NEXMD Software Package for Nonadiabatic Excited State Molecular Dynamics Simulations.

We present a versatile new code released for open community use, the nonadiabatic excited state molecular dynamics (NEXMD) package. This software aims to simulate nonadiabatic excited state molecular dynamics using several semiempirical Hamiltonian models. To model such dynamics of a molecular system, the NEXMD uses the fewest-switches surface hopping algorithm, where the probability of transition from one state to another depends on the strength of the derivative nonadiabatic coupling. In addition, there are a number of algorithmic improvements such as empirical decoherence corrections and tracking trivial crossings of electronic states. While the primary intent behind the NEXMD was to simulate nonadiabatic molecular dynamics, the code can also perform geometry optimizations, adiabatic excited state dynamics, and single-point calculations all in vacuum or in a simulated solvent. In this report, first, we lay out the basic theoretical framework underlying the code. Then we present the code's structure and workflow. To demonstrate the functionality of NEXMD in detail, we analyze the photoexcited dynamics of a polyphenylene ethynylene dendrimer (PPE, C30H18) in vacuum and in a continuum solvent. Furthermore, the PPE molecule example serves to highlight the utility of the getexcited.py helper script to form a streamlined workflow. This script, provided with the package, can both set up NEXMD calculations and analyze the results, including, but not limited to, collecting populations, generating an average optical spectrum, and restarting unfinished calculations.

Non-adiabatic Excited-State Molecular Dynamics: Theory and Applications for Modeling Photophysics in Extended Molecular Materials.

Optically active molecular materials, such as organic conjugated polymers and biological systems, are characterized by strong coupling between electronic and vibrational degrees of freedom. Typically, simulations must go beyond the Born-Oppenheimer approximation to account for non-adiabatic coupling between excited states. Indeed, non-adiabatic dynamics is commonly associated with exciton dynamics and photophysics involving charge and energy transfer, as well as exciton dissociation and charge recombination. Understanding the photoinduced dynamics in such materials is vital to providing an accurate description of exciton formation, evolution, and decay. This interdisciplinary field has matured significantly over the past decades. Formulation of new theoretical frameworks, development of more efficient and accurate computational algorithms, and evolution of high-performance computer hardware has extended these simulations to very large molecular systems with hundreds of atoms, including numerous studies of organic semiconductors and biomolecules. In this Review, we will describe recent theoretical advances including treatment of electronic decoherence in surface-hopping methods, the role of solvent effects, trivial unavoided crossings, analysis of data based on transition densities, and efficient computational implementations of these numerical methods. We also emphasize newly developed semiclassical approaches, based on the Gaussian approximation, which retain phase and width information to account for significant decoherence and interference effects while maintaining the high efficiency of surface-hopping approaches. The above developments have been employed to successfully describe photophysics in a variety of molecular materials.

Correlating Mechanical Sensitivity with Spin Transition in the Explosive Spin Crossover Complex [Fe(Htrz)3]n[ClO4]2n.

Spin crossover complexes are known to undergo bond length, volume, and enthalpy changes during spin transition. In an explosive spin crossover complex, these changes could affect the mechanical and initiation sensitivity of the explosive and lead to the development of a new class of sensitivity switchable materials. To explore this relationship, the well-known spin crossover compound [Fe(Htrz)3]n[ClO4]2n (1) was re-evaluated for its explosive properties, and its mechanical impact sensitivity was correlated to spin transition. A variable temperature impact test was developed and used to evaluate the impact sensitivity of 1 in the low spin (LS, S = 0), thermally accessed high spin (HS, S = 2), and mixed LS and HS states. For comparison, the structurally similar Ni compound, [Ni(Htrz)3]n[ClO4]2n (2), which does not undergo a spin transition at accessible temperatures, was synthesized and characterized, and its explosive properties and variable temperature impact sensitivity measured. These results reveal a correlation between impact sensitivity and spin transition, where 1 exhibits lower impact sensitivity in the LS state and increases in sensitivity upon transition to the HS state. Density functional theory was used to predict structural changes that occur upon spin transition that correlate to the change in sensitivity. This demonstrates, for the first time, an explosive spin crossover compound (ExSCO) that exhibits switchable impact sensitivity with a fully reversible internal switching mechanism.

NEXMD Modeling of Photoisomerization Dynamics of 4-Styrylquinoline.

Isomerization of molecular systems is ubiquitous in chemistry and biology, and is also important for many applications. Atomistic simulations can help determine the tunable parameters influencing this process. In this paper, we use the Nonadiabatic EXcited state Molecular Dynamics (NEXMD) software to study the photoisomerization of a representative molecule, 4-styrylquinoline (SQ). trans-SQ transforms into dihydrobenzophenanthridine (DHBP) upon irradiation with laser light, with the cis conformer acting as an intermediate. We study how varying three different external stimuli (i.e., apolar versus polar solvent, low versus high photoexcitation energy, and vacuum versus a constant temperature thermostat) affects the trans-to- cis photoisomerization of SQ. Our results show that polarization effects due to implicit solvation and the thermostat play a crucial role in the isomerization process, whereas photoexcitation energy plays a lesser role on the outcome and efficiency. We also show that NEXMD captures the correct energy profile between the ground and first singlet excited state, showing that there are two distinct reaction pathways to the final stable product that vary by the number of photons absorbed, in agreement with experiment. Ultimately, NEXMD proves to be an effective tool for investigating excited state single molecule dynamics subject to various environments and initial conditions.

Photoexcited Nonadiabatic Dynamics of Solvated Push-Pull π-Conjugated Oligomers with the NEXMD Software.

Solvation can be modeled implicitly by embedding the solute in a dielectric cavity. This approach models the induced surface charge density at the solute-solvent boundary, giving rise to extra Coulombic interactions. Herein, the Nonadiabatic EXcited-state Molecular Dynamics (NEXMD) software was used to model the photoexcited nonradiative relaxation dynamics in a set of substituted donor-acceptor oligo( p-phenylenevinylene) (PPVO) derivatives in the presence of implicit solvent. Several properties of interest including optical spectra, excited state lifetimes, exciton localization, excited state dipole moments, and structural relaxation are calculated to elucidate dependence of functionalization and solvent polarity on photoinduced nonadiabatic dynamics. Results show that solvation generally affects all these properties, where the magnitude of these effects vary from one system to another depending on donor-acceptor substituents and molecular polarizability. We conclude that implicit solvation can be directly incorporated into nonadiabatic simulations within the NEXMD framework with little computational overhead and that it qualitatively reproduces solvent-dependent effects observed in solution-based spectroscopic experiments.

Coherent exciton-vibrational dynamics and energy transfer in conjugated organics.

Coherence, signifying concurrent electron-vibrational dynamics in complex natural and man-made systems, is currently a subject of intense study. Understanding this phenomenon is important when designing carrier transport in optoelectronic materials. Here, excited state dynamics simulations reveal a ubiquitous pattern in the evolution of photoexcitations for a broad range of molecular systems. Symmetries of the wavefunctions define a specific form of the non-adiabatic coupling that drives quantum transitions between excited states, leading to a collective asymmetric vibrational excitation coupled to the electronic system. This promotes periodic oscillatory evolution of the wavefunctions, preserving specific phase and amplitude relations across the ensemble of trajectories. The simple model proposed here explains the appearance of coherent exciton-vibrational dynamics due to non-adiabatic transitions, which is universal across multiple molecular systems. The observed relationships between electronic wavefunctions and the resulting functionalities allows us to understand, and potentially manipulate, excited state dynamics and energy transfer in molecular materials.

Photoactive high explosives: linear and nonlinear photochemistry of petrin tetrazine chloride.

Pentaerythritol tetranitrate (PETN), a high explosive, initiates with traditional shock and thermal mechanisms. In this study, the tetrazine-substituted derivative of PETN, pentaerythritol trinitrate chlorotetrazine (PetrinTzCl), is being investigated for a photochemical initiation mechanism that could allow control over the chemistry contributing to decomposition leading to initiation. PetrinTzCl exhibits a photochemical quantum yield (QYPC) at 532 nm not evident with PETN. Using static spectroscopic methods, we observe energy absorption on the tetrazine (Tz) ring that results in photodissociation yielding N2, Cl-CN, and Petrin-CN as the major photoproducts. The QYPC was enhanced with increasing irradiation intensity. Experiment and theoretical calculations imply this excitation mechanism follows sequential photon absorption. Dynamic simulations demonstrate that the relaxation mechanism leading to the observed photochemistry in PetrinTzCl is due to vibrational excitation during internal conversion. PetrinTzCl's single photon stability and intensity dependence suggest this material could be stable in ambient lighting, yet possible to initiate with short-pulsed lasers.

Extremely long nonradiative relaxation of photoexcited graphane is greatly accelerated by oxidation: time-domain ab initio study.

Graphane and its derivatives are stable and extremely thin, wide band gap semiconductors that promise to replace conventional semiconductors in electronics, catalysis, and energy applications, greatly reducing device size and power consumption. In order to be useful, band-gap excitations in these materials should be long lived and nonradiative energy losses to heat should be slow. We use state-of-the-art nonadiabatic molecular dynamics combined with time-dependent density functional theory in order to determine the nonradiative lifetime and radiative line width of the lowest energy singlet excitations in pure and oxidized graphanes. We predict that pure graphane has a very long nonradiative decay time, on the order of 100 ns, while epoxy- and hydroxy-graphanes lose electronic excitation energy to heat 10-20 times faster. The luminescence line width is 1.5 times larger in pristine graphane compared to its oxidized forms, and at room temperature, it is on the order of 50 meV. Hydroxylation lowers graphane's band gap, while epoxidation increases the gap. The nonradiative decay and luminescence line width of pure graphane are governed by electron coupling to the 1200 cm(-1) vibrational mode. In the oxidized forms of graphane, the electronic excitations couple to a broad range of vibrational modes, rationalizing the more rapid nonradiative decay in these systems. The slow electron-phonon energy losses in graphane compared to other graphene derivatives, such as carbon nanotubes and nanoribbons, indicate that graphanes are excellent candidates for semiconductor applications.

Vibrational energy transfer between carbon nanotubes and nonaqueous solvents: a molecular dynamics study.

We report molecular dynamics (MD) simulation of energy exchange between single-walled carbon nanotubes (CNTs) and two aprotic solvents, acetonitrile and cyclohexane. Following our earlier study of hydrated CNTs, we find that the time scales and molecular mechanisms of the energy transfer are largely independent of the nature of the surrounding medium, and therefore, should hold for other media including polymer matrices and DNA. The vibrational energy exchange between CNT and solvents exhibits two time-scales. Over half of the energy is transferred in less than one picosecond, indicating that the dominant exchange mechanism is inertial relaxation. It occurs by collisions of solvent molecules with CNT walls, facilitated by the short-range Lennard-Jones interaction. Additional several picoseconds are required for the remainder of the vibrational energy exchange, corresponding to the diffusive relaxation mechanism and involving collective molecular motions. The faster stage of the CNT-solvent energy exchange occurs on the same time-scale, and therefore, competes with the vibrational energy relaxation inside CNTs. The energy exchange time-scales are significantly influenced by the arrangement of solvent molecules inside CNTs. Generally, the effects of confinement on the dynamics can be rationalized by analysis of the solvent structure. For the same CNT diameter, the extent of the confinement effect strongly depends on the size of the solvent molecules. Icelike properties in water seen in small CNTs disappear in CNTs with intermediate diameters. In acetonitrile and cyclohexane, medium size CNTs still show strong confinement effects. Rotational motions of acetonitrile molecules are inhibited, and the cyclohexane density is dramatically decreased. The disbalance between the local temperatures of the inside and outside regions of the solvent equilibrates through a tube-mediated interaction, rather than by a direct coupling between the two solvent subsystems. In all cases, the CNT-solvent energy transfer is mediated by slow motions in the frequency range of CNT radial breathing modes.

Vibrational energy transfer between carbon nanotubes and liquid water: a molecular dynamics study.

The rates and magnitudes of vibrational energy transfer between single-wall carbon nanotubes (CNTs) and water are investigated by classical molecular dynamics. The interactions between the CNT and solvent confined inside of the tube, the CNT and solvent surrounding the tube, as well as the solvent inside and outside of the tube are considered for the (11,11), (15,15), and (19,19) armchair CNTs. The vibrational energy transfer exhibits two time scales, subpicosecond and picosecond, of roughly equal importance. Solvent molecules confined within CNTs are more strongly coupled to the tubes than the outside molecules. The energy exchange is facilitated by slow collective motions, including CNT radial breathing modes (RBM). The transfer rate between CNTs and the inside solvent shows strong dependence on the CNT diameter. In smaller tubes, the transfer is faster and the solvent coupling to RBMs is stronger. The magnitude of the CNT-outside solvent interaction scales with the CNT surface area, while that of the CNT-inside solvent exhibits scaling that is intermediate between the CNT volume and surface. The Coulomb interaction between the solvent molecules inside and outside of the CNTs is much weaker than the CNT-solvent interactions. The results indicate that the excitation energy supplied to CNTs in chemical and biological applications is rapidly deposited to the active molecular agents and should remain localized sufficiently long in order to perform the desired function.