A simple analysis of the influence of the solvent-induced electronic polarization on the N-15 magnetic shielding of pyridine in water

Electronic polarization induced by the interaction of a reference molecule with a liquid environment is expected to affect the magnetic shielding constants. Understanding this effect using realistic theoretical models is important for proper use of nuclear magnetic resonance in molecular characterization. In this work, we consider the pyridine molecule in water as a model system to briefly investigate this aspect. Thus, Monte Carlo simulations and quantum mechanics calculations based on the B3LYP/6-311++G (d,p) are used to analyze different aspects of the solvent effects on the N-15 magnetic shielding constant of pyridine in water. This includes in special the geometry relaxation and the electronic polarization of the solute by the solvent. The polarization effect is found to be very important, but, as expected for pyridine, the geometry relaxation contribution is essentially negligible. Using an average electrostatic model of the solvent, the magnetic shielding constant is calculated as -58.7 ppm, in good agreement with the experimental value of -56.3 ppm. The explicit inclusion of hydrogen-bonded water molecules embedded in the electrostatic field of the remaining solvent molecules gives the value of -61.8 ppm.

Stereoselective synthesis of novel diels-alder adducts of p-substituted Methyl Thiocinnamates and Cyclopentadiene

This article describes the Diels-Alder reaction between methyl thiocinnamates, substituted at the para position by electron-donating and electron-withdrawing groups, with cyclopentadiene in the presence of catechol boron bromide (CBB) as a Lewis acid catalyst. The adduct configuration was confirmed by H-1 NMR coupling constants and single-crystal x-ray diffraction. Total endo stereoselectivity was observed in all reactions and was attributed to the effective secondary interaction between the boron atom and the incipient double bond in the norbonene resulting from the planar geometry of the catalyst. C-13 NMR chemical shifts of the coordinated dienophile carbonyl carbons with CBB compared to those of the non coordinated thiocinammates suggest a strong complexation with the catalyst.

Large-scale coupled-cluster calculations

Coupled-cluster theory provides one of the most successful concepts in electronic-structure theory. This work covers the parallelization of coupled-cluster energies, gradients, and second derivatives and its application to selected large-scale chemical problems, beside the more practical aspects such as the publication and support of the quantum-chemistry package ACES II MAB and the design and development of a computational environment optimized for coupled-cluster calculations. The main objective of this thesis was to extend the range of applicability of coupled-cluster models to larger molecular systems and their properties and therefore to bring large-scale coupled-cluster calculations into day-to-day routine of computational chemistry. A straightforward strategy for the parallelization of CCSD and CCSD(T) energies, gradients, and second derivatives has been outlined and implemented for closed-shell and open-shell references. Starting from the highly efficient serial implementation of the ACES II MAB computer code an adaptation for affordable workstation clusters has been obtained by parallelizing the most time-consuming steps of the algorithms. Benchmark calculations for systems with up to 1300 basis functions and the presented applications show that the resulting algorithm for energies, gradients and second derivatives at the CCSD and CCSD(T) level of theory exhibits good scaling with the number of processors and substantially extends the range of applicability. Within the framework of the ’High accuracy Extrapolated Ab initio Thermochemistry’ (HEAT) protocols effects of increased basis-set size and higher excitations in the coupled- cluster expansion were investigated. The HEAT scheme was generalized for molecules containing second-row atoms in the case of vinyl chloride. This allowed the different experimental reported values to be discriminated. In the case of the benzene molecule it was shown that even for molecules of this size chemical accuracy can be achieved. Near-quantitative agreement with experiment (about 2 ppm deviation) for the prediction of fluorine-19 nuclear magnetic shielding constants can be achieved by employing the CCSD(T) model together with large basis sets at accurate equilibrium geometries if vibrational averaging and temperature corrections via second-order vibrational perturbation theory are considered. Applying a very similar level of theory for the calculation of the carbon-13 NMR chemical shifts of benzene resulted in quantitative agreement with experimental gas-phase data. The NMR chemical shift study for the bridgehead 1-adamantyl cation at the CCSD(T) level resolved earlier discrepancies of lower-level theoretical treatment. The equilibrium structure of diacetylene has been determined based on the combination of experimental rotational constants of thirteen isotopic species and zero-point vibrational corrections calculated at various quantum-chemical levels. These empirical equilibrium structures agree to within 0.1 pm irrespective of the theoretical level employed. High-level quantum-chemical calculations on the hyperfine structure parameters of the cyanopolyynes were found to be in excellent agreement with experiment. Finally, the theoretically most accurate determination of the molecular equilibrium structure of ferrocene to date is presented.

Spectroscopic properties from hybrid QM, MM molecular dynamics simulation

The central aim of this thesis work is the application and further development of a hybrid quantum mechanical/molecular mechanics (QM/MM) based approach to compute spectroscopic properties of molecules in complex chemical environments from electronic structure theory. In the framework of this thesis, an existing density functional theory implementation of the QM/MM approach is first used to calculate the nuclear magnetic resonance (NMR) solvent shifts of an adenine molecule in aqueous solution. The findings show that the aqueous solvation with its strongly fluctuating hydrogen bond network leads to specific changes in the NMR resonance lines. Besides the absolute values, also the ordering of the NMR lines changes under the influence of the solvating water molecules. Without the QM/MM scheme, a quantum chemical calculation could have led to an incorrect assignment of these lines. The second part of this thesis describes a methodological improvement of the QM/MM method that is designed for cases in which a covalent chemical bond crosses the QM/MM boundary. The development consists in an automatized protocol to optimize a so-called capping potential that saturates the electronic subsystem in the QM region. The optimization scheme is capable of tuning the parameters in such a way that the deviations of the electronic orbitals between the regular and the truncated (and "capped") molecule are minimized. This in turn results in a considerable improvement of the structural and spectroscopic parameters when computed with the new optimized capping potential within the QM/MM technique. This optimization scheme is applied and benchmarked on the example of truncated carbon-carbon bonds in a set of small test molecules. It turns out that the optimized capping potentials yield an excellent agreement of NMR chemical shifts and protonation energies with respect to the corresponding full molecules. These results are very promising, so that the application to larger biological complexes will significantly improve the reliability of the prediction of the related spectroscopic properties.

Ab-initio study of hydrogen technology materials for hydrogen storage and proton conduction

This dissertation deals with two specific aspects of a potential hydrogen-based energy economy, namely the problems of energy storage and energy conversion. In order to contribute to the solution of these problems, the structural and dynamical properties of two promising materials for hydrogen storage (lithium imide/amide) and proton conduction (poly[vinyl phosphonic acid]) are modeled on an atomistic scale by means of first principles molecular dynamics simulation methods.rnrnrnIn the case of the hydrogen storage system lithium amide/imide (LiNH_2/Li_2NH), the focus was on the interplay of structural features and nuclear quantum effects. For these calculations, Path-Integral Molecular Dynamics (PIMD) simulations were used. The structures of these materials at room temperature were elucidated; in collaboration with an experimental group, a very good agreement between calculated and experimental solid-state 1H-NMR chemical shifts was observed. Specifically, the structure of Li_2NH features a disordered arrangement of the Li lattice, which was not reported in previous studies. In addition, a persistent precession of the NH bonds was observed in our simulations. We provide evidence that this precession is the consequence of a toroid-shaped effective potential, in which the protons in the material are immersed. This potential is essentially flat along the torus azimuthal angle, which might lead to important quantum delocalization effects of the protons over the torus.rnrnOn the energy conversion side, the dynamics of protons in a proton conducting polymer (poly[vinyl phosphonic acid], PVPA) was studied by means of a steered ab-initio Molecular Dynamics approach applied on a simplified polymer model. The focus was put on understanding the microscopic proton transport mechanism in polymer membranes, and on characterizing the relevance of the local environment. This covers particularly the effect of water molecules, which participate in the hydrogen bonding network in the material. The results indicate that these water molecules are essential for the effectiveness of proton conduction. A water-mediated Grotthuss mechanism is identified as the main contributor to proton conduction, which agrees with the experimentally observed decay on conductivity for the same material in the absence of water molecules.rnrnThe gain in understanding the microscopic processes and structures present in this materials can help the development of new materials with improved properties, thus contributing to the solution of problems in the implementation of fuel cells.

Novel cuticular hydrocarbons from the cane beetle Antitrogus parvulus - 4,6,8,10,16-penta- and 4,6,8,10,16,18-hexamethyldocosanes - Unprecedented anti-anti-anti-stereochemistry in the 4,6,8,10-methyltetrad

[GRAPHICS] The major cuticular hydrocarbons from the cane beetle species Antitrogus parvulus are 4,6,8,10,16-penta- and 4,6,8,10,16,18-hexamethyldocosanes, I and 2, respectively. Stereoisomers of 2,4,6,8-tetramethylundecanal of established relative stereochemistry were derived from 2,4,6-trimethylphenol and were then coupled with appropriate methyl-substituted phosphoranes 62 and 25 to furnish alkenes, which on reduction provided diastereomers of I and 2, respectively. Capillary gas chromatography, mass spectrometry, and high resolution C-13 NMR spectroscopy confirmed 1 as either 84a or 84b and 2 as either 15a or 15b. The novelty of these structures and their relative stereochemistry is briefly related to polyketide assembly.

Disulfide bond mutagenesis and the structure and function of the head-to-tail macrocyclic trypsin inhibitor SFTI-1

SFTI-1 is a novel 14 amino acid peptide comprised of a circular backbone constrained by three proline residues, a hydrogen-bond network, and a single disulfide bond. It is the smallest and most potent known Bowman-Birk trypsin inhibitor and the only one with a cyclic peptidic backbone. The solution structure of [ABA(3,11)]SFTI-1, a disulfide-deficient analogue of SFTI-1, has been determined by H-1 NMR spectroscopy. The lowest energy structures of native SFTI-1 and [ABA(3,11)]SFTI-1 are similar and superimpose with a root-mean-square deviation over the backbone and heavy atoms of 0.26 +/- 0.09 and 1.10 +/- 0.22 Angstrom, respectively. The disulfide bridge in SFTI-1 was found to be a minor determinant for the overall structure, but its removal resulted in a slightly weakened hydrogen-bonding network. To further investigate the role of the disulfide bridge, NMR chemical shifts for the backbone H-alpha protons of two disulfide-deficient linear analogues of SFTI-1, [ABA(3,11)]SFTI-1[6,5] and [ABA(3,11)]SFTI-1[1,14] were measured. These correspond to analogues of the cleavage product of SFTI-1 and a putative biosynthetic precursor, respectively. In contrast with the cyclic peptide, it was found that the disulfide bridge is essential for maintaining the structure of these open-chain analogues. Overall, the hydrogen-bond network appears to be a crucial determinant of the structure of SFTI-1 analogues.

Síntese, caracterização e reatividade de complexos organoestânicos contendo bases de Schiff derivadas de aminoácidos com carbonilas de Mo. W e Re

Tese (doutorado)–Universidade de Brasília, Instituto de Química, Programa de Pós-Graduação em Química, 2015.

13C NMR of a single molecule magnet: analysis of pseudocontact shifts and residual dipolar couplings

Paramagnetic triple decker complexes of lanthanides are promising Single Molecule Magnets (SMMs), with many potential uses. Some of them show preferable relaxation behavior, which enables the recording of well resolved NMR spectra. These axially symmetric complexes are also strongly magnetically anisotropic, and this property can be described with the axial component of the magnetic susceptibility tensor, χa. For triple decker complexes with phthalocyanine based ligands, the Fermi˗contact contribution is small. Hence, together with the axial symmetry, the experimental chemical shifts in 1H and 13C NMR spectra can be modeled easily by considering pseudocontact and orbital shifts alone. This results in the determination of the χa value, which is also responsible for molecular alignment and consequently for the observation of residual dipolar couplings (RDCs). A detailed analysis of the experimental 1H-13C and 1H-1H couplings revealed that contributions from RDCs (positive and negative) and from dynamic frequency shifts (negative for all observed couplings) have to be considered. Whilst the pseudocontact shifts depend on the average positions of 1H and 13C nuclei relative to the lanthanide ions, the RDCs are related to the mobility of nuclei they correspond to. This phenomenon allows for the measurement of the internal mobility of the various groups in the SMMs.

NMR study of the radiation-induced cross-linking of poly(tetrafluoroethylene-co-perfluoromethyl vinyl ether)

The gamma-radiolysis of poly(tetrafluoroethylene-co-perfuoromethyl vinyl ether) (TFE/PMVE) was investigated using solid state F-19 and C-13 NMR spectroscopy. Chain scission products identified in the polymer were saturated chain ends -CF2CF3 (G = 1.0), methyl ether end groups -CF2OCF3 (G = 0.9), acid end groups -CF2COOH (G = 0.5), and a small amount of terminal unsaturation -CF=CF2 (G = 0.2). A mechanism for the formation of these scission products was proposed and the G value for main chain scission, G(S), was determined to be 1.4. Cross-linking of TFE/PMVE was found to proceed via a Y-linking mechanism. The G value for cross-linking, G(X), was determined to be 0.9. A maximum of 0.2 mol % cross-links were formed under the experimental conditions.

Three-dimensional solution structure of alpha-conotoxin MII by NMR spectroscopy: Effects of solution environment on helicity

alpha-Conotoxin MII, a 16-residue polypeptide from the venom of the piscivorous cone snail Conus magus, is a potent and highly specific blocker of mammalian neuronal nicotinic acetylcholine receptors composed of alpha 3 beta 2 subunits. The role of this receptor type in the modulation of neurotransmitter release and its relevance to the problems of addiction and psychosis emphasize the importance of a structural understanding of the mode of interaction of MII with the alpha 3 beta 2 interface. Here we describe the three-dimensional solution structure of MIT determined using 2D H-1 NMR spectroscopy. Structural restraints consisting of 376 interproton distances inferred from NOEs and 12 dihedral restraints derived from spin-spin coupling constants were used as input for simulated annealing calculations and energy minimization in the program X-PLOR. The final set of 20 structures is exceptionally well-defined with mean pairwise rms differences over the whole molecule of 0.07 Angstrom for the backbone atoms and 0.34 Angstrom for all heavy atoms. MII adopts a compact structure incorporating a central segment of alpha-helix and beta-turns at the N- and C-termini. The molecule is stabilized by two disulfide bonds, which provide cross-links between the N-terminus and both the middle and C-terminus of the structure. The susceptibility of the structure to conformational change was examined using several different solvent conditions. While the global fold of MII remains the same, the structure is stabilized in a more hydrophobic environment provided by the addition of acetonitrile or trifluoroethanol to the aqueous solution. The distribution of amino acid side chains in MII creates distinct hydrophobic and polar patches on its surface that may be important for the specific interaction with the alpha 3 beta 2 neuronal nAChR. A comparison of the structure of MII with other neuronal-specific alpha-conotoxins provides insights into their mode of interaction with these receptors.

H-1-NMR structural studies of a cystine-linked peptide containing residues 71-93 of transthyretin and effects of a Ser84 substitution implicated in familial amyloidotic polyneuropathy

The Ile-->Ser84 substitution in the thyroid hormone transport protein transthyretin is one of over 50 variations found to be associated with familial amyloid polyneuropathy, a hereditary type of lethal amyloidosis. Using a peptide analogue of the loop containing residue 84 in transthyretin, we have examined the putative local structural effects of this substitution using H-1-NMR spectroscopy. The peptide, containing residues 71-93 of transthyretin with its termini linked via a disulfide bond, was found to possess the same helix-turn motif as in the corresponding region of the crystallographically derived structure of transthyretin in 20% trifluoroethanol (TFE) solution. It therefore, represents a useful model with which to examine the effects of amyloidogenic substitutions. In a peptide analogue containing the Ile84-->Ser substitution it was found that the substitution does not greatly disrupt the overall three-dimensional structure, but leads to minor local differences at the turn in which residue 84 is involved. Coupling constant and NOE measurements indicate that the helix-turn motif is still present, but differences in chemical shifts and amide-exchange rates reflect a small distortion. This is in keeping with observations that several other mutant forms of transthyretin display similar subunit interactions and those that have been structurally analysed possess a near native structure. We propose that the Ser84 mutation induces only subtle perturbations to the transthyretin structure which predisposes the protein to amyloid formation.

Solution structures by H-1 NMR of the novel cyclic trypsin inhibitor SFTI-1 from sunflower seeds and an acyclic permutant

SFTI-1 is a recently discovered cyclic peptide trypsin inhibitor from sunflower seeds comprising 14 amino acid residues. It is the most potent known Bowman-Birk inhibitor and the only naturally occurring cyclic one. The solution structure of SFTI-1 has been determined by H-1-NMR spectroscopy and compared with a synthetic acyclic permutant. The solution structures of both are remarkably similar. The lowest energy structures from each family of 20 structures of cyclic and acyclic SFTI-1 have an rmsd over the backbone and heavy atoms of 0.29 Angstrom and 0.66 Angstrom, respectively. The structures consist of two short antiparallel beta -strands joined by an extended loop containing the active site at one end. Cyclic SFTI-1 also has a hairpin turn completing the cycle. Both molecules contain particularly stable arrangements of cross-linking hydrogen bonds between the beta -strands and a single disulfide bridge, making them rigid and well defined in solution. These stable arrangements allow both the cyclic and acyclic variants of SFTI-1 to inhibit trypsin with very high potencies (0.5 nM and 12.1 nM, respectively). The cyclic nature of SFTI-1 appears to have evolved to provide higher trypsin inhibition as well as higher stability. The solution structures are similar to the crystal structure of the cyclic inhibitor in complex with trypsin. The lack of a major conformational change upon binding suggests that the structure of SFTI-1 is rigid and already pre-organized for maximal binding due to minimization of entropic losses compared to a more flexible ligand. These properties make SFTI-1 an ideal platform for the design of small peptidic pharmaceuticals or pesticides. (C) 2001 Academic Press.

NMR study of the gamma radiolysis of poly(dimethyl siloxane) under vacuum at 303 K

The structural changes which occur on the gamma -radiolysis of poly(dimethyl siloxane) (PDMS) under vacuum at 303 K have been investigated using Si-29 and C-13 NMR. New structural units consistent with main chain scission and crosslinking through both H-linking and Y-linking reactions have been identified. The results obtained at various absorbed doses have been used to calculate the G-values for scission and crosslinking. G-values for scission of G(S) = 1.3 +/- 0.2, for H-linking of G(D-CH2-R) = 0.34 +/- 0.02 and for Y-Linking of G(Y) = 1.70 +/- 0.09 were obtained for radiolysis under vacuum at 303 K. Thus crosslinking predominates over scission for radiolysis of PDMS under these conditions, and, by contrast with previous studies, Y-links have been shown to be the predominant form of crosslinks. (C) 2001 Elsevier Science Ltd. All rights reserved.

An NMR structural study of nickel-substituted rubredoxin

J Biol Inorg Chem (2010) 15:409–420 DOI 10.1007/s00775-009-0613-6