1,721,000 research outputs found
Accurate Biomolecular Structures by the Nano-LEGO Approach: Pick the Bricks and Build Your Geometry
Get PDFThe determination of accurate equilibrium molecular structures plays a fundamental role for understanding many physical-chemical properties of molecules, ranging from the precise evaluation of the electronic structure to the analysis of the role played by dynamical and environmental effects in tuning their overall behavior. For small semi-rigid systems in the gas phase, state-of-the-art quantum chemical computations rival the most sophisticated experimental (from, for example, high-resolution spectroscopy) results. For larger molecules, more effective computational approaches must be devised. To this end, we have further enlarged the compilation of available semi-experimental (SE) equilibrium structures, now covering the most important fragments containing H, B, C, N, O, F, P, S, and Cl atoms collected in the new SE100 database. Next, comparison with geometries optimized by methods rooted in the density functional theory showed that the already remarkable results delivered by PW6B95 and, especially, rev-DSDPBEP86 functionals can be further improved by a linear regression (LR) approach. Use of template fragments (taken from the SE100 library) together with LR estimates for the missing interfragment parameters paves the route toward accurate structures of large molecules, as witnessed by the very small deviations between computed and experimental rotational constants. The whole approach has been implemented in a user-friendly tool, termed nano-LEGO, and applied to a number of demanding case studies
Accuracy meets interpretability for computational spectroscopy by means of hybrid and double-hybrid functionals
Get PDFAccuracy and interpretability are often seen as the devil and holy grail in computational spectroscopy and their reconciliation remains a primary research goal. In the last few decades, density functional theory has revolutionized the situation, paving the way to reliable yet effective models for medium size molecules, which could also be profitably used by non-specialists. In this contribution we will compare the results of some widely used hybrid and double hybrid functionals with the aim of defining the most suitable recipe for all the spectroscopic parameters of interest in rotational and vibrational spectroscopy, going beyond the rigid rotor/harmonic oscillator model. We will show that last-generation hybrid and double hybrid functionals in conjunction with partially augmented double-and triple-zeta basis sets can offer, in the framework of second order vibrational perturbation theory, a general, robust, and user-friendly tool with unprecedented accuracy for medium-size semi-rigid molecules
Infrared Spectra, Integrated Band Intensities, and Anharmonic Force Field of H(2)C=CHF
No full textThe gas-phase infrared spectra of vinyl fluoride, H(2)C=CHF, have been examined at medium resolution in the range 400-8000 cm(-1). The assignment of the absorptions in terms of fundamental, overtone, and combination bands, assisted by quantum chemical calculations, is consistent all over the region investigated. Spectroscopic parameters, obtained from the analysis of partially resolved rotational structure of some bands, have been derived and compared with the corresponding calculated values. Accurate values of integrated band intensities have also been determined for the first time. High-level ab initio calculations with large basis sets have been performed. Correlated harmonic force fields have been obtained from coupled cluster CCSD(T) calculations with the cc-pVQZ basis set, while anharmonic force constants have been computed employing the less resource demanding cc-pVTZ basis set. A good agreement between the computed and the experimental data has been obtained including those for the integrated infrared band intensities
A computational journey across nitroxide radicals: From structure to spectroscopic properties and beyond
Get PDFNitroxide radicals are characterized by a long-lived open-shell electronic ground state and are strongly sensitive to the chemical environment, thus representing ideal spin probes and spin labels for paramagnetic biomolecules and materials. However, the interpretation of spectroscopic parameters in structural and dynamic terms requires the aid of accurate quantum chemical computations. In this paper we validate a computational model rooted into double-hybrid functionals and second order vibrational perturbation theory. Then, we provide reference quantum chemical results for the structures, vibrational frequencies and other spectroscopic features of a large panel of nitroxides of current biological and/or technological interest
Development and Validation of a Parameter-Free Model Chemistry for the Computation of Reliable Reaction Rates
Get PDFA recently developed model chemistry (jun-Cheap) has been slightly modified and proposed as an effective, reliable, and parameter-free scheme for the computation of accurate reaction rates with special reference to astrochemical and atmospheric processes. Benchmarks with different sets of state-of-the-art energy barriers spanning a wide range of values show that, in the absence of strong multireference contributions, the proposed model outperforms the most well-known model chemistries, reaching a subchemical accuracy without any empirical parameter and with affordable computer times. Some test cases show that geometries, energy barriers, zero point energies, and thermal contributions computed at this level can be used in the framework of the master equation approach based on the ab initio transition-state theory for obtaining accurate reaction rates
Gliding on Ice in search of accurate and cost-effective computational methods for Astrochemistry on Grains: the puzzling case of the HCN isomerization
Get PDFThe isomerization of hydrogen cyanide to hydrogen isocyanide on icy grain surfaces is investigated by an accurate composite method (jun-Cheap) rooted in the coupled cluster ansatz and by density functional approaches. After benchmarking density functional predictions of both geometries and reaction energies against jun-Cheap results for the relatively small model system HCN···(H2O)2, the best performing DFT methods are selected. A large cluster containing 20 water molecules is then employed within a QM/QM′ approach to include a realistic environment mimicking the surface of icy grains. Our results indicate that four water molecules are directly involved in a proton relay mechanism, which strongly reduces the activation energy with respect to the direct hydrogen transfer occurring in the isolated molecule. Further extension of the size of the cluster up to 192 water molecules in the framework of a three-layer QM/QM′/MM model has a negligible effect on the energy barrier ruling the isomerization. Computation of reaction rates by the transition state theory indicates that on icy surfaces, the isomerization of HNC to HCN could occur quite easily even at low temperatures thanks to the reduced activation energy that can be effectively overcome by tunneling.The isomerization of hydrogen cyanide to hydrogen isocyanide on icy grain surfaces is investigated by an accurate composite method (jun-Cheap) rooted in the coupled cluster ansatz and by density functional approaches. After benchmarking density functional predictions of both geometries and reaction energies against jun-Cheap results for the relatively small model system HCN···(H2O)2, the best performing DFT methods are selected. A large cluster containing 20 water molecules is then employed within a QM/QM′ approach to include a realistic environment mimicking the surface of icy grains. Our results indicate that four water molecules are directly involved in a proton relay mechanism, which strongly reduces the activation energy with respect to the direct hydrogen transfer occurring in the isolated molecule. Further extension of the size of the cluster up to 192 water molecules in the framework of a three-layer QM/QM′/MM model has a negligible effect on the energy barrier ruling the isome..
High-resolution infrared study of vinyl fluoride in the 750-1050 cm-1 region: Rovibrational analysis and resonances involving the v(8), v(10), and v(11) fundamentals
No full textThe FTIR spectra of CH2=CHF have been investigated in the v(8), v(10), and v(11) region between 750 and 1050 cm(-1) at a resolution of about 0.002 cm(-1). The v(8) vibration of symmetry species A' gives rise to an a/b-type hybrid band, while the v(10) and v(11) modes of A" symmetry produce c-type absorptions. Due to the proximity of their band origins, the three vibrations perturb each other by Coriolis and high-order anharmonic resonances. In particular, the interactions between the v(8) and v(10) modes are very strong and widespread with band origins separated by only 1.37 cm(-1). Besides the expected c-type characteristics, the v(10) band shows a very intense pseudo a- type component caused by the strong first-order Coriolis resonances with the v(8) state. Furthermore, the 2"9 " dark state" was found to be involved in the interacting band systems. The spectral analysis resulted in the identification of 3144, 3235, and 3577 transitions of the v(8), v(10), and v(11) vibrations, respectively. Almost all the assigned data were simultaneously fitted using the Watson's A- reduction Hamiltonian in the Ir representation and the perturbation operators. The model employed includes nine types of resonances within the tetrad v(8)/v(10)/v(11)/2v(9) and a set of spectroscopic constants for the v(8), v(10), and v(11) fundamentals as well as parameters for the "dark state" 2v(9), and fourteen coupling terms have been determined
DFT meets the segmented polarization consistent basis sets: Performances in the computation of molecular structures, rotational and vibrational spectroscopic properties
No full textQuantum-chemical calculations assist the analysis of laboratory spectra, and often provide the only means to determine spectroscopic data that cannot be accessed experimentally. For the purpose, reliable predictions of structural and spectroscopic parameters are required. Although coupled cluster theory in conjunction with to large basis sets and composite schemes can reach impressive accuracies for structural, thermochemical and spectroscopic properties, it is still limited to small sized molecules. DFT represents the working option for medium to large molecular systems. In this context, systematic investigations are required aimed at characterizing the performances of the different DFT model chemistries. In this work, the accuracy of the popular hybrid B3LYP and the double hybrid B2PLYP functionals coupled to the segmented polarization consistent (aug-)pcs-n basis sets in the prediction of molecular structures and rotational- and vibrational spectroscopic parameters are investigated using a benchmark set of molecules of both atmospheric and astrochemical relevance. For comparison purposes, different flavors of Dunning's triple-ζ basis sets and the SNSD basis set, are also employed. The convergence behavior of the pcs-n hierarchy with n = 1–4 is also addressed to some extent. The results indicate the B3LYP-D3 functional in conjunction with the aug-pcs-1 or SNSD basis sets as a cost-effective model chemistry for applications in the field of rotational and vibrational spectroscopies. Improved accuracy is obtained by coupling the B2PLYP-D3 functional with the aug-pcs-2 or aug-cc-pVTZ triple-ζ basis sets that show an accuracy around 0.003 Å and 0.3° for bond lengths and angles, 1% and 3% for rotational and quartic centrifugal distortion constants, respectively, 12 cm−1 for fundamental frequencies and 3 km mol−1 for IR intensities. The B2PLYP-D3/maug-cc-pVTZ-dH level keeps the same accuracy, with slightly larger deviations for intensities
Accuracy and Interpretability: The Devil and the Holy Grail. New Routes across Old Boundaries in Computational Spectroscopy
No full textThe past decade has witnessed an increasing interaction between experiment and theory in the field of molecular spectroscopy. On the computational side, ongoing developments of hardware and software have moved computational spectroscopy from a highly specialized research area to a general tool for researchers in different fields of chemical science. However, since its dawn, computational spectroscopy has been characterized by the dichotomies of qualitative and quantitative description, and of interpretation and accuracy. Indeed, the analysis of experiments is seldom straightforward because of the subtle interplay of several different effects, which are not easy to evaluate and isolate, and/or the complexity of the system under consideration. Often, the accuracy has to be set aside for a more qualitative analysis that will provide the means for a broad interpretation. In such a scenario, the most recent advances in theoretical treatments as well as computational tools have opened the way to the reconciliation of accuracy and interpretability, resulting in unequivocal analyses and assignments of experimental spectra and their unbiased interpretation. This Review aims at being a comprehensive, authoritative, critical, and readable account of general interest to the chemistry community because of the wealth of qualitative and quantitative information that can be obtained from spectroscopic investigations. Limiting ourselves to rotational and vibrational spectroscopy, emphasis will be put on accuracy and interpretability as well as on the routes toward their reconciliation and integration
Virtual Reality bridge between Chemistry and Cultural Heritage: the "Sala degli Stemmi" Case Study
Get PDFIn this contribution, we present a multiscale and multidisciplinary VR architecture that aims at creating a common environment where cultural heritage and chemistry meet in order to strengthen the role already played by chemistry in the process of restoration of cultural goods. Our aim is to create a user friendly platform where experts of both fields can share data and ideas in a direct way, in order to achieve deeper insights into cultural goods combining the scientific and historical points of view. As a case study we present the 3D reconstruction of the "Sala degli Stemmi", which is one of the two historical rooms at Palazzo della Carovana in Pisa, presenting a number of artworks that underwent a process of chemical analysis and restoration in 2012. The whole architecture has been developed using the Unity game engine, and it is usable with HTC Vive headsets. The implementation of the VR environment and the potential applications, from both the scientific and educational points of view, are discussed in some detail
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