Challenges In Conformational Analysis Of Flexible Molecules

The conformational analysis represents the first step toward a detailed characterization and understanding of the structure-function relationships of molecular systems. In this respect spectroscopic experiments on isolated bio- and organic-molecules allow detection of different binding schemes and three-dimensional (3D) conformations without perturbing effects of the environment. Detection of multiple 3D-geometries concomitantly present in an experimental mixture can be facilitated by “in situ” structural changes induced either by thermal variations, or the interaction with near-IR (NIR) to ultraviolet (UV) light. These sophisticated experiments need to be supported by accurate and reliable computational studies allowing to link the rich experimental data to the desired information on the structure and properties of complex molecular systems. Therefore a reliable computational approach should be able to provide a balanced description of all interactions allowing for extended mapping of the whole conformational space, including the accurate prediction of equilibrium structures, their relative positions on the potential energy surface (PES), free energies corresponding to the specific experimental conditions and the spectroscopic properties. Computations based on the second-order perturbation theory (VPT2) allow accounting for the anharmonicity of both wave function and properties. This results in a correct description of the intensity of non-fundamental transitions and more accurate band-shapes. Moreover, the same anharmonic force fields as employed in the determination of vibrational spectra allow considering vibrational corrections to molecular properties or thermodynamic functions. For flexible molecules, the large amplitude-motion (LAM) free approach, where all LAMs anharmonic constants are excluded, allows overcoming problems due to contaminating the overall VPT2 treatment and higher frequency vibrations. The most reliable structural, spectroscopic and energetic results can be obtained combining various computational methods ranging from density functional theory (DFT) to coupled-cluster (CC), with the latter representing also references for the benchmarking of different DFT methodologies

Interpretation and prediction of optical properties: novel fluorescent dyes as a test case

The rapid development of modern quantum mechanical theories and computational resources facilitates extended characterization of molecular systems of increasing size and complexity, including chromophores of biochemical or technological interest. Efficient and accurate computations of molecular structure and properties in the ground and excited electronic states are routinely performed using density functional theory (DFT) and its time-dependent (TD-DFT) counterpart. However, the direct comparison with experiment requires simulation of electronic absorption or emission spectra, for which inclusion of vibrational effects leads to more realistic line shapes while at the same time allowing for more reliable interpretation and prediction of optical properties and providing additional information that is not available from experimental low-resolution UV-vis spectra. Computational support can help identify the most interesting chromophores among a large number of potential candidates for designing new materials or sensors, as well as unraveling effects contributing to the overall spectroscopic phenomena. In this perspective, recently developed viologen derivatives (1,1′-disubstituted-4,4′-bipyridyl cation salts, viol) are selected as test cases to illustrate the advantages of spectroscopic theoretical methodologies, which are still not widely used in “chemical” interpretation. Although these molecules are characterized by improved stability as well as the dual function of chromism and luminescence, their detailed spectroscopic characterization is hampered due to the availability of only low-resolution experimental spectra. DFT-based absorption and emission spectra are exploited in the analysis of optical properties, allowing detailed investigation of vibrational effects and gaining more insights on the structure–spectra relationship, which can be extended to develop further viologen dyes with improved optical properties

Toward the design of alkynylimidazole fluorophores: computational and experimental characterization of spectroscopic features in solution and in poly(methyl methacrylate)

The possibilities offered by organic fluorophores in the preparation of advanced plastic materials have been increased by designing novel alkynylimidazole dyes, featuring different push and pull groups. This new family of fluorescent dyes was synthesized by means of a one-pot sequential bromination–alkynylation of the heteroaromatic core, and their optical properties were investigated in tetrahydrofuran and in poly(methyl methacrylate). An efficient in silico pre-screening scheme was devised as consisting of a step-by-step procedure employing computational methodologies by simulation of electronic spectra within simple vertical energy and more sophisticated vibronic approaches. Such an approach was also extended to efficiently simulate one-photon absorption and emission spectra of the dyes in the polymer environment for their potential application in luminescent solar concentrators. Besides the specific applications of this novel material, the integration of computational and experimental techniques reported here provides an efficient protocol that can be applied to make a selection among similar dye candidates, which constitute the essential responsive part of those fluorescent plastic materials

The ionic states of iodobenzene studied by photoionization and ab initio configuration interaction and DFT computations

New valence electron photoelectron spectra of iodobenzene obtained using synchrotron radiation have been recorded. Ionization energies (IEs) determined using multi-configuration SCF calculation (MCSCF) procedures confirmed the adiabatic IE order as: X2B1 < A2A2 < B2B2 < C2B1. Although it is convenient to retain C2v labelling, there is an evidence that minor distortion to CS symmetry occurs at the MCSCF level for the C state. The fifth ionization process shown to be D2A1 exhibits dissociation to C6H5+ + I both in the experimental and theoretical studies. The calculated Franck- Condon vibrational spectral envelopes, including hot band contributions, for the first four ionic states reproduce the observed peak positions and intensities with reasonable accuracy. In order to simulate the observed spectra, different bandwidths are required for different states. The increase in the required bandwidths for the A2A2 and B2B2 states is attributed to internal conversion to lower-lying states. The presence of relatively high intensity sequence bands leads to asymmetry of each of the X2B1 state bands

Combined theoretical and experimental study of the valence, Rydberg, and ionic states of chlorobenzene

New photoelectron (PE) and ultra violet (UV) and vacuum UV (VUV) spectra have been obtained for chlorobenzene by synchrotron study with higher sensitivity and resolution than previous work and are subjected to detailed analysis. In addition, we report on the mass-resolved (2 + 1) resonance enhanced multiphoton ionization (REMPI) spectra of a jet-cooled sample. Both the VUV and REMPI spectra have enabled identification of a considerable number of Rydberg states for the first time. The use of ab initio calculations, which include both multi-reference multi-root doubles and singles configuration interaction (MRD-CI) and time dependent density functional theoretical (TDDFT) methods, has led to major advances in interpretation of the vibrational structure of the ionic and electronically excited states. Franck-Condon (FC) analyses of the PE spectra, including both hot and cold bands, indicate much more complex envelopes than previously thought. The sequence of ionic states can be best interpreted by our multi-configuration self-consistent field computations and also by comparison of the calculated vibrational structure of the B and C ionic states with experiment; these conclusions suggest that the leading sequence is the same as that of iodobenzene and bromobenzene, namely: X2B1(3b1 121) < A2A2(1a2 121) < B2B2(6b2 121) < C2B1(2b1 121). The absorption onset near 4.6 eV has been investigated using MRD-CI and TDDFT calculations; the principal component of this band is 1B2 and an interpretation based on the superposition of FC and Herzberg-Teller contributions has been performed. The other low-lying absorption band near 5.8 eV is dominated by a 1A1 state, but an underlying weak 1B1 state (\u3c0\u3c3 17) is also found. The strongest band in the VUV spectrum near 6.7 eV is poorly resolved and is analyzed in terms of two \u3c0\u3c0 17 states of 1A1 (higher oscillator strength) and 1B2 (lower oscillator strength) symmetries, respectively. The calculated vertical excitation energies of these two states are critically dependent upon the presence of Rydberg functions in the basis set, since both manifolds are strongly perturbed by the Rydberg states in this energy range. A number of equilibrium structures of the ionic and singlet excited states show that the molecular structure is less subject to variation than corresponding studies for iodobenzene and bromobenzene

UV Irradiation and Near Infrared Characterization of Laboratory Mars Soil Analog Samples

The search for molecular biosignatures at the surface of Mars is complicated by an intense irradiation in the mid- and near-ultraviolet (UV) spectral range for several reasons: (i) many astrobiologically relevant molecules are electronically excited by efficient absorption of UV radiation and rapidly undergo photochemical reactions; (ii) even though the penetration depth of UV radiation is limited, aeolian erosion continually exposes fresh material to radiation; and (iii) UV irradiation generates strong oxidants such as perchlorates that can penetrate deep into soils and cause subsurface oxidative degradation of organics. As a consequence, it is crucial to investigate the effects of UV radiation on organic molecules embedded in mineral matrices mimicking the martian soil, in order to validate hypotheses about the nature of the organic compounds detected so far at the surface of Mars by the NASA Mars Science Laboratory’s (MSL) Curiosity rover, as well as organics that will be possibly found by the next rover missions Mars 2020 (NASA) and ExoMars 2022 (ESA-Roscosmos). In addition, studying the alteration of possible molecular biosignatures in the martian environment will help to redefine the molecular targets for life detection missions and devise suitable detection methods. Here we report the results of mid- and near-UV irradiation experiments of Mars soil analog samples obtained adsorbing relevant organic molecules on a clay mineral that is quite common on Mars, i.e. montmorillonite, doped with 1 wt% of magnesium perchlorate. Specifically, we chose to investigate the photostability of a plausible precursor of the chlorohydrocarbons detected on Mars by the Curiosity rover, namely phthalic acid, along with the biomarkers of extant life L-phenylalanine and L-glutamic acid, which are proteomic amino acids, and adenosine 5’-monophosphate, which is a nucleic acid component. We monitored the degradation of these molecules adsorbed on montmorillonite through in situ spectroscopic analysis, investigating the reflectance properties of the samples in the Near InfraRed (NIR) spectral region. Such spectroscopic characterization of molecular alteration products provides support for two upcoming robotic missions to Mars that will employ NIR spectroscopy to look for molecular biosignatures, through the instruments SuperCam on board Mars 2020, ISEM, Ma_Miss and MicrOmega on board ExoMars 2022

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

Anharmonic Ir Spectra Of Biomolecules: Nucleobases And Their Oligomers

Computational spectroscopy techniques have become in the last years effective means to predict and characterize spectra, such as infrared, for molecular systems of increasing dimensions with account for different environments. We are actively developing a comprehensive and robust computational protocol, set within a perturbative vibrational framework [1], aimed at a quantitative reproduction of the spectra of biomolecules. In order to model the vibrational spectra of weakly bound molecular complexes, dispersion interactions should be taken into proper account. In this work, we present critical assessment of dispersion-corrected DFT approaches for anharmonic vibrational frequency calculations. It is shown that fully anharmonic IR spectra, simulated through full and reduced-dimensionality generalized second-order vibrational perturbation theory (GVPT2)[1] with the potential energy surfaces computed with the B3LYP-D3 approach, may be used to interpret experimental data of nucleobases and their complexes[2] by the direct comparison of experimental IR spectra with their theoretical anharmonic counterpart, taking into account also overtones and combination bands. [1] V. Barone, M. Biczysko, J. Bloino, Phys. Chem. Chem. Phys., 2014,16, 1759-1787 [2] T. Fornaro, M. Biczysko, S. Monti, V. Barone , Phys. Chem. Chem. Phys., 2014, DOI: 10.1039/C3CP54724

Accurate Anharmonic Ir Spectra From Integrated Cc/dft Approach

The recent implementation of the computation of infrared (IR) intensities beyond the double harmonic approximation [1] paved the route to routine calculations of infrared spectra for a wide set of molecular systems. Contrary to common beliefs, second-order perturbation theory is able to deliver results of high accuracy provided that anharmonic resonances are properly managed [1,2]. It has been already shown for several small closed- and open shell molecular systems that the differences between coupled cluster (CC) and DFT anharmonic wavenumbers are mainly due to the harmonic terms, paving the route to introduce effective yet accurate hybrid CC/DFT schemes [2]. In this work we present that hybrid CC/DFT models can be applied also to the IR intensities leading to the simulation of highly accurate fully anharmonic IR spectra for medium-size molecules, including ones of atmospheric interest, showing in all cases good agreement with experiment even in the spectral ranges where non-fundamental transitions are predominant[3]. [1] J. Bloino and V. Barone, J. Chem. Phys. 136, 124108 (2012) [2] V. Barone, M. Biczysko, J. Bloino, Phys. Chem. Chem. Phys., 16, 1759-1787 (2014) [3] I. Carnimeo, C. Puzzarini, N. Tasinato, P. Stoppa, A. P. Charmet, M. Biczysko, C. Cappelli and V. Barone, J. Chem. Phys., 139, 074310 (2013