Alessio Petrone

Single-Crystal and Electronic Structure of a 1.3 nm Indium Phosphide Nanocluster.

Magic-sized nanoclusters have been implicated as mechanistically relevant intermediates in the synthesis of group III-V quantum dots. Herein we report the single-crystal X-ray diffraction structure of a carboxylate-ligated indium phosphide magic-sized nanocluster at 0.83 Å resolution. The structure of this cluster, In37P20(O2CR)51, deviates from that of known crystal phases and possesses a non-stoichiometric, charged core composed of a series of fused 6-membered rings. The cluster is completely passivated by bidentate carboxylate ligands exhibiting predominantly bridging binding modes. The absorption spectrum of the cluster shows an asymmetric line shape that is broader than what would be expected from a homogeneous sample. A combination of computational and experimental evidence suggests that the spectral line width is a result of multiple, discrete electronic transitions that couple to vibrations of the nanocrystal lattice. The product of reaction of this nanocluster with 1 equiv of water has also been structurally characterized, demonstrating site selectivity without a drastic alteration of electronic structure.

Absorption and emission spectral shapes of a prototype dye in water by combining classical/dynamical and quantum/static approaches.

We study the absorption and emission electronic spectra in an aqueous solution of N-methyl-6-oxyquinolinium betaine (MQ), an interesting dye characterized by a large change of polarity and H-bond ability between the ground (S0) and the excited (S1) states. To that end we compare alternative approaches based either on explicit solvent models and density functional theory (DFT)/molecular-mechanics (MM) calculations or on DFT calculations on clusters models embedded in a polarizable continuum (PCM). In the first approach (ClMD), the spectrum is computed according to the classical Franck-Condon principle, from the dispersion of the time-dependent (TD)-DFT vertical transitions at selected snapshots of molecular dynamics (MD) on the initial state. In the cluster model (Qst) the spectrum is simulated by computing the quantum vibronic structure, estimating the inhomogeneous broadening from state-specific TD-DFT/PCM solvent reorganization energies. While both approaches provide absorption and emission spectral shapes in nice agreement with experiment, the Stokes shift is perfectly reproduced by Qst calculations if S0 and S1 clusters are selected on the grounds of the MD trajectory. Furthermore, Qst spectra better fit the experimental line shape, mostly in absorption. Comparison of the predictions of the two approaches is very instructive: the positions of Qst and ClMD spectra are shifted due to the different solvent models and the ClMD spectra are narrower than the Qst ones, because MD underestimates the width of the vibrational density of states of the high-frequency modes coupled to the electronic transition. On the other hand, both Qst and ClMD approaches highlight that the solvent has multiple and potentially opposite effects on the spectral width, so that the broadening due to solute-solvent vibrations and electrostatic interaction with bulk solvent is (partially) counterbalanced by a narrowing of the contribution due to the solute vibrational modes. Qst analysis evidences a pure quantum broadening effect of the spectra in water due to vibronic progressions along the solute/solvent H-bonds.

Understanding THz and IR Signals beneath Time-Resolved Fluorescence from Excited-State Ab Initio Dynamics

The detailed interpretation of time-resolved spectroscopic signals in terms of the molecular rearrangement during a photoreaction or a photophysical event is one of the most important challenges of both experimental and theoretical chemistry. Here we simulate a time-resolved fluorescence spectrum of a dye in aqueous solution, the N-methyl-6-oxyquinolinium betaine, and analyze it in terms of far IR and THz frequency contributions, providing a direct connection to specific molecular motions. To obtain this result, we build up an innovative and general approach based on excited state ab-initio molecular dynamics and a wavelet-based time-dependent frequency analysis of nonstationary signals. We obtain a nice agreement with key parameters of the solvent dynamics, such as the total Stokes shift and the Stokes shift relaxation times. As an important finding, we observe a strong change of specific solute-solvent interactions upon the electronic excitation, with the migration of about 1.5 water molecules from the first solvation shell toward the bulk. In spite of this event, the Stokes shift dynamics is ruled by collective solvent motions in the THz and far IR, which guide and modulate the strong rearrangement of the dye microsolvation. By the relaxation of THz and IR contributions to the emission signal, we can follow and understand in detail the molecularity of the process. The protocol presented here is, in principle, transferable to other time-resolved spectroscopic techniques.

On the optical absorption of the anionic GFP chromophore in vacuum, solution, and protein

In spite of the large number of experimental and theoretical studies, the optical absorption trend of the green fluorescent protein (GFP) chromophore in several environments has not been fully understood. We calculated at the same level of time dependent density functional theory the vertical excitation energy of the anionic GFP chromophore in the protein and in ethanol, dioxane, methanol and water solutions. As result, we reproduced for the first time the experimental trend of the absorption peaks with 0.015 eV as the standard deviation of the accuracy. This systematic error allowed us to analyze with confidence the relative weight of several solvation effects on the vertical excitation energy. Experimental trends not correlated with the solvent polarity were therefore explained with a fine balance of different steric and electronic effects on the photophysics of the chromophore. As an indirect and remarkable result, the present analysis confirms that the optical absorption of the chromophore in the gas phase is close to the value of 2.84 eV extrapolated by Dong et al. (J. Am. Chem. Soc., 2006, 128, 12038), and, as a consequence, that the protein environment induces a red shift of 0.23 eV.

Vibrational analysis of x-ray absorption fine structure thermal factors by ab initio molecular dynamics: the Zn(II) ion in aqueous solution as a case study.

In this work, we consider a new combination of vibrational analysis and normal-like mode decomposition of Debye-Waller factors of solvated ions entirely based on molecular dynamics data. Such a novel time-dependent analysis procedure provides a direct link between x-ray absorption fine structure parameters and normal mode contributions for an ion-solvent system. The potentialities of such a methodology rely on two fundamental aspects which distinguish it from already available tools. First, a general vibrational analysis that does not require any Gaussian or harmonic model for describing atomic fluctuations in liquids. Second, a very accurate sampling of the short range motions around the structural probe via the recently developed atom centered density matrix propagation/general liquid optimized boundary method. This novel molecular dynamics methodology is based on an integrated ab initio/classical potential using localized basis functions and nonperiodic boundary conditions. As a case study we have chosen the Zn(II) ion in aqueous solution. The consistency of our results and the observed good agreement with experiments show how the key support to advanced structural techniques from molecular dynamics can be further expanded and investigated.

“Watching” Polaron Pair Formation from First-Principles Electron–Nuclear Dynamics

The formation of polaron pairs is one of the important photophysical processes that take place after the excitation in semiconducting organic polymers. First-principles Ehrenfest excited-state dynamics is a unique tool to investigate ultrafast photoinduced charge carrier dynamics and related nonequilibrium processes involving correlated electron-nuclear dynamics. In this work the formation of polaron pairs and their dynamical evolution in an oligomer of seven thiophene units is investigated with a combined approach of first-principles exciton-nuclear dynamics and wavelet analysis. The real-time formation of a polaron pair can be observed in the dipole evolution during the excited-state dynamics. The possible driving force of the polaron pair formation is investigated through qualitative correlation between the structural dynamics and the dipole evolution. The time-dependent characteristics and spectroscopic consequences of the polaron pair formation are probed using the wavelet analysis.

Investigating the role of amine in InP nanocrystal synthesis: destabilizing cluster intermediates by Z-type ligand displacement

The reaction of primary amines with In37P20(O2CR)51 is found to remove In(O2CR)3 subunits from In37P20(O2CR)51. This loss of Z-type ligands coincides with structural rearrangement to alleviate core strain and passivate phosphorus atoms. This result consolidates conflicting claims that primary amines both promote and retard precursor conversion rates for InP nanocrystals.

Direct ab Initio (Meta-)Surface-Hopping Dynamics

Tractable methods for studying the molecular dynamics of chemical processes driven by electronic nonadiabaticity are highly sought after to provide insight into, for example, photochemical reaction mechanisms, molecular collisions, and thermalized electronic band structures. Starting from the time-dependent Schrödinger equation for a many-body system, a direct ab initio trajectory surface-hopping (TSH) method relying on an analytical treatment of nonadiabatic couplings between electronic states is developed in this work. An approach that combines time-dependent perturbation theory and explicit time evolution via TSH to expedite calculation of nonadiabatic transition rates, namely, meta-surface-hopping dynamics, is presented, and an extrapolatory approach using time-dependent perturbation theory for recovering unbiased transition rates is assessed. The meta-surface-hopping method is applied to the problem of estimating nonradiative relaxation rates of a photoexcited iminium ion, CH₂NH₂⁺, and evidence for internal consistency of the combined dynamics/perturbation theory approach is presented.

Does Thermal Breathing Affect Collision Cross Sections of Gas-Phase Peptide Ions? An Ab Initio Molecular Dynamics Study

Ab initio molecular dynamics (AIMD) with density functional theory (DFT) was applied to explore conformational motions and collision cross sections (Ω) of folded (2) and extended (7) conformers of doubly charged peptide ions, (Ala-Ala-Leu-Arg + 2H)(2+), in the gas phase at 300 and 473 K. The experimental Ω of (Ala-Ala-Leu-Arg +2H)(2+) was measured as 149 ± 1.2 Å(2) at 298 K. Thermally distributed mean values of Ω for 2 and 7 at 300 and 473 K were only 0.8-1.1% larger than for the equilibrium 0 K structures. Long (>10 ps) trajectory calculations indicated entropy-driven conformational change of 2 to 7 that occurred at random within a ∼ 4 ps time window. The experimental Ω was found to fit the calculated population averaged values for 2 and 7, indicating a rapid conformer interconversion. Overall, thermal breathing had only a minor effect on the peptide ion collision cross sections.

Ab Initio Excited-State Transient Raman Analysis

Time-resolved Raman spectroscopy has proven useful for studying the formation of polarons in conjugated polymers, verifying the presence of reactive intermediates in photochemical reactions, investigating nonradiative transitions in the short lifetime of the photoexcited species, and resolving electron-phonon coupling strengths and exciton dissociation in crystalline materials. In this paper, we present an excited state transient Raman analysis protocol combining ab initio direct molecular dynamics, transient excited state Hessian, and excited state nonresonant Raman activities evaluations. Prototypical molecules are used as test cases, showing the evolution of the transient Raman signatures that follow electronic excitation. This protocol provides a direct route to assigning the vibrations implicated in the (photo)dynamics of several (photoactive) systems, complementary to the transient infrared analysis.