Posts Tagged ‘Lone pair’

VSEPR Theory: Octet-busting or not with trimethyl chlorine, ClMe3.

Sunday, November 12th, 2017

A few years back, I took a look at the valence-shell electron pair repulsion approach to the geometry of chlorine trifluoride, ClF3 using so-called ELF basins to locate centroids for both the covalent F-Cl bond electrons and the chlorine lone-pair electrons. Whereas the original VSEPR theory talks about five “electron pairs” totalling an octet-busting ten electrons surrounding chlorine, the electron density-based ELF approach located only ~6.8e surrounding the central chlorine and no “octet-busting”. The remaining electrons occupied fluorine lone pairs rather than the shared Cl-F regions. Here I take a look at ClMe3, as induced by the analysis of SeMe6.

The difference between ClF3 and ClMe3 is that octet-excess electrons (two in this case) in the former can relocate into fluorine lone pairs by occupying in effect anti-bonding orbitals and hence end up not contributing to the central atom valence shell.‡ With ClMe3 the methyl groups cannot apparently sustain such lone pairs, at least not distinct from the Cl-C bond region. So might we get an octet-busting example with this molecule? A ClMe3 calculation (ωb97xd/6-311++g(d,p)) reveals a molecule with all real vibrational modes (i.e. a minimum, FAIR data DOI: 10.14469/hpc/3241) and ELF (FAIR data DOI 10.14469/hpc/3242)† basins as shown below:

Density-derived approach: Two of the C-Cl bonds each exhibit two ELF basins; one disynaptic basin (0.94e) and one monosynaptic basin (0.20e) closer to the chlorine. The former pair integrate to 1.88e, density which largely arises from carbon (natural charge -0.84) and which contribute to a total integration for these carbons of 7.17e. The latter pair contributes to a total chlorine integration of 7.19e. The angle subtended at chlorine for the two 2.68e “lone pair” basins is 141°. Thus an inner, octet-compliant, valence-shell for chlorine is revealed, plus an expanded-octet outer one into which the two additional electrons go. The latter contribute to forming an octet-compliant carbon valence shell, but may be considered as not contributing to the valence shell of the other atom of the pair, the chlorine. An endo lone-pair rather than the more usual exo lone-pair if you will. These results reveal that the molecular feature we know as a (single) “bond” may in fact have more complex inner structures or zones, something we do not normally consider bonds as having. In this model, these zones are not invariably considered as shared between both the atoms comprising the bond.

Orbital-derived approach: NBO analysis (FAIR data DOI: 10.14469/hpc/3241) reveals the chlorine electronic configuration as [core]3S(1.83)3p(4.67)4S(0.01)3d(0.03)5p(0.02,) showing very little population of the Rydberg shells (4s, 3d, 5p) occurs (0.13e in total). This method of partitioning the electrons allocates a chlorine Wiberg bond index of 2.00 and the methyl carbon bond index of  3.83. If the regular valence of Cl is taken as 1, then the central chlorine can be regarded as non-Rydberg hypervalent (the electrons in the 0.94e basins are taken as contributing to the chlorine bond index).

The carbon-halogen bond internal structures simplify for Br (DOI: 10.14469/hpc/3248, 10.14469/hpc/3250) and I (DOI: 10.14469/hpc/3249, 10.14469/hpc/3247); for each only a single ELF basin is located and the NBO Br and I bond indices are respectively 2.10 and 2.1. This is not due to incursion of  Rydberg hypervalence (Br: [core]4S(1.83)4p(4.46)5S(0.02)4d(0.03)6p( 0.01); I: [core]5S(1.82)5p(4.29)6S(0.02)5d(0.02)6p(0.01) ) but of a merging of the carbon and halogen valence basin such that the ELF contributions to each cannot be deconvoluted. In each case the NBO bond indices of ~2 suggest hypervalency for the halogen.

What have we learnt?  That the shared electron (covalent) bond can have complex internal features, such as two discrete basins for the apparently shared electrons. How one partitions these electrons can influence the value one obtains for the total shared electron count and hence whether the octet is retained or expanded for main group elements such as the halogens. And finally, that hypervalence and hyper-coordination are related in the orbital model at least. Thus along the series MenI (n= coordination number 1,3,5,7), the values of the Wiberg bond index at the halogen progress as 1.0, 2.1, 3.1 (DOI: 10.14469/hpc/3236) and 4.01 (DOI: 10.14469/hpc/3238), or one extra atom bond index per electron pair.  Given this, it seems useful to retain the distinction between the terms hypervalence and hyper-coordination, but also recognize that we still may have much to learn about the former.

‡See the previous post on SeMe6 for a more detailed discussion.

† The FAIR Data accompanying this blog post is organised in a new way here. All the calculations are collected together with an over-arching DOI: 10.14469/hpc/3252 associated with this post, with individual entries accessible directly using the DOIs given above. The post itself has a  DOI: 10.14469/hpc/3255 and the two identifiers are associated with each-other via their respective metadata.  A set of standards (https://jats.nlm.nih.gov) with implementation guidelines for e.g. repositories, authors and publishers-editors  are expected in the future to establish infra-structures for cross-linking narratives/stories with the data on which they are based.

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A periodic table for anomeric centres, this time with quantified interactions.

Monday, August 8th, 2016

The previous post contained an exploration of the anomeric effect as it occurs at an atom centre X for which the effect is manifest in crystal structures. Here I quantify the effect, by selecting the test molecule MeO-X-OMe, where X is of two types:

  1. A two-coordinate atom across the series B-O and Al-S, and carrying the appropriate molecular charge such that X carries two lone pairs of electrons (thus the charge is 0 for O, but -3 for B).
  2. A four-coordinate atom across the series B-O and Al-S, with X-H bonds replacing the lone pairs on this centre in the previous example, and again with appropriate molecule charges (e.g. +2 for  SH2).

The donor in the anomeric interaction always originates on the oxygen of the MeO group attached to X. The acceptor is always the X-O σ* empty orbital. The results (table below, ωB97XD/Def2-TZVPP calculation, NBO E(2) in kcal/mol) confirm that as X gets more electronegative, the X-O σ* empty orbital becomes a better acceptor, and so the NBO E(2) interaction energy which quantifies the anomeric interaction gets larger. Eventually (with X=OH2) the donation of electrons into the X-O σ* empty orbital becomes so effective that the X-O bond (in this case O-O) dissociates fully and the NBO perturbation cannot be computed. Also for reference, a “normal” anomeric interaction (such as is found in e.g. sugars) is around 18 kcal/mol. Anything larger than this could be considered especially strong, and anything less than ~10 kcal/mol would be regarded as weak. 

X[1]*
BH2 CH2 NH2 OH2
12.5 17.7 18.5 dissociates
AlH2 SiH2 PH2 SH2
6.9 12.9 21.9 31.3
B C N O
8.3 11.7 12.9 14.2
Al Si P S
4.8 6.6 11.2 18.2

For the entry X=S, the E(2) term is actually larger than for the oxygen. I should note that the Me group itself is not passive in this process. The C-H bonds can also act as significant electron donors, but here I am not going to analyse this additional complexity.

This table reveals that there is nothing special about carbon as an anomeric centre, and here also the normal intimate association with the term anomeric and heterocyclohexanes such as found in sugars.

* Here I introduce a refinement to my normal process of citing the data produced for any specific calculation. Rather than including 16 individual citations for each cell in the table, I have gathered all these calculations into a collection and cite here only the DOI of that collection. When resolved, the individual members of that collection can then be inspected for the actual data.

References

  1. H. Rzepa, "Anomeric interactions at atom centres", 2016. https://doi.org/10.14469/hpc/1221

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A periodic table for anomeric centres.

Saturday, August 6th, 2016

In the last few posts, I have explored the anomeric effect as it occurs at an atom centre X. Here I try to summarise the atoms for which the effect is manifest in crystal structures.

The effect is defined by X bearing two substituents, one of which Z is a centre bearing a “lone pair” of electrons (or two electrons in a π-bond), and another Y in which the X-Y bond has a low-lying acceptor or σ* empty orbital into which the lone pair can be donated. This donation will only occur if the Z-lone pair and the X-Y bond vectors align antiperiplanar. Here is the summary so far.

X Blog entry
B 16601
C 14508,8898
N this one
O 16646
Si 16601
P 16601
S this one

As required of a good periodic table, it has gaps that need completing, in this case X=N and X=S. Firstly N, for which the small molecule below is known (FUHFAP).

FUHFAP

A ωB97XD/Def2-TZVPP calculation[1] yields an electron density distribution, which can be collected into monosynaptic basins using the ELF technique. There are two oxygen lone pairs (17 and 20) that are close to antiperiplanar to the adjacent N-O bond, having E(2) interaction energies obtained using the NBO method of 15.1 and 15.8 kcal/mol, typical of the anomeric range. The basin labelled 13 on X=N1 below is also perfectly aligned antiperiplanar with the adjacent O3-C2 bond, but its E(2) interaction energy is only 7.3 kcal/mol. Thus a strong anomeric interaction on the anomeric atom itself does not seem to occur. The same effect was noted for X=O in the previous post; the explanation remains unidentified.

FUHFAP

With the X=S gap, we have lots of opportunity with polysulfide compounds, a good example of which is the C2-symmetric and helical S8 dianion TEGWAF[2]

TEGWAF

Each of the 8 sulfur atoms exhibits antiperiplanar orientation of an S lone pair with an adjacent S-S acceptor σ* orbital;
1:2-3=23.7 kcal/mol;
2:3-4=18.5;
3:4-8=11.7, 3:2-1=7.4;
4:8-7=11.4, 4:3-2=9.2.

This just surveys the central main group elements, and it is possible that this little mini-periodic table may yet grow.

References

  1. H.S. Rzepa, "C 2 H 7 N 1 O 2", 2016. https://doi.org/10.14469/ch/195294
  2. Rybak, W.K.., Cymbaluk, A.., Skonieczny, J.., and Siczek, M.., "CCDC 880780: Experimental Crystal Structure Determination", 2012. https://doi.org/10.5517/ccykj88

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Ways to encourage water to protonate an amine: superbasing.

Friday, April 8th, 2016

Previously, I looked at models of how ammonia could be protonated by water to form ammonium hydroxide. The energetic outcome of my model matched the known equilbrium in water as favouring the unprotonated form (pKb ~4.75). I add here two amines for which R=Me3Si and R=CN. The idea is that the first will assist nitrogen protonation by stabilising the positive centre and the second will act in the opposite sense; an exploration if you like of how one might go about computationally designing a non-steric superbasic amine that becomes predominantly protonated when exposed to water (pKb <1)† and is thus more basic than hydroxide anion in this medium.

NH3-8

Before reporting any calculations, let us see what the CSD (Cambridge structure database) might contain. The search query is simple, a 3-coordinate amine forming a 4-coordinate quaternary nitrogen† with one N-H and a positive (formal) charge on the N, and a 1-coordinate oxygen with one O-H and a negative charge on the O. With the constraints R < 10%, no disorder and no errors, one gets as many as 15 hits,[1] several of which also apparently contain separate water molecules in the crystal. A warning bell (perhaps several) sounds, since if R < 5%, the number of hits drops to just 2; these are clearly difficult structures to refine!‡ So there is some tantalising evidence that in the solid state at least, the quaternary ammonium group (with at least one N-H), water and a hydroxide anion might be capable of co-existence. As noted below† some fascinating 2-coordinate amines have also been reported as having superbasic properties.

NH3-8

R=CN: the well known compound cyanamide is known to act only as an acid and its basic properties are never quoted. Shown below is the reaction path for transfer of a proton from water to the amine using an 8-water model (n=8) in which two bridges can serve to help stabilize any ionic form. The energy required to do so however is at least 24 kcal/mol (ωB97XD/Def2-TZVPPD/SCRF=water) which indicates that no protonated amine is formed. This can be attributed to the electron withdrawing cyano group strongly destablising any adjacent positive ammonium centre and thus effectively completely inhibiting its formation.

NH3-8

R=Me3Si: this too is already known[2],[3] but only in the presence of the non-coordinating counter-anion B(C6F5)4 crystallised from non-protic solution. An ionised form can now be located using the model above. This has the structure shown below; note the very short hydrogen bonds associated with the hydroxide anion and the possibility of forming only two water bridges across the ion-pair. The relative free energy of the ion-pair (table below) shows it to be if anything less basic than ammonia. 

NH3-8

n=8 R=H R=SiMe3 R=CN
ΔΔG298 7.0[4]

7.6[5],[6]

>24[7]

NBO (natural bond orbital) analysis might here  be a useful metric of basicity. Hence Me3SiNH2…H2O  suggests that donation from the N lone pair into an antiperiplanar Si-C bond is quite large (E(2) = 11.9 kcal/mol), although alternative donation by nitrogen into the H-O σ* bond  of the water is much higher (33.4 kcal/mol). 

Perhaps the basicity of simple amines is related to their ability to form stabilizing water bridges across the ion-pair? With trimethylsilyl substituents, this feature (and hence the basicity) is partially or even fully suppressed as in e.g. tris(trimethylsilyl)amine.The pKb of the latter appears to be unreported[8] but it does seem to be only weakly basic and "inert to H2O",[9] a property attributed instead to multiple character in the Si-N bonds. 

I will in a future post look at the alternative class of phosphazenium amines which do manage to achieve superbasicity.[10]

†A phosphazenium 3-coordinate amine[11] was in 1991 claimed to be the strongest metal-free neutral base. This has now been superceded by combining this base motif with that of a sterically operating proton sponge.[12],[10] I will report the computational modelling of these systems in a later post.

‡One of the structures identified with R<10% is UBEJIU[13] and which is worth showing below. Note the apparent close contact of the type N-H…H-O (1.416-1.463Å) rather than the expected N-H…OH.  If correct (this feature is not mentioned in the article itself) it would be classified as a dihydrogen bond, a type normally only found in situations such as B-H…H-N. There are a number of other inconsistencies which must be resolved if this structure is to stand as correct.

NH3-8

References

  1. H. Rzepa, "Substituted ammonium hydroxides", 2016. https://doi.org/10.14469/hpc/361
  2. Y. Sarazin, J.A. Wright, and M. Bochmann, "Synthesis and crystal structure of [C6H5Hg(H2NSiMe3)][H2N{B(C6F5)3}2], a phenyl–mercury(II) cation stabilised by a non-coordinating counter-anion", Journal of Organometallic Chemistry, vol. 691, pp. 5680-5687, 2006. https://doi.org/10.1016/j.jorganchem.2006.09.021
  3. Sarazin, Y.., Wright, J.A.., and Bochmann, M.., "CCDC 608250: Experimental Crystal Structure Determination", 2007. https://doi.org/10.5517/ccndxzx
  4. H.S. Rzepa, and H.S. Rzepa, "H21NO9", 2016. https://doi.org/10.14469/ch/191946
  5. H.S. Rzepa, and H.S. Rzepa, "C 3 H 29 N 1 O 9 Si 1", 2016. https://doi.org/10.14469/ch/191987
  6. H.S. Rzepa, and H.S. Rzepa, "C 3 H 29 N 1 O 9 Si 1", 2016. https://doi.org/10.14469/ch/191982
  7. H.S. Rzepa, "CH20N2O9", 2016. https://doi.org/10.14469/ch/191983
  8. E.W. Abel, D.A. Armitage, and G.R. Willey, "Relative base strengths of some organosilicon amines", Transactions of the Faraday Society, vol. 60, pp. 1257, 1964. https://doi.org/10.1039/tf9646001257
  9. J. Goubeau, and J. Jimenéz‐Barberá, "Tris‐(trimethylsilyl)‐amin", Zeitschrift für anorganische und allgemeine Chemie, vol. 303, pp. 217-226, 1960. https://doi.org/10.1002/zaac.19603030502
  10. Kögel, Julius F.., Oelkers, Benjamin., Kovačević, Borislav., and Sundermeyer, Jörg., "CCDC 1002088: Experimental Crystal Structure Determination", 2014. https://doi.org/10.5517/cc12mrfw
  11. R. Schwesinger, and H. Schlemper, "Peralkylated Polyaminophosphazenes— Extremely Strong, Neutral Nitrogen Bases", Angewandte Chemie International Edition in English, vol. 26, pp. 1167-1169, 1987. https://doi.org/10.1002/anie.198711671
  12. J.F. Kögel, B. Oelkers, B. Kovačević, and J. Sundermeyer, "A New Synthetic Pathway to the Second and Third Generation of Superbasic Bisphosphazene Proton Sponges: The Run for the Best Chelating Ligand for a Proton", Journal of the American Chemical Society, vol. 135, pp. 17768-17774, 2013. https://doi.org/10.1021/ja409760z
  13. P. Vianello, A. Albinati, G.A. Pinna, A. Lavecchia, L. Marinelli, P.A. Borea, S. Gessi, P. Fadda, S. Tronci, and G. Cignarella, "Synthesis, Molecular Modeling, and Opioid Receptor Affinity of 9,10-Diazatricyclo[4.2.1.1<sup>2,5</sup>]decanes and 2,7-Diazatricyclo[4.4.0.0<sup>3,8</sup>]decanes Structurally Related to 3,8-Diazabicyclo[3.2.1]octanes", Journal of Medicinal Chemistry, vol. 43, pp. 2115-2123, 2000. https://doi.org/10.1021/jm991140q

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VSEPR Theory: A closer look at trifluorothionitrile, NSF3.

Saturday, January 16th, 2016

The post on applying VSEPR ("valence shell electron pair repulsion") theory to the geometry of ClF3 has proved perennially popular. So here is a follow-up on another little molecue, F3SN. As the name implies, it is often represented with an S≡N bond. Here I take a look at the conventional analysis.

trifluoorothionitrile

This is as follows:

  1. Six valence electrons on the central S atom.
  2. Three F atoms contribute one electron each.
  3. One electron from the N σ-bond.
  4. Donate two electrons from S to the two π-bonds.
  5. Eight electrons left around central S, ≡ four valence shell electron pairs.
  6. Hence a tetrahedral geometry.
  7. The bond-bond repulsions however are not all equal. The SN bond repels the three SF bonds more than the S-F bonds repel each-other.
  8. Hence the N-S-F angle is greater than the F-S-F angle, a distorted tetrahedron.

Now for a calculation[1];  ωB97XD/Def2-TZVP, where the wavefunction is analysed using ELF (electron localisation function), which is a useful way of locating the centroids of bonds and lone pairs (click on diagram below to see 3D model).

Trifluorosulfonitrile

  • At the outset one notes that there are six ELF disynaptic basins surrounding the central S, integrating to a total of 7.05e. The sulfur is NOT hypervalent; it does not exceed the octet rule.
  • These six "electron sub-pair" basins are arranged octahedrally around the sulfur. The coordination is NOT tetrahedral, as implied above.
  • The three S-N basins have slightly more electrons (1.25e) than the three S-F basins (1.10e), resulting in …
  • the angle subtended at the S for the SN basins being 96° (a bit larger than octahedral) whilst the angle subtended at the S for the SF basins being smaller (89.9°). This matches point 7 above, but is achieved in an entirely different manner.
  • As a result, the N-S-F angle (122.5°) is larger than the ideal tetrahedral angle and the F-S-F angle (93.9°) is smaller, an alternative way of expressing point 7 above.
  • The S≡N triple bond as shown above does have some reality;  it is a "banana bond" with three connectors rather than two. Each banana bond however has only 1.25e, so the bond order of this motif is ~four (not six) but nevertheless resulting in a short S-N distance (1.406Å) with multiple character.

So we have achieved the same result as classical VSEPR, but using partial rather than full electron pairs to do so. We got the same result with ClF3 before. So perhaps this variation could be called "valence shell partial electron pair repulsions" or VSPEPR.

References

  1. H.S. Rzepa, "F 3 N 1 S 1", 2016. https://doi.org/10.14469/ch/191808

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A visualization of the anomeric effect from crystal structures.

Thursday, August 27th, 2015

The anomeric effect is best known in sugars, occuring in sub-structures such as RO-C-OR. Its origins relate to how the lone pairs on each oxygen atom align with the adjacent C-O bonds. When the alignment is 180°, one oxygen lone pair can donate into the C-O σ* empty orbital and a stabilisation occurs. Here I explore whether crystal structures reflect this effect.

Scheme

The torsion angles along each O-C bond are specified, along with the two C-O distances. All the bonds are declared acyclic, and the usual R < 5%, no disorder and no errors specified.

  1. You can see from the plot below that the hotspot occurs when both RO-CO torsions are ~65°. From this we will assume that the two (unseen)‡ lone pairs at any one of the oxygens are distributed approximately tetrahedrally around each oxygen, and if this is true then one of them must by definition be oriented ~ 180° with respect to the same RO-CO bond (the other is therefore oriented -60°). This allows it to be antiperiplanar to the adjacent C-O bond and hence interact with its σ* empty orbital. So the hotspot corresponds to structures where BOTH oxygen atoms have lone pairs which interact with the adjacent O-C anti bond.
  2. There is a tiny cluster for which both RO-CO torsions are ~180° and hence neither oxygen has an antiperiplanar lone pair.
  3. Only slightly larger are clusters where one torsion is ~65° and the other ~180°, meaning that only one oxygen has an antiperiplanar lone pair.
  4. A plot of the two C-O lengths indeed shows an overall hotspot at ~1.40Å for both distances. If the search is filtered to include only torsions in the range 150-180°, the hotspot value increases to 1.415Å for both. If one torsion is restricted to 40-80° and the other to 150-180° the hotspot shows one C-O bond is about 0.012Å shorter than the other.

Scheme

Scheme

I also include a further constraint, that the diffraction data must be collected below 140K. The hotspot moves to ~ 55/60° indicating values free of some vibrational noise.

Scheme

Interestingly, replacing  oxygen with  nitrogen reveals relatively few examples of the effect (C(NR2)4 is an exception). Replacing  O by divalent S produces only 13 hits, with the surprising result (below) that in all of them only one S sets up an anomeric interaction. Arguably, the number of examples is too low to draw any firm conclusions from this observation.

Scheme

‡Most diffractometers measure low angle scattering of X-rays by high density electrons. These are the core electrons associated with a nucleus rather than the valence electrons associated with lone pairs. Hence very few positions of valence lone pairs have ever been crystallographically measured.

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