Solid-state nuclear magnetic resonance spectroscopy studies of furanose ring dynamics in the DNA HhaI binding site

The dynamics of the furanose rings in the GCGC moiety of the DNA oligomer [d(G 1A 2T 3A 4 G 5 C 6 G 7 C 8T 9A 10T 11C 12)] 2 are studied by using deuterium solid-state NMR (SSNMR). SSNMR spectra obtained from DNAs selectively deuterated on the furanose rings of nucleotides within the 5'-GCGC-3' moiety indicated that all of these positions are structurally flexible. The furanose ring within the deoxycytidine that is the methylation target displays the largest-amplitude structural changes according to the observed deuterium NMR line shapes, whereas the furanose rings of nucleotides more remote from the methylation site have less-mobile furanose rings (i.e., with puckering amplitudes < 0.3 A). Previous work has shown that methylation reduces the amplitude of motion in the phosphodiester backbone of the same DNA, and our observations indicate that methylation perturbs backbone dynamics through the furanose ring. These NMR data indicate that the 5'-GCGC-3' is dynamic, with the largest-amplitude motions occurring nearest the methylation site. The inherent flexibility of this moiety in DNA makes the molecule more amenable to the large-amplitude structural rearrangements that must occur when the DNA binds to the HhaI methyltransferase.     

The gas-phase structure of dodecafluorooctahydrothiophene, c-C4F8SF4

The geometric structure of c-C₄F₈SF₄ has been determined by gas-phase electron diffraction. The five-membered ring has the twist form (C₂ symmetry) with a puckering amplitude q = 0.42 (2) Å. The following principle geometric parameters (r_a values) with estimated uncertainties have been derived: (C---C)_av = 1.541(10), S---C = 1.896(7), S---F_e = 1.558(6), S---F_a = 1.594(6) Å, CSC = 90.0(9)°, SCC = 109.1(8)°, CCC = 106.5(12)°, F_aSF_e = 90.5(15)° and F_eSF_e = 87.7(29)°. Vibrational amplitudes for long non-bonded CF and FF distances indicate a high barrier to pseudorotation of the ring.     

Large amplitude oscillations of protons in water clusters

Synchronous oscillations of bridge protons in molecular rings of (H₂O) _n water clusters with n = 4–6, 8, and 12 are analyzed as large amplitude motions that result in the inversion of the hydrogen bond sequence in a single ring. The corresponding one-dimensional cross sections of the potential energy surfaces (symmetric double-well potentials) are constructed at the MP2/6–31++G(d, p) level. The eigenstates of the systems in the constructed potentials in the energy range up to the top of the barrier are determined. The synchronous oscillations of protons are shown to be coupled to vibrations of the oxygen skeleton of the molecular ring, and the typical frequencies of the complex vibrations lie in the range of 230–330 cm^?1.     

Microwave spectrum of sulfolane

The microwave spectrum of sulfolane has been investigated in the frequency region 26.5 to 40.0 GHz. The rotational constants have been derived for the ground state (in MHz: A = 3780.814 ± 0.326, B = 2047.243 ± 0.006 and C = 1899.572 ± 0.006) and three excited states of the ring puckering vibration. Possible interpretations of the effect of nuclear spin statistical weights on the relative intensity measurements and of the analysis of the variation of the rotational constants with the vibrational quantum number are discussed. Two situations may be compatible with the available data: pseudorotation with the bent conformer lowest in energy or a near planar structure with a small barrier at the planar configuration with respect to the bending mode.     

Synthesis and structure of novel conformationally constrained 1',2'-azetidine-fused bicyclic pyrimidine nucleosides: their incorporation into oligo-DNAs and thermal stability of the heteroduplexes

[structures: see text] The synthesis of novel 1',2'-aminomethylene bridged (6-aza-2-oxabicyclo[3.2.0]heptane) "azetidine" pyrimidine nucleosides and their transformations to the corresponding phosphoramidite building blocks (20, 39, and 42) for automated solid-phase oligonucleotide synthesis is reported. The novel bicyclonucleoside "azetidine" monomers were synthesized by two different strategies starting from the known sugar intermediate 6-O-benzyl-1,2:3,4-bis-O-isopropylidene-D-psicofuranose. Conformational analysis performed by molecular modeling (ab initio and MD simulations) and NMR showed that the azetidine-fused furanose sugar is locked in a North-East conformation with pseudorotational phase angle (P) in the range of 44.5-53.8 degrees and sugar puckering amplitude (phi(m)) of 29.3-32.6 degrees for the azetidine-modified T, U, C, and 5-Me-C nucleosides. Thermal denaturation studies of azetidine-modified oligo-DNA/RNA heteroduplexes show that the azetidine-fused nucleosides display improved binding affinities when compared to that of previously synthesized North-East sugar constrained oxetane fused analogues.     

A novel Janus‐type AT nucleoside with benzoyl protecting groups forming a pleated‐sheet structure

The title compound, 5‐amino‐8‐(2,3,5‐tri‐O‐benzoyl‐β‐d ‐ribofuranosyl)pyrimido[4,5‐d]pyrimidine‐2,4(3H,8H)‐dione methanol monosolvate, C₃₂H₂₅N₅O₉·CH₄O, which crystallized slowly from methanol, exhibits an anti conformation with a glycosyl‐bond torsion angle of χ = −141.28 (17)°. The furanose moiety adopts an N‐type sugar puckering (³T₄). The corresponding pseudorotation phase angle and maximum amplitude are P = 24.5 (2)° and τ_m = 38.3 (2)°, respectively. In the solid state, one methanol molecule acts as a bridge joining adjacent nucleoside molecules head‐to‐head, leading to a pleated‐ribbon supramolecular structure, with the base moieties located in the centre of the ribbon and the sugar residues protruding to the outside of the layers, as in a DNA helix. The pleated‐ribbon supramolecular structure is tethered together into a two‐dimensional infinite pleated‐sheet structure through aromatic stacking between the nucleobase planes and the benzene rings of the benzoyl protecting groups on the 5′‐OH group of furanose.     

Parameterization and Application of the General Amber Force Field to Model Fluoro Substituted Furanose Moieties and Nucleosides

Molecular mechanics force field calculations have historically shown significant limitations in modeling the energetic and conformational interconversions of highly substituted furanose rings. This is primarily due to the gauche effect that is not easily captured using pairwise energy potentials. In this study, we present a refinement to the set of torsional parameters in the General Amber Force Field (gaff) used to calculate the potential energy of mono, di-, and gem-fluorinated nucleosides. The parameters were optimized to reproduce the pseudorotation phase angle and relative energies of a diverse set of mono- and difluoro substituted furanose ring systems using quantum mechanics umbrella sampling techniques available in the IpolQ engine in the Amber suite of programs. The parameters were developed to be internally consistent with the gaff force field and the TIP3P water model. The new set of angle and dihedral parameters and partial charges were validated by comparing the calculated phase angle probability to those obtained from experimental nuclear magnetic resonance experiments.     

Ab initio determination of the flexibility of 2'-aminoribonucleosides and 2'-aminoarabinonucleosides inserted in duplexes

The sugar puckering of adenosine and uridine nucleosides with an amino group at 2' in the ribo or arabino orientations are determined using high-level quantum mechanical calculations Only the conformations that have dihedrals compatible with their insertion into a duplex are retained. The amino group has always been found to be pyramidal and its orientation governs the conformation of the sugar. The energetically most favorable conformation of the 2'-aminoribonucleosides has the south puckering but must be discarded. For another orientation of the 2'-amino group, the conformation is energetically less favorable but has the north puckering. Calculations performed in the presence of a water molecule give similar results but with a smaller energy gap. The model then explains why the insertion of a 2'-aminoribonucleotide destabilizes double-stranded RNAs and also double-stranded DNAs. In the arabino orientation, an NH(2) substituent at 2' favors north puckering. In contrast to 2'-aminoribonucleosides, deoxynucleosides inserted into a duplex remain in the most energetically favorable conformation compatible with the canonical values of the torsion angles. The whole relaxed potential map, in the amplitude/pseudorotation space, shows that for natural deoxyadenosine there is only one valley in the east running from south to north puckering.     

Molecular structure of free canonical 2′-deoxyribonucleosides: a density functional study

The molecular structure of isolated canonical 2′-deoxyrinobucleosides was calculated using the density functional theory. It was demonstrated that the geometry of the base unit (BU) is almost unchanged compared to free nucleobases. Only slight out-of-plane deformation of the pyrimidine ring in deoxy-cytidine is observed. The conformation of the furanose ring strongly depends on the nature and orientation of the nucleobase. All nucleosides possess different conformations of this ring. Significant influence of the steric repulsion between the nucleobase and the sugar unit (SU) on puckering of the furanose ring and variation of the C–O and glycosyl bond lengths was demonstrated. The C(3′)-endo conformer of the furanose ring is more stable at the anti-orientation BU with respect to SU. An opposite trend is observed for the syn-orientation which is additionally stabilized by an intramolecular hydrogen bond with participation of the C(5′)OH group.     

Furanose dynamics in the HhaI methyltransferase target DNA studied by solution and solid-state NMR relaxation

Both solid-state and solution NMR relaxation measurements are routinely used to quantify the internal dynamics of biomolecules, but in very few cases have these two techniques been applied to the same system, and even fewer attempts have been made so far to describe the results obtained through these two methods through a common theoretical framework. We have previously collected both solution 13C and solid-state 2H relaxation measurements for multiple nuclei within the furanose rings of several nucleotides of the DNA sequence recognized by HhaI methyltransferase. The data demonstrated that the furanose rings within the GCGC recognition sequence are very flexible, with the furanose rings of the cytidine, which is the methylation target, experiencing the most extensive motions. To interpret these experimental results quantitatively, we have developed a dynamic model of furanose rings based on the analysis of solid-state 2H line shapes. The motions are modeled by treating bond reorientations as Brownian excursions within a restoring potential. By applying this model, we are able to reproduce the rates of 2H spin-lattice relaxation in the solid and 13C spin-lattice relaxation in solution using comparable restoring force constants and internal diffusion coefficients. As expected, the 13C relaxation rates in solution are less sensitive to motions that are slower than overall molecular tumbling than to the details of global molecular reorientation, but are somewhat more sensitive to motions in the immediate region of the Larmor frequency. Thus, we conclude that the local internal motions of this DNA oligomer in solution and in the hydrated solid state are virtually the same, and we validate an approach to the conjoint analysis of solution and solid-state NMR relaxation and line shapes data, with wide applicability to many biophysical problems.     

Centrifugal distortion and the ring puckering vibration in the microwave spectrum of 2,3-dihydrofuran

The microwave spectrum of 2,3-dihydrofuran has been reinvestigated and measurements for the ground and first five excited states of the ring puckering vibration have been extended to higher frequencies and rotational quantum numbers in order to study the vibrational dependence of the rotational and centrifugal distortion constants. The ring puckering potential function derived by Green from the far infrared spectrum does not reproduce the vibrational dependence of the rotational constants well. A slightly different potential function is derived which gives a reasonable fit both to the far infrared spectrum and the rotational constants. This changes the barrier to ring inversion from 1.00 kJ mol⁻¹ to 1.12 kJ mol⁻¹. The vibrational dependence of the centrifugal distortion constants is accounted for satisfactorily by the theory developed by Creswell and Mills. An attempt to reproduce the vibrational dependence of the rotational and centrifugal distortion constants using the ring puckering potential function and a simple model for this vibration has very limited success.     

Experimental and theoretical electron momentum spectroscopic study of the valence electronic structure of tetrahydrofuran under pseudorotation

The most populated structure of tetrahydrofuran (THF) has been investigated in our previous study using electron momentum spectroscopy (EMS). Because of the relatively low impact energy (600 eV) and low energy resolution (DeltaE = 1.20 eV) in the previous experiment, only the highest occupied molecular orbital (HOMO) of THF was investigated. The present study reports the most recent high-resolution EMS of THF in the valence space for the first time. The binding energy spectra of THF are measured at 1200 and 2400 eV plus the binding energies, respectively, for a series of azimuthal angles. The experimentally obtained binding energy spectra and orbital momentum distributions (MDs) are employed to study the orbital responses of the pseudorotation motion of THF. The outer valence Greens function (OVGF), the OVGF/6-311++G** model, and density function theory (DFT)-based SAOP/et-pVQZ model are employed to simulate the binding energy spectra. The orbital momentum distributions (MDs) are produced using the DFT-based B3LYP/aug-cc-pVTZ model, incorporating thermodynamic population analysis. Good agreement between theory and experiment is achieved. Orbital MDs of valence orbitals exhibit only slight differences with respect to the impact energies at 1200 and 2400 eV, indicating validation of the plane wave impulse approximation (PWIA). The present study has further discovered that the orbital MDs of the HOMO in the low-momentum region (p < 0.70 a.u) change significantly with the pseudorotation angle, phi, giving a v-shaped cross section, whereas the innermost valence orbital of THF does not vary with pseudorotation, revealing a very different bonding mechanism from the HOMO. The present study explores an innovative approach to study pseudorotation of sugar puckering, which sheds a light to study other biological systems with low energy barriers among ring-puckering conformations.     

2H NMR characterization of phenylene ring flip motion in poly(p-phenylene vinylene) films

Solid-state ²H quadrupole echo nuclear magnetic resonance (NMR) spectra and measurements of ²H spin lattice relaxation times have been obtained for films of poly(p-phenylene vinylene) deuterated in phenylene ring positions (PPV-d₄). NMR line shapes show that all the phenylene rings of PPV undergo 180° rotational jumps about the 1,4 ring axis (“ring flips”) at 225°C. The temperature dependence of the ²H line shapes show that the jump motion is thermally activated, with a median activation energy, E_a = 15 kcal/mol, and a distribution of activation energies of less than ±2 kcal/mol. The jump rate was also determined from the magnitude of the anisotropic T₂ relaxation associated with ²H line shapes and from the curvature of inversion recovery intensity data. The experimental activation energy for jumps is comparable to the intramolecular potential barrier for rotation about phenylene vinylene bonds. ²H NMR provides a method for determining the phenylene-vinylene rotational barrier in pristine PPV, and may potentially be used to study conjugation in conducting films.     

3‐Bromo‐1‐(2‐deoxy‐β‐d‐erythro‐pento­furan­osyl)‐1H‐pyrazolo­[3,4‐d]­pyrimidine‐4,6‐di­amine: a nucleoside which strongly enhances DNA duplex stability

The title compound, C₁₀H₁₃BrN₆O₃, exhibits an anti gly­cosylic bond conformation, with an O—C—N—C torsion angle of −105.0 (6)°. The pseudorotation phase angle and the amplitude [P = 5.8 (5)° and τ_m = 30.0 (3)°, respectively] indicate N‐type sugar puckering (³T₂).     

Symmetric ring puckering potential in thietane‐1,1‐dioxide compared with experiment and analysis of theoretical vibrational spectra

We studied the ring puckering potential in thietane‐1,1‐dioxide with different methods, using a suitable basis set, 6‐311+G**. We obtained a barrier to ring puckering of 153 cal/mol with the DFT/B3LYP (Becke3 exchange–Lee, Yang, Parr correlation functional) method, ～60% too small compared with experiment. However, using MP2, MP3, and MP4 we obtained values around 200% too large. The MP series turned out to converge far too slowly to the experimental barrier value, showing no sign of convergence even at MP4, while higher orders are out of our reach for such a system. Obviously, of all methods used, DFT worked best despite some shortcomings. The barrier corresponds to 77 K; thus, there should be rapid interconversion over the barrier at room temperature, a phenomenon actually observed at room temperature, the measured barrier corresponding to 201 K. Thus, we decided to use the DFT/6‐311+G** calculations to predict reasonable vibrational spectra and assignments of the lines found. The ring puckering mode is found at 80 cm^?1 in DFT in good agreement with the experimental value of 78.3 cm^?1 for this vibration. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Development of a novel nucleoside analogue with S-type sugar conformation: 2′-deoxy-trans-3′,4′-bridged nucleic acids

Two novel trans-3′,4′-bridged nucleic acid (trans-3′,4′-BNA) monomers, one with a 3,5,8-trioxabicyclo[5.3.0]decane structure and the other with a 4,7-dioxabicyclo[4.3.0]nonane structure, were successfully synthesized from thymidine. The locked trans-fused ring structures of the nucleoside analogues were confirmed by X-ray crystallography, which also indicated that their furanose rings had a typical S-type conformation involving C_2′-endo or C_3′-exo sugar puckering, respectively, and the same ring conformation as that observed in the B-type helical structure of the DNA duplex.     

The adiabatic correction to the ring puckering potential of oxetane

The adiabatic correction to the Hartree-Fock ring puckering potential of oxetane is presented along with the adiabatic correction to potential functions of H₂, CO, and CO₂. The oxetane calculation allows the identification of the source of the disagreement between theory and experiment for the barrier to ring planarity.     

Anomerization reaction of bare and microhydrated d‐erythrose via explicitly correlated coupled cluster approach. Two water molecules are optimal

We present a comprehensive benchmark computational study which has explored a complete path of the anomerization reaction of bare d ‐erythrose involving a pair of the low‐energy α‐ and β‐furanose anomers, the former of which was observed spectroscopically (Cabezas et al., Chem. Commun. 2013, 49, 10826). We find that the ring opening of the α‐anomer yields the most stable open‐chain tautomer which step is followed by the rotational interconversion of the open‐chain rotamers and final ring closing to form the β‐anomer. Our results indicate the flatness of the reaction's potential energy surface (PES) corresponding to the rotational interconversion path and its sensitivity to the computational level. By using the explicitly correlated coupled cluster CCSD(T)‐F12/cc‐pVTZ‐F12 energies, we determine the free energy barrier for the α‐furanose ring‐opening (rate‐determining) step as 170.3 kJ/mol. The question of the number of water molecules (n ) needed for optimal stabilization of the erythrose anomerization reaction rate‐determining transition state is addressed by a systematic exploration of the PES of the ring opening in the α‐anomer‐(H₂O)_n and various β‐anomer‐(H₂O)_n (n = 1–3) clusters using density functional and CCSD(T)‐F12 computations. These computations suggest the lowest free energy barrier of the ring opening for doubly hydrated α‐anomer, achieved by a mechanism that involves water‐mediated multiple proton transfer coupled with the furanose C O bond breakage. Among the methods used, the G4 performed best against the CCSD(T)‐F12 reference at estimating the ring‐opening barrier heights for both the hydrated and bare erythrose conformers. Our results for the hydrated species are most relevant to an experimental study of the anomerization reaction of d ‐erythrose to be carried out in microsolvation environment. © 2016 Wiley Periodicals, Inc.