Chemical Physics 328 (2006) 1–7 www.elsevier.com/locate/chemphys Conformational topology of ribose: A computational study Abraham F. Jalbout *, Ludwik Adamowicz, Lucy M. Ziurys Department of Chemistry, The University of Arizona, Tucson, AZ 85721, USA Received 17 January 2006; accepted 21 March 2006 Available online 27 March 2006 Abstract This work concerns the theoretical study of the configurational topology of the ribose molecule. MP2/6-31G** geometry optimizations of the system have yielded several structures corresponding to local minima on the ground-state potential energy surface and the lowest energy configuration was identified. The stability of a few lowest lying conformations has been recalculated at the CCSD(T)/6-31G** level of theory. Ó 2006 Published by Elsevier B.V. Keywords: Ribose; MP2; Coupled cluster theory; Ab initio; Potential energy surface 1. Introduction Increasing number of organic molecules are being identified in interstellar space. Some of those systems have fairly complicated structures and include several different functional groups. In the search for molecules involving carbon, hydrogen, nitrogen, and oxygen a special attention is directed towards finding molecular systems which are fragments of molecules of life. Sugars, which form the backbone of DNA and RNA, are among such systems. Since the detection of interstellar species is mostly achieved by the microwave spectroscopy, it is helpful if the equilibrium configuration(s) of the search for system is described by precision quantum-mechanical calculations, the rotational constants are determined, and a computer simulation of the spectrum is performed. In the present work, we perform calculations to characterize the configurational topology of R-ribose. As it will be shown the structural flexibility of this system leads to several low-energy minima that are connected with shallow pathways on the potential energy hypersurface. Previous * Corresponding author. E-mail address: [email protected] (A.F. Jalbout). 0301-0104/$ - see front matter Ó 2006 Published by Elsevier B.V. doi:10.1016/j.chemphys.2006.03.026 calculations on furanose [1] showed that the furanose ring has two minimum energy conformations at the C3 0 -endo and C2 0 -endo ring puckerings and that the barrier between these minima is only 0.6 kcal/mol. As the authors stated this result has a simple physical explanation. Their argument is based on first considering a five-membered ring of equivalent atoms like the cyclopentane ring. Because the ring closes on itself, the torsion angles about all five C–C single bonds must be close to the unfavorable eclipsed position. These unfavorable interactions make ring closure difficult, but once the ring is formed the energy is equally unfavorable for all the conformations along a path in conformational space known as pseudorotation. In the ring of the furanose system, as well as in ribose, one methylene group is replaced by an oxygen. As the barrier to internal rotation is lower about a C–O single bond than about a C–C single bond, the ring will prefer a conformation where the C–O torsion angles are most eclipsed. When these torsion angles are zero, the ring atoms across the ring from them, C3 0 and C2 0 , will be maximally puckered and these two conformations (C3 0 -endo and C2 0 -endo) become energy minima. As the COC bond angle prefers a larger value than the CCC bond angle, the ring will have a high energy when the oxygen O1 0 is maximally puckered (O1 0 -endo and O1 0 -exo). Levitt and Warshel [1] found the energy of a 2 A.F. Jalbout et al. / Chemical Physics 328 (2006) 1–7 furanose ring to be almost constant between the C3 0 -endo and C2 0 -endo conformations. However, ring conformations observed by X-ray crystallography do tend to cluster at these two extremes. They suggested a possible explanation for this in the influence of crystal packing forces acting on the C5 0 and O3 0 atoms. They also concluded that the variation of the energy of the ring system is almost the same for both the ribose and deoxyribose group since the extra hydroxyl group should not affect the conformational preferences of the ring. As ribonucleic acid double helices have only been observed in the C3 0 -endo conformation, while deoxyribonucleic acids double helices have been observed in both the C3 0 -endo and C2 0 -endo conformations [2], this difference must be due to interactions of the O2 0 hydroxyl group with the more distant parts of the sugar-phosphate backbone. Single-stranded ribonucleic acid does adopt both puckers [3]. In this work, we perform ab initio calculations to describe the configurational topology of unsubstituted dehydro R-ribose. The literature search has shown that there has been no report on the structural investigation of this system. The only similar study was recently performed on the abstraction reactions of ribose [4]. However, no account up to now deals with the stability and structure of dehydro R-ribose conformers. The variability of structural forms an isolated ribose molecule can assume results from superposition of two different puckers of the ribose five-member ring and several different intramolecular hydrogen bonds that can be formed by four OH groups. This work is important to the astrobiological study of the precursors of life among other topics. There is some evidence that suggests that various biological sugars such as ribose may be formed from simple interstellar precursors [5]. Therefore, it is important to carefully analyze the conformational behavior of ribose in order to fully understand the stable forms that may be observed. In addition, the conformational properties of ribose may be directly applied to its ability to undergo chemical reactions and modifications. 2. Methods All the calculations done in this work have been performed using the GAUSSIAN03 suit of programs [6]. The geometry optimizations have been done using the MP2/631G** method with the frozen-core (FC) approximation. That level of theory is sufficiently accurate to identify the equilibrium points of the potential energy surface of ribose. The relative energies of the different ribose configurational isomers have been determined at the MP2/6-31G** level. From our experiences [7,8] this method is sufficient for large-scale biological systems. For several low-energy conformers the relative energies have also been calculated at the CCSD (T)/6-31G** level of theory. For those conformers we also calculated the zero-point vibrational energies using the MP2/6-31G** level of theory and the harmonic approximation. The relative zero-point vibrational energies were added to the electronic relative energies to determine the final energy differences between the ribose conformational isomers. The zero-point energies were scaled by 0.9646 which is customary for this theory level used [7]. It is clear that hydrogen bonding plays an important role in the stability of a conformer. Thus we have attempted to characterize the hydrogen bonds using the ‘‘atoms in molecules’’ (AIM) methods [9]. However, this was unsuccessful due to problems with convergence. As an alternative to AIM we used natural bond orbital (NBO) analysis [7] to determine the presence of hydrogen bonds. In the Wiberg model of NBO the cutoff bond order value for a hydrogen bond is 0.0002 and for the molecular orbital (MO) model the cutoff bond order for a hydrogen bond is 0.015. We have applied the MO model to analyze the hydrogen bond structure, for each conformer and we got results consistent with the information obtained from the analysis HO–H distances. 3. Results The R-ribose equilibrium structures obtained in the calculations are shown in Fig. 1. To aid in the discussion of the structures, we will group the R-ribose isomers according to similarity in geometrical properties, which are shown in Table 1. We have presented only the most important parameters, in the interest of space. The supporting material for this manuscript contains MP2/6-31G** cartesian coordinates for all species. The data in Table 2 include the total MP2/6-31G** energies that correspond to the equilibrium structures obtained from geometry optimizations performed at that level of theory. For several lowest-energy structures we also show the CCSD(T)/6-31G**//MP2/6-31G** energies, i.e., the energies obtained using the coupled cluster method with single and double excitations and with non-iterative inclusion of triple excitations calculated at the MP2/6-31G** optimal geometries. The relative energies of the different configurational isomers calculated at the MP2/6-31G** and CCSD(T)/6-31G** levels are also shown in Table 2. Table 2 also shows the final relative energies that include the electronic contribution obtained at the CCSD(T)/631G** level and the zero-point vibrational contribution calculated at the MP2/6-31G* level using the harmonic approximation approach. The last column of the table shows dipole moments (l) in Debye (D). For the structural analysis of the isomers in this work we have followed all of the vibrational modes in order to attempt to locate more structural isomers, however, we have considered only those with positive vibrational frequencies. These 16 were the only low energy structures that we were able to locate. This is after a thorough analysis of all possible vibrational modes and configurations of this molecular species. In agreement with the previous investigation [4], we have considered two puckered orientations of the ring (the first orientation corresponding to C3 located above the C1OC4 plane and C2 below the plane, and the second A.F. Jalbout et al. / Chemical Physics 328 (2006) 1–7 3 Fig. 1. MP2/6-31G** equilibrium structures of the ribose molecule which are grouped based on similarities. Structures are organized from most to least stable (relative to 6). orientation corresponding to C3 below the plane and C2 above the plane). For each puckering orientation of the ring, we also considered all possible configurations of internal hydrogen bonds formed by hydrogens attached to O1, O2, O3, and O4. That produced the structures being the starting point for geometry optimizations. We will begin by identifying the lowest energy structure. There are many isomers for R-ribose, however, Table 2 shows that the lowest energy structure is 6. Also, this structure has atom labels that will be used throughout this work. For this isomer, two other alternatives exist, 6b and 6ab. As we can see from Fig. 1, 6 has two intermolec- ular hydrogen bond, whereas 6b has only one due to the fact that two of the hydroxyl groups (OH) have their hydrogen atoms facing each other, preventing this type of interaction. Although, the isomers of 6 are higher in energy, 6b is only 0.83 kcal/mol higher than 6 while 6ab is around 2.07 kcal/mol higher in energy. This slight difference in energy has to do with the rotation of one of the OH groups, in which the hydrogen atoms is pointing away from the molecule (HO3), relieving it from intermolecular strain. It is interesting to note that structure 6 in fact more stable than the regular R-ribose molecule (0), which has an energy that is 6.27 kcal/mol higher than it. 4 Table 1 Geometrical parameters for structures shown in Fig. 1 n R(O2O3)b \O1C1C2c \O2C2C1c \O3C3C4c \O4C5C4c \H(O1)O1C1C2c \H(O2)O2C2C1c 147.7 150.2 80.9 57.1 56.6 Group 1 1 16 3 4 2 5.215 5.667 4.969 6.048 6.004 2.118 2.149 2.196 2.144 2.146 106.4 106.5 106.2 107.8 107.7 104.5 105.1 108.6 106.9 106.9 105.3 104.9 105.5 105.5 105.4 108.0 106.9 107.8 107.3 108.0 170.8 169.9 162.3 175.9 176.0 Group 2 0 13 15 14 5.016 4.926 5.037 5.122 1.958 1.957 2.047 1.950 106.7 106.7 106.3 106.8 104.9 104.9 108.5 104.6 108.2 108.1 104.9 108.2 107.8 107.2 107.3 107.2 177.0 176.9 168.7 176.5 Group 3 12 7 9 8 1.994 2.488 2.060 2.052 2.028 1.950 1.983 1.997 106.5 106.7 104.2 104.6 108.0 105.1 107.5 105.3 105.8 108.5 105.7 108.7 108.5 104.4 108.1 107.0 Group 4 6 6b 6ab 5 11 10 2.220 2.184 2.244 2.359 1.937 1.974 2.039 2.071 2.098 2.096 2.055 2.064 106.9 107.1 107.3 107.1 105.7 105.6 104.9 105.3 105.9 108.6 108.5 105.2 107.6 107.7 108.6 95.6 104.7 107.4 105.9 106.3 104.5 107.3 108.4 107.9 a b c The distance (Å) between the interaction between O4 and O1 via an HO–HO bond. The distance (Å) between the interaction between O2 and O3 via an HO–HO bond. Bond angles are represented as \XYZ, and dihedral angles are shown as \XYWZ, both in degrees (°). \H(O3)O3C3C4c \H(O4)O4C5C4c 53.8 57.9 73.0 154.1 155.0 176.6 83.0 41.0 67.0 178.1 89.85 89.9 85.0 90.9 82.3 82.7 79.7 97.5 178.0 175.5 176.7 73.7 178.4 179.4 62.7 58.8 86.2 90.5 58.1 84.5 151.8 86.5 143.0 75.5 60.2 61.3 176.4 175.4 171.4 64.6 61.1 175.0 87.5 88.3 138.9 139.8 152.9 84.9 75.8 138.9 157.1 162.1 72.3 38.4 80.8 162.2 41.1 67.8 65.7 41.7 161.1 156.1 A.F. Jalbout et al. / Chemical Physics 328 (2006) 1–7 R(O4O1)a A.F. Jalbout et al. / Chemical Physics 328 (2006) 1–7 5 Table 2 Total MP2/6-31G** and CCSD(T) energies of ribose conformers found to be local minima on the ribose potential energy surface with the use of the MP2/ 6-31G** calculations n MP2/6-31G** 0 1 2 3 4 5 6b 7 8 9 10 11 12 13 14 15 16 571.0587076 571.0665235 571.0582391 571.0638051 571.0592873 571.0669134 571.0687070 571.0668144 571.0606408 571.0637682 571.0655256 571.0668089 571.0674584 571.0587073 571.0581445 571.0586860 571.0659204 CCSD(T)/6-31G** 571.1750194 571.1754961 571.1772456 571.1754046 571.1738721 571.1750684 571.1760640 571.1745569 DMP2/6-31G** 6.27 1.37 6.57 3.08 5.91 1.13 0.0 1.19 5.06 3.10 2.00 1.19 0.78 6.27 6.63 6.29 1.75 DMP2/6-31G**a DCCSD(T)/6-31G** DCCSD(T)/6-31G**a ZPEc 1.06 1.40 1.08 0.16099 0.80 0.0 1.25 1.10 0.0 1.15 0.78 0.0 1.22 0.16098 0.16149 0.16159 1.78 0.84 0.82 2.12 1.37 0.74 1.90 1.02 0.77 0.16114 0.16093 0.16155 1.47 1.69 1.41 0.16105 Md 3.12 4.02 2.64 4.38 1.92 4.74 1.35 3.43 6.86 4.04 4.84 1.11 2.14 3.13 3.67 3.58 2.57 Total energies in hartrees and the relative energies in kcal/mol. a Corrected for zero-point energies. b Two other isomers exist shown in Fig. 1 as 6b, and 6ab which are higher in energy by 0.83 and 2.07 kcal/mol, respectively. c ZPE scaled by 0.9646. d Dipole moment of the molecules in Debye (D). Therefore, from the results of the calculations in Table 2 we can see that there exist 7 low-lying (lowest energy) structures that are energetically similar to 6, these molecules are 12, 5, 7 = 11, 1, 16, 10. For these molecules MP2/6-31G** frequencies as well as CCSD(T)/6-31G**//MP2/6-31G** calculations have been carried out to verify their position on the potential energy surface. The structural reasons for this difference in energy will be described below based on groups. It is important to classify the conformers according to geometrical traits, in order to form general conclusions about the structures. The following figure will be used for the numbering scheme discussed in this work. 3.1. Group 1 The first set consists of molecules 1, 2, 3, 4, and 16, which share close equilibrium geometries. From previous nomenclature [4] these molecules belong to a twist configuration. We can further classify these molecules according to the position of their OH groups, as either endo (up) or exo (down). For structures 1, 3 and 2 we can say that O1, O2 (see structure 6 for numbering scheme) are endo, whereas O4, O3 are exo. However, structures 16, 4 have their O1, O3 as endo, and O2, O4 as exo. Therefore, the primary difference between 1, 3, 2 and 16, 4 is that the O2 has rotated downward and the O3 has rotated upward. Table 1 shows the geometrical parameters for the molecules shown in Fig. 1. The hydrogen bond interactions between O4 and O1 are labeled as R(O4O1) and for the interaction between O2 and O3 it is labeled as R(O2O3). As we can see for all the structures in this group, there is no hydrogen bond interaction between O4 and O1 as can be seen by the large R(O4O1) distances in the table. However, there is substantial bonding between the O2 and O3 groups as can be seen for the R(O2O3) values that are about 2.1 Å which is typical for a hydrogen bond. These structures are higher in energy than the majority of the other isomers in this study as Table 2 shows. The relative energies of 1, 2, 3, 4, and 16 are 1.37, 6.27, 3.08, 5.91, and 1.75 kcal/mol, respectively. Due to the low-lying nature of structures 1 and 16 we have performed further CCSD(T)/6-31G**//MP2/6-31G** calculations to obtain relative energy values of 1.08 and 1.41 kcal/mol, respectively. With ZPE corrections we obtain MP2/6-311G**// 6 A.F. Jalbout et al. / Chemical Physics 328 (2006) 1–7 MP2/6-311G** values of 1.04 and 1.45 kcal/mol, as well as CCSD(T)/6-31G**//MP2/6-31G** of 1.06, and 1.47 kcal/ mol, for 1 and 16, respectively. As we can see 1 has the lowest energy in this group. The table also shows dipole moments in Debye (D). As we can see from the table, 2, 3, 4, and 16, have dipole moments of 2.64, 4.38, 1.92 and 2.57 D, respectively. The highest dipole moment being for 3 due to the fact that the dipoles of the OH groups are parallel to the ring. Overall, the stability of these molecules is greatly influenced by the orientation of the H in the OH groups. They determine whether or not hydrogen bonding will form, as well as the general interatomic interactions in the molecular framework. 3.2. Group 2 The second group of molecules consists of 0, 13, 15, and 14, belong to an enveloped configuration. For 0, 13, 14 we observe that the general trend is where the O1, O2, O4 groups are endo, and the O3 is exo. The only deviation is for 15, where O1, O3, O4 are endo, and O2 is exo. Structures 0, 13, 14, and 15 have relative energies of 6.27, 6.27, and 6.63, and 6.29 kcal/mol, respectively. As we can see 0, 13, both have the lowest energy, which is also verified by a single point CCSD(T)/6-31G**//MP2/6-31G** calculation that yields a relative energy of 1.40 kcal/mol, which is very similar to the MP2/6-31G** result. The high stability of this group relative to the other three groups can be attributed to the fact the outer ACH2(OH) adopts an ‘L’ structure that should lower the energy [10]. In addition, the presence of one hydrogen bonding interaction, which is shown in Table 1 as R(O4O1), also stabilizes the structure. This interaction occurs at about 2 Å which is typical for a hydrogen bond. Structures 0 and 13 have are almost isoenergetic, with their structural differences being very small. These two structures along with 14 share a similar geometry, however 14 is partially destabilized by the rotation of C5 that causes the OH group to move slightly closer to the ring, causing minor steric interactions. Molecule 15 has a different OH configuration than then others, but is stabilized over 14 since the dihedral angle is around 177°, which causes less interactions with the ring, due its larger distance from the other atoms as a result from this rotation. In addition, we have also calculated dipole moments in Table 1 for 0, 13, 15, 14 are 3.12, 3.13, 3.58, and 3.67 D, respectively. As we can see the dipole moment for 14 is the highest which can be attributed to the orientation of the O1, and O4 groups. 3.3. Group 3 The third group consists of 7, 8, 9, and 12, which belong to a twist configuration. These molecules can be classified as have their O1, O2, O4 atoms endo, and O3 as exo. Structures 7, 8, 9, and 12, have energies of 1.19, 5.06, 3.10, and 0.78 kcal/mol, respectively. The lowest energy structures in this group are 7, and 12, for which single point CCSD(T)/ 6-31G**//MP2/6-31G** calculations reveal a relative energy of 1.15 and 0.74 kcal/mol, respectively. With ZPE corrections we obtain CCSD(T)/6-31G**//MP2/6-31G** values of 1.22 and 0.77 kcal/mol for 7, 12, respectively. These structures are stabilized due to the fact that two hydrogen bonding interactions can be observed, as can be seen for the R(O4O1) and R(O2O3) distances of about 2 Å which is typical of hydrogen bonding. Structures 12 and 7 are very similar in structure except that the direction of their hydrogen atoms in their OH groups differ (HO2, HO3), leading to a slight destabilization of 7. Molecule 9 has a similar structure as 7, however, the rotation of H (O4) and H (O1) causes it to have a higher energy since these is more interaction of H (O4) with the hydrogen atoms of C5. Structure 8, has a higher energy due to the fact that all of its groups run parallel leading to a destabilization of energy also due to unfavorable interactions as opposed to the most stable structure 12, of this group. From Table 1 we can also see dipole moments for 12, 7, 9, 8 of 2.14 D, 3.43 D, 4.04 D, 6.84 D, the highest being for 8 due again to the parallel orientation of the OH groups. 3.4. Group 4 In the final group, 5, 6, 10, and 11 are in a twist configuration with the general trend of O1, O3, and O4 as endo, and O2 as exo. Structures 5, 6, 10, and 11 have relative energies of 1.13, 0.0, 2.00, 1.19, and 1.75 kcal/mol, respectively. Since all of these structures are low lying on the potential energy surface, single point CCSD(T)/6-31G**// MP2/6-31G** calculations have been carried out that yield relative energies of 1.10, 2.12, 1.37 kcal/mol for molecules 5, 10, and 11, respectively. With ZPE corrections we get CCSD(T)/6-31G**//MP2/6-31G** for 5, 10, 11 of 0.78, 1.90, and 1.02 kcal/mol, respectively. As already mentioned structure 6 is the most stable, and is used as a reference point for the energies of the other molecules in this study. As we can see the CCSD(T)//MP2 are very similar to the results of the MP2//MP2 calculations with an average difference of 0.11 kcal/mol for the above mentioned molecules. The stability of 6 over 5 has to do with the orientation of the second H (O2) group. It is rotated away from the molecule leading to an energy that is 1.13 kcal/mol higher. Structure 10, 11 show a slight destabilization as a result of the rotation of the HO1, HO4 in an opposite direction as 6, 5. Furthermore, rotation of H (O3) in 10 causes a slight destabilization relative to 11. Table 1 shows that the \H (O2) O2C2C1 of 11 is 75.8°, whereas the angle in 10 is 138.9° as a result of this effect. Table 1 also shows that 6, 5, 11, 10 have dipole moments of 1.35, 4.75, 1.11, and 4.84 D, respectively. The highest dipole moment is seen for 10 which may be due to the orientation of the hydroxyl groups as can be seen for the variations in the dihedral angles from the table. A.F. Jalbout et al. / Chemical Physics 328 (2006) 1–7 slight energy changes. We saw that for groups 1, 2 only one hydrogen bond can form between O2 and O3 due to rotation of the C5 atom that prevents an interaction between O1 and O4. In groups 3 and 4, however, this same rotation now occurs in a favorable manner permitting a second hydrogen bonding interaction that stabilizes the molecule. This work has not only summarized our location of 16 conformers of the dehydro-R ribose molecule, but also described energetic and structural differences in these structures. The located minimum molecules can be used as a reference for future experimental studies related to this system. 6.5 6.0 5.5 -1 Relative Energy (kcal mol ) 7 5.0 4.5 4.0 3.5 3.0 2.5 2.0 1.5 1.0 0.5 Acknowledgement 0.0 r6 r12 r5 r11 r7 r1 r16 r10 r9 r3 r8 r4 r13 r0 r15 r2 r14 Ribose Isomer Fig. 2. Relative energies in kcal mol of the structures shown in Fig. 1. We would like to thank The University of Arizona for valuable resources. Appendix A. Supporting information 4. Conclusions In this work, we have explored several isomers of the dehydro R-ribose molecule. We have identified 16 stable molecules on the potential energy surface. Out of these 16 structures 6, 12, 5, 7 = 11, 1, 16, 10 (where 7 and 11 are isoenergetic) were found to be low lying. For these structures not only were their frequencies calculated at the MP2/6-31G** level, but their energies were also verified at the CCSD(T)/6-31G**//MP2/6-31G** level of theory. The relative energies of the structures in Fig. 1 are represented graphically in Fig. 2. If we refer back to Fig. 2, we can see that most stable structures are 6, 12, 5, in that order. These structures have two hydrogen bonds, however, in their formation the hydrogen atoms rotates away from the molecular structure. Such an effect can be seen by observing that H (O1), H (O3) are point away from the ring, whereas in 12 only H (O1) is in this similar orientation, and in 5 only HO3 is pointing away. In general, we have discussed that the primary reason associated with the differences in energy had to with the fact that each of them had structural deviations that caused Supplementary data associated with this article can be found, in the online version, at doi:10.1016/ j.chemphys.2006.03.026. References [1] M. Levitt, A. Warshel, J. Am. Chem. Soc. 100 (1978) 2607. [2] A. Arnott, S.D. Dover, A.J. Wonacott, Acta Crystallogr., Sect. B 25 (1969) 2192. [3] C. Altona, M. Sundaralingam, J. Am. Chem. Soc. 94 (1972) 8205. [4] N. Luo, A. Litvin, R. Osman, J. Phys. Chem. A. 103 (1999) 592. [5] S.A. Benner, A. Ricardo, M.A. Carrigan, Curr. Opin. Chem. Biol. 8 (2004) 672. [6] M.J. Frisch et al., GAUSSIAN03, Gaussian Inc., Pittsburgh, PA, 2003. [7] J.B. Foresman, Æ Frisch, Exploring Chemistry with Electronic Structure Methods, second ed., Gaussian, INC, Pittsburgh, PA, 1996; A.F. Jalbout, F. Nazari, L. Turker, J. Mol. Struct. (Theochem) 1 (2004) 627. [8] A.F. Jalbout, L. Adamowicz, Adv. Quant. 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