Search Results for "schreiner carbene"

Structure of dihydroxycarbene

Dihdroxycarbene was the subject of a post a few years ago relating to how this carbene does not undergo tunneling,1 while related hydroxycarbene do undergo a tunneling rearrangement.

Now we have a gas-phase microwave determination of the trans,cis isomer of dihydroxycarbene.2 The computed CCSD(T)/cc-pCVQZ structure is shown in Figure 1. What is truly remarkable here is the amazing agreement between the experimental and computed structure – as seen in Table 1.The bond distance are in agreement within 0.001 Å and the bond angles agree within 0.3°! Just further evidence of the quality one can expect from high-level computations. And computing this structure was certainly far easier than the experiments!

Figure 1. CCSD(T)/cc-pCVQZ optimized geometry of dihydroxycarbene.

Table 1. Experimental and computed (CCSD(T)/cc-pCVQZ) geometric parameters of dihydroxycarbene.a


 

Expt.

Comp.

C-O

1.335

1.336

C-O

1.309

1.309

O-Htrans

0.961

0.960

O-Hcis

0.976

0.975

O-C-O

107.30

107.25

C-O-H­­trans

106.8

106.8

C-O-H­­cis

110.7

110.4


aDistances in Å and angles in deg.

References

(1) Schreiner, P. R.; Reisenauer, H. P. "Spectroscopic Identification of Dihydroxycarbene," Angew. Chem. Int. Ed. 2008, 47, 7071-7074, DOI: 10.1002/anie.200802105.

(2) Womack, C. C.; Crabtree, K. N.; McCaslin, L.; Martinez, O.; Field, R. W.; Stanton, J. F.; McCarthy, M. C. "Gas-Phase Structure Determination of Dihydroxycarbene, One of the Smallest Stable Singlet Carbenes," Angew. Chem. Int. Ed. 2014, 53, 4089-4092, DOI: 10.1002/anie.201311082.

InChIs

Dihydroxycarbene: InChI=1S/CH2O2/c2-1-3/h2-3H
InChIKey=VZOMUUKAVRPMBY-UHFFFAOYSA-N

carbenes Steven Bachrach 09 Jun 2014 No Comments

Tunneling in t-butylhydroxycarbene

Sorry I missed this paper from much earlier this year – it’s from a journal that’s not on my normal reading list. Anyways, here is another fantastic work from the Schreiner lab demonstrating the concept of tunneling control (see this post).1 They prepare the t-butylhydroxycarbene 1 at low temperature to look for evidence of formation of possible products arising from a [1,2]-hydrogen shift (2), a [1,2]-methyl shift (3) or a [1,3]-CH insertion (4).

Schreiner performed CCSD(T)/cc-pVDZ optimizations of these compounds along with the transition states for the three migrations. The optimized geometries and relative energies are shown in Figure 1. The thermodynamic product is the aldehyde 2 while the kinetic product is the cyclopropane 4, with a barrier of 23.8 kcal mol-1 some 3.5 kcal mol-1 lower than the barrier leading to 2.

1
(0.0)

TS2
(27.3)

2
(-53.5)

TS3
(31.0)

3
(-41.0)

TS4
(23.8)

4
(-28.3)

Figure 1. CCSD(T)/cc-pVDZ optimized structures of 1-4 and the transition states for the three reaction. Relative energies in kcal mol-1.

At low temperature (11 K), 1 is found to slowly convert into 2 with a half-life of 1.7 h. No other product is observed. Rates for the three reactions were also computed using the Wentzel-Kramers-Brillouin (WKB) method (which Schreiner and Allen have used in all of their previous studies). The predicted rate for the conversion of 1 into 2, which takes place at 11 K solely through a tunneling process, is 0.4h, in quite reasonable agreement with experiment. The predicted rates for the other two potential reactions at 11 K are 1031 and 1040 years.

This is clearly an example of tunneling control. The reaction occurs not across the lowest barrier, but through the narrowest barrier.

References

(1) Ley, D.; Gerbig, D.; Schreiner, P. R. "Tunneling control of chemical reactions: C-H insertion versus H-tunneling in tert-butylhydroxycarbene," Chem. Sci. 2013, 4, 677-684, DOI: 10.1039/C2SC21555A.

InChI

1: InChI=1S/C5H10O/c1-5(2,3)4-6/h6H,1-3H3
InChIKey=ZGFKBRGJTPEEOC-UHFFFAOYSA-N

2: InChI=1S/C5H10O/c1-5(2,3)4-6/h4H,1-3H3

3: InChI=1S/C5H10O/c1-4(2)5(3)6/h6H,1-3H3
InChIKey=BZAZNULYLRVMSW-UHFFFAOYSA-N

4: InChI=1S/C5H10O/c1-5(2)3-4(5)6/h4,6H,3H2,1-2H3
InChIKey=MWWQKEGWQLBJBJ-UHFFFAOYSA-N

Schreiner &Tunneling Steven Bachrach 11 Nov 2013 No Comments

Cyclopropylhydroxycarbene

As we have noted in many previous posts, Schreiner has observed tunneling in hydroxycarbenes that is either very rapid (1a-c) or not at all (1d-f).1-4 In a recent paper his group investigates whether cyclopropylhydroxycarbene 2 might have an intermediate lifetime due to the π-donating effect of the three-member ring.5

Schreiner makes this carbene in his usual manner: flash pyrolysis of the cyclopropylglyoxylic acid. Let’s now consider three possible rearrangements of carbene 2. The hydrogen can migrate (Scheme 1, path a) to give cyclopropylcarboxyaldehyde 3 similar to what was observed with the related hydroxycarbenes. Carbon can migrate (Scheme 1, path b), opening up the three-member ring to give the cyclobutenol 4. This ring could open to the diene 5 and tautomerize to the ketone 6. Lastly, a hydrogen migration from carbon (Scheme 1, path c) would lead to 7. The relative energies of these species computed at CCSD(T)//cc-pVTZ//M06-2x//6-311++G(d,p) are shown in Scheme 1.

Scheme 1. Relative energies in kcal mol-1.

The computed barriers for the initial step of each pathway is +30.4 kcal mol-1 for path a, +21.9 kcal mol-1 for path b and +35.8 kcal mol-1 for path c. Thus, one might expect to see only the reaction along path b at low temperature and mostly along b at high temperature with some small percent along path a. So what actually occurs?

After capturing the flash pyrolysis product in an Ar matrix, besides the unreacted cyclopropylglyoxylic acid, 6, 3, and 2 are observed in an approximate 8:5:1 ratio. 2 is identified on the basis of the nice agreement between the experimental and computed IR frequencies. Irradiation of 2 in the matrix leads to clean conversion to 4, also identified by comparison of the observed and computed IR frequencies. This is all consistent with the computed activation barriers. In the pyrolysis, at high T, 6 is the major product and 3 is the minor product. At very low T (11 K), irradiation of 2 produces 4 (crossing only the lowest barrier) and not continuing further along the rearrangement path to 6.

What is perhaps most exciting is that 2 disappears slowly in the dark at both 11 K and 20 K, converting at the same rate to 3. The half life is 17.7 h, much longer than for the alkyl and aryl substituted hydroxycarbenes 1a-c. This confirms the stabilization effect of the cyclopropyl group, as does its large singlet-triplet gap. The computed tunneling half-life using the WKB approach is 16.6 h, in excellent agreement with experiment. And as expected for a tunneling phenomenon, the dueterated analog has a much longer half-life, computed to be 105 years. Experimentally, 2-d persists with no conversion to 3-d observed.

As with methylhydroxycarbene, we see here an example of tunneling control vs kinetic control. At high T, the reaction crosses the lowest barrier (shown in Figure 1a), proceeding to 4 and subsequent rearrangement products. At low T, the reaction crosses a higher barrier (shown in Figure 1b), but this path involves tunneling of the very light hydrogen atom only, producing 3.

TS 2 → 3

TS 2 → 4

Figure 1. M06-2X/6-311++G(d,p) optimized geometry of the transition states connecting 2 to (a) 3 and (b) 4.

References

(1) Schreiner, P. R.; Reisenauer, H. P.; Pickard Iv, F. C.; Simmonett, A. C.; Allen, W. D.; Matyus, E.; Csaszar, A. G., "Capture of hydroxymethylene and its fast disappearance through tunnelling," Nature, 2008, 453, 906-909, DOI: 10.1038/nature07010.

(2) Schreiner, P. R.; Reisenauer, H. P., "Spectroscopic Identification of Dihydroxycarbene," Angew. Chem. Int. Ed., 2008, 47, 7071-7074, DOI: 10.1002/anie.200802105

(3) Gerbig, D.; Reisenauer, H. P.; Wu, C.-H.; Ley, D.; Allen, W. D.; Schreiner, P. R., "Phenylhydroxycarbene," J. Am. Chem. Soc., 2010, 132, 7273-7275, DOI: 10.1021/ja9107885

(4) Schreiner, P. R.; Reisenauer, H. P.; Ley, D.; Gerbig, D.; Wu, C.-H.; Allen, W. D., "Methylhydroxycarbene: Tunneling Control of a Chemical Reaction," Science, 2011, 332, 1300-1303, DOI: 10.1126/science.1203761.

(5) Ley, D.; Gerbig, D.; Wagner, J. P.; Reisenauer, H. P.; Schreiner, P. R., "Cyclopropylhydroxycarbene," J. Am. Chem. Soc., 2011, 133, 13614-13621, DOI: 10.1021/ja204507j

Schreiner &Tunneling Steven Bachrach 31 Aug 2011 4 Comments

Methylhydroxycarbene and tunelling control

Another remarkable piece of science from the Schreiner and Allen groups has appeared demonstrating the critical importance of combining experiment with computations.1 (This one will surely be in the running for computational chemistry paper of the year.) Once again they examine tunneling from a carbene intermediate, but this time with an amazing conclusion that will have impact on chemistry textbooks!

Schreiner and Allen have previously examined a number of hydroxycarbenes (see these posts: A, B, C) and have found tunneling to be the main exit channel from these carbenes. The tunneling passes through barriers that are as large as 30 kcal mol-1, and as expected, the deuterium labeled analogues have tunneling half lives that are exceptionally long, like 4000 years.

Now they examine methylhydroxycarbene 1,1 which is interesting because there are two possible exit channels, leading to acetaldehyde 2 or vinyl alcohol 3. Previous gas-phase pyrolysis of pyruvic acid suggested the intermediacy of 1, which rearranges to 2 much more rapidly than to 3. However, G1 computations predict the barrier to 3 is smaller than the barrier to 2,2 which should mean that 2 is the kinetic product!

Methylhydroxycarbene 1 was prepared by flash pyrolysis of pyruvic acid with capture of the products in an argon matrix. The carbene 1 was characterized by IR. The predicted frequencies (CCSD(T)/cc-pCVTZ – with corrections for anharmonicity) of 9 of the 11 bands of 1 are within 8 cm-1 of the experimental frequencies. The OH and OD stretches, the ones not in agreement, are likely to be perturbed by the matrix. The predicted (MRCC/aug-cc-pVTZ) and experimental UV spectrum are also in close agreement.

Holding the matrix at 11 K and following the spectra of 1-3 led to the following important kinetic results: the half-life for formation of 2 is 66 min with no 3 observed to form. In addition, the rate for the deuterium labeled carbene to form 2 was too long for measuring, but was 196 minutes in Kr and 251 minutes in Xe. CCSD(T)/cc-pCVCZ computations followed by focal point methods gives the barrier to form acetaldehyde from 1 as 28.0 kcal mol-1 while that to form vinyl alcohol 3 is much lower: 22.6 kcal mol-1. (The structures of these three molecules and the transition states connecting them are shown in Figure 1.) Apparently, the reaction passes through or over the higher barrier in large preference over passing through or over the lower barrier!

1

TS12

2

TS13

3

Figure 1. CCSD(T)/cc-pCVTZ optimizes structures of 1-3 and the transition states connecting 1 to 2 and 1 to 3.

Precise mapping of the intrinsic reaction path at CCSD(T)/cc-pCVTZ allows for computing the WKB tunneling probabilities. This leads to the prediction of the half-life for the reaction 12 as 71 minutes, in excellent agreement with experiment. The computed half-life for the deuterium labeled reaction of 400 years and the computed half-life for 13 of 190 days are both in fine agreement with experiment.

Why does the reaction preferentially tunnel through the higher barrier? Well, the tunneling rate is dependent on the square root of the barrier height and linearly on the barrier width. The width is much smaller for the rearrangement to 2. The hydrogen needs to move a shorter amount in proceeding from 1to 2 than to 3, and in the rearrangement to vinyl alcohol a second hydrogen must migrate downwards to form the planar vinyl group. Basically, width beats out the height.

The important conclusion from this paper is the following: in addition to reactions being under kinetic or thermodynamic control, we must now consider a third options – a reaction under tunneling control!

A nice perspective on this paper and its implications has been written by Carpenter, who points out how this adds to our general notion of significant limitations to transition state theory.3

References

(1) Schreiner, P. R.; Reisenauer, H. P.; Ley, D.; Gerbig, D.; Wu, C.-H.; Allen, W. D., "Methylhydroxycarbene: Tunneling Control of a Chemical Reaction," Science, 2011, 332, 1300-1303, DOI: 10.1126/science.1203761.

(2) Smith, B. J.; Nguyen Minh, T.; Bouma, W. J.; Radom, L., "Unimolecular rearrangements connecting hydroxyethylidene (CH3-C-OH), acetaldehyde (CH3-CH:O), and vinyl alcohol (CH2:CH-OH)," J. Am. Chem. Soc., 1991, 113, 6452-6458, DOI: 10.1021/ja00017a015

(3) Carpenter, B. K., “Taking the High Road and Getting There Before You,” Science, 2011, 332, 1269-1270, DOI: 10.1126/science.1206693.

InChIs

1: InChI=1/C2H4O/c1-2-3/h3H,1H3
InChIKey=JVKQHDUTAFISFX-UHFFFAOYAN

2: InChI=1/C2H4O/c1-2-3/h2H,1H3
InChIKey=IKHGUXGNUITLKF-UHFFFAOYAB

3: InChI=1/C2H4O/c1-2-3/h2-3H,1H2
InChIKey=IMROMDMJAWUWLK-UHFFFAOYAT

focal point &Schreiner &Tunneling Steven Bachrach 14 Jun 2011 3 Comments

Phenylhydroxycarbene

Somehow I missed this paper when it came out a few months ago, even though I was aware it was coming – as I mentioned it in one of my previous posts!

Anyways, Schreiner and Allen reported on their third study of hydroxyl carbenes (see these posts on dihydroxymethylene and hydroxymethylene), this time examining phenylhydroxycarbene.1 As I covered in my book, there is a lot of work on phenylcarbenes which typically ring expand to the cycloheptatetraene, see Reaction 1. One might expect phenylhydroxycarbene to do the same thing, i.e. 1 converting into 2 (Reaction 2). 1 is prepared by high-vacuum flash pyrolysis of phenylglyoxylic acid 3 and then capturing the product in an argon matrix at 11 K (Reaction 3).

Reaction 1

Reaction 2

Reaction 3

The carbene 1 is identified through comparison of its experimental and computed (anharmonic frequencies at CCSD(T)/cc-pVDZ) IR frequencies.

No ring expansion is observed at all – Reaction 2 does not occur. Instead, 1 rearranges to benzaldehyde 4 (Reaction 4) at 11 K with a half life of 2.46 h (and a half life of 2.55 h at 20 K). The deuterated analogue does not convert to benzaldehyde and 1-d appears to be completely stable.

Reaction 4

So, what is going on? The cis and trans forms of 1 interconvert through a barrier of 22.7 kcal mol-1. The trans isomer can convert to benzaldehyde (the reaction is very exothermic: -50.8 kcal mol-1) with a barrier of 28.8 kcal mol-1 through TS1, shown in Figure 1. The cis isomer can cleave into benzene and CO (not observed) with a huge barrier of 55 kcal mol-1. All of these barrier were computed at CCSD(T)/cc-pVQZ.

TS1

Figure 1. MP2/cc-pVDZ optimized transition state for the conversion of 1 into 4.

Benzaldehyde seems to be produced by passing through a huge barrier, something that is impossible from a thermal perspective (we’re at 11 K!). But this can be accomplished by tunneling. Tunneling probabilities were computed from the MP2/aug-cc-pVDZ intrinsic reaction path with barrier penetration integrals computed with the WKB approximation. The bottom line: the computed half-life is 3.3 h and the deuterated species is computed to have a half-life of 8700 years(!), both in excellent agreement with experimental observation. Quantum mechanical tunneling is clearly the explanation for this chemistry.

This is another fine example of the power of joint experimental/computational studies. And be on the look-out for an even more exciting case from this group. I met with Wes Allen on my recent trip to the University of Georgia and was entertained with another hydroxycarbene that undergoes quite novel tunneling!

References

(1) Gerbig, D.; Reisenauer, H. P.; Wu, C.-H.; Ley, D.; Allen, W. D.; Schreiner, P. R., "Phenylhydroxycarbene," J. Am. Chem. Soc., 2010, 132, 7273-7275, DOI: 10.1021/ja9107885

InChIs

1: InChI=1/C7H6O/c8-6-7-4-2-1-3-5-7/h1-5,8H
InChIKey=QVZIGMRPQWIGCV-UHFFFAOYAE

2: InChI=1/C7H6O/c8-7-5-3-1-2-4-6-7/h1-6H
InChIKey=QVWDCTQRORVHHT-UHFFFAOYAM

3: InChI=1/C8H6O3/c9-7(8(10)11)6-4-2-1-3-5-6/h1-5H,(H,10,11)/f/h10H
InChIKey=FAQJJMHZNSSFSM-KZFATGLACS

4: InChI=1/C7H6O/c8-6-7-4-2-1-3-5-7/h1-6H
InChIKey=HUMNYLRZRPPJDN-UHFFFAOYAE

carbenes &Schreiner &Tunneling Steven Bachrach 21 Sep 2010 3 Comments

Dihydroxycarbene

Following on the great study of hydroxycarbene1 (see my blog post), Schreiner now reports on the synthesis and characterization of dihydroxycarbene 1.2 It is prepared by high-vacuum flash pyrolysis of oxalic acid (Scheme 1).

Scheme 1

Dihydroxycarbene can exist in three different conformations characterized by the relationship about the C-O bond, either s-cis or s-trans. The three conformations are shown in Figure 1, and the s-trans,s-trans structure is the local energy minimum (computed at CCSD(T)/cc-pVTZ).

1tt (0.0)

1ct (0.1)

1cc (6.7)

Figure 1. CCSD(T)/cc-pVTZ optimized geometries and relative energies (kcal mol-1) of the conformers of 1.2

Identification of the 1 is made through comparison of the experimental and computed IR vibrational frequencies. As an example, the experimental and computed frequencies for the s-trans,s-trans conformer are listed in Table 1. The agreement is excellent.

Table 1. Computed and experimental vibrational frequencies (cm-1) and intensities (in parentheses) of the s-trans,s-trans conformation of 1.2


vibration

computed

experiment

1

3876.4 (23.5)

3633.2 / 3628.6 (w)

2

3871.4 (234.1)

3625.1 (s)

3

1443.1 (124.4)

1386.2 (m)

4

1370.5 (58.3)

1289.0 / 1287.4 (w)

5

1157.8 (470.6)

1110.3 / 1109.3 (vs)

6

1156.6 (1.4)

 

7

742.4 (178.8)

706.6 (s)

8

672.4 (0.0)

 

9

641.6 (11.2)

 


Unlike hydroxycarbene, dihydroxycarbene is stable. The amazing instability of hydroxycarbene is due to tunneling through a large barrier: nearly 30 kcal mol-1.1 The tunneling route for the decomposition of 1 is more difficult for two reasons. First, its C-O bond is quite strong; the C-O distance is quite short, 1.325 Å. This makes a long distance that must be traversed in the tunneling mode. (The strong bond is due to π-donation from the oxygen lone pair into the empty carbon p orbital; this is noted by the large rotational barrier about the C-O bonds of 17 kcal mol-1!) Second, the activation barrier for decomposition is very high, at least 34 kcal mol-1.

References

(1) Schreiner, P. R.; Reisenauer, H. P.; Pickard Iv, F. C.; Simmonett, A. C.; Allen, W. D.; Matyus, E.; Csaszar, A. G., "Capture of hydroxymethylene and its fast disappearance through tunnelling," Nature, 2008, 453, 906-909, DOI: 10.1038/nature07010.

(2) Schreiner, P. R.; Reisenauer, H. P., "Spectroscopic Identification of Dihydroxycarbene13," Angew. Chem. Int. Ed., 2008, 47, 7071-7074, DOI: 10.1002/anie.200802105

InChIs

1: InChI=1/CH2O2/c2-1-3/h2-3H

carbenes &Schreiner &Tunneling Steven Bachrach 06 Oct 2008 2 Comments

Conformationally selective tunneling

The Schreiner group has again reported an amazing experimental and computational study demonstrating a fascinating quantum mechanical tunneling effect, this time for the trifluoromethylhydroxycarbene (CF3COH) 2.1 (I have made on a number of posts discussing a series of important studies in this field by Schreiner.) Carbene 2 is formed, in analogy to many other hydroxycarbenes, by flash vapor pyrolysis of the appropriate oxoacid 1 and capturing the products on a noble gas matrix.

Carbene 2t is observed by IR spectroscopy, and its structure is identified by comparison with the computed CCSD(T)/cc-pVTZ frequencies. When 2t is subjected to 465 nm light, the signals for 2t disappear within 30s, and two new species are observed. The first species is the cis conformer 2c, confirmed by comparison with its computed CCSD(T)/cc-pVTZ frequencies. This cis conformer remains even with continued photolysis. The other product is determined to be trifluoroacetaldehyde 3. Perhaps most interesting is that 2t will convert to 3 in the absence of light at temperatures between 3 and 30 K, with a half-life of about 144 h. There is little rate difference at these temperatures. These results are quite indicative of quantum mechanical tunneling.

To aid in confirming tunneling, they computed the potential energy surface at CCSD(T)/cc-pVTZ. The trans isomer is 0.8 kcal mol-1 lower in energy that the cis isomer, and this is much smaller than for other hydroxycarbenes they have examined. The rotational barrier TS1 between the two isomer is quite large, 26.4 kcal mol-1, precluding their interchange by classical means at matrix temperatures. The barrier for conversion of 2t to 3 (TS2) is also quite large, 30.7 kcal mol-1, and insurmountable at 10K by classical means. No transition state connecting 2c to 3 could be located. These geometries and energies are shown in Figure 1.

2c
0.8

TS1
26.4

2t
0.0

TS2
30.7

3
-49.7

Figure 1. Optimized geometries at CCSD(T)/cc-pVTZ. Relative energies (kcal mol-1) of each species are listed as well.

WKB computations at M06-2X/6-311++G(d,p) predict a half-life of 172 h, in nice agreement with experiment. The computed half-life for deuterated 2t is 106 years, and the experiment on the deuterated analogue revealed no formation of deuterated 3.

The novel component of this study is that tunneling is conformationally selective. The CF3 group stabilizes the cis form probably through some weak HF interaction, so that the cis isomer can be observed, but no tunneling is observed from this isomer. Only the trans isomer has the migrating hydrogen atom properly arranged for a short hop over to the carbon, allowing the tunneling process to take place.

References

1) Mardyukov, A.; Quanz, H.; Schreiner, P. R., "Conformer-specific hydrogen atom tunnelling in trifluoromethylhydroxycarbene." Nat. Chem. 2017, 9, 71–76, DOI: 10.1038/nchem.2609.

InChIs

1: =1S/C3HF3O3/c4-3(5,6)1(7)2(8)9/h(H,8,9)
InChIKey=GVDJEHMDNREMFA-UHFFFAOYSA-N

2: InChI=1S/C2HF3O/c3-2(4,5)1-6/h6H
InChIKey=FVJVNIREIXAWKU-UHFFFAOYSA-N

3: InChI=1S/C2HF3O/c3-2(4,5)1-6/h1H
InChIKey=JVTSHOJDBRTPHD-UHFFFAOYSA-N

carbenes &Schreiner &Tunneling Steven Bachrach 07 Feb 2017 1 Comment

Computational Organic Chemistry, Second Edition – what’s new in Chapters 5-9

This post continues my presentation of what’s new in the second edition of my book Computational Organic Chemistry. I present here a brief summary of the new materials in chapters 5-9. (See this previous post for what’s new in chapters 1-4.)

Every chapter has been updated, meaning that the topics from the First Edition that remain in this Second Edition (and that’s most of them) have been updated with any new relevant work that have appeared since 2007, when the First Edition was published. In addition, the following new subjects have been included.

Chapter 5. Diradicals and Carbenes

One of the major additions to the entire book appears in Chapter 5: the discovery of tunneling in a variety of carbenes. This work, pioneered by Schreiner and Allen, led to the discovery of tunneling control, a third means, in conjunction with thermodynamic control and kinetic control, for controlling product formation. This work is an exemplar of the synergy provided by experiments done in partnership with computations. The chapter also includes an interview with Prof. Peter Schreiner.

Chapter 6. Organic Reactions of Anions

The discussion on proline-catalyzed aldols includes many new computations, especially dealing with the possible intermediacy of oxazolidinones. A section on thiurea-catalyzed Claisen rearrangements, from the Jacobsen group, concludes the chapter, showing how the computational approaches to organocatalyzed reactions can be extended beyond the aldol and aldol-like reactions.

Chapter 7. Solution-Phase Organic Chemistry

A discussion of solvent effects on amino acid structure has been added. This work focusses on the use of microsolvation to model local solvent effects, particularly in cases where proper accounting of strong hydrogen bonds can be critical in assessing behaviors.

Chapter 8. Organic Reaction Dynamics

A great deal of new materials appears in this chapter. Since the publication of the first edition of the book, many new studies have been published that greatly expand the types of organic reactions that are subject to dynamic effects. Of particular note are the many new examples of reactions on bifurcating surfaces. Some studies, principally by Singleton, now provide some guidance and hints towards predicting what types of reactions might exhibit non-statistical dynamics. Two new non-statistical dynamic types are presented: the roaming reactions and the roundabout mechanism in the SN2 reaction. The chapter ends with a detailed case study of the Wolff rearrangement.

Chapter 9. Computational Approaches to Understanding Enzymes

The last chapter is entirely new, and features how the techniques of computational organic chemistry, as discussed in the previous eight chapters, can be employed toward explicating enzymatic reactions. The chapter is not an in-depth survey of all of the activities in computational enzyme action – that would require its own full-length book – but rather it’s an overview to inspire you. The chapter begins with a brief discussion of enzymatic models, including the Pauling paradigm and Goodman’s model. Then computational strategies for addressing the large molecules involved in enzymatic studies are presented including QM/MM, adiabatic mapping, and the use of some very large-scale computations as benchmarks. Next, I present two case studies: of chorismate mutase and of catechol-O-methyltransferase (COMT). The chapter ends with a presentation of the progress in de novo design of enzymes capable of catalyzing specific reactions as developed by Baker and Houk.

Second Edition Steven Bachrach 16 Apr 2014 1 Comment

Another example of tunneling control

The notion of tunneling control has been a topic of interest within this blog a number of times. As developed by Schreiner and Allen,1,2 tunneling control is a third means for predicting (or directing) the outcome of a reaction, alongside the more traditionally recognized kinetic and thermodynamic control. Tunneling control occurs when tunneling through a higher barrier is preferred over tunneling through a lower barrier.

Kozuch and Borden propose another example of tunneling control, this time in the rearrangement of the noradamantyl carbene 1.3 This carbene can undergo a 1,2-carbon shift, driven by strain relief to form the alkene 2. The alternative as a 1,2-hydrogen shift that produces the alkene 3.

These two reaction pathways were explored using B3LYP/6-31G(d,p) computations coupled with canonical variational theory and small curvature tunneling corrections. Structures of the reactant 1 and the two transition states leading to the two products 2 and 3 are shown in Figure 1. The activation barrier at 300 K is 5.4 kcal mol-1 leading to 2 and 8.6 kcal mol-1 leading to 3. Tunneling is expected to be much more important for the hydrogen shift than for the carbon shift, but even including tunneling, the rate to form 2 is much faster than the rate to form 3 at 300 K.

1

TS 1→2

2

TS 1→3

3

Figure 1. B3LYP/6 optimized structures of 1-3 and the transition states leading to 2 and 3.

The situation is reversed however at cryogenic temperatures (< 20 K). Tunneling is now the only route for the reactions to occur, and the rate for formation of 3 is dramatically greater than the rate of formation of 2, which is inhibited by the movement of the much heavier carbon atom. Perdeuteration of the methyl group of 1, which drastically slows the rate of tunneling in the path to 3, nonetheless still favors this pathway (forming d33) over formation of d32. Thus, at low temperatures the formation of 3 is the preferred product, a manifestation of tunneling control.

Kozuch and Borden end their paper with a hope that an experimentalist will examine this interesting case. I concur!

References

(1) Schreiner, P. R.; Reisenauer, H. P.; Ley, D.; Gerbig, D.; Wu, C.-H.; Allen, W. D. "Methylhydroxycarbene: Tunneling Control of a Chemical Reaction," Science 2011, 332, 1300-1303, DOI: 10.1126/science.1203761.

(2) Ley, D.; Gerbig, D.; Schreiner, P. R. "Tunnelling control of chemical reactions – the organic chemist’s perspective," Org. Biomol. Chem. 2012, 10, 3781-3790, DOI: 10.1039/C2OB07170C.

(3) Kozuch, S.; Zhang, X.; Hrovat, D. A.; Borden, W. T. "Calculations on Tunneling in the Reactions of Noradamantyl Carbenes," J. Am. Chem. Soc. 2013, 135, 17274-17277, DOI: 10.1021/ja409176u.

InChIs

1: InChI=1S/C11H16/c1-2-11-6-8-3-9(7-11)5-10(11)4-8/h8-10H,3-7H2,1H3
InChIKey=CXFJINASYYTBBV-UHFFFAOYSA-N

2: InChI=1S/C11H16/c1-7-10-3-8-2-9(5-10)6-11(7)4-8/h8-10H,2-6H2,1H3
InChIKey=XDANPUSLLJWVEK-UHFFFAOYSA-N

3: InChI=1S/C11H16/c1-2-11-6-8-3-9(7-11)5-10(11)4-8/h2,8-10H,1,3-7H2
InChIKey=JHEPVTWREMDEMG-UHFFFAOYSA-N

Borden &Tunneling Steven Bachrach 27 Jan 2014 No Comments

Review of tunneling in organic chemistry

Schreiner has written a very nice review of the role of tunneling in organic chemistry.1 This includes tunneling in the conformations of carboxylic acids and in hydrogen abstractions. But the major emphasis is on his own group’s contributions regarding tunneling on a variety of hydroxycarbenes (see these posts: cyclopropylhydroxycarbene, methylhydroxycarbene, phenylhydroxycarbene, dihydroxycarbene, and hydroxymethylene). This led to the development of a third means for controlling reactions: not just kinetic and thermodynamic control, but tunneling control as well.

Recommended reading for anyone interested in learning how quantum mechanical tunneling can have very real-world chemical consequences.

References

(1) Ley, D.; Gerbig, D.; Schreiner, P. R. "Tunnelling control of chemical reactions – the organic chemist’s perspective," Org. Biomol. Chem., 2012, 10, 3781-3790, DOI: 10.1039/C2OB07170C.

Schreiner &Tunneling Steven Bachrach 19 Jun 2012 No Comments

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