Carbohydrates in the gas phase: conformational preference of D-ribose and 2-deoxy-D-ribose
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1 New J. Chem ELECTRONIC SUPPLEMENTARY INFORMATION Carbohydrates in the gas phase: conformational preference of D-ribose and 2-deoxy-D-ribose Luis Miguel Azofra,*, María Mar Quesada-Moreno, Ibon Alkorta, Juan Ramón Avilés-Moreno, Juan Jesús López-González and José Elguero. Instituto de Química Médica (C.S.I.C.), Juan de la Cierva, 3, E Madrid, Spain. Department of Physical and Analytical Chemistry, University of Jaén, Campus Las Lagunillas, E Jaén, Spain. *Author to whom correspondence should be addressed: URL: FAX: Cartesian coordinates of the most stable minima in gas phase (less than 5 kj mol 1 ) at M06-2X/ G(d,p) computational level Table S1. Relative energy in kj mol 1 for the most stable minima at M06-2X and B3LYP computational levels. Both: G(d,p) Figure S1. Molecular graphs of the most stable conformers (less than 3 kj mol 1 ) for 2-deoxy-D-ribose and D-ribose in gas phase calculated at M06-2X/ G(d,p) computational level Figure S2. Topological representations for the C(sp 2 ) HC, H H and O HC interactions Page S2 S19 S20 S21 S22 S26 S27 S1
2 Cartesian coordinates of the most stable minima in gas phase (less than 5 kj mol 1 ) for the open-chain, furanose and pyranose forms of 2-deoxy-D-ribose and D-ribose calculated with the M06-2X hybrid functional and the G(d,p) Pople s basis set. Open-chain 2-deoxy-D-ribose (3) ddr01 C, , , C, , , C, , , C, , , C, , , O, , , H, , , H, , , H, , , H, , , H, , , H, , , H, , , O, , , O, , , O, , , H, , , H, , , H, , , ddr02 C, , , C, , , C, , , C, , , C, , , O, , , H, , , H, , , H, , , H, , , H, , , H, , , H, , , O, , , O, , , O, , , H, , , H, , , H, , , ddr03 C, , , C, , , C, , , C, , , C, , , O, , , H, , , H, , , S2
3 H, , , H, , , H, , , H, , , H, , , O, , , O, , , O, , , H, , , H, , , H, , , Open-chain D-ribose (9) DR01 C, , , C, , , C, , , C, , , C, , , O, , , H, , , H, , , H, , , H, , , H, , , H, , , O, , , O, , , O, , , O, , , H, , , H, , , H, , , H, , , DR02 C, , , C, , , C, , , C, , , C, , , O, , , H, , , H, , , H, , , H, , , H, , , H, , , O, , , O, , , O, , , O, , , H, , , H, , , H, , , H, , , S3
4 DR03 C, , , C, , , C, , , C, , , C, , , O, , , H, , , H, , , H, , , H, , , H, , , H, , , O, , , O, , , O, , , O, , , H, , , H, , , H, , , H, , , DR04 C, , , C, , , C, , , C, , , C, , , O, , , H, , , H, , , H, , , H, , , H, , , H, , , O, , , O, , , O, , , O, , , H, , , H, , , H, , , H, , , DR05 C, , , C, , , C, , , C, , , C, , , O, , , H, , , H, , , H, , , H, , , H, , , H, , , O, , , O, , , S4
5 O, , , O, , , H, , , H, , , H, , , H, , , DR06 C, , , C, , , C, , , C, , , C, , , O, , , H, , , H, , , H, , , H, , , H, , , H, , , O, , , O, , , O, , , O, , , H, , , H, , , H, , , H, , , DR07 C, , , C, , , C, , , C, , , C, , , O, , , H, , , H, , , H, , , H, , , H, , , H, , , O, , , O, , , O, , , O, , , H, , , H, , , H, , , H, , , DR08 C, , , C, , , C, , , C, , , C, , , O, , , H, , , S5
6 H, , , H, , , H, , , H, , , H, , , O, , , O, , , O, , , O, , , H, , , H, , , H, , , H, , , DR09 C, , , C, , , C, , , C, , , C, , , O, , , H, , , H, , , H, , , H, , , H, , , H, , , O, , , O, , , O, , , O, , , H, , , H, , , H, , , H, , , deoxy-D-ribofuranose (2) ddr f01 C, , , C, , , C, , , C, , , O, , , C, , , H, , , H, , , H, , , H, , , H, , , H, , , H, , , O, , , O, , , O, , , H, , , H, , , H, , , S6
7 ddr f02 C, , , C, , , C, , , C, , , O, , , C, , , H, , , H, , , H, , , H, , , H, , , H, , , H, , , O, , , O, , , O, , , H, , , H, , , H, , , deoxy-D-ribofuranose (4) ddr f01 C, , , C, , , C, , , C, , , O, , , C, , , H, , , H, , , H, , , H, , , H, , , H, , , H, , , O, , , O, , , O, , , H, , , H, , , H, , , ddr f02 C, , , C, , , C, , , C, , , O, , , C, , , H, , , H, , , H, , , H, , , H, , , H, , , S7
8 H, , , O, , , O, , , O, , , H, , , H, , , H, , , ddr f03 C, , , C, , , C, , , C, , , O, , , C, , , H, , , H, , , H, , , H, , , H, , , H, , , H, , , O, , , O, , , O, , , H, , , H, , , H, , , ddr f04 C, , , C, , , C, , , C, , , O, , , C, , , H, , , H, , , H, , , H, , , H, , , H, , , H, , , O, , , O, , , O, , , H, , , H, , , H, , , D-ribofuranose (5) DR f01 C, , , C, , , C, , , C, , , O, , , S8
9 C, , , H, , , H, , , H, , , H, , , H, , , H, , , O, , , O, , , O, , , O, , , H, , , H, , , H, , , H, , , DR f02 C, , , C, , , C, , , C, , , O, , , C, , , H, , , H, , , H, , , H, , , H, , , H, , , O, , , O, , , O, , , O, , , H, , , H, , , H, , , H, , , DR f03 C, , , C, , , C, , , C, , , O, , , C, , , H, , , H, , , H, , , H, , , H, , , H, , , O, , , O, , , O, , , O, , , H, , , H, , , H, , , H, , , S9
10 DR f04 C, , , C, , , C, , , C, , , O, , , C, , , H, , , H, , , H, , , H, , , H, , , H, , , O, , , O, , , O, , , O, , , H, , , H, , , H, , , H, , , DR f05 C, , , C, , , C, , , C, , , O, , , C, , , H, , , H, , , H, , , H, , , H, , , H, , , O, , , O, , , O, , , O, , , H, , , H, , , H, , , H, , , D-ribofuranose (10) DR f01 C, , , C, , , C, , , C, , , O, , , C, , , H, , , H, , , H, , , H, , , S10
11 H, , , H, , , O, , , O, , , O, , , O, , , H, , , H, , , H, , , H, , , DR f02 C, , , C, , , C, , , C, , , O, , , C, , , H, , , H, , , H, , , H, , , H, , , H, , , O, , , O, , , O, , , O, , , H, , , H, , , H, , , H, , , DR f03 C, , , C, , , C, , , C, , , O, , , C, , , H, , , H, , , H, , , H, , , H, , , H, , , O, , , O, , , O, , , O, , , H, , , H, , , H, , , H, , , DR f04 C, , , C, , , C, , , S11
12 C, , , O, , , C, , , H, , , H, , , H, , , H, , , H, , , H, , , O, , , O, , , O, , , O, , , H, , , H, , , H, , , H, , , DR f05 C, , , C, , , C, , , C, , , O, , , C, , , H, , , H, , , H, , , H, , , H, , , H, , , O, , , O, , , O, , , O, , , H, , , H, , , H, , , H, , , DR f06 C, , , C, , , C, , , C, , , O, , , C, , , H, , , H, , , H, , , H, , , H, , , H, , , O, , , O, , , O, , , O, , , H, , , H, , , S12
13 H, , , H, , , DR f07 C, , , C, , , C, , , C, , , O, , , C, , , H, , , H, , , H, , , H, , , H, , , H, , , O, , , O, , , O, , , O, , , H, , , H, , , H, , , H, , , DR f08 C, , , C, , , C, , , C, , , O, , , C, , , H, , , H, , , H, , , H, , , H, , , H, , , O, , , O, , , O, , , O, , , H, , , H, , , H, , , H, , , DR f09 C, , , C, , , C, , , C, , , O, , , C, , , H, , , H, , , H, , , H, , , H, , , S13
14 H, , , O, , , O, , , O, , , O, , , H, , , H, , , H, , , H, , , DR f10 C, , , C, , , C, , , C, , , O, , , C, , , H, , , H, , , H, , , H, , , H, , , H, , , O, , , O, , , O, , , O, , , H, , , H, , , H, , , H, , , deoxy-D-ribopyranose (1) ddr p01 C, , , C, , , C, , , C, , , C, , , O, , , H, , , H, , , H, , , H, , , H, , , H, , , H, , , O, , , O, , , O, , , H, , , H, , , H, , , ddr p01-2-deoxy-d-ribopyranose (3) S14
15 C, , , C, , , C, , , C, , , C, , , O, , , H, , , H, , , H, , , H, , , H, , , H, , , H, , , O, , , O, , , O, , , H, , , H, , , H, , , ddr p02 C, , , C, , , C, , , C, , , C, , , O, , , H, , , H, , , H, , , H, , , H, , , H, , , H, , , O, , , O, , , O, , , H, , , H, , , H, , , ddr p03 C, , , C, , , C, , , C, , , C, , , O, , , H, , , H, , , H, , , H, , , H, , , H, , , H, , , O, , , O, , , O, , , H, , , S15
16 H, , , H, , , D-ribopyranose (4) DR p01 C, , , C, , , C, , , C, , , C, , , O, , , H, , , H, , , H, , , H, , , H, , , H, , , O, , , O, , , O, , , O, , , H, , , H, , , H, , , H, , , DR p02 C, , , C, , , C, , , C, , , C, , , O, , , H, , , H, , , H, , , H, , , H, , , H, , , O, , , O, , , O, , , O, , , H, , , H, , , H, , , H, , , DR p03 C, , , C, , , C, , , C, , , C, , , O, , , H, , , H, , , S16
17 H, , , H, , , H, , , H, , , O, , , O, , , O, , , O, , , H, , , H, , , H, , , H, , , DR p04 C, , , C, , , C, , , C, , , C, , , O, , , H, , , H, , , H, , , H, , , H, , , H, , , O, , , O, , , O, , , O, , , H, , , H, , , H, , , H, , , D-ribopyranose (4) DR p01 C, , , C, , , C, , , C, , , C, , , O, , , H, , , H, , , H, , , H, , , H, , , H, , , O, , , O, , , O, , , O, , , H, , , H, , , H, , , H, , , S17
18 DR p02 C, , , C, , , C, , , C, , , C, , , O, , , H, , , H, , , H, , , H, , , H, , , H, , , O, , , O, , , O, , , O, , , H, , , H, , , H, , , H, , , DR p03 C, , , C, , , C, , , C, , , C, , , O, , , H, , , H, , , H, , , H, , , H, , , H, , , O, , , O, , , O, , , O, , , H, , , H, , , H, , , H, , , DR p04 C, , , C, , , C, , , C, , , C, , , O, , , H, , , H, , , H, , , H, , , H, , , H, , , O, , , S18
19 O, , , O, , , O, , , H, , , H, , , H, , , H, , , S19
20 Table S1. Relative energy in kj mol 1 for the most stable minima (restricted for conformers with energies less than 5 kj mol 1 ) of 2-deoxy-D-ribose and D-ribose (openchain, furanose and pyranose forms) at M06-2X/ G(d,p) and B3LYP/ G(d,p) computational levels. Open-chain 2-deoxy-D-ribose Open-chain D-ribose M06-2X B3LYP M06-2X B3LYP ddr ddr DR DR ddr ddr DR DR ddr ddr DR DR DR DR DR DR DR DR DR DR DR DR DR DR deoxy-D-ribofuranose -2-deoxy-D-ribofuranose M06-2X B3LYP M06-2X B3LYP ddr f ddr f ddr f ddr f ddr f ddr f ddr f ddr f ddr f ddr f ddr f ddr f D-ribofuranose -D-ribofuranose M06-2X B3LYP M06-2X B3LYP DR f DR f DR f DR f DR f DR f DR f DR f DR f DR f DR f DR f DR f DR f DR f DR f DR f DR f DR f DR f DR f DR f DR f DR f DR f DR f DR f DR f DR f deoxy-D-ribopyranose -2-deoxy-D-ribopyranose M06-2X B3LYP M06-2X B3LYP ddr p ddr p ddr p ddr p S20
21 ddr p ddr p ddr p ddr p D-ribopyranose -D-ribopyranose M06-2X B3LYP M06-2X B3LYP DR p DR p DR p DR p DR p DR p DR p DR p DR p DR p DR p DR p DR p DR p DR p DR p S21
22 Fig. S1. Molecular graphs of the most stable conformers (less than 5 kj mol 1 ) for 2- deoxy-d-ribose and D-ribose in gas phase calculated at M06-2X/ G(d,p) computational level. For linear forms, dihedral angles D C1C2C3C4 ( 1 ) and D C2C3C4C5 ( 2 ) in deg are shown, and for cyclic ones the ring conformation, a as well as the Q parameter in Å are included. Relative energies are in kj mol 1. Small points are BCP (red), RCP (yellow) and CCP (green). a C=chair, H=half-chair, S=skew, B=boat, T=twist and E=envelope. Superscript at left refers to endo face. Subscript at right refers to exo face. ddr ddr ddr DR DR DR DR DR DR DR DR DR S22
23 ddr f01 2 Q ddr f02 T 2 Q 1 E ddr f01 4 Q ddr f02 E 4 Q ddr f03 E 4 Q E ddr f04 Q E DR f01 2 Q DR f02 T 2 Q DR f03 1 T 3 Q 1 T S23
24 DR f04 2 Q DR f05 E 2 Q E DR f01 Q DR f02 Q DR f03 E 2 E 3 Q 2 T DR f04 1 Q DR f05 T 4 Q DR f06 Q 2 T 3 E DR f07 3 Q DR f08 T 1 Q DR f09 2 T 3 Q 2 T S24
25 DR f10 4 Q E ddr p01 4 Q C ddr p01 1 Q ddr p02 C 1 Q ddr p03 4 C 1 Q 4 C DR p01 1 Q DR p02 C 4 Q DR p03 4 C 1 Q 1 C DR p04 1 Q C S25
26 DR p01 1 Q DR p02 C 1 Q DR p03 4 C 4 Q 4 C DR p04 1 Q C S26
27 Fig. S2. (a) Electron density at BCP in au; and (b) its Laplacian at BCP in au, both versus C(sp 2 ) HC, H H or O HC distance in Å. All data are calculated at M06-2X/ G(d,p) computational level. / au C(sp 2 ) HC H H O HC d / Å (a) 2 / au C(sp 2 ) HC H H O HC d / Å (b) S27
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