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The photoisomerization of chromophores embedded in biological environments is of high importance for biomedical applications, but it is still challenging to define the photoisomerization mechanism both experimentally and computationally. We present here a computational study of the azobenzene molecule embedded in a DPPC lipid membrane, and assess the photoisomerization mechanism by means of the quantum mechanics/molecular mechanics surface hopping (QM/MM-SH) method. We observe that while the trans-to-cis isomerization is a slow process governed by a torsional mechanism due to the strong interaction with the environment, the cis-to-trans mechanism is completed in sub-ps time scale and is governed by a pedal-like mechanism in which both weaker interactions with the environment and a different geometry of the potential energy surface play a key role. S. O. thanks the Polish National Science Centre for funding (grant no. UMO-2018/31/D/ST4/01475 and UMO-2020-39-I-ST4- 01446). This research was carried out with the support of the Interdisciplinary Center for Mathematical and Computational Modeling at the University of Warsaw (ICM UW) under grants no. G83-28 and GB80-24.

Zwitterionic polymers are very promising candidates for antifouling materials that exhibit high chemical stability as compared to polyethylene glycol-based systems. A number of simulation and experimental studies have emerged over recent years for the investigation of sulfobetaine-based zwitterionic polymers. Investigating the structural and thermodynamic properties of such polymers requires access to broad time and length regimes, thus necessitating the development of multiscale simulation strategies. The present article advocates a mesoscopic dissipative particle dynamics (DPD) model capable of addressing a wide range of time and length scales. The mesoscopic force field was developed hand-in-hand with atomistic simulations based on the OPLS force field through a bottom-up parameterization procedure that matches the atomistically calculated strand-length, strand-angle and pair distribution functions. The DPD model is validated against atomistic simulations conducted in this work, and against relevant atomistic simulation studies, theoretical predictions and experimental correlations from the literature. Properties examined include the conformations of SPE polymers in dilute bulk aqueous solution, the density profile and thickness of brush arrays as functions of the grafting density and chain length. In addition, we compute the potential of mean force of an approaching hydrophilic or hydrophobic foulant via umbrella sampling as a function of its position relative to the poly-zwitterion-covered surface. The aforementioned observables lead to important insights regarding the conformational tendencies of grafted polyzwitterions and their antifouling properties.

Laurdan is one of the most used fluorescent probes for lipid membrane phase recognition. Despite its wide use for optical techniques and its versatility as a solvatochromic probe, little is known regarding its use as molecular rotor, for which clear evidence is found in the current study. Although recent computational and experimental studies suggest the existence of two stable conformations of laurdan in different membrane phases, it is difficult to experimentally probe their prevalence. By means of multiscale computational approaches, we prove now that this information can be obtained through the optical properties of the two conformers, ranging from one-photon absorption over two-photon absorption to the first hyperpolarizability. Fluorescence decay and anisotropy analyses are performed as well and stress the importance of laurdan's conformational versatility. As a molecular rotor and with reference to the distinct properties of its conformers, laurdan can be used to probe biochemical processes that change the lipid orders in cell membranes.

To assess a tumor biomarker like the cyclooxygenase-2 enzyme (COX-2), non-invasive imaging techniques are powerful tools. The (non-) linear optical properties of activatable fluorescent probes which are selectively bound to the biomarker can therefore be exploited. The here presented molecular modelling results based on multi-scale modelling techniques highlight the importance of the conformational versatility and of changes in the electronic interactions of such probes when they are embedded in water or in the COX-2 homodimer enzyme. The ANQ-IMC-6 probe, which combines the binding domain/scaffold of indomethacin (IMC) on COX-2 with the optical properties of acenaphtho[1,2–b]quinoxaline (ANQ), is found to be folded in the solvent and unfolded in the enzyme. A concerted movement of the probe and the protein is seen, while the rotational autocorrelation function exhibits also the intrinsic properties of the probe. Hybrid Quantum Mechanics/Molecular Mechanics (QM/MM) calculations are used to simulate the one-photon and two-photon absorption spectra along with the first hyperpolarizability. The transition has a local character in vacuum, but changes to a charge transfer one in the presence of the microenvironment of the enzyme. This is also visible through a change of the shape of the absorption spectrum, while at the same time the simulated signals of second harmonic generation experiments are strongly enhanced. The results of this work prove that an environment sensitive probe with an anchoring group and an optical active part can be constructed for use in absorption spectroscopy, without the need to revert to fluorescence experiments.

Background Organic fluorophores embedded in lipid bilayers can nowadays be described by a multiscale computational approach. Combining different length and time scales, a full characterization of the probe localization and optical properties led to novel insight into the effect of the environments. Scope of review Following an introduction on computational advancements, three relevant probes are reviewed that delineate how a multiscale approach can lead to novel insight into the probes' (non) linear optical properties. Attention is paid to the quality of the theoretical description of the optical techniques. Major conclusions Computation can assess a priori novel probes' optical properties and guide the analysis and interpretation of experimental data in novel studies. The properties can be used to gain information on the phase and condition of the surrounding biological environment. General significance Computation showed that a canonical view on some of the probes should be revisited and adapted.

The photoisomerization scheme of the cyanine-based 1,1'-dioctadecyl-3,3,3',3'-tetramethylindocarbocyanine (DiD) probe was investigated by means of molecular modeling techniques, accounting for differences between the potential energy surfaces in the ground and excited states. Starting from the trans conformation, the photoisomerization path to the cis conformation and its dependence on the acyl tail lengths of the probe were evaluated. Moreover, the ground-state conformational distribution was investigated and suitable topologies were built for the ground- and excited-state molecular dynamics (MD) calculations. A protocol for simulations in solvents and in liquid-disordered lipid bilayers was worked out. In a kinetic analysis, the decay of the excited singlet (S1) state via radiative and nonradiative decays and via dihedral twisting is discussed. The twisting of one of the dihedral angles in the S1 state is found to be faster than the direct decay rate, which explains the relatively low fluorescence quantum yield of the compound. The molecular dynamics simulations show that in lipid bilayers, the DiD probe with methyl groups as acyl tails from the headgroup brings the highest level of photoisomerization, while a compound with acyl tails of 18 carbon atoms does not isomerize at all.

The specific relationship between the alkyl tail lengths of four azobenzene probes embedded in DOPC liquid disorder membrane and their (non) linear optical (NLO) properties have been considered in the current study. Using extensive molecular dynamics calculations, the push/pull effect of the alkyl tails on the position and orientation of the probes in the model membrane are discussed. The simulations indicate that with increasing tail lengths the cis isomers are pushed closer to the membrane surface, while the trans ones are rather pulled toward the membrane center. Throughout hybrid quantum mechanics/molecular mechanics calculations, the linear and nonlinear optical properties of these compounds have been investigated. The pushing effect of the tails for cis azobenzene is translated in strong responses in the (non) linear I optical spectroscopies, while the opposite is seen for the trans isomers. The cis isomer can be seen as the active state of the azobenzene compound for membrane recognition. The current work highlights the correlation between the tails of photosensitive membrane probes and their NLO properties, and focuses on unexpected behaviors of azobenzene derivatives in biological environments which can be exploited in distinguishing between soft and stiff cellular compartments that are of utmost importance for ion carrier transport.

Characterization of the membrane phases is a crucial task in cell biology. Cells differ in composition of the lipids and consequently in adopted phases. The phases can be discriminated based upon lipid ordering and molecular diffusion and their identification could be used for characterization of cell membranes. Here we used molecular dynamics (MD) simulations to study the behavior of the fluorescent reporter molecule diphenylhexatriene (DPH) in different lipid phases – liquid disordered (Ld), liquid ordered (Lo), and solid ordered (So) composed of phosphatidylcholines (Ld and So) or a sphingomyelin/cholesterol (SM/Chol) mixture (Lo). To the best of our knowledge, this is the first simulation of DPH in Lo SM/Chol and So DPPC membranes. For the considered membrane compositions DPH is mostly oriented parallel to lipid tails. In the Lo phase we observed a significant fraction of DPH positioned in between membrane leaflets, which agrees with experimental findings, but which has not been observed in previous MD simulations of DPH in phosphatidylcholine membranes. Further, we calculated rotational autocorrelation functions (ROTACF) from our MD simulations in order to model the time-resolved fluorescence anisotropy decay. We observed that order parameters 〈P2〉 and 〈P4〉 are sufficient to fully describe the orientation distribution of DPH. We analyzed the ROTACFs by a so-called general model for the time-resolved fluorescence anisotropy [W. van der Meer et al., Biophys. J., 1984, 46, 515] and observed an overestimation of 〈P4〉. We suggest a rescaling of the recovered 〈P4〉 yielding an orientation distribution of DPH close to the one observed in our MD simulations.

Graphene quantum dots (GQD) are interesting materials due to the confined sizes which allow to exploit their optoelectronic properties, especially when they interface with organic molecules through physisorption. In particular, when interfaces are formed, charge transfer (CT) processes can occur, in which electrons can flow either from the GQD to the absorbed molecule, or vice versa. These processes are accessible by modelling and computational analysis. Yet, the presence of different environments can strongly affect the outcome of such simulations which, in turn, can lead to wrong results if not taken into account. In the present multiscale study, we assess the sensibility of the computational approach and compute the CT, calculated at interfaces composed by GQD and amino-acene derivatives. The hole transfer is strongly affected by dynamic disorder and the nature of the environment, and imposes stringent descriptions of the modelled systems to ensure enhanced accuracy of the transfer of charges., Comment: 19 pages, 3 figures

The development of a universal probe to assess the phase of a lipid membrane is one of the most ambitious goals for fluorescence spectroscopy. The ability of a well-known molecule as Laurdan to reach this aim is here exploited as the behavior of the probe is fully characterized in a dipalmitoyl-phosphatidylcholine (DPPC) solid gel (So) phase by means of molecular dynamics simulations. Laurdan can take two conformations, depending on whether the carbonyl oxygen points toward the beta-position of the naphthalene core (Conf-I) or to the alpha-position (Conf-II). We observe that Conf-I has an elongated form in this environment, whereas Conf-II takes an L-shape. Interestingly, our theoretical calculations show that these two conformations behave in an opposite way from what is reported in the literature for a DPPC membrane in a liquid disordered (Ld) phase, where Conf-I assumes an L-shape and Conf-II is elongated. Moreover, our results show that in DPPC (So) no intermixing between the conformations is present, whereas it has been seen in a fluid environment such as DOPC (Ld). Through a careful analysis of angle distributions and by means of the rotational autocorrelation function, we predict that the two conformers of Laurdan behave differently in different membrane environments. S.O. acknowledges the National Science Centre, Poland, grant UMO-2015/19/P/ST4/03636, for the funding from the European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement no. 665778. The Swedish Infrastructure Committee (SNIC) is acknowledged for the computational time granted through the medium allocations 1-87 and 1-415 (2016); 1-16, 1-102 (2017); and 3-397, 3-156, 3-396, 3-23 (2018). The Flemish Supercomputer Centre (VSC) (Flanders, Belgium) and the Herculesstichting (Flanders, Belgium) are acknowledged for the generously allocated computational time on the Tier-1 cluster Breniac as well as the Tier-2 cluster Thinking.

Here we describe a new BODIPY-based membrane probe (1) that provides an alternative to dialkylcarbocyanine dyes, such as DiI-C18, that can be excited in the blue spectral region. Compound 1 has unbranched octadecyl chains at the 3,5-positions and a meso-amino function. In organic solvents, the absorption and emission maxima of 1 are determined mainly by solvent acidity and dipolarity. The fluorescence quantum yield is high and reaches 0.93 in 2-propanol. The fluorescence decays are well fitted with a single-exponential in pure solvents and in small and giant unilamellar vesicles (GUV) with a lifetime of ca. 4 ns. Probe 1 partitions in the same lipid phase as DiI-C18(5) for lipid mixtures containing sphingomyelin and for binary mixtures of dipalmitoylphosphatidylcholine (DPPC) and dioleoylphosphatidylcholine (DOPC). The lipid phase has no effect on the fluorescence lifetime but influences the fluorescence anisotropy. The translational diffusion coefficients of 1 in GUVs and OLN-93 cells are of the same order as those reported for DiI-C18. The directions of the absorption and emission transition dipole moments of 1 are calculated to be parallel. This is reflected in the high steady-state fluorescence anisotropy of 1 in high ordered lipid phases. Molecular dynamic simulations of 1 in a model of the DOPC bilayer indicate that the average angle of the transition moments with respect to membrane normal is ca. 70°, which is comparable with the value reported for DiI-C18.

By reverting to spectroscopy, changes in the biological environment of a fluorescent probe can be monitored and the presence of various phases of the surrounding lipid bilayer membranes can be detected. This study highlights the important differences in orientation and location and therefore in efficiency between the probes when they are used in fluorescence microscopy to screen various lipid bilayer membrane phases. Dependent on the lipid composition, the angle between the transition state dipole moments of both probes and the normal to the membrane are found to deviate clearly from 90{\deg}. It is seen that the DiI-C18(5) probe is located in the headgroup region of the SM:Chol mixture, in close contact with water molecules. A fluorescence anisotropy study indicates also that DiI-C18(5) gives rise to a distinctive behavior in the SM:Chol membrane compared to the other considered membranes. The latter behavior has not been seen for the studied BODIPY probe, which is located deeper in the membrane., Comment: 32 pages, 8 figures

The widespread interest in phase recognition of lipid membranes has led to the use of different optical techniques to enable differentiation of healthy and not fully functional cells. In this work, we show how the combination of different (non)linear optical methods such as One Photon Absorption (OPA), Two Photon Absorption (TPA) and Second Harmonic Generation (SHG) as well as the study of the fluorescence decay time leads to an enhanced screening of membrane phases using a fluorescent dioctadecyltetramethylindocarbocyanine (DiD) probe. In the current study we consider the pure liquid disordered phases of DOPC (room temperature) and DPPC (323 K), the solid gel phase of DPPC (298 K), and the liquid ordered phase of a 2:1 binary mixture of Sphingomyelin and Cholesterol. By means of extensive hybrid quantum mechanics molecular mechanics calculations and based upon the (non) linear absorption of the embedded probes, it is found that DiD can be used to identify the lipid bilayer phase. The joint TPA and SHG as well as fluorescence analyses qualifies DiD as versatile probe for phase recognition. In particular, the SHG data obtained by means of HyperRayleigh Scattering and by Electric Field Induced Second Harmonic Generation reveal differences in polarization of the probe in the different environments. The TPA results finally confirm the particular location of the probe in between the polar head group region of the 2:1 SM:Chol mixture in the liquid ordered phase., 33 pages, 4 figures

The absorption spectrum of a representative BisBODIPY molecule is investigated using high-level quantum chemical methodology; the results are compared with experimental data. The S1 and S2 excited states are examined in detail to illuminate and to understand the electronic coupling between them. With the help of model systems in which the distance between the BODIPY monomers is increased or in which the dihedral angle between the subunits is changed, the electronic coupling is quantified, and its influence on energetics and oscillator strengths is highlighted. For the explanation of the experimental spectrum, orbital interaction effects are found to be important. Because of the large experimental Stokes shift of BisBODIPY, the nature of the emissive state is investigated and found to remain C2 symmetric as the ground state, and no localization of the excitation on one BODIPY subunit occurs. The excitonic coupling is in BisBODIPY still larger than the geometry relaxation energy, which explains the absence of a pseudo-Jahn-Teller effect.

International audience; The combination of DNA and π-conjugated polyelectrolytes (CPEs) represents a promising approach to develop DNA hybridization biosensors, with potential applications for instance in the detection of DNA lesions and single-nucleotide polymorphisms. Here we exploit the remarkable optical properties of a cationic poly[3-(6′-(trimethylphosphonium)hexyl)thiophene-2,5-diyl] (CPT) to decipher the self-assembly of DNA and CPT. The ssDNA/CPT complexes have chiroptical signatures in the CPT absorption region that are strongly dependent on the DNA sequence, which we relate to differences in supramolecular interactions between the thiophene monomers and the various nucleobases. By studying DNA–DNA hybridization and melting processes on preformed ssDNA/CPT complexes, we observe sequence-dependent mechanisms that can yield DNA-condensed aggregates. Heating–cooling cycles show that non-equilibrium mixtures can form, noticeably depending on the working sequence of the hybridization experiment. These results are of high importance for the use of π-conjugated polyelectrolytes in DNA hybridization biosensors and in polyplexes.

Results are reported of Born-Oppenheimer molecular dynamics calculations performed on the singlet dication of norbornane, starting from the neutral ground state geometry. Intramolecular rearrangements and charge dissociation processes, which probably take place in the innermost valence ionization spectrum, are discussed and an analysis by means of natural bond orders and Wiberg bond indices has been performed. The outcome of these simulations and the observed cage fragmentation might explain a tremendous rise of electron-impact ( e , 2 e ) ionization cross sections of norbornane at electron binding energies around the double-ionization threshold.

We describe the synthesis and photophysical properties of a series of derivatives of pyrrolo[3,2-b]pyrrole-2,5(1H,4H)-dione-3,6-diyl (iDPP) linked to two oligothiophenes of variable length (nT). The iso-DPP-oligothiophenes (iDPPnTs) differ from the common pyrrolo[3,4-c]pyrrole-1,4(2H,5H)-dione-3,6-diyl-oligothiophene analogues (DPPnTs) by a different orientation of the two lactam rings in the bicyclic iDPP unit compared to DPP. In contrast to the highly fluorescent DPPnTs, the new isomeric iDPPnTs exhibit only very weak fluorescence. We demonstrate with the help of quantum-chemical calculations that this can be attributed to a different symmetry of the lowest excited state in iDPPnT (A in C2 symmetry) compared to DPPnTs (B) and the corresponding loss in oscillator strength of the lowest energy transition. Upon extending the oligothiophene moiety in the iDPPnTs molecules, the charge transfer character of the lowest A excited state becomes more pronounced. This tends to preclude high fluorescence quantum yields even in extended iDPPnTs systems.

Photochromism, the change of color upon irradiation, is a general property of quinoline derivatives, yet subtle differences in the geometric structure influence its occurrence. To investigate this relation, the mechanism of photoenolization of the photochromic compounds 3-benzoyl-2-benzyl-1-methyl-1H-quinoline-4-one (1) and 3-benzoyl-1,2-dibenzyl-1H-1,8 naphtyridin-4-one (2) as well as of the structurally closely related but nonphotochromic 3-benzoyl-1-benzyl-2-methyl-1H-1,8-naphtyridin-4-one (3) has been investigated theoretically using state-of-the-art quantum chemical methods. Focusing on the difference between 2 and 3 and stressing the absence of a phenyl group in the latter, the excited state potential energy surfaces along the photoenolization coordinate have been calculated for both. While the initial proton transfer initializing photoenolization is feasible when the phenyl group is present in 1 and 2, it is suppressed in 3.

The fluorescent marker Laurdan and its new derivative, C-Laurdan, have been investigated by means of theoretical calculations in a DOPC lipid bilayer membrane at room temperature, and a comparison is made with results from fluorescence experiments. Experimentally, the latter probe is known to have a higher sensitivity to the membrane polarity at the lipid headgroup region and has higher water solubility. Results from Molecular Dynamics (MD) simulations show that C-Laurdan is oriented with the carboxyl group toward the head of the membrane, with an angle of 50° between the molecular backbone and the normal to the bilayer, in contrast to the orientation of the Laurdan headgroup whose carbonyl group is oriented toward the polar regions of the membrane and which describes an angle of ca. 70-80° with the membrane normal. This contrast in orientation reflects the differences in transition dipole moment between the two probes and, in turn, the optical properties. QM/MM results of the probes show little differences for one- (OPA) and two-photon absorption (TPA) spectra, while the second harmonic generation (SHG) beta component is twice as large in Laurdan with respect to C-Laurdan probe. The fluorescence anisotropy decay analysis of the first excited state confirms that Laurdan has more rotational freedom in the DOPC membrane, while C-Laurdan experiences a higher hindrance, making it a better probe for lipid membrane phase recognition.

Nitrodibenzofuran (NDBF) has recently been established as photolabile protecting group and efficiently used as two-photon active cage. In this work, a computational approach is exploited to rationally design improved two-photon active caging groups based on this NDBF chromophore. For this objective, first the two-photon absorption (TPA) properties of NDBF are investigated in detail and a suitable theoretical approach for the reliable simulation of TPA spectra of this class of compounds is identified. Then, virtual chemical modifications are performed by introduction of substituents at the chromophore and replacement of the central furan ring by pyrolle, thiophene, and borrole heterocycles. Subsequently, the TPA properties of the resulting compounds are computed, and the influences of the chemical modifications on TPA properties investigated in detail. The most promising candidates with largely increased two-photon uncaging efficiencies are dimethylamino-substituted derivatives of NDBF, nitrodibenzopyrrol, and nitrodibenzothiophene.

The gas-phase photoelectron spectra of ethene, formaldehyde, formic acid and difluoromethane are simulated using the reflection principle and the unrestricted second-order algebraic diagrammatic construction [UADC(2)] scheme of the polarization propagator for the computation of the vertical-excited states of the cations at the equilibrium geometry of the parent neutral molecule. Comparison is made with experimental spectra and the established highly accurate ionization IP-ADC(3) theory to gain insight into the accuracy and applicability of recently developed excitation UADC schemes. Within UADC(2), we distinguish between the strict and extended schemes UADC(2)-s and UADC(2)-x. While the latter approach is found to slightly underestimate the experimental photoelectron spectra by 0.3 eV and can thus be regarded as a reliable scheme within the limits of the applied reflection principle and the underlying approximations, the UADC(2)-s scheme tends to overestimate the excitation energies by about 0.5 eV. Time-dependent density functional theory is also applied in combination with the standard B3LYP xc functional and turns out to be a useful computational tool for the simulation of the photoelectron spectra of the studied species.

1-Butene was investigated by rotational femtosecond degenerate four-wave mixing spectroscopy (fs DFWM) under supersonic expansion conditions as well as by quantum chemical calculations. Fs DFWM is a time-resolved rotational Raman spectroscopy, which allows for precise determination of rotational constants. The experimental fs DFWM spectrum was successfully reproduced by a fitted simulation using a single structure ascribed to the gauche conformer of 1-butene. The obtained rotational constants A = 22.6 ± 1.7 GHz, B = 4.1554 ± 0.0004 GHz and C = 4.0550 ± 0.0004 GHz are in excellent agreement with the ones from microwave spectroscopy. The cis conformer was not observed in the fs DFWM spectrum recorded under the low-temperature conditions of a supersonic expansion. The absence of the cis form along with simulations of a fs DFWM spectrum indicate that the cis conformer is at most equally but most likely less stable than the gauche rotamer. The experimental findings were supplemented by high level quantum chemical calculations, which predict the gauche form to have lower total energy than the cis structure.

The ring-puckering motion in cyclopentene as well as the hindered internal rotation around the central C–C bond in 1-butene have been studied by high-level quantum chemical calculations. Relevant potential energy surfaces of these molecules along these large-amplitude motions are provided as well as rotational constants are given allowing for thorough comparison with recent results from time-resolved femtosecond degenerate four-wave mixing (fs DFWM) spectroscopy. Emphasis is put on the performance of various post-Hartree Fock methods, the required level of electron correlation as well as the basis set quality.

The vertical excited electronic states of linearly fused neutral polyacenes (PACs) and their radical cations have been investigated using the algebraic diagrammatic construction scheme of second order (ADC(2)). While strict ADC(2) (ADC(2)-s) correctly reproduces trends for mainly singly excited states, in extended ADC(2) (ADC(2)-x) the description of doubly excited states is critically improved. It is shown that a combined application of strict and extended ADC(2) nicely reveals the importance of doubly excited configurations in the description of the excited state spectrum of the neutral PACs. In contrast to general expectation, our calculations of the lowest excited states of the radical cations of the PACs employing unrestricted ADC(2)-s and ADC(2)-x identified one B1 g electronic transition whose excitation energy increases with increasing molecular size. Thorough analysis of this electronic state and the involved molecular orbitals relates this unusual phenomenon to an increasing energy gap between t...

A review of an extensive series of theoretical studies of the valence one-electron and shake-up ionization spectra of polycyclic aromatic hydrocarbons is presented, along with new results for three planar quinone derivatives, obtained using one-particle Green's function (1p-GF) theory along with the so-called third-order algebraic diagrammatic construction [ADC(3)] scheme and the outer-valence Green's function (OVGF) approximation. These results confirm both for the π- and σ-band systems the rapid spreading, upon increasing system size, of many shake-up lines with significant intensities at outer-valence energies. Linear regressions demonstrate that with large conjugated molecules the location of the shake-up onset in the π-band system is merely determined by the energy of the frontier (HOMO, LUMO) orbitals. Electron pair removal effects are found to almost compensate the electron relaxation effects induced by ionization of π-levels, whereas the latter effects strongly dominate the ionization of more localized lone-pair ( n ) levels, and may lead to inversions of the energy order of Hartree–Fock (HF) orbitals. Therefore, although it increases upon a lowering of the HF band gap, and thus upon an increase of system size, the dependence of the one-electron ionization energies onto the quality of the basis set is lesser for π-levels than for σ-levels relating to electron lone pairs ( n ). Basis sets of triple- and quadruple-zeta quality are therefore required for treatments of the outermost π- and n -ionization energies approaching chemical accuracy [1 kcal/mol, i.e. 0.04 eV]. When 1p-GF theory invalidates Koopmans’ theorem and the energy order of HF orbitals, a comparison with Kohn–Sham orbital energies confirms the validity of the meta-Koopmans’ theorem for density functional theory.

The main purpose of the present work is to simulate from many-body quantum mechanical calculations the results of experimental studies of the valence electronic structure of n-hexane employing photoelectron spectroscopy (PES) and electron momentum spectroscopy (EMS). This study is based on calculations of the valence ionization spectra and spherically averaged (e, 2e) electron momentum distributions for each known conformer by means of one-particle Green's function [1p-GF] theory along with the third-order algebraic diagrammatic construction [ADC(3)] scheme and using Kohn-Sham orbitals derived from DFT calculations employing the Becke 3-parameters Lee-Yang-Parr (B3LYP) functional as approximations to Dyson orbitals. A first thermostatistical analysis of these spectra and momentum distributions employs recent estimations at the W1h level of conformational energy differences, by Gruzman et al. [J. Phys. Chem. A 2009, 113, 11974], and of correspondingly obtained conformer weights using MP2 geometrical, vibrational, and rotational data in thermostatistical calculations of partition functions beyond the level of the rigid rotor-harmonic oscillator approximation. Comparison is made with the results of a focal point analysis of these energy differences using this time B3LYP geometries and the corresponding vibrational and rotational partition functions in the thermostatistical analysis. Large differences are observed between these two thermochemical models, especially because of strong variations in the contributions of hindered rotations to relative entropies. In contrast, the individual ionization spectra or momentum profiles are almost insensitive to the employed geometry. This study confirms the great sensitivity of valence ionization bands and (e, 2e) momentum distributions on the molecular conformation and sheds further light on spectral fingerprints of through-space methylenic hyperconjugation, in both PES and EMS experiments.

The main purpose of the present work is to predict from benchmark many-body quantum mechanical calculations the results of experimental studies of the valence electronic structure of dimethoxymethane employing electron momentum spectroscopy, and to establish once and for all the guidelines that should systematically be followed in order to reliably interpret the results of such experiments on conformationally versatile molecules. In a first step, accurate calculations of the energy differences between stationary points on the potential energy surface of this molecule are performed using Hartree-Fock (HF) theory and post-HF treatments of improving quality (MP2, MP3, CCSD, CCSD(T), along with basis sets of increasing size. This study focuses on the four conformers of this molecule, namely the trans-trans (TT), trans-gauche (TG), gauche-gauche (G+G+), and gauche-gauche (G+G-) structures, belonging to the C2v, C1, C2, and Cs symmetry point groups, respectively. A focal point analysis supplemented by suited extrapolations to the limit of asymptotically complete basis sets is carried out to determine how the conformational energy differences at 0 K approach the full CI limit. In a second step, statistical thermodynamics accounting for hindered rotations is used to calculate Gibbs free energy corrections to the above energy differences, and to evaluate the abundance of each conformer in the gas phase. It is found that, at room temperature, the G+G+ species accounts for 96% of the conformational mixture characterizing dimethoxymethane. In a third step, the valence one-electron and shake-up ionization spectrum of dimethoxymethane is analyzed according to calculations on the G+G+ conformer alone by means of one-particle Green's function [1p-GF] theory along with the benchmark third-order algebraic diagrammatic construction [ADC(3)] scheme. A complete breakdown of the orbital picture of ionization is noted at electron binding energies above 22 eV. A comparison with available (e,2e) ionization spectra enables us to identify specific fingerprints of through-space orbital interactions associated with the anomeric effect. At last, based on our 1p-GF/ADC(3) assignment of spectral bands, accurate and spherically averaged (e,2e) electron momentum distributions at an electron impact energy of 1200 eV are computed from the related Dyson orbitals. Very significant discrepancies are observed with momentum distributions obtained for several outer-valence levels using standard Kohn-Sham orbitals.

Results of an experimental study of the valence electronic structure of difluoromethane employing high-resolution Electron Momentum Spectroscopy with various impact energies are reported. One-particle Green’s Function theory is utilized, for the first time, for computing accurate spherically averaged electron momentum distributions. These are derived from Dyson orbitals obtained using the third-order Algebraic Diagrammatic Construction (ADC(3)) scheme. The corresponding eigen-energies also accurately reproduce the (e, 2e) ionization spectrum. Shortcomings of empirical analyses of (e, 2e) experiments based on Kohn–Sham orbitals and eigen-energies are comparatively discussed. A failure of the target Hartree-Fock approximation is noted for the momentum distribution pertaining to the 1b 1 + 3b 2 + 5a 1 levels.

The valence one-electron and shake-up ionization spectra of stella-2,6-diene, stella-2,6-dione, bicyclo- (2.2.2)-octane-2,5-dione, and bicyclo-(2.2.1)-heptane-2,5-dione have been exhaustively studied, up to the double ioni- zation threshold and beyond, by means of one-particle Green's function theory. This study is based on calculations employing the outer-valence Green's function and the third-order algebraic diagrammatic construction schemes, along with a variety of basis sets. A comparison is made with available ultraviolet (He I) photoelectron and (e, 2e) electron- impact ionization spectra, with main focus on the identification of spectral fingerprints for cyclic strains and through- bond � -conjugation. As a byproduct, our results demonstrate that it is impossible to reliably assign complex (e, 2e) ionization spectra by resorting only to Hartree-Fock or Kohn-Sham orbital energies and to the related electron mo- mentum distributions.

In continuation of a recent study of the electronic structure of norbornane [J. Chem. Phys., 2004, 121, 10525] by means of electron momentum spectroscopy (EMS), we present Green's Function calculations of the ionization spectrum of this compound at the ADC(3) level using basis sets of varying quality, along with accurate evaluations at the CCSD(T) level of the vertical (26.5 eV) and adiabatic (22.1 eV) double ionization thresholds under C(2v) symmetry. The obtained results are compared with newly recorded ultraviolet photoemission spectra (UPS), up to binding energies of 40 eV. The theoretical predictions are entirely consistent with experiment and indicate that, in a vertical depiction of ionization, shake-up states at binding energies larger than approximately 26.5 eV tend to decay via emission of a second electron in the continuum. A band of s-type symmetry that has been previously seen at approximately 25 eV in the electron impact ionization spectra of norbornane is entirely missing in the UPS measurements and theoretical ADC(3) spectra. With regard to these results and to the time scales characterizing electron-electron interactions in EMS (10(-17) s) as compared with that (10(-13) s) of photon-electron interactions in UPS, and considering the p-type symmetry of the electron momentum distributions for the nearest 1b(1) and 1b(2) orbitals, this additional band can certainly not be due to adiabatic double ionization processes starting from the ground electronic state of norbornane, or to exceptionally strong vibronic coupling interactions between cationic states derived from ionization of the latter orbitals. It is therefore tentatively ascribed to autoionization processes via electronically excited and possibly dissociating states.

We report on the results of an exhaustive study of the valence electronic structure of norbornane (C7H12), up to binding energies of 29 eV. Experimental electron momentum spectroscopy and theoretical Green's function and density functional theory approaches were all utilized in this investigation. A stringent comparison between the electron momentum spectroscopy and theoretical orbital momentum distributions found that, among all the tested models, the combination of the Becke-Perdew functional and a polarized valence basis set of triple-zeta quality provides the best representation of the electron momentum distributions for all of the 20 valence orbitals of norbornane. This experimentally validated quantum chemistry model was then used to extract some chemically important properties of norbornane. When these calculated properties are compared to corresponding results from other independent measurements, generally good agreement is found. Green's function calculations with the aid of the third-order algebraic diagrammatic construction scheme indicate that the orbital picture of ionization breaks down at binding energies larger than 22.5 eV. Despite this complication, they enable insights within 0.2 eV accuracy into the available ultraviolet photoemission and newly presented (e,2e) ionization spectra, except for the band associated with the 1a(2)(-1) one-hole state, which is probably subject to rather significant vibronic coupling effects, and a band at similar to25 eV characterized by a momentum distribution of "s-type" symmetry, which Green's function calculations fail to reproduce. We note the vicinity of the vertical double ionization threshold at similar to26 eV. (C) 2004 American Institute of Physics.

In line with a recent study of the electronic structure of the cage compound norbornane (J. Chem. Phys. 121 (2004), 10525; J. Phys. Chem. A 109 (2005), 4267), symmetry adapted cluster expansion configuration interaction (SAC-CI) general R calculations have been performed and compared with results obtained by the third order algebraic diagrammatic construction scheme [ADC(3)]. Comparison has been made with previously performed electron momentum spectroscopy (EMS) and ultraviolet photo-electron measurements. The region around ∼25 eV (band 12), characterized by an elaborated band in the EMS spectrum which is missing in previous Green's function and ADC calculations, is investigated. This study is completed with outer-valence Green's function (OVGF) and SAC-CI/SD-R calculations, and results are obtained by employing (single and double) ionization extended second order ADC [ADC(2)-x]. Since ADC(3) only includes 2h-1p shake-up states, while SAC-CI general-R also includes higher order states, the agreement between both methods assures that the higher order shake-up states do not play an important role in the ionization spectrum of norbornane. While the band-12 issue of norbornane is therefore still open for further discussion, a tentative description in terms of ultrafast nuclear dynamical effects and autoionization processes has become more plausible.

The ring-puckering vibration in cyclopentene was studied by rotational time-resolved femtosecond degenerate four-wave mixing (fs DFWM) spectroscopy. The fs DFWM spectra of cyclopentene were measured both in a supersonic expansion and in a gas cell at room temperature. The room temperature fs DFWM spectrum has been satisfactorily reproduced by a fitted simulation based on a one-dimensional model for the ring-puckering vibration. This has allowed for the determination of energetic parameters of the ring-puckering motion such as the energy barrier to ring inversion of 274(+12/-20) cm(-1) and the equilibrium ring-puckering angle of 24.3 degrees . The derived dependences of the rotational constants A and B on the puckering angle resemble very closely those obtained by microwave spectroscopy. In addition, previous theoretical estimates of the ring inversion barrier of cyclopentene were improved by performing high level ab initio calculations. Zero-point vibrational energy correction was found to be essential for an accurate evaluation of the puckering potential. Altogether, this study provides a proof-of-principle of the applicability of the fs DFWM technique for investigating large amplitude intramolecular motions.

The potential energy surface of norbornane in its dicationic singlet ground state has been investigated in detail using density functional theory along with the nonlocal hybrid and gradient-corrected Becke three-parameter Lee-Yang-Parr functional (B3LYP) and the cc-pVDZ basis set. For the sake of more quantitative insight into the chemical reactions induced by double ionization of norbornane, this study was supplemented by a calculation of basic thermodynamic state functions coupled to a focal point analysis of energy differences obtained using correlation treatments and basis sets of improving quality, enabling an extrapolation of these energy differences at the CCSD(T) level in the limit of an asymptotically complete (cc-pV infinity Z) basis set. Our results demonstrate the likelihood of an ultrafast intramolecular rearrangement of the saturated hydrocarbon cage after a sudden removal of two electrons into a kinetically metastable five-membered cyclic C5H8+-CH+-CH3 intermediate, prior to a Coulomb explosion into C5H7+=CH2 and CH3+ fragments, which might explain a tremendous rise of electron-impact (e, 2e) ionization cross sections at electron binding energies around the double-ionization threshold. The first step is straightforward and strongly exothermic (DeltaH298 = -114.0 kcal mol-1). The second step is also exothermic (DeltaH298 = -10.2 kcal mol-1) but requires an activation enthalpy (DeltaH298) of 39.7 kcal/mol. The various factors governing the structure of this intermediate, such as electrostatic interactions, inductive effects, cyclic strains, and methylenic hyperconjugation interactions, are discussed in detail.

Results of a study of the valence electronic structure of norbornene (C(7)H(10)), up to binding energies of 30 eV, are reported. Experimental electron momentum spectroscopy (EMS) and theoretical Green's function and density functional theory approaches were utilized in this investigation. A stringent comparison between the electron momentum spectroscopy and theoretical orbital momentum distributions found that, among the tested models, the combination of the Becke-Perdew functional and a polarized valence basis set of triple-zeta quality provides the best representation of the electron momentum distributions for all 19 valence orbitals of norbornene. This experimentally validated model was then used to extract other molecular properties of norbornene (geometry, infrared spectrum). When these calculated properties are compared to corresponding results from independent measurements, reasonable agreement is typically found. Due to the improved energy resolution, EMS is now at a stage to very finely image the effective topology of molecular orbitals at varying distances from the molecular center, and the way the individual atomic components interact with each other, often in excellent agreement with theory. This will be demonstrated here. Green's Function calculations employing the third-order algebraic diagrammatic construction scheme indicate that the orbital picture of ionization breaks down at binding energies larger than about 22 eV. Despite this complication, they enable insights within 0.2 eV accuracy into the available ultraviolet emission and newly presented (e,2e) ionization spectra. Finally, limitations inherent to calculations of momentum distributions based on Kohn-Sham orbitals and employing the vertical depiction of ionization processes are emphasized, in a formal discussion of EMS cross sections employing Dyson orbitals.

An earlier proposed approach to molecular response functions based on the intermediate state representation (ISR) of polarization propagator and algebraic-diagrammatic construction (ADC) approximations is for the first time employed for calculations of nonlinear response properties. The two-photon absorption (TPA) spectra are considered. The hierarchy of the first- and second-order ADC∕ISR computational schemes, ADC(1), ADC(2), ADC(2)-x, and ADC(3/2), is tested in applications to H(2)O, HF, and C(2)H(4) (ethylene). The calculated TPA spectra are compared with the results of coupled cluster (CC) models and time-dependent density-functional theory (TDDFT) calculations, using the results of the CC3 model as benchmarks. As a more realistic example, the TPA spectrum of C(8)H(10) (octatetraene) is calculated using the ADC(2)-x and ADC(2) methods. The results are compared with the results of TDDFT method and earlier calculations, as well as to the available experimental data. A prominent feature of octatetraene and other polyene molecules is the existence of low-lying excited states with increased double excitation character. We demonstrate that the two-photon absorption involving such states can be adequately studied using the ADC(2)-x scheme, explicitly accounting for interaction of doubly excited configurations. Observed peaks in the experimental TPA spectrum of octatetraene are assigned based on our calculations.

Orbital imaging experiments employing Electron Momentum Spectroscopy are subject to many complications, such as distorted wave effects, conformational mobility in the electronic ground state, ultra-fast nuclear dynamics in the final state, or a dispersion of the ionization intensity over electronically excited (shake-up) configurations of the cation. The purpose of the present contribution is to illustrate how a proper treatment of these complications enables us to probe in momentum space the consequences of electron correlation and nuclear dynamics in neutral and cationic states.

The scope of the present work is to reconcile electron momentum spectroscopy with elementary thermodynamics, and refute conclusions drawn by Saha et al. in J. Chem. Phys. 123, 124315 (2005) regarding fingerprints of the gauche conformational isomer of 1,3-butadiene in electron momentum distributions that were experimentally inferred from gas phase (e,2e) measurements on this compound [M. J. Brunger et al., J. Chem. Phys. 108, 1859 (1998)]. Our analysis is based on thorough calculations of one-electron and shake-up ionization spectra employing one-particle Green's function theory along with the benchmark third-order algebraic diagrammatic construction [ADC(3)] scheme. Accurate spherically averaged electron momentum distributions are correspondingly computed from the related Dyson orbitals. The ionization spectra and Dyson orbital momentum distributions that were computed for the trans-conformer of 1,3-butadiene alone are amply sufficient to quantitatively unravel the shape of all available experimental (e,2e) electron momentum distributions. A comparison of theoretical ADC(3) spectra for the s-trans and gauche energy minima with inner- and outer-valence high-resolution photoelectron measurements employing a synchrotron radiation beam [D. M. P. Holland et al., J. Phys. B 29, 3091 (1996)] demonstrates that the gauche structure is incompatible with ionization experiments in high-vacuum conditions and at standard temperatures. On the other hand, outer-valence Green's function calculations on the s-trans energy minimum form and approaching basis set completeness provide highly quantitative insights, within approximately 0.2 eV accuracy, into the available experimental one-electron ionization energies. At last, analysis of the angular dependence of relative (e,2e) ionization intensities nicely confirms the presence of one rather intense pi(-2) pi(*+1) satellite at approximately 13.1 eV in the ionization spectrum of the s-trans conformer.