Development, validation, and pilot application of a generalized fluctuating charge model for computational spectroscopy in solution

A general approach enforcing nonperiodic boundary conditions for the computation of spectroscopic properties in solution has been improved including an effective description of charge-transfer contributions and coordination number adjustment for explicit solvent molecules. Both contributions are obtained from a continuous description of intermolecular hydrogen bonds, which has been employed also for an effective clustering of molecular dynamics trajectories. Fine tuning of the model has been performed for several water clusters, and then its efficiency and reliability have been demonstrated by computing the absorption spectra of different creatinine tautomers in aqueous solution

Quantum ESPRESSO: One Further Step toward the Exascale

We review the statusof the Quantum ESPRESSO softwaresuite for electronic-structure calculations based on plane waves,pseudopotentials, and density-functional theory. We highlight therecent developments in the porting to GPUs of the main codes, usingan approach based on OpenACC and CUDA Fortran offloading.We describe, in particular, the results achieved on linear-responsecodes, which are one of the distinctive features of the QuantumESPRESSO suite. We also present extensive performance benchmarkson different GPU-accelerated architectures for the main codes of thesuite

An integrated experimental and quantum-chemical investigation on the vibrational spectra of chlorofluoromethane

The vibrational analysis of the gas-phase infrared spectra of chlorofluoromethane (CH2ClF, HCFC-31) was carried out in the range 200-6200 cm(-1). The assignment of the absorption features in terms of fundamental, overtone, combination, and hot bands was performed on the medium-resolution (up to 0.2 cm(-1)) Fourier transform infrared spectra. From the absorption cross section spectra accurate values of the integrated band intensities were derived and the global warming potential of this compound was estimated, thus obtaining values of 323, 83, and 42 on a 20-, 100-, and 500-year horizon, respectively. The set of spectroscopic parameters here presented provides the basic data to model the atmospheric behavior of this greenhouse gas. In addition, the obtained vibrational properties were used to benchmark the predictions of state-of-the-art quantum-chemical computational strategies. Extrapolated complete basis set limit values for the equilibrium geometry and harmonic force field were obtained at the coupled-cluster singles and doubles level of theory augmented by a perturbative treatment of triple excitations, CCSD(T), in conjunction with a hierarchical series of correlation-consistent basis sets (cc-pVnZ, with n = T, Q, and 5), taking also into account the core-valence correlation effects and the corrections due to diffuse (aug) functions. To obtain the cubic and quartic semi-diagonal force constants, calculations employing second-order Moller-Plesset perturbation (MP2) theory, the double-hybrid density functional B2PLYP as well as CCSD(T) were performed. For all anharmonic force fields the performances of two different perturbative approaches in computing the vibrational energy levels (i.e., the generalized second order vibrational treatment, GVPT2, and the recently proposed hybrid degeneracy corrected model, HDCPT2) were evaluated and the obtained results allowed us to validate the spectroscopic predictions yielded by the HDCPT2 approach. The predictions of the deperturbed second-order perturbation approach, DVPT2, applied to the computation of infrared intensities beyond the double-harmonic approximation were compared to the accurate experimental values here determined. Anharmonic DFT and MP2 corrections to CCSD(T) intensities led to a very good agreement with the absorption cross section measurements over the whole spectral range here analysed. (C) 2013 AIP Publishing LLC

Computer simulations of prebiotic systems

Computer simulations are powerful tools in order to figure out the physical and chemical phenomena occurring in the prebiotic environments, shedding light on the processes that led to the emergence of life on Earth. Indeed, the state-of-the-art theoretical methods have been developed for predicting molecular properties of the isolated systems and for describing the intermolecular interactions and the reactivity in a wide range of environments and boundary conditions. Such studies strongly help to unravel the various molecular contributions to the intricate experimental outcomes, allowing a deeper understanding of the underlying phenomena. This contribution provides an overview of the theoretical studies of prebiotic systems, drawing attention to some application of specific computational tool

Optical rotatory dispersion of methyloxirane in aqueous solution: assessing the performance of density functional theory in combination with a fully polarizable QM/MM/PCM approach

We report a study on the performance of a recently developed fully polarizable QM/MM/PCM approach based on Fluctuating Charges (FQ) combined with 11 different Density Functionals for the description of the Optical Rotation at different wavelengths of (R)-Methyloxirane in aqueous solution. The results are compared with those obtained for the isolated system and for the solvated one as described by the Polarizable Continuum Model. In all cases, a comparison with experimental data is also shown. The results show that the effect of the solvent is much more significant than the effect of the density functional

Reliable structural, thermodynamic, and spectroscopic properties of organic molecules adsorbed on silicon surfaces from computational modeling: the case of glycine@Si(100)

Chemisorption of glycine on Si(100) has been studied by an integrated computational strategy based on perturbative anharmonic computations employing geometries and harmonic force fields evaluated by hybrid density functionals coupled to purposely tailored basis sets. It is shown that such a strategy allows the prediction of spectroscopic properties of isolated and chemisorbed molecules with comparable accuracy, paving the route toward a detailed analysis of surface-induced changes of glycine vibrational spectra

Toward Feasible and Comprehensive Computational Protocol for Simulation of the Spectroscopic Properties of Large Molecular Systems: The Anharmonic Infrared Spectrum of Uracil in the Solid State by the Reduced Dimensionality/Hybrid VPT2 Approach

Feasible and comprehensive computational protocols for simulating the spectroscopic properties of large and complex molecular systems are very sought after. Indeed, due to the great variety of intra- and intermolecular interactions that may take place, the interpretation of experimental data becomes more and more difficult as the system under study increases in size or is placed in a complex environment, such as condensed phases. In this framework, we are actively developing a comprehensive and robust computational protocol aimed at quantitative reproduction of the spectra of nucleic acid base complexes, with increasing complexity toward condensed phases and monolayers of biomolecules on solid supports. We have resorted to fully anharmonic quantum mechanical computations within the generalized second-order vibrational perturbation theory (GVPT2) approach, combined with the cost-effective B3LYP-D3 method, in conjunction with basis sets of double-ζ plus polarization quality. Such an approach has been validated in a previous work (Phys. Chem. Chem. Phys. 2014, 16, 10112−10128) for simulating the IR spectra of the monomers of nucleobases and some of their dimers. In the present contribution we have extended such computational protocol to simulate spectroscopic properties of a molecular solid, namely polycrystalline uracil. First we have selected a realistic molecular model for representing the spectroscopic properties of uracil in the solid state, the uracil heptamer, and then we have computed the relative anharmonic frequencies combining less demanding approaches such as the hybrid B3LYP-D3/DFTBA one, in which the harmonic frequencies are computed at a higher level of theory (B3LYP-D3/N07D) whereas the anharmonic shifts are evaluated at a lower level of theory (DFTBA), and the reduced dimensionality VPT2 (RD-VPT2) approach, where only selected vibrational modes are computed anharmonically along with the couplings with other modes. The good agreement between the theoretical results and the experimental findings allowed us to extend the interpretation of experimental data. Our results indicate that hybrid and reduced dimensionality models pave a way for the definition of system-tailored computational protocols able to provide more and more accurate results for very large molecular systems, such as molecular solids and molecules adsorbed on solid supports

Accurate Vibrational-Rotational Parameters and Infrared Intensities of 1-Bromo-1-fluoroethene: A Joint Experimental Analysis and Ab Initio Study

The medium-resolution gas-phase infrared (IR) spectra of 1-bromo-1-fluoroethene (BrFC═CH2, 1,1-C2H2BrF) were investigated in the range 300-6500 cm(-1), and the vibrational analysis led to the assignment of all fundamentals as well as many overtone and combination bands up to three quanta, thus giving an accurate description of its vibrational structure. Integrated band intensity data were determined with high precision from the measurements of their corresponding absorption cross sections. The vibrational analysis was supported by high-level ab initio investigations. CCSD(T) computations accounting for extrapolation to the complete basis set and core correlation effects were employed to accurately determine the molecular structure and harmonic force field. The latter was then coupled to B2PLYP and MP2 computations in order to account for mechanical and electrical anharmonicities. Second-order perturbative vibrational theory was then applied to the thus obtained hybrid force fields to support the experimental assignment of the IR spectra.The medium-resolution gas-phase infrared (IR) spectra of 1-bromo-1-fluoroethene (BrFC=CH2, 1,1-C2H2BrF) were investigated in the range 300-6500 cm(-1), and the, vibrational analysis led to the assignment of all fundamentals as well as many overtone and combination bands up to three quanta, thus giving an accurate description of its vibrational structure. Integrated band intensity data were determined with high precision from the measurements of their corresponding absorption cross sections. The vibrational analysis was supported by high-level ab initio investigations. CCSD (T) computations accounting for extrapolation to the complete basis set and core correlation effects were employed to accurately determine the molecular structure and harmonic force field. The latter was then coupled to B2PLYP and MP2 computations in order to account for mechanical and electrical anharmonicities. Second-order perturbative vibrational theory was then applied to the thus obtained hybrid force fields to support the experimental assignment of the IR spectra

Ultrafast resonance energy transfer in the umbelliferone-alizarin bichromophore

In this work we present the synthesis, time-resolved spectroscopic characterization and computational analysis of a bichromophore composed of two very well-known naturally occurring dyes: 7-hydroxycoumarin (umbelliferone) and 1,2-dihydroxyanthraquinone (alizarin). The umbelliferone donor (Dn) and alizarin acceptor (Ac) moieties are linked to a triazole ring via sigma bonds, providing a flexible structure. By measuring the fluorescence quantum yields and the ultrafast transient absorption spectra we demonstrate the high efficiency (similar to 85%) and the fast nature (similar to 1.5 ps) of the energy transfer in this compound. Quantum chemical calculations, within the density functional theory (DFT) approach, are used to characterize the electronic structure of the bichromophore (Bi) in the ground and excited states. We simulate the absorption and fluorescence spectra using the TD-DFT methods and the vertical gradient approach (VG), and include the solvent effects by adopting the conductor-like polarizable continuum model (CPCM). The calculated electronic structure suggests the occurrence of weak interactions between the electron densities of Dn and Ac in the excited state, indicating that the Forster-type transfer is the appropriate model for describing the energy transfer in this system. The average distance between Dn and Ac moieties calculated from the conformational analysis (12 angstrom) is in very good agreement with the value estimated from the Forster equation (similar to 11 angstrom ). At the same time, the calculated rate constant for energy transfer, averaged over multiple conformations of the system (3.6 ps), is in reasonable agreement with the experimental value (1.6 ps) estimated by transient absorption spectroscopy. The agreement between experimental results and computational data leads us to conclude that the energy transfer in Bi is well described by the Forster mechanism