Theoretical and Computational Chemistry Lab
The THC2-Lab involves 7 permanent research scientists and two associate researchers thus representing one of the largest research teams settled in a single CNR Institute and working in the field of molecular modeling and theoretical and computational chemistry. Our research is aimed at the development of new theoretical and computational models and methods and their application to the study of systems and processes relevant for materials chemistry and biology, pursuing a fully dynamical description of the phenomena under investigation. We have a long-standing expertise in the investigation of the optical properties of molecular dyes in complex environments, e.g. in solution, or in natural/synthetic polymeric matrix, that has been exploited to study the photochemical and photobiological behavior of DNA segments and natural pigments, as well as the properties of functionalized polymers, focusing not only on their optical response but also on the dynamical processes triggered by light absorption like, chemical reactions, internal conversions, energy, proton and electron transfers. With this background we recently conveyed part of our efforts to the study of models systems for dye-sensitized solar cells and artificial photosynthesis. We also have a long experience in the simulation of the structure, growth and properties of metallic nanoclusters and nanoalloys, both free and in diverse enviroments such as colloidal and supported systems (heterogeneous catalysis). Low-dimensional (2D) oxide materials both as supports and for their emerging properties are also part of our expertise. Closing the loop, the ability to simulate the anchorage of molecular and biological fragments on clusters and heterogeneous surfaces allows us to study biosensors. Our technical expertise covers many tools of computational chemistry and physics ranging from DFT, post-HF, hybrid QM/MM, plane-wave approaches for solids, implicit and explicit solvation models, classical and quantum molecular dynamics (MD). Nonetheless, a significant part of our work is devoted to the developments of new models, methods and computational protocols. In this framework we quote methods to optimize force fields for MD and to simulate vibronically resolved electronic spectra in large systems, fragmentation methods to evaluate electronic couplings for electron and energy transfers and (reactive) global optimizations algorithm for the exploration of multi-minima potential energy surfaces typical for nanoclusters and nanoalloys. Some of these developments have been implemented in open source codes that are freely shared with the scientific community (see Available software)

Research topics

  • Developments of  models and methods
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    A substantial part of our work is devoted to the development of models, methods and novel computational approaches that support our investigations in the different fields described below. We elaborate methods for vibrational and vibronic spectroscopy, for parametrization of force fields, for classical, semi-classical and quantum dynamical simulations, for describing electron transfer and transport in molecular devices, and for global optimization of the structure of nano-clusters and nano-alloys. In some cases these developments have been implemented in freely available or commercial codes
  • Materials Chemistry
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    State-of-the-art computational techniques, based both on classical and quantum mechanics, are employed for the in silico design of advanced materials, ranging from liquid crystals, to organic dyes embedded in complex systems (nano-particles, polymers, etc.), Particular attention is given to a reliable modeling of the chemical interactions among all material-constituting components and both quantum mechanical and multi-level approaches are employed to investigate this issue.Materials are characterized by simulating their structural, dynamic and possibly spectroscopic properties, and the validity of the models is checked against experimental data, where available. Finally, computational screening protocols are devised and implemented to flank the experiment in novel synthetic routes
  • Energy 
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     In the field of dye sensitized solar cells, we investigate the light harvesting properties of potential dyes inquiring the role of their intrinsic properties (electronic and vibronic states) and of the environment (solvent and semiconductor surface) on the position and width of the absorption spectra. Moreover we aim at investigating the dynamics of charge injection. We also actively study the oxygen reduction reaction in electrochemical fuel cells based on nanoporous materials, Li-ion batteries for energy storage, and the catalytic conversion of CO2 
  • Photochemistry, Photobiology and Photophysics
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    We study the basic mechanisms ruling the radiative and noradiative processes induced by Uv/vis excitation. We focus in particular on processes taking place around conical intersections of the molecular potential energy surfaces. Such dynamical processes are investigated at both quantum and semiclassical level. For semi-rigid systems we mostly work in a quantum dynamical framework and we aim at developing computational approaches suitable for systems with many degrees of freedom, exploiting the potentialities of hierarchical representations of the Hamiltonian, system/bath partitions of the system and hybrid quantum/classical descriptions. This approach is not suited for flexible systems in complex environments. We plan to approach these systems in the general framework of classical molecular dynamics simulation based on parametrized force field. Current applications are mostly limited spectroscopic absorption/emission behavior.
  • Biosensors
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    DNA detection systems (bio-sensors) based on hydridization processes between single-stranded target/probe DNA pairs are investigated through multi-layered protocols, involving quantum mechanical calculations, accurate force-field parameterizations and state-of-the-art molecular dynamics simulations. The insight granted by a computational approach is exploited to unravel the roles that many different players (substrate nature and coverage, hybridization mechanisms, tethered dynamics, etc.) play in the efficiency of these devises
  • Molecular electronics
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    work in progress
  • Metal nanoclusters and nanoalloys
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    Pure and alloy nanoclusters are investigated, with attention to the useof quantum mechanical approaches and the simulation of kinetics anddynamic phenomena. Structural dynamics: a Reactive Glocal Optimization(RGO) approach is proposed to explore [the reactive phase space ofsystems composed by supported sub-nanometer metal aggregates in thepresence of reactant molecules (heterogeneous ultrananocatalysis). Thisis framed within the general theme of the long-term structural dynamicsof kinetics-driven off-lattice activated processes, and applied to thekinetics of elemental diffusion in nanoalloys.Electron dynamics: the optical response of pure and mixed metal nanostructures both bare and ligand-coated is predicted using time-dependent density-functional-theory (TDDFT) methods, from bare systems to coupled plasmonics effects]. Spin dynamics: the magnetic anisotropy of supported alloy nanoparticles is studied, linking with non-scalable effects in nanomaterials science and their significance for multi-scale modeling.
  • Ultrathin oxide films
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    Self-assembled low-dimensional (2D, 1D, 0D) oxide nanostructures andtheir emergent properties in terms of structure and growth, electronics,magnetism and catalytic chemistry are investigated via first-principlesapproaches in close collaboration with leading surface scienceexperimental groups. [The stabilization mechanism of polar oxidesurfaces in nanoscale oxide objects, the catalytic chemistry ofnanoscale "inverse catalysts" consisting of oxide nanowires coupled toarrays of one-dimensional metal step atoms, and the electronic andmagnetic properties of surface-supported oxide quantum dots arespecifically investigated
  • Systems of biological relevance
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    We study the fundamental interactions responsible for DNA structure, like stacking and hydrogen bonds both in the ground and in the electronic excited states.   In the ground state, we study the proton transfer in base pair and the mechanism (step-to-step or concerted) of  double proton transfer, both with and without the explicit inclusion of  solvent water molecules. We also consider the coupling between the proton transfer of several base pairs. Concerning the photoexcited DNA we focus on the mechanisms that allow a fast and efficient dissipation of the electronic energy and avoid damages with possible mutagenic consequences. Therefore we investigate both at static and a quantum-dynamical level the competition of different decay channels like those involving single nucleobases and those involving collective exciton and charge-transfer states. Other fields of interest are the electronic spectroscopy and the photophysical behavior of some classes of proteins like Rhodopsins and  green fluorescent proteins, and the interactions of biological macromolecules with metallic and semiconductor surfaces
  • Computational spectroscopy 
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    We are interested in linear and non-linear steady-state and time-resolved electronic and vibrational spectroscopies. We develop time-independent and time-dependent methods to compute the lineshape of electronic spectra, with a special focus on large systems. To that end we adopt both quantum and classical/semi-classical approaches. Due to the dimensions of the systems, quantum methods, able to describe the vibrational structure associated to the spectra, are mainly routed in harmonic approximation, including Duschinsky and Herzberg-Teller effects, and describing the vibrational modes either in Cartesian or in internal coordinates. The developed methodologies have been applied to one- and two-photon absorption, emission, one- and two-photo circular dichroism, circularly-polarized luminescence, magnetic circular dichroism and vibrational resonance Raman, and we aim at extending them to new spectroscopies. Classical methods are based on molecular dynamics or Monte Carlo simulations to sample the initial-state distribution and application of the classical Franck-Condo principle. When needed, we develop ad hoc parametrizations of the force fields in order to properly describe large amplitude motions and include explicitly the solvent effect.  In the field of vibrational spectroscopy our min interest is toward efficient calculation of the anharmonic effects both on the frequencies and on the intensities of IR and vibrational circular dichroism spectra. We also simulate time-resolved pump-probe spectroscopies and we are recently tackling the problem of the simulation of two-dimensional IR and UV/vis spectra both at quantum and at classical level.

Expertise

  • postHF and DFT based methods for molecular properties in electronic excited states
  • Molecular dynamics and development of force fields
  • Plane-wave DFT methods for solids and clusters
  • Implicit and explicit solvation models
  • Conical Intersections, quantum and semiclassical dynamics of nonadiabatic processes
  • Vibrational and electronic spectroscop
  • Transitions from metastable states
  • Drug design
  • Multi-scale methods
  • Accelerated dynamics techniques

Instruments

  • Cluster Sole e Baleno (392 CORE +28 TB STORAGE)
    • 4 nodes / 32 CPU core Intel(R) Xeon(R) CPU E5-2640 v3 @ 2.60GHz, 128GB RAM 2TB SATA HD
    • 4 nodes / 32 CPU core Intel(R) Xeon(R) CPU E5620 @ 2.40GHz, 32 GB RAM 500GB SATA HD
    • 4 nodes / 48 CPU core Intel(R) Xeon(R) CPU E5650 @ 2.67GHz, 52 GB RAM 500GB SATA HD
    • 6 nodes / 72 CPU cores Intel(R) Xeon(R) CPU E5650 @ 2.67GHz, 96 GB RAM 250GB SATA HD
    • 4 nodes/ 64 CPU core Intel(R) Xeon(R) CPU E5-2670 @ 2.60GHz, 128GB RAM 2TB SATA HD
    • 1 node/ 48 CPU Core AMD Opteron 6176SE @ 2.3 GHz, 256 GB 6HDD SATA 2TB
  • Cluster FORM Fortunelli
    • 16 nodes / 128 CPU Quad-Core AMD Opteron Processor 2380, 32 GB RAM, 250GB SATA HD
  • Cluster GROWTH Fortunelli
    • 12 nodes / 96 CPU AMD Opteron Processor 2354, 16 GB RAM, 250GB SATA HD
    • 4 nodes / 16 CPU AMD Opteron Processor 265, 8 GB RAM, 250GB SATA HD
  • Cluster DPM
    • 8 nodes / 64 CPU cores HP BladeSystem c3000 tower, 8x HP ProLiant BL460c G1 (2x Intel(R) Xeon(R) CPU E5440 @ 2.83GHz, 16GB RAM 150GB SATA HD)