Computed Absorption Spectrum Research Articles

Development of a charged model of the SARS-CoV-2 viral surface

A recent study provided experimental evidence of inactivation of viral activity after radio-frequency (RF) exposures in the 6–12 GHz band that was hypothesized to be caused by vibrations of an acoustic dipole mode in the virus that excited the viral membrane to failure. Here, we develop an atomic-scale molecular dynamics (MD) model of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral surface to estimate the electric fields necessary to rupture the viral membrane via dipole shaking of the virus. We computed the absorption spectrum of the system via unbiased MD simulations and found no particular strong absorption in the GHz band. We investigated the mechanical resiliency of the viral membrane by introducing uniaxial strains in the system and observed no pore formation in the membrane for strains up to 50%. Because the computed absorption spectrum was found to be essentially flat, and the strain required to break the viral membrane was >0.5, the field strength associated with rupture of the virus was greater than the dielectric breakdown value of air. Thus, RF disinfection of enveloped viruses would occur only once sufficient heat was transferred to the virus via a thermal mechanism and not by direct action (shaking) of the RF field oscillations on the viral membrane.

An ab initio quantum dynamics simulation of UV absorption spectrum of methyl vinyl ketone oxide.

The spectroscopy of the four-carbon Criegee intermediate, methyl vinyl ketone oxide (MVK-oxide), following UV excitation to the B state (corresponding to the first π* ← π electronic transition), is studied theoretically, which relied on a single reference electronic wave function and a quantum dynamical approach for the nuclear motion. Two interacting electronic states BA'1 and CA'1, together with two nuclear degrees of freedom (O-O stretching and C-O-O bending modes), are considered in the dynamical approach. The computed absorption spectrum is found to agree well with the available experimental recordings. The existence of the weak oscillatory structures in the absorption spectrum is argued likely due to the fact that the excitation energy range of the first π* ← π electronic transition is below the energy barrier of the diabatic B state (∼215 nm) and, thus, below the sufficiently deep well occurring at the intermediate O-O distances. This suggests the recurrences of the wavepacket, which might be considered the origin of the weak oscillatory structures in the absorption spectrum. The computed electronic excitation profile of MVK-oxide is predicted to peak at 373nm.

Structural, electronic, thermodynamic and optical properties of SnlSemSn clusters: A DFT study

• DFT study of electronic, thermodynamic and optical properties of SnlSemSn clusters. • Band gap energy of Sn l Se m S n clusters lie in the semiconducting range (1.035–3.463 eV). • Sn 1 Se 1 S 2 is found to be the most reactive cluster. • Absorption spectra can be tailored by varying thecomposition of atoms in clusters. Density Functional Theory (DFT) calculations are performed to investigate the structural, electronic, thermodynamic, and optical properties of Sn l Se m S n clusters with the variation in the number of Sn, Se, and S atoms using B3LYP/321-G ∗ level of theory. We have obtained 23 optimized clusters and their calculated properties are dependent on the size, geometry, and structure of clusters. We observed that Sn 1 Se 1 S 2 is found to be highly reactive owing to its largest values of electronegativity, vertical ionization potential, vertical electron affinity with the least values of binding energy and band gap energy. The least reactive cluster is Sn 1 Se 1 S 8 with the maximum values of band gap and hardness. The band gap energies of all clusters lie in the semiconducting range (1.035 eV–3.463 eV). The optical absorption is observed in ultraviolet and visible regions. The theoretically computed absorption spectrum for excited states is compared experimentally confirming their applications in optoelectronics.

Pt2Cu34(PET)22Cl4]2-: An Atomically Precise, 10-Electron PtCu Bimetal Nanocluster with a Direct Pt-Pt Bond.

Heteroatom-doped metal nanoclusters (NCs) are highly desirable to gain fundamental insights into the effect of doping on the electronic structure and catalytic properties. Unfortunately, their controlled synthesis is highly challenging when the metal atomic sizes are largely different (e.g., Cu and Pt). Here, we design a metal-exchange strategy that enables simultaneous doping and resizing of NCs. Specifically, [Pt2Cu34(PET)22Cl4]2- NC, the first example of a Pt-doped Cu NC, is synthesized by utilizing the unique reactivity of [Cu32(PET)24Cl2H8]2- NC with Pt4+ ions. The single-crystal X-ray structure reveals that two directly bonded Pt atoms occupy the two centers of an unusually interpenetrating, incomplete biicosahedron core (Pt2Cu18), which is stabilized by a Cu16(PET)22Cl4 shell. The molecular structure and composition of the NC are validated by combined experimental and theoretical results. Electronic structure calculations, using the density functional theory, show that the Pt2Cu34 NC is a 10-electron superatom. The computed absorption spectrum matches well with the measured data and allows for assignment of the absorption peaks. The calculations also rationalize energetics for ligand exchange observed in the mass spectrometry data. The synergistic effects induced by Pt doping are found to enhance the catalytic activity of Cu NCs by ∼300-fold in silane to silanol conversion under mild conditions. Furthermore, our synthetic strategy has potential to produce Ni-, Pd-, and Au-doped Cu NCs, which will open new avenues to uncover their molecular structures and catalytic properties.

Computation of the S1 ← S0 Vibronic Absorption Spectrum of Formaldehyde by Variational Gaussian Wavepacket and Semiclassical IVR Methods.

The vibronic absorption spectrum of the electric dipole forbidden and vibronically allowed S1(1 A2) ← S0(1 A1) transition of formaldehyde is calculated by Gaussian wavepacket and semiclassical methods, along with numerically exact reference calculations, using the potential energy surface of Fu, Shepler, and Bowman ( J. Am. Chem. Soc. 2011, 133, 7957). Specifically, the variational multiconfigurational Gaussian (vMCG) approach and the Herman-Kluk semiclassical initial value representation (HK-SCIVR) are compared to assess the accuracy and convergence of these methods, benchmarked against numerically exact time-dependent wavepacket propagation (TDWP) on the reference potential energy surface. The vMCG calculation is shown to converge quite well with about 100 variationally evolving Gaussian functions and using a local cubic expansion instead of the conventional local harmonic approximation. By contrast, the HK-SCIVR approach with ∼105 trajectories reproduces the vibrationally structured spectral envelope correctly but yields a strongly broadened spectrum. The comparison of the computed absorption spectrum with experiment shows that the relevant vibronic progressions are reasonably reproduced by all computations, but deviations of the order of 10-100 cm-1 occur, underscoring that both electronic structure calculations and dynamical approaches remain challenging in the calculation of typical small-molecule excited-state spectra by trajectory-based methods.

Slice imaging of the UV photodissociation of CH2BrCl from the maximum of the first absorption band.

The photodissociation dynamics of bromochloromethane (CH2BrCl) have been investigated at the maximum of the first absorption band, at the excitation wavelengths 203 and 210 nm, using the slice imaging technique in combination with a probe detection of bromine-atom fragments, Br(2P3/2) and Br*(2P1/2), via (2 + 1) resonance enhanced multiphoton ionization. Translational energy distributions and angular distributions reported for both Br(2P3/2) and Br*(2P1/2) fragments show two contributions for the Br(2P3/2) channel and a single contribution for the Br*(2P1/2) channel. High level ab initio calculations have been performed in order to elucidate the dissociation mechanisms taking place. The computed absorption spectrum and potential energy curves indicate the main contribution of the populated 4A″, 5A', and 6A' excited states leading to a C-Br cleavage. Consistently with the results, the single contribution for the Br*(2P1/2) channel has been attributed to direct dissociation through the 6A' state as well as an indirect dissociation of the 5A' state requiring a 5A' → 4A' reverse non-adiabatic crossing. Similarly, a faster contribution for the Br(2P3/2) channel characterized by a similar energy partitioning and anisotropy than those for the Br*(2P1/2) channel is assigned to a direct dissociation through the 5A' state, while the slower component appears to be due to the direct dissociation on the 4A″ state.

Computed and Experimental Absorption Spectra of the Perovskite CH3NH3PbI3.

Electronic structure and light absorption properties of the perovskite CH3NH3PbI3 are investigated by relativistic density functional theory with quasiparticle GW corrections and many-body interactions. The nature of the Wannier exciton is studied by solving the Bethe-Salpeter equation augmented with the analysis of a conceptual hydrogen-like model. The computed absorption spectrum unravels a remarkable absorption "gap" between the first two absorption peaks. This discontinuity is maintained in the calculated tetragonal structure that, however, is not stable at low temperature. Most importantly, the discontinuity is also observed in the experimental absorption spectrum of the orthorhombic single crystal at low temperature (4 K). However, in contrast to the single crystal, in a polycrystalline perovskite film at 5 K the "gap" is filled by a monotonously increasing absorption throughout the visible range. This feature of thin films points to the potential significance of defect absorption for the excellent light harvesting properties of perovskite-based solar cells.

Massively-parallel electron dynamics calculations in real-time and real-space: Toward applications to nanostructures of more than ten-nanometers in size

A highly efficient program of massively parallel calculations for electron dynamics has been developed in an effort to apply the method to optical response of nanostructures of more than ten-nanometers in size. The approach is based on time-dependent density functional theory calculations in real-time and real-space. The computational code is implemented by using simple algorithms with a finite-difference method in space derivative and Taylor expansion in time-propagation. Since the computational program is free from the algorithms of eigenvalue problems and fast-Fourier-transformation, which are usually implemented in conventional quantum chemistry or band structure calculations, it is highly suitable for massively parallel calculations. Benchmark calculations using the K computer at RIKEN demonstrate that the parallel efficiency of the program is very high on more than 60 000 CPU cores. The method is applied to optical response of arrays of C60 orderly nanostructures of more than 10 nm in size. The computed absorption spectrum is in good agreement with the experimental observation.

Ground and Excited State Properties of New Porphyrin Based Dyads: A Combined Theoretical and Experimental Study.

The properties of the ground and excited states of several porphyrins appended with external chelates coordinated to ruthenium-bisbipyridine units are reported. The important modification of the absorption spectrum upon coordination with the ruthenium complex showed that a significant electronic communication between the two subunits was present in the ground state. Experimental results were compared with quantum chemistry calculations performed at density functional theory and time-dependent density functional theory level. The influence of the exchange-correlation functional on the quality of the computed absorption spectrum is shown, and the better behavior of hybrid functionals over long-range corrected ones was rationalized. The excited states topology analysis, performed using natural transition orbitals, gave a more evident confirmation of the communication between the subunits and showed that these new compounds can be promising as dyes in dye-sensitized solar cells.

Electronic Absorption and Resonance Raman Spectroscopy from Ab Initio Quantum Molecular Dynamics

The absorption and resonance Raman excitation profiles of ethylene following π → π* excitation and taking full account of anharmonicity and Duschinsky rotation effects are calculated from first principles molecular dynamics using the ab initio multiple spawning (AIMS) method and a correlation function approach. The AIMS method solves the nuclear and electronic Schrodinger equations simultaneously and it associates a unique nuclear wave function with each electronic state. The computed absorption spectrum has a full width at half maximum of 9800 ± 1300 cm-1 (in agreement with the experimental value, 9500 cm-1) and a high-frequency structure spaced by 800 ± 10 cm-1, attributed to CC stretching. The resonance Raman excitation profile exhibits fundamental activity in all totally symmetric modes with the CC stretching mode being the most dominant. In addition, overtone activity is observed in the torsional motion, out-of-plane wagging motions and the out-of-plane rocking motions. This activity is consistent wi...

Far-infrared absorption in liquid carbon tetrachloride: A theoretical study of the lineshape and intensity

Liquid carbon tetrachloride displays a far-infrared absorption spectrum which is primarily the result of collisional processes involving octapolar and hexadecapolar induction of dipole moments. These moments are modulated by both the rotational and translational motions of the CCl 4 molecules. The rotational motion is essentially free; to treat the more complicated many-body translational problem we apply information theory, which uses as input only spectral moments. We thus avoid assumptions concerning the system dynamics. At 295 K our computed absorption spectrum agrees well with experiment, both in shape and in absolute intensity.

Information theory of the lineshape for collision-induced absorption: Liquid tetrafluoromethane

In liquid tetrafluoromethane collision-induced absorption arises through octopolar and hexadecapolar induction. Induced dipoles are modulated by both the relative rotation and translation of interacting groups of molecules. To a good approximation the molecules rotate freely. To treat the more complicated many-body translational problem we apply information theory, which uses as input only spectral moments. We thus avoid the need to make assumptions about the system dynamics. At 110 K our computed absorption spectrum agrees well with experiment. The calculations are sensitive to the assumed values of the molecular octopole and hexadecapole moments. Our results suggest, subject to certain provisos, that the current values for these moments are accurate to ±5%.