Potential energy surface and MULTIMODE vibrational analysis of C2H3+

A full dimensional, ab initio-based semiglobal potential energy surface for C(2)H(3) (+) is reported. The ab initio electronic energies for this molecule are calculated using the spin-restricted, coupled cluster method restricted to single and double excitations with triples corrections [RCCSD(T)]. The RCCSD(T) method is used with the correlation-consistent polarized valence triple-zeta basis augmented with diffuse functions (aug-cc-pVTZ). The ab initio potential energy surface is represented by a many-body (cluster) expansion, each term of which uses functions that are fully invariant under permutations of like nuclei. The fitted potential energy surface is validated by comparing normal mode frequencies at the global minimum and secondary minimum with previous and new direct ab initio frequencies. The potential surface is used in vibrational analysis using the "single-reference" and "reaction-path" versions of the code MULTIMODE.     

Specifying Rewrite Strategies for Interactive Exercises

Strategies specify how a wide range of exercises can be solved incrementally, such as bringing a logic proposition to disjunctive normal form, reducing a matrix, or calculating with fractions. In this paper we introduce a language for specifying strategies for solving exercises. This language makes it easier to automatically calculate feedback, for example when a user makes an erroneous step in a calculation. We can automatically generate worked-out examples, track the progress of a student by inspecting submitted intermediate answers, and report back suggestions in case the student deviates from the strategy. Thus it becomes less labor-intensive and less ad-hoc to specify new exercise domains and exercises within that domain. A strategy describes valid sequences of rewrite rules, which turns tracking intermediate steps into a parsing problem. This is a promising view at interactive exercises because it allows us to take advantage of many years of experience in parsing sentences of context-free languages, and transfer this knowledge and technology to the domain of stepwise solving exercises. In this paper we work out the similarities between parsing and solving exercises incrementally, we discuss generating feedback on strategies, and the implementation of a strategy recognizer.     

New diphosphine ligands based on diphenyl ether for the Pd-catalyzed CO/ethene copolymerization

The catalytic activity and selectivity of palladium(II) complexes of new, flexible bidentate ligands in the CO/ethene copolymerization reaction have been found to change considerably with the steric properties of the ligands.     

Squared error as a measure of perceived phase distortion

Based on two well-known auditory models, it is investigated whether the squared error between an original signal and a phase-distorted signal is a perceptually relevant measure for distortions in the Fourier phase spectrum of periodic signals obtained from speech. Both the performance of phase vector quantizers and the direct relationship between the squared error and two perceptual distortion measures are studied. The results indicate that for small values the squared error correlates well to the perceptual measures. However, for large errors, an increase in squared error does not, on average, lead to an increase in the perceptual measures. Empirical rate-perceptual distortion curves and listening tests confirm that, for low to medium codebook sizes, the average perceived distortion does not decrease with increasing codebook size when the squared error is used as encoding criterion.     

Ro-vibrational spectra of C2H2 based on variational nuclear motion calculations

A published ab initio-based potential energy surface and newly constructed dipole moment surface of acetylene have been used to compute vibrational band intensities. The line intensity calculations employed the variational nuclear motion code WAVR4 for computation of wave functions and energy levels, and a newly developed code DIPOLE4 for computation of dipole transitions. Owing to the high computational cost of J > 0 transitions using direct variational methods only J = 0 and J = 1 states and transitions have been computed variationally. The intensities of J > 1 transitions were extrapolated from J = 0 and J = 1 using Hönl–London coefficients. The resulting effective rotational constants B and transition intensities are compared with experimental data for the (3ν₄ + ν₅) combination band, the ν₃ and the ν₅ fundamental band. The prospects of using this procedure for extensive calculations of a hot line list, important for cool stars and extrasolar planets are discussed.     

Dynamic spatial and structural organization in artificial cells regulates signal processing by protein scaffolding

Structural and spatial organization are fundamental properties of biological systems that allow cells to regulate a wide range of biochemical processes. This organization is often transient and governed by external cues that initiate dynamic self-assembly processes. The construction of synthetic cell-like materials with similar properties requires the hierarchical and reversible organization of selected functional components on molecular scaffolds to dynamically regulate signaling pathways. The realization of such transient molecular programs in synthetic cells, however, remains underexplored due to the associated complexity of such hierarchical platforms. In this contribution, we effectuate dynamic spatial organization of effector protein subunits in a synthetic biomimetic compartment, a giant unilamellar vesicle (GUV), by associating in a reversible manner two fragments of a split luciferase to the membrane. This induces their structural dimerization, which consequently leads to the activation of enzymatic signaling. Importantly, such organization and activation are dynamic processes, and can be autonomously regulated – thus opening up avenues toward continuous spatiotemporal control over supramolecular organization and signaling in an artificial cell.

Engineered artificial cells respond to environmental cues through a pre-programmed enzymatic machinery that induces spatio-structural organization and activation of effector proteins at the lipid membrane.     

Quantum and classical studies of vibrational motion of CH5+ on a global potential energy surface obtained from a novel ab initio direct dynamics approach

We report a full dimensional, ab initio based potential energy surface for CH(5) (+). The ab initio electronic energies and gradients are obtained in direct-dynamics calculations using second-order M?ller-Plesset perturbation theory with the correlation consistent polarized valence triple zeta basis. The potential energy and the dipole moment surfaces are fit using novel procedures that ensure the full permutational symmetry of the system. The fitted potential energy surface is tested by comparing it against additional electronic energy calculations and by comparing normal mode frequencies at the three lowest-lying stationary points obtained from the fit against ab initio ones. Well-converged diffusion Monte Carlo zero-point energies, rotational constants, and projections along the CH and HH bond lengths and the tunneling coordinates are presented and compared with the corresponding harmonic oscillator and standard classical molecular dynamics ones. The delocalization of the wave function is analyzed through comparison of the CH(5) (+) distributions with those obtained when all of the hydrogen atoms are replaced by (2)H and (3)H. The classical dipole correlation function is examined as a function of the total energy. This provides a further probe of the delocalization of CH(5) (+).     

The theoretical prediction of infrared spectra of trans- and cis-hydroxycarbene calculated using full dimensional ab initio potential energy and dipole moment surfaces

Accurate infrared spectra of the two hydroxycarbene isomers are computed by diagonalizing the Watson Hamiltonian including up to four mode couplings using full dimensional potential energy and dipole moment surfaces calculated at the CCSD(T)/cc-pVTZ (frozen core) and CCSD6-311G(**) (all electrons correlated) levels, respectively. Anharmonic corrections are found to be very important for these elusive higher-energy isomers of formaldehyde. Both the energy levels and intensities of stretching fundamentals and all overtone transitions are strongly affected by anharmonic couplings between the modes. The results for trans-HCOHHCOD are in excellent agreement with the recently reported IR spectra, which validates our predictions for the cis-isomers.     

Strip-based regression: A method to obtain comprehensive co-polymer architectures from matrix-assisted laser desorption ionisation-mass spectrometry data

A method aimed to obtain the relative abundances of all molecular species in highly overlapped mass spectra is presented. Its performance is demonstrated with an example of matrix-assisted laser desorption ionization (MALDI) spectra obtained from a polysterene-co-polyisoprene sample, retrieving the full co-polymer architecture. The method is based on a multiple regression operation, applied locally at consecutive regions. The method is designed in such a way that it is not necessary to locate regions in the spectrum that are not influenced by adjacent ones. This increases its applicability, since the method is able to tackle the analysis of highly complex spectra, tending to minimise the need of user intervention. The method allows to correct for non-idealities (such as wrong calibration) or to adjust the variations of spectral resolution with mass. Additionally, the algorithm calculates the precision of the computation in a straightforward way.     

The reduced density matrix method for electronic structure calculations and the role of three-index representability conditions

The variational approach for electronic structure based on the two-body reduced density matrix is studied, incorporating two representability conditions beyond the previously used P, Q, and G conditions. The additional conditions (called T1 and T2 here) are implicit in the work of Erdahl [Int. J. Quantum Chem. 13, 697 (1978)] and extend the well-known three-index diagonal conditions also known as the Weinhold-Wilson inequalities. The resulting optimization problem is a semidefinite program, a convex optimization problem for which computational methods have greatly advanced during the past decade. Formulating the reduced density matrix computation using the standard dual formulation of semidefinite programming, as opposed to the primal one, results in substantial computational savings and makes it possible to study larger systems than was done previously. Calculations of the ground state energy and the dipole moment are reported for 47 different systems, in each case using an STO-6G basis set and comparing with Hartree-Fock, singly and doubly substituted configuration interaction, Brueckner doubles (with triples), coupled cluster singles and doubles with perturbational treatment of triples, and full configuration interaction calculations. It is found that the use of the T1 and T2 conditions gives a significant improvement over just the P, Q, and G conditions, and provides in all cases that we have studied more accurate results than the other mentioned approximations.