The writhing on the wall: first tentative steps toward a comprehensive theory of liquid crystal surfaces

A Commentary on the paper “Theory of the nematic-isotropic transition in a restricted geometry„, by A. Poniewierski and T.J. Sluckin. First published in Liquid Crystals, 2, 281-311 (1987).     

The writhing on the wall: first tentative steps toward a comprehensive theory of liquid crystal surfaces

A Commentary on the paper ”Theory of the nematic‐isotropic transition in a restricted geometry?, by A. Poniewierski and T.J. Sluckin. First published in Liquid Crystals, 2, 281‐311 (1987).     

Implementation of a microcanonical variational transition state theory for direct dynamics calculations of rate constants

Calculation of microcanonical rate constants has been an important field in chemical dy-namic studies for many years because it can be used not only to give good prediction of rate con-stants in microcanonical assembly, but also to calculate rate constants with certain conserved quantum numbers such as the total angular momentum, and in turn, can be easily converted into thermal rate constants[1—3]. The widely used method for calculating microcanonical rate constants of unimolecular reac-tions…     

Reactive orbital energy theory serving a theoretical foundation for the electronic theory of organic chemistry

It is established that the reactive orbital energy theory (ROET) theoretically reproduces the rule-based electronic theory diagrams of organic chemistry by a comparative study on the charge transfer natures of typical organic carbon–carbon and carbon–heteroatom bond formation reactions: aldol, Mannich, α-aminooxylation, and isogyric reactions. The ROET, which is an expansion of the reaction electronic theories (e.g., the frontier orbital theory) in terms of orbital energies, elucidates the reactive orbitals driving reactions and the charge transferability indices of the reactions. Performing the ROET analyses of these reactions shows that the charge transfer directions given in the rule-based diagrams of the electronic theory are reproduced even for the functional groups of charge transfer destinations in all but only two processes for 38 reaction processes. The ROET analyses also make clear the detailed orbital-based pictures of these bond formation reactions: that is, the use of the out-of-plane antibonding π orbitals in acidic conditions (enol-mode) and in-plane antibonding π orbitals in basic conditions (enolate-mode), which explain the experimentally assumed mechanisms such as the π-bond formations in acidic conditions and σ-bond formations at α-carbons in basic conditions. Furthermore, the ROET analyses explicate that the methyl group initially accepts electrons and then donates them to the bond formations in the target reactions. It is, consequently, suggested that the ROET serves a theoretical foundation for the electronic theory of organic chemistry.     

Some applications of local density functional theory to the calculation of reaction energetics

Summary We report the results of a local density functional investigation of the energetics of some isomerization reactions, involving the conversions of several unsaturated systems to highly strained molecules related to triprismane and tetrahedrane. The program DMol was used at the DNP level to compute the activation barriers and total energy changes associated with these processes. We also show, for more than 70 first- and second-row atoms and molecules, that the errors (non-local corrections) in their energies correlate very well with the number of electrons, within isonuclear series. This should provide a useful empirical means for improving dissociation energies obtained within the local approximation.     

Theoretical studies toward understanding the excited state dynamics of a bichromophoric molecule

By means of the time-dependent density functional theory, the authors study the torsional dynamics of the lowest singlet electronic excited state (S1) of a bichromophoric molecule, 2-(9-anthryl)-1H-imidazo [4,5-f]-phenanthroline (AIP). The intramolecular dynamical relaxation process, the S1 potential energy surface, and the vibrationally resolved electronic absorption and fluorescence spectra are estimated. The results reveal that the strong electron-nuclear coupling leads to a dynamic structural distortion in S1 state so that the mirror-image symmetry of absorption and fluorescence spectra of AIP breaks down. The torsional motion between the donor and acceptor moieties in AIP favors the intramolecular electronic energy transfer process. The transfer rate is dominated by the relaxation time along S1 low-frequency torsional motion.     

Density functional theory for efficient ab initio molecular dynamics simulations in solution

We present a density functional for first-principles molecular dynamics simulations that includes the electrostatic effects of a continuous dielectric medium. It allows for numerical simulations of molecules in solution in a model polar solvent. We propose a smooth dielectric model function to model solvation into water and demonstrate its good numerical properties for total energy calculations and constant energy molecular dynamics.     

Parallelization of a multiconfigurational perturbation theory

In this work, we present a parallel approach to complete and restricted active space second‐order perturbation theory, (CASPT2/RASPT2). We also make an assessment of the performance characteristics of its particular implementation in the Molcas quantum chemistry programming package. Parallel scaling is limited by memory and I/O bandwidth instead of available cores. Significant time savings for calculations on large and complex systems can be achieved by increasing the number of processes on a single machine, as long as memory bandwidth allows, or by using multiple nodes with a fast, low‐latency interconnect. We found that parallel efficiency drops below 50% when using 8–16 cores on the shared‐memory architecture, or 16–32 nodes on the distributed‐memory architecture, depending on the calculation. This limits the scalability of the implementation to a moderate amount of processes. Nonetheless, calculations that took more than 3 days on a serial machine could be performed in less than 5 h on an InfiniBand cluster, where the individual nodes were not even capable of running the calculation because of memory and I/O requirements. This ensures the continuing study of larger molecular systems by means of CASPT2/RASPT2 through the use of the aggregated computational resources offered by distributed computing systems. © 2013 Wiley Periodicals, Inc.     

On the applicability of density functional theory to manganese‐based complexes with catalytic activity toward water oxidation

The present contribution assesses the performance of several popular and accurate density functionals, namely B3LYP, BP86, M06, MN12L, mPWPW91, PBE0, and TPSSh toward manganese‐based coordination complexes. These compounds show promising properties toward application to catalytic water oxidation. Although manganese with N‐ and O‐biding ligands tends to give rise to high spin complexes, the results show that BP86, mPWPW91, and specially MN12L, tend to yield low‐spin complexes. The usage of these functionals for such compounds is, thus, discouraged. All the functionals considered deliver accurate geometries. The present results show, however, that B3LYP delivers geometries deviating from experimental values when compared to the other functionals of the set. M06, PBE0, and TPSSh deliver geometries of similar accuracy, PBE0 outstanding slightly with respect to the other two. © 2017 Wiley Periodicals, Inc.     

Revisiting the foundations of the quantum theory of atoms in molecules: Some open problems

In a series of papers in the last 10 years, various aspects of the mathematical foundations of the quantum theory of atoms in molecules have been considered by this author and his coworkers in some details. Although these considerations answered part of the questions raised by some critics on the mathematical foundations of the quantum theory of atoms in molecules, however, new mathematical problems also emerged during these studies that were reviewed elsewhere [Sh. Shahbazian Int. J. Quantum Chem. 2011 , 111, 4497.]. Beyond mathematical subtleties of the formalism that were the original motivation for initial exchanges and disputes, the questions raised by critics had a constructive effect and prompted the author to propose a novel extension of the theory, now called the multi‐component quantum theory of atoms in molecules [M. Goli, Sh. Shahbazian Theor. Chem. Acc. 2013 , 132, 1365.]. Taking this background into account, in this paper a new set of open problems is put forward that the author believes proper answers to these questions, may open new doors for future theoretical developments of the quantum theory of atoms in molecules. Accordingly, rather than emphasizing on the rigorous mathematical formulation, the practical motivations behind proposing these questions are discussed in detail and the relevant literature are reviewed while when possible, evidence and routes to answers are also provided. The author hopes that proposing these open questions as a compact package may motivate more mathematically oriented people to participate in future developments of the quantum theory of atoms in molecules and its multi‐component version.     

Some late-term thoughts of a density-functional theorist

Fourteen problems are stated within the density-functional theory of molecular electronic structure. Their alleviation will bring the subject closer to maturity. An erratum to this article is available at .     

State conditions transferability of vapor–liquid equilibria via fluctuation solution theory with correlation function integrals from molecular dynamics simulation

The ‘State Conditions Transferability’ category of IFPSC 2006 tests prediction of binary vapor–liquid isotherms for mixtures of ethanol and the refrigerant HFF-227ea (1,1,1,2,3,3,3-heptafluoropropane). We predict these isotherms using fluctuation solution theory (FST). The method is based on isobaric–isothermal molecular dynamics (NPT-MD) simulations, using force field parameters published in the literature and fitted CHARMM force field parameters. Systems studied previously [S. Christensen, G.H. Peters, F.Y. Hansen, J.P. O’Connell, J. Abildskov, Molecular Simulation 33 (2007) 449–457] comprise the nearly ideal benzene/methyl acetate system, and the less ideal benzene/ethanol system at ambient temperatures. Both are at low pressures and remote from the pure component critical points. For the IFPSC system, we have used the same method even though predictions are for conditions remote from those of the provided data, the pressures are elevated, and the temperatures are near the critical temperature of one of the components. We first describe the computational method and thermodynamic modeling for the entry submitted, which assumed the vapor was an ideal gas and no Poynting correction was included. Then we discuss the effects of using common modeling methods to estimate the effects of elevated pressures.     

Outline of a transition-state hydrogen-bond theory

Though the H-bond is well characterized as a D–H:A three-center-four-electron interaction, the formulation of a general H-bond theory has turned out to be a rather formidable problem because of the extreme variability of the bonds formed (for instance, O–HO energies range from 0.1 to 31 kcal mol⁻¹). This paper surveys our previous contributions to the problem, including: (a) the H-bond chemical leitmotifs (CLs), showing that there are only four classes of strong H-bonds and one of moderately strong ones; (b) the PA/pK_a equalization principle, showing that the four CLs forming strong H-bonds are actually molecular devices apt to equalize the acid–base properties (PA or pK_a) of the H-bond donor and acceptor groups; (c) the driving variable of the H-bond strength, which remains so identified as the difference ΔpK_a=pK_AH(D–H)−pK_BH(A–H⁺) or, alternatively, ΔPA=PA(D⁻)−PA(A); and, in particular, (d) the transition-state H-bond theory (TSHBT), which interprets the H-bond as a stationary point along the complete proton transfer pathway going from D–HA to DH–A via the DHA transition state. TSHBT is verified in connection with a series of seven 1-(X-phenylazo)-2-naphthols, a class of compounds forming a strong intramolecular resonance-assisted H-bond (RAHB), which is switched from N–HO to NH–O by the decreasing electron-withdrawing properties of the substituent X. The system is studied in terms of: (i) variable-temperature X-ray crystallography; (ii) DFT emulation of stationary points and full PT pathways; (iii) Marcus rate-equilibrium analysis correlated with substituent LFER Hammett parameters.     

Molecular dynamics simulation and density functional theory insight into the cocrystal explosive of hexaazaisowurtzitane/nitroguanidine

Theoretical methods involving molecular dynamics (MD) simulation and density functional theory were performed to investigate the different molecular ratios, mechanical Properties, structure, trigger bond, and intermolecular interaction of hexaazaisowurtzitane (CL‐20)/nitroguanidine (NQ) cocrystal explosive. Results of MD simulation show that CL‐20 and NQ packed in ratios of 1:1 present the larger binding energy and better mechanical properties than any other molecular ratios, which indicates 1:1 cocrystal can form the stable crystal structure. Shorter length and larger dissociation energy of trigger bond in composite structure than in isolated CL‐20 component suggests that the cocrystal may exhibit less sensitive than CL‐20. Analyses of atoms in molecules, reduced density gradient, and natural bond orbital confirm that intermolecular interactions are mainly derived from a series of weak hydrogen bond and strong vdW forces, involving of NH···O, CH···O, CH···N, O···N, and O···O. Additionally, composite structures of 2 and 3 bringing us more attractive performance will act as a key role in constructing of CL‐20/NQ cocrystal explosive. © 2015 Wiley Periodicals, Inc.     

The dynamics of band (peak) shape development in capillary zone electrophoresis in light of the linear theory of electromigration

The continuity equations that describe the movement of ions in liquid solutions under the influence of an external stationary electric field, as it is utilized in electrophoresis, were introduced a long time ago starting with Kohlrausch in 1897. From that time on, there have been many attempts to solve the equations and to discuss the results. In electrophoresis, special attention has always been devoted to the peak shapes obtained by the detector since the shapes have a tight connection with the phenomena taking place during electromigration and influence the efficiency and selectivity of the separation. Among these phenomena, the most important is electromigration dispersion. In this commented review paper, we compare various models of electromigration, try to find points that connect them, and discuss the range of their validity in light of the linear and nonlinear theory of electromigration.     

On a formal treatment of the Rayleigh-Schrödinger perturbation theory

The formal treatment of the Rayleigh-Schrödinger perturbation theory based on a first-order iteration procedure as described in a previous publication is discussed with reference to the properties of the terms of a Taylor series. The formalism is generalized to allow for multiple perturbation.     

Evaluation of a spectroscopic tandem method using information theory

To obtain vital spectroscopic data, a specific tandem spectroscopic method consisting of excitation in the DC are separated from the evaporation process was applied. Recently developed tandem spectroscopic methods require a complex evaluation process that can be described by metrological characteristics and from them derived parameters. Evaluation of the novel method optimization process is a part of the application of some chosen, specific, and generally accepted statistical methods. For this purpose, it is suitable to determine parameters of the information theory. It is necessary to compare experimental parameters of the information theory with tolerance parameters representing the values which are supposed to be achieved. To evaluate the given parameters, influence of the concentration range used was taken into account.     

A nuclear magnetic resonance study of dynamics in toluene-polyisobutylene solutions: 1. Penetrant diffusion and Fujita theory

The self-diffusion coefficients of toluene in polyisobutylene (PIB) solutions were determined using the pulsed field gradient nuclear magnetic resonance technique. The volume fraction of toluene in the polymer was varied from 0.045 up to 0.712 and the temperature was varied from 225 K up to 368 K. The concentration dependence of the data was interpreted using the Fujita free volume theory and the temperature dependence was interpreted with the WLF equation. These models describe separately the concentration and temperature dependencies of the toluene self-diffusion coefficients very well and the resulting free volume parameters are in good agreement with the ones extracted from the analysis of viscosity data on the same system. ©1995 John Wiley & Sons, Inc.     

Exploring odd-even effects of simple oligomer-like DRCNnT series: a study based on density functional theory/time-dependent density functional theory calculations

Odd-even effects of short-circuit current density and power conversion efficiency (PCE) are an interesting phenomenon in some organic solar cells. Although some explanations have been given, why they behave in such a way is still an open question. In the present work, we investigate a set of acceptor-donor-acceptor simple oligomer-like small molecules, named the DRCNnT (n = 5-9) series, to give an insight into this phenomenon because the solar cells based on them have high PCE (up to 10.08%) and show strong odd-even effects in experiments. By modeling the DRCNnT series and using density functional theory, we have studied the ground-state electronic structures of the DRCNnT (n = 5-9) series in condensed phase. The calculated results reproduce the experimental trends well. Furthermore, we find that the exciton-binding energies of the DRCNnT series may be one of the key parameters to explain this phenomenon because they also show odd-even effects. In addition, by studying the effects of alkyl branch and terminal group on odd-even effects of dipole moment, we find that eliminating one or two alkyl branches does not break the odd-even effects of dipole moments, but eliminating one or two terminal groups does. Finally, we conclude that removing one alkyl branch close to the terminal group of DRCN5T can decrease highest occupied molecular orbital (HOMO) energy (thus increasing open circuit voltage) and increase dipole moment (thus enhancing charge separation and short-circuit current). This could be a new and simple method to increase the PCE of DRCN5T-based solar cells.