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A complex polarization propagator approach has been developed to third order and implemented in density functional theory (DFT), allowing for the direct calculation of nonlinear molecular properties in the X-ray wavelength regime without explicitly addressing the excited-state manifold. We demonstrate the utility of this propagator method for the modeling of coherent near-edge X-ray two-photon absorption using, as an example, DFT as the underlying electronic structure model. Results are compared with the corresponding near edge X-ray absorption fine structure spectra, illuminating the differences in the role of symmetry, localization, and correlation between the two spectroscopies. The ramifications of this new technique for nonlinear X-ray research are briefly discussed., QC 20160707

A successful elucidation of the near-ultraviolet electronic circular dichroism spectrum of a short double-stranded DNA is reported. Time-dependent density functional theory methods are shown to accurately predict spectra and assign bands on the microscopic base-pair scale, a finding that opens the field for using circular dichroism spectroscopy as a sensitive nanoscale probe of DNA to reveal its complex interactions with the environment., Funding Agencies|Swedish Research Council [621-2014-4646]; FNRS (Belgium) [2.4615.11-BINDER]

We present a computational study of the Magnetic circular dichroism (MCD) spectra in the 200-300 nm wavelength region of purine and its derivative hypoxanthine, as well as of the pyrimidine bases of nucleic acids uracil,thymine, and cytosine, Using the B3LYP and CAM-B3LYP functionals. Solvent effects, are investigated within the polarizable continuum model and by inclusion of explicit water molecules. In, general; the computed spectra are found to be in good agreement with the experimental ones, aprt from some overall blue shifts. Both the pseudo-A term shape of the MCD spectra of the purines and the B term shape of the spectra of pyrimidine base are reproduced. Our calculations also correctly reproduce the reversed phase of the MCD bands in purine compared to,that of its derivatives present in nucleic acids. Solvent effects are sizable and system specific,but they do not in general alter the qualitative shape of the spectra. The bands are dominated the-bright pi -greater than pi* transitions; and our calculations in solution nicely reproduce theft energy differences, improving the estimates obtained in the gas phase. Shoulders are predicted for purine and uracil due to n -greater than pi* excitations, but they are too weak to be observed in the. experiment., Funding Agencies|PRIN [2010ERFKXL_008]; University of Trieste [CHIM02-Ricerca]

The first-order hyperpolarizability, beta, has been calculated for a group Of marine natural products, the makaluvamines. These compounds possess a common Cationic pyrroloiminoquinone structure that is substituted to varying degrees. Calculations at the MP2 level indicate that makaluvamines possessing phenolic side Chains conjugated with the pyrroloiminoquinone moiety display large beta values, while breaking this conjugation leads to a dramatic decrease in the calculated hyperpolarizability. This is consistent with a charge-transfer donor-pi-acceptor (D-pi-A) structure type, characteristic of nonlinear optical Chromophores. Dynamic hyperpolarizabilities calculated using resonance-convergent time-dependent density functional theory coupled to polarizable continuum model (PCM) solvation suggest that significant resonance, enhancement, effects can be expected for incident radiation with wavelengths around 800 nm. The results of the current Work suggest that the pyrroloiminoquinone moiety represents a potentially useful new Chromophore subunit, in particular for the development of molecular probes for biological imaging. The introduction of solvent solute interactions in the theory is conventionally made in a density matrix formalism, and the Present work will provide detailed account of the approximations that need to be introduced in wave function theory, and our program implementation. The program implementation as such is achieved by a mere combination of existing modules from previous developments, and it is here only briefly reviewed., Funding Agencies|Swedish Research Council [621-2010-5014]; Portuguese Foundation for Science and Technology [PTDC/FIS/103587/2008]; Donostia International Physics centre; Centre de Fisica de Materiales, University of the Basque Country

Ultraviolet and X-ray photoelectron spectroscopies in combination with density functional theory (DFT) calculations were used to study the change in the work function (Phi) of graphene, supported by quartz, as induced by adsorption of hexaazatriphenylene-hexacarbonitrile (HATCN). Near edge X-ray absorption fine structure spectroscopy (NEXAFS) and DFT modeling show that a molecular-density-dependent reorientation of HATCN from a planar to a vertically inclined adsorption geometry occurs upon increasing surface coverage. This, in conjunction with the orientation-dependent magnitude of the interface dipole, allows one to explain the evolution of graphene (Phi) from 4.5 eV up to 5.7 eV, rendering the molecularly modified graphene-on-quartz a highly suitable hole injection electrode.

The relative position of L-a and L-b pi pi* electronic states in purine nucleobases is a much debated topic, since it can strongly affect our understanding of their photoexcited dynamics. To assess this point, we calculated the absorption and magnetic circular dichroism (MCD) spectra of adenine, guanine, and their nucleosides in gas-phase and aqueous solution,. exploiting recent developments in MCD computational technology within time-dependent density functional theory. MCD spectroscopy allows us to resolve the intense S-0 -greater than L-a transition from the weak S-0 -greater than L-b transition. The spectra obtained in water solution, by using B3LYP and CAM-B3LYP functionals and describing solvent effect by cluster models and by the polarizable continuum model (PCM), are in very good agreement with the experimental counterparts, thus providing direct and unambiguous evidence that the energy ordering predicted by TD-DFT, L-a less than L-b, is the correct one.

We present a combination of the polarizable embedding (PE) scheme with the complex polarization propagator (CPP) method with the aim of calculating response properties including relaxation for large and complex systems. This new approach, termed PE-CPP, will benefit from the highly advanced description of the environmental electrostatic potential and polarization in the PE method as well as the treatment of near-resonant effects in the CPP approach. The PE-CPP model has been implemented in a Kohn-Sham density functional theory approach, and we present pilot calculations exemplifying the implementation for the UV/vis and carbon K-edge X-ray absorption spectra of the protein plastocyanin. Furthermore, technical details associated with a PE-CPP calculation are discussed.

Molecular spectra can be determined from molecular response functions, by solving the so-called damped response equations using the complex polarization propagator approach. The overall structure of response equations is identical for variational wave functions such as the Hartree-Fock, multi-configuration self-consistent field, and Kohn-Sham density functional theory, and the key program module is the linear response equation solver. We present an implementation of the solver using the algorithm with symmetrized vectors, optimized for addressing spectral regions of a width of some 5-10 eV and a resolution below 0.1 eV. The work is illustrated by the consideration of UV-vis as well as near carbon K -edge absorption spectra of the C-60 fullerene. We demonstrate that it is possible to converge tightly response equations for hundreds of optical frequencies in resonance regions of the spectrum at a cost not much exceeding the solution of a single response equation in the nonresonant region. Our work is implemented in the molecular orbital based module of the Dalton program and serves as a documentation of the code distributed in the Dalton2013 release version.

A methodological development is reported for the study of luminescence properties of conjugated polyelectrolytes, encompassing systems in which dihedral rotational barriers are easily overcome at room temperature. The components of the model include (i) a molecular mechanics (MM) force field description of the solvent in its electronic ground state well as the chromophore in its electronic ground and excited states, (ii) a conformational sampling by means of classical molecular dynamics (MD) in the respective electronic states, and (in) ii) spectral response calculations by means of the quantum mechanics/molecular mechanics QM/MM approach. A detailed analysis of the combined polarization effects of the ionic moiety and the polar water solvent is presented. At an increased computational cost of 30% compared to a calculation excluding the solvent, the error in the transition wavelength of the dominant absorption band is kept as small as 1 nm as compared to the high-quality benchmark result, based largely on a QM description of the solvent. At a reduced computational cost the error of the same quantity is kept as small as 6 nm, with the cost reduction being the result of an effective description of the effects of the solvent by means of replacing the carboxylate ions with neutral hydrogens. In absorption spectroscopy, the obtained best theoretical results are in excellent agreement with the experimental benchmark measurement, regarding excitation energies as well as band intensities and profiles. In fluorescence spectroscopy, the experimental spectrum shows a vibrational progression that is not addressed by theory, but the theoretical band position is in excellent agreement with experiment, with a highly accurate description of the Stokes shift as a result.

A complete understanding of the physics underlying the varied colors of firefly bioluminescence remains elusive because it is difficult to disentangle different enzyme-lumophore interactions. Experiments on isolated ions are useful to establish a proper reference when there are no microenvironmental perturbations. Here, we use action spectroscopy to compare the absorption by the firefly oxyluciferin lumophore isolated in vacuo and complexed with a single water molecule. While the process relevant to bioluminescence within the luciferase cavity is light emission, the absorption data presented here provide a unique insight into how the electronic states of oxyluciferin are altered by microenvironmental perturbations. For the bare ion we observe broad absorption with a maximum at 548 +/- 10 nm, and addition of a water molecule is found to blue-shift the absorption by approximately 50 nm (0.23 eV). Test calculations at various levels of theory uniformly predict a blue-shift in absorption caused by a single water molecule, but are only qualitatively in agreement with experiment highlighting limitations in what can be expected from methods commonly used in studies on oxyluciferin. Combined molecular dynamics simulations and time-dependent density functional theory calculations closely reproduce the broad experimental peaks and also indicate that the preferred binding site for the water molecule is the phenolate oxygen of the anion. Predicting the effects of microenvironmental interactions on the electronic structure of the oxyluciferin anion with high accuracy is a nontrivial task for theory, and our experimental results therefore serve as important benchmarks for future calculations., Funding Agencies|Lundbeckfonden||Human Frontier Science Project|RGY0081/2011|Kyoto Universitys Hakubi Project||Portuguese Foundation for Science and Technology|PTDC/FIS/103587/2008|Swedish Research Council|621-2010-5014|SERC (Swedish e-Science Research Center)

We present an implementation of the damped coupled-cluster linear response function based on an asymmetric Lanczos chain algorithm for the hierarchy of coupled-cluster approximations CCS (coupled-cluster singles), CC2 (coupled. cluster singles and approximate doubles), and CCSD (coupled-cluster singles and doubles). Triple corrections to the excitation energies can be included via the CCSDR(3) (coupled-cluster singles and doubles with noniterative-triples-corrected excitation energies) approximation. The performance and some of the potentialities of the approach are investigated in calculations of the visible/ultraviolet absorption spectrum and the dispersion of the real polarizability in near-resonant regions of pyrimidine, the near-edge absorption fine structure (NEXAFS) of ammonia, and the direct determination of the C-6 dipole-dipole dispersion coefficient of the benzene dimer., Funding Agencies|FP7-PEOPLE-2009-IEF|254326|Swedish Research Council|621-2010-S014|National Supercomputer Centre (NSC), Sweden

In this work, it is shown that a well-organized monolayer of phenylboronic ester-terminated thiol (BOR-capped) on gold surfaces can be prepared. Our results also show that the BOR-capped molecular system can be cleaved directly on the surface, resulting in an unprotected BOR-uncapped monolayer with the boronic acid functional groups available for coordination to diol molecules in the ambient media. The monolayers of BOR-capped and BOR-uncapped were characterized using infrared spectroscopy, near edge X-ray absorption fine structure spectroscopy, X-ray photoelectron spectroscopy, ellipsometry, and contact angle goniometry. The X-ray photoelectron spectroscopy results showed that both BOR-capped and BOR-uncapped are chemically linked to the gold substrate. According to the infrared spectroscopy results, the main component of the CO vibrational mode present in the amide moiety is perpendicular oriented relative to the gold surface normal for the BOR-capped molecular system. The near edge X-ray absorption fine structure spectroscopy resonance peak located at approximately 285 eV, assigned to pi(1)* transitions, was used to estimate the average tilt angle of the vector parallel to the pi* orbitals of the aromatic ring relative to the gold surface normal. The average tilt angle is estimated to be approximately 63 degrees for the BOR-capped monolayer on gold surfaces. The aromatic ring of the BOR-uncapped molecule has a more tilted orientation compared to the BOR-capped one. The experimental infrared spectroscopy and near edge X-ray absorption fine structure spectroscopy results were supported with theoretical modeling including calculations of vibrational modes and of excitation processes., Funding Agencies|Swedish research council Carl Tryggers Foundation|621-2010-5014|CeNano at LiU

Geometries, UV absorption bands, and resonance Raman (RR) cross sections of TNT and RDX are investigated using density functional theory (DFT) in conjunction with the Coulomb attenuated B3LYP exchange-correlation functional. The absorption and RR spectra are determined with use of vibronic (VB) theory, excited-state gradient, and complex polarizability (CPP) approximations. We examined lowenergy isomers (two for TNT and four for RDX) whose energies differ by less than 1 kcal/mol, such that they would appreciably be populated at room temperature. The two TNT isomers differ by an internal rotation of the methyl group, while the four conformers of RDX differ by the arrangements of the nitro group relative to the ring. Our theoretical optical properties of the TNT and RDX isomers are in excellent agreement with experimental and recent CCSD-EOM results, respectively. For the two TNT isomers, the ultraviolet RR (UVRR) spectra are similar and in good agreement with recently measured experimental results. Additionally, the UVRR spectra computed using the excited-state and CPP approaches compare favorably with the VB theory results. On the other hand, the RR spectra of the RDX conformers differ from one another, reflecting the importance of the positioning of the NO2 groups with respect to the ring. In the gas phase or in solution, RDX would give a spectrum associated with a conformationally averaged structure. It is encouraging that the computed spectra of the conformers show similarities to recent measured RDX spectra in acetonitrile solution, and reproduce the 10-fold decrease in the absolute Raman cross sections of RDX compared to TNT for the observed 229 nm excitation. We show that in TNT and RDX vibrational bands that couple to NO2 or the ring are particularly resonance enhanced. Finally, the computed RDX spectra of the conformers present a benchmark for understanding the RR spectra of the solid-phase polymorphs of RDX., Funding Agencies|Swedish Research Council|621-2010-5014

Self-assembled monolayers and multilayers of a noradrenaline analogue (Nor-Pt) on gold substrates as well as multilayers of noradrenaline have been investigated by means of the molecular orientation, the molecule surface interaction, the molecular composition and the functional group availability for further biointeraction processes, using X-ray photoelectron spectroscopy (XPS), infrared reflection absorption spectroscopy (IRAS), and near-edge X-ray absorption fine structure (NEXAFS) spectroscopy. A chemical shift (1.7 eV) of the S 2p peak to lower binding energies is observed, in the XPS spectrum, indicating that the Nor-Pt molecules are chemisorbed onto the gold substrate. The IR results show that Nor-Pt adsorbate has the C=O stretching vibration modes parallel oriented relative to the gold substrate. The average tilt angle of the aromatic ring relative to the gold surface normal is determined to be approximately 51 degrees, based on the NEXAFS measurements on Nor-Pt monolayers. The experimental results and assignments are supported with theoretical studies where we use the building block principle in the spectral analysis and compare with the measurements of noradrenaline and Nor-Pt. The theoretical calculations are shown to be useful; for angle dependence NEXAFS studies as resonances with fully pi* or sigma* character are preferred for correct analysis.

A presentation of the complex polarization propagator in the restricted open-shell self-consistent field approximation is given. It rests on a formulation of a resonant-convergent, first-order polarization propagator approach that makes it possible to directly calculate the X-ray absorption cross section at a particular frequency without explicitly addressing the excited states. The quality of the predicted X-ray spectra relates only to the type of density functional applied without any separate treatment of dynamical relaxation effects. The method is applied to the calculation of the near K-edge X-ray absorption fine structure spectra of allyl and copper phthalocyanine. Comparison is made between the spectra of the radicals and those of the corresponding cations and anions to assess the effect of the increase of electron charge in the frontier orbital. The method offers the possibility for unique assign-lent of symmetry-independent atoms. The overall excellent spectral agreement motivates the application of the method as a routine precise tool for analyzing X-ray absorption of large systems of technological interest.

A series of chiral synthetic compounds is reported that show intricate but specific hierarchical assembly because of varying positions of coordination and hydrogen bonds. The evolution of the aggregates (followed by absorption spectroscopy and temperature-dependent circular dichroism studies in solution) reveal the influence of the proportion of stereogenic centers in the side groups connected to the chromophore ring in their optical activity and the important role of pyridyl groups in the self-assembly of these chiral macrocycles. The optical activity spans two orders of magnitude depending on composition and constitution. Two of the aggregates show very high optical activity even though the isolated chromophores barely give a circular dichroism signal. Molecular modeling of the aggregates, starting from the pyridine-zinc(II) porphyrin interaction and working up, and calculation of the circular dichroism signal confirm the origin of this optical activity as the chiral supramolecular organization of the molecules. The aggregates show a broad absorption range, between approximately 390 and 475 nm for the transitions associated with the Soret region alone, that spans wavelengths far more than the isolated chromophore. The supramolecular assemblies of the metalloporphyrins in solution were deposited onto highly oriented pyrolitic graphite in order to study their hierarchy in assembly by atomic force microscopy. Zero and one-dimensional aggregates were observed, and a clear dependence on deposition temperature was shown, indicating that the hierarchical assembly took place largely in solution. Moreover, scanning electron microscopy images of porphyrins and metalloporphyrins precipitated under out-of-equilibrium conditions showed the dependence of the number and position of chiral amide groups in the formation of a fibrillar nanomaterial. The combination of coordination and hydrogen bonding in the complicated assembly of these molecules - where there is a clear hierarchy