Electron dynamics in complex environments with real-time time dependent density functional theory in a QM-MM framework

Modeling of High-Harmonic Generation in the C60 Fullerene Using Ab Initio, DFT-Based, and Semiempirical Methods

We report calculations of the high-harmonic generation spectra of the C60 fullerene molecule carried out by employing a diverse set of real-time time-dependent quantum chemical methods. All methodologies involve expanding the propagated electronic wave function in bases consisting of the ground and singly excited time-independent eigenstates obtained through the solution of the corresponding linear-response equations. We identify the correlation and exchange effect in the spectra by comparing the results from methods relying on the Hartree-Fock reference determinant with those obtained using approaches based on the density functional theory with different exchange-correlation functionals. The effect of the full random-phase approximation treatment of the excited electronic states is also analyzed and compared with the configuration interaction singles and the Tamm-Dancoff approximation. We also showcase the fact that the real-time extension of the semiempirical method INDO/S can be effectively applied for an approximate description of laser-driven dynamics in large systems.

Dynamic chromatin accessibility tuning by the long noncoding RNA ELDR accelerates chondrocyte senescence and osteoarthritis

Epigenetic reprogramming plays a critical role in chondrocyte senescence during osteoarthritis (OA) pathology, but the underlying molecular mechanisms remain to be elucidated. Here, using large-scale individual datasets and genetically engineered (Col2a1-CreER^T2;Eldr^flox/flox and Col2a1-CreER^T2;ROSA26-LSL-Eldr^+/+ knockin) mouse models, we show that a novel transcript of long noncoding RNA ELDR is essential for the development of chondrocyte senescence. ELDR is highly expressed in chondrocytes and cartilage tissues of OA. Mechanistically, exon 4 of ELDR physically mediates a complex consisting of hnRNPL and KAT6A to regulate histone modifications of the promoter region of IHH, thereby activating hedgehog signaling and promoting chondrocyte senescence. Therapeutically, GapmeR-mediated silencing of ELDR in the OA model substantially attenuates chondrocyte senescence and cartilage degradation. Clinically, ELDR knockdown in cartilage explants from OA-affected individuals decreased the expression of senescence markers and catabolic mediators. Taken together, these findings uncover an lncRNA-dependent epigenetic driver in chondrocyte senescence, highlighting that ELDR could be a promising therapeutic avenue for OA.

Tailoring Cooperative Emission in Molecules: Superradiance and Subradiance from First-Principles Simulations

Cooperative optical effects provide a pathway to both the amplification (superradiance) and the suppression (subradiance) of photon emission from electronically excited states. These captivating phenomena offer a rich variety of possibilities for photonic technologies aimed at electromagnetic energy manipulation, including lasers and high-speed emitting devices in the case of superradiance or optical energy storage in that of subradiance. The employment of molecules as the building pieces in these developments requires a precise understanding of the roles of separation, orientation, spatial distribution, and applied fields, which remains challenging for theory and experiments. These questions are addressed here through ab initio quantum dynamics simulations of collective emission on the basis of a novel semiclassical formalism and time-dependent density functional theory. By establishing the configurations leading to decoherence and how the fine-tuning of a pulse can accumulate or release optical energy in H₂ arrays, this report provides fundamental insight toward the design of real superradiant and subradiant devices.

Non-Aromatic Fluorescence in Biological Matter: The Exception or the Rule?

While in the vast majority of cases fluorescence in biological matter has been attributed to aromatic or conjugated groups, peptides associated with neurodegenerative diseases, such as Alzheimer's, Parkinson's, or Huntington's, have been recently shown to display an intrinsic visible fluorescence even in the absence of aromatic residues. This has called the attention of researchers from many different fields, trying to understand the origin of this peculiar behavior and, at the same time, motivating the search for novel strategies to control the optical properties of new biophotonic materials. Today, after nearly 15 years of its discovery, there is a growing consensus about the mechanism underlying this phenomenon, namely, that electronic interactions between non-optically active molecules can result in supramolecular assemblies that are fluorescent. Despite this progress, many aspects of this phenomenon remain uncharted territory. In this Perspective, we lay down the state-of-the-art in the field highlighting the open questions from both experimental and theoretical fronts in this fascinating emerging area of non-aromatic fluorescence.

Environment Effects on X-Ray Absorption Spectra With Quantum Embedded Real-Time Time-Dependent Density Functional Theory Approaches

In this work we implement the real-time time-dependent block-orthogonalized Manby-Miller embedding (rt-BOMME) approach alongside our previously developed real-time frozen density embedding time-dependent density functional theory (rt-TDDFT-in-DFT FDE) code, and investigate these methods' performance in reproducing X-ray absorption spectra (XAS) obtained with standard rt-TDDFT simulations, for model systems comprised of solvated fluoride and chloride ions ([X@( H 2 O ) 8 - , X = F, Cl). We observe that for ground-state quantities such as core orbital energies, the BOMME approach shows significantly better agreement with supermolecular results than FDE for the strongly interacting fluoride system, while for chloride the two embedding approaches show more similar results. For the excited states, we see that while FDE (constrained not to have the environment densities relaxed in the ground state) is in good agreement with the reference calculations for the region around the K and L1 edges, and is capable of reproducing the splitting of the 1s1 (n + 1)p1 final states (n + 1 being the lowest virtual p orbital of the halides), it by and large fails to properly reproduce the 1s1 (n + 2)p1 states and misses the electronic states arising from excitation to orbitals with important contributions from the solvent. The BOMME results, on the other hand, provide a faithful qualitative representation of the spectra in all energy regions considered, though its intrinsic approximation of employing a lower-accuracy exchange-correlation functional for the environment induces non-negligible shifts in peak positions for the excitations from the halide to the environment. Our results thus confirm that QM/QM embedding approaches are viable alternatives to standard real-time simulations of X-ray absorption spectra of species in complex or confined environments.

Doping and coupling strength in molecular conductors: polyacetylene as a case study

The doping mechanisms responsible for elevating the currents up to eleven orders of magnitude in semiconducting polymer films are today well characterized. Doping can also improve the performance of nanoscale devices or single molecule conductors, but the mechanism in this case appears to be different, with theoretical studies suggesting that the dopant affects the electronic properties of the junctions. In the present report, multiscale time-dependent DFT transport simulations help clarify the way in which n-type doping can raise the current flowing through a polymer chain connected to a pair of electrodes, with the focus on polyacetylene. In particular, our multiscale methodology offers control over the magnitude of the chemical coupling between the molecule and the electrodes, which allows us to analyze the effect of doping in low and strong coupling regimes. Interestingly, our results establish that the impact of dopants is the highest in weakly coupled devices, while their presence tends to be irrelevant in low-resistance junctions. Our calculations point out that both the equalization of the frontier orbitals with the Fermi level and a small gap between the HOMO and the LUMO must result from doping in order to observe any significant increase of the currents.

Exploring space-energy matching via quantum-molecular mechanics modeling and breakage dynamics-energy dissipation via microhydrodynamic modeling to improve the screening efficiency of nanosuspension prepared by wet media milling

Introduction: The preparation of nanosuspensions by wet media milling is a promising technique that increases the bioavailability of insoluble drugs. The nanosuspension is thermodynamically unstable, where its stability might be influenced by the interaction energy between the stabilizers and the drugs after milling at a specific collision energy. However, it is difficult to screen the stabilizers and the parameters of milling accurately and quickly by using traditional analysis methods. Quantum-molecular mechanics and microhydrodynamic modeling can be applied to improve screening efficiency.Areas covered: Quantum-molecular mechanics model, which includes molecular docking, molecular dynamics simulations, and data on binding energy, provides insights into screening stabilizers based on their molecular behavior at the atomic level. The microhydrodynamic model explores the mechanical processes and energy dissipation in nanomilling, and even combines information on the mechanical modulus and an energy vector diagram for the milling parameters screening of drug crystals.Expert opinion: These modeling methods improve screening efficiency and support screening theories based on thermodynamics and physical dynamics. However, how to reasonably combine different modeling methods with their theoretical characteristics and further multidimensional and cross-scale simulations of nanosuspension formation remain challenges.

Real-Time Electron Dynamics Study of Plasmon-Mediated Photocatalysis on an Icosahedral Al13-1 Nanocluster

Nitrogen bond dissociation is one of the important steps in the Haber-Bosch process, where N₂ is catalytically converted to NH₃; however, the dissociation of the nitrogen triple bond is difficult to achieve. In this study, we investigate the possibility of nitrogen activation using plasmonic excitation of an icosahedral aluminum nanocluster. Real-time time-dependent density functional theory is employed to study the electron dynamics of the Al₁₃^-1 and [Al₁₃N₂]^-1 systems. Step and trapezoidal electric fields with field strengths of 0.001 and 0.01 au and different polarization directions are applied to the systems, and the electron dynamics are analyzed. Because the occupation of nitrogen antibonding orbitals could potentially activate the N-N bond, we investigated the single-particle electronic transitions corresponding to an excitation from an occupied (O) to virtual (V) molecular orbitals (P_OV) of [Al₁₃N₂]^-1. We found that N₂ antibonding orbitals are more likely to become populated with stronger fields and also by using off-resonance fields.

Short hydrogen bonds enhance nonaromatic protein-related fluorescence

Intrinsic fluorescence of nonaromatic amino acids is a puzzling phenomenon with an enormous potential in biophotonic applications. The physical origins of this effect, however, remain elusive. Herein, we demonstrate how specific hydrogen bond networks can modulate fluorescence. We highlight the key role played by short hydrogen bonds, present in the protein structure, on the ensuing fluorescence. We provide detailed experimental and molecular evidence to explain these unusual nonaromatic optical properties. Our findings should benefit the design of novel optically active biomaterials for applications in biosensing and imaging.

Fluorescence in biological systems is usually associated with the presence of aromatic groups. Here, by employing a combined experimental and computational approach, we show that specific hydrogen bond networks can significantly affect fluorescence. In particular, we reveal that the single amino acid L-glutamine, by undergoing a chemical transformation leading to the formation of a short hydrogen bond, displays optical properties that are significantly enhanced compared with L-glutamine itself. Ab initio molecular dynamics simulations highlight that these short hydrogen bonds prevent the appearance of a conical intersection between the excited and the ground states and thereby significantly decrease nonradiative transition probabilities. Our findings open the door to the design of new photoactive materials with biophotonic applications.

Electron transfer pathways from quantum dynamics simulations

This work explores the possibility of simulating an electron transfer process between a donor and an acceptor in real time using time-dependent density functional theory electron dynamics. To achieve this objective, a central issue to resolve is the definition of the initial state. This must be a non-equilibrium electronic state able to trigger the charge transfer dynamics; here, two schemes are proposed to prepare such states. One is based on the combination of the density matrices of the donor and acceptor converged separately with appropriate charges (for example, -1 for the donor and +1 for the acceptor). The second approach relied on constrained DFT to localize the charge on each fragment. With these schemes, electron transfer processes are simulated in different model systems of increasing complexity: an atomic hydrogen dimer, a polyacetylene chain, and the active site of the T. cruzi hybrid type A heme peroxidase, for which two possible electron transfer paths have been postulated. For the latter system, the present methodology applied in a hybrid Quantum Mechanics - Molecular Mechanics framework allows us to establish the relative probabilities of each path and provides insight into the inhibition of the electron transfer provoked by the substitution of tryptophan by phenylalanine in the W233F mutant.

Dissipative Equation of Motion for Electromagnetic Radiation in Quantum Dynamics

The dynamical description of the radiative decay of an electronically excited state in realistic many-particle systems is an unresolved challenge. In the present investigation electromagnetic radiation of the charge density is approximated as the power dissipated by a classical dipole, to cast the emission in closed form as a unitary single-electron theory. This results in a formalism of unprecedented efficiency, critical for ab initio modeling, which exhibits at the same time remarkable properties: it quantitatively predicts decay rates, natural broadening, and absorption intensities. Exquisitely accurate excitation lifetimes are obtained from time-dependent DFT simulations for C^{2+}, B^{+}, and Be, of 0.565, 0.831, and 1.97 ns, respectively, in accord with experimental values of 0.57±0.02, 0.86±0.07, and 1.77-2.5 ns. Hence, the present development expands the frontiers of quantum dynamics, bringing within reach first-principles simulations of a wealth of photophysical phenomena, from fluorescence to time-resolved spectroscopies.

A simple approximation to the electron-phonon interaction in population dynamics

The modeling of coupled electron-ion dynamics including a quantum description of the nuclear degrees of freedom has remained a costly and technically difficult practice. The kinetic model for electron-phonon interaction provides an efficient approach to this problem, for systems evolving with low amplitude fluctuations, in a quasi-stationary state. In this work, we propose an extension of the kinetic model to include the effect of coherences, which are absent in the original approach. The new scheme, referred to as Liouville-von Neumann + Kinetic Equation (or LvN + KE), is implemented here in the context of a tight-binding Hamiltonian and employed to model the broadening, caused by the nuclear vibrations, of the electronic absorption bands of an atomic wire. The results, which show close agreement with the predictions given by Fermi's golden rule (FGR), serve as a validation of the methodology. Thereafter, the method is applied to the electron-phonon interaction in transport simulations, adopting to this end the driven Liouville-von Neumann equation to model open quantum boundaries. In this case, the LvN + KE model qualitatively captures the Joule heating effect and Ohm's law. It, however, exhibits numerical discrepancies with respect to the results based on FGR, attributable to the fact that the quasi-stationary state is defined taking into consideration the eigenstates of the closed system rather than those of the open boundary system. The simplicity and numerical efficiency of this approach and its ability to capture the essential physics of the electron-phonon coupling make it an attractive route to first-principles electron-ion dynamics.

Real-time time-dependent density functional theory using density fitting and the continuous fast multipole method

An implementation of real-time time-dependent density functional theory (RT-TDDFT) within the TURBOMOLE program package is reported using Gaussian-type orbitals as basis functions, second and fourth order Magnus propagator, and the self-consistent field as well as the predictor-corrector time integration schemes. The Coulomb contribution to the Kohn-Sham matrix is calculated combining density fitting approximation and the continuous fast multipole method. Performance of the implementation is benchmarked for molecular systems with different sizes and dimensionalities. For linear alkane chains, the wall time for density matrix time propagation step is comparable to the Kohn-Sham (KS) matrix construction. However, for larger two- and three-dimensional molecules, with up to about 5,000 basis functions, the computational effort of RT-TDDFT calculations is dominated by the KS matrix evaluation. In addition, the maximum time step is evaluated using a set of small molecules of different polarities. The photoabsorption spectra of several molecular systems calculated using RT-TDDFT are compared to those obtained using linear response time-dependent density functional theory and coupled cluster methods.

Fluorescence Quantum Yields in Complex Environments from QM-MM TDDFT Simulations: The Case of Indole in Different Solvents

Fluorescence is commonly exploited to probe microscopic properties. An important example is tryptophan in protein environments, where variations in fluorescence quantum yield, and in absorption and emission maxima, are used as indicators of changes in the environment. Modeling the fluorescence quantum yield requires the determination of both radiative and nonradiative decay constants, both on the potential energy surface of the excited fluorophore. Furthermore, the inclusion of complex environments implies their accurate representation as well as extensive configurational sampling. In this work, we present and test various methodologies based on time-dependent density functional theory (TDDFT) and quantum mechanics/molecular mechanics (QM/MM) dynamics that take all of these requirements into account to provide a quantitative prediction of the effect of the environment on the fluorescence quantum yield of indole, a tryptophan fluorophore. This investigation paves the way for applications to the realistic spectroscopic characterization of the local protein environment of tryptophan from computer simulations.

Vibronic Dynamics of Photodissociating ICN from Simulations of Ultrafast X-Ray Absorption Spectroscopy

Ultrafast UV-pump/soft-X-ray-probe spectroscopy is a subject of great interest since it can provide detailed information about dynamical photochemical processes with ultrafast resolution and atomic specificity. Here, we focus on the photodissociation of ICN in the 1 Π1 excited state, with emphasis on the transient response in the soft-X-ray spectral region as described by the ab initio spectral lineshape averaged over the nuclear wavepacket probability density. We find that the carbon K-edge spectral region reveals a rich transient response that provides direct insights into the dynamics of frontier orbitals during the I-CN bond cleavage process. The simulated UV-pump/soft-X-ray-probe spectra exhibit detailed dynamical information, including a time-domain signature for coherent vibration associated with the photogenerated CN fragment.

Self-interaction correction, electrostatic, and structural influences on time-dependent density functional theory excitations of bacteriochlorophylls from the light-harvesting complex 2

First-principles calculations offer the chance to obtain a microscopic understanding of light-harvesting processes. Time-dependent density functional theory can have the computational efficiency to allow for such calculations. However, the (semi-)local exchange-correlation approximations that are computationally most efficient fail to describe charge-transfer excitations reliably. We here investigate whether the inexpensive average density self-interaction correction (ADSIC) remedies the problem. For the systems that we study, ADSIC is even more prone to the charge-transfer problem than the local density approximation. We further explore the recently reported finding that the electrostatic potential associated with the chromophores' protein environment in the light-harvesting complex 2 beneficially shifts spurious excitations. We find a great sensitivity on the chromophores' atomistic structure in this problem. Geometries obtained from classical molecular dynamics are more strongly affected by the spurious charge-transfer problem than the ones obtained from crystallography or density functional theory. For crystal structure geometries and density-functional theory optimized ones, our calculations confirm that the electrostatic potential shifts the spurious excitations out of the energetic range that is most relevant for electronic coupling.

Environmental Effects with Frozen-Density Embedding in Real-Time Time-Dependent Density Functional Theory Using Localized Basis Functions

Frozen-density embedding (FDE) represents a versatile embedding scheme to describe the environmental effect on electron dynamics in molecular systems. The extension of the general theory of FDE to the real-time time-dependent Kohn-Sham method has previously been presented and implemented in plane waves and periodic boundary conditions [Pavanello, M.; J. Chem. Phys. 2015, 142, 154116]. In the current paper, we extend our recent formulation of the real-time time-dependent Kohn-Sham method based on localized basis set functions and developed within the Psi4NumPy framework to the FDE scheme. The latter has been implemented in its "uncoupled" flavor (in which the time evolution is only carried out for the active subsystem, while the environment subsystems remain at their ground state), using and adapting the FDE implementation already available in the PyEmbed module of the scripting framework PyADF. The implementation was facilitated by the fact that both Psi4NumPy and PyADF, being native Python API, provided an ideal framework of development using the Python advantages in terms of code readability and reusability. We employed this new implementation to investigate the stability of the time-propagation procedure, which is based on an efficient predictor/corrector second-order midpoint Magnus propagator employing an exact diagonalization, in combination with the FDE scheme. We demonstrate that the inclusion of the FDE potential does not introduce any numerical instability in time propagation of the density matrix of the active subsystem, and in the limit of the weak external field, the numerical results for low-lying transition energies are consistent with those obtained using the reference FDE calculations based on the linear-response TDDFT. The method is found to give stable numerical results also in the presence of a strong external field inducing nonlinear effects. Preliminary results are reported for high harmonic generation (HHG) of a water molecule embedded in a small water cluster. The effect of the embedding potential is evident in the HHG spectrum reducing the number of the well-resolved high harmonics at high energy with respect to the free water. This is consistent with a shift toward lower ionization energy passing from an isolated water molecule to a small water cluster. The computational burden for the propagation step increases approximately linearly with the size of the surrounding frozen environment. Furthermore, we have also shown that the updating frequency of the embedding potential may be significantly reduced, much less than one per time step, without jeopardizing the accuracy of the transition energies.

Reaction Path Analysis from Potential Energy Contributions Using Forces: An Accessible Estimator of Reaction Coordinate Adequacy

The calculation of potential energy and free-energy profiles along complex chemical reactions or rare event processes is of great interest because of their importance for many areas in chemistry, molecular biology, and material science. One typical way to generate these profiles is to add a bias potential to modify the energy surface, which can act on a selected degree of freedom in the system. However, in these cases, the quality of the result is strongly dependent on the selection of the degree of freedom over which this bias potential acts. The present work introduces a simple method for the analysis of the degree of freedom selected to describe a chemical process. The proposed methodology is based on the decomposition of contributions to the potential energy profiles by the integration of forces along a reaction path, which allows evaluating the different contributions to the energy change. This could be useful for discriminating the contributions to the energy arising from different regions of the system, which is particularly useful in systems with complex environments that must be represented using hybrid quantum mechanics/molecular mechanics schemes. Furthermore, this methodology allows in generating a quick and simple analysis of the degree of freedom which is used to describe the potential energy profile associated with the reactive process. This is computationally more accessible than the corresponding free-energy profile and can therefore be used as a simple estimator of reaction coordinate adequacy.

Molecular Simulations with in-deMon2k QM/MM, a Tutorial-Review

deMon2k is a readily available program specialized in Density Functional Theory (DFT) simulations within the framework of Auxiliary DFT. This article is intended as a tutorial-review of the capabilities of the program for molecular simulations involving ground and excited electronic states. The program implements an additive QM/MM (quantum mechanics/molecular mechanics) module relying either on non-polarizable or polarizable force fields. QM/MM methodologies available in deMon2k include ground-state geometry optimizations, ground-state Born-Oppenheimer molecular dynamics simulations, Ehrenfest non-adiabatic molecular dynamics simulations, and attosecond electron dynamics. In addition several electric and magnetic properties can be computed with QM/MM. We review the framework implemented in the program, including the most recently implemented options (link atoms, implicit continuum for remote environments, metadynamics, etc.), together with six applicative examples. The applications involve (i) a reactivity study of a cyclic organic molecule in water; (ii) the establishment of free-energy profiles for nucleophilic-substitution reactions by the umbrella sampling method; (iii) the construction of two-dimensional free energy maps by metadynamics simulations; (iv) the simulation of UV-visible absorption spectra of a solvated chromophore molecule; (v) the simulation of a free energy profile for an electron transfer reaction within Marcus theory; and (vi) the simulation of fragmentation of a peptide after collision with a high-energy proton.

Chemical Reactivity and Spectroscopy Explored From QM/MM Molecular Dynamics Simulations Using the LIO Code

In this work we present the current advances in the development and the applications of LIO, a lab-made code designed for density functional theory calculations in graphical processing units (GPU), that can be coupled with different classical molecular dynamics engines. This code has been thoroughly optimized to perform efficient molecular dynamics simulations at the QM/MM DFT level, allowing for an exhaustive sampling of the configurational space. Selected examples are presented for the description of chemical reactivity in terms of free energy profiles, and also for the computation of optical properties, such as vibrational and electronic spectra in solvent and protein environments.

Quantum Chemical Topology of the Electron Localization Function in the Field of Attosecond Electron Dynamics

We report original analyses of attosecond electron dynamics of molecules subject to collisions by high energy charged particles based on Real-Time Time-Dependent-Density-Functional-Theory simulations coupled to Topological Analyses of the Electron Localization Function (TA-TD-ELF). We investigate irradiation of water and guanine. TA-TD-ELF enables qualitative and quantitative characterizations of bond breaking and formation, of charge migration within topological basins, or of electron attachment to the colliding particle. Whereas the Lewis-VSEPR structure of gas phase water is blown out within a few attoseconds after collision, that of guanine is far more robust and reconstitutes rapidly after impact even though the molecule remains electronically excited. This difference is accounted by the presence of the electron bath surrounding the impact point which enables energy relaxation within the molecule. Our approach should stimulate future studies to unravel the early steps following irradiation of various types of systems (isolated molecules, biomolecules, nanoclusters, solids, etc.) and is also readily applicable to irradiation by photons of various energies.

Electron transport in real time from first-principles

While the vast majority of calculations reported on molecular conductance have been based on the static non-equilibrium Green's function formalism combined with density functional theory (DFT), in recent years a few time-dependent approaches to transport have started to emerge. Among these, the driven Liouville-von Neumann equation [C. G. Sánchez et al., J. Chem. Phys. 124, 214708 (2006)] is a simple and appealing route relying on a tunable rate parameter, which has been explored in the context of semi-empirical methods. In the present study, we adapt this formulation to a density functional theory framework and analyze its performance. In particular, it is implemented in an efficient all-electron DFT code with Gaussian basis functions, suitable for quantum-dynamics simulations of large molecular systems. At variance with the case of the tight-binding calculations reported in the literature, we find that now the initial perturbation to drive the system out of equilibrium plays a fundamental role in the stability of the electron dynamics. The equation of motion used in previous tight-binding implementations with massive electrodes has to be modified to produce a stable and unidirectional current during time propagation in time-dependent DFT simulations using much smaller leads. Moreover, we propose a procedure to get rid of the dependence of the current-voltage curves on the rate parameter. This method is employed to obtain the current-voltage characteristic of saturated and unsaturated hydrocarbons of different lengths, with very promising prospects.

Nitrosodisulfide [S2NO]- (perthionitrite) is a true intermediate during the "cross-talk" of nitrosyl and sulfide

Nitrosodisulfide S₂NO^- is a controversial intermediate in the reactions of S-nitrosothiols with HS^- that produce NO and HNO. QM-MM molecular dynamics simulations combined with TD-DFT analysis contribute to a clear identification of S₂NO^- in water, acetone and acetonitrile, accounting for the UV-Vis signatures and broadening the mechanistic picture of N/S signaling in biochemistry.

Real-Time Quantum Dynamics Reveals Complex, Many-Body Interactions in Solvated Nanodroplets

Electronic excitations in the liquid phase are surprisingly rich and considerably more complex than either gas-phase or solid-state systems. While the majority of physical and biological processes take place in solvent, our understanding of nonequilibrium excited-state processes in these condensed phase environments remains far from complete. A central and long-standing issue in these solvated environments is the assessment of many-body interactions, particularly when the entire system is out of equilibrium and many quantum states participate in the overall process. Here we present a microscopic picture of solute-solvent electron dynamics and solvatochromic effects, which we uncover using a new real-time quantum dynamics approach for extremely large solvated nanodroplets. In particular, we find that a complex interplay of quantum interactions underlies our observations of solute-solvent effects, and simple macroscopic solvatochromic shifts can even be qualitatively different at the microscopic molecular level in these systems. By treating both the solvent and the solute on the same footing at a quantum-mechanical level, we demonstrate that the electron dynamics in these systems are surprisingly complex, and the emergence of many-body interactions underlies the dynamics in these solvated systems.

Quantum Chemical Studies of Light Harvesting

The design of optimal light-harvesting (supra)molecular systems and materials is one of the most challenging frontiers of science. Theoretical methods and computational models play a fundamental role in this difficult task, as they allow the establishment of structural blueprints inspired by natural photosynthetic organisms that can be applied to the design of novel artificial light-harvesting devices. Among theoretical strategies, the application of quantum chemical tools represents an important reality that has already reached an evident degree of maturity, although it still has to show its real potentials. This Review presents an overview of the state of the art of this strategy, showing the actual fields of applicability but also indicating its current limitations, which need to be solved in future developments.

Improving Efficiency in SMD Simulations Through a Hybrid Differential Relaxation Algorithm

The fundamental object for studying a (bio)chemical reaction obtained from simulations is the free energy profile, which can be directly related to experimentally determined properties. Although quite accurate hybrid quantum (DFT based)-classical methods are available, achieving statistically accurate and well converged results at a moderate computational cost is still an open challenge. Here, we present and thoroughly test a hybrid differential relaxation algorithm (HyDRA), which allows faster equilibration of the classical environment during the nonequilibrium steering of a (bio)chemical reaction. We show and discuss why (in the context of Jarzynski's Relationship) this method allows obtaining accurate free energy profiles with smaller number of independent trajectories and/or faster pulling speeds, thus reducing the overall computational cost. Moreover, due to the availability and straightforward implementation of the method, we expect that it will foster theoretical studies of key enzymatic processes.

Insights into the mechanism of the reaction between hydrogen sulfide and peroxynitrite

Hydrogen sulfide and peroxynitrite are endogenously generated molecules that participate in biologically relevant pathways. A revision of the kinetic features of the reaction between peroxynitrite and hydrogen sulfide revealed a complex process. The rate constant of peroxynitrite decay, (6.65 ± 0.08) × 10(3) M(-1) s(-1) in 0.05 M sodium phosphate buffer (pH 7.4, 37°C), was affected by the concentration of buffer. Theoretical modeling suggested that, as in the case of thiols, the reaction is initiated by the nucleophilic attack of HS(-) on the peroxide group of ONOOH by a typical bimolecular nucleophilic substitution, yielding HSOH and NO2(-). In contrast to thiols, the reaction then proceeds to the formation of distinct products that absorb near 408 nm. Experiments in the presence of scavengers and carbon dioxide showed that free radicals are unlikely to be involved in the formation of these products. The results are consistent with product formation involving the reactive intermediate HSSH and its fast reaction with a second peroxynitrite molecule. Mass spectrometry and UV-Vis absorption spectra predictions suggest that at least one of the products is HSNO2 or its isomer HSONO.