Singlet-triplet perturbations in formaldehyde

The magnetic rotation spectrum of formaldehyde in the region of 3260 Å has been studied under high resolution using magnetic flux densities ranging from 80–5000 G. Approximately 40 magnetically sensitive rotational levels have been identified. Matrix elements and possible mechanisms are discussed.     

Periodic perturbations of a polymer

The reduction of the short range translational symmetry of a polymer chain (caused by, for example, the loss of an isoconformational structure) is accommodated as a periodic perturbation in a semi-empirical tight-binding LCAO calculation. Using the results of a calculation on an unperturbed chain in a perturbational mixing procedure an energy matrix can be calculated whose order is equal to (or even less than) that of the unperturbed structure. The method is applied to the generation of various chain conformations from all-trans polyacetylene and is shown to work successfully.     

Bonding charge density from atomic perturbations

Charge transfer among individual atoms is the key concept in modern electronic theory of chemical bonding. In this work, we present a first‐principles approach to calculating the charge transfer. Based on the effects of perturbations of an individual atom or a group of atoms on the electron charge density, we determine unambiguously the amount of electron charge associated with a particular atom or a group of atoms. We computed the topological electron loss versus gain using ethylene, graphene, MgO, and SrTiO₃ as examples. Our results verify the nature of chemical bonds in these materials at the atomic level. © 2015 Wiley Periodicals, Inc.     

Single-molecule charge-transport measurements that reveal technique-dependent perturbations

We compare scanning tunneling microscopy (STM) imaging with single-molecule conductive atomic force microscopy (C-AFM) measurements by probing a series of structurally related thiol-terminated oligo(phenylenevinylene)s (OPVs) designed to have unique charge-transport signatures. When one or two methylene spacers are inserted between the thiol points of attachment and the OPV core, a systematic reduction in the imaged molecular transconductance and the current transmitted through a metal-molecule-metal junction containing the molecule is observed, indicating good agreement between STM and C-AFM measurements. However, a structure where the OPV backbone is interrupted by a [2.2]paracyclophane core has a low molecular transconductance, as determined from STM images, and a high measured single-molecule conductance. This apparent disconnect can be understood by comparing the calculated molecular orbital topology of the OPV with one thiol bound to a gold surface (the geometry in the STM experiment) with the topology of the molecule with both thiol termini bound to gold (relevant to C-AFM). In the former case, a single contact splits low-lying molecular orbitals into two discrete fragments, and in the latter case, molecular orbitals that span the entire molecule are observed. Although the difference in observed conductance between the two different measurements is resolved, the overall set of observations highlights the importance of using combined techniques to better characterize charge-transport properties relevant to molecular electronics.     

Molecular conformation search by distance matrix perturbations

Three-dimensional molecular structure is fundamental in chemical function identification and computer-aided drug design. The enumeration of a small number of feasible conformations provides a rigorous way to determine the optimal or a few acceptable conformations. Our contribution concerns a heuristic enhancement of a method based on distance geometry, typically in relation with experiments of the NMR type. Distance geometry has been approached by different viewpoints; ours is expected to help in several subtasks arising in the process that determines 3D structure from distance information. More precisely, the input to our algorithm consists of a set of approximate distances of varying precision; some are specified by the covalent structure and others by Nuclear Magnetic Resonance (NMR) experiments (or X-ray crystallography which, however, requires crystallization). The output is a valid tertiary structure in a specified neighborhood of the input. Our approach should help in detecting outliers of the NMR experiments, and handles inputs with partial information. Moreover, our technique is able to bound the number of degrees of freedom of the conformation manifold. We have used numerical linear algebra algorithms for reasons of speed, and because they are well-implemented, fully documented and widely available. Our main tools include, besides distance matrices, structure-preserving matrix perturbations for minimizing singular values. Our MATLAB (or SCILAB) implementation is described and illustrated.AMS subject Classification: 92E10 Molecular structure, 92C40 Biochemistry, molecular biology, 65F15 Eigenvalues, eigenvectors, 15A18 Eigenvalues, singular values, and eigenvectors     

Rapid protein-ligand costructures using chemical shift perturbations

Structure-based drug discovery requires the iterative determination of protein-ligand costructures in order to improve the binding affinity and selectivity of potential drug candidates. In general, X-ray and NMR structure determination methods are time consuming and are typically the limiting factor in the drug discovery process. The application of molecular docking simulations to filter and evaluate drug candidates has become a common method to improve the throughput and efficiency of structure-based drug design. Unfortunately, molecular docking methods suffer from common problems that include ambiguous ligand conformers or failure to predict the correct docked structure. A rapid approach to determine accurate protein-ligand costructures is described based on NMR chemical shift perturbation (CSP) data routinely obtained using 2D 1H-15N HSQC spectra in high-throughput ligand affinity screens. The CSP data is used to both guide and filter AutoDock calculations using our AutoDockFilter program. This method is demonstrated for 19 distinct protein-ligand complexes where the docked conformers exhibited an average rmsd of 1.17 +/- 0.74 A relative to the original X-ray structures for the protein-ligand complexes.     

Non-linear relaxation methods: III. Current-controlled perturbations

A functional expression is derived valid for evaluating all orders of perturbation in potential when a current of known profile is super-imposed. Generalised expressions for the distortion and the rectification potential are given. The problems of “iR-drop” and “charging current” compensation are also discussed.     

Half-Heusler phase related structural perturbations near stoichiometric composition FeZnSb

Half-Heusler phases XYZ (Pearson symbol cF12) are chemically versatile and rich in physical properties. The half-Heusler phase in the Fe-Zn-Sb ternary system was reported in the year 2000. In this work, two new ternary phases are identified in the vicinity of the equiatomic composition FeZnSb in the same system: Fe_1−xZnSb (tetragonal, space group P4/nmm, Pearson symbol tP6−δ, Z=2: a=4.1113(6) Å, c=6.0127(12) Å for x=0.08 (1), and a=4.1274(6) Å, c=6.0068(12) Å for x=0.12 (2)); and Fe_7.87Zn_6.72Sb₈ (Fe_0.98Zn_0.84Sb) (3) (cubic, space group Fm-3m, Pearson symbol cF96−δ, Z=4, a=11.690(13) Å). 1 and 2 crystallize in the PbFCl-type structure, and 3 adopts a unique 2×2×2 supercell of a normal half-Heusler structure. The structures of both the tetragonal and cubic phases can be described as assemblies of half-Heusler structure related subunits. Electrical resistivity measurement on the pure sample of 2 shows it has metallic-like behavior, and its thermal and magnetic properties are also characterized.     

Calculating expectations with time-dependent perturbations in quantum Monte Carlo

We show that a small perturbation periodic in imaginary time can be used to compute expectation values of nondifferential operators that do not commute with the Hamiltonian within the framework of quantum diffusion Monte Carlo. Some results for the harmonic oscillator and the helium atom are presented showing the validity of the proposed method.     

Field induced perturbations in the ultraviolet spectrum of s-triazine

It is shown that on application of an external magnetic or electric field, resulting mixing of states enables new transitions to be induced in optical spectra. These transitions behave non-linearly with field, and enable extension of spectroscopic techniques to previously unobserved electronic states. Selection rules for this phenomenon are the same as Raman or two photon spectroscopy.Electric field induced perturbations are observed in several vibronic bands associated with the ν₆ vibration in the ¹E″←¹′_t, transition in s-triazine. Evidence is presented that the states mixed by the field are Jahn-Teller doublets. From observed splittings and field dependence we determine a coupling parameter of D = 0.1 cm⁻¹.     

Electronic states of an infinite polyene under local perturbations

A perturbation theory method is developed in the tight-binding LCAO MO treatment of a one-dimensional polymer under local perturbation with the aid of the Wannier function. As the first step, electronic states of an infinite polyene under a few of significant cases of perturbation are formulated in the scheme of the Hückel MO approach, giving the changes in total energies, electron densities, and bond orders of the perturbed systems.     

Errors in the calculations of first-order and second-order energy perturbations

We consider the calculation of first-order and second-order atomic and molecular properties from approximate ground-state wave-functions by using variational procedures for solving the first- and second-order perturbation equations. We evaluate the errors in the final results due to the error in the unperturbed wave-function and to the errors caused by the approximations in solving the perturbation equations. By combining slightly different results we can eliminate all first-order errors. Our analysis covers situations where perturbation expansions of the error in the ground-state wave-function are not feasible and it includes the effects due to approximations in solving the perturbation equations.     

Hyperconjugative and inductive perturbations in poly(p-phenylene vinylenes)

New polymers having high solid-state fluorescence quantum yields and the ability to tune their electron affinity without effecting their band gap using hyperconjugative interactions is reported. The novel three-dimensional poly(phenylene vinylenes) having [2.2.2] bicyclic ring systems shown were synthesized, and the different hyperconjugative perturbations provide differential fluorescence sensory quenching responses to electron-rich and electron-deficient analytes in solution and solid thin films.