All the bound vibrational states of H3+: A reappraisal

Two-dimensional Infrared Spectroscopy Reveals Better Insights of Structure and Dynamics of Protein

Proteins play an important role in biological and biochemical processes taking place in the living system. To uncover these fundamental processes of the living system, it is an absolutely necessary task to understand the structure and dynamics of the protein. Vibrational spectroscopy is an established tool to explore protein structure and dynamics. In particular, two-dimensional infrared (2DIR) spectroscopy has already proven its versatility to explore the protein structure and its ultrafast dynamics, and it has essentially unprecedented time resolutions to observe the vibrational dynamics of the protein. Providing several examples from our theoretical and experimental efforts, it is established here that two-dimensional vibrational spectroscopy provides exceptionally more information than one-dimensional vibrational spectroscopy. The structural information of the protein is encoded in the position, shape, and strength of the peak in 2DIR spectra. The time evolution of the 2DIR spectra allows for the visualisation of molecular motions.

Low-temperature chemistry using the R-matrix method

Techniques for producing cold and ultracold molecules are enabling the study of chemical reactions and scattering at the quantum scattering limit, with only a few partial waves contributing to the incident channel, leading to the observation and even full control of state-to-state collisions in this regime. A new R-matrix formalism is presented for tackling problems involving low- and ultra-low energy collisions. This general formalism is particularly appropriate for slow collisions occurring on potential energy surfaces with deep wells. The many resonance states make such systems hard to treat theoretically but offer the best prospects for novel physics: resonances are already being widely used to control diatomic systems and should provide the route to steering ultracold reactions. Our R-matrix-based formalism builds on the progress made in variational calculations of molecular spectra by using these methods to provide wavefunctions for the whole system at short internuclear distances, (a regime known as the inner region). These wavefunctions are used to construct collision energy-dependent R-matrices which can then be propagated to give cross sections at each collision energy. The method is formulated for ultracold collision systems with differing numbers of atoms.

Structural sensitivity of CH vibrational band in methyl benzoate

The CH vibrational bands of methyl benzoate are studied to understand its coupling pattern with other vibrational bands of the biological molecule. This will facilitate to understand the biological structure and dynamics in spectroscopic as well as in microscopic study. Due to the congested spectroscopic pattern, near degeneracy, and strong anharmonicity of the CH stretch vibrations, assignment of the CH vibrational frequencies are often misleading. Anharmonic vibrational frequency calculation with multidimensional potential energy surface interprets the CH vibrational spectra more accurately. In this article we have presented the importance of multidimensional potential energy surface in anharmonic vibrational frequency calculation and discuss the unexpected red shift of asymmetric CH stretch vibration of methyl group. The CD stretch vibrational band which is splitted to double peaks due to the Fermi resonance is also discussed here.

Vibrational spectroscopy of Methyl benzoate

Methyl benzoate is studied as a model compound for the development of new IR pulse schemes with possible applicability to biomolecules.

Vibrational Levels of Ar4: New Odd-Parity Bosonic States

Vibrational levels of Ar4 are computed using the Lanczos algorithm and a large basis set. We find both even- and odd-parity states with wave functions that are invariant with respect to permutations of the Ar atoms. The odd-parity bosonic levels have not been computed previously. The even-parity levels are close to those obtained using the correlation-function Monte Carlo method (CFMC).

Use of a nondirect-product basis for treating singularities in triatomic rotational–vibrational calculations

A technique has been developed which in principle allows the determination of the full rotational-vibrational eigenspectrum of triatomic molecules by treating the important singularities present in the triatomic rotational-vibrational kinetic energy operator given in Jacobi coordinates and the R(1) embedding. The singular term related to the diatom-type coordinate, R(1), deemed to be unimportant for spectroscopic applications, is given no special attention. The work extends a previous [J. Chem. Phys., 2005, 122, 024101] vibration-only approach and employs a generalized finite basis representation (GFBR) resulting in a nonsymmetric Hamiltonian matrix [J. Chem. Phys., 2006, 124, 014110]. The basis set to be used is obtained by taking the direct product of a 1-D DVR basis, related to R(1), with a 5-D nondirect-product basis, the latter formed by coupling Bessel-DVR functions depending on the distance-type coordinate causing the singularity, associated Legendre polynomials depending on the Jacobi angle, and rotational functions depending on the three Euler angles. The robust implicitly restarted Arnoldi method within the ARPACK package is used for the determination of a number of eigenvalues of the nonsymmetric Hamiltonian matrix. The suitability of the proposed approach is shown by the determination of the rotational-vibrational energy levels of the ground electronic state of H(3)(+) somewhat above its barrier to linearity. Convergence of the eigenenergies is checked by an alternative approach, employing a Hamiltonian expressed in Radau coordinates, a standard direct-product basis, and no treatment of the singularities.

The role of asymptotic vibrational states in H3+

Calculations are discussed which characterize all the vibrational bound states of the H3+ and D2H+ molecular ions using a realistic ab initio potential energy surface. Graphical analysis and calculation of rotational constants show that both ions support a series of atom-diatom-like long-range states: asymptotic vibrational states. The role of these states in the H3+ system and other molecules is discussed. The vibrational calculations are extended above dissociation where the resulting (Feshbach) resonances are shown to be too short-lived to be of importance for the H3+ photodissociation spectrum.

Calculating vibrational energies and wave functions of vinylidene using a contracted basis with a locally reorthogonalized coupled two-term Lanczos eigensolver

We use a contracted basis+Lanczos eigensolver approach to compute vinylidene-like vibrational states of the acetylene-vinylidene system. To overcome problems caused by loss of orthogonality of the Lanczos vectors we reorthogonalize Lanczos vector and use a coupled two-term approach. The calculations are done in CC-HH diatom-diatom Jacobi coordinates which make it easy to compute states one irreducible representation at a time. The most costly parts of the calculation are parallelized and scale well. We estimate that the vinylidene energies we compute are converged to approximately 1 cm(-1).

Treating singularities present in the Sutcliffe-Tennyson vibrational Hamiltonian in orthogonal internal coordinates

Two methods are developed, when solving the related time-independent Schrodinger equation (TISE), to cope with the singular terms of the vibrational kinetic energy operator of a triatomic molecule given in orthogonal internal coordinates. The first method provides a mathematically correct treatment of all singular terms. The vibrational eigenfunctions are approximated by linear combinations of functions of a three-dimensional nondirect-product basis, where basis functions are formed by coupling Bessel-DVR functions, where DVR stands for discrete variable representation, depending on distance-type coordinates and Legendre polynomials depending on angle bending. In the second method one of the singular terms related to a distance-type coordinate, deemed to be unimportant for spectroscopic applications, is given no special treatment. Here the basis set is obtained by taking the direct product of a one-dimensional DVR basis with a two-dimensional nondirect-product basis, the latter formed by coupling Bessel-DVR functions and Legendre polynomials. With the basis functions defined, matrix representations of the TISE are set up and solved numerically to obtain the vibrational energy levels of H3+. The numerical calculations show that the first method treating all singularities is computationally inefficient, while the second method treating properly only the singularities having physical importance is quite efficient.

Vibrational spectroscopy and the development of new force fields for biological molecules

The role of vibrational spectroscopy in the testing of force fields of biological molecules and in the determination of improved force fields is discussed. Analysis shows that quantitative testing of potential energy surfaces by comparison with spectroscopic data generally requires calculations that include anharmonic couplings between different vibrational modes. Applications of the vibrational self-consistent field (VSCF) method to calculations of spectroscopy of biological molecules are presented, and comparison with experiment is used to determine the merits and flaws of various types of force fields. The main conclusions include the following: (1) Potential surfaces from ab initio methods at the level of MP2 yield very satisfactory agreement with spectroscopic experimental data. (2) By the test of spectroscopy, ab initio force fields are considerably superior to the standard versions of force fields such as AMBER or OPLS. (3) Much of the spectroscopic weakness of AMBER and OPLS is due to incorrect description of anharmonic coupling between different vibrational modes. (4) Potential surfaces of the QM/MM (Quantum Mechanics/Molecular Mechanics) type, and potentials based on improved versions of semi-empirical electronic structure theory, which are feasible for large biological molecules, yield encouraging results by the test of vibrational spectroscopy.