Weijie Hua

Vibrationally resolved high-resolution NEXAFS and XPS spectra of phenanthrene and coronene

We performed a combined experimental and theoretical study of the C1s Near-Edge X-ray Absorption Fine-Structure (NEXAFS) spectroscopy and X-ray Photoelectron Spectroscopy in the gas phase of two polycyclic aromatic hydrocarbons (phenanthrene and coronene), typically formed in combustion reactions. In the NEXAFS of both molecules, a double-peak structure appears in the C1s → LUMO region, which differ by less than 1 eV in transition energies. The vibronic coupling is found to play an important role in such systems. It leads to weakening of the lower-energy peak and strengthening of the higher-energy one because the 0 - n (n > 0) vibrational progressions of the lower-energy peak appear in nearly the same region of the higher-energy peak. Vibrationally resolved theoretical spectra computed within the Frank-Condon (FC) approximation and linear coupling model agree well with the high-resolution experimental results. We find that FC-active normal modes all correspond to in-plane vibrations.

First-principles study on core-level spectroscopy of arginine in gas and solid phases.

First-principles simulations have been performed for near-edge X-ray absorption fine-structure (NEXAFS) spectra of neutral arginine at different K-edges in the solid phase as well as X-ray photoelectron spectra (XPS) of neutral, deprotonated, and protonated arginines in the gas phase. Influences of the intra- and intermolecular hydrogen bonds (HBs) and different charge states have been carefully examined to obtain useful structure-property relationships. Our calculations show a noticeable difference in the NEXAFS/XPS spectra of the canonical and zwitterionic species that can be used for unambiguously identifying the dominant form in the gas phase. It is found that the deprotonation/protonation always results in red/blue shifts of several electronvolts for the core binding energies (BEs) at all edges. The normal hydrogen bond Y-H···X (X, Y = N, O) can cause a blue/red shift of ca. 1 eV to the core BEs of the proton acceptor X/donor Y, while the weak C-H···Y hydrogen bond may also lead to a weak red shift (less than 1 eV) of the C1s BEs. Moreover, the influence of intermolecular interactions in the solid state is reflected as a broadening in the σ* region of the NEXAFS spectra at each edge, while in the π* region, these interactions lead to a strengthening or weakening of individual transitions from different carbons, although no evident visual change is found in the resolved total spectra. Our results provide a better understanding of the influences of the intra- and intermolecular forces on the electronic structure of arginine.

Refinement of DNA Structures through Near-Edge X-ray Absorption Fine Structure Analysis: Applications on Guanine and Cytosine Nucleobases, Nucleosides, and Nucleotides

In this work we highlight the potential of NEXAFS—near-edge X-ray absorption fine structure—analysis to perform refinements of hydrogen-bond structure in DNA. For this purpose we have carried out first-principle calculations of the N1s NEXAFS spectra of the guanine and cytosine nucleobases and their tautomers, nucleosides, and nucleotides in the gas phase, as well as for five crystal structures of guanine, cytosine, or guanosine. The spectra all clearly show imine (π1*) and amine (π2*) nitrogen absorption bands with a characteristic energy difference (Δ). Among all of the intramolecule covalent connections, the tautomerism of hydrogens makes the largest influence, around ±0.4−0.5 eV change of Δ, to the spectra due to a switch of single−double bonds. Deoxyribose and ribose sugars can cause at most 0.2 eV narrowing of Δ, while the phosphate groups have nearly negligible effects on the spectra. Two kinds of intermolecule interactions are analyzed, the hydrogen bonds and the stacking effect, by comparing “compressed” and “expanded” models or by comparing models including or excluding the nearest stacking molecules. The shortening of hydrogen-bond length by 0.2−0.3 Å can result in the reduction of Δ by 0.2−0.8 eV. This is because the hydrogen bonds make the electrons more delocalized, and the amine and imine nitrogens become less distinguishable. Moreover, the hydrogen bond has a different ability to influence the spectra of different crystals, with guanine crystals as the largest (change by 0.8 eV) and the guanosine crystal as the smallest (change by 0.2 eV). The stacking has negligible effects on the spectra in all studied systems. A comparison of guanosine to guanine crystals shows that the sugars in the crystal could create “blocks” in the π-and hydrogen bonds network of bases and thus makes the imine and amine nitrogens more distinguishable with a larger Δ. Our theoretical calculations offer a good match with experimental findings and explain earlier discrepancies in the NEXAFS analysis.

X-ray spectroscopy of blocked alanine in water solution from supermolecular and supermolecular-continuum solvation models: a first-principles study

The N1s near-edge X-ray absorption fine structure (NEXAFS) and X-ray emission spectra (XES) of blocked alanine in water solution have been investigated at the first-principles level based on cluster models constructed from classical molecular dynamics simulations. The bulk solvent has been described by both supermolecular and combined supermolecular-continuum models. With the former model we show that NEXAFS spectra convergent with respect to system size require at least the inclusion of the second solvation shell and that averaged spectra over several hundreds of snapshots can well represent the statistical effect of different instantaneous configurations of the solvation shells. With the combined model we demonstrate that calculations of a medium-sized peptide-water supermolecule qualitatively predict the NEXAFS spectrum of the solvated peptide even considering a single geometry. Furthermore, sampling over hundreds of snapshots by the combined model, the explicit inclusion of even a few waters yields an averaged spectrum in good quantitative agreement with the discrete model results. In comparison, the XES spectra show little dependence on the structures of either the solvent shell or the peptide itself. The ramifications of these findings are discussed.

Structures of neutral and protonated water clusters confined in predesigned hosts: a quantum mechanical/molecular mechanical study.

Hybrid quantum mechanical/molecular mechanical (QM/MM) calculations have been carried out to investigate the structures of the neutral (H(2)O)(21) and protonated H(+)(H(2)O)(21) clusters confined in the crystal hosts. The influence of other cocrystallized species and the local electrostatic environments of the crystal hosts on the structures of water clusters has been analyzed. For the neutral (H(2)O)(21) cluster in the tetrahedral host, its low-lying structures are found to exist as a dodecahedral cage with one interior water molecule, which is in good accord with the corresponding X-ray data. The confined (H(2)O)(21) cluster possesses the main structural features of the lowest-energy structure of the free (H(2)O)(21) cluster in the gas phase. For the protonated H(+)(H(2)O)(21) cluster confined in the cubic cavity, its low-lying structures are found to have a common hexahedral (H(2)O)(20) shell, which is consistent with the experimental X-ray structure, but the position of the additional H(2)O (or the H(3)O(+) ion) in different low-lying structures is different, while the H(3)O(+) ion is situated at the center of the cage in the corresponding X-ray structure. The overall shape of the confined H(+)(H(2)O)(21) cluster is significantly different from that of the free cluster in the gas phase, and the confined cluster has much less intrinsic hydrogen bonds (H-bonds) than the free cluster, due to the need to form extrinsic H-bonds with acetonitrile molecules in the crystal host. The local electrostatic environment of the crystal host is found to exert a negligible influence on the structure of the (H(2)O)(21) cluster but play a significant role in modulating the structure of the H(+)(H(2)O)(21) cluster. This may be attributed to the fact that the protonated water cluster is much more easily polarized by the external electrostatic field of the crystal host than the neutral water cluster.

Systematic Study of Soft X-ray Spectra of Poly(Dg)·Poly(Dc) and Poly(Da)·Poly(Dt) DNA Duplexes

In the present work, we have undertaken a combined experimental and theoretical study of X-ray spectroscopies for DNA base pairs, more precisely near-edge X-ray absorption, X-ray emission, and resonant inelastic X-ray scattering applied to poly(dG).poly(dC) and poly(dA).poly(dT) DNA duplexes. We have derived several conclusions on the nature of these X-ray spectra: the stacking of pairs has very little influence on the spectra; the spectra of a DNA composed of mixed Watson-Crick base pairs are well reproduced by linear combinations of GC and AT base pairs involved; the amine and imine nitrogens show noticeable differences as building blocks in the absorption, emission, and resonant emission spectra. The calculated spectra are in good agreement with experimental results. The ramifications of these conclusions for the use of X-ray spectroscopy for DNA are discussed.

Monitoring conical intersections in the ring opening of furan by attosecond stimulated X-ray Raman spectroscopy.

Attosecond X-ray pulses are short enough to capture snapshots of molecules undergoing nonadiabatic electron and nuclear dynamics at conical intersections (CoIns). We show that a stimulated Raman probe induced by a combination of an attosecond and a femtosecond pulse has a unique temporal and spectral resolution for probing the nonadiabatic dynamics and detecting the ultrafast (∼4.5 fs) passage through a CoIn. This is demonstrated by a multiconfigurational self-consistent-field study of the dynamics and spectroscopy of the furan ring-opening reaction. Trajectories generated by surface hopping simulations were used to predict Attosecond Stimulated X-ray Raman Spectroscopy signals at reactant and product structures as well as representative snapshots along the conical intersection seam. The signals are highly sensitive to the changes in nonadiabatically coupled electronic structure and geometry.

Mechanistic Insight on the Diels–Alder Reaction Catalyzed by a Self-Assembled Molecular Capsule

We combined Monte Carlo simulations and density functional theory calculations to study the mechanism of the Diels-Alder reaction of p-quinone and cyclohexadiene catalyzed by a self-assembled molecular capsule. Our calculations show that the encapsulation of the reactants into the cage is driven by hydrogen-bonding interactions and π-π stacking interactions between two reactants and the capsule. The encapsulated Diels-Alder reaction at different locations inside the capsule may have quite different reactivity due to different guest-host interactions. A comparison of the free energy profiles of the Diels-Alder reaction in the capsule and in the bulk solution reveals that the Diels-Alder reaction in the capsule is accelerated because the host-guest interaction leads to a relatively smaller barrier for the cycloaddition step.

Multidimensional resonant nonlinear spectroscopy with coherent broadband x-ray pulses

New x-ray free electron laser (XFEL) and high harmonic generation (HHG) light sources are capable of generating short and intense pulses that make x-ray nonlinear spectroscopy possible. Multidimens ...

Nonlinear Spectroscopy of Core and Valence Excitations Using Short X-Ray Pulses: Simulation Challenges.

Measuring the nonlinear response of electrons and nuclei to attosecond broadband X-ray radiation has become possible by newly developed free electron lasers and high harmonic generation light sources. The design and interpretation of these novel experiments poses considerable computational challenges. In this chapter we survey the basic description of nonlinear X-ray spectroscopy signals and the electronic structure protocols which may be used for their simulation.