Updated geo.txt with new molecules. #6
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geo.txt
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| and thermodynamics of beryllium dihalides. Struct Chem 26 (5-6):1451-1458 | ||
| # Date first added: 2023-07-05 (by Sichao Xiong) | ||
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| Be I (T = 501(5) K) 2.163(6) |
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The temperature at which the experiment was done, is something that would more appropriately be in the comments section. An extra line in the comments section can be added for "Additional comments".
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Just to clarify these are two set of bond length values for two temperatures.
Be I (T = 501(5) K) 2.163(6)
I Be I (T = 501(5) K) 165(3)
Be I (T = 722(10) K) 2.172(7)
I Be I (T = 722(10) K) 162(4)
Should I make this
# T = 501(5) K
Be I 2.163(6)
I Be I 165(3)
# T = 722(10) K
Be I 2.172(7)
I Be I 162(4)
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For AgHS we had three sets of bond lengths:
Ag S 2.31219(75)
S H 1.375(15)
Ag S H 92.49(81)
# Bond lengths: rs (angstroms)
# Bond angles: thetas (degrees)
Ag S 2.313(20)
S H 1.373(15)
Ag S H 92.21(42)
# Bond lengths: rz (angstroms)
# Bond angles: thetaz (degrees)
Ag S 2.313713(99)
S H 1.3472(18)
Ag S H 93.120(90)
Following what I did for that molecule, you have the right idea, but an extra space between the temperature and the first line of the data might make things more aesthetically pleasing when reading.
Also, I prefer "Temperature" and "Kelvins" rather than "T" and "K".
geo.txt
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| # Dihedral angles: taue (degrees) | ||
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| S=O 1.4340(7) | ||
| S Cl 2.0700(3) |
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It would be nice, for aesthetics and easy of reading, if all columns of atoms were aligned, as in the examples that I currently have in the main fork. I guess this means that double-bonds would need to be made a bit longer: S==O (for example). Have you considered what notation to use for triplet bonds? The Chromium dimer (Cr2) has a sextuple bond, so I'm not sure how that would be denoted either 😂
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Yes, I can see how we will have an alignment problem with symbols like "...", "=" and elements with a different number of characters in their name. I have two proposals.
(1) We can leave a fixed amount of spacing in our columns each time (this will also standardize our representation across different molecules) i.e. ###### where ## represents element names (supposing we don't have any of the newer elements) and *** represents how they are bonded. Single bonds are default to three spaces, double bonds " = ", triple bonds " ≡ " and the intermolecular forces are represented by "...". i.e.
S = O 1.434(9)
S Cl 2.072(3)
Cl S = O 108.00(6)
Cl S Cl 97.08
Cl S = O...Cl 104.0(3)
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If you think we'll end up taking too long on fomatting using (1) then
(2) we can keep our previous convention but we use (2) to denote a double bond, (3) for a triple bond etc. i.e.
S O (2) 1.4340(7)
S Cl 2.0700(3)
Cl S O (2) 107.703(6)
Cl S Cl 96.929
Cl S O (2)...Cl 103.58(3)
I prefer the first one much more.
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Thanks for making these proposals!
I also (along with you) prefer the first one.
For sextuple bonds like in the Cr2 molecule, we can maybe have something like:
Cr-6-Cr
to denote that the bond order is 6, but it's not really crucial (for our purposes) to know the order of a bond, especially when it gets to such a high bond order.
I will make one more aesthetic suggestion though. Please notice the alignment of the digits in your example, versus in my version below:
S = O 1.434(9)
S Cl 2.072(3)
Cl S = O 108.00(6)
Cl S Cl 97.08
Cl S = O...Cl 104.0(3)
Okay, that did not work at all because the font in this edit box is not fixed-width, even within code blocks. Discord's editor had the same problem. StackExchange's editor was helpful though:
S = O 1.434(9)
S Cl 2.072(3)
Cl S = O 108.00(6)
Cl S Cl 97.08
Cl S = O...Cl 104.0(3)
| Ag...N 2.15444(6) | ||
| N H 1.0129 | ||
| H N...Ag 113.48(2) | ||
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If you take a look at the triatomics that I added earlier, you might notice that I didn't always report the geometry data in the same order as in the book. I reported the geometry data in such a way that the structure could be un-ambiguously inferred without needing an image. Is this possible for this molecule? Or do we absolutely need an image? Preferably the computer can just read this data and make a z-matrix, without having to refer to an image to know that NH3 is the pyramidal part and AgCl is the linear part (for example).
These Van der Waals complexes / weakly bound systems (for which we have dotted lines) present a much more challenging case than ordinary molecules in this sense.
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Sorry for the late response. Lets do this to solve both problems (refering to the next comment)
Ag Cl 2.26333(6)
Ag...N(H3) 2.15444(6)
N H 1.0129
H N...Ag 113.48(2)
The brackets will serve to show that this wasn't originally in the book and the fact that it's the pyramidal complex that the Ag is interacting with.
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This might be confusing for some people, because parenthesis are part of the standard chemical notation for molecules, for example rhodizonic acid is: (CO)4(COH)2.
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For Ar---H2 we were given the length R_cm which is presumably the distance between the Ar atom and the centre of mass of the H2 molecule. For that reason I could just write: "H2 Ar 3.957" and it can be inferred that the length given is between the centre of mass of H2 and Ar, and I guess the fact that the point group was C2v, means that the H2---Ar complex would form a T shape rather than something less symmetric.
In the case of Ag---NH3, they have not given us the length R_cm, which would be the distance between the Ag atom and the centre of mass of the NH3 molecule. Instead they've given us the distance between N and Ag, and the N-H bond lengths.
They have told us that the point group for the entire complex is C3v, but you were smart enough to describe the "Shape" as: Trigonal pyramidal --- Linear.
Perhaps we can treat such Van der Waals complexes by specifying each molecule in the somewhat complex separately. For example:
1) Trigonal pyramidal --- Linear
2) C3v --- Coov
3) N H 1.0129 --- Ag Cl 2.26333(6)
combined with:
N...Ag 2.15444(6)
would be enough for one to be able to reconstruct the entire molecule?
While copying and pasting the above N-H bond length, I noticed a footnote that says that the N-H bond length was "assumed" at the r_e value from CCSD(T)/cc-pVQZ, and I hope they did that CCSD(T) calculation for the whole NH3---Ag complex rather than just for NH3, but it would take longer to confirm this for certain (Section 3.3, Table 2 and the below quote are what I found so far). I'm guessing for now that the calculation included the entire complex, because otherwise they could have just used established NH3 bong lengths (and could have obtained more accurate results than CCSD(T)/cc-pVQZ).
"It is not possible to obtain a full r0-geometry for H3N...Ag–Cl because the distance r0(N–H) and the angle HNH are not separately determinable from the available data. We therefore fixed the value of r(N–H) at 1.0129 Å, as determined in the ab initio calculation described in Section 3.3 [...]"
geo.txt
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| # Date first added: 2023-07-05 (by Sichao Xiong) | ||
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| Ag I 2.5375(3) | ||
| Ag...N 2.180(1) |
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Looking back at what I did for the triatomics that I added earlier, I had:
H2 Ar 3.957
To denote the length between the center-of-mas of H2 and the Ar atom.
Similarly, something here would ideally denote that Ag is not just interacting with N, but with NH3.
geo.txt
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| Ag I 2.5483(1) | ||
| P...Ag 2.3488(20) | ||
| P H 1.4086 | ||
| H P H 118.92 |
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The book has a footnote on the number 118.92. The footnote says "Assumed". I think it's important for our database to retain the information that 118.92 is an "assumed" angle.
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Ag I 2.5483(1)
P...Ag 2.3488(20)
P H 1.4086
H P H 118.92
# Angle H P H of 118.92 is assumed
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- This comment can be moved up to where the rest of the comments/meta-data are.
- "H P H" can be "HPH or H-P-H".
- 118.92 doesn't need to be repeated in the comment.
- Assumed can be put in inverted commas: "assumed".
| Al Br 2.229(5) | ||
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| # Bond lengths: re(M)(a,b) (angstroms) | ||
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"a" and "b" are footnotes. All information is valuable in some way, but footnotes "a" and "b" are such detail for which, if someone was interested, they could get the information from the original paper, so we don't need to clutter our database with such information (or maybe it wouldn't be a bad idea to do so, if it weren't for it taking so much more time/energy to include such footnotes).
"rg(a)" therefore needs to be changed to just "rg", and "re(M)(a,b)" needs to be changed to just "re^M", the superscript symbol being more appropriate (and simpler, and more close to the original presentation) than the parentheses.
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I think in this case it was used to cite two different sources so I kept it in this case.
a. Varga Z, Kolonits M, Hargittai M (2012) Comprehensive study of the structure of aluminum trihalides from
electron diffraction and computation. Struct Chem 23 (3):879-893
b. Hargittai M, Kolonits M, Gödörházy L (1996) Molecular geometry of monomeric and dimeric aluminium
tribromide from gas phase electron diffraction. Chem Phys Lett 257:321-326.
Are you suggesting that I simply include both sources without making distinctions towards the contributions?
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There's two sets of "a" and "b":
The first are footnotes, the second are references. Please include both citations in the comments section, and remove the (a,b) from re^M(a,b)
| # Bond lengths: re(M)(a,b) (angstroms) | ||
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| Al F 1.621(4) | ||
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You included AlBr3, AlCl3, and AlF3, but seem to have skipped AlI3 which was next in the book?
geo.txt
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| # Date first added: 2023-07-05 (by Sichao Xiong) | ||
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| Rcm(b) 3.957 | ||
| (b) Distance between Ar and the center-of-mass of H2. |
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ArH2 was already included by me! Please take this opportunity to see how I did it, compared to how you did it.
| NAME = AsP3 2010 | ||
| # Point Group: C3v | ||
| # Shape: Tetrahedral | ||
| # Bond lengths: rg (angstroms) |
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In addition to the rg values at T = 388 K, there's also r0 values that are given in the book, but seem to be accidentally neglected here.
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I also added the source for the other experiment.
NAME = AsP3
# Point Group: C3v (assumed)
# Shape: Tetrahedral
# Bond lengths: rg (angstroms)
# Source Paper: a. Cossairt BM, Cummins CC, Head AR, Lichtenberger DL, Berger RJF, Hayes SA, Mitzel NW, Wu G (2010)
On the molecular and electronic structures of AsP3 and P4. J Am Chem Soc 132 (24):8459-8465 b. Daly AM, Cossairt BM, Southwood G, Carey SJ, Cummins CC, Kukolich SG (2012) Microwave spectrum of
arsenic triphosphide. J Mol Spectrosc 278:68-71
# Date first added: 2023-07-05 (by Sichao Xiong)
# Temperature = 388 Kelvin
As P 2.1949(28)
P P 2.3041(12)
# Bond lengths: r0 (angstroms)
As P 2.311
P P 2.201
| # Date first added: 2023-07-05 (by Sichao Xiong) | ||
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| H H 0.92(1) | ||
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It's strange that they only gave the H-H bond length, and nothing about the distance between the H2 molecule and the ClAu molecule. Fortunately one of the authors of the original paper is quite a close friend of mine (who I saw in person just a couple weeks ago!), so I can ask for clarification about the geometry, if you can't find any more information in the original paper.
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Nope I couldn't find any details on the Cl-Au bond length or the distance between Au and the H-H centre of mass.
geo.txt
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| NAME = BFH2O | ||
| # Point Group: Cs (syn) | ||
| # Shape: Planar | ||
| # Bond lengths: re(se) (angstroms) |
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Maybe a superscript for "se" is better than parentheses, for the same reasons why I said earlier that this was the case for r^M vs r(M).
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Fixed.
# Bond lengths: re^se (angstroms)
# Bond angles: thetae^se (degrees)
| B H 1.197(2) | ||
| H B H 129.6(2) | ||
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| NAME = BH6N |
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I have reviewed everything up to here, with a fair amount of rigor. As it is now almost midnight here, if you can implement the changes suggested in my above comments, for the above molecules and also the molecules below, then when I return to this review I might not need to make as many comments for the rest of the molecules.
geo.txt
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| Ag...N 2.180(1) | ||
| Ag N H 110.86(5) | ||
| Ag I 2.5375(3) | ||
| Ag...NH3 2.180(1) |
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I wrote a comment here a moment ago but can't find what I wrote anymore. I was saying that Ag...NH3 suggests that you're providing the length between Ag and the center-of-mass of NH3, when really the book looks like it's denoting the distance between Ag and N.
geo.txt
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| H P H 118.92 | ||
| H P H 118.92(b) | ||
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| (b) assumed |
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I wrote a comment here a moment ago but can't find what I wrote anymore.
The number in parentheses is the uncertainty in the last digit shown. Putting a letter there can be confusing and would make it harder for a computer program to parse.
I suggest putting a comment like: "The HPH angle of 118.92 degrees is an "assumed" angle.
…as added for Chatper 8.
geo.txt
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| Phys Chem A 112(19):4477-4482 | ||
| # Date first added: 2023-07-05 (by Sichao Xiong) | ||
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| B...N 1.6576(16) |
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Here we have the same issue as in Ag---NH3. I'm not sure how the computer will know how to make the z-matrix based on the data given here alone (without the diagram for guidance).
| # Temperature = 501(5) Kelvin | ||
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| Be I 2.163(6) | ||
| I Be I 165(3) |
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Lining up the digits would be nice.
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| Be I 2.172(7) | ||
| I Be I 162(4) | ||
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I wonder why you included BeI2, but not Be2O?
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I was slightly confused with it being an ion. So I wasn't really sure if the two Be were in fact identical but given that it only provides one bond length I would assume so. Also I think I realised at some point that I should exclude 3 atom molecules but then but then forgot so I included BeI2.
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I see. It's the whole molecule that's an ion, so I would just have treated it just like all of the other molecules (in terms of the way that you add all of the data), then I would have just added a comment with the charge of the molecule. Now you know for next time, to please include ions when adding molecules. But you don't need to add this one because it's a triatomic. I will hold of on clicking "Resolve conversation" until I've seen what Arpit did in his pull request for this triatomic.
| Si H 1.46948(9) | ||
| F Si H 108.304(9) | ||
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| # Bond lengths: r0 (angstroms) |
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The second reference (b) would probably be more appropriate directly before this line.
| I Si I 111.27(13) | ||
| H Si H 105.9(19) | ||
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| NAME = H2O2Si |
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How is this (Dioxasilacyclopropane) distinguished from the other H2O2Si in the book (Dihydroxysilylene)? I had been putting years next to the chemical formulas in my entries. That is not a perfect solution, so I'm open to suggestions.
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Hmmm we do need a way to deal with structural isomers. I guess one is Cs and the other is C2v. I would need to think about the case where two isomers have the same geometry.
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Good point. If a user were to ask for the z-matrix for H2O2Si without specifying the point group, then the program can say: "Warning, the database has two entries for that molecule, one with point group C2v and one with point group Cs. Which one do you want?". Alternatively, if the user asks for the C2v molecule, then they will get the C2v one.
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Sure and if we have two of the same geometry then the user can choose once again.
geo.txt
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| Si(1) N = Si(2) 180.0 | ||
| H Si(1) N 109.99(6) | ||
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| # Angle Si(1) N = Si(2) is assumed to be 180.0 by symmetry |
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This can go with the other comments.
| F C F 108.06(6) | ||
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| NAME = CHNS | ||
| # Point Group: Coov |
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How is this distinguished from the other two CHNS structures? Unfortunately all three are published in 2016. The Coov point group distinguishes them, but the other two are both Cs so we might need to think of a different way to distinguish them.
geo.txt
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| H C H 107.66 | ||
| Br C I 113.53 | ||
| Br C H 107.27 | ||
| F C F 108.06(6) |
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Alignment of atoms slipped here.
| S...N 3.3233(2) | ||
| NH3 SCO 4.3607(2) | ||
| α 25.23(4) | ||
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I understand that "alpha" is all they gave in the book (along with a footnote), but it's not clear to me what it its, and it would be even less clear to the users of this database who haven't seen the footnote. I don't know what the best solution is here, because the footnote isn't enough for me to know immediately what angles this is.
| C H 1.140(9) | ||
| Zn C H 110.2(3) | ||
| H C H 108.7(3) | ||
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You have included a lot of linear tetraatomics so far, so I wonder why you didn't include CN2Si?
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Sorry I think I was scrolling through too fast. Added in now.
geo.txt
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| C Cl 1.635(6) | ||
| Ag...Cl 4.8722(2) | ||
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| # Bond length C ≡ C 1.2219 assumed at the CCSD(T)/aug-cc-pV5Z value |
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Can go with the other comments.
| Ag C 2.015(14) | ||
| C ≡ C 1.2219 | ||
| C Cl 1.635(6) | ||
| Ag...Cl 4.8722(2) |
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2.015+1.2219+1.635 = 4.8719 so I'm confused about the meaning of 4.8722 here.
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Could it be that when they measured the length between Ag and Cl it was subject to error because the molecules was not perfectly linear?
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I think I need to look at how the length of 4.8722(3) for Ag...Cl was determined.
| I...C 3.4281(12) | ||
| ϕ 4.0(5) | ||
| φ 10(3) | ||
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Instead of Rcm, please put CO F3I. These angles also need to be explained somehow.
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I'm kind of confused with the justification for ϕ and φ.
Are they reusing the notation Rcm in this case to denote the line connecting the centers of mass?
| # ϕ: Angle between the C3 axis of CF3I subunit and Rcm. | ||
| # φ: Angle between the OC axis and Rcm | ||
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| NAME = C2HAl 2012 |
| # Date first added: 2023-07-11 (by Sichao Xiong) | ||
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| OC1 HCN 4.842(1) | ||
| C(1)...H 2.572(2) |
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Parentheses are probably not needed for C(1). C1 is probably just as good. I saw this before, but didn't comment on it. If the parentheses can be removed universally without me finding all previous examples, I would appreciate it!
When we have C2, then we won't know if it means there's a C2 molecule for which we're describing a distance from the centre of mass, or a single C atom that is labeled as the "second" C atom.
Therefore OC1 would probably be better labeled as OC(1).
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OC_1, OC_2, OC_3, ...
or
OCa, OCb, OCc, ...
would require even fewer characters than:
OC(1), OC(2), OC(3), ...
But we can fix that later quite easily when we decide on a notation.
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| H...N 2.3980(7) | ||
| NH3 HCCH 4.0594(6) | ||
| α 23.29(2) |
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I commented about alpha earlier, but I think that this is essentially the CHN bond angle (in this case, and something similar in the other case), although this isn't clear from the book. We might have to look at the paper to confirm what this angle is.
| # Date first added: 2023-07-11 (by Sichao Xiong) | ||
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| S2C2O SC1S 3.5553(8) | ||
| C(1)...C(2) = S(2) 104.82(22) |
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S2C2O is a pentaatomic molecule, but the books is only giving us a triatomic molecule here.
These labels in parentheses also won't help without the diagram.
Also, all four bonds are double bonds, so C(2) = S(2) won't tell us to which pair of C and S atoms is being referred.
Maybe this will work:
COS(1) CS2 3.5553(8)
C C S(1) 104.82(22)
Or even better, I think the CCO angle is just 180 minus the CCS(1) angle, so we could do:
COS CS2 3.5553(8)
C C O 180-104.82(22)
But we might need to label one of the C atoms because there's two possible CCO angles. Only one of them avoids jumping from molecule 1 to molecule 2 and back to molecule 1 though.
P.S. sorry for the spacing in my code blocks. I would fix that using StackExchagne's markdown editor but it's now 3:18am here!
| [http://dx.doi.org/10.1063/1.4932043] | ||
| # Date first added: 2023-07-11 (by Sichao Xiong) | ||
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| OCO OC 3.583 |
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- I guess we know the orientation is a T shape because it's the only way that we can get C2v?
- I think in addition to "Linear --- Linear" we should specify what type of "Linear --- Linear" it is (not just for this molecule but for all of them). We could have Linear --- Linear: Linear, or Linear --- Linear: T, or something else.
- I wonder how the program would know that the O atom in the CO molecule is the one closer to the CO2 molecule?
geo.txt
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| θ2 78.7 (25) | ||
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| # θ1: Angle between Rcm and the O=C=O axis (measured from the inner O end) | ||
| # θ2: Angle between Rcm and the O=C=S axis (measured from the S end). |
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Ideally our data format would have some mechanism to portray this information without having to write it.
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| # θ1: Angle between Rcm and the O=C=O axis (measured from the inner O end) | ||
| # θ2: Angle between Rcm and the O=C=S axis (measured from the S end). | ||
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You can put the S-interior first, then the O-interior with the (a) reference, then move the (b) reference here, and then put the O-interior data from the (b) reference here.
geo.txt
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| # Shape: Linear --- Linear | ||
| # Bond lengths: r0 (angstroms) | ||
| # Source paper: a. Dehghany M, Norooz Oliaee J, Afshari M, Moazzen-Ahmadi N, McKellar ARW (2009) Infrared spectra of | ||
| the OCS-CO2 complex: Observation of two distinct slipped near-parallel isomers. J Chem Phys 130(22):224310/1-224310/5 doi: 10.1063/1.3152743 b. Sedo G, van Wijngaarden J (2009) Fourier transform microwave spectra of a “new” isomer of OCS-CO2. J |
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There's something strange happening with the word wrapping.
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| C ≡ Ge 1.7695(1) | ||
| C = C 1.2893 | ||
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The order of the atoms won't be obvious with just this much information.
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Not sure with molecules with many duplicate names if it's worth identifying the Cs as C1, C2 and C3. May help with identifying the order but will in some cases unnecessarily clutter the document.
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| C ≡ Ge 1.7695(1) | ||
| C = C 1.2893 | ||
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| # C = C 1.2893 assumed at the CCSD(T)/cc-pwCVQZ value |
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This can move up to where the other comments are.
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| C(4)...H 2.65315(27) | ||
| C(4)...D 2.64962(27) | ||
| OC4 HC1C2C3N 6.2031 |
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Maybe the following would work:
OC(1) C3HN 6.2031
C(1) H 2.65315(27)
But the only problem is that it's not obvious that the H is the atom closest to CO.
Also, C...H and C...D belong in separate sections. D is an isotope of H.
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| # ϕ: Angle of torsional oscillation about the a axis, defined as the angle between this axis and the HCCCN axis | ||
| # φ: Angle of torsional oscillation about an axis parallel to b one (bꞌ), defined as the angle between bꞌ and the | ||
| O=C=O axis |
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Hopefully these angle descriptions can be built into our notation/format instead.
| ϕ2 8.7 | ||
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| # ϕ1: Angle between the a axis and the axis of the HCCCN(1) subunit. | ||
| # ϕ2: Angle between the a axis and the axis of the other HCCCN subunit |
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A Coov molecule wouldn't have an angle though, so this is similar to the previous case in which we had two different point groups for the same molecule, but the book didn't list them both equally at the beginning.
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I managed to work on this review non-stop from around 1:17am (which was when I wrote the first comment) to 3:51am :) |
| @@ -1681,15 +1705,14 @@ NAME = C3Pd | |||
| # Source paper: Bittner DM, Zaleski DP, Tew DP, Walker NR, Legon AC (2016) Highly unsaturated platinum and palladium | |||
| carbenes PtC3 and PdC3 isolated and characterized in the gas phase. Angew Chem 128(11):3832-3835; Angew | |||
| Chem Int Ed Engl 55(11):3768-3771 | |||
| # C(1) = C(2) 1.3009 and C(2) = C(3) 1.2789 fixed to the value calculated at the level CCSD(T)_ae/aug-cc-pwCV5Z-PP(for Pd) and corrected for r0 ‒ re | |||
| difference assumed to that for PtC3. | |||
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It seems that the line wrapped a bit too early?
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Think ill need to make a new line.
Please review the changes in geo.txt. I will continue entering new molecules after the feedback.