| 1. |
- Hua, Shugui, et al.
(författare)
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An Efficient Implementation of the Generalized Energy-Based Fragmentation Approach for General Large Molecules
- 2010
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Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 114:31, s. 8126-8134
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Tidskriftsartikel (refereegranskat)abstract
- An efficient implementation of the generalized energy-based fragmentation (GEBF) approach (Li, W.; Li, S.; Jiang, Y. J Phys. Chem. A 2007, 111, 2193) for treating a wide range of large molecules is presented. In this implementation, the fragmentation process can be automatically done for a general molecule, with only some functional groups defined by users. A new and fast scheme is designed for the generation of various subsystems and the derivation of their coefficients. The newly implemented GEBF approach has been applied to several large molecules including proteins, nucleic acids, and supermolecules with fused aromatic rings. Test calculations within the Hartree-Fock (HF) and density functional theory (DFT) framework demonstrate that the GEBF approach can provide reasonably accurate ground-state energies and optimized structures, which are in good agreement with those from conventional HF or DFT calculations. The GEBF approach implemented in this work can now be employed by nonexpert users to compute energies, optimized structures, and some molecular properties at various ab initio levels for a broad range of large molecules on ordinary PC workstations.
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| 2. |
- Bennett, Kochise, et al.
(författare)
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Multidimensional resonant nonlinear spectroscopy with coherent broadband x-ray pulses
- 2016
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Ingår i: Physica Scripta. - : IOP PUBLISHING LTD. - 0031-8949 .- 1402-4896. ; T169
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Tidskriftsartikel (refereegranskat)abstract
- 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. Multidimensional spectroscopic techniques, which have long been used in the nuclear magnetic resonance, infrared, and optical regimes to probe the electronic structure and nuclear dynamics of molecules by sequences of short pulses with variable delays, can thus be extended to the attosecond x-ray regime. This opens up the possibility of probing core-electronic structure and couplings, the real-time tracking of impulsively created valence-electronic wavepackets and electronic coherences, and monitoring ultrafast processes such as nonadiabatic electron-nuclear dynamics near conical-intersection crossings. We survey various possible types of multidimensional x-ray spectroscopy techniques and demonstrate the novel information they can provide about molecules.
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| 3. |
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| 4. |
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| 5. |
- Cheng, Xiao, et al.
(författare)
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Vibrationally-Resolved X-ray Photoelectron Spectra of Six Polycyclic Aromatic Hydrocarbons from First-Principles Simulations
- 2022
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Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 126:33, s. 5582-5593
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Tidskriftsartikel (refereegranskat)abstract
- Vibrationally resolved C 1s X-ray photoelectron spectra (XPS) of a series of six polycyclic aromatic hydrocarbons (PAHs; phenanthrene, coronene, naphthalene, anthracene, tetracene, and pentacene) were computed by combining the full core hole density functional theory and the Franck–Condon simulations with the inclusion of the Duschinsky rotation effect. Simulated spectra of phenanthrene, coronene, and naphthalene agree well with experiments both in core binding energies (BEs) and profiles, which validate the accuracy of our predictions for the rest molecules with no high-resolution experiments. We found that three types of carbons i (inner C), p (peripheral C bonded to three C atoms), and h (peripheral C bonded to an H atom) show decreasing BEs. In linear PAHs (the latter four), h-type carbons further split into h1 or h2 (on inner or edge benzene ring) subtypes with chemical shifts of ca. 0.2–0.4 eV. All major Franck–Condon-active modes are characterized to be in-plane vibrations: low-frequency (<800 cm–1) C–C ring deformation modes play an essential role in determining the peak asymmetries; and for each h-type carbon a high-frequency (ca. 3600 cm–1) C*–H stretching mode is responsible for the high-energy tail. We found that core ionization leads to reduction of all C*–C and C*–H bond lengths and ring deformation with a definite direction. Based on theoretical spectra of four linear PAHs, we found asymptotic relations and anticipated possible spectral features for even larger linear PAHs. Our calculations provide accurate reference spectra for XPS characterizations of PAHs, which are useful in understanding the vibronic coupling effects in this family.
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| 6. |
- Fronzoni, Giovanna, et al.
(författare)
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Vibrationally resolved high-resolution NEXAFS and XPS spectra of phenanthrene and coronene
- 2014
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 141:4, s. 044313-
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 7. |
- Hua, Weijie, et al.
(författare)
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Fe L-Edge X-ray Absorption Spectra of Fe(II) Polypyridyl Spin Crossover Complexes from Time-Dependent Density Functional Theory
- 2013
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Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 117:51, s. 14075-14085
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Tidskriftsartikel (refereegranskat)abstract
- L-edge near-edge X-ray fine structure spectroscopy (NEXAFS) has become a powerful tool to study the electronic structure and dynamics of metallo-organic and biological compounds in solution. Here, we present a series of density functional theory calculations of Fe L-edge NEXAFS for spin crossover (SCO) complexes within the time-dependent framework. Several key factors that control the L-edge excitations have been carefully examined using an Fe(II) polypyridyl complex [Fe(tren(py)(3))](2+) (where tren(py)(3) = tris(2-pyridylmethyliminoethyl)amine) as a model system. It is found that the electronic spectra of the low-spin (LS, singlet), intermediate-spin (IS, triplet), and high-spin (HS, quintet) states have distinct profiles. The relative energy positions, but not the spectral profiles, of different spin states are sensitive to the choice of the functionals. The inclusion of the vibronic coupling leads to almost no visible change in the resulting NEXAFS spectra because it is governed only by low-frequency modes of less than 500 cm(-1). With the help of the molecular dynamics sampling in acetonitrile at 300 K, our calculations reveal that the thermal motion can lead to a noticeable broadening of the spectra. The main peak position is strongly associated with the length of the Fe-N bond.
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| 8. |
- Hua, Weijie, et al.
(författare)
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First-Principles Simulation of Soft X-Ray Spectroscopy
- 2012
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Ingår i: Huaxue jinzhan. - 1005-281X. ; 24:6, s. 964-980
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Tidskriftsartikel (refereegranskat)abstract
- Soft x-ray spectroscopy represents a category of instrumental techniques to effectively probe the electronic and chemical structure of molecules, surfaces, and a variety of complexes by core excitations or de-excitations. The basic computational methods, based on the density functional theory, for different absorption and emission processes are reviewed in this paper. Special attention has been paid to the practical implementations and applications of different methods. Details on the simulations of commonly used K-edge x-ray photoelectron, absorption, and emission spectra for a wide range of illustrative examples including molecules, fullerenes, carbon nanotubes, graphenes and DNA, are provided.
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| 9. |
- Hua, Weijie
(författare)
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MCNOX : A code for computing and interpreting ultrafast nonlinear X-ray spectra of molecules at the multiconfigurational level
- 2024
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Ingår i: Computer Physics Communications. - : Elsevier BV. - 0010-4655 .- 1879-2944. ; 296
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Tidskriftsartikel (refereegranskat)abstract
- This work describes a program for computing and analyzing the ultrafast (attosecond and femtosecond) nonlinear X-ray spectra of molecules at the multiconfigurational quantum chemistry level, called MCNOX. It is aimed at cutting-edge current and future photochemistry/photophysics applications enabled by X-ray free-electron lasers and high harmonic generation light sources. It can compute steady-state X-ray absorption spectroscopy (XAS) and three types of ultrafast nonlinear X-ray spectra: transient XAS, all-X-ray four-wave mixing, and stimulated Raman spectra. It is especially capable of picking out major electronic transitions, and further computing the natural transition orbitals for these transitions, which help finally yield the physical and chemical insights from complex signals. Following a research paradigm of "electronic structure-*molecular dynamics-*signal", in this paper, methods for the former two steps are reviewed, and then the theory, implementations, and technical details for signal simulations are presented along illustrative examples on uracil.
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| 10. |
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| 11. |
- Hua, Weijie, et al.
(författare)
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Refinement of DNA Structures through Near-Edge X-ray Absorption Fine Structure Analysis : Applications on Guanine and Cytosine Nucleobases, Nucleosides, and Nucleotides
- 2010
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 114:41, s. 13214-13222
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Tidskriftsartikel (refereegranskat)abstract
- 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 (pi*(1)) and amine (pi*(2)) nitrogen absorption bands with a characteristic energy difference (Delta). Among all of the intramolecule covalent connections, the tautomerism of hydrogens makes the largest influence, around +/- 0.4-0.5 eV change of Delta, to the spectra due to a switch of single-double bonds. Deoxyribose and ribose sugars can cause at most 0.2 eV narrowing of Delta, 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 angstrom can result in the reduction of Delta 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 pi-and hydrogen bonds network of bases and thus makes the imine and amine nitrogens More distinguishable with a larger Delta. Our theoretical calculations offer a good match with experimental findings and explain earlier discrepancies in the NEXAFS analysis.
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| 12. |
- Hua, Weijie
(författare)
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Structure and spectroscopy of bio- and nano-materials from first-principles simulations
- 2011
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- This thesis is devoted to first-principles simulations of bio- and nano-materials,focusing on various soft x-ray spectra, ground-state energies and structures of isolated largemolecules, bulk materials, and small molecules in ambient solutions. K-edge near-edge x-ray absorption fine structure (NEXAFS) spectra, x-ray emission spectra, andresonant inelastic x-ray scattering spectra of DNA duplexes have been studied by means oftheoretical calculations at the density functional theory level. By comparing a sequence of DNAduplexes with increasing length, we have found that the stacking effect of base pairs has verysmall influence on all kinds of spectra, and suggested that the spectra of a general DNA can bewell reproduced by linear combinations of composed base pairs weighted by their ratio. The NEXAFS spectra study has been extended to other realistic systems. We have used cluster modelswith increasing sizes to represent the infinite crystals of nucleobases and nucleosides, infinitegraphene sheet, as well as a short peptide in water solution. And the equivalent core holeapproximation has been extensively adopted, which provides an efficient access to these largesystems. We have investigated the influence of external perturbations on the nitrogen NEXAFSspectra of guanine, cytosine, and guanosine crystals, and clarified early discrepancies betweenexperimental and calculated spectra. The effects of size, stacking, edge, and defects to theabsorption spectra of graphene have been systematically analyzed, and the debate on theinterpretation of the new feature has been resolved. We have illustrated the influence of watersolvent to a blocked alanine molecule by using the snapshots generated from molecular dynamics. Multi-scale computational study on four short peptides in a self-assembled cage is presented. It isshown that the conformation of a peptide within the cage does not corresponds to its lowest-energyconformation in vacuum, due to the Zn-O bond formed between the peptide and the cage, and theconfinement effect of the cage. Special emphasis has been paid on a linear-scaling method, the generalized energy basedfragmentation energy (GEBF) approach. We have derived the GEBF energy equation at the Hartree-Focklevel with the Born approximation of the electrostatic potential. Numerical calculations for amodel system have explained the accuracy of the GEBF equation and provides a starting point forfurther refinements. We have also presented an automatic and efficient implementation of the GEBFapproach which is applicable for general large molecules.
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| 13. |
- Hua, Weijie, et al.
(författare)
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Study of double core hole excitations in molecules by X-ray double-quantum-coherence signals : a multi-configuration simulation
- 2016
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Ingår i: Chemical Science. - : Royal Society of Chemistry. - 2041-6520 .- 2041-6539. ; 7:9, s. 5922-5933
-
Tidskriftsartikel (refereegranskat)abstract
- The multi-configurational self-consistent field method is employed to simulate the two-dimensional all-X-ray double-quantum-coherence (XDQC) spectroscopy, a four-wave mixing signal that provides direct signatures of double core hole (DCH) states. The valence electronic structure is probed by capturing the correlation between the single (SCH) and double core hole states. The state-averaged restricted-activespace self-consistent field (SA-RASSCF) approach is used which can treat the valence, SCH, and DCH states at the same theoretical level, and applies to all types of DCHs (located on one or two atoms, K-edge or L-edge), with both accuracy and efficiency. Orbital relaxation introduced by the core hole(s) and the static electron correlation is properly accounted for. The XDQC process can take place via different intermediate DCH state channels by tuning the pulse frequencies. We simulate the XDQC signals for the three isomers of aminophenol at 8 pulse frequency configurations, covering all DCH pathways involving the N1s and O1s core hole (N1sN1s, O1sO1s and N1sO1s), which reveal different patterns of valence excitations.
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| 14. |
- Hua, Weijie, et al.
(författare)
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Systematic Study of Soft X-ray Spectra of Poly(Dg)center dot Poly(Dc) and Poly(Da)center dot Poly(Dt) DNA Duplexes
- 2010
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 114:20, s. 7016-7021
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Tidskriftsartikel (refereegranskat)abstract
- 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)center dot poly(dC) and poly(dA)center dot 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.
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| 15. |
- Hua, Weijie, et al.
(författare)
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Transient X-ray Absorption Spectral Fingerprints of the S1 Dark State in Uracil
- 2019
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Ingår i: The Journal of Physical Chemistry Letters. - : American Chemical Society (ACS). - 1948-7185. ; 10:22, s. 7172-7178
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Tidskriftsartikel (refereegranskat)abstract
- Low-lying dark nÏ€∗ states play an important role in many photophysical and photochemical processes of organic chromophores. Transient X-ray absorption spectroscopy (TXAS) provides a powerful technique for probing the dynamics of valence states by exciting the electrons into high-lying core excited states. We employ multiconfigurational self-consistent field calculations to investigate the TXAS of uracil along its nonradiative photodecay pathways. An open issue is whether dark nÏ€∗ state S1 (n is the lone pair localized on an oxygen atom) is accessible when bright ππ∗ state S2 is selectively excited. Vertical core excitations were calculated along the potential energy surfaces of the three lowest states, S0-S2, interpolated between two minima and two minimum-energy conical intersections. Computed TXAS data from the C, N, and O K edges show distinct spectral fingerprints of the dark state in all spectral regimes. At the O 1s edge, the nÏ€∗ state has a very strong absorption at 526-527 eV, while at the C (N) 1s edge, by contrast, there is almost zero (very weak) absorption at 279-282 eV (397-398 eV). All K-edge spectra can be used to sensitively detect the dark states. Our proposed O 1s feature has already been observed in a recent TXAS experiment with thymine. Natural transition orbital analysis is used to interpret all dominant features of the three lowest-valence states along the reaction coordinate and reveal some important valence fine-structure information from the core excitation.
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| 16. |
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| 17. |
- Hua, Weijie, et al.
(författare)
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Understanding the Influence of Guest-Host Interactions on the Conformation of Short Peptides in a Hydrophobic Cavity : A Computational Study
- 2011
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Ingår i: ChemPhysChem. - : Wiley. - 1439-4235 .- 1439-7641. ; 12:7, s. 1325-1333
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Tidskriftsartikel (refereegranskat)abstract
- We performed a computational investigation to understand the conformational preferences of four short peptides in a self-assembled cage based on the experimental work by Y. Hatakeyama et al. (Angew. Chem. Int. Ed. 2009, 48, 8695). For this purpose, we combined molecular dynamics simulations, Monte Carlo simulations, and quantum mechanical calculations to obtain energies and structures for several low-lying conformers of four peptides and the corresponding peptide-cage inclusion complexes. Our calculations at both B3LYP and MP2 levels show that for each peptide, the corresponding conformation within the host (as revealed by the crystal structure) does not represent the lowest-energy conformation of this peptide in vacuum. By comparing some low-lying conformers in vacuum and in the cavity (for the same peptide), we found that the cage has a significant influence on the conformational propensities of peptides. First, one carbonyl oxygen of each peptide tends to bind to one Zn (II) atom of the cage, forming a Zn-O bond. The formation of this bond leads to significant charge transfer from the cage to the peptide. Second, this Zn-O bond causes the peptide to go through some local conformational changes. For larger peptides, such as penta-and hexapeptides, our calculations also show that some of their conformers must undergo significant structural changes, due to the confinement of the host. This computational study reveals the noticeable influence of the guest-host interaction on the conformational preferences of short peptides.
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| 18. |
- Hua, Weijie, et al.
(författare)
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X-ray absorption spectra of graphene from first-principles simulations
- 2010
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Ingår i: Physical Review B. Condensed Matter and Materials Physics. - 1098-0121 .- 1550-235X. ; 82:15, s. 155433-
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Tidskriftsartikel (refereegranskat)abstract
- Near edge x-ray absorption fine-structure spectra of graphenes are calculated using hybrid density-functional theory with the equivalent core hole approximation, aiming to resolve the ongoing debate on the interpretation of corresponding experimental spectra. Effects of size, stacking, edges, and defects on the spectra have been analyzed in detail for both C 1s-pi* and C 1s-sigma* transitions. The infinite graphene sheet has been modeled by graphene nanoribbons of different size. The size dependence and convergence of the spectra have been revealed. It is found that the pi-pi interaction between layers have mainly effects on the C 1s-pi* transitions in two different energy regions. The stacking effect smears out the double-peaks structure of the first main pi* peak around 285 eV and results in blueshift of the second pi* structure by almost 2 eV. The calculations show that the pi spectrum of hydrogen saturated edge carbons is redshifted with respect to the central ones and that a new weak sigma* peak around 288 eV appears. The presence of defects can also introduce new spectral features in both pi and sigma regions.
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| 19. |
- Hua, Weijie, et al.
(författare)
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X-ray spectroscopy of blocked alanine in water solution from supermolecular and supermolecular-continuum solvation models : a first-principles study
- 2012
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Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry (RSC). - 1463-9076 .- 1463-9084. ; 14:27, s. 9666-9675
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Tidskriftsartikel (refereegranskat)abstract
- 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
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| 20. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Forskningsöversikt (refereegranskat)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 21. |
- Li, Hongbao, et al.
(författare)
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First-Principles Study on Core-Level Spectroscopy of Arginine in Gas and Solid Phases
- 2012
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 116:42, s. 12641-12650
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Tidskriftsartikel (refereegranskat)abstract
- 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 center dot center dot center dot 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 center dot center dot center dot 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 sigma* region of the NEXAFS spectra at each edge, while in the pi* 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.
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| 22. |
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| 23. |
- Li, Xin, et al.
(författare)
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Effects of domain size on x-ray absorption spectra of boron nitride doped graphenes
- 2016
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Ingår i: Applied Physics Letters. - : American Institute of Physics (AIP). - 0003-6951 .- 1077-3118. ; 109:8
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Tidskriftsartikel (refereegranskat)abstract
- Doping is an efficient way to open the zero band gap of graphene. The control of the dopant domain size allows us to tailor the electronic structure and the properties of the graphene. We have studied the electronic structure of boron nitride doped graphenes with different domain sizes by simulating their near-edge X-ray absorption fine structure (NEXAFS) spectra at the N K-edge. Six different doping configurations (five quantum dot type and one phase-separated zigzag-edged type) were chosen, and N K-edge NEXAFS spectra were calculated with large truncated cluster models by using the density functional theory with hybrid functional and the equivalent core hole approximation. The opening of the band gap as a function of the domain size is revealed. We found that nitrogens in the dopant boundary contribute a weaker, red-shifted pi* peak in the spectra as compared to those in the dopant domain center. The shift is related to the fact that these interfacial nitrogens dominate the lowest conduction band of the system. Upon increasing the domain size, the ratio of interfacial atom decreases, which leads to a blue shift of the pi* peak in the total NEXAFS spectra. The spectral evolution agrees well with experiments measured at different BN-dopant concentrations and approaches to that of a pristine h-BN sheet.
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| 24. |
- Li, Xin, et al.
(författare)
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Electronic Structure of Nitrogen-Doped Graphene in the Ground and Core-Excited States from First-Principles Simulations
- 2015
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Ingår i: The Journal of Physical Chemistry C. - : American Chemical Society (ACS). - 1932-7447 .- 1932-7455. ; 119:29, s. 16660-16666
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Tidskriftsartikel (refereegranskat)abstract
- We have calculated the N 1s near-edge X-ray absorption fine structure (NEXAFS) spectra of nitrogen-doped monolayer graphene (NG) using density functional theory (DFT) with the equivalent core hole approximation. The hexavacancy (6V) defect and its dependence on the nitrogen-doping concentration have been analyzed in detail via both N 1s -> pi* and N 1s -> sigma* transitions. The NEXAFS spectra are sensitive to the doping concentration of N in the pi* region: diluted doping weakens the main pi* peak and smears the oscillations in this region. The vacancy defect leads to a red-shift in both the pi and sigma spectra. A pyridinic nitrogen at the 6V defect center exhibits a sharp pi* peak at 398.4 eV, which agrees well with the experimental pre-edge structure at 398.6 eV. The sigma* peak is split in two, which can serve as the fingerprint to reveal the nature of the defect. A structural change from pyridinic to pyrrolic NG results in a distinctive difference in the spectral shape. The ground-state band structure has also been simulated at the DFT level with periodic boundary conditions. Similar profiles are found in the N 2p projected density of states above the Fermi level and in the N 1s NEXAFS spectra.
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| 25. |
- Lindblad, Rebecka, Dr, 1984-, et al.
(författare)
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Experimental and theoretical near-edge x-ray-absorption fine-structure studies of NO
- 2022
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Ingår i: Physical Review A: covering atomic, molecular, and optical physics and quantum information. - : American Physical Society. - 2469-9926 .- 2469-9934. ; 106:4
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Tidskriftsartikel (refereegranskat)abstract
- Experimental near-edge x-ray-absorption fine-structure (NEXAFS) spectra of the nitrosonium NO+ ion are presented and theoretically analyzed. While neutral NO has an open shell, the cation is a closed-shell species, which for NEXAFS leads to the simplicity of a closed-shell spectrum. Compared to neutral NO, the electrons in the cation experience a stronger Coulomb potential, which introduces a shift of the ionization potential towards higher energies, a depletion of intensity in a large interval above the pi* resonance, and a shift of the sigma* resonance from the continuum to below the ionization threshold. NEXAFS features at the nitrogen and oxygen K edges of NO+ are compared, as well as NEXAFS features at the nitrogen edges of the isoelectronic closed-shell species NO+, N2, and N2H+.
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