Effects Of Large-amplitude Motion Research Articles

Benchmark Theoretical and Experimental Study on (15)N NMR Shifts of Oxidatively Damaged Guanine.

The (15)N NMR shifts of 9-ethyl-8-oxoguanine (OG) were calculated and measured in liquid DMSO and in crystal. The OG molecule is a model for oxidatively damaged 2'-deoxyguanosine that occurs owing to oxidative stress in cell. The DNA lesion is repaired with human 8-oxoguanine glycosylase 1 (hOGG1) base-excision repair enzyme, however, the exact mechanism of excision of damaged nucleobase with hOGG1 is currently unknown. This benchmark study on (15)N NMR shifts of OG aims their accurate structural interpretation and calibration of the calculation protocol utilizable in future studies on mechanism of hOGG1 enzyme. The effects of NMR reference, DFT functional, basis set, solvent, structure, and dynamics on calculated (15)N NMR shifts were first evaluated for OG in crystal to calibrate the best performing calculation method. The effect of large-amplitude motions on (15)N NMR shifts of OG in liquid was calculated employing molecular dynamics. The B3LYP method with Iglo-III basis used for B3LYP optimized geometry with 6-311++G(d,p) basis and including effects of solvent and molecular dynamic was the calculation protocol used for calculation of (15)N NMR shifts of OG. The NMR shift of N9 nitrogen of OG was particularly studied because the atom is involved in an N-glycosidic bond that is cleaved with hOGG1. The change of N9 NMR shift owing to oxidation of 9-ethylguanine (G) measured in liquid was -27.1 ppm. The calculated N9 NMR shift of OG deviated from experiment in crystal and in liquid by 0.45 and 0.65 ppm, respectively. The calculated change of N9 NMR shift owing to notable N9-pyramidalization of OG in one previously found polymorph was 20.53 ppm. We therefore assume that the pyramidal geometry of N9 nitrogen that could occur for damaged DNA within hOGG1 catalytic site might be detectable with (15)N NMR spectroscopy. The calculation protocol can be used for accurate structural interpretation of (15)N NMR shifts of oxidatively damaged guanine DNA residue.

The effect of large amplitude motions on the vibrational intensities in hydrogen bonded complexes.

We have developed a model to calculate accurately the intensity of the hydrogen bonded XH-stretching vibrational transition in hydrogen bonded complexes. In the Local Mode Perturbation Theory (LMPT) model, the unperturbed system is described by a local mode (LM) model, which is perturbed by the intermolecular modes of the hydrogen bonded system that couple with the intramolecular vibrations of the donor unit through the potential energy surface. We have applied the model to three complexes containing water as the donor unit and different acceptor units, providing a series of increasing complex binding energy: H2O⋯N2, H2O⋯H2O, and H2O⋯NH3. Results obtained by the LMPT model are presented and compared with calculated results obtained by other vibrational models and with previous results from gas-phase and helium-droplet experiments. We find that the LMPT model reduces the oscillator strengths of the fundamental hydrogen bonded OH-stretching transition relative to the simpler LM model.

Importance of C*-H based modes and large amplitude motion effects in vibrational circular dichroism spectra: the case of the chiral adduct of dimethyl fumarate and anthracene.

The role played by the C*-H based modes (C* being the chiral carbon atom) and the large amplitude motions in the vibrational absorption (VA) and vibrational circular dichroism (VCD) spectra is investigated. The example of an adduct of dimethyl fumarate and anthracene, i.e., dimethyl-(+)-(11R,12R)-9,10-dihydro-9,10-ethanoanthracene-11,12-dicarboxylate, and two deuterated isotopomers thereof specially synthesized for this goal, are considered. By comparing the experimental and DFT calculated spectra of the undeuterated and deuterated species, we demonstrate that the C*-H bending, rocking, and stretching modes in the VA and VCD spectra are clearly identified in well defined spectroscopic features. Further, significant information about the conformer distribution is gathered by analyzing the VA and VCD data of both the fingerprint and the C-H stretching regions, with particular attention paid to the band shape data. Effects related to the large amplitude motions of the two methoxy moieties have been simulated by performing linear transit (LT) calculations, which consists of varying systematically the relative positions of the two methoxy moieties and calculating VCD spectra for the partially optimized structures obtained in this way. The LT method allows one to improve the quality of calculated spectra, as compared to experimental results, especially in regard to relative intensities and bandwidths.

The effect of large amplitude motions on the transition frequency redshift in hydrogen bonded complexes: a physical picture.

We describe the vibrational transitions of the donor unit in water dimer with an approach that is based on a three-dimensional local mode model. We perform a perturbative treatment of the intermolecular vibrational modes to improve the transition wavenumber of the hydrogen bonded OH-stretching transition. The model accurately predicts the transition wavenumbers of the vibrations in water dimer compared to experimental values and provides a physical picture that explains the redshift of the hydrogen bonded OH-oscillator. We find that it is unnecessary to include all six intermolecular modes in the vibrational model and that their effect can, to a good approximation, be computed using a potential energy surface calculated at a lower level electronic structure method than that used for the unperturbed model.

A pass too far: dissociation of internal energy selected paracyclophane cations, theory and experiment

The vacuum ultraviolet (VUV) photoionization and dissociative photoionization of three hydroxy-substituted [2.2]paracyclophane derivatives were studied yielding adiabatic ionization energies and dissociative photoionization energies (appearance energies). The simplest dissociation pathway is the breaking of both CH(2)-CH(2) bridge units and fragmenting the molecular ion in half to yield xylylene neutral and cationic fragments. The experimental data show that this process is outcompeted by a faster, higher energy channel, possibly yielding cyclooctatetraene derivatives. The role of the reaction coordinate, the effect of large amplitude motions on the density of states function at low and high energies and the temperature dependent 'population gap' in the internal energy distribution in large molecules are discussed in the context of applying statistical models to the dissociation. Computational approaches to the binding energy of paracyclophanes are marred with pitfalls. Noncovalent interactions play a major role in keeping paracyclophanes bound by some 200 kJ mol(-1) with respect to the two xylylene motifs, and the covalent CH(2)-CH(2) bonds are mostly counteracted by the geometric strain. The stabilizing effects are twofold: first, paracyclophanes are aromatic compounds, whereas xylylenes are not. Thus, the aromaticity of the molecule is induced by dimerization. Second, dispersive π-π interactions also stabilize the molecule. We evaluated 23 different computational chemistry approaches, and found that very few of the favorably scaling ones give an adequate description of this system. Among the DFT functionals tested, only PBE-D3 and perhaps M06-2X yielded consistently accurate results, comparable with MP3 and CCSD, or the G4 and CBS-QB3 composite methods. MP2 results in general suffer from significant overbonding.

A code for analysis of the fine structure in near-rigid weakly-bonded open-shell complexes that consist of a diatomic radical in a [formula omitted] state and a closed-shell molecule

A code for analysis of the fine structure in near-rigid weakly-bonded open-shell complexes that consist of a diatomic radical in a [formula omitted] state and a closed-shell molecule

μ-H-Bridged Bicyclo[3.3.3]undecyl Cations. Theoretical Calculations of Physical and Chemical Properties

μ-H-Bridged carbocations 1 and 2, which are still unknown experimentally, are structures with fascinating possibilities as intermediates for the synthesis of very strained in-bicyclic and tricyclic alkanes and alkenes. They are also expected to possess record high pKa values. In conjunction with our experimental program to try to prepare 1 and 2, we have carried out ab initio calculations on these structures and various reference compounds, with the aim of assessing just how stable these cations might be, and what physical and chemical properties they might possess. The results of these studies confirm that 1 and 2 should be viable species; they have energies similar to those of the conventional out-cations, and the μ-H bond distances are not very different from those calculated for known μ-H cations. The calculated 1H NMR chemical shift for the mu-H of 1 is –12 ± 0.5 and –9.5 ± 0.5 for 2, both values considerably more negative than in known μ-H cations. The possible effect of large amplitude motions of the μ-H on the 1H NMR chemical shift was investigated and not found to be significant. The pKas for 1 and 2 are estimated to be 17-18 with respect to an alkene conjugate base, a virtually unimaginable size for a formally alkyl cation. The paper also discusses the possibility of the μ-H being involved in the acid-conjugate base chemistry, since this is shown to be a hugely exothermic reaction. Finally, the alkenes and alkanes associated with cations 1 and 2 have been calculated, the in-alkene 7 from cation 1 is shown, for example, to possess a large steric strain, yet this structure should be accessible via deprotonation of 1 with a strong base.

Large-amplitude vibrations and their effects on lowering onset of intramolecular vibrational redistribution in jet-cooled N-methylaniline

Laser-induced fluorescence (LIF) spectroscopy of isolated jet-cooled N-methylaniline (NMA) is reported in detail for the first time. The low-frequency, large-amplitude vibrations involving internal methyl rotation, N–aryl torsion and inversion of the methylamino NHCH3 group have been examined especially and their potential barrier heights determined. We present two hypotheses to describe the behaviour of the lone pair of electrons on the nitrogen atom in the methylamino group and to explain the conjugation between the nitrogen lone pair and methyl group as well as the benzene ring system from which the observed spectra are well interpreted and the geometry of the molecule determined. A link between changes in the torsional potential and π-electron density on the methyl group and the effect of large-amplitude motions on relaxation processes such as intramolecular vibrational redistribution (IVR) is illustrated. A rather low onset of IVR has been observed, which is mainly attributed to the activity of the methylated amino group.