COSY‐ und HSQC‐NMR‐Spektroskopie

The present state of the routine 2D COSY‐ and HSQC‐NMR spectroscopy is reported. After a short introduction into the basic theory of 2D NMR the pulse sequences of COSY and HSQC are explained. Using an example from natural product chemistry the procedures during the analysis of these 2D NMR spectra are demonstrated.     

Signatures of beta-peptide unfolding in two-dimensional vibrational echo spectroscopy: a simulation study.

An ensemble of exciton Hamiltonians for the amide-I band of the folded and unfolded states of a helical beta-heptapeptide is generated using a molecular dynamics (MD) simulation. The correlated fluctuations of its parameters and their signatures in two-dimensional (2D) vibrational echo spectroscopy are computed. This technique uses infrared pulse sequences to provide ultrafast snapshots of molecular structural fluctuations, in analogy with multidimensional NMR. The present study demonstrates that, by combining a method of calculating the vibrational Hamiltonian from MD snapshots and the nonlinear exciton equations (NEE), it may be possible to simulate realistic multidimensional IR spectra of chemically and biologically interesting systems.     

NMR experiments for the analysis of mixtures: beyond 1D 1H spectra

State-of-the-art technologies and methodologies in NMR spectroscopy make it possible to obtain very informative and high-quality spectra in much less experimental time than classical methods by making better choices of NMR pulse sequences and acquisition parameters. This review presents some recent NMR methods allowing rapid identification, assignment and structural characterization of the components in mixtures. The relative merits of the different NMR pulse sequences are briefly discussed and recommendations are made for the preferred choice of sequences to obtain rapidly artifact-free data. This review covers diffusion experiments (DOSY), HSQC and HMBC experiments, ultra-resolved 2D spectra exploiting the property of aliasing and NOESY/ROESY experiments. It will be in particular shown that selective 1D NOESY/ROESY sequences can be more informative and reach higher resolution in less experimental time than the corresponding 2D sequences.     

Elucidation of structural restraints for phosphate residues with different hydrogen bonding and ionization states

Solid state NMR spectroscopy and gauge including atomic orbital (GIAO) theoretical calculations were employed to establish structural restraints (ionization, hydrogen bonding, spatial arrangement) for O-phosphorylated l-threonine derivatives in different ionization states and hydrogen bonding strengths. These structural restraints are invaluable in molecular modeling and docking procedures for biological species containing phosphoryl groups. Both the experimental and the GIAO approach show that 31P delta ii chemical shift tensor parameters are very sensitive to the ionization state. The negative values found for the skew kappa are typical for -2 phosphates. The distinct span Omega values reflect the change of strength of hydrogen bonding. For species in the -1 ionization state, engaged in very strong hydrogen bonds, Omega is smaller than for a phosphate group involved in weak hydrogen bonding. For phosphates in the -2 ionization state, Omega is significantly smaller compared to -1 species, although the kappa for -1 samples never reaches negative values. For -1 phosphate residues, in the case when 1H one pulse and/or combined rotation and multiple pulse spectroscopy (CRAMPS) sequences fail and assignment of proton chemical shift is ambiguous, a combination of 1H-(13)C and 1H-(31)P 2D heteronuclear correlation (HETCOR) correlations is found to be an excellent tool for the elucidation of 1H isotropic chemical shifts. In addition, a 2D strategy using 1H-(1)H double quantum filter (DQF) correlations [a back-to-back (BABA) sequence in this work] is useful for analyzing the topology of hydrogen bonding. In the case of a multicenter phosphorus domain, 2D 31P-(31)P proton driven spin diffusion experiments give information about the spatial arrangement of the phosphate residues.     

Slice-selected LED and BPPLED: application of slice selection to DOSY

High-resolution DOSY (Diffusion-ordered spectroscopy) is a series of 2-dimensional and 3-dimensional NMR techniques based on the differing diffusivity of constituent molecules in the solution state, with which the individual NMR spectrum of each component in a chemical mixture can be observed. All of the DOSY pulse sequences are derived from the spin-echo or stimulated-echo techniques under the effect of PFG (pulsed field gradient). One of the requirements for successful DOSY experiments and data fitting is that PFG must be uniform across the active sample volume. However, PFG, in general, is not uniform across the active sample volume in commercial high-resolution NMR probes and this nonuniformity of PFG is known to produce systematic errors in DOSY experiments. In fact, a strong and uniform gradient field can be realized only in the central region of the gradient coil and the slice-selection technique, widely used in Magnetic Resonance (MR) imaging, can be employed in resolving problems associated with the nonuniformity of PFG. We have developed a slice-selection pulse block, which can be generally applied to any DOSY pulse sequence with proper care of the phase cycling and experimental parameters. We applied the slice-selection technique to LED and BPPLED pulse sequences, which are among the most popular DOSY pulse sequences, and obtained good experimental results for a chemical mixture.     

Probing the transition state ensemble of a protein folding reaction by pressure-dependent NMR relaxation dispersion

The F61A/A90G mutant of a redesigned form of apocytochrome b562 folds by an apparent two-state mechanism. We have used the pressure dependence of 15N NMR relaxation dispersion rate profiles to study the changes in volumetric parameters that accompany the folding reaction of this protein at 45 degrees C. The experiments were performed under conditions where the folding/unfolding equilibrium could be studied at each pressure without addition of denaturants. The exquisite sensitivity of the methodology to small changes in folding/unfolding rates facilitated the use of relatively low-pressure values (between 1 and 270 bar) so that pressure-induced changes to the unfolded state ensemble could be minimized. A volume change for unfolding of -81 mL/mol is measured (at 1 bar), a factor of 1.4 larger (in absolute value) than the volume difference between the transition state ensemble (TSE) and the unfolded state. Notably, the changes in the free energy difference between folded and unfolded states and in the activation free energy for folding were not linear with pressure. Thus, the difference in the isothermal compressibility upon unfolding (-0.11 mL mol(-1) bar(-1)) and, for the first time, the compressibility of the TSE relative to the unfolded state (0.15 mL mol(-1) bar(-1)) could be calculated. The results argue for a TSE that is collapsed but loosely packed relative to the folded state and significantly hydrated, suggesting that the release of water occurs after the rate-limiting step in protein folding. The notion of a collapsed and hydrated TSE is consistent with expectations based on earlier temperature-dependent folding studies, showing that the barrier to folding at 45 degrees C is entropic (Choy, W. Y.; Zhou, Z.; Bai, Y.; Kay, L. E. J. Am. Chem. Soc. 2005, 127, 5066-5072).     

Two-Dimensional NMR Spectroscopy: Background and Overview of the Experiments [New Analytical Methods (36)]

An exact knowledge of the structure, dynamics, and reactions of molecules provides the key to understand their functions and properties. NMR spectroscopy has developed, through the introduction of two-dimensional methods, into the most important method for the investigation of these questions in solution. A great variety of different techniques is available. However, for their successful application not only the appropriate equipment is required, but also the right choice of experiments and optimum measurement parameters, as well as a careful evaluation of the spectra. This contribution describes the necessary background for modern NMR spectroscopy. With the aid of the so-called product operator formalism it is possible to understand pulsed Fourier transform NMR spectroscopy both qualitatively and quantitatively. Very few, readily understandable assumptions are sufficient for confident application of these methods. This article attempts to introduce in a simple manner this formalism as well as phase cycles necessary for the understanding of pulse sequences, and to train the reader through the discussion of several 2D NMR techniques. An overview of the most important techniques is given in the second part of this article.     

TReNDS—Software for reaction monitoring with time-resolved non-uniform sampling

NMR spectroscopy, used routinely for structure elucidation, has also become a widely applied tool for process and reaction monitoring. However, the most informative of NMR methods—correlation experiments—are often useless in this kind of applications. The traditional sampling of a multidimensional FID is usually time-consuming, and thus, the reaction-monitoring toolbox was practically limited to 1D experiments (with rare exceptions, e.g., single-scan or fast-sampling experiments). Recently, the technique of time-resolved non-uniform sampling (TR-NUS) has been proposed, which allows to use standard multidimensional pulse sequences preserving the temporal resolution close to that achievable in 1D experiments. However, the method existed only as a prototype and did not allow on-the-fly processing during the reaction. In this paper, we introduce TReNDS: free, user-friendly software kit for acquisition and processing of TR-NUS data. The program works on Bruker, Agilent, and Magritek spectrometers, allowing to carry out up to four experiments with interleaved TR-NUS. The performance of the program is demonstrated on the example of enzymatic hydrolysis of sucrose.     

Next‐Generation Heteronuclear Decoupling for High‐Field Biomolecular NMR Spectroscopy

Ultra‐high‐field NMR spectroscopy requires an increased bandwidth for heteronuclear decoupling, especially in biomolecular NMR applications. Composite pulse decoupling cannot provide sufficient bandwidth at practical power levels, and adiabatic pulse decoupling with sufficient bandwidth is compromised by sideband artifacts. A novel low‐power, broadband heteronuclear decoupling pulse is presented that generates minimal, ultra‐low sidebands. The pulse was derived using optimal control theory and represents a new generation of decoupling pulses free from the constraints of periodic and cyclic sequences. In comparison to currently available state‐of‐the‐art methods this novel pulse provides greatly improved decoupling performance that satisfies the demands of high‐field biomolecular NMR spectroscopy.     

Solid state separated-local-field NMR spectroscopy on half-integer quadrupolar nuclei: principles and applications to borane analysis

New multidimensional NMR methods correlating the quadrupolar and heteronuclear dipolar interactions affecting a half-integer quadrupolar spin in the solid state are introduced and exemplified. The methods extend separated-local-field magic-angle spinning (SLF MAS) NMR techniques that have been used successfully in spin-(1)/(2) spectroscopy to the study of S >/= (3)/(2) nuclei. In our implementation, these techniques avoid homonuclear proton decoupling requirements by relying on moderately fast MAS rates (6-15 kHz) and use rotor-synchronized constant-time pulse sequences to achieve nearly arbitrary amplifications of the apparent dipolar coupling strengths. The result is a suite of simple 2D NMR experiments, whose line shapes carry valuable information about the structure and dynamics of solids containing quadrupolar and proton nuclei. The potential of these sequences was exploited to gather new insight into the structure and dynamics of a variety of boron-containing samples. These experimental SLF schemes were also extended to 3D NMR experiments that incorporate multiple-quantum MAS, thus enabling the resolution needed to study multiple chemical sites in a solid and providing a useful tool for the assignment of inequivalent sites.     

Phenylene Ethynylene‐Tethered Perylene Bisimide Folda‐Dimer and Folda‐Trimer: Investigations on Folding Features in Ground and Excited States

In this work, we have elucidated in detail the folding properties of two perylene bisimide (PBI) foldamers composed of two and three PBI units, respectively, attached to a phenylene ethynylene backbone. The folding behaviors of these new PBI folda‐dimer and trimer have been studied by solvent‐dependent UV/Vis absorption and 1D and 2D NMR spectroscopy, revealing facile folding of both systems in tetrahydrofuran (THF). In CHCl₃ the dimer exists in extended (unfolded) conformation, whereas partially folded conformations are observed in the trimer. Temperature‐dependent ¹H NMR spectroscopic studies in [D₈]THF revealed intramolecular dynamic processes for both PBI foldamers due to, on the one hand, hindered rotation around C?N imide bonds and, on the other hand, backbone flapping; the latter process being energetically more demanding as it was observed only at elevated temperature. The structural features of folded conformations of the dimer and trimer have been elucidated by different 2D‐NMR spectroscopy (e.g., ROESY and DOSY) in [D₈]THF. The energetics of folding processes for the PBI dimer and trimer have been assessed by calculations applying various methods, particularly the semiempirical PM6‐DH2 and the more sophisticated B97D approach, in which relevant dispersion corrections are included. These calculations corroborate the results of NMR spectroscopic studies. Folding features in the excited states of these PBI foldamers have been characterized by using time‐resolved fluorescence and transient absorption spectroscopy in THF and CHCl₃, exhibiting similar solvent‐dependent behavior as observed for the ground state. Interestingly, photoinduced electron transfer (PET) process from electron‐donating backbone to electron‐deficient PBI core for extended, but not for folded, conformations was observed, which can be explained by a fast relaxation of excited PBI stacks in the folded conformation into fluorescent excimer states.     

Protonation/deprotonation effects on the stability of the Trp-cage miniprotein

The Trp-cage miniprotein is a 20 amino acid peptide that exhibits many of the properties of globular proteins. In this protein, the hydrophobic core is formed by a buried Trp side chain. The folded state is stabilized by an ion pair between aspartic acid and an arginine side chain. The effect of protonating the aspartic acid on the Trp-cage miniprotein folding/unfolding equilibrium is studied by explicit solvent molecular dynamics simulations of the protein in the charged and protonated Asp9 states. Unbiased Replica Exchange Molecular Dynamics (REMD) simulations, spanning a wide temperature range, are carried out to the microsecond time scale, using the AMBER99SB forcefield in explicit TIP3P water. The protein structural ensembles are studied in terms of various order parameters that differentiate the folded and unfolded states. We observe that in the folded state the root mean square distance (rmsd) from the backbone of the NMR structure shows two highly populated basins close to the native state with peaks at 0.06 nm and 0.16 nm, which are consistent with previous simulations using the same forcefield. The fraction of folded replicas shows a drastic decrease because of the absence of the salt bridge. However, significant populations of conformations with the arginine side chain exposed to the solvent, but within the folded basin, are found. This shows the possibility to reach the folded state without formation of the ion pair. We also characterize changes in the unfolded state. The equilibrium populations of the folded and unfolded states are used to characterize the thermodynamics of the system. We find that the change in free energy difference due to the protonation of the Asp amino acid is 3 kJ mol(-1) at 297 K, favoring the charged state, and resulting in ΔpK(1) = 0.5 units for Asp9. We also study the differences in the unfolded state ensembles for the two charge states and find significant changes at low temperature, where the protonated Asp side chain makes multiple hydrogen bonds to the protein backbone.     

Dynamics of water probed with vibrational echo correlation spectroscopy

Vibrational echo correlation spectroscopy experiments on the OD stretch of dilute HOD in H(2)O are used to probe the structural dynamics of water. A method is demonstrated for combining correlation spectra taken with different infrared pulse bandwidths (pulse durations), making it possible to use data collected from many experiments in which the laser pulse properties are not identical. Accurate measurements of the OD stretch anharmonicity (162 cm(-1)) are presented and used in the data analysis. In addition, the recent accurate determination of the OD vibrational lifetime (1.45 ps) and the time scale for the production of vibrational relaxation induced broken hydrogen bond "photoproducts" ( approximately 2 ps) aid in the data analysis. The data are analyzed using time dependent diagrammatic perturbation theory to obtain the frequency time correlation function (FTCF). The results are an improved FTCF compared to that obtained previously with vibrational echo correlation spectroscopy. The experimental data and the experimentally determined FTCF are compared to calculations that employ a polarizable water model (SPC-FQ) to calculate the FTCF. The SPC-FQ derived FTCF is much closer to the experimental results than previously tested nonpolarizable water models which are also presented for comparison.     

NOAH: NMR Supersequences for Small Molecule Analysis and Structure Elucidation

Nested NMR experiments combining up to five conventional NMR pulse sequences into one supersequence are introduced. The core 2D NMR techniques routinely employed in small molecule NMR spectroscopy, such as HSQC, HMQC, HMBC, COSY, NOESY, TOCSY, and similar, can be recorded in a single measurement. In this way the data collection time may be dramatically reduced and sample throughput increased for basic NMR applications, such as structure elucidation and verification in synthetic, medicinal, and natural product chemistry.     

Different Behaviors of Glutathione in Aqueous and DMSO Solutions: Molecular Dynamics Simulation and NMR Experimental Study

An all-atom molecular simulation and NMR experiments have been carried out to investigate the interactions and conformations of glutathione (GSH) in aqueous and DMSO solutions. The simulations started, from different initial conformations, are characterized by intramolecular distance, radius of gyration, root-mean-square deviation, and solvent-accessible surface. Interestingly, different behaviors are found in the two different solutions. GSH is highly flexible in an aqueous solution with transitions to the extended, semifolded, and folded states. However, once GSH reaches the folded state in DMSO, it remains there and becomes difficult to break down. The NMR results show agreement with the MD simulations. The water molecule is small. It is also a good proton donor and a good proton acceptor. Water molecules can easily break down the “folded” conformation. In DMSO solution, the stronger hydrogen bonds and the hydrophobic interactions are more important, which can make the GSH in the folded state stable. Variations in the distribution of conformations and the hydrogen-bonding network may play an important role in its function under physiological conditions.     

Effective Hamiltonians by optimal control: solid-state NMR double-quantum planar and isotropic dipolar recoupling

We report the use of optimal control algorithms for tailoring the effective Hamiltonians in nuclear magnetic resonance (NMR) spectroscopy through sophisticated radio-frequency (rf) pulse irradiation. Specifically, we address dipolar recoupling in solid-state NMR of powder samples for which case pulse sequences offering evolution under planar double-quantum and isotropic mixing dipolar coupling Hamiltonians are designed. The pulse sequences are constructed numerically to cope with a range of experimental conditions such as inhomogeneous rf fields, spread of chemical shifts, the intrinsic orientation dependencies of powder samples, and sample spinning. While the vast majority of previous dipolar recoupling sequences are operating through planar double-or zero-quantum effective Hamiltonians, we present here not only improved variants of such experiments but also for the first time homonuclear isotropic mixing sequences which transfers all I(x), I(y), and I(z) polarizations from one spin to the same operators on another spin simultaneously and with equal efficiency. This property may be exploited to increase the signal-to-noise ratio of two-dimensional experiments by a factor of square root 2 compared to conventional solid-state methods otherwise showing the same efficiency. The sequences are tested numerically and experimentally for a powder of (13)C(alpha),(13)C(beta)-L-alanine and demonstrate substantial sensitivity gains over previous dipolar recoupling experiments.     

Rapid acquisition of 1H and 19F NMR experiments for direct and competition ligand-based screening

Direct and competition ligand-based NMR experiments are often used in the screening of chemical fragment libraries against a protein target due to the high relative sensitivity of NMR for protein-binding events. A plethora of NMR methods has been proposed for this purpose. Two of these techniques are the (19)F T(2) filter and the (1)H selective T(2) filter experiments. Modifications of the pulse sequences of these experiments have resulted in a ～2-fold reduction in the experiment time thus allowing an increase in the screening throughput and making NMR an attractive technique for screening large compound collections.     

Solid phase synthesis of aromatic oligoamides: application to helical water-soluble foldamers

Synthetic helical aromatic amide foldamers and in particular those based on quinolines have recently attracted much interest due to their capacity to adopt bioinspired folded conformations that are highly stable and predictable. Additionally, the introduction of water-solubilizing side chains has allowed to evidence promising biological activities. It has also created the need for methods that may allow the parallel synthesis and screening of oligomers. Here, we describe the application of solid phase synthesis to speed up oligomer preparation and allow the introduction of various side chains. The synthesis of quinoline-based monomers bearing protected side chains is described along with conditions for activation, coupling, and deprotection on solid phase, followed by resin cleavage, side-chain deprotection, and HPLC purification. Oligomers having up to 8 units were thus synthesized. We found that solid phase synthesis is notably improved upon reducing resin loading and by applying microwave irradiation. We also demonstrate that the introduction of monomers bearing benzylic amines such as 6-aminomethyl-2-pyridinecarboxylic acid within the sequences of oligoquinolines make it possible to achieve couplings using a standard peptide coupling agent and constitute an interesting alternative to the use of acid chloride activation required by quinoline residues. The synthesis of a tetradecameric sequence was thus smoothly carried out. NMR solution structural studies show that these alternate aminomethyl-pyridine residues do not perturb the canonical helix folding of quinoline monomers in protic solvents, contrary to what was previously observed in nonprotic solvents.     

Optimal control design of NMR and dynamic nuclear polarization experiments using monotonically convergent algorithms

Optimal control theory has recently been introduced to nuclear magnetic resonance (NMR) spectroscopy as a means to systematically design and optimize pulse sequences for liquid- and solid-state applications. This has so far primarily involved numerical optimization using gradient-based methods, which allow for the optimization of a large number of pulse sequence parameters in a concerted way to maximize the efficiency of transfer between given spin states or shape the nuclear spin Hamiltonian to a particular form, both within a given period of time. Using such tools, a variety of new pulse sequences with improved performance have been developed, and the NMR spin engineers have been challenged to consider alternative routes for analytical experiment design to meet similar performance. In addition, it has lead to increasing demands to the numerical procedures used in the optimization process in terms of computational speed and fast convergence. With the latter aspect in mind, here we introduce an alternative approach to numerical experiment design based on the Krotov formulation of optimal control theory. For practical reasons, the overall radio frequency power delivered to the sample should be minimized to facilitate experimental implementation and avoid excessive sample heating. The presented algorithm makes explicit use of this requirement and iteratively solves the stationary conditions making sure that the maximum of the objective is reached. It is shown that this method is faster per iteration and takes different paths within a control space than gradient-based methods. In the present work, the Krotov approach is demonstrated by the optimization of NMR and dynamic nuclear polarization experiments for various spin systems and using different constraints with respect to radio frequency and microwave power consumption.     

Precise measurement of <Superscript>1</Superscript>H 90° pulse in solid-state NMR spectroscopy for complex and heterogeneous molecular systems

The 90 degrees pulse calibration is essential in NMR spectroscopy to prevent artefacts in the liquid state or to enhance cross-polarization efficiency in the solid state. We verified pulse-angle (PA) errors due to circuit impedances in solid-state NMR and suggested a possible solution to prevent the inconvenience of PA errors. The classic pulse sequences used to calibrate (1)H 90 degrees pulse lengths by direct detection of protons or by cross-polarization were modified in order to replace single (1)H pulses with (1)H pulse trains. Pulse trains were found to decrease the effect of PA imperfections in the calibration of basic pulses (i.e. 90 degrees and 180 degrees ) for a number of organic substrates. The modified sequences are especially important to rapidly obtain pulse calibration of complex and heterogeneous molecular systems such as humic substances, which usually require a long time when using single (1)H pulses.