Investigating the Optical Properties of BOIMPY Dyes with ab initio Tools

Physical Chemistry Chemical Physics
Using a computational approach combining the Time-Dependent Density Functional Theory (TD-DFT) and the second-order Coupled Cluster (CC2) approaches, we investigate the spectral properties of a large panel of BOIMPY dyes. BOIMPY derivatives constitute a new class of fluorophores that appeared only very recently [Angew. Chem. Int. Ed., 2016, 55, 13340-13344] and display intriguing properties. First, we show that theory is able to reproduce the experimental 0-0 energies with a reasonable accuracy, and more importantly an excellent consistency (R=0.99). Next, by analyzing the nature of the excited-states, we show that the first electronic transition does not imply a significant charge-transfer character and significantly differs from the one of the parent BODIPYs. Third, we unravel the vibrational modes responsible for the specific band shapes of the BOIMPY derivatives. Finally, using theory to design new compounds, we propose new substitution patterns leading to redshifted absorption...  Read more

Atomistic non-adiabatic dynamics of the LH2 complex with a GPU-accelerated ab initio exciton model

Physical Chemistry Chemical Physics
We recently outlined an efficient multi-tiered parallel ab initio excitonic framework that utilizes time dependent density functional theory (TDDFT) to calculate ground and excited state energies and gradients of large supramolecular complexes in atomistic detail – enabling us to undertake non-adiabatic simulations which explicitly account for the coupled anharmonic vibrational motion of all the constituent atoms in a supramolecular system. Here we apply that framework to the 27 coupled bacterio-cholorophyll-a chromophores which make up the LH2 complex, using it to compute an on-the-fly nonadiabatic surface-hopping (SH) trajectory of electronically excited LH2. Part one of this article is focussed on calibrating our ab initio exciton Hamiltonian using two key parameters: a shift δ, which corrects for the error in TDDFT vertical excitation energies; and an effective dielectric constant ε, which describes the average screening of the transition-dipole coupling between chromophores....  Read more

Production of doubly-charged highly reactive species from the long-chain amino acid GABA initiated by Ar9+ ionization

Physical Chemistry Chemical Physics
We present a combined experimental and theoretical study of the fragmentation of multiply- charged γ-aminobutyric acid molecules (GABAz+, z = 2,3) in the gas phase. The combination of ab initio molecular dynamics simulations with multiple-coincidence mass spectrometry techniques allows us to observe and identify doubly-charged fragments in coincidence with another charged moiety. The present results indicate that double and triple electron capture lead to the formation of doubly-charged reactive nitrogen and oxygen species (RNS and ROS) with different probability due to the different charge localisation and fragmentation behaviour of GABA2+ and GABA3+. The MD simulations unravel the fast (femtosecond) formation of large doubly charged species, observed in the experimental microsecond timescale. The excess of positive charge is stabilised by the presence of cyclic X −member (X = 3 − 5) ring structures....  Read more

Unique agreement of experimental and computational infrared spectroscopy: a case study of lithium bromide solvation in an important electrochemical solvent

Physical Chemistry Chemical Physics
Infrared (IR) spectroscopy is a widely used and invaluable tool in the studies of solvation phenomena in electrolyte solutions. Using state-of-the-art chemometric analysis of a spectral series measured in a concentration-dependent manner, the spectrum of the solute-affected solvent can be extracted, providing a detailed view of the structural and energetic states of the solvent molecules influenced by the solute. Concurrently, ab initio molecular dynamics (AIMD) simulations provide the solvation shell picture at an atomistic detail level and allow for a consistent decomposition of the theoretical IR spectrum in terms of distance-dependent contributions of the solvent molecules. Here, we show for the first time how the chemometric techniques designed with the analysis of experimental data in mind can be harnessed to extract corresponding information from the computed IR spectra for mutual benefit, but without any mutual input. The wide applicability of this two-track approach...  Read more

Structure and unconventional dihydrogen bonding of a pressure-stabilized hydrogen-rich (NH3BH3)(H2)x (x = 1.5) compound

Journal of Materials Chemistry A
Combining X-ray diffraction, Raman spectroscopy, and ab initio simulations we characterize an extremely hydrogen-rich phase with the chemical formula (NH3BH3)(H2)x (x = 1.5). This phase was formed by compressing ammonia borane (AB, NH3BH3) in an environment with excess of molecular hydrogen (H2). This compound can store a total of 26.8 wt% hydrogen, both as molecular hydrogen and chemically bonded hydrogen in AB, making it one of the most hydrogen-rich solids currently known. The new compound possesses a layered AB structure where additional H2 molecules reside in channels created through the weaving of AB layers. The unconventional dihydrogen bonding network of the new compound is significantly modified from its parent AB phase and contains H…H contacts between adjacent AB molecules and between AB and H2 molecules. H-H can be either a proton donor or a proton acceptor that forms new types of dihydrogen bonding with the host AB molecules, which are depicted as H-H…H-B or...  Read more

A quantum-rovibrational-state-selected study of the H2O+(X2B1; v1+v2+v3+; N+Ka+Kc+ ) + CO reaction in the collision energy range of 0.05-10.00 eV: translational, rotational, and vibrational energy effects

Physical Chemistry Chemical Physics
We report detailed absolute integral cross sections (σ’s) for the quantum-rovibrational-state-selected ion-molecule reaction H2O+(X2B1: v1+v2+v3+; N+Ka+Kc+) + CO in the center-of-mass collision energy (Ecm) range of 0.05-10.00 eV, where (v1+v2+v3+) = (000), (100), and (020), and N+Ka+Kc+ = 000, 111, and 211. Three product channels, HCO++ OH, HOCO++ H, and CO+ + H2O, are identified. The measured σ(HCO+) curve [σ(HCO+) versus Ecm plot] supports that the formation of the HCO+ + OH channel follows an exothermic pathway with no potential energy barriers. Although the HOCO+ + H channel is the most exothermic, the σ(HOCO+) is found to be significantly lower than the σ(HCO+). The σ(HOCO+) curve is bimodal, indicating two distinct mechanisms for the formation of HOCO+. The σ(HOCO+) is strongly inhibited at Ecm < 0.4 eV, but is enhanced at Ecm > 0.4 eV by (100) vibrational excitation. The Ecm onsets of σ(CO+) determined for the (000) and (100) vibrational states are in excellent...  Read more

Insight into the Role of Oxygen in Phase-Change Material GeTe

Journal of Materials Chemistry C
Oxygen is widely used to tune the performance of chalcogenide phase-change materials in the usage of phase-Change random access memory (PCRAM) which is considered as the most promising next-generation non-volatile memory. However, the microscopic role of oxygen in the write-erase process, i.e., the reversible phase transition between crystalline and amorphous state of phase-change materials, remains unclear. Using oxygen doped GeTe as an example, this work unravels the role of oxygen at the atomic scale by means of ab initio total energy calculations and ab initio molecular dynamics simulations. Our main finding is that after the amorphization and the subsequent re-crystallization process simulated by ab initio molecular dynamics, oxygen will drag one Ge atom out of its lattice site and both atoms stay in the interstitial region near the Te vacancy that was originally occupied by the oxygen, forming a “dumbbell-like” defect (O-VTe-Ge), which is in sharp...  Read more

Adsorption of small inorganic molecules on a defective MoS2 monolayer

Physical Chemistry Chemical Physics
We present a theoretical study of molecular adsorption on defects on a MoS2 monolayer. Based on Density Functional Theory, our calculations confirm that small inorganic molecules, such as CO2, CO, H2O, NO, NO2, H2 and N2, remain bonded to the pristine monolayer through weak van der Waals interactions, suggesting that the molecules may easily diffuse over the clean monolayer. On the other hand, the introduction of defects can lead to three different situations, depending on the defect and the molecule considered: physisorption, chemical (strong) bonding to the metallic defects, namely the Mo substitutional atoms on the S vacancies, and dissociation, that can take place spontaneously at 0K in some specific cases or by the effect of thermal agitation in molecules such as CO2 or NO2...  Read more

A study of the water molecule using frequency control over nuclear dynamics in resonant X-ray scattering

Physical Chemistry Chemical Physics
In this combined theoretical and experimental study we report a full analysis of the resonant inelastic X-ray scattering spectra (RIXS) of H2O, D2O and HDO. We demonstrate that there is an inherent capability for the electronically-elastic RIXS to map the potential energy surface and to perform vibrational analysis of the electronic ground state in multimode systems. We show, that the control and selection of vibrational excitation can be performed by tuning the X-ray frequency across core-excited molecular bands and it is clearly reflected in the RIXS spectra. Using high level ab initio electronic structure and quantum nuclear wave packet calculations together with high resolution RIXS measurements we discuss in great detail the mode coupling, mode localization and anharmonicity in the studied systems.Read more

π-Hole interactions at work: crystal engineering with nitro-derivatives

CrystEngComm
In this manuscript we report the design, synthesis and X-ray characterization of nitrodiene derivatives that present crucial π-hole interactions involving the nitro group as π-hole donor. Solid state structures of 1,4-dinitro-1,3-butadiene (1), its co-crystal 1Diox and homologous 1,4-dinitro-1,3-pentadiene (2) and 2,4-dinitro-2,4-hexadiene (3) feature competition of the latters with common weak CHO bonding and gradually increased role of lone pair- π-hole NO2NO2 interactions. Regular evolution of the supramolecular patterns (1 to 3) results in generation of unprecedented 3D non-covalent framework in 3 that is controlled exclusively by short π-hole contacts (O•••N = 2.9615(18), 3.1304(18) Å). These findings complement results of high level ab initio calculations (MP2/def2-TZVP) and unite theory and experiment thus supporting the functional relevance of this novel π-hole interaction.Read more

Intermolecular anharmonicity in molecular crystals: interplay between experimental low-frequency dynamics and quantum quasi-harmonic simulations of solid purine

Chemical Communications
The intermolecular anharmonic potential of crystalline purine is probed by means of temperature-dependent terahertz time-domain spectroscopy, low-frequency Raman scattering, X-ray diffraction, and ab initio quasi-harmonic quantum-chemical simulations. As temperature increases, anharmonicity in the intermolecular interactions results in strongly anisotropic thermal expansion – with a negative thermal expansion along the b crystallographic axis – yielding corresponding bulk structural modifications. The observed thermally-induced shifts of most vibrational bands in the terahertz region of the spectra are shown to arise from volume-dependent thermal changes of the hydrogen-bond pattern along the a and b crystallographic axes.Read more

FDHALO17: The anomalous Halogen Bonding Interactions between Chlorine and Bromine with Water in Clathrate Hydrates

Faraday Discussions
Clathrate hydrate phases of Cl2 and Br2 guest molecules have been known for about 200 years. The crystal structure of these phases was recently re-determined with high accuracy by single crystal X-ray diffraction. In these structures, the water oxygen-halogen atom distances are determined to be shorter than the sum of the van der Waals radii, which indicates the action of some type of non-covalent interaction between the dihalogens and water molecules. Given that both lone pairs of each water oxygen atom are engaged in hydrogen bonding with other water molecules of the lattice, the nature of the oxygen-halogen interactions may not be the standard halogen bonds characterized recently in the solid state materials and enzyme-substrate compounds. The nature of the halogen-water interactions for the Cl2 and Br2 molecules in two isolated clathrate hydrate cages has recently been studied with ab initio calculations (Ochoa-Resendiz et al. J. Chem. Phys. 2016, 145, 161104). Here we present the...  Read more

Bismuth based half-Heusler alloys with giant thermoelectric figures of merit

Journal of Materials Chemistry A
Half-Heusler thermoelectric materials have attracted extensive research interest over the last two decades owing to their thermal stability, mechanical strength, and moderate efficiency. This article presents an ab initio theoretical evaluation of the electrical and thermal transport properties of three bismuth-based most promising thermoelectric alloys, selected out of 54 stable half-Heusler compounds. These are brand new compounds which are recently proposed to be stable (Nature Chem.7, 308 (2015)) and may have interesting properties. The calculated band structures of the three compounds, namely HfRhBi, ZrIrBi and ZrRhBi, served as a hint for their promising thermoelectric properties. HfRhBi and ZrIrBi turn out to be narrow band gap semiconductors while ZrRhBi is a moderate band gap semiconductor. A detailed study of the carrier concentration and temperature dependence of the Seebeck coefficient, power factor, lattice and electronic thermal...  Read more

The Prediction of Strong O-H/M Hydrogen Bonding between Water and Square-planar Ir and Rh Complexes

Physical Chemistry Chemical Physics
Intermolecular O-H/M interactions, between a water molecule and square-planar acac complexes ([M(acac)L2]), with different types of L ligands (en, H2O, CO, CN-, and OH-) and different types of metal atoms (Ir(I), Rh(I), Pt(II), and Pd(II) were studied by high level ab initio calculations. Among the studied neutral complexes, the [Pd(acac)(CN)(CO)] complex forms the weakest interaction, -0.62 kcal/mol, while the [Ir(acac)(en)] complex forms the strongest interaction, -9.83 kcal/mol, which is remarkably stronger than the conventional hydrogen bond between two water molecules (-4.84 kcal/mol).Read more

Temperature effects on the viscosity and the wavelength-dependent refractive index of imidazolium-based ionic liquids with a phosphorus-containing anion

Physical Chemistry Chemical Physics
A systematic study on the viscosity and refractive index of 1-alkyl-3-methylimidazolium based ionic liquids (alkyl = methyl, butyl and hexyl) combined with three phosphorus containing anions, i.e. dimethylphosphate, methyl methylphosphonate and methylphosphonate, is reported. Experimental measurements account for temperature effects, while the refractive index is determined at multiple wavelengths in the visible and near infrared region. Despite the structural similarity of these anions, significant differences in the physical properties of the resulting ILs are identified, along with the clear trend of viscosity increase – and refractive index decrease – with increasing alkyl chain length on the cation. Ab initio theoretical calculations are carried out to support and rationalise the observed behaviour.Read more

High level potential energy surface and mechanism of the Al(CH3)2OCH3 promoted lactone polymerization. Initiation and propagation

Physical Chemistry Chemical Physics
Despite increasing experimental interest in aliphatic polyesters as biodegradable and bioassimil- able polymers the theoretical description of the ring-opening polymerization (ROP) is not yet fully established. We report a detailed theoretical account for the mechanism of the ROP of three lactons (glycolide , 1,5-dioxepan-2-one and ε-caprolactone) using dimethylaluminium methoxide (Al(CH 3 ) 2 OCH 3 ) as initiator. Both the initiation and propagation steps of the ROP are investi- gated using a composite method consisting of explicitly correlated Moller-Plesset (DF-MP2-F12) and explicitly correlated local coupled cluster methods (DF-LCCSD(T)-F12), for an accurate and definitive determination of transition state and intermediate electronic energies. A hithero unre- ported transition state is found in the initiation reaction, which is the highest energy stationary state for all three lactones. Computed reaction free energies suggest a thermodynamically favourable polymerization of the...  Read more

In search of the best DFT functional for dealing with organic anionic species

Physical Chemistry Chemical Physics
Quantum chemical computational methods are thought to have problems in dealing with unstable organic anions. This work assesses the ability of different Density Functional Theory (DFT) functionals to reproduce electron affinity and reduction potential of organic compounds. The performance of 23 DFT functionals was evaluated computing negative electron affinities (from 0 eV to -3.0 eV) and reduction potentials in acetonitrile (from 0 to -2.7 V). In general, most of the hybrid GGA functionals work fine in the prediction of electron affinities, being BPW91, B3PW91 and M06 the bests on each class of functionals (pure, hybrid and meta-GGA functionals, respectively). On the other hand, the ab initio post Hartree-Fock methods, MP2 and coupled-cluster (CCSD(T)), as well as the double hybrid functionals, B2PLYP, mPW2PLYP, usually fail. For compounds with EAs lower than -1.75 eV, a method for stabilizing the anion, based on solvation with the IEFPCM model was employed. In this case, BPW91, PBE0...  Read more

Emergence of novel hydrogen chlorides under high pressure

Physical Chemistry Chemical Physics
HCl is a textbook example of a polar covalent molecule, and has a wide range of industrial applications. Inspired by the discovery of unexpected stable sodium and potassium chlorides, we performed systematic ab initio evolutionary searches for all stable compounds in the H–Cl system at pressures up to 400 GPa. Besides HCl, four new stoichiometries (H2Cl, H3Cl, H5Cl and H4Cl7) are found to be stable under pressure. Our predictions substantially differ from previous theoretical studies. We evidence a high significance of zero-point energy in determining phase stability. The newly discovered compounds display a rich variety of chemical bonding characteristics. At ambient pressure, H2, Cl2 and HCl molecular crystals are formed by weak intermolecular van der Waals interactions, and adjacent HCl...  Read more

Modulation of electronic and mechanical properties of phagraphene via hydrogenation and fluorination

Physical Chemistry Chemical Physics
Recently, a new carbon sheet, phagraphene, was proposed by theoretical calculations [Nano Lett. 2015, 15, 6182]. In this paper, the hydrogenated and fluorinated phagraphene (denoted as H-PHA and F-PHA) sheets have been systematically studied using first-principles calculations. The results of formation energy, ab initio molecular dynamics, phonon dispersion and elastic constants confirm that the modified phagraphene sheets are thermodynamically and dynamically as well as mechanically stable. We find that hydrogenation or fluorination is an effective way to modulate the bandgap, and we also find that adsorption-induced semimetal-semiconductor transition and adsorption-induced semimetal-insulator transition occur. Configuration-dependent bandgap for partially H-PHA and configuration-independent bandgap for fully H-PHA are determined. Adsorption-ratio-dependent bandgaps of H-PHA and F-PHA are also identified. Calculated bandgaps from HSE06 and PBE functionals of fully H-PHA are larger...  Read more

An sd2 hybridized transition-metal monolayer with a hexagonal lattice: reconstruction between the Dirac and kagome bands

Physical Chemistry Chemical Physics
Graphene-like two-dimensional materials have garnered tremendous interest as emerging device materials due to their remarkable properties. However, their applications in spintronics have been limited by the lack of intrinsic magnetism. Here, we perform an ab initio simulation on the structural and electronic properties of several transition-metal (TM) monolayers (TM = Cr, Mo and W) with a honeycomb lattice on a 1/3 monolayer Cl-covered Si(111) surface. Due to the template effect from the halogenated Si substrate, the TM-layers will be maintained in an expanded lattice which is nearly 60% larger than that of the freestanding case. All these isolated TM-layers exhibit ferromagnetic coupling with kagome band structures related to sd2 hybridization and a strong interfacial interaction may destroy the topological bands. Interestingly, the W-monolayer on the Cl-covered Si substrate shows a half-metallic behavior. A Dirac point formed at the K...  Read more