We present an all atom potential energy function for the simulation of proteins and nucleic acids. This work is an extension of the CH united atom function recently presented by S.J. Weiner et al. J. Amer. Chem. Soc., 106, 765 (1984). The parameters of our function are based on calculations on ethane, propane, n−butane, dimethyl ether, methyl ethyl ether, tetrahydrofuran, imidazole, indole, deoxyadenosine, base paired dinucleoside phosphates, adenine, guanine, uracil, cytosine, thymine, insulin, and myoglobin. We have also used these parameters to carry out the first general vibrational analysis of all five nucleic acid bases with a molecular mechanics potential approach.

An all atom force field for simulations of proteins and nucleic acids.

https://www.pci.uni-heidelberg.de/tc/usr/mctdh/lit/rev.pdf

The multiconfiguration time-dependent Hartree (MCTDH) method: a highly efficient algorithm for propagating wavepackets

Mise au point. Theorie des effets de couplage vibronique multimodes. Probleme a 2 etats. Couplage vibronique mettant en jeu des modes et des etats degeneres. Effets du couplage vibronique multimodes en spectroscopie. Comportement statistique des niveaux d'energie vibroniques. Intersections coniques et evolution temporelle de la fluorescence

Multimode molecular dynamics beyond the Born-Oppenheimer approximation

https://www.physik.uni-augsburg.de/theo1/hanggi/Papers/213.pdf

Driven quantum tunneling

A new method for the calculation of bound state eigenvalues and eigenfunctions of the Schrodinger equation is presented. The Fourier grid Hamiltonian method is derived from the discrete Fourier transform algorithm. Its implementation and use is extremely simple, requiring the evaluation of the potential only at certain grid points and yielding directly the amplitude of the eigenfunctions at the same grid points.

The Fourier grid Hamiltonian method for bound state eigenvalues and eigenfunctions

A simple method using the techniques of transformation theory for the generation of the matrix elements of unusual potential functions for one‐dimensional quantum‐mechanical problems is described. It is applicable both to functions which exist as a set of points, for example, a curve or table, as well as to those in explicit form. Some representative calculations have been made for anharmonic oscillators.

/pdf/calculation-of-matrix-elements-for-one-dimensional-quantum-1hybk3v12z.pdf

Calculation of Matrix Elements for One‐Dimensional Quantum‐Mechanical Problems and the Application to Anharmonic Oscillators

The microwave spectrum of tetrahydrofuran has been studied. Nine complete rotational spectra have been observed. These arise from the ground and eight excited states. All of these states are less than 200 cm−1 from the ground state. The rotational constants and dipole moments exhibit a strong nonlinear dependence on the quantum number of the excited state. Vibration–rotation interaction is strong and the spectra of the first four states deviate from that of rigid rotor spectra. These deviations permit the determination of two energy separations: Δ01 = 0.67 cm−1 and Δ23 = 1.5 cm−1. All of the results are interpreted in terms of a model of restricted pseudorotation with a potential function of [30(1‐cos2φ) / 2] + [40(1‐cos4φ) / 2] cm−1, where φ is the angle of pseudorotation. The dipole moment varies from 1.52 to 1.76 D depending upon the pseudorotation state. The details of this variation indicate that the twisted configuration is at lower energy than the bent configuration.

Ring Puckering in Five‐Membered Rings. II. The Microwave Spectrum, Dipole Moment, and Barrier to Pseudorotation in Tetrahydrofuran

As a general introduction to a subsequent series of papers on pseudorotation and five‐membered rings, the two‐ring puckering modes of a five‐membered ring are discussed in general terms. Five cases are separated depending upon the nature of the potential function for each mode. Correlation diagrams connecting the various cases are given. Consistent with our basic policy, we have gone directly from fundamental theory to an arithmetical development using large digital computers. The classical section of this development is outlined. The quantum‐mechanical section is developed in the following paper.

Ring Puckering in Five‐Membered Rings. I. General Theory

Refinements in the experimental application of the energy‐distribution‐difference (EDD) method for resolving fine structure in ionization‐efficiency curves are presented. These include data acquisition and computer‐processing techniques by which first‐differential EDD curves can be obtained with a good signal‐to‐noise ratio. Using these techniques, a study has been made of the fine structure observed in the first‐differential EDD ionization‐efficiency curves of C2H2+ and Xe+ near their thresholds. Distinct “steps” are resolved in the first‐differential ionization‐efficiency curve of C2H2+. The energy separations between these steps agree quite well with energy separations between vibrational levels of the C2H2+ ion determined by photoionization techniques. However, the relative cross sections for these processes determined by electron impact are drastically different from those reported for photoionization. Possible explanations for these differences are discussed. The electron‐impact results for xenon in...

Gail G. Engerholm

Papers

Calculation of Matrix Elements for One‐Dimensional Quantum‐Mechanical Problems and the Application to Anharmonic Oscillators

Ring Puckering in Five‐Membered Rings. II. The Microwave Spectrum, Dipole Moment, and Barrier to Pseudorotation in Tetrahydrofuran

Ring Puckering in Five‐Membered Rings. I. General Theory

Fine Structure in Energy‐Distribution‐Difference Ionization‐Efficiency Curves

Microwave spectrum and pseudorotation in tetrahydrofuran.