Photoionization Bands of Cyanogen: Multi-Mode Vibronic Coupling and Renner-Teller Effects

Multi-mode vibronic coupling in the , , and electronic states of Cyanogen radical cation (C N ) is investigated with the aid of ab initio quantum chemistry and first principles quantum dynamics methods. The electronic degenerate states of Π symmetry of C N undergo Renner-Teller (RT) splitting along degenerate vibrational modes of π symmetry. The RT split components form symmetry allowed conical intersections with those from nearby RT split states or with non-degenerate electronic states of Σ symmetry. A parameterized vibronic Hamiltonian is constructed using standard vibronic coupling theory in a diabatic electronic basis and symmetry rules. The parameters of the Hamiltonian are derived from ab initio calculated adiabatic electronic energies. The vibronic spectrum is calculated, assigned and compared with the available experimental data. The impact of various electronic coupling on the vibronic structure of the spectrum is discussed.     

Adsorption of Acetate on Au(111): An in-situ Scanning Tunnelling Microscopy Study and Implications on Formic Acid Electrooxidation

The adsorption of acetate on an Au(111) electrode surface in contact with acetic acid at pH 2.7 was imaged in-situ using scanning tunnelling microscopy (STM). Two different ordered structures were imaged for acetate adsorbed in the bidentate configuration on the unreconstructed surface at 0.95 V (vs. the saturated calomel electrode, SCE). The first structure, , is metastable and transforms at constant potential within 20 minutes to a structure, which is thermodynamically more favourable. The acetate adlayer starts to form at step edges and propagates via nucleation and growth onto terraces. The findings from in-situ STM are in agreement with the electrochemical behaviour of acetate on Au(111) characterized by voltammetry. A comparison is made with formate adsorption on Au(111). While acetate is not reactive, in contrast to formate, it can act as a spectator species in formic acid electrooxidation.     

Quantum Phase Diagram of a Frustrated Spin-1/2 Ferro-Antiferromagnetic Normal Ladder

In this work, we consider a frustrated two-leg spin-1/2 ladder composed of Heisenberg ferromagnetic and antiferromagnetic spin-1/2 chains, and nearest spins from different legs interact via Heisenberg type rung exchange interactions that can be either ferromagnetic or antiferromagnetic in nature. The competing exchange interactions in the system lead to five different quantum phases like ferromagnetic, non-collinear ferrimagnetic (NCF), , antiferromagnetic and dimer phases. The  quantum phase diagram is constructed for the Heisenberg spin-1/2 model and the phases are characterized using the correlation functions which are calculated by the density matrix renormalization group method. We also analyze the  stability of phase and calculate the pitch angle in the NCF phase.     

Emergence of Spinmerism for Molecular Spin-Qubits Generation**

Molecular platforms are regarded as promising candidates in the generation of units of information for quantum computing. Herein, a strategy combining spin-crossover metal ions and radical ligands is proposed from a model Hamiltonian first restricted to exchange interactions. Unusual spin states structures emerge from the linkage of a singlet/triplet commutable metal centre with two doublet-radical ligands. The ground state nature is modulated by charge transfers and can exhibit a mixture of triplet and singlet local metal spin states. Besides, the superposition reaches a maximum for , suggesting a necessary competition between the intramolecular and inter-metal-ligand and direct exchange interactions. The results promote spinmerism, an original manifestation of quantum entanglement between the spin states of a metal centre and radical ligands. The study provides insights into spin-coupled compounds and inspiration for the development of molecular spin-qubits.     

Trihydrogen Cation Helium Clusters: A New Potential Energy Surface

We present a new analytical potential energy surface (PES) for the interaction between the trihydrogen cation and a He atom, , in its electronic ground state. The proposed PES has been built as a sum of two contributions: a polarization energy term due to the electric field generated by the molecular cation at the position of the polarizable He atom, and an exchange-repulsion and dispersion interactions represented by a sum of “atom-bond” potentials between the three bonds of and the He atom. All parameters of this new PES have been chosen and fitted from data obtained from high-level ab-initio calculations. Using this new PES plus the Aziz-Slaman potential for the interaction between Helium atoms and assuming pair-wise interactions, we carry out classical Basin-Hopping (BH) global optimization, semiclassical BH with Zero Point Energy corrections, and quantum Diffusion Monte Carlo simulations. We have found the minimum energy configurations of small He clusters doped with , , with N=1–16. The study of the energies of these clusters allows us to find a pronounced anomaly for N=12, in perfect agreement with previous experimental findings, which we relate to a greater relative stability of this aggregate.     

Catalytic Reaction Mechanism of Bacterial GH92 α-1,2-Mannosidase: A QM/MM Metadynamics Study

The catalytic mechanism of a -dependent family 92 -mannosidase, which is abundantly present in human gut flora and malfunctions leading to the lysosomal storage disease α-mannosidosis, has been investigated using quantum mechanics/molecular mechanics and metadynamics methods. Computational efforts show that the enzyme follows a conformational itinerary of and the ion serves a dual purpose, as it not only distorts the sugar ring but also plays a crucial role in orchestrating the arrangement of catalytic residues. This orchestration, in turn, contributes to the facilitation of conformers for the ensuing reaction. This mechanistic insight is well-aligned with the experimental predictions of the catalytic pathway, and the computed energies are of the same order of magnitude as the experimental estimations. Hence, our results extend the mechanistic understanding of glycosidases.     

Coordination Dynamics of Zinc Triggers the Rate Determining Proton Transfer in Human Carbonic Anhydrase II

We present, for the first time, how transient changes in the coordination number of zinc ion affects the rate determining step in the enzyme human carbonic anhydrase (HCA) II. The latter involves an intramolecular proton transfer between a zinc-bound water and a distant histidine residue (His-64). In the absence of time-resolved experiments, results from classical and QM-MM molecular dynamics and transition path sampling simulations are presented. The catalytic zinc ion is found to be present in two possible coordination states; viz. a stable tetra-coordinated state, T and a less stable penta-coordinated state, P with tetrahedral and trigonal bipyramidal coordination geometries, respectively. A fast dynamical inter-conversion occurs between T and P due to reorganization of active site water molecules making the zinc ion more positively charged in state P. When initiated from different coordination environments, the most probable mechanism of proton transfer is found to be deprotonation of the equatorial water molecule from state P and transfer of the excess proton via a short path formed by hydrogen bonded network of active site water molecules. We estimate the rate constant of proton transfer as from P and from T. A quantitative match of estimated k_P with the experimental value, ( ) suggests that dynamics of Zn coordination triggers the rate determining proton transfer step in HCA II.     

A Case Study on the Use of Binding Free Energies to Screen Inhibitors of Human Carbonic Anhydrase II

We present in this article a case study on the thermodynamics of binding to human carbonic anhydrase II (HCA II) by three well-known inhibitors, viz. (a) acetazolamide (AZM) that directly binds to the catalytic Zn(II) ion at the active site, (b) non-zinc binding 6-hydroxy-2-thioxocoumarin (FC5) (c) 2-[(S)-benzylsulfinyl]benzoic acid (3G1). In each case, the crystal structure or its analogue of inhibitor-bound HCA II has been used to perform classical molecular dynamics (MD) simulation in water till . AZM and FC5 are found to undergo repeated binding and unbinding with markedly different dynamics from the partially buried, substrate-binding hydrophobic pocket near the active site. 3G1, on the other hand, is found to remain mostly at its crystallographic binding site occluded from the active site of HCA II. The associated binding free energies ( ) have been computed using the known MM/GBSA method and compared to the available experimental data. Our results show that encounters several issues including limited sampling of multiple binding sites and incorrect prediction of the affinity of the chosen ligands. Possible use of the simulation results in further construction of Markov state models is also discussed.     

Second Harmonic Generation Signatures of Supramolecular Assemblies Based on Amide Moieties

Targeting the use of the second harmonic generation (SHG) as a bioimaging technique to unravel the formation of aggregates, the SHG first hyperpolarizabilities ( ) of assemblies of benzene-1,3,5-tricarboxamide derivatives have been evaluated at the density functional theory level. Calculations have revealed that i) the assemblies exhibit SHG responses and the total first hyperpolarizability responses of the aggregates are evolving with their size. The largest aggregation effect is a 18-times increase for of B4 when going from the monomer to the pentamer, that ii) the intrinsic SHG responses described by the hyper-Rayleigh Scattering are enhanced in presence of iodine atoms on the phenyl core, that iii) the side chains affect the relative orientation of the dipole moment and first hyperpolarizability vectors, which impacts more the EFISHG quantities than their moduli, and that iv) the radial component to is dominant for the compounds having the largest responses. These results have been obtained using the sequential molecular dynamics then quantum mechanics approach to account for dynamic structural effects on the SHG responses.     

Investigating Possible Dipole-Bound States of Cyanopolyynes: the Case for the C5N− Anion Detected in Interstellar Space

We present results of quantum structure calculations aimed at demonstrating the possible existence of dipole-bound states (DBS) for the anion , a species already detected in the Interstellar medium (ISM). The positive demonstration of DBS existence using ab initio studies is an important step toward elucidating possible pathways for the formation of the more tightly bound valence bound states (VBS) in environments where free electrons from starlight ionization processes are known to be available to interact with the radical partner of the title molecule. Our current calculations show that such excited DBS states can exist in , in agreement with what we had previously found for the smallercyanopolyyne in the series: the anion. This system has a very weakly bound anion with binding energies of about 3 and 9 cm⁻¹ for the and DBS, respectively.     

On the Mechanical Properties of Popgraphene-Based Nanotubes: a Reactive Molecular Dynamics Study

Carbon-based tubular materials have sparked a great interest in future electronics and optoelectronics device applications. In this work, we computationally studied the mechanical properties of nanotubes generated from popgraphene (PopNTs). Popgraphene is a 2D carbon allotrope composed of 5-8-5 rings. We carried out fully atomistic reactive (ReaxFF) molecular dynamics for PopNTs of different chiralities ( and ) and/or diameters and at different temperatures (from 300 up to 1200 K). Results showed that the tubes are thermally stable (at least up to 1200 K). All tubes presented stress/strain curves with a quasi-linear behavior followed by an abrupt drop of stress values. Interestingly, armchair-like PopNTs ( ) can stand a higher strain load before fracturing when contrasted to the zigzag-like ones ( ). Moreover, it was obtained that Young's modulus (Y_Mod) (750–900 GPa) and ultimate strength (σ_US) (120–150 GPa) values are similar to the ones reported for conventional armchair and zigzag carbon nanotubes. Y_Mod values obtained for PopNTs are not significantly temperature-dependent. While the σ_US values for the showed a quasi-linear dependence with the temperature, the exhibited no clear trends.     

Potential of AMnO3 (A=Ca,Sr, Ba,La) as Active Layer in Inorganic Perovskite Solar Cells

Inorganic perovskite CaMnO was proposed as a substitution for the TiO anatase in electron transport layers of solar cells containing the hybrid perovskite CH NH PbI based on increased mobility of electrons and better optical matching. Due to a suitable band gap concerning the absorption of sunlight, we investigate the potential of CaMnO and similar manganite perovskites, where Ca is replaced by either Sr, Ba or La, as an absorber layer in inorganic perovskite solar cells. In this study, we have used optical measurements on the synthesized AMnO (A=Ca, Sr, Ba, La) samples to aid density functional theory calculations (DFT) in order to accurately simulate the electronic and optical properties of AMnO compounds and gauge their potential for the role of absorber layer. Both experimental measurements and theoretical calculations show suitable band gap of 1.1-1.5 eV, depending on the compound, and absorption coefficients of the order of cm in the visible part of the spectrum.     

The role of dimers in complex forming reactions at low temperature: full dimension potential and dynamics of (H2CO)2+OH reaction

The (H CO) +OH and H CO-OH+H CO reaction dynamics are studied theoretically for temperatures below 300 K. For this purpose, a full dimension potential energy surface is built, which reproduces well accurate ab initio calculations. The potential presents a submerged reaction barrier, as an example of the catalytic effect induced by the presence of the third molecule. However, quasi-classical and ring polymer molecular dynamics calculations show that the dominant channel is the dimer-exchange mechanism below 200 K, and that the reactive rate constant tends to stabilize at low temperatures, because the effective dipole of either dimer is reduced with respect to that of formaldehyde alone. The reaction complex formed at low temperatures does not live long enough to produce complete energy relaxation, as assumed in statistical theories. These results show that the reactivity of the dimers cannot explain the large rate constants measured at temperatures below 100 K.     

The Reaction of Sulfur Dioxide Radical Cation with Hydrogen and its Relevance in Solar Geoengineering Models

SO₂ has been proposed in solar geoengineering as a precursor of H₂SO₄ aerosol, a cooling agent active in the stratosphere to contrast climate change. Atmospheric ionization sources can ionize SO₂ into excited states of , which quickly reacts with trace gases in the stratosphere. In this work we explore the reaction of with excited by tunable synchrotron radiation, leading to ( ), where H contributes to O₃ depletion and OH formation. Density Functional Theory and Variational Transition State Theory have been used to investigate the dynamics of the title barrierless and exothermic reaction. The present results suggest that solar geoengineering models should test the reactivity of with major trace gases in the stratosphere, such as H₂ since this is a relevant channel for the OH formation during the nighttime when there is not OH production by sunlight. OH oxides SO₂, triggering the chemical reactions leading to H₂SO₄ aerosol.     

Molecular Oxygen Trimer: Multiplet Structures and Stability

We present a detailed theoretical study of the molecular oxygen trimer where the potential energy surfaces of the seven multiplet states have been calculated by means of a pair approximation with very accurate dimer ab initio potentials. In order to obtain all the states a matrix representation of the potential using the uncoupled spin representation has been applied. The and states are nearly degenerate and low-lying isomers appear for most multiplicities. A crucial point in deciding the relative stabilities is the zero-point energy which represents a sizable fraction of the electronic well-depth. Therefore, we have performed accurate diffusion Monte Carlo studies of the lowest state in each multiplicity. Analysis of the wavefunction allows a deeper interpretation of the cluster structures, finding that they are significantly floppy in most cases.     

Size Evolution of Photoabsorption Spectra of Small Clusters: A Computational Study

Photoabsorption spectra of clusters, N=5–9, have been calculated using a diatomics-in-molecules like electronic structure model and a path-integral Monte Carlo sampling method. A qualitative change in the calculated spectra has been observed at N=9, which has been interpreted in terms of a structural transformation in the clusters consisting in a transition from trimer-like ionic cores observed for N≤7 to dimer-like ionic cores prevailing in through an intermediate state (comparable abundances of both types of ionic cores) observed in . The calculated spectra have been thoroughly compared with an earlier calculation on , , and reported from our group and data available for the same cluster sizes from an experiment.     

Proton Relaxometry of Long-Lived Spin Order

A study of long-lived spin order in chlorothiophene carboxylates at both high and low magnetic fields is presented. Careful sample preparation (removal of dissolved oxygen in solution, chelating of paramagnetic impurities, reduction of convection) allows one to obtain very long-lived singlet order of the two coupled protons in chlorothiophene derivatives, having lifetimes of about 130 s in D₂O and 240 s in deuterated methanol, which are much longer than the T₁-relaxation times (18 and 30 s, respectively, at a field =9.4 T). In protonated solvents the relaxation times become shorter, but the lifetime is still substantially longer than . In addition, long-lived coherences are shown to have lifetimes as long as 30 s. Thiophene derivatives can be used as molecular tags to study slow transport, slow dynamics and slow chemical processes, as has been shown in recent years.     

Fluorine Substitution of TCNQ Alters the Redox-Driven Catalytic Pathway for the Ferricyanide-Thiosulfate Reaction

Mechanistic variation in catalysis through substituent-based redox tuning is well established. Fluorination of TCNQ (TCNQ=tetracyanoquinodimethane) provides ~850 mV variation in the redox potentials of the and (n=0, 2, 4) processes. With , catalysis of the kinetically very slow ferrocyanide-thiosulfate redox reaction in aqueous solution occurs via a mechanism in which the catalyst is reduced to when reacting with which is oxidised to . Subsequently, reacts with to form and reform the catalyst, in another thermodynamically favoured process. An analogous mechanism applies with as a catalyst. In contrast, since the reaction of with is thermodynamically unfavourable, an alternative mechanism is required to explain the catalytic activity observed in this non-fluorinated system. Here, upon addition of , reduction of to occurs with concomitant oxidation of to , which then acts as the catalyst for oxidation. Thermodynamic data explain the observed differences in the catalytic mechanisms. (n=0, 4) also act as catalysts for the ferricyanide-thiosulfate reaction in aqueous solution. The present study shows that homogeneous pathways are available following addition of these dissolved materials. Previously, these (n=0, 4) coordination polymers have been regarded as insoluble in water and proposed as heterogeneous catalysts for the ferricyanide-thiosulfate reaction. Details and mechanistic differences were established using UV-visible spectrophotometry and cyclic voltammetry.     

Microsecond Protein Dynamics from Combined Bloch-McConnell and Near-Rotary-Resonance R1p Relaxation-Dispersion MAS NMR

Studying protein dynamics on microsecond-to-millisecond (μs-ms) time scales can provide important insight into protein function. In magic-angle-spinning (MAS) NMR, μs dynamics can be visualized by rotating-frame relaxation dispersion experiments in different regimes of radio-frequency field strengths: at low RF field strength, isotropic-chemical-shift fluctuation leads to “Bloch-McConnell-type” relaxation dispersion, while when the RF field approaches rotary resonance conditions bond angle fluctuations manifest as increased rate constants (“Near-Rotary-Resonance Relaxation Dispersion”, NERRD). Here we explore the joint analysis of both regimes to gain comprehensive insight into motion in terms of geometric amplitudes, chemical-shift changes, populations and exchange kinetics. We use a numerical simulation procedure to illustrate these effects and the potential of extracting exchange parameters, and apply the methodology to the study of a previously described conformational exchange process in microcrystalline ubiquitin.