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Theoretical Studies on Molecular Recognition and Self-Assembly
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Supramolecular chemistry now has become a central part of the research activities. Basically, it mostly concerns molecular recognition and self aggregation by non-covalent weak intermolecular interactions, such as hydrogen bonding, π-π stacking, and van der Waals interactions. The computational applications on such large systems are limited for their structural complexity. Several examples of the computational approaches to understand molecular recognition and self-aggregation are discussed. Firstly, bifunctional (fluorescence and visible light absorption) anion sensing mechanism is supported by the DFT calculations. Secondly, an experimentally observed selective recognition of Cu2+ by an azobenzene-appended receptor, which can exhibit Cu2+ selectivity by color change, is discussed based on computational approach. Finally, the intermolecular interaction, which is useful for predicting the self-assembled structures, can be understood by replicating the monomer unit and manipulating the translation and rotation.
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Rules for Migrating from Entity Relationship (ER) Diagrams to Object Relationship (OR) Diagrams
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In this paper, we provide detailed mapping rules (a methodology) to convert an ER schema into an object relationship (OR) schema. The mapping rules are presented in a manner that will keep as much of the semantics of the database intact, in order to smoothen the important step of data migration from an ER schema to an OR schema. This OR schema should also serve as a conceptual design tool for object-oriented data models, very much like the ER diagrams are a conceptual design tool for relational databases. Since we are mainly discussing the conversion from an ER model to an OR model, we are limiting the discussion in this paper to the structural aspects of the OR model.
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B-spline Method for Solving General Singularly Perturbed Boundary Value Problems Using Fitted Mesh
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In this paper we develop B-spline method for solving a class of Singularly Perturbed two point boundary value problems given as
Ly = εy″ = F(x,y,y′), x ∈ (0,1) (1)
y(0) = ν0 y(1) = ν1, ν0,ν1 ∈ R (2)
We use the Fitted mesh technique to generate piecewise uniform mesh, and use B-spline method which leads to a tridiagonal linear system. In case of non-linear problems we first linearize the equation using Quasilinearization technique and the resulting problem is solved by B-spline. The convergence analysis is given and the method is shown to have uniform convergence. Numerical illustrations are given in the end to demonstrate the efficiency of our method.
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Theoretical Modeling of the N-H and N-D Stretching Bands of Hydrogen-Bonded 1-Methylthymine Crystal and Its Deuterated Form
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Theoretical model for vibrational interactions in the hydrogen bonds in molecular crystals with four molecules forming two centrosymmetric dimers in the unit cell is presented. The model takes into account anharmonic-type couplings between the high-frequency N-H(D) and the low-frequency N…O stretching vibrations in each hydrogen bond, resonance interactions (Davydov coupling) between equivalent hydrogen bonds in each dimer, resonance interdimer interactions within an unit cell and Fermi resonance between the N-H(D) stretching fundamental and the first overtone of the N-H(D) in-plane bending vibrations. The vibrational Hamiltonian, selection rules, and expressions for the integral properties of an absorption spectrum are derived. The model is used for theoretical simulation of the νs stretching bands of 1-methylthymine and its ND derivative at 300 K. The effect of deuteration is successfully reproduced by our model.
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Geometry Optimization of ZnnCdm and (AlTiNi)n Clusters by the Modified Diffusion Monte Carlo Method
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General information about the problem of determining ground-state geometries of atomic clusters has been given. Modified diffusion Monte Carlo (MDMC) method which was recently developed for this problem has been reviewed. A technique, called the rotation operation, has been proposed to escape from local minima. Information about empirical potential energy functions, used in the computations, has been given. Binding energy results for ZnnCdm and (AlTiNi)n clusters obtained by the combination of the MDMC method and the rotation operation have been presented and these results have been compared with the molecular dynamics (MD) results. Efficiency of the method has been investigated by comparing the results and the computation times with the results of the single walker MDMC method - rotation operation combination.
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Exploring Vibrational Optical Activity with PyVib2
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In this work we present a practical example of the automatic correlation of the vibrations of two molecules based on an approach which introduces a new formalism for comparing force fields in cartesian coordinates via the normal modes they entail. We consider two partially deuterated isotopomers of (+)-(R)-1-methylindane, a molecule the absolute configuration of which was successfully verified with vibrational optical activity. The isotopomers are obtained by substituting four hydrogen atoms either in the aromatic or in the aliphatic ring by deuterium atoms. This substitution gives rise to the mixing of the normal modes of the parent system. The automatic correlation of the vibrations will be demostrated with the PyVib2 program.
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Theoretical Design of Optical Switches Using the Spin Transition Phenomenon
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The spin characteristics of octahedrically coordinated Fe(II) compounds are determined from first-principles quantum chemical calculations. Four novel Fe(II) spin transition materials are suggested for use in optical switching applications.
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Understanding Normal Modes of Molecules and Clusters
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Traditional methods for characterizing molecular vibrations were developed for small molecules and are not well suited for understanding nuclear motions of large molecules and of clusters. We present a procedure based on representing normal modes, including translations and rotations, as vectors in 3N dimensional space, where N is the number of nuclei. Double-contracting dyads formed from them allows for a quantitative definition of the overlap and the similarity of nuclear motions of whole molecules, of clusters of molecules, and of arbitrary fragments.
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Structure and Polarizability of Small (GaAs)n Clusters (n= 2, 3, 4, 5, 6, and 8)
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We studied the structure and polarizability of small stoichiometric gallium arsenide clusters (GaAs)n (n= 2, 3, 4, 5, 6 and 8) with conventional ab-initio and density functional methods relying on correlation consistent large-core relativistic pseudo potential basis set. Our results show that computations based on those basis sets yield reasonable results compared to all electron basis sets and the polarizability/atom of small gallium arsenide clusters up to the octamer, is predicted to be larger than the Clausius-Mosotti bulk value.
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Relativistic and Electron Correlation Effects as a Tool for Explaining Some Trends in Molecular Properties and Interactions
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In this paper we discuss relatively routine Douglas–Kroll–Hess spin–free relativistic calculations as a tool for understanding some trends of molecular properties within the series of related molecules. Electron correlation effects are considered by the Coupled Cluster method with iterative treatment of the single and double excitation operators and perturbative treatment of triples, CCSD(T). For our analysis we use accumulated data on relativistic effects on ionization potentials, electron affinities and polarizabilities of the coinage elements, Cu, Ag, and Au and related series like Ia and IIa group elements. Next we analyze electric properties of diatomic molecules as CuF, AgF, and AuF, and compare electric properties and bonding energies of these molecules with intermetalics CuAl, AgAl, AuAl. Electric dipole moments and dipole polarizabilities of the series of oxides including a heavy atom, GeO, SnO, and PbO in their 1Σ ground states are also analyzed. Particular attention is paid to the dissociation energy of PbO and its electron affinity. The bonding character of the MeL series of complexes (Me=Cu, Ag, Au; L=H2O, NH3, and H2S) is explained by stressing the importance of the charge transfer from the lone pair of the ligand to the metal element. Relativistic effects which affect the Me electron affinity and polarizability facilitate understanding the trends of Me interactions with different ligands. We also mention using of the optimized virtual orbital space (OVOS) as an instrument which allows to circumvent problems with proper contraction needed for a specific approximate relativistic Hamiltonian. OVOS allows to reduce the computer time of correlated relativistic calculation by an order of magnitude.
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