How to detect internal motion by homonuclear NMR

NOESY and ROESY cross-peak intensities depend on internuclear distances and internal motion. Internal motion is usually ignored, and NOESY cross-peak intensities are interpreted in terms of internuclear distances only. Off-resonance ROESY experiments measure a weighted average of NOE and ROE. The weight can be described and experimentally set by an angle theta;. For large enough molecules, NOE and ROE have opposite signs. Therefore, each cross-peak intensity becomes zero for an angle theta;(0). For any sample, the maximum angle theta;(0) is determined by the overall motion of the molecule. Smaller theta;(0) values reflect the angular component of internal motions. Because individual cross-peaks are analyzed, the method evaluates internal motions of individual H,H vectors. The reduction of theta;(0) is largest for internal motions on a time scale of 100-300 ps. The sensitivity of theta;(0) for internal motions decreases with increasing molecular weight. We estimate that detecting internal motions will be practicable for molecules up to about 15 kDa. We describe a protocol to measure theta;(0) from a series of off-resonance ROESY spectra. For such a series, we describe the choice of experimental parameters, a procedure to extract theta;(0) from the raw data, and the interpretation of theta;(0) in terms of internal motions. In the small protein BPTI, we analyzed 75 cross-peaks. The precision of theta;(0) was 0.25 degrees, as compared to typical reductions of theta;(0) of 3 degrees. We found a well-defined maximum theta;(0) for cross-peaks in rigid parts of the molecule, which reflects the overall motion of the molecule. For BPTI, also many structurally important long-range cross-peaks appear rigid. The lower theta;(0) values of long-range contacts involving methyl groups are consistent with methyl rotation on the 25-ps time scale. The lower theta;(0) values of the flexible C-terminus and of flexible side chains translate into upper limits for the angular order parameter of 0.4 and 0.5-0.8, respectively. Off-resonance ROESY can monitor internal motions of H,H contacts that are used in a structure calculation. Because no isotope labeling is needed, off-resonance ROESY can be used to detect internal motions in a wide range of natural products.     

A microwave study of hydrogen-transfer-triggered methyl-group rotation in 5-methyltropolone

We present here the first experimental and theoretical study of the microwave spectrum of 5-methyltropolone, which can be visualized as a seven-membered "aromatic" carbon ring with a five-membered hydrogen-bonded cyclic structure at the top and a methyl group at the bottom. The molecule is known from earlier studies in the literature to exhibit two large-amplitude motions, an intramolecular hydrogen transfer and a methyl torsion. The former motion is particularly interesting because transfer of the hydrogen atom from the hydroxyl to the carbonyl group induces a tautomerization in the molecule, which then triggers a 60° internal rotation of the methyl group. Measurements were carried out by Fourier-transform microwave spectroscopy in the 8-24 GHz frequency range. Theoretical analysis was carried out using a tunneling-rotational Hamiltonian based on a G(12)(m) extended-group-theory formalism. Our global fit of 1015 transitions to 20 molecular parameters gave a root-mean-square deviation of 1.5 kHz. The tunneling splitting of the two J=0 levels arising from a hypothetical pure hydrogen-transfer motion is calculated to be 1310 MHz. The tunneling splitting of the two J=0 levels arising from a hypothetical pure methyl top internal-rotation motion is calculated to be 885 MHz. We have also carried out ab initio calculations, which support the structural parameters determined from our spectroscopic analysis and give estimates of the barriers to the two large-amplitude motions.     

Raman study of ratational diffusion in methyl iodide

The usefulness of Raman and NMR spin relaxation spectroscopic methods in probing the details of molecular motions in liquids is demonstrated in a study of methyl iodide. Analysis of the lineshape of the ν₃ Raman band of methyl iodide as a function of temperature yields values of the perpendicular component D_⊥ of the diffusion tensor D_i and an activation energy of reorientation perpendicular to the C₃ axis of the molecule of 2.1 kcal/mole. Coupling the Raman data with ²D NMR spin relaxation data yields values of D_| and an activation energy for reorientation about the C₃ axis of 0.4 kcal/mole indicating quasi-free rotation for this motion. Thus the reorientational motions of methyl iodide are shown to be highly anisotropic in the liquid state.     

Carbon-13 NMR. The analysis of the relaxation times T1 of benzofuran and of a series of its methyl derivatives. Correlations between molecular motions and structural properties

Carbon-13 relaxation times (T₁) and nuclear Overhauser enhancements (η) have been measured for benzofuran and a series of its methyl derivatives. The contributions of dipolar (T₁ ^DD) and spin rotation (T₁^SR) mechanisms have both been determined. The temperature dependence of T₁ has been studied. The relationships between molecular motions and structural properties have been emphasized. The overall motional anisotropy of the benzofuran molecule is increased by substitution in positions 2 and 5. The internal rotation of a methyl group may change depending on its position in the molecule and on the influence of other methyl groups in its close neighbourhood.     

Internal dynamics features in the free jet rotational spectrum of the acetaldehyde-Kr molecular complex

The structure and the dynamics of internal motions in the complex formed between acetaldehyde and Kr are studied by free jet absorption microwave spectroscopy performed in the range 60-78 GHz. The fourfold structure of each rotational line is evidence of the vibration-rotation coupling between the overall rotation of the complex, a tunneling motion of the Kr atom between two equivalent positions and the internal rotation of the methyl group in the acetaldehyde moiety. The four sets of transitions could be fitted with a coupled Hamiltonian which allows for the Coriolis interaction obtaining the energy separation between the vibrational energy levels related to the tunneling motion, while the observed splittings due to the methyl group internal rotation were analyzed independently with an appropriate model. The potential energy barriers for the tunneling motion and the internal rotation of the methyl group have been calculated and the interaction of the rare gas atom with the acetaldehyde moiety is reflected in the change of the V(3) barrier to internal rotation in going from the molecule to the weakly bound complex.     

Methoxy and Methyl Group Rotation: Solid‐State NMR 1H Spin‐Lattice Relaxation,Electronic Structure Calculations,X‐ray Diffractometry,and Scanning Electron Microscopy

We report solid‐state ¹H nuclear magnetic resonance (NMR) spin‐lattice relaxation experiments, X‐ray diffractometry, field‐emission scanning electron microscopy, and both single‐molecule and cluster ab initio electronic structure calculations on 1‐methoxyphenanthrene ( 1 ) and 3‐methoxyphenanthrene ( 2 ) to investigate the rotation of the methoxy groups and their constituent methyl groups. The electronic structure calculations and the ¹H NMR relaxation measurements can be used together to determine barriers for the rotation of a methoxy group and its constituent methyl group and to develop models for the two coupled motions.     

Rotationally resolved electronic spectra of 2- and 3-methylanisole in the gas phase: a study of methyl group internal rotation

Rotationally resolved fluorescence excitation spectra of several torsional bands in the S1 <-- S0 electronic spectra of 2-methylanisole (2MA) and 3-methylanisole (3MA) have been recorded in the collision-free environment of a molecular beam. Some of the bands can be fit with rigid rotor Hamiltonians; others exhibit perturbations produced by the coupling between the internal rotation of the methyl group and the overall rotation of the entire molecule. Analyses of these data show that 2MA and 3MA both have planar heavy-atom structures; 2MA has trans-disposed methyl and methoxy groups, whereas 3MA has both cis- and trans-disposed substituents. The preferred orientations (staggered or eclipsed) in two of the conformers and the internal rotation barriers of the methyl groups in all three conformers change when they are excited by light. Additionally, the values of the barriers opposing their motion depend on the relative positions of the substituent groups, in both electronic states. In contrast, no torsional motions of the attached methoxy groups were detected. Possible reasons for these behaviors are discussed.     

Impact of extended pi conjugation on methyl rotor-induced IVR in aromatic molecules

Laser-induced fluorescence excitation and resolved fluorescence spectra following excitations of the single vibronic levels (SVL) of p-vinyltoluene (p-VT) and p-vinylfluorobenzene (p-VFB) have been measured in a seeded supersonic free-jet expansion. A complete vibronic assignment of the fluorescence spectrum measured following excitation of the 0(0)0-band of p-VT has been presented. Normal vibrational modes in the S0 and S1 states of the molecule have been calculated by CASSCF method, and the correlation between the two set of modes is made by expressing the excited-state normal modes in terms of those of the ground state. The calculations predict that in the excited state methyl and vinyl torsional motions of p-VT are extensively mixed with many of the out-of-plane modes of the aromatic ring. Our resolved fluorescence spectral data measured following SVL excitations essentially agree with such predictions. In the excited state, the molecule exhibits a dramatically low threshold for the rotor-induced IVR in a supersonic jet expansion. Several mechanisms have been discussed to explain the phenomenon.     

Theoretical study on the lowest-frequency mode of the flavin ring

The dynamic aspects along the normal vibrational motions of the lowest frequencies in the oxidized, radical, and reduced states of flavin (isoalloxazine) have been studied. In comparison with the twist motions in the oxidized state, the butterfly motions in the radical and reduced states turned out to bring more significant variations to the frontier molecular orbital energies and to the charge distributions on the atoms of the pyrazine ring in isoalloxazine. It can be considered that the electron transfers from and to the isoalloxazine ring can be adjusted or controlled by these variations. In the reduced states the electron release from the molecule, and in the radical states the electron release from or acceptance by the molecule, could be impelled by the butterfly motions, while in the oxidized state the electron acceptance by the molecule could be accelerated slightly by the twist motion. Received: 30 September 1998 / Accepted: 20 January 1999 / Published online: 7 June 1999     

On the gearing of methyl groups in hexamethylbenzene

Empirical force field calculations were performed on hexamethylbenzene to elucidate the internal motions of the methyl groups. When the benzene ring is constrained to be planar (as in solid-phase studies), the methyl groups undergo a geared, disrotatory motion. When this constraint is relaxed, results are force field dependent. Calculated barriers are in good agreement with experimentally determined values.     

On the separation of motions in the theory of polyatomic molecular spectra

A method has been suggested for the separation of rotational and vibrational motions of nuclei in polyatomic molecules. The method is based on the introduction of the angular velocity vector associated with the kinetic moment and provides the complete separation of motions in the case of arbitrary molecule deformations. The method requires no a priori assumptions on vibrational amplitudes.     

Adsorption of methyl red on sterchamol

The mode of retention of methyl red on Sterchamol is studied by the adsorption of compounds containing some of the functional groups active for hydrogen bonding in the methyl red molecule. It is shown that two types of adsorbing centres exist on the Sterchamol surface. An adsorbate with an oxygen or nitrogen electron-donor atom in its molecule deactivates only one type of centre. Both electron donors are present in a methyl red molecule, allowing both types of active sites to be deactivated by this adsorbate.     

Challenge of large-scale motion for residual dipolar coupling based analysis of configuration: the case of fibrosterol sulfate A

Fibrosterol sulfate A is a polysulfated bis-steroid with an atypical side chain. Due to the flexibility of the linker, large-scale motions that change dramatically the shape of the entire molecule are expected. Such motions pose major challenges to the structure elucidation and the correct determination of configuration. In this study, we will describe the determination of the relative configuration of fibrosterol sulfate A through a residual dipolar coupling based multiple alignment tensor analysis complemented by molecular dynamics. For completeness, we applied also the single tensor approach which is unreliable due to the large-scale motions and compare the results.     

Comparative study on the nonadditivity of methyl group in lithium bonding and hydrogen bonding

Quantum chemical calculations at the second‐order Moeller–Plesset (MP2) level with 6‐311++G(d,p) basis set have been performed on the lithium‐bonded and hydrogen‐bonded systems. The interaction energy, binding distance, bond length, and stretch frequency in these systems have been analyzed to study the nonadditivity of methyl group in the lithium bonding and hydrogen bonding. In the complexes involving with NH₃, the introduction of one methyl group into NH₃ molecule results in an increase of the strength of lithium bonding and hydrogen bonding. The insertion of two methyl groups into NH₃ molecule also leads to an increase of the hydrogen bonding strength but a decrease of the lithium bonding strength relative to that of the first methyl group. The addition of three methyl groups into NH₃ molecule causes the strongest hydrogen bonding and the weakest lithium bonding. Although the presence of methyl group has a different influence on the lithium bonding and hydrogen bonding, a negative nonadditivity of methyl group is found in both interactions. The effect of methyl group on the lithium bonding and hydrogen bonding has also been investigated with the natural bond orbital and atoms in molecule analyses. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

Slow internal dynamics in proteins: application of NMR relaxation dispersion spectroscopy to methyl groups in a cavity mutant of T4 lysozyme

Recently developed carbon transverse relaxation dispersion experiments (Skrynnikov, N. R.; et al. J. Am. Chem. Soc. 2001, 123, 4556-4566) were applied to the study of millisecond to microsecond time scale motions in a cavity mutant of T4 lysozyme (L99A) using methyl groups as probes of dynamics. Protein expressed in E. coli cells with (13)CH(3)-pyruvate as the sole carbon source contained high levels of (13)C enrichment at a total of 80 Val gamma, Leu delta, Ile gamma (2), Ala beta, and Met epsilon methyl positions with little extraneous incorporation. Data for 72 methyl groups were available for analysis. Dispersion profiles with large amplitudes were measured for many of these residues and were well fit to a two-state exchange model. The interconversion rates and populations of the states, obtained from fitting relaxation dispersion profiles of each individual probe, were remarkably homogeneous and data for nearly all methyl groups in the protein could be collectively fit to a single cooperative conformational transition. The present study demonstrates the general applicability of methyl relaxation dispersion measurements for the investigation of millisecond time scale protein motions at a large number of side-chain positions. Potential artifacts associated with the experiments are described and methods to minimize their effects presented. These experiments should be particularly well suited for probing dynamics in high molecular weight systems due to the favorable NMR spectroscopic properties of methyl groups.     

Intermediate motions as studied by solid-state separated local field NMR experiments

In this report, the application of a class of separated local field NMR experiments named dipolar chemical shift correlation (DIPSHIFT) for probing motions in the intermediate regime is discussed. Simple analytical procedures based on the Anderson-Weiss (AW) approximation are presented. In order to establish limits of validity of the AW based formulas, a comparison with spin dynamics simulations based on the solution of the stochastic Liouville-von-Neumann equation is presented. It is shown that at short evolution times (less than 30% of the rotor period), the AW based formulas are suitable for fitting the DIPSHIFT curves and extracting kinetic parameters even in the case of jumplike motions. However, full spin dynamics simulations provide a more reliable treatment and extend the frequency range of the molecular motions accessible by DIPSHIFT experiments. As an experimental test, molecular jumps of imidazol methyl sulfonate and trimethylsulfoxonium iodide, as well as the side-chain motions in the photoluminescent polymer poly[2-methoxy-5-(2'-ethylhexyloxy)-1,4-phenylenevinylene], were characterized. Possible extensions are also discussed.     

Molecular dynamics simulations of atomistic hydration structures of poly(vinyl methyl ether)

Molecular dynamics simulations have been performed on the aqueous solutions of poly(vinyl methyl ether) (PVME) at various concentrations. Both radial and spatial distribution functions are used to investigate the detailed hydration structures. The structures of water are found to get increasingly concentrated when polymers are introduced and the water motions are severely hindered by the polymer matrix. At low concentrations, larger populations of tt conformers in meso dyads than those at higher concentrationsare found and this phenomenon is believed to be due to the increasing in bonding of water molecule to two ether oxygens in meso dyad. At higher concentrations, the size and conformations of polymers are quite similar to those in bulk. A transition of hydrogen bond fractions between PVME and water at around the concentration of 0.3 is observed and this value is perfectly in agreement with the results of conformational analysis and Raman spectra. Second neighbor hydrogen bond statistics revealed the domination of complicated hydrogen bond networks at low concentrations, but single hydrogen bonds as well as isolated clusters composed of 2-4 water molecules are usual around each polymer repeat unit.     

Slow dynamics in glassy methyl alpha-l-rhamnopyranoside studied by 1D NMR exchange experiments

It is widely known that the ability of sugar glasses to preserve anhydrobiotic systems in nature is important but the process is not yet fully understood. Molecular motions in the glassy state are likely to be important in the process but until now have remained largely uncharacterized. Here we describe the use of 1D 13C NMR exchange experiments using CODEX (centreband only detection of exchange) methods to study the dynamics of the well characterised model glassy monosaccharide, methyl alpha-l-rhamnopyranoside. The glass was prepared by fast cooling of a melt inside an NMR rotor. Molecular motions in the range of seconds to milliseconds were observed in the glass, whereas identical experiments using the crystalline material displayed no observable motions in the time-scales covered by the experiment. At 13 to 14 K above Tg the nature of the motion in the glass changed probably due to the onset of larger scale reorientation. A bimodal distribution of jump angles combined with a broad distribution of correlation times was found to best represent the observed motions.