Theoretical studies of low energy electron collisions with small molecular clusters

We developed and tested a new approach to treat low energy electron collisions with molecular clusters, called Multiple Scattering, which simplifies the scattering process by dividing the target cluster into molecular sub-units; ab initio methods are employed to calculate collisional data for the electron - sub-unit scattering process, which is later combined by the Multiple Scattering method to account for the interference between sub-units. We applied the novel method to the scattering from water and formic acid clusters; the results (cross sections) were compared to other theoretical and experimental results, showing good agreement. The ab initio R-matrix method was employed both for producing the collisional information on the sub-units and also for calculating comparison cross sections where previous results were not available

Excited state gradients within a polarizable QM/MM formulation

Multiscale approaches that partition the system into an active site (where the electronic process under study occurs) and a remaining region, the environment, have proven to be good strategies for the computation of electronic excitations in complex systems. In this work the implementation of a polarizable QM/MM scheme for the computation of excited state gradients is presented and are applied to a test case

Dissecting the nature of exciton interactions in ethyne-linked tetraarylporphyrin arrays

We investigate how electronic energy transfer in a series of three ethyne-linked Zinc- and free base-tetraarylporphyrin dimers is tuned by the type of linker and by substitution on the porphyrin rings. We use TD-DFT combined with a recently developed fully polarizable QM/MM/PCM method. This allows us to dissect the bridge-mediated contributions to energy transfer in terms of superexchange (through-bond) interactions and Coulomb (through space) terms mediated by the polarizability of the bridge. We explore the effects of the substituents and of the bridge-chromophore mutual orientation on these contributions. We find that bridge-mediated superexchange contributions largely boost energy transfer between the porphyrin units. When the effect of the solvent is also considered through PCM, we find good agreement with the through-bond versus through-space contributions determined experimentally, thus indicating the need to properly include both solvent and bridge effects in the study of energy transfer in bridged molecular dyads

Toward a unified modeling of environment and bridge-mediated contributions to electronic energy transfer: A fully polarizable QM/MM/PCM approach

Recent studies have unveiled the similar nature of solvent (screening) effects and bridge-mediated contributions to electronic energy transfer, both related to the bridge/solvent polarizability properties. Here, we exploit the similarity of such contributions to develop a fully polarizable mixed QM/discrete/continuum model aimed at studying electronic energy transfer processes in supramolecular systems. In the model, the definition of the three regions is completely flexible and allows us to explore the possibility to describe bridge-mediated contributions by using a polarizable MM description of the linker. In addition, we show that the classical MMPol description of the bridge can be complemented either with an analogous atomistic or with a continuum description of the solvent. Advantages and drawbacks of the model are finally presented and discussed with respect to the system under study

Achieving Linear Scaling in Computational Cost for a Fully Polarizable MM/Continuum Embedding

In this paper, we present a new, efficient implementation of a fully polarizable QM/MM/continuum model based on an induced-dipoles polarizable force field and on the Conductor-like Screening Model as a polarizable continuum in combination with a self-consistent field QM method. The paper focuses on the implementation of the MM/continuum embedding, where the two polarizable methods are fully coupled to take into account their mutual polarization. With respect to previous implementations, we achieve for the first time a linear scaling with respect to both the computational cost and the memory requirements without limitations on the molecular cavity shape. This is achieved thanks to the use of the recently developed ddCOSMO model for the continuum and the Fast Multipole Method for the force field, together with an efficient iterative procedure. Therefore, it becomes possible to include in the classical layer as much as several tens of thousands of atoms with a limited computational effort

Twin-to-twin transfusion syndrome: diagnostic imaging and its role in staving off malpractice charges and litigation

The study aims to expound upon the imaging-based diagnostic methodologies aimed at identifying twin-to-twin transfusion syndrome (TTTS), a serious, somewhat rare prenatal condition that takes place in pregnancies where identical twins, or other multiples, share a placenta (monochorionic placenta), highlighting how medico-legal outcomes can be affected by provable compliance with consolidated diagnostic guidelines or best practices. It is of utmost importance to produce a prompt identification of TTTS instances; an early diagnosis is in fact critical in order to effectively treat and manage TTTS. By virtue of TTTS being a highly progressive condition, a delay in diagnosis can result in disastrous outcomes; just a few weeks delay in the diagnosis of TTTS can turn out fatal for one or both twins. Hence, most TTTS malpractice claims involve allegations of medical negligence, namely the failure to recognize the condition in a timely fashion, or to proceed with adequate diagnostic and therapeutic pathways. In that regard, case law databases have been pored over (Justia, Lexis, Leagle), and five significant court cases have been examined and discussed in an attempt to identify objective medico-legal standards and bring to the forefront relevant forensic dynamics. In fact, when health professionals are capable of proving adherence to guidelines or best practices, this can shield them from malpractice allegations and ensuing litigation

Geometry Optimization in Polarizable QM/MM Models: The Induced Dipole Formulation

We present the mathematical derivation and the computational implementation of the analytical geometry derivatives for a polarizable QM/MM model (QM/MMPol). In the adopted QM/MMPol model, the focused part is treated at QM level of theory, while the remaining part (the environment) is described classically as a set of fixed charges and induced dipoles. The implementation is performed within the ONIOM procedure, resulting in a polarizable embedding scheme, which can be applied to solvated and embedded systems and combined with different polarizable force fields available in the literature. Two test cases characterized by strong hydrogen-bond and dipole-dipole interactions, respectively, are used to validate the method with respect to the nonpolarizable one. Finally, an application to geometry optimization of the chromophore of Rhodopsin is presented to investigate the impact of including mutual polarization between the QM and the classical parts in conjugated systems

Efficient photoinduced charge separation in a BODIPY-C60 dyad

A donor-acceptor dyad composed of a BF2-chelated dipyrromethene (BODIPY) and a C60 fullerene has been newly synthesized and characterized. The two moieties are linked by direct addition of an azido substituted BODIPY on the C60, producing an imino-fullerene-BODIPY adduct. The photoinduced charge transfer process in this system was studied by ultrafast transient absorption spectroscopy. Electron transfer toward the fullerene was found to occur selectively exciting both the BODIPY chromophore at 475 nm and the C60 unit at 266 nm on a time scale of a few picoseconds, but the dynamics of charge separation was different in the two cases. Eletrochemical studies provided information on the redox potentials of the involved species and spectroelectrochemical measurements allowed to unambiguously assign the absorption band of the oxidized BODIPY moiety, which helped in the interpretation of the transient absorption spectra. The experimental studies were complemented by a theoretical analysis based on DFT computations of the excited state energies of the two components and their electronic couplings, which allowed identification of the charge transfer mechanism and rationalization of the different kinetic behavior observed by changing the excitation conditions

A multiple-scattering approach to electron collisions with small molecular clusters

We present a method based on multiple-scattering to determine elastic cross sections for electron collisions with molecular clusters. The method is based on the calculation of accurate collisional information for the molecules constituting the cluster that is then combined to obtain a cross section for interaction with the whole system. Themethod provides a computationally cost-effectiveway of treating low energy electron scattering from (homogeneous and heterogeneous) molecular clusters and aggregates.Results for (H2O)n (n D 2,5) and (HCOOH)2 are presented; the cross sections agree well with more accurate ab initio data

Theoretical description of protein field effects on electronic excitations of biological chromophores

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 system