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1.
Angew Chem Int Ed Engl ; 60(31): 17037-17044, 2021 Jul 26.
Article in English | MEDLINE | ID: mdl-33955632

ABSTRACT

In the development of 3D printing fuels, there is a need for new photoinitiating systems working under mild conditions and/or leading to polymers with new and/or enhanced properties. In this context, we introduce herein N-heterocyclic carbene-borane complexes as reagents for a new type of photo-click reaction, the borane-(meth)acrylate click reaction. Remarkably, the higher bond number of boranes relative to thiols induced an increase of the network density associated with faster polymerization kinetics. Solid-state NMR evidenced the strong participation of the boron centers on the network properties, while DMA and AFM showed that the materials exhibit improved mechanical properties, as well as reduced solvent swelling.

2.
RSC Adv ; 11(47): 29870-29876, 2021 Sep 01.
Article in English | MEDLINE | ID: mdl-35479571

ABSTRACT

Fast (60 kHz) magic angle spinning solid-state NMR allows very sensitive proton detection in highly paramagnetic organometallic powders. We showcase this technique with the complete assignment of 1H and 13C resonances in a high-spin Fe(ii) polymerisation catalyst with less than 2 mg of sample at natural abundance.

3.
J Am Chem Soc ; 142(39): 16757-16765, 2020 09 30.
Article in English | MEDLINE | ID: mdl-32871082

ABSTRACT

Most of our understanding of chemistry derives from atomic-level structures obtained with single-crystal X-ray diffraction. Metal centers in X-ray structures of small organometallic or coordination complexes are often extremely well-defined, with errors in the positions on the order of 10-4-10-5 Å. Determining the metal coordination geometry to high accuracy is essential for understanding metal center reactivity, as even small structural changes can dramatically alter the metal activity. In contrast, the resolution of X-ray structures in proteins is limited typically to the order of 10-1 Å. This resolution is often not sufficient to develop precise structure-activity relations for the metal sites in proteins, because the uncertainty in positions can cover all of the known ranges of bond lengths and bond angles for a given type of metal complex. Here we introduce a new approach that enables the determination of a high-definition structure of the active site of a metalloprotein from a powder sample, by combining magic-angle spinning (MAS) nuclear magnetic resonance (NMR) spectroscopy, tailored radio frequency (RF) irradiation schemes, and computational approaches. This allows us to overcome the "blind sphere" in paramagnetic proteins, and to observe and assign 1H, 13C, and 15N resonances for the ligands directly coordinating the metal center. We illustrate the method by determining the bond lengths in the structure of the CoII coordination sphere at the core of human superoxide dismutase 1 (SOD) with 0.7 pm precision. The coordination geometry of the resulting structure explains the nonreactive nature of the CoII/ZnII centers in these proteins, which allows them to play a purely structural role.


Subject(s)
Cobalt/chemistry , Coordination Complexes/chemistry , Metalloproteins/chemistry , Superoxide Dismutase-1/chemistry , Zinc/chemistry , Binding Sites , Humans , Nuclear Magnetic Resonance, Biomolecular
4.
Inorg Chem ; 59(14): 10071-10082, 2020 Jul 20.
Article in English | MEDLINE | ID: mdl-32633944

ABSTRACT

In order to develop novel, more efficient, and/or selective contrast agents for magnetic resonance imaging (MRI), different modi operandi are explored as alternatives to water-relaxation enhancement. In this work, cobalt(II/III) complexes of bis(N-trifluoroethyl)cyclam derivatives with two acetate or two phosphonate pendant arms, H2te2f2a and H4te2f2p, were prepared and investigated. X-ray diffraction structures confirmed octahedral coordination with a very stable trans-III cyclam conformation and with fluorine atoms located about 5.3 Å from the metal center. The Co(II) complexes are kinetically inert, decomposing slowly even in 1 M aqueous HCl at 80 °C. The Co(II) complexes exhibited well-resolved paramagnetically shifted NMR spectra. These were interpreted with the help of quantum chemistry calculations. The 13C NMR shifts of the trans-[CoII(te2f2p)]2- complex were successfully assigned based on spin density delocalization within the ligand molecule. The obtained spin density also helps to describe d-metal-induced NMR relaxation properties of 19F nuclei, including the contribution of a Fermi contact relaxation mechanism. The paramagnetic complexes show convenient relaxation properties to be used as 19F MRI contrast agents.

5.
J Chem Phys ; 150(14): 144101, 2019 Apr 14.
Article in English | MEDLINE | ID: mdl-30981251

ABSTRACT

Pseudocontact shifts are traditionally described as a function of the anisotropy of the paramagnetic susceptibility tensor, according to the semiempirical theory mainly developed by Kurland and McGarvey [J. Magn. Reson. 2, 286-301 (1970)]. The paramagnetic susceptibility tensor is required to be symmetric. Applying point-dipole approximation to the quantum chemistry theory of hyperfine shift, pseudocontact shifts are found to scale with a non-symmetric tensor that differs by a factor gT/ge from the paramagnetic susceptibility tensor derived within the semiempirical framework. We analyze the foundations of the Kurland-McGarvey pseudocontact shift expression and recall that it is inherently based on the Russell-Saunders (LS) coupling approximation for the spin-orbit coupling. We show that the difference between the semiempirical and quantum chemistry pseudocontact shift expressions arises directly from the different treatment of the orbital contribution to the hyperfine coupling.

6.
Phys Chem Chem Phys ; 21(10): 5661-5673, 2019 Mar 06.
Article in English | MEDLINE | ID: mdl-30794275

ABSTRACT

Transient and fuzzy intermolecular interactions are fundamental to many biological processes. Despite their importance, they are notoriously challenging to characterize. Effects induced by paramagnetic ligands in the NMR spectra of interacting biomolecules provide an opportunity to amplify subtle manifestations of weak intermolecular interactions observed for diamagnetic ligands. Here, we present an approach to characterizing dynamic interactions between a partially flexible dimeric protein, HIV-1 protease, and a metallacarborane-based ligand, a system for which data obtained by standard NMR approaches do not enable detailed structural interpretation. We show that for the case where the experimental data are significantly averaged to values close to zero the standard fitting of pseudocontact shifts cannot provide reliable structural information. We based our approach on generating a large ensemble of full atomic models, for which the experimental data can be predicted, ensemble averaged and finally compared to the experiment. We demonstrate that a combination of paramagnetic NMR experiments, quantum chemical calculations, and molecular dynamics simulations offers a route towards structural characterization of dynamic protein-ligand complexes.


Subject(s)
Boranes/chemistry , HIV Protease/chemistry , Metals/chemistry , Molecular Dynamics Simulation , Ligands , Magnetic Resonance Spectroscopy/methods , Protein Binding , Protein Conformation , Quantum Theory
7.
Organometallics ; 36(3): 605-613, 2017 Feb 13.
Article in English | MEDLINE | ID: mdl-31031510

ABSTRACT

The use of the dialkene divinyltetramethyldisiloxane (dvtms) allows easy access to the reactive 16 valence-electron complexes [Fe0(L-L)(dvtms)], (L-L) = dppe (1,2-bis(diphenylphosphino)ethane), (1), dppp (1,2-bis(diisopropylphosphino)propane), (2), pyNMeP(iPr)2 (N-(diisopropylphosphino)-N-methylpyridin-2-amine), (4), dipe (1,2-bis(diisopropylphosphino)ethane), (5), and [Fe0(L)2(dvtms)], L = PMe3, (3), by a mild reductive route using AlEt2(OEt) as reducing agent. In contrast, by the same methodology, the 18 valence-electron complexes [Fe0(L-L)2(ethylene)], (L-L) = dppm (1,2-bis(diphenylphosphino)methane), 6, (L-L) = dppa (1,2-bis(diphenylphosphino)amine) 7 or (L-L)=dppe, 8, were obtained, which do not contain dvtms. In addition, a combined DFT and solid-state paramagnetic NMR methodology is introduced for the structure determination of 5. A comparative study of the reactivity of 1,2,4-6 and 8 with 3-hexyne highlights emerging mechanistic implications for C-C coupling reactions using these complexes as catalysts.

8.
Angew Chem Int Ed Engl ; 55(47): 14713-14717, 2016 11 14.
Article in English | MEDLINE | ID: mdl-27781358

ABSTRACT

Long-range pseudo-contact NMR shifts (PCSs) provide important restraints for the structure refinement of proteins when a paramagnetic metal center is present, either naturally or introduced artificially. Here we show that ab initio quantum-chemical methods and a modern version of the Kurland-McGarvey approach for paramagnetic NMR (pNMR) shifts in the presence of zero-field splitting (ZFS) together provide accurate predictions of all PCSs in a metalloprotein (high-spin cobalt-substituted MMP-12 as a test case). Computations of 314 13 C PCSs using g- and ZFS tensors based on multi-reference methods provide a reliable bridge between EPR-parameter- and susceptibility-based pNMR formalisms. Due to the high sensitivity of PCSs to even small structural differences, local structures based either on X-ray diffraction or on various DFT optimizations could be evaluated critically by comparing computed and experimental PCSs. Many DFT functionals provide insufficiently accurate structures. We also found the available 1RMZ PDB X-ray structure to exhibit deficiencies related to binding of a hydroxamate inhibitor. This has led to a newly refined PDB structure for MMP-12 (5LAB) that provides a more accurate coordination arrangement and PCSs.

9.
J Phys Chem B ; 119(33): 10682-92, 2015 Aug 20.
Article in English | MEDLINE | ID: mdl-26193890

ABSTRACT

The phosphate group (PO2(-)) is an important building block occurring in many components of living matter including nucleic acids. It provides distinct features in vibrational spectra and is useful as a local probe of NA conformation and interactions with the environment. For this purpose, it is desirable to explore in detail various factors influencing spectral shapes of characteristic phosphate vibrations. In the present study, effects of the solvent and conformational averaging are analyzed for simple model molecules, dimethylphosphate, ethylmethylphosphate, and ethylmethylthiophosphate. Infrared absorption (IR) and Raman spectra were measured and calculated using a combination of molecular dynamics (MD) and density functional theory (DFT). To fully understand the link between the structure and the spectra, the solvent has to be explicitly included in the computational modeling. The results indicate that vibrational properties of the phosphate moiety are very sensitive to its conformation and interactions with the aqueous environment indeed. Polarizable continuum solvent models without explicit water molecules provided significantly worse agreement with the experiment. The combined MD/DFT approach captures well spectral characteristics for the model systems and constitutes the most reliable basis for exploration of phosphate vibrational properties in biomolecular structural studies.


Subject(s)
Molecular Dynamics Simulation , Phosphates/chemistry , Quantum Theory , Vibration , Hydrogen Bonding , Molecular Conformation , Thermodynamics
10.
J Phys Chem B ; 118(24): 6864-74, 2014 Jun 19.
Article in English | MEDLINE | ID: mdl-24853047

ABSTRACT

The microscopic structure of ethanol in the liquid state is characterized as a dynamic equilibrium of hydrogen-bonded clusters of different sizes and topologies. We have developed a novel method for determination of the average size of the clusters that combines the measurement of diffusion coefficient by means of NMR diffusometry technique and hydrodynamic simulations. The approach includes the use of HydroNMR [J. Garcìa de la Torre, M. L. Huertas, and B. Carrasco, J. Magn. Reson. 147, 2000, 138] for small molecules, which is attained here by the calibration procedure using a dilute solution of tetramethylsilane. It is thus possible to correlate the experimentally determined diffusion coefficient of ethanol with calculated diffusion coefficients of the modeled clusters of different sizes. We found that average size of the clusters in 0.16 M solution of ethanol in n-hexane corresponds to the monomer above 300 K and to the pentamer/hexamer below 240 K. The clusters in the case of 0.44 M solution are generally slightly larger, from the average size corresponding to the dimer at 320 K and the hexamer at 210 K.

11.
J Biomol NMR ; 55(1): 59-70, 2013 Jan.
Article in English | MEDLINE | ID: mdl-23202985

ABSTRACT

Density functional theory was employed to study the influence of O-phosphorylation of serine, threonine, and tyrosine on the amidic (15)N chemical shielding anisotropy (CSA) tensor in the context of the complex chemical environments of protein structures. Our results indicate that the amidic (15)N CSA tensor has sensitive responses to the introduction of the phosphate group and the phosphorylation-promoted rearrangement of solvent molecules and hydrogen bonding networks in the vicinity of the phosphorylated site. Yet, the calculated (15)N CSA tensors in phosphorylated model peptides were in range of values experimentally observed for non-phosphorylated proteins. The extent of the phosphorylation induced changes suggests that the amidic (15)N CSA tensor in phosphorylated proteins could be reasonably well approximated with averaged CSA tensor values experimentally determined for non-phosphorylated amino acids in practical NMR applications, where chemical surrounding of the phosphorylated site is not known a priori in majority of cases. Our calculations provide estimates of relative errors to be associated with the averaged CSA tensor values in interpretations of NMR data from phosphorylated proteins.


Subject(s)
Nuclear Magnetic Resonance, Biomolecular , Proteins/chemistry , Serine/chemistry , Threonine/chemistry , Tyrosine/chemistry , Anisotropy , Nitrogen Isotopes/chemistry , Peptides/chemistry , Phosphates/chemistry , Phosphorylation , Solvents/chemistry
12.
J Phys Chem A ; 116(32): 8313-20, 2012 Aug 16.
Article in English | MEDLINE | ID: mdl-22803635

ABSTRACT

The Hg(2+) ion stabilizes the thymine-thymine mismatched base pair and provides new ways of creating various DNA structures. Recently, such T-Hg-T binding was detected by the Raman spectroscopy. In this work, detailed differences in vibrational frequencies and Raman intensity patterns in the free TpT dinucleotide and its metal-mediated complex (TpT·Hg)(2) are interpreted on the basis of quantum chemical modeling. The computations verified specific marker Raman bands indicating the effect of mercury binding to DNA. Although the B3LYP functional well-describes the Raman frequencies, a dispersion correction had to be added for all atoms including mercury to obtain realistic geometry of the (TpT·Hg)(2) dimer. Only then, the DFT complex structure agreed with those obtained with the wave function-based MP2 method. The aqueous solvent modeled as a polarizable continuum had a minor effect on the dispersion interaction, but it stabilized conformations of the sugar and phosphate parts. A generalized definition of internal coordinate force field was introduced to monitor covalent bond mechanical strengthening and weakening upon the Hg(2+) binding. Induced vibrational frequency shifts were rationalized in terms of changes in electronic structure. The simulations thus also provided reliable insight into the complex structure and stability.


Subject(s)
Coordination Complexes/chemistry , Mercury/chemistry , Oligonucleotides/chemistry , Thymine/chemistry , Base Pair Mismatch , Computer Simulation , DNA/chemistry , Electrons , Models, Molecular , Molecular Structure , Quantum Theory , Solutions , Spectrum Analysis, Raman , Vibration , Water
13.
J Phys Chem B ; 116(12): 3823-33, 2012 Mar 29.
Article in English | MEDLINE | ID: mdl-22380464

ABSTRACT

Determination of nucleic acid (NA) structure with NMR spectroscopy is limited by the lack of restraints on conformation of NA phosphate. In this work, the (31)P chemical shielding tensor, the Γ(P,C5'H5'1) and Γ(P,C5'H5'2) cross-correlated relaxation rates, and the (2)J(P,C3'), (2)J(P,C5'), and (3)J(P,C4') coupling constants were calculated in dependence on NA backbone torsion angles ζ and α. While the orientation of the (31)P chemical shielding tensor was almost independent of the NA phosphate conformation, the principal tensor components varied by up to ~40 ppm. This variation and the dependence of the phosphate geometry on torsion angles ζ and α had only a minor influence on the calculated Γ(P,C5'H5'1) and Γ(P,C5'H5'2) cross-correlated relaxation rates, and therefore, the so-called rigid tensor approximation was here validated. For the first time, the (2)J(P,C) spin-spin coupling constants were correlated with the conformation of NA phosphate. Although each of the two J-couplings was significantly modulated by both torsions ζ and α, the (2)J(P,C3') coupling could be structurally assigned to torsion ζ and the (2)J(P,C5') coupling to torsion α. We propose qualitative rules for their structural interpretation as loose restraints on torsion angles ζ and α. The (3)J(P,C4') coupling assigned to torsion angle ß was found dependent also on torsions ζ and α, implying that the uncertainty in determination of ß with standard Karplus curves could be as large as ~25°. The calculations provided a unified picture of NMR parameters applicable for the determination of NA phosphate conformation.


Subject(s)
Magnetic Resonance Spectroscopy , Nucleic Acids/chemistry , Nucleic Acid Conformation , Phosphorus/chemistry , Quantum Theory
14.
Nucleic Acids Res ; 40(12): 5766-74, 2012 Jul.
Article in English | MEDLINE | ID: mdl-22383582

ABSTRACT

Developing applications for metal-mediated base pairs (metallo-base-pair) has recently become a high-priority area in nucleic acid research, and physicochemical analyses are important for designing and fine-tuning molecular devices using metallo-base-pairs. In this study, we characterized the Hg(II)-mediated T-T (T-Hg(II)-T) base pair by Raman spectroscopy, which revealed the unique physical and chemical properties of Hg(II). A characteristic Raman marker band at 1586 cm(-1) was observed and assigned to the C4=O4 stretching mode. We confirmed the assignment by the isotopic shift ((18)O-labeling at O4) and density functional theory (DFT) calculations. The unusually low wavenumber of the C4=O4 stretching suggested that the bond order of the C4=O4 bond reduced from its canonical value. This reduction of the bond order can be explained if the enolate-like structure (N3=C4-O4(-)) is involved as a resonance contributor in the thymine ring of the T-Hg(II)-T pair. This resonance includes the N-Hg(II)-bonded state (Hg(II)-N3-C4=O4) and the N-Hg(II)-dissociated state (Hg(II+) N3=C4-O4(-)), and the latter contributor reduced the bond order of N-Hg(II). Consequently, the Hg(II) nucleus in the T-Hg(II)-T pair exhibited a cationic character. Natural bond orbital (NBO) analysis supports the interpretations of the Raman experiments.


Subject(s)
Mercury/chemistry , Thymine/chemistry , Base Pairing , Cations/chemistry , Spectrum Analysis, Raman
15.
J Phys Chem A ; 115(11): 2385-95, 2011 Mar 24.
Article in English | MEDLINE | ID: mdl-21366222

ABSTRACT

Dependence of NMR (31)P shielding tensor and (2)J(P,C) coupling constants on solvation of nucleic acid phosphate by Mg(2+) and water was studied using methods of bioinformatic structural analyses of crystallographic data and DFT B3LYP calculations of NMR parameters. The effect of solvent dynamics on NMR parameters was calculated using molecular dynamic. The NMR calculations for representative solvation patterns determined in crystals of B-DNA and A-RNA molecules pointed out the crucial importance of local Mg(2+) coordination geometry, including hydration by explicit water molecules and necessity of dynamical averaging over the solvent reorientation. The dynamically averaged (31)P chemical shift decreased by 2-9.5 ppm upon Mg(2+) coordination, the chemical shielding anisotropy increased by 0-20 ppm, and the (2)J(P,C5') coupling magnitude decreased by 0.2-1.8 Hz upon Mg(2+) coordination. The calculated decrease of the (31)P chemical shift is in excellent agreement with the 1.5-10 ppm decrease of the phosphorothioate (31)P chemical shift upon Cd(2+) coordination probed experimentally in hammerhead ribozyme (Suzumura; et al. J. Am. Chem. Soc. 2002, 124, 8230-8236; Osborne; et al., Biochemistry 2009, 48, 10654-10664). None of the dynamically averaged NMR parameters unequivocally distinguishes the site-specific Mg(2+) coordination to one of the two nonesterified phosphate oxygen atoms of the phosphate determined by bioinformatic analyses. By comparing the limit cases of static and dynamically averaged solvation, we propose that mobility of the solvent has a dramatic impact on NMR parameters of nucleic acid phosphate and must be taken into account for their accurate modeling.


Subject(s)
Magnesium/chemistry , Magnetic Resonance Spectroscopy/methods , Nucleic Acids/chemistry , Phosphates/chemistry , Cations , Nucleic Acid Conformation , Phosphorus Isotopes , Water/chemistry
16.
Phys Chem Chem Phys ; 13(1): 100-3, 2011 Jan 07.
Article in English | MEDLINE | ID: mdl-21049099

ABSTRACT

Metal atoms with a closed-shell electronic structure and positive charge as for example the Au(I), Pt(II), Ag(I), Tl(I) or Hg(II) atoms do not in some compounds repel each other due to the so-called metallophilic attraction (P. Pyykkö, Chem. Rev., 1997, 97, 597-636). Here we highlight the role of the Hg(II)Hg(II) metallophilic attraction between the consecutive metal-mediated mismatched base pairs of nucleic acids. Usually, the base stacking dominates the non-covalent interactions between steps of native nucleic acids. In the presence of metal-mediated base pairs these non-covalent interactions are enriched by the metal-base interactions and the metallophilic attraction. The two interactions arising due to the metal linkage of the mismatches were found in this study to have a stabilizing effect on nucleic acid structure. The calculated data are consistent with recent experimental observations. The stabilization due to the metallophilic attraction seems to be a generally important concept for the nucleic acids containing heavy metals with short contacts.


Subject(s)
Mercury/chemistry , Nucleic Acids/chemistry , Organometallic Compounds/chemistry , Uracil/chemistry , Base Pairing , Models, Molecular , Molecular Structure
17.
J Phys Chem B ; 114(10): 3574-82, 2010 Mar 18.
Article in English | MEDLINE | ID: mdl-20175531

ABSTRACT

Hydration envelopes of metallic ions significantly influence their chemical properties and biological functioning. Previous computational studies, nuclear magnetic resonance (NMR), and vibrational spectra indicated a strong affinity of the Mg(2+) cation to water. We find it interesting that, although monatomic ions do not vibrate themselves, they cause notable changes in the water Raman signal. Therefore, in this study, we used a combination of Raman spectroscopy and computer modeling to analyze the magnesium hydration shell and origin of the signal. In the measured spectra of several salts (LiCl, NaCl, KCl, MgCl(2), CaCl(2), MgBr(2), and MgI(2) water solutions), only the spectroscopic imprint of the hydrated Mg(2+) cation could clearly be identified as an exceptionally distinct peak at approximately 355 cm(-1). The assignment of this band to the Mg-O stretching motion could be confirmed on the basis of several models involving quantum chemical computations on metal/water clusters. Minor Raman spectral features could also be explained. Ab initio and Fourier transform (FT) techniques coupled with the Car-Parrinello molecular dynamics were adapted to provide the spectra from dynamical trajectories. The results suggest that even in concentrated solutions magnesium preferentially forms a [Mg(H(2)O)(6)](2+) complex of a nearly octahedral symmetry; nevertheless, the Raman signal is primarily associated with the relatively strong metal-H(2)O bond. Partially covalent character of the Mg-O bond was confirmed by a natural bond orbital analysis. Computations on hydrated chlorine anion did not provide a specific signal. The FT techniques gave good spectral profiles in the high-frequency region, whereas the lowest-wavenumber vibrations were better reproduced by the cluster models. Both dynamical and cluster computational models provided a useful link between spectral shapes and specific ion-water interactions.


Subject(s)
Ions/chemistry , Magnesium/chemistry , Models, Theoretical , Fourier Analysis , Molecular Dynamics Simulation , Molecular Imprinting , Spectrum Analysis, Raman , Water/chemistry
18.
J Phys Chem B ; 113(15): 5273-81, 2009 Apr 16.
Article in English | MEDLINE | ID: mdl-19301831

ABSTRACT

The dependence of the effective chemical shielding anisotropy (effective CSA, Deltasigma(eff)) on the phi and psi peptide backbone torsion angles was calculated in the l-alanyl-l-alanine (LALA) peptide using the DFT method. The effects of backbone conformation, molecular charge including the cation, zwitterion, and anion forms of the LALA peptide, and the scaling taking into account the length of the dipolar vector were calculated for the effective CSAs in order to assess their structural behaviors and to predict their magnitudes which can be probed for the beta-sheet and alpha-helix backbone conformations via measurement of the cross-correlated relaxation rates (CCR rates). Twenty different CSA-DD cross-correlation mechanisms involving the amide nitrogen and carbonyl carbon chemical shielding tensors and the C(alpha)H(alpha) (alpha-carbon group), NH(N) (amide group), C(alpha)H(N), NH(alpha), C'H(alpha), and C'H(N) (alpha = alpha1, alpha2) dipolar vectors were investigated. The X-C(alpha)H(alpha) (X = N, C'; alpha = alpha1, alpha2) cross-correlations, which had already been studied experimentally, exhibited overall best performance of the calculated effective CSAs in the LALA molecule; they spanned the largest range of values upon variation of the psi and phi torsions and depended dominantly on only one of the two backbone torsion angles. The X-NH(N) (X = N, C') cross-correlations, which had been also probed experimentally, depended on both backbone torsions, which makes their structural assignment more difficult. The N-NH(alpha2) and N-C'H(alpha1) cross-correlations were found to be promising for the determination of various backbone conformations due to the large calculated range of the scaled effective CSA values and due to their predominant dependence on the psi and phi torsions, respectively. The 20 calculated dependencies of effective CSAs on the two backbone torsion angles can facilitate the structural interpretation of CCR rates.


Subject(s)
Computer Simulation , Dipeptides/chemistry , Models, Chemical , Anisotropy
19.
J Phys Chem A ; 112(23): 5167-74, 2008 Jun 12.
Article in English | MEDLINE | ID: mdl-18491850

ABSTRACT

The rotation of a trimethylsiloxy (TMSO) group in three silylated phenols (with three different ortho substituents -H, -CH3, and -C(CH3)3) was studied with the NMR (n)J(Si,C), n = 2, 3, 4, 5, scalar spin-spin coupling between the (29)Si nucleus of the TMSO group and the (13)C nuclei of the phenyl ring. The internal rotation potential calculated with the B3LYP and MP2 calculation methods including the effect of a solvent environment (gas phase, chloroform, and water) was used for the calculation of the dynamical averages of the scalar coupling constants in the framework of the rigid-bender formalism. Solvent effects, the quality of the rotational potential, and the applicability of the classical molecular dynamic to the problem is discussed. Quantum effects have a sizable impact on scalar couplings, particularly for the internal rotational states well localized within the wells of the potential surfaces for the TMSO group. The overall difference between the experimental and theoretical scalar couplings calculated for the global energy-minima structures (static model) decreases substantially for both model potentials (B3LYP, MP2) when the molecular motion of the TMSO group is taken into account. The calculated data indicate that the inclusion of molecular motion is necessary for the accurate calculation of the scalar coupling constants and their reliable structural interpretation for any system which possesses a large-amplitude motion.

20.
J Phys Chem B ; 112(6): 1796-805, 2008 Feb 14.
Article in English | MEDLINE | ID: mdl-18171047

ABSTRACT

The l-alanyl-l-alanine (AA) molecule behaves differently in acidic, neutral, and basic environments. Because of its molecular flexibility and strong interaction with the aqueous environment, its behavior has to be deduced from the NMR spectra indirectly, using statistical methods and comparison with ab initio predictions of geometric and spectral parameters. In this study, chemical shifts and indirect spin-spin coupling constants of the AA cation, anion, and zwitterion were measured and compared to values obtained by density functional computations for various conformers of the dipeptide. The accuracy and sensitivity of the quantum methods to the molecular charge was also tested on the (mono)-alanine molecule. Probable AA conformers could be identified at two-dimensional potential energy surfaces and verified by the comparison of the computed parameters with measured NMR data. The results indicate that, whereas the main-chain peptide conformations of the cationic (AA+) and zwitterionic (AAZW) forms are similar, the anion (AA-) adopts also another, approximately equally populated conformer in the aqueous solution. Additionally, the NH2 group can rotate in the two main chain conformations of the anionic form AA-. According to a vibrational quantum analysis of the two-dimensional energy surfaces, higher-energy conformers might exist for all three charged AA forms but cannot be detected directly by NMR spectroscopy because of their small populations and short lifetimes. In accord with previous studies, the NMR parameters, particularly the indirect nuclear spin-spin coupling constants, often provided an excellent probe of a local conformation. Generalization to peptides and proteins, however, has to take into account the environment, molecular charge, and flexibility of the peptide chain.


Subject(s)
Dipeptides/chemistry , Electrochemistry , Hydrogen-Ion Concentration , Magnetic Resonance Spectroscopy , Models, Molecular , Protein Conformation , Solvents
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