Diverging conformations guide dipeptide self-assembly into crystals or hydrogels.

The prediction of dipeptide assembly into crystals or gels is challenging. This work reveals the diverging conformational landscape that guides self-organization towards different outcomes. In silico and experimental data enabled deciphering of the electronic circular dichroism (ECD) spectra of self-assembling dipeptides to reveal folded or extended conformers as key players.

Electronic circular dichroism from real-time propagation in state space.

In this paper, we propose to compute the electronic circular dichroism (ECD) spectra of chiral molecules using a real-time propagation of the time-dependent Schrödinger equation (TDSE) in the space of electronic field-free eigenstates, by coupling TDSE with a given treatment of the electronic structure of the target. The time-dependent induced magnetic moment is used to compute the ECD spectrum from an explicit electric perturbation. The full matrix representing the transition magnetic moment in the space of electronic states is generated from that among pairs of molecular orbitals. In the present work, we show the ECD spectra of methyloxirane, of several conformers of L-alanine, and of the Λ-Co(acac)3 complex, computed from a singly excited ansatz of time-dependent density functional theory eigenstates. The time-domain ECD spectra properly reproduce the frequency-domain ones obtained in the linear-response regime and quantitatively agree with the available experimental data. Moreover, the time-domain approach to ECD allows us to naturally go beyond the ground-state rotationally averaged ECD spectrum, which is the standard outcome of the linear-response theory, e.g., by computing the ECD spectra from electronic excited states.

The Conformational Dynamics of the Ligands Determines the Electronic Circular Dichroism of the Chiral Au38(SC2H4Ph)24 Cluster.

Effects of the conformational dynamics of 2-PET protective ligands on the electronic circular dichroism (ECD) of the chiral Au38(SC2H4Ph)24 cluster are investigated. We adopt a computational protocol in which ECD spectra are calculated via the first principle polTDDFT approach on a series of conformations extracted from MD simulations by using Essential Dynamics (ED) analysis, and then properly weighted to predict the final spectrum. We find that the experimental spectral features are well reproduced, whereas significant discrepancies arise when the spectrum is calculated using the experimental X-ray structure. This result unambiguously demonstrates the need to account for the conformational effects in the ECD modeling of chiral nanoclusters. The present procedure proved to be able of capturing the essential conformational features of the dynamic Au38(SC2H4Ph)24 system, opening the possibility to model the ECD of soluble chiral nanoclusters in a realistic way.

PECD study of a single-conformer molecule: a critical comparison of experiment and theory.

In this work we address a specific experimental and theoretical question regarding the influence of a conformational population in the modeling of photoelectron circular dichroism (PECD) spectroscopy. In the past two decades, PECD has revealed a rich and complex phenomenology in molecular processes with unprecedented insight, especially in molecular geometry sensitivity. Since the early development of this spectroscopy, theory has pointed out the importance of conformer influence on PECD; in particular, the rotation of methyl groups was surprisingly found to be responsible for strong modulation of the PECD signal. Here, to advance understanding of the effect of rotations, we have chosen to study norcamphor, a single-conformer molecule, as a benchmark for a PECD comparison between experiment and theory at the density functional theory (DFT) and time-dependent density functional theory (TDDFT) levels. The excellent agreement between experimental data and theory for norcamphor sheds light on the influence of rotations and gives a solid explanation for the reasonable qualitative agreement in the PECD of camphor, where three methyl groups are added to the same molecular structure.

Revealing the electronic properties of the B-B bond: the bis-catecholato diboron molecule.

The electronic properties of a diboron molecule, namely bis(catecholato)diboron (2-(1,3,2-benzodioxaborol-2-yl)-1,3,2-benzodioxaborole) (B2Cat2), have been studied by comparing the results of photoemission (XPS) and near edge X-ray absorption spectroscopy (NEXAFS) experiments with the outcome of DFT calculations. The B 1s, C 1s and O 1s K-edges have been investigated for both the isolated gas phase molecule and the adsorbed one on the Au(111) surface. The main features of the polarized NEXAFS spectra at each of the three edges considered are not significantly affected by the presence of the substrate, with respect to the isolated molecule, indicating that the molecule-gold interaction is weak. Moreover, the comparison between the observed dichroism in the NEXAFS spectra of the adsorbed B2Cat2 and that in the NEXAFS spectra of the isolated molecule has confirmed the orbital symmetry assigned in the gas phase absorption spectra. The transitions to π(B-B) bonding and π*(B-B) anti-bonding final states represent the most relevant probe of the chemistry of the B2Cat2 molecule. We show that their theoretical description requires that the treatment of the relaxation changes among different excited state configurations, which we successfully implemented by using ΔSCF-DFT (ΔSCF) calculations.

Time-Resolved Excited-State Analysis of Molecular Electron Dynamics by TDDFT and Bethe-Salpeter Equation Formalisms.

In this work, a theoretical and computational set of tools to study and analyze time-resolved electron dynamics in molecules, under the influence of one or more external pulses, is presented. By coupling electronic-structure methods with the resolution of the time-dependent Schrödinger equation, we developed and implemented the time-resolved induced density of the electronic wavepacket, the time-resolved formulation of the differential projection density of states (ΔPDOS), and of transition contribution map (TCM) to look at the single-electron orbital occupation and localization change in time. Moreover, to further quantify the possible charge transfer, we also defined the energy-integrated ΔPDOS and the fragment-projected TCM. We have used time-dependent density-functional theory (TDDFT), as implemented in ADF software, and the Bethe-Salpeter equation, as provided by MolGW package, for the description of the electronic excited states. This suite of postprocessing tools also provides the time evolution of the electronic states of the system of interest. To illustrate the usefulness of these postprocessing tools, excited-state populations have been computed for HBDI (the chromophore of GFP) and DNQDI molecules interacting with a sequence of two pulses. Time-resolved descriptors have been applied to study the time-resolved electron dynamics of HBDI, DNQDI, LiCN (being a model system for dipole switching upon highest occupied molecular orbital-lowest unoccupied molecular orbital (HOMO-LUMO) electronic excitation), and Ag22. The computational analysis tools presented in this article can be employed to help the interpretation of fast and ultrafast spectroscopies on molecular, supramolecular, and composite systems.

Electronic Structure Characterization of a Thiophene Benzo-Annulated Series of Common Building Blocks for Donor and Acceptor Compounds Studied by Gas Phase Photoelectron and Photoabsorption Synchrotron Spectroscopies.

The near-edge x-ray-absorption fine-structure (NEXAFS) and X-ray photoelectron spectroscopy (XPS) spectra of benzo[ b]thiophene (BBT) and dibenzothiophene (DBT) in the gas phase have been measured at the carbon K-edge and sulfur LII,III-edge regions. The assignment of the spectral features has been provided by theoretical calculations based on density functional theory (DFT) and its time-dependent generalization (TDDFT) in the linear response regime. Observed trends in computed C 1s and S 2p ionization potentials (IPs) have been rationalized in terms of both the inductive effects due to the presence of S and the increased π-electrons delocalization arising from the benzo-annulation process. The analysis of the NEXAFS carbon K-edge and sulfur LII,III-edge regions provided information on both low-lying delocalized virtual π orbitals, and higher-lying localized σ*(C-S) states. The evolution of the NEXAFS carbon K-edge spectral features along the series thiophene (T) and derivatives, BBT and DBT, is informative of a stabilizing effect due to increased aromaticity. This effect is however more pronounced in going from T to BBT compared to the introduction of a second annulated phenyl ring in DBT. The nature of the most intense sulfur LII,III-edge NEXAFS spectral features is instead conserved along the series reflecting thus the localized nature of the virtual states involved in the S 2p core-excitation process.

Study of the electronic structure of short chain oligothiophenes.

The electronic structure of short-chain thiophenes (thiophene, 2,2'-bithiophene, and 2,2':5',2″-terthiophene) in the gas phase has been investigated by combining the outcomes of Near-Edge X-ray-Absorption Fine-Structure (NEXAFS) and X-ray Photoemission Spectroscopy (XPS) at the C K-edge with those of density functional theory (DFT) calculations. The calculated NEXAFS spectra provide a comprehensive description of the main experimental features and allow their attribution. The evolution of the C1s NEXAFS spectral features is analyzed as a function of the number of thiophene rings; a tendency to stabilization for increasing chain length is found. The computation of the binding energy allows to assign the experimental XPS peaks to the different carbon sites on the basis of both the inductive effects generated by the presence of the S atom as well as of the differential aromaticity effects.

S2p core level spectroscopy of short chain oligothiophenes.

The Near-Edge X-ray-Absorption Fine-Structure (NEXAFS) and X-ray Photoemission Spectroscopy (XPS) of short-chain oligothiophenes (thiophene, 2,2'-bithiophene, and 2,2':5',2″-terthiophene) in the gas phase have been measured in the sulfur L2,3-edge region. The assignment of the spectral features is based on the relativistic two-component zeroth-order regular approximation time dependent density functional theory approach. The calculations allow us to estimate both the contribution of the spin-orbit splitting and of the molecular-field splitting to the sulfur binding energies and give results in good agreement with the experimental measurements. The deconvolution of the calculated S2p NEXAFS spectra into the two manifolds of excited states converging to the LIII and LII edges facilitates the attribution of the spectral structures. The main S2p NEXAFS features are preserved along the series both as concerns the energy positions and the nature of the transitions. This behaviour suggests that the electronic and geometrical environment of the sulfur atom in the three oligomers is relatively unaffected by the increasing chain length. This trend is also observed in the XPS spectra. The relatively simple structure of S2p NEXAFS spectra along the series reflects the localized nature of the virtual states involved in the core excitation process.

Delocalization of a Vacancy across Two Neon Atoms Bound by the van der Waals Force.

We experimentally study 2p photoionization of neon dimers (Ne_{2}) at a photon energy of hν=36.56 eV. By postselection of ionization events which lead to a dissociation into Ne^{+}+Ne we obtain the photoelectron angular emission distribution in the molecular frame. This distribution is symmetric with respect to the direction of the charged vs neutral fragment. It shows an inverted Cohen-Fano double slit interference pattern of two spherical waves emitted coherently but with opposite phases from the two atoms of the dimer.

Designing ligand-enhanced optical absorption of thiolated gold nanoclusters.

The optical spectra of thiolated Au25(SR)18/Au23(SR)16 clusters with different R residues are investigated via TDDFT simulations. Significant enhancements in the optical region and effective electron delocalization are simultaneously achieved by tuning the ligands' steric hindrance and electronic conjugating features, producing a resonance phenomenon between the Au-S core motif and the ligand fragments.

Selecting core-hole localization or delocalization in CS2 by photofragmentation dynamics.

Electronic core levels in molecules are highly localized around one atomic site. However, in single-photon ionization of symmetric molecules, the question of core-hole localization versus delocalization over two equivalent atoms has long been debated as the answer lies at the heart of quantum mechanics. Here, using a joint experimental and theoretical study of core-ionized carbon disulfide (CS2), we demonstrate that it is possible to experimentally select distinct molecular-fragmentation pathways in which the core hole can be considered as either localized on one sulfur atom or delocalized between two indistinguishable sulfur atoms. This feat is accomplished by measuring photoelectron angular distributions within the frame of the molecule, directly probing entanglement or disentanglement of quantum pathways as a function of how the molecule dissociates.

Off-resonance photoemission dynamics studied by recoil frame F1s and C1s photoelectron angular distributions of CH3F.

F1s and C1s photoelectron angular distributions are considered for CH3F, a molecule which does not support any shape resonance. In spite of the absence of features in the photoionization cross section profile, the recoil frame photoelectron angular distributions (RFPADs) exhibits dramatic changes depending on both the photoelectron energy and polarization geometry. Time-dependent density functional theory calculations are also given to rationalize the photoionization dynamics. The RFPADs have been compared with the theoretical calculations, in order to assess the accuracy of the theoretical method and rationalize the experimental findings. The effect of finite acceptance angles for both ionic fragments and photoelectrons has been included in the calculations, as well as the effect of rotational averaging around the fragmentation axis. Excellent agreement between theory and experiment is obtained, confirming the good quality of the calculated dynamical quantities (dipole moments and phase shifts).

Angular correlation between B K-VV Auger electrons of BF3 molecules and coincident fragment ions: manifestation of the difference between the angular correlation and molecular frame Auger electron angular distribution.

We have measured the angular correlation between the B K-VV Auger electrons of BF(3) molecules and the coincident fragment-ion pairs of BF(2)(+)-F(+). Then, we have found that the measured angular correlation patterns depending on the mutual angle between the light polarization direction and molecular orientation are affected by the anisotropic axis distribution of the molecular ensemble of BF(3)(+) reflecting the anisotropic nature of photon-molecule interaction. In this context, we have pointed out generally that for coincidence experiments, so-called molecular frame Auger electron angular distributions are realized only if the axis distribution of the molecular ion ensemble is isotropic.

Resonant circular dichroism of chiral metal-organic complex.

A sizable enhancement of the circular dichroism in photoelectron spectroscopy has been measured and computed for the metal complex Δ-cobalt(III) tris-acetylacetonate highest occupied molecular orbital state in the region of the Co 3p→3d Fano resonance. In the resonance the dichroism reaches the maximum value of 5% and even changes its sign as compared to the direct photoionization channel. We ascribe this enhancement to electron correlation processes, namely, with the coupling between discrete excitations and the continuum, which is correctly described in the time dependent density functional theory (TDDFT) framework. These findings open new physical aspects of photoelectron circular dichroism that now can be interpreted not only via the simple direct ionization, but also through more complex electron correlation processes.

Theoretical study of near-edge X-ray absorption fine structure spectra of metal phthalocyanines at C and N K-edges.

The inner shell excitation of CuPc, NiPc, and H(2)Pc phthalocyanines at both C and N K-edges has been investigated theoretically by density functional theory calculations. The selected molecules allow one to study the effect on the spectra of the presence and the nature of the atom in the central cavity of the macrocycle. The individual characteristics of the spectra can be rationalized in terms of the position of the unequivalent C and N atomic sites, showing that sensible changes are present in the spectral features deriving from the N atoms directly bound to the atom at the center of the Pc macrocycle. The minor variations present in the spectral C 1s profiles of the phthalocyanines reflect the little perturbation experienced by the peripheral atomic sites.

Recoil frame photoelectron angular distributions of BF3: a sensitive probe of the shape resonance in the F 1s continuum.

Recoil frame photoelectron angular distributions (RFPADs) of BF(3) molecules are presented over the energy region of the shape resonance in the F 1s continuum. Time-dependent density functional theory calculations are also given to understand the shape resonance dynamics. The RFPADs have been compared with the theoretical calculations. It is found that the RFPADs calculated by the localized core-hole model are in better agreement with the experimental, compared with those by the delocalized core hole. Dipole matrix elements and dipole prepared continuum wavefunctions show that the shape resonance in the F 1s ionization continuum of BF(3) is induced by p-partial waves as previously reported by Swanson et al. [J. Chem. Phys. 75, 619 (1981)]. However, due to the couplings with the other partial waves the feature characteristic of the p-partial waves has not been observed in the RFPADs.

The valence electronic structure and conformational flexibility of epichlorohydrin.

The electronic structure of epichlorohydrin is investigated in the whole valence region by a combined experimental and theoretical study. The issue of controversial assignments of the molecular electronic structure is here addressed. Photoelectron spectra (PES) and Threshold Photoelectron spectra (TPES) of room temperature molecules in the gas phase are recorded. Geometries and energies of the stable conformers due to internal rotation of the C-C-C-Cl dihedral angle, gauche-II (g-II), gauche-I (g-I), and cis, are calculated, and the effect of the conformational flexibility on the photoionization energetics is studied by DFT and 2h-1p Configuration Interaction (CI) methods. Strong breakdown of the Koopmans Theorem (KT) is obtained for the four outermost ionizations, which are further investigated by higher level ab initio calculations. The full assignment of the spectrum is put on a firm basis by the combination of experimental and theoretical results. The orbital composition from correlated calculations is found closer to the DFT orbitals, which are then used to analyze the electronic structure of the molecule. The Highest Occupied Molecular Orbital (HOMO) and HOMO--2 are n(O)/n(Cl) mixed orbitals. The nature of each valence MO is generally preserved in all the conformers, although the magnitude of the n(O)/n(Cl) mixing in HOMO and HOMO--2 varies to some extent with the C-C-C-Cl dihedral angle. The low energy part of the HOMO PE band is predicted to be substantially affected by the conformational flexibility, as experimentally observed in the spectra. The rest of the spectrum is described in terms of the dominant conformer g-II, and a good agreement between experiment and theory is found. The inner-valence PE spectrum is characterized by satellite structures, due to electron correlation effects, which are interpreted by means of 2h-1p CI calculations.

Photoabsorption and S 2p photoionization of the SF6 molecule: resonances in the excitation energy range of 200-280 eV.

Photoabsorption and S 2p photoionization of the SF(6) molecule have been studied experimentally and theoretically in the excitation energy range up to 100 eV above the S 2p ionization potentials. In addition to the well-known 2t(2g) and 4e(g) shape resonances, the spin-orbit-resolved S 2p photoionization cross sections display two weak resonances between 200 and 210 eV, a wide resonance around 217 eV, a Fano-type resonance around 240 eV, and a second wide resonance around 260 eV. Calculations based on time-dependent density functional theory allow us to assign the 217-eV and 260-eV features to the shape resonances in S 2p photoionization. The Fano resonance is caused by the interference between the direct S 2p photoionization channel and the resonant channel that results from the participator decay of the S 2s(-1)6t(1u) excited state. The weak resonances below 210-eV photon energy, not predicted by theory, are tentatively suggested to originate from the coupling between S 2p shake-up photoionization and S 2p single-hole photoionization. The experimental and calculated angular anisotropy parameters for S 2p photoionization are in good agreement.

Theoretical study of sulfur L-edge XANES of thiol protected gold nanoparticles.

The Scalar Relativistic-Zero Order Regular Approximation-Time Dependent Density Functional Theory has been employed to study the sulfur L-edge XANES spectrum of the [Au(25)(SCH(3))(18)](+) model cluster, with the aim to reproduce and rationalize previous experimental data. The salient experimental features are properly described by the present calculation. The model cluster contains two different types of bidentate "staple" ligand thiol fragments, and it has been possible to assign the spectral features according to the different location of the initial core orbital on one of the two different fragments. This finding suggests that in the real nanoparticle two different non-equivalent type of sulfur bidentate ligands are present, arranged with the typical staple geometry.