A new form of electric-field-dependent basis functions for the calculation of electric polarizabilities and dipole moments

An ab-initio molecular orbital theory of electrical polarization is presented in which the molecular orbitals are written as linear combinations of atomic functions which depend explicitly on the strength of a uniform external electric field. The wavefunctions in the presence of such a field are determined using self-consistent field perturbation theory. It is shown that the use of field-dependent atomic functions provides an efficient technique for the calculation of electric polarizability tensors. Polarizability tensors and electric-dipole moments calculated using both a minimal and a split-valence-shell basis set are compared with experimental results. Both polarizability-tensor components and dipole moments are seriously underestimated at the minimal bases-set level. The split-valence basis approach yields substantially better results; the calculated values at this level are in reasonable agreement with the corresponding experimental values. The experimental ordering of isotropic polarizabilities for a set of small molecules is duplicated quite closely by both the minimal and the split-valence-shell calculations.     

The inclusion of electrostatic hydration energies in molecular mechanics calculations

Summary The problem of including solvent effects in molecular mechanics calculations is discussed. It is argued that the neglect of charge-solvent (solvation) interactions can introduce significant errors. The finite difference Poisson-Boltzmann (FDPB) method for calculating electrostatic interactions is summarized and is used as a basis for introducing a new pairwise energy term which accounts for charge-solvent interactions. This term acts between all pairs of atoms usually considered in molecular mechanics calculations and can be easily incorporated into existing force fields. As an example, a parameterization is developed for the CHARMm force field and the results compared to the predictions of the FDPB method. An approach to the realistic incorporation of solvent screening into force fields is also outlined.     

Misphasing of ion motion in quadratic potential induced by space-periodic disturbance

An ideally quadratic potential used in different types of ion mass analyzer such as Paul trap, Kingdon trap and quadratic field reflectron may be space-periodically disturbed due to inaccuracy of fabrication and design features. If ion motion in such devices is computer-simulated, disturbances of potential may be caused by the peculiarity of the computation method. The problem investigated in this work is the effect that weak space-periodic disturbance of a quadratic potential takes on the ion motion in such a potential. The effect of the disturbance we considered is the misphasing of an ion cloud oscillating in a disturbed quadratic potential. A method to evaluate the characteristic misphasing time is presented. For the case of disturbance amplitude being constant along ion trajectories, the designated problem may be considered analytically. If the disturbance amplitude depends on oscillation co-ordinate, the result can be obtained by use of numerical integration. An example of numerical calculation is presented.     

The role of quantum interference in determining transport properties of molecular bridges

An analytical approach to the electron transport phenomena in molecular devices is presented. The analyzed devices are composed of various molecular bridges attached to two semi-infinite electrodes. Molecular system is described within the tight-binding model, while the coupling to the electrodes is analyzed through the use of Newns-Anderson chemisorption theory. The current-voltage (I-V) characteristics are calculated through the integration of transmission function in the standard Landauer formulation. The essential question of quantum interference effect of electron waves is diseussed in three aspects: (i) the geometry of a molecular bridge, (ii) the presence of an external magnetic field and (iii) the location of chemical substituent.     

Some remarks on the SCRF theory of solvent effects and the calculation of proton potentials

Some aspects concerning the self-consistent reaction field theory of solvent effects are discussed. In particular, the variational solution to the non-linear Schrödinger equation is considered; a necessary and sufficient constraint to be added to the standard variational procedure is discussed. The exact solution of the non-linear equation is presented within the molecular orbital approach; correlation defaults to the Hartree-Fock like solutions are stated. Some thermodynamical correspondences are established with the magnitudes calculated with the self-consistent reaction field theory. Finally, we have commented upon the proton potentials calculated within this theory. An INDO calculation of a water trimer has been used as an example to discuss different types of proton translocation potentials.     

Accurate calculation of transport properties for organic molecular semiconductors with spin-component scaled MP2 and modern density functional theory methods

At ambient temperatures, intermolecular hopping of charge carriers dominates the field effect mobility and thus the performance of organic molecular semiconductors for organic-based electronic devices. We have used a wide variety of modern and accurate computational methods to calculate the main parameters associated with charge transport, taking oligoacenes, and its derivatives as the exemplary organic materials. We tackle the problem from a combined inter- and intramolecular approach, in which the parameters are calculated for an isolated single molecule concomitantly with the stability of the dimers found in experimentally determined crystalline structures. Considering that most of the future applications within the field would need a full understanding of the transport mechanism, we assess the reliability of the methods to be employed according to the nature of the problem. Finally, we perform a computationally guided molecular engineering of a new set of materials derived from tetracene (rubrene and highly twisted oligoacenes) which allows to robustly anticipate the reasons for their expected performance in organic-based electronic devices.     

The supermolecule method,as applied to studies of liquid-phase reaction mechanisms taking cyclocarbonate aminolysis in dioxane as an example: specific features

The supermolecule method was used to describe the mechanism of liquid-phase processes taking the reaction of ethylene carbonate with methylamine as an example. Specific features of the approach are considered. The problem of choosing the reference point for calculating the relative energies of individual reaction steps was solved by introducing the idea of the structure of noninteracting solvated reactants. In this case, no basis set superposition error (BSSE) correction is required because the solvated reactants, the pre-reaction complex, and the transition state have the same atomic composition and are calculated in the same basis set. To calculate the title reaction in dioxane by the supermolecule method with acceptable accuracy, it is sufficient to consider one solvent molecule.     

Microfabricated porous glass channels for electrokinetic separation devices

Electrically insulated porous SiO2 channels for electrokinetic separation devices were fabricated based on a mask-less etching process for creation of high aspect ratio needles in silicon. The silicon needles are converted to SiO2 by oxidation and integrated within the interior of a fluidic channel network. The channels are about 5 microm high with a pore size of 0.5+/-0.2 microm. An electrophoretic separation of a mixture of fluorescein and 5-carboxyfluorescein using epi-fluorescence detection was performed to verify proper electrokinetic transport in the porous channels. The plate height was about 170,000 m-1 for a field strength of 170 V cm-1. In the near future, it is intended to extend the fabrication scheme to include an array of porous pillars for capillary electrochromatography experiments.     

Radioactive contaminants in the subsurface: the influence of complexing ligands on trace metal speciation

Equilibrium thermodynamics is one of the pillars which support safety analyses of repositories for radioactive waste. The research summarized in this review deals with approaches to resolve the problems related to thermodynamic equilibrium constants and solubility of solid phases in the field of radioactive waste management. The results have been obtained at the Paul Scherrer Institut between 1995 and 2005 and comprise the scientific basis of the author’s habilitation thesis in the field of nuclear environmental chemistry. The topics are grouped according to three different levels of problem solving strategies: (1) Critical and comprehensive reviews of the available literature, which are necessary in order to establish a reliable chemical thermodynamic database that fulfils the requirements for rigorous modeling of the behavior of the actinides and fission products in the environment. (2) In many case studies involving inorganic and simple organic ligands a serious lack of reliable thermodynamic data is encountered. There, a new modeling approach to estimate the effects of these missing data was applied. This so called “backdoor approach” begins with the question, “What total concentration of a ligand is necessary to significantly influence the speciation, and hence the solubility, of a given trace metal?” (3) In the field of natural organics, mainly humic and fulvic acids, we face an ill-defined problem concerning the molecular structure of the ligands. There, a pragmatic approach for performance assessment purposes was applied, the “conservative roof” approach, which does not aim to accurately model all experimental data, but allows estimates of maximum effects on metal complexation by humic substances to be calculated.     

Thermoresponsive hydrogels with ultrasound-controlled properties

Possibility of creation of materials with transport properties operated by ultrasound on the basis of thermosensitive hydrogels modified by a solid phase of inorganic compounds is shown. The kinetic model of drug release from the hydrogel matrix, which allows to optimize the parameters of ultrasound exposure is proposed. Various options of devices with operated ultrasound an outlet of medicinal substance are offered.     

Analysis on the contribution of molecular orbitals to the conductance of molecular electronic devices

We present a theoretical approach which allows one to extract the orbital contribution to the conductance of molecular electronic devices. This is achieved by calculating the scattering wave functions after the Hamiltonian matrix of the extended molecule is obtained from a self-consistent calculation that combines the nonequilibrium Green's function formalism with density functional theory employing a finite basis of local atomic orbitals. As an example, the contribution of molecular orbitals to the conductance of a model system consisting of a 4,4-bipyridine molecule connected to two semi-infinite gold monatomic chains is explored, illustrating the capability of our approach.     

Time-dependent density functional theory for calculating origin-independent optical rotation and rotatory strength tensors

An approach to calculate origin-independent electronic chiroptical property tensors using time-dependent density functional theory (TDDFT) and gauge-including atomic orbital (GIAO) basis sets is evaluated. Computations of origin-dependent optical rotation tensors and of rotatory strengths needed to simulate circular dichroism spectra are presented. The optical rotation tensor computations employ solutions of coupled perturbed Kohn-Sham equations for a dynamic electric field and a static magnetic field. Because the magnetic field is time independent, the GIAO treatment is somewhat simplified compared to a previously reported method, at some added computational cost if hybrid functionals are employed. GIAO rotatory strengths are also calculated, using transition density matrices from a standard TDDFT excitation energy module. A new implementation in the NWChem quantum chemistry package is employed for representative computations of origin-invariant chiroptical response tensors for methyloxirane, norbornenone, and the ketosteroid androstadienone. For the steroid molecule the vibrational structure of the CD spectrum is modeled explicitly by using calculated Franck-Condon factors. The agreement with experiment is favorable.     

Benchmarking the multipole shielding polarizability/reaction field approach to solvation against QM/MM: applications to the shielding constants of N-methylacetamide

We present a benchmark study of a combined multipole shielding polarizability/reaction field (MSP/RF) approach to the calculation of both specific and bulk solvation effects on nuclear magnetic shielding constants of solvated molecules. The MSP/RF scheme is defined by an expansion of the shielding constants of the solvated molecule in terms of electric field and field gradient property derivatives derived from single molecule ab initio calculations. The solvent electric field and electric field gradient are calculated based on data derived from molecular dynamics simulations, thereby accounting for solute-solvent dynamical effects. The MSP/RF method is benchmarked against polarizable quantum mechanics/molecular mechanics (QM/MM) calculations. The best agreement between the MSP/RF and QM/MM approaches is found by truncating the electric field expansion in the MSP/RF approach at the linear electric field level which is due to the cancelation of errors. In addition, we investigate the sensitivity of the results due to the choice of one-electron basis set in the ab initio calculations of the property derivatives and find that these derivatives are affected by the basis set in a way similar to the shielding constants themselves.     

The coupling constant polarizability and hyperpolarizabilty of 1J(NH) in N-methylacetamide, and its application for the multipole spin-spin coupling constant polarizability/reaction field approach to solvation

We present a benchmark study of a combined multipole spin-spin coupling constant (SSCC) polarizability/reaction field (MJP/RF) approach to the calculation of both specific and bulk solvation effects on SSCCs of solvated molecules. The MJP/RF scheme is defined by an expansion of the SSCCs of the solvated molecule in terms of coupling constant dipole and quadrupole polarizabilities and hyperpolarizabilities derived from single molecule ab initio calculations. The solvent electric field and electric field gradient are calculated based on data derived from molecular dynamics (MD) simulations thereby accounting for solute-solvent dynamical effects. The MJP/RF method is benchmarked against polarizable QM/MM calculations for the one-bond N-H coupling constant in N-methylacetamide. The best agreement between the MJP/RF and QM/MM approaches is found by truncating the electric field expansion in the MJP/RF approach at the linear electric field level. In addition, we investigate the sensitivity of the results due to the choice of one-electron basis set in the ab initio calculations of the coupling constant (hyper-)polarizabilities and find that they are affected by the basis set in a way similar to the coupling constants themselves.     

Hierarchical classification designs for the estimation of different sources of variability in proficiency testing experiments

An approach to the estimation of possible different sources of variation found in proficiency testing experiments is described. Four errors namely, technique, analyst, laboratory and geographical location are considered and calculated by using a rational experimental design based on hierarchical classification. The treatment of the confidence of the design over different experimental arrangements is explored and visualised by calculating a function that depends only on the design and not on the experimental response. An illustrative example based on simulated data is used to show how the theory could be applied in practice.     

Limiting current in a redox system on a vertical electrode under conditions of natural convection

The problem of calculating the limiting current in a redox system on a vertical plane electrode under the natural convection conditions is solved. By way of example, the reaction of ferrocyanide oxidation on platinum in a solution containing a mixture of potassium ferrocyanide and ferricyanide (in excess). An equation for the effective Rayleigh number determining the limiting current is derived by Kármán’s method with allowance made for the migration current of an indifferent electrolyte. Limiting currents in the electrochemical system under study are determined experimentally. The calculated and measured limiting currents are compared.     

Vibronic energies and spectra of molecular dimers

We consider three distinct methods of calculating the vibronic levels and absorption spectra of molecular dimers coupled by dipole-dipole interactions. The first method is direct diagonalization of the vibronic Hamiltonian in a basis of monomer eigenstates. The second method is to use creation and annihilation operators leading in harmonic approximation to the Jaynes-Cummings Hamiltonian. The adiabatic approximation to this problem provides insight into spectral behavior in the weak and strong coupling limits. The third method, which serves as a check on the accuracy of the previous methods, is a numerically exact solution of the time-dependent Schrodinger equation. Using these methods, dimer spectra are calculated for three separate dye molecules and show good agreement with measured spectra.     

MBPT studies of van der Waals molecules. III. The reliability of apparently accurate calculations for the magnesium dimer

The interaction potential for the magnesium dimer is calculated by using the diagrammatic many-body perturbation theory within the framework of the supermolecule approach. Different approximations for the perturbation treatment of the electron correlation effects are analysed with particular emphasis on the results of the complete fourth-order many-body perturbation theory. The influence of the composition of the basis set on the calculated interaction potentials and the basis set superposition effects are investigated. It is concluded that the interaction potentials for van der Waals systems calculated by the supermolecule technique might be highly uncertain because of the basis set superposition effects at the correlated level. The advantages and disadvantages of different methods for the calculation of the energy of weakly interacting systems are discussed in the light of their ability to cope with both the electron correlation problem and the basis set superposition effect.     

Influence of ring position on the temporal dependence of charge movement in a switchable [2]rotaxane

Switchable mechanically interlocked molecular architectures (MIMAs) are promising candidates for the components of nanoscale devices. An example of a MIMA-based switch used in nanoscale devices is the electrochemically switchable Stoddart-Heath-type [2]rotaxane. This system's two coconformations differ in electrical conductance, a feature that has been harnessed for electronic and information storage applications. Herein we study the flow of charge in two coconformations of a bistable Stoddart-Heath-type [2]rotaxane and report statistical predictions of electron transfer times using a probabilistic approach for characterizing the timescale of quantum particle transit. The ratio of predicted transfer times for the two coconformations is consistent with the experimentally reported difference in electrical conductance. Path information offered by the probabilistic method gives insight into the influence of ring position on the mechanism of electron transit in this mechanically interlocked assembly.     

An approach to the interpretation of backpropagation neural network models in QSAR studies

An approach to the interpretation of backpropagation neural network models for quantitative structure-activity and structure-property relationships (QSAR/QSPR) studies is proposed. The method is based on analyzing the first and second moments of distribution of the values of the first and the second partial derivatives of neural network outputs with respect to inputs calculated at data points. The use of such statistics makes it possible not only to obtain actually the same characteristics as for the case of traditional "interpretable" statistical methods, such as the linear regression analysis, but also to reveal important additional information regarding the non-linear character of QSAR/QSPR relationships. The approach is illustrated by an example of interpreting a backpropagation neural network model for predicting position of the long-wave absorption band of cyane dyes.