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In this work, a theoretical and computational set of tools to study and analyze time-resolved electron dynamics in molecules, under the influence of one or more external pulses, is presented. By coupling electronic-structure methods with the resolution of the time-dependent Schrödinger equation, we developed and implemented the time-resolved induced density of the electronic wavepacket, the time-resolved formulation of the differential projection density of states (ΔPDOS), and of transition contribution map (TCM) to look at the single-electron orbital occupation and localization change in time. Moreover, to further quantify the possible charge transfer, we also defined the energy-integrated ΔPDOS and the fragment-projected TCM. We have used time-dependent density-functional theory (TDDFT), as implemented in ADF software, and the Bethe-Salpeter equation, as provided by MolGW package, for the description of the electronic excited states. This suite of postprocessing tools also provides the time evolution of the electronic states of the system of interest. To illustrate the usefulness of these postprocessing tools, excited-state populations have been computed for HBDI (the chromophore of GFP) and DNQDI molecules interacting with a sequence of two pulses. Time-resolved descriptors have been applied to study the time-resolved electron dynamics of HBDI, DNQDI, LiCN (being a model system for dipole switching upon highest occupied molecular orbital-lowest unoccupied molecular orbital (HOMO-LUMO) electronic excitation), and Ag22. The computational analysis tools presented in this article can be employed to help the interpretation of fast and ultrafast spectroscopies on molecular, supramolecular, and composite systems.

Time-dependent density functional theory (TDDFT) simulations are conducted on a series of chiral gold nanowires to explore whether an enhancement of circular dichroism at the plasmon resonance is possible and identify its quantum-mechanical origin. We find that in linear two-dimensional chiral nanowires the dichroic response is suppressed by destructive interference of nearly degenerate components with opposite signs, pointing to this phenomenon as a common and likely origin of the difficulty encountered so far in achieving a plasmonic CD response in experiment and suggesting nevertheless that these opposite components could be "decoupled" by using multiwall arrangements. In contrast, we predict a giant dichroic response for nanowires with three-dimensional helical coiling. We rationalize this finding via an electronic structure analysis of longitudinal and transversal plasmonic excitations and their coupling into chiral components, and we propose a simple formula for the chiral response as a function of structural parameters (nanowire length and coiling number).

TurboRVB is a computational package for {\it ab initio} Quantum Monte Carlo (QMC) simulations of both molecular and bulk electronic systems. The code implements two types of well established QMC algorithms: Variational Monte Carlo (VMC), and Diffusion Monte Carlo in its robust and efficient lattice regularized variant. A key feature of the code is the possibility of using strongly correlated many-body wave functions. The electronic wave function (WF) is obtained by applying a Jastrow factor, which takes into account dynamical correlations, to the most general mean-field ground state, written either as an antisymmetrized geminal product with spin-singlet pairing, or as a Pfaffian, including both singlet and triplet correlations. This wave function can be viewed as an efficient implementation of the so-called resonating valence bond (RVB) ansatz, first proposed by L. Pauling and P. W. Anderson in quantum chemistry and condensed matter physics, respectively. The RVB ansatz implemented in TurboRVB has a large variational freedom, including the Jastrow correlated Slater determinant as its simplest, but nontrivial case. Moreover, it has the remarkable advantage of remaining with an affordable computational cost, proportional to the one spent for the evaluation of a single Slater determinant. The code implements the adjoint algorithmic differentiation that enables a very efficient evaluation of energy derivatives, comprising the ionic forces. Thus, one can perform structural optimizations and molecular dynamics in the canonical NVT ensemble at the VMC level. For the electronic part, a full WF optimization is made possible thanks to state-of-the-art stochastic algorithms for energy minimization. The code has been efficiently parallelized by using a hybrid MPI-OpenMP protocol, that is also an ideal environment for exploiting the computational power of modern GPU accelerators., 41 pages, 21 figures, 3 tables

Ultrafast two-pulse experiments on single molecules are invaluable tools to investigate the microscopic dynamics of a fluorophore. The first pulse generates electronic or vibronic coherence and the second pulse probes the time-evolution of the coherence. A protocol that is able to simulate ultrafast experiments on single molecules is applied in this study. It is based on a coupled quantum-mechanical description of the fluorophore and real-time dynamics of the system vibronic wave packet interacting with an electric field, described by means of the stochastic Schro¨dinger equation within the Markovian limit. This approach is applied to the DNQDI fluorophore, previously investigated experimentally [D. Brinks et al., Nature, 2010, 465, 905–908]. We find this to be in good agreement with the experimental outcomes and provide microscopic and atomistic interpretation.

The formation of hybrid light–molecule states (polaritons) offers a new strategy to manipulate the photochemistry of molecules. To fully exploit its potential, one needs to build a toolbox of polaritonic phenomenologies that supplement those of standard photochemistry. By means of a state-of-the-art computational photochemistry approach extended to the strong-coupling regime, here we disclose various mechanisms peculiar of polaritonic chemistry: coherent population oscillations between polaritons, quenching by trapping in dead-end polaritonic states and the alteration of the photochemical reaction pathway and quantum yields. We focus on azobenzene photoisomerization, that encompasses the essential features of complex photochemical reactions such as the presence of conical intersections and reaction coordinates involving multiple internal modes. In the strong coupling regime, a polaritonic conical intersection arises and we characterize its role in the photochemical process. Our chemically detailed simulations provide a framework to rationalize how the strong coupling impacts the photochemistry of realistic molecules., Manipulation of the photochemistry of molecules is traditionally achieved through synthetic chemical modifications. Here the authors use computational photochemistry to show how to control azobenzene photoisomerization through hybrid light–molecule states (polaritons).

We report an extension of diffusion Monte Carlo (DMC) to the calculation of the molecular rotational energies by means of the generalized, symmetry-adapted, imaginary-time correlation functions (SAITCFs) originally introduced in the reptation quantum Monte Carlo (RQMC) framework (Skrbic in J Phys Chem A 111:12749, 2007). We studied the a-type and b-type rotational lines of the CO( $$^{4}$$ He) $$_{N}$$ clusters with $$N=$$ 1–8 that correlate, in the dimer limit, with the end-over-end and free-rotor transitions. We compare the SAITCF–DMC results with accurate DVR (for the dimer case), RQMC and other DMC data, and with reference experimental findings (Surin in Phys Rev Lett 101:233401, 2008). A good agreement is generally found, but a systematic underestimation of the SAITCF–DMC rotational energies of the b-type series is observed. Sources of inaccuracy in our theoretical approach and in the computational protocol are discussed and analyzed in detail.

Coupling the real-time description of the ultrafast electron dynamics in strong laser fields with quantum chemistry techniques still represents an open challenge for theoreticians. In this work, high-harmonic generation (HHG) spectrum of the argon atom has been computed by means of the time-dependent configuration with singly excited configurations approach (TDCIS), using Gaussian basis sets. We show that adding a number of continuum-optimal Gaussian functions to basis sets routinely used in quantum chemistry calculations provides the expected position of the intensity minimum in the HHG spectrum, for a given selection of laser intensities and ionisation parameters. Advantages and weaknesses of the proposed computational strategy are discussed. We give evidence here that Gaussian-based TDCIS simulations are accurate enough to correctly reproduce the features of ultrafast and highly nonlinear optical processes, as HHG.

The interpretation of nanoplasmonic effects on molecular properties, such as metal-enhanced absorption or fluorescence, typically assumes a fully coherent picture (in the quantum-mechanical sense) of the phenomena. Yet, there may be conditions where the coherent picture breaks down, and decoherence effect should be accounted for. Using a state-of-the-art multiscale model approach able to include environment-induced dephasing, here we show that metal nanoparticle effects on the light absorption by a nearby molecule is strongly affected (even qualitatively, i.e., suppression vs enhancement) by molecular electronic decoherence. The present work shows that decoherence can be thought as a further design element of molecular nanoplasmonic systems., Final Accepted Version

This study arises from the attempt to answer the following question: how different descriptions of electronic exchange and correlation affect the high-harmonic generation (HHG) spectroscopy of H2, N2, and CO2 molecules? We compare HHG spectra for H2, N2, and CO2 with different ab initio electronic structure methods: real-time time-dependent configuration interaction and real-time time-dependent density functional theory (RT-TDDFT) using truncated basis sets composed of correlated wave functions expanded on Gaussian basis sets. In the framework of RT-TDDFT, we employ Perdew-Burke-Ernzerhof (PBE) and long-range corrected Perdew-Burke-Ernzerhof (LC-ωPBE) functionals. We study HHG spectroscopy by disentangling the effect of electronic exchange and correlation. We first analyze the electronic exchange alone, and in the case of RT-TDDFT with LC-ωPBE, we use ω = 0.3 and ω = 0.4 to tune the percentage of long-range Hartree-Fock exchange and short-range exchange PBE. Then, we added the correlation as described by the PBE functional. All the methods give very similar HHG spectra, and they seem not to be particularly sensitive to the different description of exchange and correlation or to the correct asymptotic behavior of the Coulomb potential. Despite this general trend, some differences are found in the region connecting the cutoff and the background. Here, the harmonics can be resolved with different accuracy depending on the theoretical schemes used. We believe that the investigation of the molecular continuum and its coupling with strong fields merits further theoretical investigations in the near future.

The multidisciplinary nature of the research in molecular nanoplasmonics, i.e., the use of plasmonic nanostructures to enhance, control, or suppress properties of molecules interacting with light, led to contributions from different theory communities over the years, with the aim of understanding, interpreting, and predicting the physical and chemical phenomena occurring at molecular- and nano-scale in the presence of light. Multiscale hybrid techniques, using a different level of description for the molecule and the plasmonic nanosystems, permit a reliable representation of the atomistic details and of collective features, such as plasmons, in such complex systems. Here, we focus on a selected set of topics of current interest in molecular plasmonics (control of electronic excitations in light-harvesting systems, polaritonic chemistry, hot-carrier generation, and plasmon-enhanced catalysis). We discuss how their description may benefit from a hybrid modeling approach and what are the main challenges for the application of such models. In doing so, we also provide an introduction to such models and to the selected topics, as well as general discussions on their theoretical descriptions.

Revealing possible long-living coherence in ultrafast processes allows detecting genuine quantum mechanical effects in molecules. To investigate such effects from a quantum chemistry perspective, we have developed a method for simulating the time evolution of molecular systems, based on ab initio calculations that includes relaxation and environment-induced dephasing of the molecular wave function, whose rates are external parameters. The proposed approach combines a quantum chemistry description of the molecular target with a real-time propagation scheme within the time-dependent stochastic Schroedinger equation. Moreover, it allows a quantitative characterization of the state and dynamics coherence, through the l1-norm of coherence and the linear entropy, respectively. To test the approach, we have simulated femtosecond pulse-shaping ultrafast spectroscopy of terrylenediimide, a well studied fluorophore in single-molecule spectroscopy. Our approach is able to reproduce the experimental findings [R. Hildner et al.,Nature Phys., 7, 172 (2011)], confirming the usefulness of the approach and the correctness of the implementation., Comment: This is the final version accepted for publication of a work that is appearing in Journal of Chemical Physics (Copyright AIP)

We present the extension of variational Monte Carlo (VMC) to the calculation of electronic excitation energies and oscillator strengths using time-dependent linear-response theory. By exploiting the analogy existing between the linear method for wave-function optimisation and the generalised eigenvalue equation of linear-response theory, we formulate the equations of linear-response VMC (LR-VMC). This LR-VMC approach involves the first-and second-order derivatives of the wave function with respect to the parameters. We perform first tests of the LR-VMC method within the Tamm-Dancoff approximation using single-determinant Jastrow-Slater wave functions with different Slater basis sets on some singlet and triplet excitations of the beryllium atom. Comparison with reference experimental data and with configuration-interaction-singles (CIS) results shows that LR-VMC generally outperforms CIS for excitation energies and is thus a promising approach for calculating electronic excited-state properties of atoms and molecules.

The penta-2,4-dieniminium cation (PSB3) displays similar ground state and first excited state potential energy features as those of the retinal protonated Schiff base (RPSB) chromophore in rhodopsin. Recently, PSB3 has been used to benchmark several electronic structure methods, including highly correlated multireference wave function approaches, highlighting the necessity to accurately describe the electronic correlation in order to obtain reliable properties even along the ground state (thermal) isomerization paths. In this work, we apply two quantum Monte Carlo approaches, the variational Monte Carlo and the lattice regularized diffusion Monte Carlo, to study the energetics and electronic properties of PSB3 along representative minimum energy paths and scans related to its thermal cis-trans isomerization. Quantum Monte Carlo is used in combination with the Jastrow antisymmetrized geminal power ansatz, which guarantees an accurate and balanced description of the static electronic correlation thanks to the multiconfigurational nature of the antisymmetrized geminal power term, and of the dynamical correlation, due to the presence of the Jastrow factor explicitly depending on electron-electron distances. Along the two ground state isomerization minimum energy paths of PSB3, CASSCF calculations yield wave functions having either charge transfer or diradical character in proximity of the two transition state configurations. Here, we observe that at the quantum Monte Carlo level of theory, only the transition state with charge transfer character can be located. The conical intersection, which becomes highly sloped, is observed only if the path connecting the two original CASSCF transition states is extended beyond the diradical one, namely by increasing the bond-length-alternation (BLA). These findings are in good agreement with the results obtained by MRCISD+Q calculations, and they demonstrate the importance of having an accurate description of the static and dynamical correlation when studying isomerization and transition states of conjugated systems. © 2015 American Chemical Society.

International audience; We propose a method for obtaining effective lifetimes of scattering electronic states for avoiding the artificially confinement of the wave function due to the use of incomplete basis sets in time-dependent electronic-structure calculations of atoms and molecules. In this method, using a fitting procedure, the lifetimes are extracted from the spatial asymptotic decay of the approximate scattering wave functions obtained with a given basis set. The method is based on a rigorous analysis of the complex-energy solutions of the Schrödinger equation. It gives lifetimes adapted to any given basis set without using any empirical parameters. The method can be considered as an ab initio version of the heuristic lifetime model of Klinkusch et al. [J. Chem. Phys. 131, 114304 (2009)]. The method is validated on the H and He atoms using Gaussian-type basis sets for calculation of high-harmonic-generation spectra.

Photoinitiated phenomena play a crucial role in many living organisms. Plants, algae, and bacteria absorb sunlight to perform photosynthesis, and convert water and carbon dioxide into molecular oxygen and carbohydrates, thus forming the basis for life on Earth. The vision of vertebrates is accomplished in the eye by a protein called rhodopsin, which upon photon absorption performs an ultrafast isomerisation of the retinal chromophore, triggering the signal cascade. Many other biological functions start with the photoexcitation of a protein-embedded pigment, followed by complex processes comprising, for example, electron or excitation energy transfer in photosynthetic complexes. The optical properties of chromophores in living systems are strongly dependent on the interaction with the surrounding environment (nearby protein residues, membrane, water), and the complexity of such interplay is, in most cases, at the origin of the functional diversity of the photoactive proteins. The specific interactions with the environment often lead to a significant shift of the chromophore excitation energies, compared with their absorption in solution or gas phase. The investigation of the optical response of chromophores is generally not straightforward, from both experimental and theoretical standpoints; this is due to the difficulty in understanding diverse behaviours and effects, occurring at different scales, with a single technique. In particular, the role played by ab initio calculations in assisting and guiding experiments, as well as in understanding the physics of photoactive proteins, is fundamental. At the same time, owing to the large size of the systems, more approximate strategies which take into account the environmental effects on the absorption spectra are also of paramount importance. Here we review the recent advances in the first-principle description of electronic and optical properties of biological chromophores embedded in a protein environment. We show their applications on paradigmatic systems, such as the light-harvesting complexes, rhodopsin and green fluorescent protein, emphasising the theoretical frameworks which are of common use in solid state physics, and emerging as promising tools for biomolecular systems

The structures of three negatively charged forms (anionic keto-1 and enol-1, dianonic enol-2) of oxyluciferin (OxyLuc), which are the most probable emitters responsible for the firefly bioluminescence, have been fully relaxed at the variational Monte Carlo (VMC) level. Absorption energies of the S1, Comment: This document is the Accepted Manuscript version of a Published Work that appeared in final form in J. Chem. Theory Comput. copyright American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see http://dx.doi.org/10.1021/acs.jctc.7b00505

International audience; High-harmonic generation (HHG) is used to produce coherent XUV and soft X-ray radiation with attosecond resolution and is a sensitive tool for probing atomic and molecular structures. In this work, we have used time-dependent configuration interaction with a Gaussian basis set to compute the HHG spectrum of the hydrogen atom. To get a correct description of the HHG optical spectrum, the Gaussian basis set has to provide an accurate representation of the bound and the continuum states. Two strategies have been proposed: (1) multicentered (defining ghost atoms around the hydrogen) and (2) optimal-continuum Gaussian basis sets. We have systematically investigated these two approaches for the hydrogen atom, which permits a non-biased analysis of the basis set. Several basis sets have been constructed and tested by combining multicentered and optimal-continuum functions together in order to obtain a reliable and accurate Gaussian basis set to be used for HHG. We have studied the effect of changing the number of ghost atoms and the distance between the ghosts and the hydrogen atom, with and without optimal-continuum Gaussian functions. We conclude that multicentered basis sets are less efficient than basis sets using only optimal-continuum Gaussian functions for a proper description of HHG.

Electron correlation plays a crucial role in the energetics of reactions catalyzed by transition metal complexes, such as water splitting. In the present work we exploit the performance of various methods to describe the thermodynamics of a simple but representative model of water splitting reaction, based on a single cobalt ion as catalyst. Density Functional Theory (DFT) calculations show a significant dependence on the adopted functional, and not negligible differences with respect to CCSD(T) findings are found along the reaction cycle. We performed quantum Monte Carlo calculations using an unrestricted single Slater determinant wave function multiplied by a Jastrow factor using both DFT and fully optimized orbitals. Variational and Lattice Regularized Diffusion Monte Carlo results are in overall agreement with the CCSD(T) free-energy profile, even though differences in the description of the thermodynamics of the reaction cycle are found. NEVPT2 calculations reveal that the role of the static correlation of the different reaction steps is not large, and it is limited to only a few intermediate structures. Finally, the free-energy difference of the overall water splitting reaction computed at the quantum Monte Carlo level shows an excellent match with the experimental value of 4.92 eV, underlining the capability of these techniques to properly describe the dynamical correlation of such reactions.

"The accurate determination of the geometrical details of the dark state of 11-cis Retinal in Rhodopsin represents a fundamental step for the rationalization of the protein role in the optical spectral tuning in the vision mechanism. We have calculated geometries of the full Retinal Protonated Schiff base chromophore in gas phase and in protein environment using the correlated Variational Monte Carlo method. The Bond Length Alternation of the conjugated carbon chain of the chromophore in gas phase shows a significant reduction when moving from the ß-ionone ring to the nitrogen whereas, as expected, the protein environment reduces the electronic conjugation. The proposed dark state structure is fully compatible with solid-state NMR data reported by Carravetta et. al. [J. Am. Chem. Soc. 2004, 126, 3948-3953]. TDDFT\/B3LYP calculations on such geometries show a blue opsin shift of 0.28 and 0.24 eV induced by the protein for S1 and S2 states, consistently with literature spectroscopic data. The effect of the geometrical distortion alone is a red shift of 0.21 and 0.16 eV with respect to the optimized gas phase chromophore. Our results open new perspectives for the study of the properties of chromophores in their biological environment using correlated methods."

We used Quantum Monte Carlo (QMC) methods to study the polarizability and the quadrupole moment of the ethyne molecule using the Jastrow-Antisymmetrised Geminal Power (JAGP) wave function, a compact and strongly correlated variational ansatz. The compactness of the functional form and the full optimization of all its variational parameters, including linear and exponential coefficients in atomic orbitals, allow us to observe a fast convergence of the electrical properties with the size of the atomic and Jastrow basis sets. Both variational results on isotropic polarizability and quadrupole moment based on Gaussian type and Slater type basis sets are very close to the Lattice Regularized Diffusion Monte Carlo values and in very good agreement with experimental data and with other quantum chemistry calculations. We also study the electronic density along the C≡C and C-H bonds by introducing a generalization for molecular systems of the small-variance improved estimator of the electronic density proposed by Assaraf et al. (Assaraf, R.; Caffarel, M.; Scemama, A. Phys. Rev. E, 2007, 75, 035701).

In this work, we study the electronic and geometrical properties of the ground state of the Retinal Minimal Model C5H6NH2+ using the variational Monte Carlo (VMC) method by means of the Jastrow antisymmetrized geminal power (JAGP) wavefunction. A full optimization of all wavefunction parameters, including coefficients, and exponents of the atomic basis, has been achieved, giving converged geometries with a compact and correlated wavefunction. The relaxed geometries of the cis and trans isomers present a pronounced bond length alternation pattern characterized by a CC central double bond slightly shorter than that reported by the CASPT2 structures. The comparison between different basis sets indicates converged values of geometrical parameters, energy differences, and dipole moments even when the smallest wavefunction is used. The compactness of the wavefunction as well as the scalability of VMC optimization algorithms on massively parallel computers opens the way to perform full structural optimizations of conjugated biomolecules of hundreds of electrons by correlated methods like Quantum Monte Carlo. © 2012 Wiley Periodicals, Inc.

The possible existence of bound states in small helium clusters containing atomic and molecular hydrogen has been investigated by means of three completely independent sets of calculations. The first set employs the Jacobi-Davidson filtering procedure recently implemented in the Distributed Gaussian Functions (DGF) approach, the second one is based on the solution of the Faddeev equation by means of the hyperspherical adiabatic expansion method and the third follows the Quantum Monte Carlo approach. The partners within each complex are taken to interact via two-body potentials chosen among the most accurate existing in the literature. All the present quantum treatments show that no bound states are found for H(4He)2 and for D(4He)2 while only one very diffuse bound state is present in T(4He)2, where H, D and T are the three isotopes of hydrogen. The substitution of the atomic dopant with its molecular counterpart, H2, also gives rise to only one bound state whose spatial attributes are reported and analysed, underlining again the ultraweak nature of the interaction forces and the need to implement highly specific tools for the investigation of the ensuing bound states., The financial support of the University of Rome Research Committee, of the CASPUR Supercomputing Center and of the PRIN 2006 Research Programme is gratefully acknowledged. This work has been supported by the Spanish MICINN under projects FIS2007-62006 and FIS2008-01301. We also acknowledge the support of the INTAS collaboration and of the Italy-Spain Integrated Action Programme.

Light harvesting from the Sun by antenna complexes surrounding the reaction center of Photosystem II represents the first step of the natural oxygenic photosynthesis performed by plants, algae and cyanobacteria. The excitation energy derived from the sunlight is absorbed by the chlorophylls of the antenna and subsequently conveyed to the reaction center of Photosystem II through resonant energy transfer mechanisms. In the special pair of chlorophylls of the reaction center the charge separation occurs, eventually leading to the oxidation of water molecules into protons, electrons and molecular oxygen. The adsorption properties of the antenna chlorophylls are ad hoc modulated by the protein environment to guarantee fast energy transfer and minimize side and back reactions. At the same time these properties are influenced by the molecular fluctuations occurring at physiological temperature. In the present work, combining classical molecular dynamics simulations with the Charge Density Coupling method, we estimated the impact of the thermal fluctuations on the site energy shift of the chlorophylls embedded in the Photosystem II complex. Our results show how the effect of the molecular fluctuations is not homogeneous throughout the complex, although the symmetry of the homodimer is maintained. Many peripheral chromophores undergo fluctuations larger then 10 kJ/mol around the average values. Possible physiological roles of such fluctuations are discussed.