Archive for the 'Uncategorized' Category

Extremely short non-bonding HH distance

What is the closest non-bonding HH distance within a single molecule? The world record had been 1.617 Å in a pentacyclodecane.1 This record now appears to be broken by the preparation of the disilane 1.2 The 1H NMR and IR suggest the interior hydrogens are very close. The x-ray structure of 1 indicates a very short Si-Si distance of 4.433 Å, a distance that must accommodate two S-H bonds, typically about 1.48 Å and the HH non-bonded distance, which might be as short then as 1.47 Å! The crystal is unfortunately not large enough for a neutron diffraction study, which would enable precise location of the hydrogens.


However, computations can help here, and they suggest a HH separation of only 1.57 Å: this is the distance obtained with B3PW91/6-311+G(2d,p), M062x/6-311+G(2d,p) and MP2/6-31G(d). The M062x/6-311+G(2d,p) structure is shown in Figure 1.

Figure 1. The M062x/6-311+G(2d,p) optimized structure of 1.

Any ideas for a compound with an even shorter non-bonded HH distance?


(1) Ermer, O.; Mason, S. A.; Anet, F. A. L.; Miura, S. S. "Ultrashort nonbonded hydrogenhydrogen distance in a half-cage pentacyclododecane," J. Am. Chem. Soc. 1985, 107, 2330-2334, DOI: 10.1021/ja00294a023.

(2) Zong, J.; Mague, J. T.; Pascal, R. A. "Exceptional Steric Congestion in an in,in-Bis(hydrosilane)," J. Am. Chem. Soc. 2013, 135, 13235-13237, DOI: 10.1021/ja407398w.


1: InChI=1S/C39H32S3Si2/c1-7-19-34-28(13-1)25-40-31-16-4-10-22-37(31)44-38-23-11-5-17-32(38)41-26-29-14-2-8-20-35(29)43(34)36-21-9-3-15-30(36)27-42-33-18-6-12-24-39(33)44/h1-24,43-44H,25-27H2

Uncategorized Steven Bachrach 01 Oct 2013 12 Comments

thiourea-catalyzed hydroamination

Jacobsen reports on another application of thiourea-based organocatalysts, this time for the
catalysis of hydroamination.1 To support the synthetic effort, he examined the uncatalyzed intramolecular hydroamination that takes 1, through TS1 into product 2. The geometry of TS1 optimized at B3LYP/6-31+G(d,p) is shown in Figure 1. The computed barrier for this reaction is 22.2 kcal mol-1. Using a model thiourea as the catalyst (MeHN)2C=S, 3), Jacobsen locates a
catalyzed transition state TS2 shown in Figure 1. The activation barrier for this catalyzed reaction is 19.1 kcal mol-1, suggesting that a thiourea can afford a real catalytic effect.



Figure 1. B3LYP/6-31+G(d,p) optimized geometries of TS1 and TS2(the catalyzed transition state).

Jacobsen then goes on to show that 4 can act as both an excellent catalyst for the hydroamination reaction along with inducing significant enantioselectivity. An example is Reaction 1, where 10 mol% of catalyst 3 gives an overall yield of 83% and an ee of 91%, while in the absence of catalyst the yield is only 8%.


(1) Brown, A. R.; Uyeda, C.; Brotherton, C. A.; Jacobsen, E. N. "Enantioselective Thiourea-Catalyzed Intramolecular Cope-Type Hydroamination," J. Am. Chem. Soc. 2013, 135, 6747-6749, DOI: 10.1021/ja402893z.


1: InChI=1S/C5H11NO/c1-2-3-4-5-6-7/h2,6-7H,1,3-5H2

2: InChI=1S/C5H11NO/c1-5-3-2-4-6(5)7/h5,7H,2-4H2,1H3

3: InChI=1S/C3H8N2S/c1-4-3(6)5-2/h1-2H3,(H2,4,5,6)

4: InChI=1S/C44H49N3OS/c1-44(2,3)42(41(48)36-25-15-24-35(36)34-23-14-21-30-16-10-11-22-33(30)34)46-43(49)45-37-26-12-13-27-40(37)47-38(31-17-6-4-7-18-31)28-29-39(47)32-19-8-5-9-20-32/h4-11,14,16-23,28-29,35-37,40,42H,12-13,15,24-27H2,1-3H3,(H2,45,46,49)/t35-,36?,37-,40-,42-/m1/s1

Uncategorized Steven Bachrach 10 Jul 2013 No Comments

Second edition of Computational Organic Chemistry

After much delay, the second edition of my book Computational Organic Chemistry has been sent off to the publisher! This edition is an update from the first, including many new examples of the major themes covered in the first edition. In addition there are some entirely new sections and chapters, extending the scope of the book into areas not mentioned in the first edition. There are also some new interviews of major players in the field. Comments from this blog where helpful in guiding my choices for what new materials to include in the book.

I suspect that editing of the book and making it all ready for print will take through the rest of the year. Later on this year I will discuss in the blog the new features of the book in some detail.

I intend to continue to blog on new papers through the publication of the second edition and beyond. So continue to monitor this blog for new papers and for information on where and when to purchase the second edition!

Uncategorized Steven Bachrach 10 Jun 2013 6 Comments

Covalently linked cycloparaphenylenes – onwards to nanotubes

Nanotubes are currently constructed in ways that offer little control of their size and chirality. The recent synthesis of cycloparaphenylenes (CPP) provides some hope that fully controlled synthesis of nanotubes might be possible in the near future. Jasti has now made an important step forward in preparing dimers of CPP such as 1.1



They also performed B3LYP-D/6-31G(d,p) computations on 1 and the directly linked dimer 2. The optimized geometries of these two compounds in their cis and trans conformations are shown in Figure 1. Interestingly, both compounds prefer to be in the cis conformation; cis-1 is 10 kcal mol-1 more stable than trans-1 and cis-2 is 30 kcal mol-1 more stable than the trans isomer. While a true transition state interconnecting the two isomers was not located, a series of constrained optimizations to map out a reaction surface suggests that the
barrier for 1 is about 13 kcal mol-1. The authors supply an interesting movie of this pseudo-reaction path (download the movie).





Figure 1. B3LYP-D/6-31G(d,p) optimized geometries of the cis and trans conformers of 1 and 2. (Be sure to click on these images to launch a 3-D viewer; these structures come to life in 3-D!)


(1) Xia, J.; Golder, M. R.; Foster, M. E.; Wong, B. M.; Jasti, R. "Synthesis, Characterization, and Computational Studies of Cycloparaphenylene Dimers," J. Am. Chem. Soc. 2012, 134, 19709-19715, DOI: 10.1021/ja307373r.


1: InChI=1S/C106H82/c1-5-13-79-21-9-17-76-29-37-85(38-30-76)95-59-63-98(64-60-95)103-71-69-101(82(16-8-4)24-12-20-77-27-35-84(36-28-77)90-51-55-94(56-52-90)91-45-41-86(79)42-46-91)73-105(103)99-65-67-100(68-66-99)106-74-102-70-72-104(106)97-61-57-88(58-62-97)81(15-7-3)23-10-18-75-25-33-83(34-26-75)89-49-53-93(54-50-89)92-47-43-87(44-48-92)80(14-6-2)22-11-19-78-31-39-96(102)40-32-78/h5-16,21-74H,1-4,17-20H2/b21-9-,22-11-,23-10-,24-12-,79-13+,80-14+,81-15+,82-16+

2: InChI=1S/C100H78/c1-5-13-75-21-9-17-72-29-37-81(38-30-72)91-59-63-94(64-60-91)97-67-65-95(78(16-8-4)24-12-20-73-27-35-80(36-28-73)86-51-55-90(56-52-86)87-45-41-82(75)42-46-87)69-99(97)100-70-96-66-68-98(100)93-61-57-84(58-62-93)77(15-7-3)23-10-18-71-25-33-79(34-26-71)85-49-53-89(54-50-85)88-47-43-83(44-48-88)76(14-6-2)22-11-19-74-31-39-92(96)40-32-74/h5-16,21-70H,1-4,17-20H2/b21-9-,22-11-,23-10-,24-12-,75-13+,76-14+,77-15+,78-16+

Uncategorized Steven Bachrach 22 Jan 2013 No Comments

Long C-O bonds

I have written a number of posts discussing long C-C bonds (here and here). What about very long bonds between carbon and a heteroatom? Well, Mascal and co-workers1 have computed the structures of some oxonium cations that express some very long C-O bonds. The champion, computed at MP2/6-31+G**, is the oxatriquinane 1, whose C-O bond is predicted to be 1.602 Å! (It is rather disappointing that the optimized structures are not included in the supporting materials!) The long bond is attributed not to dispersion forces, as in the very long C-C bonds (see the other posts), but rather to σ(C-H) or σ(C-C) donation into the σ*(C-O) orbital.


Inspired by these computations, they went ahead and synthesized 1 and some related species. They were able to get crystals of 1 as a (CHB11Cl11)- salt. The experimental C-O bond lengths for the x-ray crystal study are 1.591, 1.593, and 1.622 Å, confirming the computational prediction of long C-O bonds.

As an aside, they also noted many examples of very long C-O distances within the Cambridge
Structural database that are erroneous – a cautionary note to anyone making use of this database to identify unusual structures.


(1) Gunbas, G.; Hafezi, N.; Sheppard, W. L.; Olmstead, M. M.; Stoyanova, I. V.; Tham, F. S.; Meyer, M. P.; Mascal, M. "Extreme oxatriquinanes and a record C–O bond length," Nat. Chem. 2012, 4, 1018-1023, DOI: 10.1038/nchem.1502


1: InChI=1S/C21H39O/c1-16(2,3)19-10-12-20(17(4,5)6)14-15-21(13-11-19,22(19)20)18(7,8)9/h10-15H2,1-9H3/q+1/t19-,20+,21-

Uncategorized Steven Bachrach 07 Jan 2013 1 Comment

The longest straight chain alkane

The role of dispersion in understanding organic chemistry, both structure and reactivity, is truly coming into prominence (see for example this blog post for a compound whose stability is the result of dispersion). This has been driven in part by new computational techniques to properly account for dispersion. An interesting recent example is the structure of long chain alkanes, with a question posed and answered by Mata and Suhm:1 What is the largest alkane whose most stable conformation is the extended chain?

The question is attacked by computation and experiment. The computational methodology involves corrections to the local MP2-F12 energy involving the separation of orbital pairs that are treated with a coupled clusters method. The straight chain (having only anti arrangements about the C-C bonds) and the hairpin conformer (having three gauche arrangements) were completely optimized. The C17H36 hairpin isomer is shown in Figure 1. For chains with 16 or fewer carbons, the all-anti straight chain is lower in energy, but for chains with 17 or more carbon atoms, the hairpin is lower in energy. Gas-phase low temperature IR and Raman spectra suggest that dominance of the hairpin occurs when the chain has 18 carbons, though careful analysis suggests that this is likely an upper bound. At least tentatively the answer to the question is that heptadecane is likely the longest alkane with a straight chain, but further lower temperature experiments are needed to see if the C16 chain might fold as well.

Figure 1. Optimized geometry of the hairpin conformation of heptadecane.

(I thank Dr. Peter Schreiner for bringing this paper to my attention.)


(1) Lüttschwager, N. O. B.; Wassermann, T. N.; Mata, R. A.; Suhm, M. A. "The Last Globally Stable Extended Alkane," Angew. Chem. Int. Ed. 2012, ASAP, DOI: 10.1002/anie.201202894.


Heptadecane: InChI=1S/C17H36/c1-3-5-7-9-11-13-15-17-16-14-12-10-8-6-4-2/h3-17H2,1-2H3

Uncategorized Steven Bachrach 10 Sep 2012 3 Comments

Structure of 1-Methyl-Piperidone

The combined supersonic jet expansion and Fourier transform microwave spectroscopy provides an excellent opportunity for the synergistic workings of experiments and computations. This is nicely demonstrated in the study of 1-methyl-4-piperidone.1

The careful microwave study allows for the full structural characterization of the equatorial form 1e along with obtaining a good deal of information concerning the axial form 1a. To help evaluate the experimental data, the authors have optimized the structure of the two isomers at MP2, B3LYP and M06-2x using the 6-311++G(d,p) basis set.

The rotational parameters computed with the three methods are in very fine agreement with the experimental values. Of particular note is that the three computations predict a different sign for the nuclear quadrupole coupling tensor elements χaa and χbb, and this is observed in the experiment as well. It is perhaps the critical identifier of the axial isomer. The computed and experimental geometries of 1e are in fine agreement, with the largest deviation of a few degrees in the dihedral angle of the carbonyl to the ring. The experiment suggests an energy difference of 11.9 kJ mol-1, which is corroborated by MP2, B3LYP and M06-2x computations. In fact, these first two methods predict an enthalpy difference within a kJ of the experimental value.


(1) Evangelisti, L.; Lesarri, A.; Jahn, M. K.; Cocinero, E. J.; Caminati, W.; Grabow, J.-U., "N-Methyl Inversion and Structure of Six-Membered Heterocyclic Rings: Rotational Spectrum of 1-Methyl-4-piperidone," J. Phys. Chem. A, 2011,
115, 9545–9551, DOI: 10.1021/jp112425w


1: InChI=1/C6H11NO/c1-7-4-2-6(8)3-5-7/h2-5H2,1H3

Uncategorized Steven Bachrach 20 Sep 2011 No Comments

Topics for a new edition of Computational Organic Chemistry

I am very much contemplating a second edition of my book Computational Organic Chemistry, which is the basis of this blog. I have been in touch with Wiley and they are enthusiastic about a second edition.

Here is a list of some of the things I am contemplating as new topics for the second edition

  1. Discussion of the failures of many of the standard functionals (like B3LYP) to treat simple organics
  2. Predicting NMR, IR and ORD spectra
  3. Möbius compounds, especially aromatics
  4. π-π-stacking
  5. tunneling in carbenes (Schreiner and Allen’s great work)
  6. acidity of amino acids and remote protons
  7. bifurcating potential energy surfaces and the resultant need for dynamic considerations
  8. even more examples of dynamics – especially the roundabout SN2

So, I would like to ask my readers for suggestions of other ideas for new topics to add to the book. These can be extensions of the topics already covered, or brand new areas!

Additionally, I am planning on interviewing a few more people for the book, similar in spirit to the 6 interviews in the first addition. Again, I welcome any suggestions for computational chemists to interview!

Uncategorized Steven Bachrach 09 Aug 2011 6 Comments

Cyclopentane IR spectra

Laane has utilized high level computations to examine the high resolution IR and raman spectra of cyclopentane and some deuterated isomers.1 What is particularly of interest here is the excellent agreement between the experiment and computations. The barrier for planarity is estimated from experiment to be 1808 cm-1 and CCSD/cc-pVTZ predicts a value of 1887 cm-1 – excellent agreement. The B3LYP/cc-pVTZ computed frequencies for the C2 and Ci conformations were scaled by 0.985 for frequencies less than 1450 cm-1, 0.975 for frequencies between 1450 and 200 cm-1 and by 0.961 for frequencies above 2000 cm-1. These frequencies are very similar to one another. In comparison of these averaged frequencies with the experimental frequencies the root mean squared error is only 8.8 cm-1! As stressed by these authors, computational is important partner with experiment in characterizing spectra.


(1) Ocola, E. J.; Bauman, L. E.; Laane, J., "Vibrational Spectra and Structure of Cyclopentane and its Isotopomers," J. Phys. Chem. A, 2011, 115, 6531–6542, DOI: 10.1021/jp2032934.


Cyclopentane: InChI=1/C5H10/c1-2-4-5-3-1/h1-5H2 InChIKey=RGSFGYAAUTVSQA-UHFFFAOYAL

Uncategorized Steven Bachrach 26 Jul 2011 2 Comments

Conformation of propyphenazone

Compounds like antipyrine 1 might be expected to have two pyramidal nitrogens with their substituents on opposite sides of the ring. Interestingly, a new polymorph of propyphenazone 2 has both N-methyl and N-phenyl groups on the same side of the ring. Just how unusual is this?



Roumanos and Kertesz1 have sampled the crystallographic database and found 334 structures with the antipyrine backbone. The vast majority of them have the nitrogen substituents on opposite sides, and a few structures have these groups essential co-planar with the ring. The new propyphenazone structure does seem to be unusual. However, they also performed a BLYP/DNP scan of the potential energy surface of 2. When this surface is overlayed on the distribution of the x-ray structures, one sees that most structures are within 3 kcal mol-1 of the energy minimum (with the nitrogen groups on opposite sides). However, the structure with both groups on the same side is about 4 kcal mol-1 higher in energy than the minimum energy structure, and the nearly planar structures are higher in energy still. Thus, the authors conclude that while this new structure is unusual, it is not an outlier.


(1) Roumanos, M.; Kertesz, M., "Conformations of Antipyrines," J. Phys. Chem.A, 2011, ASAP, DOI: 10.1021/jp201510w


1: InChI=1/C11H12N2O/c1-9-8-11(14)13(12(9)2)10-6-4-3-5-7-10/h3-8H,1-2H3

2: InChI=1/C14H18N2O/c1-10(2)13-11(3)15(4)16(14(13)17)12-8-6-5-7-9-12/h5-10H,1-4H3

Uncategorized Steven Bachrach 08 Jun 2011 1 Comment

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