Two topological approaches to resonance energy and the relation between them

Two of the present authors recently put forward a novel approach to resonance energy which is based on a similar topological reasoning as a previously elaborated resonance energy concept. It is shown that these two approaches are not completely equivalent. Several other properties of the new resonance energy are pointed out.     

Excitonic coupling in polythiophenes: comparison of different calculation methods

In conjugated polymers the optical excitation energy transfer is usually described as Forster-type hopping between so-called spectroscopic units. In the simplest approach using the point-dipole approximation the transfer rate is calculated based on the interaction between the transition dipoles of two spectroscopic units. In the present work we compare this approach with three others: The line-dipole approximation, the Coulomb integral between the transition densities, and a quantum-chemical calculation of the interacting dimer as entity. The latter two approaches are based on the semiempirical method ZINDO. The line-dipole approximation is an attractive compromise between computational effort and precision for calculations of the excitonic coupling in extended conjugated polymers.     

Theory of vibronic interactions in D2 and H2: a comparison between multichannel-quantum-defect and coupled-equation approaches

New experimental energy levels for the 2pπC(1)Π(u)(-) state of D(2) are reported extending up to the dissociation limit and including rotational quantum numbers up to N = 10. These data are extracted from recent high resolution optical emission spectra, and they are used for a detailed comparison of two theoretical approaches, both of which are fully ab initio and are based on the same state-of-the-art clamped-nuclei potential energy curves. These are the coupled differential equations (CE) and the multichannel quantum defect theory (MQDT) approaches, each of which accounts for adiabatic corrections and non-adiabatic couplings. Both theoretical approaches reproduce the experimental levels to within a fraction of a wavenumber unit (cm(-1)) for the lower vibrational quantum numbers, with the MQDT surpassing the CE method. As the dissociation limit is approached, the residuals observed-calculated increase up to several cm(-1) and the MQDT method is up to a factor of two less accurate than the CE method. The same analysis is carried out with existing data for the H(2) isotopomer and yields similar results. An analogous comparison is also made for the 3pπD(1)Π(u)(-) and 4pπD('1)Π(u)(-) states for both isotopomers, where the MQDT is found to be superior to the CE approach.     

Analysis of molecular shape changes along reaction paths

In this work, a detailed discussion and illustrative example are given for a new conceptual approach to the notion of similarity between nuclear configurations. We analyze the changes in molecular shape, as described by a topological characterization of molecular envelope surfaces, along reaction paths. This approach provides an independent definition of formal species along the path, defined in terms of molecular shape, rather than based on the curvature properties of the potential energy function. The two approaches are compared in this work, using the [1,3] hydrogen-shift in formic acid as an illustrative example. The reaction is studied at SCF and MP 2 ab initio levels. Although the actual reaction paths are different, the molecular shape changes encountered along them are similar, indicating that the essential shape changes provide chemical information on a more fundamental level than do detailed reaction paths.     

Toward a consistent treatment of polarization in model QM/MM calculations

The concept of model chemistries within hybrid QM/MM calculations has been addressed through analysis of the polarization energy determined by two distinct approaches based on (i) induced charges and (ii) induced dipoles. The quantum mechanical polarization energy for four configurations of the water dimer has been determined for a range of basis sets using Morokuma energy decomposition analysis. This benchmark value has been compared to the fully classical polarization energy determined using the induced dipole approach, and the molecular mechanics polarization energy calculated using induced charges within the MM region of hybrid QM/MM calculations. From the water dimer calculations, it is concluded that the induced charge approach is consistent with medium sized basis set calculations whereas the induced dipole approach is consistent with large basis set calculations. This result is highly relevant to the concept of QM/MM model chemistries.     

A tutorial comparison of the NMRIT and LAOCOON approaches for analyses of complex solution‐phase nuclear magnetic resonance spectra

For spin ½ nuclei the two most frequently used iterative approaches for determinations of NMR chemical shifts (h_i) and coupling constants (J_i), NMRIT and LAOCOON, are discussed. When multiple pulse techniques for extraction of these parameters fail or lead to complicated spectra in the cases of very strongly coupled spin systems and systems involving magnetically nonequivalent, chemical shift equivalent nuclei, recourse to these iterative methods is necessary. The former approach employs the energy levels derived from the observed transition frequencies, whereas the latter approach uses the observed transition frequencies. Derivations of the general iterative equations for both approaches are given, along with the specific equations for the ABC spin system. The matrix nature of the derivation of these equations is stressed. Also discussed is the modified NMRIT program, NMRENIT, which has major advantages over the former in cases with symmetry and in cases where not enough lines can be assigned to link all the energy levels. The advantages of the latter program over LAOCOON in certain cases are discussed. Some general advice on the use of both approaches is presented. The Hoffman energy level approach is also discussed and it is shown that it yields the same iterative equations as the LAOCOON approach. Copyright © 2002 John Wiley & Sons, Ltd.     

Flexible polyelectrolyte simulations at the Poisson-Boltzmann level: a comparison of the kink-jump and multigrid configurational-bias Monte Carlo methods

We present a new approach for simulating the motions of flexible polyelectrolyte chains based on the continuous kink-jump Monte Carlo technique coupled to a lattice field theory based calculation of the Poisson-Boltzmann (PB) electrostatic free energy "on the fly." This approach is compared to the configurational-bias Monte Carlo technique, in which the chains are grown on a lattice and the PB equation is solved for each configuration with a linear scaling multigrid method to obtain the many-body free energy. The two approaches are used to calculate end-to-end distances of charged polymer chains in solutions with varying ionic strengths and give similar numerical results. The configurational-bias Monte Carlo/multigrid PB method is found to be more efficient, while the kink-jump Monte Carlo method shows potential utility for simulating nonequilibrium polyelectrolyte dynamics.     

Noise reduction method for molecular interaction energy: application to in silico drug screening and in silico target protein screening

We developed a new method to improve the accuracy of molecular interaction data using a molecular interaction matrix. This method was applied to enhance the database enrichment of in silico drug screening and in silico target protein screening using a protein-compound affinity matrix calculated by a protein-compound docking software. Our assumption was that the protein-compound binding free energy of a compound could be improved by a linear combination of its docking scores with many different proteins. We proposed two approaches to determine the coefficients of the linear combination. The first approach is based on similarity among the proteins, and the second is a machine-learning approach based on the known active compounds. These methods were applied to in silico screening of the active compounds of several target proteins and in silico target protein screening.     

Entropy-energy decomposition from nonequilibrium work trajectories

We derive expressions for the equilibrium entropy and energy changes in the context of the Jarzynski equality relating nonequilibrium work to equilibrium free energy. The derivation is based on a stochastic path integral technique that reweights paths at different temperatures. Stochastic dynamics generated by either a Langevin equation or a Metropolis Monte Carlo scheme are treated. The approach enables the entropy-energy decomposition from trajectories evolving at a single-temperature and does not require simulations or measurements at two or more temperatures. Both finite difference and analytical formulae are derived. Testing is performed on a prototypical model system and the method is compared with existing thermodynamic integration and thermodynamic perturbation approaches for entropy-energy decomposition. The new formulae are also put in the context of more general, dynamics-independent expressions that derive from either a fluctuation theorem or the Feynman-Kac theorem.     

Calculation of solvation and binding free energy differences between VX-478 and its analogs by free energy perturbation and AMSOL methods

Summary VX-478 belongs to a novel class of HIV-1 protease inhibitors that are based on N,N-disubstituted benzene sulfonamides. Force field parameters for the N,N-dialkyl benzene sulfonamide moiety have been assembled from the literature and from our own ab initio calculations. These parameters were employed to calculate solvation and binding free energy differences between VX-478 and two analogs. The free energy perturbation method has been used to determine these differences using two approaches. In the first approach, intergroup interaction terms only were included in the calculation of free energies (as in most reports of free energy calculations using AMBER). In the second approach, both the inter- and intragroup interaction terms were included. The results obtained with the two approaches are in excellent agreement with each other and are also in close agreement with the experimental results. The solvation free energies of N,N-dimethyl benzene sulfonamide derivatives (truncated models of the inhibitors), calculated using continuum solvation (AMSOL) methods, are found to be in qualitative agreement with the experimental and free energy perturbation results. The binding and solvation free energy results are discussed in the context of structure-based drug design to show how physicochemical properties (for example aqueous solubilities and bioavailabilities) of these HIV-1 protease inhibitors were improved, while maintaining their inhibitory potency.     

Comparative studies of quasi-relativistic density functional methods for the description of lanthanide and actinide complexes

We present a comparative Density Functional Theory (DFT) study based on two different implementations of relativistic effects within the Kohn-Sham (KS) approach, to describe the metal-ligand interaction in I(3)M-L complexes (L = NH(3), NCCH(3), CO and M = La, Nd, U). In the first model, the scalar corrections were included by a quasi-relativistic approach (QR) via the so-called ZORA or Pauli Hamiltonians, while in the second, these effects are taken into account in a quasi-Relativistic Effective Core Potential (RECP). These relativistic approaches were used in conjunction with various gradient corrected (GGA) or hybrid (SCH) functionals. The structural parameters obtained from geometry optimizations have been compared to experimental structural trends, and rationalized by a KS orbital analysis. Both approaches provide similar results for mainly ionic metal-ligand bonds (e.g., for the sigma-donor ligand L = NH(3)). For the pi-acceptor ligands (NCCH(3), CO), the QR approach is in agreement with experimental trends and consistent with the presence of a backbonding interaction between U(III) and the neutral ligand, which does not exist in the lanthanide homologues. The GGA/RECP methods also reproduce this phenomenon, while the SCH/RECP scheme fails to describe this interaction. The role of the RECP, of its size, and of additional polarization functions has also been examined. Finally, the failure of the SCH/RECP approach was interpreted as a consequence of a bad estimation of frontier orbital energy levels in the uranium and ligand species.     

Chemical shift anisotropic mapping of a coherent optical absorber using magnetic field induced quantum beats

A new method for mapping the spatial structure of optical coherent materials which relies on imposing a set of linear orthogonal gradient magnetic fields for a controlled hyperfine splitting of energy levels to create characteristic quantum beats when illuminated with a laser pulse with sufficient bandwidth to excite these levels is proposed. In this approach, a spectroscopic fingerprint of the dopant sites due to concentration and field susceptibilities in the sample is achieved through a Fourier decomposition of the radiative relaxation decay in an approach analogous to nuclear magnetic resonance spectroscopy due to the imposition of a controlled spatial-spectral encoding scheme. A three pulse sequence necessary to interrogate a gradient resolved voxel is also discussed. This three pulse approach can be combined with the conventional confocal imaging technique to provide information about the underlying chemistry of dopant distribution along each imaging plane which is useful in guiding the design and manufacturing process of optical crystals. In combination with gradient induced quantum beats, the entire inhomogeneous bandwidth can be interrogated. The proposed approach would scan this entire bandwidth at much faster rate enabling characterization of a large number of crystals than is currently possible through mechanical scanning with a confocal microscopy based spectroscopic technique as well as providing functional dopant profiling which is not currently possible with conventional approaches.     

An efficient fragment-based approach for predicting the ground-state energies and structures of large molecules

An efficient fragment-based approach for predicting the ground-state energies and structures of large molecules at the Hartree-Fock (HF) and post-HF levels is described. The physical foundation of this approach is attributed to the "quantum locality" of the electron correlation energy and the HF total energy, which is revealed by a new energy decomposition analysis of the HF total energy proposed in this work. This approach is based on the molecular fractionation with conjugated caps (MFCC) scheme (Zhang, D. W.; Zhang, J. Z. H. J. Chem. Phys. 2003, 119, 3599), by which a macromolecule is partitioned into various capped fragments and conjugated caps formed by two adjacent caps. We find that the MFCC scheme, if corrected by the interaction between non-neighboring fragments, can be used to predict the total energy of large molecules only from energy calculations on a series of small subsystems. The approach, named as energy-corrected MFCC (EC-MFCC), computationally achieves linear scaling with the molecular size. Our test calculations on a broad range of medium- and large molecules demonstrate that this approach is able to reproduce the conventional HF and second-order Moller-Plesset perturbation theory (MP2) energies within a few millihartree in most cases. With the EC-MFCC optimization algorithm described in this work, we have obtained the optimized structures of long oligomers of trans-polyacetylene and BN nanotubes with up to about 400 atoms, which are beyond the reach of traditional computational methods. In addition, the EC-MFCC approach is also applied to estimate the heats of formation for a series of organic compounds. This approach provides an appealing approach alternative to the traditional additivity rules based on either bond or group contributions for the estimation of thermochemical properties.     

Possible Mechanisms of String Formation in Complex Plasmas at Elevated Pressures

Possible mechanisms of particle attraction providing formation of the field aligned microparticle strings in complex plasmas at elevated gas pressures are theoretically investigated in the light of the Plasmakristall-4 (PK-4) experiment on board the International Space Station. The particle interaction energy is addressed by two different approaches: (i) using the dynamically screened wake potential for small Mach numbers derived by Kompaneets et al., in 2016, and (ii) introducing effect of polarization of the trapped ion cloud by discharge electric fields. Is is found that both approaches yield the particle interaction energy which is independent of the operational discharge mode. In the parameter space of the performed experiments, the first approach can provide onset of the particle attraction and string formation only at gas pressures higher than 40–45 Pa, whilst the mechanism based on the trapped ion effect yields attraction in the experimentally important pressure range 20–40 Pa and may reconcile theory and observations.     

Production of certified reference materials for mycotoxins: IRMM’s view on the assessment of uncertainties

Analytical difficulty and the economic importance of controlling mycotoxin levels in food and feed led the Community Bureau of Reference (BCR) to prepare a series of certified reference materials (CRM) for various mycotoxins. Because of the wide acceptance of these CRM and the need to ensure the comparability and traceability of measurements in the future it is necessary to prepare and certify new batches of mycotoxin reference materials (RM). In the following text two different approaches for evaluation of the characterisation uncertainty of CRM will be compared using the certification of aflatoxin M₁ (AfM₁) in milk powder as an example. The conventional approach is based on evaluation of characterisation exercise data; the alternative approach is based on measurement uncertainties of the employed analytical methods. Because laboratories are using totally different approaches to estimate the measurement uncertainties, combination of the uncertainties obtained from the participating laboratories was not recommended. Therefore, a new integrated approach for assessment of the measurement uncertainties of the analytical methods on the basis of additional data collected during the characterisation exercise will be described. The conventional approach was found to be the most appropriate and economical approach to evaluate the characterisation uncertainty as a characterisation exercise must be performed anyway to establish the property values of candidate (C)RM, irrespective of whether or not reliable measurement uncertainties can be provided by the laboratories. An integrated approach for assessment of measurement uncertainties based on additional characterisation data as applied here to enable use of an uncertainty-based approach provides more information but is too time-consuming and cost-intensive to become common practice.     

Innenrücktitelbild: Developing Conjugated Polymers with High Electron Affinity by Replacing a C?C Unit with a B←N Unit (Angew. Chem. 12/2015)

The key parameters of conjugated polymers are lowest unoccupied molecular orbital (LUMO) and highest occupied molecular orbital (HOMO) energy levels. Few approaches can simultaneously lower LUMO and HOMO energy levels of conjugated polymers to a large extent (>0.5 eV). Disclosed herein is a novel strategy to decrease both LUMO and HOMO energy levels of conjugated polymers by about 0.6 eV through replacement of a C C unit by a B←N unit. The replacement makes the resulting polymer transform from an electron donor into an electron acceptor, and is proven by fluorescence quenching experiments and the photovoltaic response. This work not only provides an effective approach to tune the LUMO/HOMO energy levels of conjugated polymers, but also uses organic boron chemistry as a new toolbox to develop conjugated polymers with high electron affinity for polymer optoelectronic devices.     

Developing Conjugated Polymers with High Electron Affinity by Replacing a CC Unit with a B←N Unit

The key parameters of conjugated polymers are lowest unoccupied molecular orbital (LUMO) and highest occupied molecular orbital (HOMO) energy levels. Few approaches can simultaneously lower LUMO and HOMO energy levels of conjugated polymers to a large extent (>0.5 eV). Disclosed herein is a novel strategy to decrease both LUMO and HOMO energy levels of conjugated polymers by about 0.6 eV through replacement of a C? C unit by a B←N unit. The replacement makes the resulting polymer transform from an electron donor into an electron acceptor, and is proven by fluorescence quenching experiments and the photovoltaic response. This work not only provides an effective approach to tune the LUMO/HOMO energy levels of conjugated polymers, but also uses organic boron chemistry as a new toolbox to develop conjugated polymers with high electron affinity for polymer optoelectronic devices.     

Comparison of global models of sub-bituminous coal devolatilization by means of thermogravimetric analysis

Coal gasification and combustion are strongly dependent on devolatilization step. Aim of this work is to obtain the parameters of global kinetics of devolatilization of a sub-bituminous coal with high sulfur content. The kinetic parameters are obtained by means of TG experimental data, and applying different approaches to extrapolate the data to industrial relevant conditions. The simpler method is a model-free one which supposes a single step process whose Arrhenius kinetic parameters (A and E _a) have to be determined. Another common approach is the distributed activation energy model (DAEM) which assumes a series of first order parallel reactions occurring and sharing the same pre-exponential factor, A, with a continuous distribution of the activation energy. For the fitting of the experimental data, a numerical solution to DAEM and two approximate methods have been evaluated. Moreover, the results of these kinetic methods based on empirical approaches were compared with simulated data obtained using a more complex model based on percolation theory with cross-linking mechanism and vapor–liquid equilibrium (chemical percolation devolatilization, CPD model), which allows to simulate the coal pyrolysis from volatile yield data.     

Adsorption energy distribution from the Aranovich-Donohue lattice density functional theory

We propose a new methodology projected for the estimation of the adsorption energy distribution from the monolayer part of a single nitrogen adsorption isotherm determined at 77 K based on the lattice density functional theory (DFT) via the Aranovich-Donohue formalism. At first sight, the presented approach is computationally more difficult than a classical one. However, it is more flexible and comprehensible. Next, we developed a numerical program and used it for the estimation of the adsorption energy distribution from the experimental data on carbon black samples. The main nitrogen molecule-carbon black surface interaction energy can be estimated as approximately 7-8 kJ/mol, but the heterogeneity of the investigated materials differs significantly. Furthermore, we compare the results obtained from the lattice DFT via the Aranovich-Donohue formalism with the solution of the integral equation with the kernel represented by the classical monolayer localized Fowler-Guggenheim isotherm equation. The similarity between these two independent approaches is observed. The proposed methodology can be used for the investigation of the energetic heterogeneity of not only the carbonaceous materials but also the other "flat-surfaced" solids.