Archive for the 'MP' Category

Structure of benzene dication

Benzene is certainly one of the most iconic chemical compounds – its planar hexagonal structure is represented often in popular images involving chemists, and its alternating single and double bonds the source of one of chemistry’s most mythic stories: Kekule’s dream of a snake biting its own tail. So while the structure of benzene is well-worn territory, what of the structure of the benzene dication? Jasik, Gerlich and Rithova probe that question using a combined experimental and computational approach.1

The experiment involves generation of the benzene dication at low temperature and complexed
to helium. Then, using infrared predissociation spectroscopy (IRPD), they obtained a spectrum that suggested two different structures.

Next, employing MP2/aug-cc-pVTZ computations, they identified a number of possible geometries, and the two lowest energy singlet dications have the geometries shown in Figure 1. The first structure (1) has a six member ring, but the molecule is no longer planar. Lying a bit lower in energy is 2, having a pentagonal pyramid form. The combination of the computed IR spectra of each of these two structures matches up extremely well with the experimental spectrum.

1

2

Figure 1. MP2/aug-cc-pVTZ geometries of benzene dication 1 and 2.

References

(1) Jašík, J.; Gerlich, D.; Roithová, J. "Probing Isomers of the Benzene Dication in a Low-Temperature Trap," J. Am. Chem. Soc. 2014, 136, 2960-2962, DOI: 10.1021/ja412109h.

Aromaticity &MP Steven Bachrach 08 Apr 2014 2 Comments

Gas phase structure of 2-deoxyribose

2-deoxyribose 1 is undoubtedly one of the most important sugars as it is incorporated into the backbone of DNA. The conformational landscape of 1 is complicated: it can exist as an open chain, as a five-member ring (furanose), or a six-member ring (pyranose), and intramolecular hydrogen bonding can occur. This internal hydrogen bonding is in competition with hydrogen bonding to water in aqueous solution. Unraveling all this is of great interest in predicting structures of this and a whole host of sugar and sugar containing-molecules.


1

In order to get a firm starting point, the gas phase structures of the low energy conformers of 1 would constitute a great set of structures to use as a benchmark for gauging force fields and computational methods. Cocinero and Alonso1 have performed a laser ablation molecular beam Fourier transform microwave (LA-MB-FTMW) experiment (see these posts for other studies using this technique) on 1 and identified the experimental conformations by comparison to structures obtained at MP2/6-311++G(d,p). Unfortunately the authors do not include these structures in their supporting materials, so I have optimized the low energy conformers of 1 at ωB97X-D/6-31G(d) and they are shown in Figure 1.

1a (0.0)

1b (4.7)

1c (3.3)

1d (5.6)

1e (8.9)

1f (9.4)

Figure 1. ωB97X-D/6-31G(d) optimized structures of the six lowest energy conformers of 1. Relative free energy in kJ mol-1.

The computed spectroscopic parameters were used to identify the structures responsible for the six different ribose conformers observed in the microwave experiment. To give a sense of the agreement between the computed and experimental parameters, I show these values for the two lowest energy conformers in Table 1.

Table 1. MP2/6-311++G(d,p) computed and observed spectroscopic parameters for the two lowest energy conformers of 1.

 

1a

1c

 

Expt

Calc

Expt

Calc

A(MHz)

2484.4138

2492

2437.8239

2447

B (MHz)

1517.7653

1533

1510.7283

1527

C (MHz)

1238.9958

1250

1144.9804

1158

ΔG (kJ mol-1)

 

0.0

 

3.3

This is yet another excellent example of the symbiotic relationship between experiment and computation in structure identification.

References

(1) Peña, I.; Cocinero, E. J.; Cabezas, C.; Lesarri, A.; Mata, S.; Écija, P.; Daly, A. M.; Cimas, Á.; Bermúdez, C.; Basterretxea, F. J.; Blanco, S.; Fernández, J. A.; López, J. C.; Castaño, F.; Alonso, J. L. "Six Pyranoside Forms of Free 2-Deoxy-D-ribose," Angew. Chem. Int. Ed. 2013, 52, 11840-11845, DOI: 10.1002/anie.201305589.

InChIs

1a: InChI=1S/C5H10O4/c6-3-1-5(8)9-2-4(3)7/h3-8H,1-2H2/t3-,4+,5-/m0/s1
InChIKey=ZVQAVWAHRUNNPG-LMVFSUKVSA-N

MP &sugars Steven Bachrach 16 Dec 2013 No Comments

Gas-phase structure of cytosine

Alonso and coworkers have again (see this post employed laser-ablation molecular-beam Fourier-transform microwave (LA-MB-MW)spectroscopy to discern the gas phase structure of an important biological compound: cytosine.1 They identified five tautomers of cytosine 1-5. Comparison between the experimental and computational (MP2/6-311++G(d,p) microwave rotational constants and nitrogen nuclear quadrupole coupling constants led to the complete assignment of the spectra. The experimental and calculated rotational constants are listed in Table 1.

Table 1. Rotational constants (MHz) for 1-5.

 

1

2

3

4

5

 

Expt

calc

Expt

calc

Expt

calc

Expt

calc

Expt

calc

A

3951.85

3934.5

3889.46

3876.5

3871.55

3856.0

3848.18

3820.1

3861.30

3844.2

B

2008.96

1999.1

2026.32

2014.7

2024.98

2012.3

2026.31

2019.0

2011.41

1999.7

C

1332.47

1326.8

1332.87

1326.9

1330.34

1323.3

1327.99

1324.0

1323.20

1318.4

The experimental and computed relative free energies are listed in Table 2. There is both not a complete match of the relative energetic ordering of the tautomers, nor is there good agreement in their magnitude. Previous computations2 at CCSD(T)/cc-pVQZ//CCSD//cc-pVTZ are in somewhat better agreement with the gas-phase experiments.

Table 2. Relative free energies (kcal mol-1) of 1-5.

 

expt

MP2/
6-311++G(d,p)

CCSD(T)/cc-pVQZ//
CCSD//cc-pVTZ

1

0.0

0.0

0.0

2

0.47

0.70

0.7

3

0.11

1.19

0.2

4

0.83

3.61

0.7

5

 

5.22

 

References

(1) Alonso, J. L.; Vaquero, V.; Peña, I.; López, J. C.; Mata, S.; Caminati, W. "All Five Forms of Cytosine Revealed in the Gas Phase," Angew. Chem. Int. Ed. 2013, 52, 2331-2334, DOI: 10.1002/anie.201207744.

(2) Bazso, G.; Tarczay, G.; Fogarasi, G.; Szalay, P. G. "Tautomers of cytosine and their excited electronic states: a matrix isolation spectroscopic and quantum chemical study," Phys. Chem. Chem. Phys., 2011, 13, 6799-6807, DOI:10.1039/C0CP02354J.

InChIs

cytosine: InChI=1S/C4H5N3O/c5-3-1-2-6-4(8)7-3/h1-2H,(H3,5,6,7,8)
InChIKey=OPTASPLRGRRNAP-UHFFFAOYSA-N

MP &nucleic acids Steven Bachrach 22 Apr 2013 1 Comment

Benchmarking conformations: melatonin

Conformational analysis is one of the tasks that computation chemistry is typically quite adept at and computational chemistry is frequently employed for this purpose. Thus, benchmarking methods for their ability to predict accurate conformation energies is quite important. Martin has done this for alkanes1 (see this post), and now he has looked at a molecule that contains weak intramolecular hydrogen bonds. He examined 52 conformations of melatonin 1.2 The structures of the two lowest energy conformations are shown in Figure 1.


1

1a

1b

Figure 1. Structures of the two lowest energy conformers of 1 at SCS-MP2/cc-pVTZ.

The benchmark (i.e. accurate) relative energies of these conformers were obtained at MP2-F12/cc-pVTZ-F12 with a correction for the role of triples: (ECCSD(T)/cc-pVTZ)-E(MP2/cc-pVTZ)). The energies of the conformers were computed with a broad variety of basis sets and quantum methodologies. The root mean square deviation from the benchmark energies is used as a measure of the utility of these alternate methodologies. Of particular note is that HF predicts the wrong ordering of the two lowest energy isomers, as do some DFT methods that use small basis sets and do not incorporate dispersion.

In fact, other than the M06 family or double hybrid functionals, all of the functionals examined here (PBE. BLYP, PBE0, B3LYP, TPSS0 and TPSS) have RMSD values greater than 1 kcal mol-1. However, inclusion of a dispersion correction, Grimme’s D2 or D3 variety or the Vydrov-van Voorhis (VV10) non-local correction (see this post for a review of dispersion corrections), reduces the error substantially. Among the best performing functionals are B2GP-PLYP-D3, TPSS0-D3, DSD-BLYP and M06-2x. They also find the MP2.5 method to be a practical ab initio alternative. One decidedly unfortunate result is that large basis sets are needed; DZ basis sets are simply unacceptable, and truly accurate performance requires a QZ basis set.

References

(1) Gruzman, D.; Karton, A.; Martin, J. M. L. "Performance of Ab Initio and Density Functional Methods for Conformational Equilibria of CnH2n+2 Alkane Isomers (n = 4-8)," J. Phys. Chem. A 2009, 113, 11974–11983, DOI: 10.1021/jp903640h.

(2) Fogueri, U. R.; Kozuch, S.; Karton, A.; Martin, J. M. L. "The Melatonin Conformer Space: Benchmark and Assessment of Wave Function and DFT Methods for a Paradigmatic Biological and
Pharmacological Molecule," J. Phys. Chem. A 2013, 117, 2269-2277, DOI: 10.1021/jp312644t.

InChIs

1: InChI=1S/C13H16N2O2/c1-9(16)14-6-5-10-8-15-13-4-3-11(17-2)7-12(10)13/h3-4,7-8,15H,5-6H2,1-2H3,(H,14,16)
InChIKey=DRLFMBDRBRZALE-UHFFFAOYSA-N

DFT &MP Steven Bachrach 11 Apr 2013 2 Comments

Gaunine tautomers

Here’s another fine paper from the Alonso group employing laser ablation molecular beam Fourier transform microwave spectroscopy coupled with computation to discern molecular structure. In this work they examine the low-energy tautomers of guanine.1 The four lowest energy guanine tautomers are shown in Figure 1. (Unfortunately, Alonso does not include the optimized coordinates of these structures in the supporting information – we need to more vigorously police this during the review process!) These tautomers are predicted to be very close in energy (MP2/6-311++G(d,p), and so one might expect to see multiple signals in the microwave originating from all four tautomers. In fact, they discern all four, and the agreement between the computed and experimental rotational constants are excellent (Table 1), especially if one applies a scaling factor of 1.004. Once again, this group shows the power of combined experiment and computations!


1 (0.0)


2 (0.28)


3 (0.40)


4 (0.99)

Figure 1. Four lowest energy (kcal mol-1, MP2/6-311++G(d,p)) tautomers of guanine.

Table 1. Experimental and computed rotational constants (MHz) of the four guanine tautomers.

 

1

2

3

4

 

Exp

Comp

Exp

Comp

Exp

Comp

Exp

Comp

A

19.22155

1909.0

19.222780

1909.7

1916.080

1908.6

1923.460

1915.6

B

1121.6840

119.2

1116.6710

1113.5

1132.360

1128.2

1136.040

1131.9

C

709.0079

706.6

706.8580

704.2

712.1950

709.5

714.7000

712.0

References

(1) Alonso, J. L.; Peña, I.; López, J. C.; Vaquero, V., "Rotational Spectral Signatures of Four Tautomers of Guanine," Angew. Chem. Int. Ed. 2009, 48, 6141-6143, DOI: 10.1002/anie.200901462

InChIs

Guanine: InChI=1/C5H5N5O/c6-5-9-3-2(4(11)10-5)7-1-8-3/h1H,(H4,6,7,8,9,10,11)/f/h8,10H,6H2
InChIKey=UYTPUPDQBNUYGX-GSQBSFCVCX

MP &nucleic acids Steven Bachrach 05 Oct 2009 3 Comments

Benzene dimer again

Yet more on the benzene dimer. Lesczynski has optimized 9 different benzene dimer configurations, shown in Scheme 1.1 There are two T-shaped isomers, where a hydrogen from one benzene interacts with the center of the π-cloud of the second. There are two bent versions of the T-shape, called Bent-T-shape. There are two sandwich configurations and two variants where the benzenes are parallel but displaced. Lastly, they report on a new variant, the V-shape configuration. (Once again, the author has not deposited the structures and so I can’t produce interactive figures!)

Scheme 1


T-1


T-2


BT-1


BT-2


SW-1


SW-2


PD-1


PD-2


V

The structures were optimized at MP2/aug-cc-pVDZ and then single point energies computed at MP4(SDTQ)/aug-cc-pVDZ and corrected for basis set superposition error. I list these energies in Table 1. They authors note that in comparison with CCSD(T) computations one has to adjust the amount of BSSE correction – which just supports my long-held contention that the standard counterpoise correction overcompensates and that we really have no reliable way of correcting for BSSE.

Table 1. Dimerization energies (kcal mol-1) at MP4(SDTQ)/aug-cc-pVDZ.1

T-1
-2.15

T-2
-2.15

BT-1
-2.21

BT-2
-2.30

SW-1
-1.25

SW-2
-1.23

PD-1
-2.13

PD-2
-2.13

V
-0.83

The relative energies of the 9 configurations are similar, indicating a very flat potential energy surface. The lowest energy structure is BT-2, and the V-shape configuration is the least favorable of the nine geometries examined.

References

(1) Dinadayalane, T. C.; Leszczynski, J., "Geometries and stabilities of various configurations of benzene dimer: details of novel V-shaped structure revealed " Struct. Chem. 2009, 20, 11-20, DOI: 10.1007/s11224-009-9411-6.

Aromaticity &MP Steven Bachrach 28 May 2009 5 Comments