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Ab initio Hartree-Fock/6-31G** calculation on 9-?-D-arabinofuranosyladenine-5?-monophosphate molecule: Application to the analysis of its IR and Raman spectra

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Ab initio Hartree-Fock/6-31G** calculation on 9-?-D-arabinofuranosyladenine-5?-monophosphate molecule: Application to the analysis of its IR and Raman spectra
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  Vibrational Force Field Calculations of Ara-A. Application to the Analysis of Its Infraredand Raman Spectra Bele ´ n Herna ´ ndez, † Abdelaziz Elass, ‡ Raquel Navarro, † Ge ´ rard Vergoten, ‡ andAntonio Hernanz* ,†  Departamento de Ciencias y Te ´ cnicas Fisicoquı ´ micas, Uni V  ersidad Nacional de Educacio ´ n a Distancia(UNED), Senda del Rey s/n, E-28040 Madrid, Spain, and CRESIMM, Uni V  ersite ´  des Sciences et Technologiesde Lille I, UFR de Chimie, Ba ˆ t. C8, 1 er  e ´ t. 59655 Villeneu V  e d’Ascq Cedex, France Recei V  ed: December 4, 1997; In Final Form: March 13, 1998  The vibrational spectra of the arabinonucleoside 9-   - D -arabinofuranosyladenine, ara-A, are reported. Ara-Ais of interest because of its antiviral activity. An accurate knowledge of the vibrational modes is a valuablehelp for the elucidation of drug - nucleotide and drug - enzyme interactions. The FTIR and FT-Raman spectraof ara-A were recorded from 4000 to 30 cm - 1 . A hexadeuterated derivative (deuteration at C8, the aminoand hydroxyl groups) was synthesized, and its spectra were also used for the vibrational analysis of ara-A.Theoretical frequencies as well as the potential energy distribution of the vibrational modes of ara-A werecalculated using the ab initio HF/3-21G method, the semiempirical PM3 method, and two valence forcefields. The results obtained are compared in order to show the accuracy and reliability of each method. Theobserved spectra and the vibrational frequencies of ara-A are assigned considering the potential energydistributions and the observed band shifts by deuteration. Scaled ab initio and PM3 frequencies are in agood agreement with the experimental data. The valence force field was found to reproduce them withenough accuracy when a large set of harmonic force constants is used. Previous normal coordinate analysesof the adenine and related molecules are compared with these results. Introduction Nucleoside analogues are an important group of antiviraldrugs. Arabinosides have attracted great attention owing to theirantiviral activity of broad spectrum against DNA viruses andRNA tumor viruses (oncoviruses). The arabinonucleosidesdiffer from their ribo and deoxyribo analogues in the bonds atthe C2 ′  position. The hydroxyl group is cis-oriented to theglycosidic C1 ′ - N9 bond, this group is trans in ribonucleosides,and no hydroxyl group exists in this position for deoxyribo-nucleosides. These changes have small effects on the bondlengths and angles of the furanose ring, keeping a similarpuckering range. 1 Adenine arabinoside, 9- beta - D -arabinofuranosyledenine (vi-darabine or ara-A), Figure 1, is a purine nucleoside, synthesizedin the early 1960s, 2 active against DNA viruses of the herpesgroup. 3 - 6 Ara-A is an effective chemotherapeutic agent 3,7 - 10 used in combination with inhibitors of adenosine deaminase. 3,8 The compound is curative against L 1210 leukemia in mice 11 and for several types of mammalian tumors. 12 Some studieshave indicated that the mechanism involves the phosphorylationof ara-A by cellular kinases to active 5 ′ -triphosphate, 8,13 whichhas been proved to inhibit the viral DNA polymerase. 14 X-ray diffraction studies of this compound were performedby Bunick and Voet, 15 who observed orthorhombic crystals withunit cell dimensions  a ) 5.08 Å,  b ) 10.485 Å,  c ) 21.419 Åand four molecules per unit cell. There are infinite stacks of adenine residues in which neighboring rings are related by the “a”  axis. The arabinose puckering for ara-A is  3 T 4 , one of thepreferred puckering modes for the ribose ring. Hence, the sugarconformation of ara-A is quite similar to that of adenosine. 16 Both molecules are C3 ′ -endo, gauche - trans oriented about theirC4 ′ - C5 ′  exocyclic bond and within the orientation range antiabout the glycosidic bond. The conformational similaritiesbetween ara-A and adenosine are such that ara-A is acceptedinto many biosynthetic pathways that normally incorporateadenosine. Several authors 12,17,18 have suggested that once ara-Ais included into various biomolecules, the configurationaldifferences between adenosine and ara-A render these aggregatespartially or even totally inactive in their biochemical processes.An accurate knowledge of the vibrational modes of thisarabinonucleoside would be an important help for the elucidationof drug - target interactions.Raman spectra of ara-A, ara-A ‚ HCl, adenosine and adenosinehydrochloride have been reported by Theophanides et al., 19 butthe region around 3000 cm - 1 was not recorded. The observedfrequencies were assigned on the basis of correlated groupfrequencies. In the present work, the vibrational study isextended to infrared and Raman spectroscopy (4000 - 30 cm - 1 ) † Universidad Nacional de Educacio´n a Distancia. ‡ CRESIMM. Figure 1.  Numbering of atoms in ara-A. 4233  J. Phys. Chem. B  1998,  102,  4233 - 4239S1089-5647(98)00425-8 CCC: $15.00 © 1998 American Chemical SocietyPublished on Web 05/06/1998  for ara-A and a hexadeuterated derivative, ara-A- d  6  (deuterationat C8, the amino and hydroxyl groups), synthesized for thispurpose. The assignment of the vibrational spectra of ara-A isbased on normal coordinate treatments using the ab initio HF/ 3-21G method, the semiempirical PM3 method, and twodifferent valence force fields: one built transferring forceconstants from related molecules and the other using the forceconstants obtained from the ab initio calculation of ara-Amolecule reported here. The results obtained from all thesetreatments are compared to evaluate their reliability. They arealso compared with previous normal coordinate analyses of related molecules. 19 - 30 Experimental SectionMaterials and Instrumentation.  Adenine 9-   - D -arabino-furanoside was purchased from Sigma Chemical Co. and usedas supplied. The ara-A- d  6  isotopomer (deuteration at C8, theamino and hydroxyl groups) was obtained heating a solutionof ara-A in  2 H 2 O at 80  ° C for 20 h and subsequent recrystal-lization. Deuteration was confirmed by  1 H NMR spectroscopy.The FTIR spectra were recorded in a Bomem-DA3 interfer-ometer, working under vacuum (pressure  e  133.3 Pa). Themid-infrared spectra of polycrystalline ara-A and ara-A- d  6  inKBr pellets, Figures 2 and 3, were recorded coadding 500interferograms with an effective apodized resolution  s  )  0.89cm - 1 (RES ) 1.0 and Hamming apodizing function). A DTGS/ MIR detector, a Globar source, and a KBr beam splitter wereused. Far-infrared, FIR, spectra of ara-A and ara-A- d  6  inpolyethylene pellets, from 700 to 200 cm - 1 and from 200 to 40cm - 1 , Figure 4, were obtained coadding 1000 interferograms, s  )  1.77 cm - 1 (RES  )  2 and Hamming apodizing function)using a DTGS/FIR detector and a high-pressure mercury lamp.Mylar beam splitters of 3 and 12  µ m were used for the formerand the latter far-IR regions, respectively.The FT-Raman spectra of the polycrystalline ara-A wererecorded using a Bruker Raman RFS 100 spectrometer. AKrypton discharge lamp pumped Nd 3 + :YAG laser working at1064 nm was the exciting source. Raman emission wascollected at 180 ° , i.e., with backscattering geometry . A quartzbeam splitter and a germanium detector working at 77 K (cooled Figure 2.  3500 - 2000 cm - 1 spectral region. (a) FT-Raman spectrumof ara-A; (b) FTIR spectrum of ara-A; (c) FTIR spectrum of ara-A- d  6  . Figure 3.  1700 - 700 cm - 1 spectral region. (a) FT-Raman spectrumof ara-A. (b) FTIR spectrum of ara-A; (c) FTIR spectrum of ara-A- d  6  . Figure 4.  700 - 30 cm - 1 spectral region. (a) FT-Raman spectrum of ara-A. (b) FTIR spectrum of ara-A; (c) FTIR spectrum of ara-A- d  6  . 4234  J. Phys. Chem. B, Vol. 102, No. 21, 1998   Herna´ndez et al.  by liquid N 2 ) were used to obtain the FT-Raman spectrum,Figures 2a - 4a. One hundred interferograms were coadded, witha nominal resolution of 8 cm - 1 after Blackman - Harris apodiza-tion. Normal Coordinate TreatmentsAb Initio and PM3 Treatments.  Ab initio at level HF, usingthe basis set 3-21G, and PM3 molecular orbital calculations werecarried out using both methods as implemented in Gaussian 94. 31 Total geometry optimizations, ab initio and PM3, were per-formed using the crystalline structure obtained from X-ray data 15 as initial geometry. After each change of atomic coordinates,the energy of the fundamental state of the system was evaluatedby the self-consistent field, SCF (ab initio and PM3), using therestricted Hartree - Fock, RHF, spin-pairing treatment withoutconfiguration interaction. The optimizations are completedwhen the maximum force, rms force, maximum displacement,and rms displacement were less than 0.000 450, 0.000 300,0.001 800, and 0.001 200 internal units (hartrees - bohrs - radians), respectively. The optimized geometries and forceconstants resulting from the second derivatives of the energieshave been used to compute the wavenumbers corresponding tothe normal modes. The force fields were scaled applying theRedong program. 32 Valence Force Field.  The normal coordinate treatment basedon the Wilson’s GF method 33 was applied to ara-A with somespecific details. The molecular geometry to built the G matrixwas taken from crystallographic data. 15 This matrix was writtenin internal coordinates representation, using an extended basisset of 119 coordinates, Table 1, including 29 redundancies whichwere eliminated by diagonalization, as their correspondingeigenvalues are zero. The GF product results in the secularequation, whose eigenvalues yield the 90 harmonic vibrationwavenumbers (32 atoms). A complete set of valence forceconstants for the ara-A molecule was not found in the literatureuntil now. Nevertheless, the overlay technique has proved tobe a reasonable approach. 29,30,34 - 36 Thus, a valence force fieldwith 119 diagonal force constants and 237 off-diagonal termswas built from force constants published for adenine, 20 assumedto be valid for the base residue: from guanine and 5 ′ -dGMP 34 for the glycosidic bond and C - N - H bonds, from 5’-dGMP 34 and tetrahydrofuran (THF) 37 for the arabinose moiety, Tables2 and 3.The second force field was built using the resulting F matrixfrom our ab initio calculation. In this case, a set of 130 internalcoordinates was used. In this case, the out-of-plane bends, opb’s(92 to 97), have been replaced by the opb’s listed in Table 1.This has been done in order to be coherent with the definitionin the ab initio treatment. The 130 diagonal force constantsand the 2102 off-diagonal elements were transferred from theab initio F matrix, Table 1S. Calculations with the first andsecond force field, Bioviban A and B, respectively, have beendone using the program Bioviban developed by this research TABLE 1: Internal Coordinates Definition ( ν ) Stretching,  δ ) In-Plane Bending,  π  ) Out-of-Plane Bending,  τ  ) Torsion) Bioviban A: Internal Coordinates for the Ara-A Molecule1  ν  N1 - C2 34  ν  O5 ′ - H 67  δ  C3 ′ - C4 ′ - O4 ′  100  τ   C2 - N3 - C4 - C52  ν  N1 - C6 35  δ  N1 - C2 - N3 68  δ  C4 ′ - O4 ′ - C1 ′  101  τ   N3 - C4 - C5 - C63  ν  C2 - H 36  δ  C2 - N3 - C4 69  δ  H - C2 ′ - C3 ′  102  τ   C4 - C5 - C6 - N14  ν  C2 - N3 37  δ  N3 - C4 - C5 70  δ  C2 ′ - C3 ′ - O3 ′  103  τ   C5 - C6 - N1 - C25  ν  N3 - C4 38  δ  C4 - C5 - C6 71  δ  C3 ′ - C2 ′ - O2 ′  104  τ   C5 - C4 - N9 - C86  ν  C4 - C5 39  δ  C5 - C6 - N1 72  δ  O2 ′ - C2 ′ - H 105  τ   C4 - N9 - C8 - N77  ν  N9 - C4 40  δ  C6 - N1 - C2 73  δ  C2 ′ - O2 ′ - H 106  τ   N9 - C8 - N7 - C58  ν  C5 - C6 41  δ  N7 - C5 - C4 74  δ  H - C3 ′ - C2 ′  107  τ   C8 - N7 - C5 - C49  ν  C5 - N7 42  δ  C5 - N7 - C8 75  δ  O3 ′ - C3 ′ - C4 ′  108  τ   N1 - C6 - N7 - H2210  ν  C6 - N6 43  δ  N7 - C8 - N9 76  δ  C4 ′ - C3 ′ - H  τ   N1 - C6 - N7 - H2311  ν  N6 - H 44  δ  C8 - N9 - C4 77  δ  H - C4 ′ - C3 ′  109  τ   C4 - N9 - C1 ′ - O4 ′ 12  ν  N6 - H ′  45  δ  N1 - C2 - H 78  δ  C3 ′ - C4 ′ - C5 ′  110  τ   C2 ′ - C1 ′ - O4 ′ - C4 ′ 13  ν  N7 - C8 46  δ  N3 - C2 - H 79  δ  H - C3 ′ - O3 ′  111  τ   O4 ′ - C1 ′ - C2 ′ - C3 ′ 14  ν  C8 - H 47  δ  N3 - C4 - N9 80  δ  C3 ′ - O3 ′ - H 112  τ   C1 ′ - C2 ′ - C3 ′ - C4 ′ 15  ν  N9 - C8 48  δ  C4 - N9 - C1 ′  81  δ  H - C4 ′ - C5 ′  113  τ   C2 ′ - C3 ′ - C4 ′ - O4 ′ 16  ν  N9 - C1 ′  49  δ  O4 ′ - C1 ′ - N9 82  δ  C4 ′ - C5 ′ - H 114  τ   C3 ′ - C4 ′ - O4 ′ - C1 ′ 17  ν  C1 ′ - H 50  δ  N9 - C1 ′ - C2 ′  83  δ  C4 ′ - C5 ′ - H ′  115  τ   HO2 ′ - O2 ′ - C2 ′ - H2 ′ 18  ν  C1 ′ - O4 ′  51  δ  N9 - C1 ′ - H 84  δ  C4 ′ - C5 ′ - O5 ′  116  τ   H3 ′ - C3 ′ - O3 ′ - HC3 ′ 19  ν  C2 ′ - C1 ′  52  δ  C8 - N9 - C1 ′  85  δ  H - C5 ′ - H ′  117  τ   HC4 ′ - C4 ′ - C5 ′ - O5 ′ 20  ν  C4 ′ - O4 ′  53  δ  N9 - C8 - H 86  δ  H - C5 ′ - O5 ′  118  τ   C4 ′ - C5 ′ - O5 ′ - HO5 ′ 21  ν  C2 ′ - O2 ′  54  δ  H - C8 - N7 87  δ  H ′ - C5 ′ - O5 ′  119  δ  C5 ′ - C4 ′ - O4 ′ 22  ν  C2 ′ - C3 ′  55  δ  N7 - C5 - C6 88  δ  C5 ′ - O5 ′ - H23  ν  C2 ′ - H 56  δ  C5 - C6 - N6 89  δ  C5 - C4 - N924  ν  O2 ′ - H 57  δ  C6 - N6 - H 90  δ  O4 ′ - C4 ′ - H25  ν  C3 ′ - O3 ′  58  δ  H - N6 - H ′  91  δ  O4 ′ - C1 ′ - H26  ν  O3 ′ - H 59  δ  C6 - N6 - H 92  π   H - C8 - N7 - N927  ν  C3 ′ - C4 ′  60  δ  N1 - C6 - N6 93  π   H - C2 - N1 - N328  ν  C3 ′ - H 61  δ  O4 ′ - C1 ′ - C2 ′  94  π   N6 - C6 - N1 - C529  ν  C4 ′ - C5 ′  62  δ  C2 ′ - C1 ′ - H ′  95  π   H - N6 - N1 - C530  ν  C4 ′ - H 63  δ  O2 ′ - C2 ′ - C1 ′  96  π   H ′ - N6 - N1 - C531  ν  C5 ′ - O5 ′  64  δ  C1 ′ - C2 ′ - H 97  π   N9 - C1 ′ - C4 - C832  ν  C5 ′ - H 65  δ  C1 ′ - C2 ′ - C3 ′  98  τ   C6 - N1 - C2 - N333  ν  C5 ′ - H ′  66  δ  C2 ′ - C3 ′ - C4 ′  99  τ   N1 - C2 - N3 - C4Bioviban B, ab Initio HF/3 - 21G and PM3 Out - of  - Plane Bends π   N1 - C5C6N6 (opb N1 1 )  π   C5 - N3C4N9 (opb C5 1 )  π   N9 - N7C8H (opb N9 1 ) π   N1 - N3C2H (opb N1 2 )  π   C5 - C6N1N6 (opb C5 2 )  π   N9 - N3C4C5 (opb N9 2 ) π   N3 - N1C2H (opb N3 1 )  π   N7 - C4C5C6 (opb N7 1 )  π   C1 ′ - N1N9C8 (opb C1 ′ ) π   N3 - C5C4N9 (opb N3 2 )  π   N7 - N9C8H (opb N7 2 )  π   N6 - N1C5C6 (opb N6) π   C4 - C5C6N7 (opb C4 1 )  π   C8 - C4N9C1 ′  (opb C8)  π   H - C2N1N3 (opb H - C2) π   C4 - C8N9C1 ′  (opb C4 2 )  π   H - C8N9N7 (opb H - C8) Vibrational Force Field Calculations of Ara-A  J. Phys. Chem. B, Vol. 102, No. 21, 1998   4235  group 16,18 and modified for its application to biological sys-tems. 29,30 Results The optimized ab initio geometry is closer to the crystallinestructure 15 than the geometry obtained from PM3, Table 4. Thebond distances are similar to the experimental data except forC1 ′ - N9, which lengthen from 1.48 to 1.53 Å in the PM3optimized structure and shorten to 1.43 Å in the ab initiostructure. Concerning the arabinose ring, the ab initio treatmentkeeps a degree of pucker similar to those found by X-raydiffraction; PM3 tends to systematically produce sugar ringscloser to planarity. Table 4 lists the geometrical parameters of the three mentioned structures.The spectra of ara-A and ara-A- d  6  are shown in Figures 2 - 5.The wavenumber of fundamentals and the potential energydistributions, PEDs, calculated by ab initio  ,  PM3, and Bioviban(A and B) treatments as well as the observed wavenumbers arelisted in Tables IIS and IIIS. Most of the scale factors takevalues between 0.95 and 0.80. The lowest value, 0.65,corresponds to four torsions. The standard deviation betweencalculated and observed wavenumbers for the ab initio treatmentis 6.16 cm - 1 , whereas for the PM3 calculation it is 12.0 cm - 1 (the largest deviations being localized on C8H, C2H, C4 ′ H, andC2 ′ H stretching frequencies; a standard deviation of 6.74 cm - 1 is obtained without considering these frequencies). No forcefield refinement has been done on Bioviban treatments. As-signments proposed by the different methods are discussed andcompared. Discussion The assignment of the observed bands is discussed by spectralregions considering the nature of the normal modes. 3550 - 2000 cm - 1 .  Intense IR bands appear in this regiondue to N - H, O - H, and C - H stretching vibrations. The twointense bands at 3545 and 3450 cm - 1 are attributed to theantisymmetric and symmetric N - H stretching modes,  ν a (NH 2 )and  ν s (NH 2 ), respectively, in agreement with previous studiesfor adenine, adenosine, and ara-A ‚ HCl 20,21,24,29,30 and the resultsof the ab initio, PM3, and Bioviban calculations. These bandsshift by deuteration to lower wavenumbers in the neighborhoodof  ≈ 2600 cm - 1 . The broad IR bands observed at 3382, 3332,and 3212 cm - 1 are due to the stretching modes of the hydroxylgroups  ν (O2 ′ H),  ν (O3 ′ H), and  ν (O5 ′ H), respectively. Thebroadening of these bands suggests that these groups areinvolved in hydrogen bonds, as indicated by Bunick and Voet 15 from X-ray diffraction data. This group of bands shifts bydeuteration to the region of   ≈ 2500 - 2300 cm - 1 . The  ν (CH)bands overlap with the  ν (OH) bands in the IR spectrum. The ν (C8H) and  ν (C2H) stretching modes appear at wavenumbers ≈ 3000 cm - 1 , in agreement with published values for adenine,adenosine, and ara-A ‚ HCl. 20,21,24,29,30 The IR band at 3116 cm - 1 is assigned to the  ν (C8H) mode; it shifts upon deuteration to2290 cm - 1 . The C - H sugar stretches are observed at lowerwavenumbers, 2900 - 2800 cm - 1 . Concerning the Biovibancalculations, we found in this spectral region that the calculationB reproduces very well the observed wavenumbers, whilecalculation A seems less suitable. 1700 - 1000 cm - 1 .  The bands in this region are mainly dueto in-plane base 19 - 24,26,28,38 and sugar vibrations. Calculations TABLE 2: Bioviban A: Diagonal Valence Force Constants(In-Plane and Out-of-Plane Modes) for the Set of 119Internal Coordinates for Ara-A, Transferred from ValuesPublished for Adenine (Dhaouadi et al. 20 ), Guanine(Majoube 25 ), 5 ′ -dGMP (Ghomi and Taillandier 34 ), andTetrahydrofuran (Eyster and Prohofsky 37 ). Units:Stretching Force Constants (mdyn Å - 1 ), Bending ForceConstants (mdyn Å), Out-of-Plane Bending, and TorsionalForce Constants (mdyn) Stretch1 6.21 10 6.2 19 4.2697 28 4.57092 6.2 11 5.86 20 5.4953 29 4.6523 5.13 12 5.86 21 4.745 30 4.64404 6.88 13 7.0 22 4.2697 31 4.3425 6.4 14 5.41 23 4.5709 32 4.6446 6.4 15 5.92 24 5.534 33 4.6447 5.92 16 4.86 25 4.745 34 5.5348 5.73 17 4.6440 26 5.5349 5.51 18 5.4953 27 4.2697Bend35 1.53 50 1.588 65 1.0079 80 0.53036 1.9 51 0.5017 66 1.0079 81 0.734637 1.23 52 1.380 67 1.1633 82 0.734638 1.0 53 0.425 68 1.3081 83 0.734639 1.29 54 0.425 69 0.656 84 0.163340 1.998 55 1.350 70 1.1633 85 0.501741 1.23 56 1.44 71 1.1633 86 0.78142 1.68 57 0.415 72 0.718 87 0.78143 1.39 58 0.452 73 0.530 88 0.53044 1.4 59 0.415 74 0.656 89 1.645 0.52 60 1.28 75 1.1633 90 0.78146 0.52 61 1.1633 76 0.656 91 0.78147 1.0 62 0.7346 77 0.7346 119 1.163348 1.380 63 1.1633 78 1.007949 1.363 64 0.656 79 0.781Wag92 0.362 93 0.3 94 0.43 95 0.004496 0.0044 97 0.43Torsion98 0.257 104 0.55 110 0.0101 116 0.01099 0.43 105 0.55 111 0.0208 117 0.010100 0.257 106 0.61 112 0.0208 118 0.010101 0.585 107 0.55 113 0.0208102 0.455 108 0.0935 114 0.0101103 0.43 109 0.1 115 0.010 Figure 5.  Comparison between the FTIR spectra of ara-A and ara-A- d  6  in the region 1750 - 1550 cm - 1 . Second derivative spectra in dots. 4236  J. Phys. Chem. B, Vol. 102, No. 21, 1998   Herna´ndez et al.  TABLE 3: Bioviban A: Off-Diagonal Valence Force Constants (In-Plane and Out-of-Plane Modes) for the Set of 119 InternalCoordinates for Ara-A, Transferred from Values Published for Adenine (Dhaouadi et al. 20 ), Guanine (Majoube 25 ), 5 ′ -dGMP(Ghomi and Taillandier 34 ), and Tetrahydrofuran (Eyster and Prohofsky 37 ). Units: Stretching Force Constants (mdyn Å - 1 ),Bending Force Constants (mdyn Å), Out-of-Plane Bending, and Torsional Force Constants (mdyn) Adenine and Glycoside BondStretch - Stretch (In-Plane)1 - 2 0.641 2 - 13 0.22 5 - 8  - 0.15 7 - 8 0.151 - 4 0.5 2 - 8 0.65 5 - 7 0.2 8 - 10 0.751 - 6 0.35 2 - 5 0.2 6 - 8 0.44 8 - 9  - 0.151 - 5 0.2 4 - 13  - 0.17 6 - 9 0.15 9 - 13 0.91 - 8  - 0.15 4 - 6  - 0.15 6 - 7 0.15 13 - 15 0.92 - 4 0.15 4 - 5 0.25 6 - 13 0.15 15 - 16 0.22 - 6 0.35 4 - 8 0.65 7 - 15 0.2 7 - 16 0.22 - 10 0.801 5 - 6 0.35 7 - 13  - 0.71 16 - 19  - 0.15Bend - Bend (In-Plane)60 - 39 0.39 56 - 55  - 0.45 56 - 60 0.25 57 - 56 0.256 - 39  - 0.1 59 - 60 0.25 59 - 56 0.2Stretch - Bend (In-Plane)1 - 35 0.701 5 - 36 0.701 8 - 38 0.2 13 - 43 0.581 - 40 0.701 5 - 37 0.701 8 - 39 0.2 15 - 43 0.551 - 45 0.54 5 - 47 0.55 8 - 55  - 0.3 15 - 44 0.82 - 39 6.2 6 - 37 0.3 9 - 42 0.75 15 - 53 0.762 - 40 0.4 6 - 38 0.75 9 - 55 0.75 15 - 48  - 0.032 - 60 0.78 6 - 89 0.3 10 - 39 0.901 15 - 52  - 0.034 - 35 0.75 7 - 89 0.9 10 - 40 0.901 16 - 44  - 0.034 - 36 0.75 7 - 44 0.9 10 - 38 0.901 16 - 89  - 0.034 - 46 0.35 7 - 47 0.55 13 - 42 0.58 16 - 43  - 0.03Wag - Wag (Out-of-Plane)95 - 94  - 0.03 96 - 94  - 0.062 92 - 93 0.02 94 - 93  - 0.01Wag - Torsion (Out-of-Plane)92 - 105 0.12 92 - 106  - 0.245 93 - 98 0.115 93 - 99  - 0.0694 - 102 0.14 94 - 103 0.11Torsion - Torsion (Out-of-Plane)104 - 105 0.195 105 - 101  - 0.05 108 - 103  - 0.01 102 - 101  - 0.08104 - 106  - 0.05 104 - 107  - 0.14 99 - 100  - 0.04 103 - 99 0.09101 - 100  - 0.12 105 - 106 0.035 98 - 99 0.0625 103 - 101  - 0.08105 - 107 0.05 107 - 101 0.1 98 - 103 0.02 99 - 101  - 0.01106 - 101 0.12 101 - 104 0.22 102 - 103 0.05 100 - 102 0.195Deoxyribose Ring and Glycosidic BondStretch - Stretch18 - 20 0.2956 19 - 22 0.101 22 - 27 0.101 27 - 20 0.10118 - 19 0.1016 21 - 22 0.101 25 - 27 0.101 29 - 31 0.10119 - 21 0.101 22 - 25 0.101 27 - 29 0.101 33 - 32  - 0.0652Bend - Bend49 - 61  - 0.041 66 - 74  - 0.052 69 - 74  - 0.021 78 - 119 0.113961 - 91  - 0.031 66 - 76  - 0.052 70 - 74 0.0158 81 - 82  - 0.088161 - 68 0.285 66 - 69  - 0.052 70 - 79  - 0.031 81 - 83  - 0.088161 - 62 0.0158 66 - 77  - 0.031 71 - 72  - 0.031 81 - 84 0.015861 - 65 0.1139 66 - 71 0.1139 71 - 74 0.0158 81 - 90 0.036361 - 64 0.0158 66 - 70 0.1139 74 - 76 0.012 81 - 119 0.15863 - 72  - 0.031 66 - 75 0.1139 74 - 79 0.0363 82 - 83  - 0.088163 - 62 0.0158 66 - 67 0.1139 75 - 76 0.0158 82 - 84 0.015863 - 65 0.1139 66 - 78 0.1139 75 - 77 0.0158 82 - 87 0.036363 - 64 0.0158 67 - 78 0.1139 75 - 78 0.1139 82 - 119 0.015862 - 65  - 0.031 67 - 76 0.0158 75 - 79  - 0.031 83 - 84 0.015862 - 64 0.0314 67 - 77 0.0158 76 - 77  - 0.0664 83 - 119 0.015864 - 65  - 0.052 67 - 90  - 0.031 76 - 78  - 0.052 83 - 86 0.036364 - 69  - 0.021 67 - 68 0.0285 76 - 79 0.0363 84 - 86  - 0.03164 - 72 0.0363 68 - 119 0.0285 77 - 78  - 0.031 84 - 87  - 0.03165 - 71 0.1139 68 - 90 0.0844 77 - 90 0.0363 86 - 87  - 0.082465 - 74  - 0.052 68 - 91 0.0844 78 - 81  - 0.031 90 - 119  - 0.03165 - 66 0.1139 69 - 70 0.0158 78 - 82  - 0.03165 - 69  - 0.152 69 - 71 0.0158 78 - 83  - 0.03165 - 70 0.1139 69 - 72 0.0363 78 - 84 0.1139Stretch - Bend16 - 49 0.347 20 - 67 0.4197 22 - 66 0.417 27 - 77 0.428816 - 50 0.347 20 - 119 0.4197 22 - 65 0.417 29 - 119 0.365618 - 61 0.4197 20 - 68 0.8257 25 - 79 0.3842 29 - 84 0.365618 - 68 0.8752 20 - 90 0.3842 25 - 75 0.4197 29 - 78 0.41718 - 91 0.3842 21 - 63 0.4197 25 - 70 0.4197 29 - 81 0.428819 - 61 0.3656 21 - 71 0.4197 27 - 66 0.417 29 - 82 0.428119 - 63 0.3656 22 - 71 0.3656 27 - 78 0.417 29 - 83 0.428119 - 65 0.417 22 - 70 0.3656 27 - 75 0.3656 31 - 86 0.384219 - 62 0.4288 22 - 74 0.328 27 - 67 0.3656 31 - 87 0.384219 - 64 0.328 22 - 69 0.328 27 - 76 0.328 31 - 84 0.419719 - 69 0.0703 22 - 64 0.0703 27 - 74 0.0703 Vibrational Force Field Calculations of Ara-A  J. Phys. Chem. B, Vol. 102, No. 21, 1998   4237
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