A scrutinous study of the catalytic cycle for electrochemical CO2 reduction by the ruthenium 2,2:6,2-terpyridine (tpy) 2,2-bipyridine (bpy) class of catalysts is presented. An unprecedented 2-(C,O)-carboxycarboxylatoruthenium(II) metalacyclic intermediate, critical for C-O bond dissociation at low overpotentials, so far precluded from mechanistic considerations of polypyridyl transition metal complex catalysts, is unearthed by infra-red spectroscopy coupled to controlled potential electrolysis in corroboration with density functional theory (DFT) investigations. Thermodynamic and kinetic analyses of the intermediate reveal the important role of the structural flexibility of polypyridyl ligands and fine electronic tunability of the metal center, along with kinetic trans effect, in propelling catalysis at lower overpotentials. The choice of metal center, Ru in the present case, points to the fact that the requirement of an additional Lewis acid to enhance C-O bond dissociation, hence increase the catalytic rate or turnover, can be circumvented.

Within the self-consistent field approximation, computationally tractable expressions for the isotropic second-order hyperpolarizability have been derived and implemented for the calculation of two-photon absorption cross sections. The novel tensor average formulation presented in this work allows for the evaluation of isotropic damped cubic response functions using only similar to 3.3% (one-photon off-resonance regions) and similar to 10% (one-photon resonance regions) of the number of auxiliary Fock matrices required when explicitly calculating all the needed individual tensor components. Numerical examples of the two-photon absorption cross section in the one-photon off-resonance and resonance regions are provided for alanine-tryptophan and 2,5-dibromo-1,4-bis(2-(4-diphenylaminophenyl)vinyl)-benzene. Furthermore, a benchmark set of 22 additional small- and medium-sized organic molecules is considered. In all these calculations, a quantitative assessment is made of the reduced and approximate forms of the cubic response function in the one-photon off-resonance regions and results demonstrate a relative error of less than similar to 5% when using the reduced expression as compared to the full form of the isotropic cubic response function.

Control over the photophysical properties and molecular organization of pi-conjugated oligothiophenes is essential to their use in organic electronics. Herein we synthesized and characterized a variety of anionic pentameric oligothiophenes with different substitution patterns of L- or D-tyrosine at distinct positions along the thiophene backbone. Spectroscopic, microscopic, and theoretical studies of L- or D-tyrosine substituted pentameric oligothiophene conjugates revealed the formation of optically active pi-stacked self-assembled aggregates under acid conditions. The distinct photophysical characteristics, as well as the supramolecular structures of the assemblies, were highly influenced by the positioning of the L- or D-tyrosine moieties along the thiophene backbone. Overall, the obtained results clearly demonstrate how fundamental changes in the position of the enantiomeric side-chain functionalities greatly affect the optical properties as well as the architecture of the self-assembled supramolecular structures.

Nd3+-sensitized upconversion nanoparticles (UCNPs) can be excited by both 980 and 808 nm light, which is regarded as a particularly advantageous property of these particles. In this work, we demonstrate that the nanoparticles can exhibit significantly different response when excited at these two excitation wavelengths, showing dependence on the intensity of the excitation light and the way it is distributed in time. Specifically, with 808 nm excitation saturation in the emitted luminescence is more readily reached with increasing excitation intensities than upon 980 nm excitation. This is accompanied by delayed upconversion luminescence (UCL) kinetics and weaker UCL intensities. The different luminescence response at 808 and 980 nm excitation reported in this work is relevant in a manifold of applications using UCNPs as labels and sensors. This could also open new possibilities for multi-wavelength excitable UCNPs for upconversion color display and in laser-scanning microscopy providing selective readouts and sub-sectioning of samples.

We investigate the extent to which the class of Dirac materials in two-dimensions provides general statements about the behavior of both fermionic and bosonic Dirac quasiparticles in the interacting regime. For both quasiparticle types, we find common features for the interaction induced renormalization of the conical Dirac spectrum. We perform the perturbative renormalization analysis and compute the self-energy for both quasiparticle types with different interactions and collate previous results from the literature whenever necessary. Guided by the systematic presentation of our results in table1, we conclude that long-range interactions generically lead to an increase of the slope of the single-particle Dirac cone, whereas short-range interactions lead to a decrease. The quasiparticle statistics does not qualitatively impact the self-energy correction for long-range repulsion but does affect the behavior of short-range coupled systems, giving rise to different thermal power-law contributions. The possibility of a universal description of the Dirac materials based on these features is also mentioned.

An in-depth analysis of the vibronic absorption spectra for the recently synthesized blue-fluorescent OLED emitters bis[(1,2)(5,6)]indoloanthracene and biscarbazolo[3,4-a:3',4'-h]anthracene has been carried out computationally at the density functional theory level within the Franck-Condon approximation. These molecules are characterized by extended and rich electronic absorption spectra with most absorption bands being of vibronic origin. The first excited singlet state of bis[(1,2)(5,6)]indoloanthracene compound demonstrates a clear observable double-peak vibronic progression for two different active modes in the absorption spectrum, while the S-2 state is vibronically inactive. In contrast, for the larger biscarbazolo[3,4-a:3',4'-h]anthracene compound the S-0 -> S-2 transition demonstrates well-resolved intense vibronic bands which overlap the less intense progressions of few modes in the S-0 -> S-1 transition. We have also found, that even the higher-lying and very intense S-0 -> S-4 and S-0 -> S-5 transitions for bis[(1,2)(5,6)]indoloanthracene and biscarbazolo[3,4-a:3',4'-h]anthracene, respectively, are characterized by clear vibronic progressions in excellent agreement with experimental spectra.

The electronic structure, absorption and emission spectra, aromaticity and photophysical behavior of the recently synthesized tetrasilatetrathia[8]circulene and tetragermatetrathia[8]circulene compounds have been studied computationally. Both compounds demonstrate a specific bifacial aromaticity, which is unusual for hetero[8]circulenes; the inner eight-membered core sustains an expected strong paratropic magnetically-induced ring current, while the outer perimeter contains saturated Si(Et)(2) and Ge(Et)(2) moieties which break the conjugation between the thiophene rings. The overall magnetically-induced ring current for both studied circulenes is close to zero because of the strong local diatropic currents in each thiophene ring that compensate the paratropic counterpart. The electronic absorption and emission spectra of tetrasilatetrathia[8]circulene and tetragermatetrathia[8]circulene demonstrate a clear visible vibronic progression. The 0-0 band is the most active one in the absorption spectra, while in the fluorescence spectra the 0-1 band composed of several normal vibrations is more intense compared with the 0-0 band in excellent agreement with experiment. Accounting for spin-orbit coupling effects, an analysis of the photophysical constants for the two compounds demonstrates: (1) a clear manifestation of the internal heavy atom effect on the inter-system crossing efficiency; (2) one to two order domination of non-radiative rates over the fluorescence rate; and (3) that the S-1-S-0 internal conversion is extremely slow and can not compete with the fluorescence, while the S-1-T-n inter-system crossing is a main deactivation channel of the S-1 excited state. These results provide new insight into the electronic structure and photophysics of tetrasilatetrathia[8]circulene and tetragermatetrathia[8]circulene as novel standalone representatives of hetero[8]circulenes - tetraannelated derivatives of tetrathienylene.

Cyclo[18]carbon (C-18) is studied computationally at the density functional theory (DFT) and ab initio levels to obtain insight into its electronic structure, aromaticity, and adsorption properties on a NaCl surface. DFT functionals with a small amount of Hartree-Fock exchange fail to determine the experimentally observed polyyne molecular structure, revealing a cumulene-type geometry. Exchange-correlation functionals with a large amount of Hartree-Fock exchange as well as ab initio CASSCF calculations yield the polyyne structure as the ground state and the cumulene structure as a transition state between the two inverted polyyne structures through a Kekule distortion. The polyyne and the cumulene structures are found to be doubly Huckel aromatic. The calculated adsorption energy of cyclo[18]carbon on the NaCl surface is small (37 meV/C) and almost the same for both structures, implying that the surface does not stabilize a particular geometry.

The recently synthesized twisted thia-norhexaphyrin and its multiply annulated polypyrrolic derivatives have been studied computationally. Gauge-including magnetically induced current calculations predict a global nonaromatic character of the initial thia-norhexaphyrin due to the highly-twisted conformation of the macrocycle. Upon the oxidation of the thia-norhexaphyrin four multiply annulated polypyrrolic aromatic macrocycles are formed for which the global aromatic character is confirmed in agreement with experimentally measured H-1 NMR spectra. The calculation of the proton chemical shifts for the studied compounds by direct comparison with the tetramethylsilane standard leads to a significant mean absolute error. At the same time a linear regression procedure for the two selected groups of protons (CH and NH protons) provides much better values of calculated chemical shifts and tight correlation with experiment. The separate consideration of NH protons is motivated by the numerous intermolecular hydrogen bonds in which the protons are involved, which induce considerable upfield shifts, leading to a significant underestimation of the corresponding chemical shifts. Such a selected correlation can be used for accurate estimation of proton chemical shifts of the related porphyrinoids. Bader's theory of Atoms in Molecules has been applied for the studied twisted thia-norhexaphyrin and its multiply annulated polypyrrolic derivatives to characterize intramolecular H-bonds and other non-covalent interactions.

Owing to the fact that weakly-coupled Cu(II) complexes are potentially applicable in the fields of spintronics and single-molecule magnets we have studied one particularly conspicuous case – a tetranuclear square-planar complex of Cu(II) ions with a π-extended tetraporphyrin ligand (Tetrahedron, 2008, 64, 11433), the structural criteria of which, with very long distances between the paramagnetic centers, can sensibly define the exchange coupling constants and magnetic behaviour. We use the “broken symmetry” density functional theory formalism for various spin states (open-shell singlet, triplet and quintet states). The calculated value of the magnetic exchange integral corresponds to a very weak antiferromagnetic coupling between the neighboring Cu(II) ions (Jcalc = –1.48 cm−1(calculated) Jexp = −1.16 cm−1 (experiment)). The opposite Cu(II) ions are coupled ferromagnetically with an extremely small exchange constant (jcalc = 0.09 cm−1 (calculated) that corresponds to the open-shell singlet ground state of the following spin configuration↑↓↑↓. The exchange mechanism between the [Cu(n) + 4N] localized singly-occupied “magnetic” orbitals of the dxy(Cu) + 4sp2(N) nature indicates a diffuse non-zero overlap between them on the Carbon atoms of the organic ligand. The numerical analysis of atomic spin densities and corresponding decomposition coefficients for the singly-occupied “magnetic” orbitals confirm the proposed exchange mechanism. This superexchange pathway is mediated by the in-plane sp2-hybrid orbitals of the Carbon atoms that couple four [Cu + 4N] fragments by the σ-bond system. For more detailed characterization of the target system a topological analysis of electron density distributions in the high-spin quintet states has been carried out using the Bader's method “quantum theory of atoms in molecules”.

New perspective 1.4 nm thick spin-polarized triple heterostructures based on graphene sandwiched between two vanadium ditelluride monolayers (VTe2/graphene/VTe2) were studied using ab initio DFT technique. Both possible trigonal prismatic (H-VTe2) and octahedral (T-VTe2) VTe2 phases were considered to design and study graphene-based heterostructures. It was shown that the interaction with graphene changes the electronic structure of 2D T-VTe2 from metallic to half-metallic, making T phase perspective to be used for magnetic tunnel junctions. The electronic subsystem of graphene fragment is slightly hole doped. Calculated tunnel magne-toresistance ratio for the favorable heterostructure configuration estimated within the Julliere model is 220%, which opens a way to use VTe2/graphene/VTe2 as prospective magnetic tunnel junction in novel spintronic nanodevices based on tunnel magnetic resistance and spin transfer torque effects.

In this study, we systematically investigate the decay characteristics of upconversion luminescence (UCL) under anti-Stokes excitation through numerical simulations based on rate-equation models. We find that a UCL decay profile generally involves contributions from the sensitizer's excited-state lifetime, energy transfer and cross-relaxation processes. It should thus be regarded as the overall temporal response of the whole upconversion system to the excitation function rather than the intrinsic lifetime of the luminescence emitting state. Only under certain conditions, such as when the effective lifetime of the sensitizer's excited state is significantly shorter than that of the UCL emitting state and of the absence of cross-relaxation processes involving the emitting energy level, the UCL decay time approaches the intrinsic lifetime of the emitting state. Subsequently, Stokes excitation is generally preferred in order to accurately quantify the intrinsic lifetime of the emitting state. However, possible cross-relaxation between doped ions at high doping levels can complicate the decay characteristics of the luminescence and even make the Stokes-excitation approach fail. A strong cross-relaxation process can also account for the power dependence of the decay characteristics of UCL.

Charge separation dynamics after the absorption of a photon is a fundamental process relevant both for photosynthetic reaction centers and artificial solar conversion devices. It has been proposed that quantum coherence plays a role in the formation of charge carriers in organic photovoltaics, but experimental proofs have been lacking. Here we report experimental evidence of coherence in the charge separation process in organic donor/acceptor heterojunctions, in the form of low frequency oscillatory signature in the kinetics of the transient absorption and nonlinear two-dimensional photocurrent spectroscopy. The coherence plays a decisive role in the initial 200 femtoseconds as we observe distinct experimental signatures of coherent photocurrent generation. This coherent process breaks the energy barrier limitation for charge formation, thus competing with excitation energy transfer. The physics may inspire the design of new photovoltaic materials with high device performance, which explore the quantum effects in the next-generation optoelectronic applications.

Featured Application Herein, an innovative methodology, called X-ray chronoscopy, is proposed for exploration of ultrafast processes in matter with attosecond precision using current XFEL sources. The method is based on measuring the change in an X-ray pulse temporal profile induced by interaction with a medium. X-ray free electron lasers (XFELs) have provided scientists opportunities to study matter with unprecedented temporal and spatial resolutions. However, access to the attosecond domain (i.e., below 1 femtosecond) remains elusive. Herein, a time-dependent experimental concept is theorized, allowing us to track ultrafast processes in matter with sub-fs resolution. The proposed X-ray chronoscopy approach exploits the state-of-the-art developments in terahertz streaking to measure the time structure of X-ray pulses with ultrahigh temporal resolution. The sub-femtosecond dynamics of the saturable X-ray absorption process is simulated. The employed rate equation model confirms that the X-ray-induced mechanisms leading to X-ray transparency can be probed via measurement of an X-ray pulse time structure.

The GALILEO gamma-ray spectrometer, installed at the Laboratori Nazionali di Legnaro (LNL), benefits from intense stable beams provided by the Tandem-ALPI-PIAVE accelerator complex and from radioactive beams to be delivered in the near future by the SPES facility. The spectrometer is complemented with a variety of ancillary devices to allow for nuclear structure and reaction studies. The 4 pi Si-ball array EUCLIDES coupled to the GALILEO gamma-ray spectrometer represents one of the commonly used setup for experiments aiming at spectroscopic studies. High-efficiency detection of light-charged particles in a fusion-evaporation reaction guarantees good discrimination of different reaction channels and provides essential information for the kinematic reconstruction. In this paper we discuss a configuration of the EUCLIDES array developed for the lifetime measurements of nuclear excited states populated in a fusion-evaporation reaction. In such a configuration a part of the EUCLIDES detectors is disassembled allowing for the installation of a plunger device in the reaction chamber. The reduced configuration of EUCLIDES provides high detection efficiency necessary for reliable light charged-particle discrimination. We report on the commissioning experiment focused on the Ni-58(Ni-58,3p)I-113 reaction. The lifetimes of 11/2(-) and 15/2(-) states were measured by applying the Recoil Distance Doppler Shift method to be equal to 206(20) ps and 7.9(12) ps correspondingly and were in good agreement with the values cited in the literature. Thus, the combination of the GALILEO and EUCLIDES arrays, and the plunger device has resulted in a powerful experimental setup to determine lifetimes of excited states in neutron-deficient nuclei in the picosecond range.

While the anomalous non-additive size-dependencies of static dipole polarizabilities and van der Waals C-6 dispersion coefficients of carbon fullerenes are well established, the widespread reported scalings for the latter (ranging from N-2.2 to N-2.8) call for a comprehensive first-principles investigation. With a highly efficient implementation of the linear complex polarization propagator, we have performed Hartree-Fock and Kohn-Sham density functional theory calculations of the frequency-dependent polarizabilities for fullerenes consisting of up to 540 carbon atoms. Our results for the static polarizabilities and C-6 coefficients show scalings of N-1.2 and N-2.2, respectively, thereby deviating significantly from the previously reported values obtained with the use of semi-classical/empirical methods. Arguably, our reported values are the most accurate to date as they represent the first ab initio or first-principles treatment of fullerenes up to a convincing system size.

We demonstrate that contemporary computational resources allow for accurate theoretical studies of systems matching recent advances in experimental helicene chemistry. Concerned with first-principles calculations of carbohelicenes, our work surpasses CH[12] as the largest system investigated to date and unravels trends in the electronic structure of the low-lying states of the homologous series. Utilizing a highly efficient implementation of linear response algorithms, we present electronic circular dichroism (CD) spectra of carbohelicenes ranging from CH[5] to CH[30] at the level of Kohn-Sham density-functional theory. Our results for a systematic increase in system size show the emergence of new CD bands that subsequently rise to intensities dominating the spectrum. The spectral band progressions exhibit a periodicity directly linked to the number of overlapping layers of conjugation. While our findings rectify the current understanding of the electronic structure of carbohelicenes, they also serve as a general call for caution regarding the extrapolation of trends from small system ranges.

Expressions for analytical molecular gradients of core-excited states have been derived and implemented for the hierarchy of algebraic diagrammatic construction (ADC) methods up to extended second-order within the core-valence separation (CVS) approximation. We illustrate the use of CVS-ADC gradients by determining relaxed core-excited state potential energy surfaces and optimized geometries for water, formic acid, and benzene. For water, our results show that in the dissociative lowest core-excited state, a linear configuration is preferred. For formic acid, we find that the O K-edge lowest core-excited state is non-planar, a fact that is not captured by the equivalent core approximation where the core-excited atom with its hole is replaced by the "Z + 1" neighboring atom in the periodic table. For benzene, the core-excited state gradients are presented along the Jahn-Teller distorted geometry of the 1s -> pi* excited state. Our development may pave a new path to studying the dynamics of molecules in their core-excited states.

A methodology implemented to compute photoionization cross sections beyond the electric dipole approximation using Gaussian type orbitals for the initial state and plane waves for the final state is applied to molecules of various sizes. The molecular photoionization cross sections computed for valence molecular orbitals as a function of photon energy present oscillations due to the wave-like nature of both the outgoing photoelectron and of the incoming photon. These oscillations are damped by rotational and vibrational averaging or by performing a k-point summation for the solid state case. For core orbitals, the corrections introduced by going beyond the electric dipole approximation are comparable to the atomic case. For valence orbitals, nondipole corrections to the total photoinization cross sections can reach up to 20% at photon energies above 1 keV. The corrections to the differential cross sections calculated at the magic angle are larger, reaching values between 30% and 50% for all molecules included. Our findings demonstrate that photoelectron spectroscopy, especially angle-resolved, on, e.g., molecules and clusters on surfaces, using high photon energies, must be accompanied by theories that go beyond the electric dipole approximation.

The influence of core-hole delocalization for x-ray photoelectron, x-ray absorption, and x-ray emission spectrum calculations is investigated in detail using approaches including response theory, transition-potential methods, and ground state schemes. The question of a localized/delocalized vacancy is relevant for systems with symmetrically equivalent atoms, as well as near-degeneracies that can distribute the core orbitals over several atoms. We show that the issues relating to core-hole delocalization are present for calculations considering explicit core-hole states, e.g., when using a core-excited or core-ionized reference state or for fractional occupation numbers. As electron correlation eventually alleviates the issues, but even when using coupled-cluster single-double and perturbative triple, there is a notable discrepancy between core-ionization energies obtained with localized and delocalized core-holes (0.5 eV for the carbon K-edge). Within density functional theory, the discrepancy correlates with the exchange interaction involving the core orbitals of the same spin symmetry as the delocalized core-hole. The use of a localized core-hole allows for a reasonably good inclusion of relaxation at a lower level of theory, whereas the proper symmetry solution involving a delocalized core-hole requires higher levels of theory to account for the correlation effects involved in orbital relaxation. For linear response methods, we further show that if x-ray absorption spectra are modeled by considering symmetry-unique sets of atoms, care has to be taken such that there are no delocalizations of the core orbitals, which would otherwise introduce shifts in absolute energies and relative features.

A methodology is developed to compute photoionization cross sections beyond the electric dipole approximation from response theory, using Gaussian type orbitals and plane waves for the initial and final states, respectively. The methodology is applied to compute photoionization cross sections of atoms and ions from the first four rows of the periodic table. Analyzing the error due to the plane wave description of the photoelectron, we find kinetic energy and concomitant photon energy thresholds above which the plane wave approximation becomes applicable. The correction introduced by going beyond the electric dipole approximation increases with photon energy and depends on the spatial extension of the initial state. In general, the corrections are below 10% for most elements, at a photon energy reaching up to 12 keV. 2019 Author(s).

It is established that density functional theory (DFT) + U is a better choice compared to DFT for describing the correlated electron metal center in organometallics. The value of the Hubbard U parameter may be determined from linear response, either by considering the response of the metal site alone or by additionally considering the response of other sites in the compound. We analyze here in detail the influence of ligand shells of increasing size on the U parameter calculated from the linear response for five transition metal phthalocyanines. We show that the calculated multiple-site U ligand atoms that are mainly responsible for this difference are is larger than the single-site U by as much as 1 eV and the ligand atoms that are mainly responsible for this difference are the isoindole nitrogen atoms directly bonded to the central metal atom. This suggests that a different U value may be required for computations of chemisorbed molecules compared to physisorbed and gas-phase cases.

A new series of TADF emitters with donor-acceptor or donor-acceptor-donor structure containing 2,7-dimethoxycarbazole donor moiety and diphenylsulfone acceptor unit were synthesized and employed in non-doped sky-blue organic light emitting diodes with the external quantum efficiency reaching 9.0%. Thermal, optical and photophysical properties of for D-A and D-A-D compounds containing one or two tert-butyl groups attached to C-3 and C-6 positions of 2,7-dimethoxycarbazole moiety were studied and compared with those of the corresponding compounds containing no tert-butyl groups. Studies of photophysical properties of the compounds confirmed TADF nature of their emission. Computational studies revealed that small modification of the donor moiety could have a significant impact on the TADF mechanism turning it from vibronically induced TADF mediated by the T-2 state to the common TADF which occurs through the direct reverse intersystem crossing between the S-1 and T-1 states. New principle of purposeful of molecular design of TADF emitters with controlled efficiency of reverse intersystem crossing by only small functionalization of donor fragments is proposed.

Dioxygen (O-2) activation is a vital step in many oxidation reactions, and a graphitic carbon nitride (g-C3N4) sheet is known as a famous semiconductor catalytic material. Here, we report that the atomic boron (B)-doped g-C3N4 (B/g-C3N4) can be used as a highly efficient catalyst for O-2 activation. Our first-principles results show that O-2 can be easily chemisorbed at the B site and thus can be highly activated, featured by an elongated O-O bond (similar to 1.52 angstrom). Interestingly, the O-O cleavage is almost barrier free at room temperatures, independent of the doping concentration. It is revealed that the B atom can induce considerable spin polarization on B/g-C3N4, which accounts for O-2 activation. The doping concentration determines the coupling configuration of net-spin and thus the magnitude of the magnetism. However, the distribution of net-spin at the active site is independent of the doping concentration, giving rise to the doping concentration-independent catalytic capacity. The unique monolayer geometry and the existing multiple active sites may facilitate the adsorption and activation of O-2 from two sides, and the newly generated surface oxygen-containing groups can catalyze the oxidation coupling of methane to ethane. The present findings pave a new way to design g-C3N4-based metal-free catalysts for oxidation reactions.

In this paper we put forward some historical notes on the development of computational chemistry toward applications of x-ray spectroscopies. We highlight some of the important contributions by Enrico Clementi as method and program developer and as a supporter of this branch of computational research. We bring up a modern example based on the very recent experimental development of x-ray absorption of cationic molecules. As we show this spectroscopy poses new challenges for electronic structure theory and the electron correlation problem.

The distribution and protonation states of amino acids in water droplets are of considerable concern in studies on the formation of clouds in the atmosphere as well as in many biological contexts. In the present work we use the amino acid cysteine as a prototypical example and explore the protonation states of this molecule in aqueous solution, which are strongly affected by the acidity of the environment and also can show different distributions between surface and bulk. We use a combination of X-ray photoelectron chemical shift measurements, density functional theory calculations of the shifts, and reactive force field molecular dynamics simulations of the underlying structural dynamics. We explore how the photoelectron spectra distinctly reflect the different protonation states that are generated by variation of the solution acidity and how the distribution of these protonation states can differ between bulk and surface regions. At specific pH values, we find that the distribution of the cysteine species at the surface is quite different from that in bulk, in particular, for the appearance in the surface region of species which do not exist in bulk. Some ramifications of this finding are discussed.

Electron transport through metal-organic frameworks by ahopping mechanism between discrete redox active sites is coupled to diffusion-migration of charge-balancing counter cations. Experimentally determinedapparent diffusion coefficients,Deapp, that characterize this form of chargetransport thus contain contributions from both processes. While this is wellestablished for MOFs, microscopic descriptions of this process are largelylacking. Herein, we systematically lay out different scenarios for cation-coupledelectron transfer processes that are at the heart of charge diffusion throughMOFs. Through systematic variations of solvents and electrolyte cations, it isshown that theDeappfor charge migration through a PIZOF-type MOF,Zr(dcphOH-NDI) that is composed of redox-active naphthalenediimide(NDI) linkers, spans over 2 orders of magnitude. More importantly, however,the microscopic mechanisms for cation-coupled electron propagation arecontingent on differing factors depending on the size of the cation and its propensity to engage in ion pairs with reduced linkers,either non-specifically or in defined structural arrangements. Based on computations and in agreement with experimental results, weshow that ion pairing generally has an adverse effect on cation transport, thereby slowing down charge transport. In Zr(dcphOH-NDI), however, specific cation-linker interactions can open pathways for concerted cation-coupled electron transfer processes thatcan outcompete limitations from reduced cationflux.

Observing and controlling molecular motion and in particular rotation are fundamental topics in physics and chemistry. To initiate ultrafast rotation, one needs a way to transfer a large angular momentum to the molecule. As a showcase, this was performed by hard X-ray C1s ionization of carbon monoxide accompanied by spinning up the molecule via the recoil "kick" of the emitted fast photoelectron. To visualize this molecular motion, we use the dynamical rotational Doppler effect and an X-ray "pump-probe" device offered by nature itself: the recoil-induced ultrafast rotation is probed by subsequent Auger electron emission. The time information in our experiment originates from the natural delay between the C1s photoionization initiating the rotation and the ejection of the Auger electron. From a more general point of view, time-resolved measurements can be performed in two ways: either to vary the "delay" time as in conventional time-resolved pump-probe spectroscopy and use the dynamics given by the system, or to keep constant delay time and manipulate the dynamics. Since in our experiment we cannot change the delay time given by the core-hole lifetime tau, we use the second option and control the rotational speed by changing the kinetic energy of the photoelectron. The recoil-induced rotational dynamics controlled in such a way is observed as a photon energy-dependent asymmetry of the Auger line shape, in full agreement with theory. This asymmetry is explained by a significant change of the molecular orientation during the core-hole lifetime, which is comparable with the rotational period.

Neomorphic mutation R140Q in the metabolic enzyme isocitrate dehydrogenase 2 (IDH2) is found to be a driver mutation in cancers. Recent studies revealed that allosteric inhibitors could selectively inhibit IDH2/R140Q and induce differentiation of TF-1 erythroleukemia and primary human AML cells. However, the allosteric inhibition mechanism is not very clear. Here, we report the results from computational studies that AGI-6780 binds tightly with the divalent cation binding helices at the homodimer interface and prevents the transition of IDH2/R140Q homodimer to a closed conformation that is required for catalysis, resulting in the decrease of the binding free energy of NADPHs. If the allosteric inhibitor is removed, the original open catalytic center of IDH2/R140Q will gradually reorganize to a quasi-closed conformation and the enzymatic activity might recover. Unlike IDH2/R140Q, AGI-6780 locks one monomer of the wild-type IDH2 in an inactive open conformation and the other in a half-closed conformation, which can be used to explain the selectivity of AGI-6780. Our results suggest that conformational changes are the primary contributors to the inhibitory potency of the allosteric inhibitor. Our study will also facilitate the understanding of the inhibitory and selective mechanisms of AG-221 (a promising allosteric inhibitor that has been approved by FDA) for mutant IDH2.

Photo-/ion-induced ionization and dissociation processes are commonly observed for polycyclic aromatic hydrocarbon (PAH) molecules. This work performs theoretical studies of PAHs and their fragments. Molecular dynamics simulations in combination with static quantum chemical calculations reveal that following a single hydrogen atom loss, the fragments, PAH-H, are extremely reactive. They catch a neighbor molecule within picoseconds to form a covalently bonded large molecule regardless of orientations/angles and temperatures. We calculate the infrared spectra of the covalently bonded molecules, which indicate that such species could be the carrier of unidentified infrared emission bands. It also implies that regular PAHs might be less abundant in space than what is expected. 

Aims. Large compact polycyclic aromatic hydrocarbon molecules (PAHs) present special interest in the astrochemical community. A key issue in analyses of large PAHs is understanding the effect that temperature and anharmonicity have on different vibrational bands, and thus interpreting the infrared (IR) spectra for molecules under various conditions. Methods. Because of the huge amount of interactions/resonances in large PAHs, no anharmonic IR spectrum can be produced with static/time-independent ab initio method, especially for the molecules with D6h symmetry, e.g., coronene and circumcoronene. In this work, we performed molecular dynamics simulations to generate anharmonic IR spectra of coronene and circumcoronene. Results. The method is validated for small PAHs, i.e., naphthalene and pyrene. We find that the semiempirical method PM3 produces accurate band positions with an error <5 cm(-1). Furthermore, we calculate the spectra at multiple temperatures and find a clear trend toward band shifting and broadening.

Anharmonic infrared (IR) spectra are crucial for the study of interstellar polycyclic aromatic hydrocarbon (PAH) molecules. This work aims to provide a comprehensive study of the features that may influence the accuracy of anharmonic IR spectra of PAHs so that a reliable spectrum that incorporates all necessary features for interpreting the observational IR spectra can be obtained. Six PAHs are investigated: naphthalene, anthracene, pyrene, chrysene, 9,10-dimethylanthracene, and 9,10-dihydroanthracene. The NIST spectra and high-resolution IR absorption spectra are utilized as the reference for the comparisons. The influences of different resonances and resonant thresholds are studied. Four methods for electronic structure calculations are tested. The quantitative comparisons indicate that for the NIST data, B3LYP/NO7D provides the best agreement with measured spectra concerning band positions and B3LYP/cc-pVTZ is superior in the description of the relative intensities. The importance of 1-3 Darling-Dennison resonances, which are required for generating triple combination bands, is investigated through a comparison to a high-resolution experimental spectrum. For interpreting the bandwidths and profiles of the observational spectra, the temperature effects are included through the Wand-Landau random walk technique. The comparisons between calculated high-temperature anharmonic and observational spectra indicate that small and compact PAHs might be responsible for the 3.3 mu m aromatic infrared bands.

Context. As the fourth most abundant element in the universe, carbon (C) is widespread in the interstellar medium (ISM) in various allotropic forms (e.g. fullerenes have been identified unambiguously in many astronomical environments, the presence of polycyclic aromatic hydrocarbon molecules in space has been commonly acknowledged, and presolar graphite, as well as nanodiamonds, have been identified in meteorites). As stable allotropes of these species, whether carbon nanotubes (CNTs) and their hydrogenated counterparts are also present in the ISM or not is unknown. Aims. The aim of the present works is to explore the possible routes for the formation of CNTs in the ISM and calculate their fingerprint vibrational spectral features in the infrared (IR). Methods. We studied the hydrogen-abstraction and acetylene-addition (HACA) mechanism and investigated the synthesis of nanotubes using density functional theory (DFT). The IR vibrational spectra of CNTs and hydrogenated nanotubes (HNTs), as well as their cations, were obtained with DFT. Results. We find that CNTs could be synthesized in space through a feasible formation pathway. CNTs and cationic CNTs, as well as their hydrogenated counterparts, exhibit intense vibrational transitions in the IR. Their possible presence in the ISM could be investigated by comparing the calculated vibrational spectra with astronomical observations made by the Infrared Space Observatory, Spitzer Space Telescope, and particularly the upcoming James Webb Space Telescope.

In this work, we perform molecular dynamic (MD) simulations to investigate the stability and fragmentation processes of vibrationally excited linear polycyclic aromatic hydrocarbons (PAHs). The program of CP2K in combination with the semi-empirical method PM3 is utilized for the MD simulations. The simulations show that the formation of molecular hydrogens (H-2) is different than previous studies, in particular, different than compact PAHs. At high temperatures, linear PAHs tend to open aromatic rings and convert the sp(3) C-C or sp(2) C=C bonds to sp C C bonds by removing H-2; i.e. polyynes are formed in such process. Besides polyynes, PAHs attached with sp-bonded polyyne chains are commonly observed at high temperatures. We notice that due to the addition of flexible tails (polyynes), the ring-polyyne molecules do not dissociate for a long period of time at high temperatures. Such structures facilitate the molecules to survive in the harsh environment of the interstellar medium. In addition, the ring-polyyne structures induce dipole moments that could, in principle, be detected by radio astronomy.

Aims. Due to the limitations of current computational technology, the fragmentation and isomerization products of vibrationally-excited polycyclic aromatic hydrocarbon (PAH) molecules and their derivatives have been poorly studied. In this work, we investigate the intermediate products of PAHs and their derivatives as well as the gas-phase reactions relevant to the interstellar medium, with coronene as a case study. Methods. Based on the semi-empirical method of PM3 as implemented in the CP2K program, molecular dynamics simulations were performed to model the major processes (e.g., vibrations, fragmentations, and isomerizations) of coronene and its derivatives (e.g., methylated coronene, hydrogenated coronene, dehydrogenated coronene, nitrogen-substituted coronene, and oxygen-substituted coronene) at temperatures of 3000 K and 4000 K. Results. We find that the anharmonic effects are crucial for the simulation of vibrational excitation. For the molecules studied here, H-2, CO, HCN, and CH2 are the major fragments. Following the dissociation of these small units, most of the molecules could maintain their ring structures, but a few molecules would completely break into carbon chains. The transformation from a hexagon to a pentagon or a heptagon may occur and the heteroatomic substitutions (e.g., N- or O-substitutions) would facilitate the transformation.

Context. The 3.3 mu m aromatic C-H stretching band of polycyclic aromatic hydrocarbon (PAH) molecules seen in a wide variety of astrophysical regions is often accompanied by a series of weak satellite bands at similar to 3.4-3.6 mu m. One of these sources, IRAS 21282 +5050, a planetary nebula, also exhibits a weak band at similar to 1.68 mu m. While the satellite features at similar to 3.4-3.6 mu m are often attributed to the anharmonicities of PAHs, it is not clear whether overtones or combination bands dominate the 1.68 mu m feature. Aims. In this work, we examine the anharmonic spectra of eight PAH molecules, including anthracene, tetracene, pentacene, phenanthrene, chrysene, benz[a]anthracene, pyrene, and perylene, to explore the origin of the infrared bands in the 1.6-1.7 mu m wavelength region. Methods. Density functional theory (DFT) in combination with the vibrational second-order perturbation theory (VPT2) was used to compute the anharmonic spectra of PAHs. To simulate the vibrational excitation process of PAHs, the Wang-Landau random walk technique was employed. Results. All the dominant bands in the 1.6-1.7 mu m wavelength range and in the 3.1-3.5 mu m C-H stretching region are calculated and tabulated. It is demonstrated that combination bands dominate the 1.6-1.7 mu m region, while overtones are rare and weak in this region. We also calculate the intensity ratios of the 3.1-3.5 mu m C-H stretching features to the bands in the 1.6-1.7 mu m region, I3.1-3:5/I1.6-1.7, for both ground and vibrationally excited states. On average, we obtain < I3.1-3.5=/I1.6-1.7 > approximate to 12.6 and < I3.1-3.5=/I1.6-1.7 > approximate to 17:6 for PAHs at ground states and at vibrationally excited states, respectively.

Aims. Infrared (IR) spectroscopy is a powerful tool to study molecules in space. A key issue in such analyses is understanding the effect that temperature and anharmonicity have on different vibrational bands, and thus interpreting the IR spectra for molecules under various conditions. Methods. We combined second order vibrational perturbation theory and the Wang-Landau random walk technique to produce accurate IR spectra of highly excited polycyclic aromatic hydrocarbons. We fully incorporated anharmonic effects, such as resonances, overtones, combination bands, and temperature effects. Results. The results are validated against experimental results for the pyrene molecule (C16H10). In terms of positions, widths, and relative intensities of the vibrational bands, our calculated spectra are in excellent agreement with gas-phase experimental data.

In this work, we utilize a method based on Wang-Landau Monte Carlo sampling for studying the temperature effects of astrophysically relavant molecules. Anharmonic effects, e.g., resonances, overtones, and combination bands, are fully incoportated in this method. The calculated infrared (IR) spectra are consistent with the experimental data measured by National Institute of Standards and Technology (NIST).

Context. Polycyclic aromatic hydrocarbons (PAHs) and fullerenes are the largest molecules found in the interstellar medium (ISM). They are abundant and widespread in various astronomical environments. However, the detailed connection between these two species is unknown; in particular, no quantum chemical studies have been performed.Aims. In this work, we investigate a vital step in transforming planar PAHs to fullerenes, that is, the tubulation processes of PAHs.Methods. We used density functional theory for this study. The molecular structures and vibrational frequencies were calculated using the hybrid density functional B3LYP method. To better describe intermolecular forces, we considered Grimme's dispersion correction in the calculations for this work. Intrinsic reaction coordinate calculations were also performed to confirm that the transition state structures are connected to their corresponding local potential energy surface minima.Results. As expected, we find that it is easier to bend a molecule as it gets longer, whereas it is harder to bend the molecule if it gets "wider" (i.e., with more rows of benzene rings). The change of multiplicity slightly alters the bending energies, while (a complete) dehydrogenation alleviates the bending barrier significantly and facilitates the formation of pentagons, which may act as an indispensable step in the formation of fullerenes in the ISM.

The detection of the 11.3 mu m emission feature characteristic of the Si-C stretch in carbon-rich evolved stars reveals that silicon carbide (SiC) dust grains are condensed in the outflows of carbon stars. SiC dust could be a significant constituent of interstellar dust since it is generally believed that carbon stars inject a considerable amount of dust into the interstellar medium (ISM). The presence of SiC dust in the ISM is also supported by the identification of pre-solar SiC grains of stellar origin in primitive meteorites. However, the 11.3 mu m absorption feature of SiC has never been seen in the ISM, and oxidative destruction of SiC is often invoked. In this work, we quantitatively explore the destruction of interstellar SiC dust through oxidation based on molecular dynamics simulations and density functional theory calculations. We find that the reaction of an oxygen atom with SiC molecules and clusters is exothermic and could cause CO-loss. Nevertheless, even if this is extrapolable to bulk SiC dust, the destruction rate of SiC dust through oxidation could still be considerably smaller than the (currently believed) injection rate from carbon stars. Therefore, the lack of the 11.3 mu m absorption feature of SiC dust in the ISM remains a mystery. A possible solution may lie in the currently believed stellar injection rate of SiC (which may have been overestimated) and/or the size of SiC dust (which may actually be considerably smaller than submicron in size).

A systematic study, using ion trap time-of-flight mass spectrometry, is presented for the photo-dissociation processes of Bisanthenquinone (Bq) cations, C28H12O2+, a ketone substituted Polycyclic Aromatic Hydrocarbon (PAH). The Bq cation fragments through sequential loss of the two neutral carbonyl (CO) units upon laser (626nm) irradiation, resulting in a PAH-like derivative C26H12+. Upon further irradiation, C26H12+ exhibits both stepwise dehydrogenation and C2/C2H2 loss fragmentation channels. Quantum chemistry calculations reveal a detailed picture for the first CO-loss, which involves a transition state with a barrier of ∼ 3.4 eV, which is lower than the energy required for the lowest H-loss pathway (∼ 5.0 eV). The barrier for the second CO-loss is higher (∼ 4.9 eV). The subsequent loss of this unit changes the Bq geometry from a planar to a bent one. It is concluded that the photodissociation mechanism of the substituted PAH cations studied here is site selective in the substituted subunit. This work also shows that an acetone substituted PAH cation is not photo-stable upon irradiation. 

Long-standing radical species have raised noteworthy concerns in organic functional chemistry and materials. However, there remains a substantial challenge to produce long-standing radicals by light, because of the structural dilemmas between photoproduction and stabilization. Herein, we present a pyrrole and chloride assisted photochromic structure to address this issue. In this well-selected system, production and stabilization of a radical species were simultaneously found accompanied by a photochemical process in chloroform. Theoretical study and mechanism construction indicate that the designed π-system provides a superior spin-delocalization effect and a large steric effect, mostly avoiding possible consumptions and making the radical stable for hours even under an oxygen-saturated condition. Moreover, this radical system can be applied for a visualized and quantitative detection towards peroxides, such as 2,2,6,6-tetramethylpiperidine-1-oxyl, hydrogen peroxide, and ozone. As the detection relies on a radical capturing mechanism, a higher sensing rate was achieved compared to traditional redox techniques for peroxide detection.

The gated photochromic systems have attracted great interest in scientific researches due to their merits in the opto-electronic fields, whereas the multi-stimuli gating function in a unimolecular platform has rarely been addressed. Herein, a new strategy to realize multi-stimuli gated photochromic function was devised relying on a simple Schiff-based diarylethene derivative. The compound shows no photoswitching properties in solution under irradiation with any wavelength of light. It is noteworthy that mecury(II) ions, water and protons can trigger its photo-reactivity independently with different absorption changes, respectively. Therefore, a molecular logic circuit with four inputs, including mecury(II) ions, water, protons and UV light, was fabricated on the basis of the unimolecular platform, suggesting promise for application in multi-controlled photoswitchings. These results could be valuable for the further development of photoswitchings with multiple stimuli responses.

The atmospheric CO2 concentration has increased by more than 20% since 1980s and has now reached the highest level than at any point in the past 800 000 years. Electrochemical CO2 reductions are receiving particular in- terest as the apparatus are relatively easy to maintain and cheap to operate. However, the direct reduction of CO2 into CO2 radical requires a very high over-potential, meaning a substantial waste in energy. In order to lower the over-potential required, a large number of catalysts has been synthesised and studied. Among these catalysts, three are studied in this work due to their interesting reactivities. We believe the further understanding gained in our studies will benefit the development of new and better catalysts.

Ru(6-Mebpy)(tBu3-tpy) reduces CO2 at its first reduction potential and can therefore lower the over-potential required significantly. This observation is unique for Ru(tpy)(bpy) type of catalysts. Density functional theory (DFT) cal- culations revealed that the steric hindrance provided by the 6-methyl group weakens Ru-solvent interactions and hence allows solvent detachment to take place after only one reduction, which is otherwise not possible. Furthermore, we proposed a new mechanism for CO2 to CO reduction at the first reduc- tion potential and identified a cyclic intermediate by Infra-red spectroscopy in collaboration with experimentalists. Such intermediate was not reported pre- viously for Ru-based electrocatalysts.

Co(TPP)/CNTs as a heterogenous catalyst exhibits superior reactivity as compared to in solution. DFT calculations with implicit solvent model ac- counts its enhanced reactivity to the increased proton concentration in water. The inverse-loading effect was studied by potential mean force (PME) sam- pling. Our results suggest that aggregation is triggered by the strong inter- molecular p - p interactions among the catalysts. Flatter nanotubes have better contact with Co(TPP) and hence reduces aggregation tendency. The same cat- alyst was also used as an example to study catalysis at interfaces in an electric field. Our full-explicit EVB -MD (Empirical Valence Bond-Molecular Dynam- ics) model illustrates that the electric double layer concentrates cations, which significantly stabilises polarised CO2 at a higher concentration and hence eases CO2 binding. Furthermore, we have also shown that either the electric field or the cations along provides only a minor, almost negligible stabilisation.

In 2019, CoPc/CNTs was reported to be the first early-period transition metal complex that can catalyse CO2-to-CH3OH conversion at a decent yield. Literature search on previous work suggests that the presence of well-dispersed, monomeric CoPc is crucial to further reduce CO into CH3OH. We calculated the reaction profiles for both monomeric CoPc and dimeric CoPc, which is the simplest form of aggregates. Our DFT results demonstrate that after the formation of catalyst-CO- complex, monomers tend to go though further reac- tions to afford CH3OH while dimers tend to dissociate CO as reductions are slightly harder, which in turn, is raised from a less degree of solvation stabili- sation upon reductions.