yes. (2) Depends on the definition. (3) Because there are pretty many of them in one DNA strand. $\endgroup$ – Ivan Neretin Dec 4 '20 at 9:32
  • $\begingroup$ @IvanNeretin, then what definition is correct and/or official? Are there any formal parameters to split between the case of two water compounds and DNA strands? Maybe, the number of h-bonds or some kind of h-bonds total strength or something like this? $\endgroup$ – ademchenko Dec 4 '20 at 10:28
  • $\begingroup$ The definition you quoted is official enough to me. But it is not complete. You may look for the complete one; you may even found some, but they won't be complete either. There are always borderline cases. You are looking for strict formal criteria where there are none. $\endgroup$ – Ivan Neretin Dec 4 '20 at 10:47
  • $\begingroup$ @ademchenko 1)True 2)NO. DNA is a polymeric macro molecule, It is consisted of 2 strands connected by Hydrogen bonds. Each Strand is also a polymeric macro molecule. therefore the term "molecule" results from covalent bonds of phosphodiester in each strand. I suppose you're not familiar with proteins 4 types of structure see : en.wikipedia.org/wiki/Protein_structure. The hydrogen bonds are created in 2nd, 3rd , 4th structure of a protein but 1st structure ALWAYS contains ONLY covalent bonds.Almost the same thing goes with DNA. 3) Because H2O**H2O is not polymer as DNA is. $\endgroup$ – Sam Dec 4 '20 at 10:50
  • $\begingroup$ @Sam, I'm sorry about that, I'm really confused because of my lack of knowledge. But do you mean that polymeric molecule is not a molecule by definition? I know what the polymeric molecule is but I thought it is a type of molecule. So, I thought the term "molecule" suits "polymeric molecule" as well. So, according to what you have said could we say that: the only type of molecule which parts can be connected by exclusively h-bonds (no covalent bonds are presented) is the polymeric one? $\endgroup$ – ademchenko Dec 4 '20 at 10:57
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There are some grey areas in the normal usage of the word 'molecule'

The normal usage of the term molecule is accurately described by your quote from the Khan Academy. The majority of molecules chemists talk about are groups of atoms joined with covalent bonds. But, like many things in chemistry, there are some grey areas and the normal usage gets bent a little.

One of the major areas where the terminology gets fuzzy is in polymers. While on a strict interpretation of the normal definition a single polymer strand (be it DNA or a single strand of polyethylene) is a molecule the terminology is not particularly helpful as the key things that matter in bulk polymer properties are not easily reduced to the properties of individual 'molecules' so the very idea of molecules is less relevant. In polyethylene (a very simple polymer) there will not be a mix of identical molecules but, rather, a wide range of very similar molecules (even for linear polyethylene there will be a wide range of chain lengths (say from 1,000 to 10,000 carbons). So polymer chemists tend not to talk about molecules much.

DNA is a polymer but, by its nature, one where the structure of a given strand is constant (and can be precisely replicated). We do tend to say DNA molecule at least in casual conversation despite the fact that the two strands are connected only by hydrogen bonds. But there are good reasons why this is not an abuse of the normal definition of molecule. One is that many hydrogen bonds along a polymeric chain add up to a strong overall bond even though the individual bonds are merely hydrogen bonds. But the relative weakness of each bond is a key part of the process of replicating DNA as the two strands can be easily unzipped by the machinery in the cell nucleus. You could argue that a DNA strand consists of two molecules using the normal definition but this doesn't help much and, in normal discussion, we talk about both a DNA molecule with two hydrogen-bonded strands and a DNA strand as a molecule. This mild abuse of a strict definition of "molecule" doesn't matter much as it doesn't interfere with any understanding of how DNA works.

Mostly, though, chemists don't consider hydrogen-bonded units as "molecules" even when the bonds have significant effects on the bulk properties of the substance. The physical properties of, for example, acetic acid are heavily influenced by hydrogen bonding. In solution molecules often form pairs (joined by two hydrogen bonds) and this leads to a big elevation in their expected boiling point compared to a similar hypothetical molecule of the same size that couldn't do hydrogen bonds. But there is no benefit in describing this a "molecule" and nobody does this.

But the main point is that many properties in chemistry have an almost continuous range with no clear point where a black and white distinction can be made. The definition of what counts as a molecule is like this. Describing hydrogen bonded DNA as a molecule isn't a terrible use of the terminology; describing an acetic acid hydrogen-bonded pair as a molecule probably is. The term molecule can be useful in some circumstances but not others. The utility of the term is what matters not a simple black or white definition.

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