Computational infrared and Raman spectra by hybrid QM/MM techniques: a study on molecular and catalytic material systems

Vibrational spectroscopy is one of the most well-established and important techniques for characterizing chemical systems. To aid the interpretation of experimental infrared and Raman spectra, we report on recent theoretical developments in the ChemShell computational chemistry environment for modelling vibrational signatures. The hybrid quantum mechanical and molecular mechanical approach is employed, using density functional theory for the electronic structure calculations and classical forcefields for the environment. Computational vibrational intensities at chemical active sites are reported using electrostatic and fully polarizable embedding environments to achieve more realistic vibrational signatures for materials and molecular systems, including solvated molecules, proteins, zeolites and metal oxide surfaces, providing useful insight into the effect of the chemical environment on the signatures obtained from experiment. This work has been enabled by the efficient task-farming parallelism implemented in ChemShell for high-performance computing platforms.  This article is part of a discussion meeting issue 'Supercomputing simulations of advanced materials'

The dipolar endofullerene HF@C60

The cavity inside fullerenes provides a unique environment for the study of isolated atoms and molecules. We report encapsulation of hydrogen fluoride inside C60 using molecular surgery to give the endohedral fullerene HF@C60. The key synthetic step is the closure of the open fullerene cage while minimizing escape of HF. The encapsulated HF molecule moves freely inside the cage and exhibits quantization of its translational and rotational degrees of freedom, as revealed by inelastic neutron scattering and infrared spectroscopy. The rotational and vibrational constants of the encapsulated HF molecules were found to be redshifted relative to free HF. The NMR spectra display a large 1H-19F J coupling typical of an isolated species. The dipole moment of HF@C60 was estimated from the temperature-dependence of the dielectric constant at cryogenic temperatures and showed that the cage shields around 75% of the HF dipole

Prediction of optically-induced vibrations in large biomolecules

openNon-covalent van Der Waals (vdW) forces are due to coupled dipole oscillations, and play a key role in determining structural properties of large molecules, actively influencing their vibrational spectra. Upon optical excitation, charge oscillation modes can be activated, causing a dramatic change of vdW interactions and introducing non-local stress in the molecular structure. Vibrational modes are thus expected to be activated by energy transfer from optically-excited charge-fluctuation modes. A quantum-mechanical model for the interaction between charge oscillations and vibrational modes is proposed here, based on the many body dispersion (MBD) model, where the problem is reduced to a set of coupled quantum harmonic oscillators. The aim is to study the vibrational modes activation, analyzing the transition between relevant quantum states within a perturbative framework, and to specifically analyze molecular systems such as photo-receptors and host-guest complexes.Non-covalent van Der Waals (vdW) forces are due to coupled dipole oscillations, and play a key role in determining structural properties of large molecules, actively influencing their vibrational spectra. Upon optical excitation, charge oscillation modes can be activated, causing a dramatic change of vdW interactions and introducing non-local stress in the molecular structure. Vibrational modes are thus expected to be activated by energy transfer from optically-excited charge-fluctuation modes. A quantum-mechanical model for the interaction between charge oscillations and vibrational modes is proposed here, based on the many body dispersion (MBD) model, where the problem is reduced to a set of coupled quantum harmonic oscillators. The aim is to study the vibrational modes activation, analyzing the transition between relevant quantum states within a perturbative framework, and to specifically analyze molecular systems such as photo-receptors and host-guest complexes

The Quantum Dynamics of H2 in a C60 Lattice

Since its onset in 1941, matrix isolation has become a popular and common technique for studying species using spectroscopy by isolating them in an inert host solid [1]. Due to the large, spherical shape of the molecules, solid C60 has large interstitial voids making it a good host for matrix isolation. These voids come in two varieties. The larger of the two, the octahedral sites, have an ideal size for studying the dynamics of H2 molecules because the sites are large enough that a hydrogen molecule can be trapped, resulting in quantized translational motion, and can rotate nearly freely within the site. On the other hand, the sites are also small enough that each will contain only one hydrogen molecule thus eliminating H2-H2 interactions. The dynamics of a single hydrogen molecule isolated within the potential well of an octahedral site are very interesting because it represents a real-life example of the famous quantum mechanical situation of a “particle-in-a-box”. While the quantum dynamics of hydrogen within a C60 host lattice is worthy of investigation purely on the basis of the interesting physics involved in the system, there is also a practical importance for gaining a better understanding of the C60-H2, host-guest interaction because of the continuing interest in the possible use of carbon nanostructures as devices for hydrogen storage 3]. Using infrared spectroscopy to study H2 intercalated within a C60 lattice gives insight into the nature of the C60-H2 interaction because H2 is not infrared-active under normal conditions and so the H2 absorption peaks in our spectra are purely due to interaction with the C60 host. Initial results the H2 absorbance spectrum were published in 2002 by Professor Stephen FitzGerald, Scott Forth, and Marie Rinkoski [4]. This paper presents a continuation and a further understanding of using Fourier transform infrared spectroscopy to study the quantum behavior of H2 molecules within the octahedral lattice sites of C60

Fluorescent Silicon Clusters and Nanoparticles

The fluorescence of silicon clusters is reviewed. Atomic clusters of silicon have been at the focus of research for several decades because of the relevance of size effects for material properties, the importance of silicon in electronics and the potential applications in bio-medicine. To date numerous examples of nanostructured forms of fluorescent silicon have been reported. This article introduces the principles and underlying concepts relevant for fluorescence of nanostructured silicon such as excitation, energy relaxation, radiative and non-radiative decay pathways and surface passivation. Experimental methods for the production of silicon clusters are presented. The geometric and electronic properties are reviewed and the implications for the ability to emit fluorescence are discussed. Free and pure silicon clusters produced in molecular beams appear to have properties that are unfavourable for light emission. However, when passivated or embedded in a suitable host, they may emit fluorescence. The current available data show that both quantum confinement and localised transitions, often at the surface, are responsible for fluorescence. By building silicon clusters atom by atom, and by embedding them in shells atom by atom, new insights into the microscopic origins of fluorescence from nanoscale silicon can be expected.Comment: 5 figures, chapter in "Silicon Nanomaterials Sourcebook", editor Klaus D. Sattler, CRC Press, August 201

Computation Vibration Spectroscopy as a Tool for Investigation of Complicated Systems

Short overview for the computation vibration spectroscopy methodology has been done. The main features of the used methods to compute parameters for complete vibration spectra, including inelastic neutron spectroscopy, infrared and Raman, has been described, too. Matrix method to solve inverted vibration problem, its limitation and modifications are discussed. All these algorithms are implemented into software called ''COSPECO''

Microscopic mechanism of structural and volume relaxation below glass transition temperature in a soda-lime silicate glass revealed by Raman spectroscopy and its first principle calculations

To elucidate the atomistic origin of volume relaxation in soda-lime silicate glass annealed below the glass transition temperature (Tg), the experimental and calculated Raman spectra were compared. By decomposing the calculated Raman spectra into a specific group of atoms, we found that the Raman peak at 1050 cm-1 corresponds to bridging oxygen with a small Si-O-Si bond angle. The experimental Raman spectra indicated that, during annealing below Tg, a homogenization reaction Q2+Q4->2Q3 proceeds in the early stage of structural relaxation. Then, the Si-O-Si units with relatively small angles decrease even in the later stages, which is first evidence of ring deformation causing volume relaxation of soda-lime silicate glass because decreasing small Si-O-Si angles corresponds to the reduce of acute O-O-O angle in a ring and can expand the space inside the rings, and Na can be inserted into the ring center. In conclusion the ring deformation and Na displacement is the origin of the volume relaxation of soda-lime silicate glass below Tg.Comment: 15 figures and 1 table for main text, 8 figures and 1 table for supplemental inf

Characterization, Stability, and Transport Through Defects in Graphene Nanoribbons

Graphene nanoribbons (GNRs) constitute a new class of nanostructured materials with unique properties and significant potential for applications. During production of GNRs, defects are generally introduced within the lattice. Assessment of defects\u27 stability and characterization of their effects on GNRs are therefore very important for predicting GNRs performance under realistic circumstances. Here we consider various possible defects, namely the ones caused by removal/addition of carbon atoms from/to the lattice as well as those caused by bond rotation/rearrangement. Our study is based on ab initio geometry optimization and electronic structure calculations. We determine which defects can be stable in graphene nanoflakes and/or GNRs, by calculating the corresponding vibration modes. We further investigate how the presence of defects would modify electronic transport through defected GNRs. Among the defects considered, only some turn out to be stable within the GNR lattice. Transport in presence of defects is generally less compared to the pristine case, however, different defects cause different levels of conductance reduction. We also investigate the effects of a spin-polarized defect on transport characteristics