Enantiomeric syntheses of conformationally restricted D- and L-2', 3'-dideoxy-2',3'-endo-methylene nucleosides from carbohydrate chiral templates

D- and L-2',3'-dideoxy-2',3'-endo-methylene nucleosides were synthesized as potential antiviral agents. The key intermediates 5-O-tert-butyldiphenylsilyl-D- and L-2,3-dideoxy-2, 3-endo-methylenepentofuranoses (20 and 33, respectively) were obtained by selective protection of the D- and L-2,3-dideoxy-2, 3-endo-methylenepentose derivatives 19 and 32 which were prepared from 1,2:5,6-di-O-isopropylidene-D-mannitol and L-gulonic gamma-lactone, respectively, and converted to 5-O-tert-butyldiphenylsilyl-D- and L-2,3-dideoxy-2, 3-endo-methylenepentofuranosyl acetates (21 and 34, respectively) or the chlorides 22 and 35. The acetates and chlorides were condensed with pyrimidine and purine bases by Vorbrüggen conditions or S(N)2-type condensation. Vorbrüggen conditions using the acetates gave mostly alpha-isomers. In contrast, S(N)2-type condensation using the chlorides greatly improved the beta/alpha ratio. From the synthesis, several D- and L-2',3'-dideoxy-2',3'-endo-methylene nucleoside analogues have been obtained, and their structures have been elucidated by NMR spectroscopy and X-ray crystallography. The synthesized D- and L-adenine derivatives were tested as substrates of adenosine deaminase, which indicated that the D-adenosine derivative 4a was a good substrate of a mammalian adenosine deaminase from calf intestinal mucosa (EC 3.5.4.4) while its L-enantiomer 10a was a poor substrate. Either the D-adenine derivative 4a or its L-enantiomer 10a did not serve as an inhibitor of the enzyme.     

Enzymatic and chemical stability of 2',3'-dideoxy-2',3'-didehydropyrimidine nucleosides: potential anti-acquired immunodeficiency syndrome agents

The enzymatic and chemical stability of three 2',3'-dideoxy-2',3'-didehydropyrimidine nucleosides has been studied. Chemical degradtion of the analogues was measured in the pH range of 1.0-9.0. 2',3'-Dideoxy-2',3'-didehydrocytidine (DDCN) degraded rapidly under acidic conditions, but the chemical stability was greater under basic conditions. The chemical degradation of 2',3'-dideoxy-2',3'-didehydrouridine (DDUN) and 2',3'-dideoxy-2',3'-didehydrothymidine (DDTN) was not pH dependent and was faster than that of cytarabine. Enzymatic degradation of DDCN, DDUN and DDTN was not observed in human plasma, though cytarabine was degraded enzymatically under the same conditions. DDCN was also not degraded in the presence of mouse kidney cytidine deaminase.     

Synthesis of 3'-fluoro-2',3'-dideoxy-2',3'-didehydro-4'-ethynyl-D- and -L-furanosyl nucleosides

An efficient procedure has been developed for the synthesis of 3'-fluoro-2',3'-dideoxy-2',3'-didehydro-4'-ethynyl D- and L-furanosyl nucleosides (1 and 2) starting from 2,3-O-isopropylidene-d-glyceraldehyde. The key intermediate 1-O-benzoyl-3E-fluoro-3,4-unsaturated-5,6-di(tert-butyldimethylsilyloxy)-2-hexanone 8 was obtained in nine steps with the overall yield of 22%. The alpha,beta-unsaturated ketone 8 was then treated with ethynylmagnesium bromide in a typical Grignard reaction procedure to afford the two intermediates 9 and 10, which after deprotection, oxidation, and acetylation gave the corresponding 4-ethynyl-substituted D- and L-sugar moieties 15 and 16, respectively. A series of D- and L-pyrimidine and purine nucleosides were prepared by the coupling of the sugar moieties with various silylprotected bases. The anomeric mixtures were obtained after condensation. After separation, the beta-isomers were further deprotected to yield the target nucleosides. All the newly synthesized 4'-substituted nucleosides were tested for their activities against HIV, among which the D-adenine derivative showed moderate anti-HIV activity (EC(50) = 25.1 microM) without significant cytotoxicity.     

Stereoselective synthesis and conformational study of novel 2',3'-Didehydro-2',3'-dideoxy-4'-selenonucleosides

Stereoselective synthesis of novel 2',3'-didehydro-2',3'-dideoxy-4'-selenonucleosides (4'-seleno-d4Ns) 4a- c was accomplished via 4'-selenoribofuranosyl pyrimidines 11a- c, as key intermediates. 4'-Selenoribofuranosyl pyrimidines 11a- c were efficiently synthesized from d-ribose or d-gulonic gamma-lactone using a Pummerer-type condensation as a key step. Introduction of 2',3'-double bond was achieved by treating cyclic 2',3'-thiocarbonate with 1,3-dimethyl-2-phenyl-1,3,2-diazaphospholidine.     

2',3'-二脱氧-2',3'-二去氢鸟嘌呤核苷构象稳定性的理论研究

采用密度泛函方法在B3LYP/6-31＋G**水平上研究了2',3'-二脱氧-2',3'-二去氢鸟嘌呤核苷分子(D4G)的构象. 分别研究在气相中的孤立分子和一水合物异构体的相对稳定性和异构体之间的相互转变过程, 分析了水分子的参与对D4G异构体的相对稳定性和几何结构参数以及自然电荷的影响. 结果表明, 孤立的D4G分子在气相中存在8种稳定构象, 其中构象d4g-2是所有构象中最稳定的, 气相中D4G主要以d4g-2存在. 气相中各构象的相对稳定性为: d4g-2＞d4g-1＞d4g-5＞d4g-3＞d4g-6＞d4g-4＞d4g-8＞d4g-7. 计算得到的各构象键长和键角数据与实验值接近. 一个水分子的加入对D4G分子的构型参数有所影响, 基本不改变D4G分子各构象的稳定性顺序, 但构象转变的能垒有所提高. 氢键在分子构象中发挥了重要作用.     

Chemical and structural implications of 1',2'- versus 2',4'- conformational constraints in the sugar moiety of modified thymine nucleosides

In order to understand how the chemical nature of the conformational constraint of the sugar moiety in ON/RNA(DNA) dictates the duplex structure and reactivity, we have determined molecular structures and dynamics of the conformationally constrained 1',2'-azetidine- and 1',2'-oxetane-fused thymidines, as well as their 2',4'-fused thymine (T) counterparts such as LNA-T, 2'-amino LNA-T, ENA-T, and aza-ENA-T by NMR, ab initio (HF/6-31G** and B3LYP/6-31++G**), and molecular dynamics simulations (2 ns in the explicit aqueous medium). It has been found that, depending upon whether the modification leads to a bicyclic 1',2'-fused or a tricyclic 2',4'-fused system, they fall into two distinct categories characterized by their respective internal dynamics of the glycosidic and the backbone torsions as well as by characteristic North-East type sugar conformation (P = 37 degrees +/- 27 degrees , phi(m) = 25 degrees +/- 18 degrees ) of the 1',2'-fused systems, and (ii) pure North type (P = 19 degrees +/- 8 degrees , phi(m) = 48 degrees +/- 4 degrees ) for the 2',4'-fused nucleosides. Each group has different conformational hyperspace accessible, despite the overall similarity of the North-type conformational constraints imposed by the 1',2'- or 2',4'-linked modification. The comparison of pK(a)s of the 1-thyminyl aglycon as well as that of endocyclic sugar-nitrogen obtained by theoretical and experimental measurements showed that the nature of the sugar conformational constraints steer the physicochemical property (pK(a)) of the constituent 1-thyminyl moiety, which in turn can play a part in tuning the strength of hydrogen bonding in the basepairing.     

2',3'-二脱氧-2',3'-二去氢鸟嘌呤核苷构象稳定性的理论研究

采用密度泛函方法在B3LYP/6-31＋G**水平上研究了2',3'-二脱氧-2',3'-二去氢鸟嘌呤核苷分子(D4G)的构象. 分别研究在气相中的孤立分子和一水合物异构体的相对稳定性和异构体之间的相互转变过程, 分析了水分子的参与对D4G异构体的相对稳定性和几何结构参数以及自然电荷的影响. 结果表明, 孤立的D4G分子在气相中存在8种稳定构象, 其中构象d4g-2是所有构象中最稳定的, 气相中D4G主要以d4g-2存在. 气相中各构象的相对稳定性为: d4g-2＞d4g-1＞d4g-5＞d4g-3＞d4g-6＞d4g-4＞d4g-8＞d4g-7. 计算得到的各构象键长和键角数据与实验值接近. 一个水分子的加入对D4G分子的构型参数有所影响, 基本不改变D4G分子各构象的稳定性顺序, 但构象转变的能垒有所提高. 氢键在分子构象中发挥了重要作用.     

Comprehensive structural studies of 2',3'-difluorinated nucleosides: comparison of theory, solution, and solid state

The conformations of three 2',3'-difluoro uridine nucleosides were studied by X-ray crystallography, NMR spectroscopy, and ab initio calculations in an attempt to define the roles that the two vicinal fluorine atoms play in the puckering preferences of the furanose ring. Two of the compounds examined contained fluorine atoms in either the arabino or xylo dispositions at C2' and C3' of a 2',3'-dideoxyuridine system. The third compound also incorporated fluorine atoms in the xylo configuration on the furanose ring but was substituted with a 6-azauracil base in place of uracil. A battery of NMR experiments in D 2O solution was used to identify conformational preferences primarily from coupling constant and NOE data. Both (1)H and (19)F NMR data were used to ascertain the preferred sugar pucker of the furanose ring through the use of the program PSEUROT. Compound-dependent parameters used in the PSEUROT calculations were newly derived from complete sets of conformations calculated from high-level ab initio methods. The solution and theoretical data were compared to the conformations of each molecule in the solid state. It was shown that both gauche and antiperiplanar effects may be operative to maintain a pseudodiaxial arrangement of the C2' and C3' vicinal fluorine atoms. These data, along with previously reported data by us and others concerning monofluorinated nucleoside conformations, were used to propose a model of how fluorine influences different aspects of nucleoside conformations.     

Gas-phase structure, rotational barrier, and vibrational properties of methyl methanethiosulfonate, CH3SO2SCH3: an experimental and computational study

The molecular structure of methyl methanethiosulfonate, CH3SO2SCH3, has been determined in the gas phase from electron-diffraction data supplemented by ab initio (HF, MP2) and density functional theory (DFT) calculations using 6-31G(d), 6-311++G(d,p), and 6-311G(3df,3pd) basis sets. Both experimental and theoretical data indicate that although both anti and gauche conformers are possible by rotating about the S-S bond, the preferred conformation is gauche. The barrier to internal rotation in the CSSC skeleton has been calculated using the RHF/6-31G(d), MP2/6-31G(d), and B3LYP/6-31G(d) methods as well as MP2 with a 6-31G(3df) basis set on sulfur and 6-31G(d) on C, H, and O. A 6-fold decomposition of the rotational barrier has been performed in terms of a Fourier-type expansion, enabling us to analyze the nature of the potential function, showing that the coefficients V1 and V2 are the dominant terms; V1 is associated with nonbonding interactions, and V2 is associated with hyperconjugative interactions. A natural bond orbital analysis showed that the lone pair --> sigma* hyperconjugative interactions favor the gauche conformation. Furthermore, the infrared spectra for the liquid and solid phases and the Raman spectrum for the liquid have been recorded, and the observed bands have been assigned to the vibrational normal modes. The experimental vibrational data, along with calculated theoretical force constants, were used to define a scaled quantum mechanical force field for the target system that enabled us to estimate the measured frequencies with a final root-mean-square deviation of 6 cm-1.     

Nucleophilic addition of benzenethiol to 1',2'-unsaturated nucleosides: 1'-C-phenylthio-2'-deoxynucleosides as anomeric radical precursors

The addition reaction of benzenethiol to the glycal portion of 1',2'-unsaturated uridine proceeds efficiently in the presence of Et(3)N. The mechanism involves nucleophilic attack of thiolate at the anomeric position in the rate-determining step, wherein conjugation between the nucleobase and the glycal portion is crucial. The derivative having a methyl group either at the 2'- or 6-position did not undergo this addition reaction, due to their sterically prohibited coplanarity. The 1',2'-unsaturated derivatives of thymine and adenine can also be used as substrates for this addition reaction. It was also shown that the resulting 1'-C-phenylthio-2'-deoxynucleosides serve as precursors for radical-mediated C-C bond formation at the anomeric position.     

Hydrolysis of 2',3'-O-methyleneadenos-5'-yl bis(2',5'-di-O-methylurid-3'-yl) phosphate, a sugar O-alkylated trinucleoside 3',3',5'-monophosphate: implications for the mechanism of large ribozymes

Hydrolytic reactions of 2',3'-O-methyleneadenos-5'-yl bis(2',5'-di-O-methylurid-3'-yl) phosphate (1), a sugar O-alkylated trinucleoside 3',3',5'-monophosphate, have been followed by RP HPLC over a wide pH range. Under neutral and mildly acidic conditions, the only reaction observed was a pH-independent cleavage of the O-C5' bond of the 5'-linked nucleoside. Under more alkaline conditions nucleophilic attack by hydroxide ion starts to compete. The reaction is first order in [OH(-)] and becomes predominant at pH 10. Each of the 3'-linked nucleosides is displaced 2.9 times as readily as the 5'-linked one. To determine the beta(lg) value for the hydroxide ion catalyzed hydrolysis of 1, two diesters (2a,b) having 2',3'-O-methyleneadenosine (7) and 2',5'-di-O-methyluridine (4) as leaving groups were hydrolyzed under alkaline conditions. Since the beta(lg) value for this reaction is known, DeltapK(a) between 4 and 7 could be calculated. The beta(lg) for the hydrolysis of 1 was estimated to be -0.5 with use of this information. The mechanisms of the partial reactions and the role of leaving group properties in ribozyme reactions of large ribozymes are discussed.     

1,2-Dibromoethyl-trichlorosilane (CH2BrCHBrSiCl3): conformational structure and vibrational properties by gas-phase electron diffraction, infrared and Raman spectroscopy, and ab initio molecular orbital and density functional theory calculations

The molecular structure and conformational properties of 1,2-dibromoethyl-trichlorosilane (CH2BrCHBrSiCl3) have been investigated using gas-phase electron diffraction (GED) data recorded at a temperature of 100 degrees C, together with ab initio molecular orbital (MO) and density functional theory (DFT) calculations, infrared (IR) and Raman spectroscopy in the liquid and solid phases, and normal coordinate analysis (NCA). The molecule exists in the gas- and liquid phases as a mixture of three conformers, gauche(-) [G(-)], with a refined torsion angle phi(BrCCBr)=-71(6) degrees, anti [A], with a torsion angle phi(BrCCBr) approximately -170 degrees , and gauche(+) [G(+)], with a torsion angle phi(BrCCBr) approximately +70 degrees . The second torsion angle of importance, the rotation about the CSi bond, has been refined to a value of +175(13) degrees . Torsion angles were only refined for the more abundant G(-) conformer. In the solid phase, only the G(-) conformer was observed. The temperature-dependent Raman spectra have provided an estimate of the relative conformational entropies, DeltaS. The obtained composition from GED refinements was (%) G(-)/A/G(+)=64(27)/23(13)/13(18) (values with estimated 2sigma uncertainties), giving a conformational stability order in agreement with both the Raman enthalpy measurements and the ab initio MO and DFT calculations using the 6-311G(d) basis set and scaled zero-point energies. Relevant structural parameter values obtained from the GED refinements (with the ab initio HF values used as constraints) were as follows (G(-) values with estimated 2sigma uncertainties): bond lengths (r(g)):r(C-C)=1.501(18)A, r(SiC)=1.865(15)A, r(CBr)=1.965(8)A (average), r(SiCl)=2.028(3)A (average). Bond angles ( anglealpha):angleCCSi=114.1(33) degrees , angleC1C2Br=114.0(21) degrees , angleCSiCl=109.6(7) degrees (average). Experimental IR/Raman and obtained vibrational wavenumbers based on both the unscaled, fixed-scaled as well as the scale-refined quantum-mechanical force fields [HF/6-311G(d)] are presented. The results are discussed and compared with some similar molecules from the literature.     

Nucleic-Acid Analogues with Constraint Conformational Flexibility in the Sugar-Phosphate Backbone (‘Bicyclo-DNA’). Part 1. Preparation of (3S,5′R)-2′-Deoxy-3′,5′-ethano-αβ-D-ribonucleosides (‘Bicyclonucleosides’)

We describe the synthesis of 2′-deoxy-3′,5′-ethano-D -ribonucleosides 1 – 8 (= (5′,8′-dihydroxy-2′-oxabicyclo-[3.3.0]oct-3′-yl)purines or -pyrimidines) of the nucleobases adenine, thymine, cytosine, and guanine. They differ from natural 2′-deoxyribonucleosides only by an additional ethylene bridge between the centers C(3′) and C(5′). The configuration at these centers (3S,5′R) was chosen as to match the geometry of a repeating nucleoside unit in duplex DNA as close as possible. These nucleosides were designed to confer, as constituents of an oligonucleotide chain, a higher degree of preorganization of a single strand for duplex formation with respect to natural DNA, thus leading to an entropic advantage for the pairing process. The synthesis of these ‘bicyclonucleosides’ was achieved by construction of an enantiomerically pure carbohydrate precursor 18 / 19 (Schemes 1), which was then converted to the corresponding nucleosides by known methods in nucleoside synthesis (Schemes 2 and 3). In all cases, both anomeric forms of the nucleosides were obtained in pure crystalline form, the relative configuration of which was established by ¹H-NMR-NOE spectroscopy. A conformational analysis of the nucleosides with β-configuration at the anomeric center by means of X-ray and ¹H-NMR (including NOE) spectroscopy show the furanose part of the molecules to adopt uniformly a 1′exo-conformation with the base substituents preferentially in the anti-range in the pyrimidine nucleosides (anti/syn ca. 2:1) distribution in the purine nucleosides (in solution).     

Stereoelectronic effect on one-electron reductive release of 5-fluorouracil from 5-fluoro-1-(2-oxocycloalkyl)uracils as a new class of radiation-activated antitumor prodrugs

A series of 5-fluoro-1-(2'-oxocycloalkyl)uracils (3-11) that are potentially novel radiation-activated prodrugs for the radiotherapy of hypoxic tumor cells have been synthesized to evaluate a relationship between the molecular structure and the reactivity of one-electron reductive release of antitumor 5-fluorouracil (1) in anoxic aqueous solution. All the compounds 3-11 bearing the 2'-oxo group were one-electron reduced by hydrated electrons (eaq-) and thereby underwent C(1')-N(1) bond dissociation to release 5-fluorouracil 1 in 47-96% yields upon radiolysis of anoxic aqueous solution, while control compounds (12, 13) without the 2'-oxo substituent had no reactivity toward such a reductive C(1')-N(1) bond dissociation. The decomposition of 2-oxo compounds in the radiolytic one-electron reduction was more enhanced, as the one-electron reduction potential measured by cyclic voltammetry in N,N-dimethylformamide became more positive. The efficiency of 5-fluorouracil release was strongly dependent on the structural flexibility of 2-oxo compounds. X-ray crystallographic studies of representative compounds revealed that the C(1')-N(1) bond possesses normal geometry and bond length in the ground state. MO calculations by the AM1 method demonstrated that the LUMO is primarily localized at the pi* orbital of C(5)-C(6) double bond of the 5-fluorouracil moiety, and that the LUMO + 1 is delocalized between the pi* orbital of 2'-oxo substituent and the sigma* orbital of adjacent C(1')-N(1) bond. The one-electron reductive release of 5-fluorouracil 1 in anoxic aqueous solution was presumed to occur from the LUMO + 1 of radical anion intermediates possessing a partial mixing of the antibonding C(2')=O pi* and C(1')-N(1) sigma* MO's, that may be facilitated by a dynamic conformational change to achieve higher degree of (pi* + sigma*) MO mixing.     

Chlorocarbonyl trifluoromethanesulfonate, ClC(O)OSO2CF3: structure and conformational properties in the gaseous and condensed phases

Pure chlorocarbonyl trifluoromethanesulfonate, ClC(O)OSO(2)CF(3), has been prepared in about 58% yield by the ambient-temperature reaction between ClC(O)SCl and AgCF(3)SO(3). The conformational properties of the gaseous molecule have been studied by vibrational spectroscopy [IR(gas), IR(matrix), and Raman(liquid)] and quantum chemical calculations (HF and B3LYP with 6-31+G* basis sets); in addition, the solid-state structure has been determined by X-ray crystallography. ClC(O)OSO(2)CF(3) exists in the gas phase as a mixture of trans [ClC(O) group trans with respect to the CF(3) group] and gauche conformers, with the trans form being the more abundant [66(8)% from IR(matrix) measurements]. In both conformers, the C=O bond of the ClC(O) group is oriented synperiplanar with respect to the S-O single bond. The experimental free energy difference between the two forms, DeltaG degrees = 0.8(2) kcal mol(-1) (IR), is slightly smaller than the calculated value (1.0-1.5 kcal mol(-1)). The crystalline solid at 150 K [monoclinic, P2(1)/n, a = 7.3951(9) angstroms, b = 24.897(3) angstroms, c = 7.4812(9) angstroms, beta = 99.448(2) degrees, Z = 8] consists surprisingly of both trans and gauche forms. Whereas the more stable conformer for the more or less discrete molecules and the polarization effects would tend to favor the trans form, the packing effects would stabilize the gauche rotamer in the solid state.     

Trifluoromethyl chlorosulfonate, CF3OSO2Cl: gas phase and crystal structure, conformation and vibrational analysis studied by experimental and theoretical methods

The geometric structure and conformational properties of trifluoromethyl chlorosulfonate (chlorosulfuric acid trifluoromethyl ester), CF(3)OSO(2)Cl, have been determined by X-ray crystallography, gas electron diffraction (GED), and vibrational spectroscopy (IR(gas), IR(matrix), and Raman(liquid)). These experimental investigations were supplemented by quantum chemical calculations (B3LYP with 6-311G* and 6-311+G(3df) basis sets). All experimental methods result in a single conformer with gauche orientation of the CF(3) group relative to the S[bond]Cl. The dihedral angle delta(COSCl) is determined to be 91.7(3) degrees in the crystal and 94(3) degrees in the gas phase. This dihedral angle corresponds to a near-eclipsed orientation of the O[bond]C relative to one of the S[double bond]O bonds (delta(CO[bond]SO) = -23.0(3) degrees and -21(3) degrees in the crystal and gas phase, respectively).     

Trans-hydrogen-bond (h2)J(NN) and (h1)J(NH) couplings in the DNA A-T base pair: natural bond orbital analysis

Natural bond orbital (NBO) analysis described here demonstrates that trans-hydrogen-bond (trans-H-bond) NMR J couplings in the DNA A-T base pair, h2JNN and h1JNH, are determined largely by three terms: two Lewis-type contributions (the single-orbital contribution from the adenine lone pair and the contribution from the sigmaN3H3 natural bond orbital of the thymine ring) and one contribution from pairwise delocalization of spin density (between the lone pair in adenine and the sigma* antibonding orbital linking N3 and H3 of thymine). For h2JNN coupling, all three contributions are positive, whereas for h1JNH coupling, the delocalization term is negative, and the other two terms are positive, resulting in a small net positive coupling constant. This result rationalizes the experimental findings that the two-bond coupling (h2JNN approximately 9 Hz) is larger than the one-bond coupling (h1JNH approximately 3 Hz) and demonstrates that the same hyperconjugative and steric mechanisms that stabilize the H-bond are involved in the transmission of J coupling information. The N1...H3-N3 H-bond of the DNA A-T base pair is found to exhibit significant covalent character, but steric effects contribute almost equally to the trans-H-bond coupling.     

Computational analysis of aza analogues of [2',5'-bis-O-(tert-butyldimethylsilyl)-beta-D-ribofuranose]-3'-spiro-5"-(4"-amino-1",2"-oxathiole-2",2"-dioxide) (TSAO) as HIV-1 reverse transcriptase inhibitors: relevance of conformational properties on the inhibitory activity

We have carried out a theoretical analysis of aza analogues of [2',5'-bis-O-(tert-butyldimethylsilyl)-beta-D-ribofuranosyl]-3'-spiro-5"-(4"-amino-1",2"-oxathiole-2",2"-dioxide) by a variety of computational tools, aimed to account for the effect of the endocyclic amino moiety N-2" on the inhibitory activity against HIV-1. Docking studies suggest that compounds substituted at the N-3 and N-2' ' positions present the same binding mode to the [2',5'-bis-O-(tert-butyldimethylsilyl)-beta-D-ribofuranosyl]-3'-spiro-5"-(4"-amino-1",2"-oxathiole-2",2"-dioxide)thymine prototype, where the endocyclic amino group remains mostly exposed to the solvent. A careful conformational analysis performed through different theoretical levels, from molecular mechanics to high-level quantum mechanical calculations, provides a rationalization based on conformational preferences, which appears as strongly determined by the substitution at N-2", and on electrostatic effects from the bulk water.     

Sugar pucker modulates the cross-correlated relaxation rates across the glycosidic bond in DNA

The dependence of N1/9 and C1' chemical shielding (CS) tensors on the glycosidic bond orientation (chi) and sugar pucker (P) in the DNA nucleosides 2'-deoxyadenosine, 2'-deoxyguanosine, 2'-deoxycytidine, and 2'-deoxythymidine was studied using the calculation methods of quantum chemistry. The results indicate that these CS-tensors exhibit a significant degree of conformational dependence on chi and P structural parameters. The presented data test underlying assumptions of currently established methods for interpretation of cross-correlated relaxation rates between the N1/9 chemical shielding tensor and C1'-H1' dipole-dipole (Ravindranathan et al. J. Biomol. NMR 2003, 27, 365-75. Duchardt et al. J. Am. Chem. Soc. 2004, 126, 1962-70) and highlight possible limitations of these methods when applied to DNA.