Total Electron Detachment and Induced Cationic Fragmentation Cross Sections for Superoxide Anion (O2−) Collisions with Benzene (C6H6) Molecules

In this study, novel experimental total electron detachment cross sections for O₂⁻ collisions with benzene molecules are reported for the impact energy range (10–1000 eV), as measured with a transmission beam apparatus. By analysing the positively charged species produced during the collision events, relative total ionisation cross sections were derived in the incident energy range of 160–900 eV. Relative partial ionisation cross sections for fragments with m/z ≤ 78 u were also given in this energy range. We also confirmed that heavier compounds (m/z > 78 u) formed for impact energies between 550 and 800 eV. In order to further our knowledge about the collision dynamics governing the fragmentation of such heavier molecular compounds, we performed molecular dynamics calculations within the framework of the Density Functional Theory (DFT). These results demonstrated that the fragmentation of these heavier compounds strongly supports the experimental evidence of m/z = 39–42, 50, 60 (u) cations formation, which contributed to the broad local maximum in the total ionisation observed from 550 to 800 eV. This work reveals the reactivity induced by molecular anions colliding with hydrocarbons at high energies, processes that can take place in the interstellar medium under various local conditions.     

Thermodynamics of π–π Interactions of Benzene and Phenol in Water

The π–π interaction is a major driving force that stabilizes protein assemblies during protein folding. Recent studies have additionally demonstrated its involvement in the liquid–liquid phase separation (LLPS) of intrinsically disordered proteins (IDPs). As the participating residues in IDPs are exposed to water, π–π interactions for LLPS must be modeled in water, as opposed to the interactions that are often established at the hydrophobic domains of folded proteins. Thus, we investigated the association of free energies of benzene and phenol dimers in water by integrating van der Waals (vdW)-corrected density functional theory (DFT) and DFT in classical explicit solvents (DFT-CES). By comparing the vdW-corrected DFT and DFT-CES results with high-level wavefunction calculations and experimental solvation free energies, respectively, we established the quantitative credibility of these approaches, enabling a reliable prediction of the benzene and phenol dimer association free energies in water. We discovered that solvation influences dimer association free energies, but not significantly when no direct hydrogen-bond-type interaction exists between two monomeric units, which can be explained by the enthalpy–entropy compensation. Our comprehensive computational study of the solvation effect on π–π interactions in water could help us understand the molecular-level driving mechanism underlying the IDP phase behaviors.     

Geometry relaxation in singlet excited states of oligomers containing cyclopentadiene and fulvene and their cyano derivatives

Using the singles configuration interaction (CIS) theoretical approach, we investigated the nature of the geometric conformations and electronic transitions in π-conjugated oligo(cyclopentadiene)s and oligo(fulvene)s, and their cyano derivatives. Geometry optimizations were first carried out with the restricted Hartree-Fock (RHF/3-21G*) method which was followed by calculations of excitation energies using CIS (CIS/3-21G*) method. The trends in excitation energies as a function of chain lengths show that the band gaps in the cyano substituted compounds are lowered by approximately 0.5 eV relative to their parent polymers. The results of CIS/3-21G* oligomer calculations also show that delocalized singlet excited states are accompanied by a geometry relaxation in comparison to their ground state (HF) geometries.     

Electron Attachment Studies with the Potential Radiosensitizer 2-Nitrofuran

Nitrofurans belong to the class of drugs typically used as antibiotics or antimicrobials. The defining structural component is a furan ring with a nitro group attached. In the present investigation, electron attachment to 2-nitrofuran (C₄H₃NO₃), which is considered as a potential radiosensitizer candidate for application in radiotherapy, has been studied in a crossed electron–molecular beams experiment. The present results indicate that low-energy electrons with kinetic energies of about 0–12 eV effectively decompose the molecule. In total, twelve fragment anions were detected within the detection limit of the apparatus, as well as the parent anion of 2-nitrofuran. One major resonance region of ≈0–5 eV is observed in which the most abundant anions NO₂⁻, C₄H₃O⁻, and C₄H₃NO₃⁻ are detected. The experimental results are supported by ab initio calculations of electronic states in the resulting anion, thermochemical thresholds, connectivity between electronic states of the anion, and reactivity analysis in the hot ground state.     

Experimental and Theoretical Studies of Dissociative Electron Attachment to Metabolites Oxaloacetic and Citric Acids

In this contribution the dissociative electron attachment to metabolites found in aerobic organisms, namely oxaloacetic and citric acids, was studied both experimentally by means of a crossed-beam setup and theoretically through density functional theory calculations. Prominent negative ion resonances from both compounds are observed peaking below 0.5 eV resulting in intense formation of fragment anions associated with a decomposition of the carboxyl groups. In addition, resonances at higher energies (3–9 eV) are observed exclusively from the decomposition of the oxaloacetic acid. These fragments are generated with considerably smaller intensities. The striking findings of our calculations indicate the different mechanism by which the near 0 eV electron is trapped by the precursor molecule to form the transitory negative ion prior to dissociation. For the oxaloacetic acid, the transitory anion arises from the capture of the electron directly into some valence states, while, for the citric acid, dipole- or multipole-bound states mediate the transition into the valence states. What is also of high importance is that both compounds while undergoing DEA reactions generate highly reactive neutral species that can lead to severe cell damage in a biological environment.     

Picosecond carrier dynamics induced by coupling of wavefunctions in a Si-nanodisk array fabricated by neutral beam etching using bio-nano-templates

The picosecond carrier dynamics in a closely packed Si-nanodisk (Si-ND) array with ultrathin potential barrier fabricated by neutral beam etching using bio-nano-templates was investigated by time-resolved photoluminescence (PL). The PL decay curves were analyzed as a function of photon energy by the global fitting method. We show three spectral components with different decay times, where the systematic energy differences of the spectral peaks are clarified: 2.03 eV for the fastest decaying component with a decay time τ = 40 ps, 2.02 eV for τ = 300 ps, and 2.00 eV for τ = 1.6 ns. These energy separations ranging from 10 to 30 meV among the emissive states can be attributed to the coupling of wavefunctions of carriers between neighboring NDs.     

Excited States and Photodebromination of Selected Polybrominated Diphenyl Ethers: Computational and Quantitative Structure—Property Relationship Studies

This paper presents a density functional theory (DFT)/time-dependent DFT (TD-DFT) study on the lowest lying singlet and triplet excited states of 20 selected polybrominateddiphenyl ether (PBDE) congeners, with the solvation effect included in the calculations using the polarized continuum model (PCM). The results obtained showed that for most of the brominated diphenyl ether (BDE) congeners, the lowest singlet excited state was initiated by the electron transfer from HOMO to LUMO, involving a π–σ* excitation. In triplet excited states, structure of the BDE congeners differed notably from that of the BDE ground states with one of the specific C–Br bonds bending off the aromatic plane. In addition, the partial least squares regression (PLSR), principal component analysis-multiple linear regression analysis (PCA-MLR), and back propagation artificial neural network (BP-ANN) approaches were employed for a quantitative structure-property relationship (QSPR) study. Based on the previously reported kinetic data for the debromination by ultraviolet (UV) and sunlight, obtained QSPR models exhibited a reasonable evaluation of the photodebromination reactivity even when the BDE congeners had same degree of bromination, albeit different patterns of bromination.     

Signatures of Conical Intersection Dynamics in the Time-Resolved Photoelectron Spectrum of Furan: Theoretical Modeling with an Ensemble Density Functional Theory Method

The non-adiabatic dynamics of furan excited in the ππ* state (S₂ in the Franck–Condon geometry) was studied using non-adiabatic molecular dynamics simulations in connection with an ensemble density functional method. The time-resolved photoelectron spectra were theoretically simulated in a wide range of electron binding energies that covered the valence as well as the core electrons. The dynamics of the decay (rise) of the photoelectron signal were compared with the excited-state population dynamics. It was observed that the photoelectron signal decay parameters at certain electron binding energies displayed a good correlation with the events occurring during the excited-state dynamics. Thus, the time profile of the photoelectron intensity of the K-shell electrons of oxygen (decay constant of 34 ± 3 fs) showed a reasonable correlation with the time of passage through conical intersections with the ground state (47 ± 2 fs). The ground-state recovery constant of the photoelectron signal (121 ± 30 fs) was in good agreement with the theoretically obtained excited-state lifetime (93 ± 9 fs), as well as with the experimentally estimated recovery time constant (ca. 110 fs). Hence, it is proposed to complement the traditional TRPES observations with the trXPS (or trNEXAFS) measurements to obtain more reliable estimates of the most mechanistically important events during the excited-state dynamics.     

Asymmetric Non-Fullerene Small Molecule Acceptor with Unidirectional Non-Fused π-Bridge and Extended Terminal Group for High-Efficiency Organic Solar Cells

We designed and synthesized an asymmetric non-fullerene small molecule acceptor (NF-SMA) IDT-TNIC with an A–D–π–A structure, based on an indacenodithiophene (IDT) central core, with a unidirectional non-fused alkylthio-thiophene (T) π-bridge, and 2-(3-oxo-2,3-dihydro-1H-cyclopenta[b]naphthalen-1-ylidene)malononitrile (NIC) extended terminal groups. IDT-TNIC molecules still maintain a good coplanar structure, which benefits from the non-covalent conformational locks (NCL) between O···S and S···S. The asymmetric structure increases the molecular dipole moment, and the extended terminal group broadens the absorption of the material, resulting in an excellent photovoltaic performance of IDT-TNIC. The photovoltaic device, based on PBDB-T:IDT-TNIC, exhibits an energetic PCE of 11.32% with a high V_oc of 0.87 V, high J_sc of 19.85 mA cm⁻², and a low energy loss of 0.57 eV. More importantly, IDT-TNICs with asymmetric structures show a superior property compared to symmetric IDT-Ns. The results demonstrate that it is an effectual strategy to enhance the properties of asymmetric A–D–π–A-based NF-SMAs with non-fused NCL π-bridges and extended terminal groups.     

The Valence Band Structure of the [Ni(Salen)] Complex: An Ultraviolet,Soft X-ray and Resonant Photoemission Spectroscopy Study

The valence band photoemission (VB PE) spectra of the [Ni(Salen)] molecular complex were measured by ultraviolet, soft X-ray and resonant photoemission (ResPE) using photons with energies ranging from 21.2 eV to 860 eV. It was found that the Ni 3d atomic orbitals’ (AOs) contributions are most significant for molecular orbitals (MOs), which are responsible for the low-energy PE band at a binding energy of 3.8 eV in the VB PE spectra. In turn, the PE bands in the binding energies range of 8–16 eV are due to the photoionization of the MOs of the [Ni(Salen)] complex with dominant contributions from C 2p AOs. A detailed consideration was made for the ResPE spectra obtained using photons with absorption resonance energies in the Ni 2p_3/2, N 1s, and O 1s Near-Edge X-ray Absorption Fine Structure (NEXAFS) spectra. A strong increase in the intensity of the PE band ab was found when using photons with an energy 854.4 eV in the Ni 2p_3/2 NEXAFS spectrum. This finding is due to the high probability of the participator-Auger decay of the Ni 2p_3/2⁻¹3d⁹ excitation and confirms the relationship between the PE band ab with the Ni 3d-derived MOs.     

Systematic Approach to Find the Global Minimum of Relaxation Dispersion Data for Protein-Induced B–Z Transition of DNA

Carr–Purcell–Meiboom–Gill (CPMG) relaxation dispersion spectroscopy is commonly used for quantifying conformational changes of protein in μs-to-ms timescale transitions. To elucidate the dynamics and mechanism of protein binding, parameters implementing CPMG relaxation dispersion results must be appropriately determined. Building an analytical model for multi-state transitions is particularly complex. In this study, we developed a new global search algorithm that incorporates a random search approach combined with a field-dependent global parameterization method. The robust inter-dependence of the parameters carrying out the global search for individual residues (GSIR) or the global search for total residues (GSTR) provides information on the global minimum of the conformational transition process of the Zα domain of human ADAR1 (hZα_ADAR1)–DNA complex. The global search results indicated that a α-helical segment of hZα_ADAR1 provided the main contribution to the three-state conformational changes of a hZα_ADAR1—DNA complex with a slow B–Z exchange process. The two global exchange rate constants, k_ex and k_ZB, were found to be 844 and 9.8 s⁻¹, respectively, in agreement with two regimes of residue-dependent chemical shift differences—the “dominant oscillatory regime” and “semi-oscillatory regime”. We anticipate that our global search approach will lead to the development of quantification methods for conformational changes not only in Z-DNA binding protein (ZBP) binding interactions but also in various protein binding processes.     

Double and Triple Differential Cross Sections for Single Ionization of Benzene by Electron Impact

Experimental results for the electron impact ionization of benzene, providing double (DDCS) and triple differential cross sections (TDCS) at the incident energy of 90 eV, measured with a multi-particle momentum spectrometer, are reported in this paper. The most intense ionization channel is assigned to the parent ion (C₆H₆⁺) formation. The DDCS values are presented for three different transferred energies, namely 30, 40 and 50 eV. The present TDCS are given for two fixed values of the ejected electron energy (E₂), at 5 and 10 eV, and an electron scattering angle (θ₁) of 10°. Different features related to the molecular orbitals of benzene from where the electron is extracted are observed. In addition, a semi-empirical formula to be used as the inelastic angular distribution function in electron transport simulations has been derived from the present DDCS result and compared with other expressions available in the literature.     

FeIII,CuII and ZnII Complexes of the Rigid 9-Oxido-phenalenone Ligand—Spectroscopy,Electrochemistry, and Cytotoxic Properties

The three complexes [Fe(opo)₃], [Cu(opo)₂], and [Zn(opo)₂] containing the non-innocent anionic ligand opo⁻ (opo⁻ = 9-oxido-phenalenone, Hopo = 9-hydroxyphenalonone) were synthesised from the corresponding acetylacetonates. [Zn(opo)₂] was characterised using ¹H nuclear magnetic resonance (NMR) spectroscopy, the paramagnetic [Fe(opo)₃] and [Cu(opo)₂] by electron paramagnetic resonance (EPR) spectroscopy. While the EPR spectra of [Cu(opo)₂] and [Cu(acac)₂] in dimethylformamide (DMF) solution are very similar, a rather narrow spectrum was observed for [Fe(opo)₃] in tetrahydrofuran (THF) solution in contrast to the very broad spectrum of [Fe(acac)₃] in THF (Hacac = acetylacetone, 2,4-pentanedione; acac⁻ = acetylacetonate). The narrow, completely isotropic signal of [Fe(opo)₃] disagrees with a metal-centred S = 5/2 spin system that is observed in the solid state. We assume spin-delocalisation to the opo ligand in the sense of an opo⁻ to Fe^III electron transfer. All compounds show several electrochemical opo-centred reduction waves in the range of −1 to −3 V vs. the ferrocene/ferrocenium couple. However, for Cu^II and Fe^III the very first one-electron reductions are metal-centred. Electronic absorption in the UV to vis range are due to π–π* transitions in the opo core, giving Hopo and [Zn(opo)₂] a yellow to orange colour. The structured bands ranging from 400 to 500 for all compounds are assigned to the lowest energy π−π* transitions. They show markedly higher intensities and slight shifts for the Cu^II (brown) and Fe^III (red) complexes and we assume admixing metal contributions (MLCT for Cu^II, LMCT for Fe^III). For both complexes long-wavelength absorptions assignable to d–d transitions were detected. Detailed spectroelectrochemical experiments confirm both the electrochemical and the optical assignments. Hopo and the complexes [Cu(opo)₂], [Zn(opo)₂], and [Fe(opo)₃] show antiproliferative activities against HT-29 (colon cancer) and MCF-7 (breast cancer) cell lines in the range of a few µM, comparable to cisplatin under the same conditions.     

Distribution of Alpha Thalassaemia Gene Variants in Diverse Ethnic Populations in Malaysia: Data from the Institute for Medical Research

Alpha thalassaemia is highly prevalent in the plural society of Malaysia and is a public health problem. Haematological and molecular data from 5016 unrelated patients referred from various hospitals to the Institute for Medical Research for α thalassaemia screening from 2007 to 2010 were retrieved. The aims of this retrospective analysis were to describe the distribution of various alpha thalassaemia alleles in different ethnic groups, along with their genotypic interactions, and to illustrate the haematological changes associated with each phenotype. Amongst the patients, 51.2% (n = 2567) were diagnosed with α thalassaemia. Of the 13 α thalassaemia determinants screened, eight different deletions and mutations were demonstrated: three double gene deletions, – – ^SEA, – – ^THAI, ––^FIL; two single-gene deletions, α–^3.7 and – α^4.2; and three non-deletion mutations, Cd59G > A (haemoglobin [Hb] Adana), Cd125T > C (Hb Quong Sze) and Cd142 (Hb Constant Spring). A high incidence of α–^3.7 deletion was observed in Malays, Indians, Sabahans, Sarawakians and Orang Asli people. However, the – – ^SEA deletion was the most common cause of alpha thalassaemia in Chinese, followed by the α–^3.7 deletion. As many as 27 genotypic interactions showed 1023 α thalassaemia silent carriers, 196 homozygous α⁺ thalassaemia traits, 973 heterozygous α⁰ thalassaemia carriers and 375 patients with Hb H disease. Statistical analysis showed a significant difference in the distribution of α thalassaemia determinants amongst the various ethnic groups. Hence, the heterogeneous distribution of common determinants indicated that the introduction of an ethnicity-targeted hierarchical α thalassaemia screening approach in this multi-ethnic Malaysian population would be effective.     

Excited States Computation of Models of Phenylalanine Protein Chains: TD-DFT and Composite CC2/TD-DFT Protocols

The present benchmark calculations testify to the validity of time-dependent density functional theory (TD-DFT) when exploring the low-lying excited states potential energy surfaces of models of phenylalanine protein chains. Among three functionals suitable for systems exhibiting charge-transfer excited states, LC-ωPBE, CAM-B3LYP, and ωB97X-D, which were tested on a reference peptide system, we selected the ωB97X-D functional, which gave the best results compared to the approximate coupled-cluster singles and doubles (CC2) method. A quantitative agreement for both the geometrical parameters and the vibrational frequencies was obtained for the lowest singlet excited state (a ππ* state) of the series of capped peptides. In contrast, only a qualitative agreement was met for the corresponding adiabatic zero-point vibrational energy (ZPVE)-corrected excitation energies. Two composite protocols combining CC2 and DFT/TD-DFT methods were then developed to improve these calculations. Both protocols substantially reduced the error compared to CC2 and experiment, and the best of both even led to results of CC2 quality at a lower cost, thus providing a reliable alternative to this method for very large systems.     

Neutral Dissociation of Pyridine Evoked by Irradiation of Ionized Atomic and Molecular Hydrogen Beams

The interactions of ions with molecules and the determination of their dissociation patterns are challenging endeavors of fundamental importance for theoretical and experimental science. In particular, the investigations on bond-breaking and new bond-forming processes triggered by the ionic impact may shed light on the stellar wind interaction with interstellar media, ionic beam irradiations of the living cells, ion-track nanotechnology, radiation hardness analysis of materials, and focused ion beam etching, deposition, and lithography. Due to its vital role in the natural environment, the pyridine molecule has become the subject of both basic and applied research in recent years. Therefore, dissociation of the gas phase pyridine (C₅H₅N) into neutral excited atomic and molecular fragments following protons (H⁺) and dihydrogen cations (H₂⁺) impact has been investigated experimentally in the 5–1000 eV energy range. The collision-induced emission spectroscopy has been exploited to detect luminescence in the wavelength range from 190 to 520 nm at the different kinetic energies of both cations. High-resolution optical fragmentation spectra reveal emission bands due to the CH(A²Δ→X²Π_r; B²Σ⁺→X²Π_r; C²Σ⁺→X²Π_r) and CN(B²Σ⁺→X²Σ⁺) transitions as well as atomic H and C lines. Their spectral line shapes and qualitative band intensities are examined in detail. The analysis shows that the H₂⁺ irradiation enhances pyridine ring fragmentation and creates various fragments more pronounced than H⁺ cations. The plausible collisional processes and fragmentation pathways leading to the identified products are discussed and compared with the latest results obtained in cation-induced fragmentation of pyridine.     

Synthesis and Characterization of New Conjugated Azomethines End-Capped with Amino-thiophene-3,4-dicarboxylic Acid Diethyl Ester

A new series of thiophene-based azomethines differing in the core structure was synthesized. The effect of the central core structure in azomethines on the thermal, optical and electrochemical properties was investigated. The obtained compounds exhibited the ability to form a stable amorphous phase with a high glass transition temperature above 100 °C. They were electrochemically active and undergo oxidation and reduction processes. The highest occupied (HOMO) and the lowest unoccupied molecular (LUMO) orbitals were in the range of −3.86–−3.60 eV and −5.46–−5.17 eV, respectively, resulting in a very low energy band gap below 1.7 eV. Optical investigations were performed in the solvents with various polarity and in the solid state as a thin film deposited on a glass substrate. The synthesized imines absorbed radiation from 350 to 600 nm, depending on its structure and showed weak emission with a photoluminescence quantum yield below 2.5%. The photophysical investigations were supported by theoretical calculations using the density functional theory. The synthesized imines doped with lithium bis-(trifluoromethanesulfonyl)imide were examined as hole transporting materials (HTM) in hybrid inorganic-organic perovskite solar cells. It was found that both a volume of lithium salt and core imine structure significantly impact device performance. The best power conversion efficiency (PCE), being about 35–63% higher compared to other devices, exhibited cells based on the imine containing a core tiphenylamine unit.     

Thermal stability of the optical properties of plasma deposited diamond-like carbon thin films

In present paper we studied the optical constants of the diamond-like carbon (DLC) films and their changes with annealing. The multisample modification of combined variable angle spectroscopic ellipsometry and near normal spectroscopic reflectometry was used. The optical constants of the DLC films were simulated by our recently published six-parameter dispersion model employing a parameterization of the density of electronic states (DOS). Based on the dispersion model parameters the density of π and σ electrons were evaluated. We showed that from our model and the independently determined hydrogen atomic fraction of the films before and after annealing the ratio between momentum matrix elements of π → π* and σ → σ* transitions and the correct sp³-to-sp² carbon bonding configuration ratio can be calculated. It is worth to notice that the first quantity is usually assumed to be equal to unity but we showed that this assumption may cause a significant error in the determination of the sp³-to-sp² ratio. Therefore, our suggested method represents a novelty in this field.     

Introducing DInaMo: A Package for Calculating Protein Circular Dichroism Using Classical Electromagnetic Theory

The dipole interaction model is a classical electromagnetic theory for calculating circular dichroism (CD) resulting from the π-π* transitions of amides. The theoretical model, pioneered by J. Applequist, is assembled into a package, DInaMo, written in Fortran allowing for treatment of proteins. DInaMo reads Protein Data Bank formatted files of structures generated by molecular mechanics or reconstructed secondary structures. Crystal structures cannot be used directly with DInaMo; they either need to be rebuilt with idealized bond angles and lengths, or they need to be energy minimized to adjust bond lengths and bond angles because it is common for crystal structure geometries to have slightly short bond lengths, and DInaMo is sensitive to this. DInaMo reduces all the amide chromophores to points with anisotropic polarizability and all nonchromophoric aliphatic atoms including hydrogens to points with isotropic polarizability; all other atoms are ignored. By determining the interactions among the chromophoric and nonchromophoric parts of the molecule using empirically derived polarizabilities, the rotational and dipole strengths are determined leading to the calculation of CD. Furthermore, ignoring hydrogens bound to methyl groups is initially explored and proves to be a good approximation. Theoretical calculations on 24 proteins agree with experiment showing bands with similar morphology and maxima.