Mechanistic Insight and Intersystem Crossing Dynamics of the C(3P) + H2CO/D2CO Reaction.

The reaction of atomic carbon, C(3P), with H2CO has been investigated using the direct dynamics trajectory surface hopping (DDTSH) method with Tully's fewest switches algorithm. The lowest lying ground triplet and single states are considered for the dynamics study at a reagent collision energy of 8.0 kcal/mol. From the trajectory calculations, we observed that CH2 + CO and H + HCCO are the two major product channels for the title reaction. The insertion mechanism of the C(3P) + H2CO reaction is rather complex and is followed by three distinct intermediates with no entrance channel barrier to the reaction on the B3LYP/6-31G(d,p) potential energy surfaces. The triplet insertion complexes are formed by three different approaches; "Sideways", "End-on" and "Head-on" attack of the triplet carbon atom toward H2CO molecule. Our dynamics calculations predict a new product channel (H + HCCO(X 2A'')) with a contribution of ∼46% of the overall products formation via ketocarbene intermediate through "Head-on" approach. Despite the weak spin-orbit coupling (SOC) interactions, intersystem crossing (ISC) via a ketocarbene intermediate has a small but significant contribution, about 2.3%, for the CH2 + CO channel. To understand the kinetic isotope effects on the reaction dynamics, we have extended our study for the C(3P) + D2CO reaction. It is seen that isotopic substitution of both the H atoms has a small reduction in the extent of ISC dynamics for the carbene formation. Our results, certainly, reveal the importance of the ketocarbene intermediate and the H + HCCO products channel as one of the major product formation channels in the title reaction, which was not reported earlier.

The interplay of vibronic and spin-orbit coupling in the fluorescence quenching in trans-dithionated PDI.

Organic chromophores such as the thionated derivatives of perylene diimides (PDIs) show prolonged triplet-excited state lifetimes in contrast to their pristine parent PDI molecule, which shows near unity fluorescence quantum yield. The excited state dynamics in the trans-dithionated PDI (S2-PDI) are studied here. Unlike PDI, the photo absorbing ππ* state of S2-PDI is in close proximity to quasi-degenerate nπ* states. The latter exhibits an interesting vibronic problem leading to the breaking of orbital symmetry mediated through non-totally symmetric vibrations. The time-dependent quantum dynamics are studied with a diabatic model Hamiltonian involving three singlet and three triplet states coupled via 22 vibrational modes. A combined effect of multiple internal-conversion and inter-system crossing (ISC) pathways leads to population transfer from the 1ππ* state to the 3ππ* state via the nπ* states, with an overall ISC rate of 0.70 ps that compares well with the experimental value. The calculated absorption spectra for PDI and S2-PDI reproduce the essential vibronic features in the observed experimental spectra. The dominant vibronic progressions are found to have significant contributions from the vinyl stretching modes of the PDI core.

Spin-vibronic coupling in the quantum dynamics of a Fe(III) trigonal-bipyramidal complex.

The presence of a high density of excited electronic states in the immediate vicinity of the optically bright state of a molecule paves the way for numerous photo-relaxation channels. In transition-metal complexes, the presence of heavy atoms results in a stronger spin-orbit coupling, which enables spin forbidden spin-crossover processes to compete with the spin-allowed internal conversion processes. However, no matter how effectively the states cross around the Franck-Condon region, the degree of vibronic coupling, of both relativistic and non-relativistic nature, drives the population distribution among these states. One such case is demonstrated in this work for the intermediate-spin Fe(III) trigonal-bipyramidal complex. A quantum dynamical investigation of the photo-deactivation mechanism in the Fe(III) system is presented using the multi-configurational time-dependent Hartree approach based on the vibronic Hamiltonian whose coupling terms are derived from the state-averaged complete active space self-consistent field/complete active space with second-order perturbation theory (CASPT2) calculations and spin-orbit coupling of the scalar-relativistic CASPT2 states. The results of this study show that the presence of a strong (non-relativistic) vibronic coupling between the optically bright intermediate-spin state and other low-lying states of the same spin-multiplicity overpowers the spin-orbit coupling between the intermediate-spin and high-spin states, thereby lowering the chances of spin-crossover while exhibiting ultrafast relaxation among the intermediate-spin states. In a special case, where the population transfer pathway via the non-relativistic vibronic coupling is blocked, the probability of the spin-crossover is found to increase. This suggests that a careful modification of the complex by incorporation of heavier atoms with stronger relativistic effects can enhance the spin-crossover potential of Fe(III) intermediate-spin complexes.

Vibronic Coupling in the First Five Electronic States of Dicyanodiacetylene Radical Cation.

We examine vibronic coupling in the first five electronic states (X̃2Πg-Ã2Πu-B̃2Σg+-C̃2Σu+-D̃2Πg-E2Πu) of dicyanodiacetylene radical cation (C6N2•+) in this article. Prompted by the prediction of its existence in the astrophysical environment, the vibronic band structure of these electronic states of C6N2•+ has been probed in spectroscopic measurements in laboratory by various groups. Inspired by numerous experimental data, we undertook the task of investigating topographical details of electronic potential energy surfaces, their coupling mechanism and nuclear dynamics on them. The degenerate Π electronic states of this radical are prone to Renner-Teller instability, and in addition symmetry allowed Σ-Π and Π-Π vibronic coupling is expected to play crucial role in the detailed vibronic structure of each of the above electronic states. A vibronic coupling model is developed here and first-principles nuclear dynamics study is carried out employing quantum mechanical methods. The vibronic band structure thus calculated is compared with experimental results and the progressions are identified and assigned. The nonradiative internal conversion dynamics among electronic states is also examined and discussed in relation to the various coupling of electronic states.

Photophysics of phenol and pentafluorophenol: The role of nonadiabaticity in the optical transition to the lowest bright 1ππ* state.

We report multimode vibronic coupling of the energetically low-lying electronic states of phenol and pentafluorophenol in this article. First principles nuclear dynamics calculations are carried out to elucidate the optical absorption spectrum of both of the molecules. This is motivated by the recent experimental measurements [S. Karmakar et al., J. Chem. Phys. 142, 184303 (2015)] on these systems. Diabatic vibronic coupling models are developed with the aid of adiabatic electronic energies calculated ab initio by the equation of motion coupled cluster quantum chemistry method. A nuclear dynamics study on the constructed electronic states is carried out by both the time-independent and time-dependent quantum mechanical methods. It is found that the nature of low-energy πσ* transition changes, and in pentafluorophenol the energy of the first two 1πσ* states, is lowered by about half an eV (vertically, relative to those in phenol), and they become energetically close to the optically bright first excited 1ππ* (S1) state. This results in strong vibronic coupling and multiple multi-state conical intersections among the ππ* and πσ* electronic states of pentafluorophenol. The impact of associated nonadiabatic effects on the vibronic structure and dynamics of the 1ππ* state is examined at length. The structured vibronic band of phenol becomes structureless in pentafluorophenol. The theoretical results are found to be in good accord with the experimental finding at both high energy resolution and low energy resolution.

Trajectory surface hopping study of the O((3)P) + C2H2 reaction dynamics: effect of collision energy on the extent of intersystem crossing.

Intersystem crossing (ISC) dynamics plays an important role in determining the product branching in the O((3)P) + C2H2 reaction despite the necessarily small spin-orbit coupling constant values. In this study we investigate the effect of collision energy on the extent of the contribution of a spin non-conserving route through ISC dynamics to the product distributions at the initial collision energies 8.2, 9.5, and 13.1 kcal/mol. A direct dynamics trajectory surface hopping method is employed with potential energy surfaces generated at the unrestricted B3LYP/6-31G(d,p) level of theory to perform nonadiabatic dynamics. To make our calculation simpler, nonadibatic transitions were only considered at the triplet-singlet intersections. At the crossing points, Landau-Zener transition probabilities were calculated using spin-orbit coupling constant values computed at the same geometry. The Landau-Zener model for the title reaction is validated against a more rigorous Tully's fewest switches method and found to be working reasonably well as expected because of weak spin-orbit coupling. We have compared our results with the recent crossed molecular beam experiments and observed a very good agreement with respect to the primary product branching ratios. Our calculation revealed that there is no noticeable effect of the initial collision energy on the overall product distributions that corroborates the recent experimental findings. Our calculation indicates, however, that the extent of intersystem crossing contributions varies significantly with collision energy, needed to be verified, experimentally.

Identification of potential inhibitors against FemX of Staphylococcus aureus: A hierarchial in-silico drug repurposing approach.

Staphylococcus aureus causes a wide range of common diseases in both community-acquired and hospital-acquired environments. The treatment becomes challenging due to the emergence of multi-drug resistant strains such as Methicillin-Resistant Staphylococcus aureus (MRSA). This study aims to find some drugs that can be used in repurposing. Virtual screening has been performed against S. aureus FemX using 1,918 FDA-approved drugs, which provides the top 10 drugs with good binding affinity. These drugs are re-docked to understand their interaction patterns with FemX. Docking study shows a high score for three drugs, Lumacaftor, Dihydroergocornine and Olaparib, and they are selected for molecular dynamics and quantum mechanical analysis. Molecular dynamics calculation shows that drug-FemX forms a stable structure compared to apo-FemX. Besides, the free energy landscape reveals that drug-protein complexes possess a single global minimum indicating their thermodynamic stability. MM/GBSA calculations show that Lumacaftor, Dihydroergocornine and Olaparib have the binding free energy of -30.03, -19.22 and -16.54 kcal/mol, respectively. The analysis of the wavefunctions from quantum chemical calculations reveals the presence of non-covalent interactions between drug and receptor, dominated by aromatic π-π interactions. The drug-receptor interaction energy estimated from quantum mechanical methods suggests an important role of dispersion interactions in stabilizing the drug molecules with FemX. The hierarchy of computational methods of increasing accuracy employed in this work finds Lumacaftor to be the most potent inhibitor against FemX.

Communications: Direct dynamics study of the O((3)P)+C(2)H(2) reaction: Contribution from spin nonconserving route.

The importance of intersystem crossing dynamics for the O((3)P)+C(2)H(2) reaction is demonstrated in this work. A direct dynamics trajectory surface hopping method has been employed to study the intersystem crossing effects. Our study reveals that there is a significant contribution from the spin nonconserving route to the chemical dynamics of the O((3)P)+C(2)H(2) reaction, despite small spin-orbit coupling constant values (<70 cm(-1)).

Aging-Dependent Morphological Crystallinity Determines Membrane Activity of l-Phenylalanine Self-Assembles.

Amyloid polymorphism has emerged as an important topic of research in recent years to identify the particular species responsible for several neurodegenerative disorders, whereas the concept is overlooked in the case of the simplest building block, that is, l-phenylalanine (l-Phe) self-assembly. Here, we report the first evidence of l-Phe polymorphism and the conversion of metastable helical fibrillar to thermodynamically stable rodlike crystalline morphologies with increasing time and temperature. Furthermore, only the fibrillar l-Phe polymorph shows a significant modulation of the model membrane. In addition, the l-Phe molecules prefer to arrange in a multilayered rodlike fashion than in a lateral arrangement, which reduces the membrane binding ability of the l-Phe polymorph due to the decrease in the partial charge of the N-terminal of l-Phe units. The present work exemplifies a different approach to understanding l-Phe self-assembly and provides an effective strategy for the therapy of phenylketonuria by scrutinizing the discrete membrane activity of different l-Phe polymorphs.