Vibronic coupling simulations for linear and nonlinear optical processes: simulation results

A vibronic coupling model based on time-dependent wavepacket approach is applied to simulate linear optical processes, such as one-photon absorbance and resonance Raman scattering, and nonlinear optical processes, such as two-photon absorbance and resonance hyper-Raman scattering, on a series of small molecules. Simulations employing both the long-range corrected approach in density functional theory and coupled cluster are compared and also examined based on available experimental data. Although many of the small molecules are prone to anharmonicity in their potential energy surfaces, the harmonic approach performs adequately. A detailed discussion of the non-Condon effects is illustrated by the molecules presented in this work. Linear and nonlinear Raman scattering simulations allow for the quantification of interference between the Franck-Condon and Herzberg-Teller terms for different molecules.     

Graph-based molecular alignment (GMA)

We describe a combined 2D/3D approach for the superposition of flexible chemical structures, which is based on recent progress in the efficient identification of common subgraphs and a gradient-based torsion space optimization algorithm. The simplicity of the approach is reflected in its generality and computational efficiency: the suggested approach neither requires precalculated statistics on the conformations of the molecules nor does it make simplifying assumptions on the topology of the molecules being compared. Furthermore, graph-based molecular alignment produces alignments that are consistent with the chemistry of the molecules as well as their general structure, as it depends on both the local connectivities between atoms and the overall topology of the molecules. We validate this approach on benchmark sets taken from the literature and show that it leads to good results compared to computationally and algorithmically more involved methods. The results suggest that, for most practical purposes, graph-based molecular alignment is a viable alternative to molecular field alignment with respect to structural superposition and leads to structures of comparable quality in a fraction of the time.     

Analytic calculation of isotropic hyperfine structure constants using the normalized elimination of the small component formalism

Based on the normalized elimination of the small component relativistic formalism, a new approach to the calculation of hyperfine structure parameters of paramagnetic molecules is developed and implemented. The new method is tested in the calculation of the isotropic hyperfine structure constant for a series of open-shell molecules containing mercury. The results of calculations carried out in connection with ab initio methods of increasing complexity demonstrate the high accuracy of the formalism developed. In view of its computational simplicity, the new approach provides the basis for an efficient and accurate calculation of the HFS parameters of large molecules.     

Application of potential constants: Charge transfer and electric dipole moment change in the formation of heteronuclear diatomic molecules—IV

The harmonic and anharmonic potential (force) constants of heteronuclear diatomic molecules, which are usually available from normal coordinate analyses, are applied to problems of determining the number of electrons transferred (charge transfer) and electric dipole moment functions of such molecules. The approach developed here is mainly based on Slater's orbital expansion method, that is, in a non-spin-polarized calculation atomic energies in a molecule are expanded with respect to the occupation number of electrons of atomic orbitals. To confirm the accuracy and the reliability of the approach, we have calculated the number of electrons transferred and electric dipole moments for alkali halides and other heteronuclear diatomic molecules. Specially, detailed analyses of electric dipole moment functions have been carried out on hydrogen fluoride (HF) and hydrogen oxide (OH) for which reliable experimental dipole moment functions are presently known over a wide range of internuclear distances. It is concluded from these analyses that the present approach is simple and useful in evaluating the charge transfer and the dipole moment change in the formation of heteronuclear diatomic molecules.     

Genius: a genetic algorithm for automated structure elucidation from 13C NMR spectra

The automated structure elucidation of organic molecules from experimentally obtained properties is extended by an entirely new approach. A genetic algorithm is implemented that uses molecular constitution structures as individuals. With this approach, the structure of organic molecules can be optimized to meet experimental criteria, if in addition a fast and accurate method for the prediction of the used physical or chemical features is available. This is demonstrated using 13C NMR spectrum as readily obtainable information. By means of artificial neural networks a fast and accurate method for calculating the 13C NMR spectrum of the generated structures exists. The method is implemented and tested successfully for organic molecules with up to 18 non-hydrogen atoms.     

How to Predict Excited State Geometry by Using Empirical Parameters Obtained from Franck-Condon Analysis of Optical Spectrum

Excited state geometries of molecules can be calculated with highly reliable wavefunction schemes. Most of such schemes, however, are applicable to small molecules and can hardly be viewed as error-free for excited state geometries. In this study, a theoretical approach is presented in which the excited state geometries of molecules can be predicted by using vibrationally resolved experimental absorption spectrum in combination with the theoretical modelling of vibrational pattern based on Franck-Condon approximation. Huang-Rhys factors have been empirically determined and used as input for revealing the structural changes occurring between the ground and the excited state geometries upon photoexcitation. Naphthalene molecule has been chosen as a test case to show the robustness of the proposed theoretical approach. Predicted 1B_2u excited state geometry of the naphthalene has similar but slightly different bond length alternation pattern when compared with the geometries calculated with CIS, B3LYP, and CC2 methods. Excited state geometries of perylene and pyrene molecules are also determined with the presented theoretical approach. This powerful method can be applied to other molecules and specifically to relatively large molecules rather easily as long as vibrationally resolved experimental spectra are available to use.     

Quantitative Structure-Property Relationship: XVII. Properties of Branched Hydrocarbon Molecules

A simple approach to estimating properties of branched molecules is suggested: A property of any nonlinear molecule is considered as a sum of the property of the corresponding linear molecule and correction "for branching,"] determined by the interaction of atoms of the substituting group with atoms of the main chain. The potential of this approach is demonstrated by the calculation of the melting points, heat capacities, entropies, and enthalpies and free energies of formation for 117 saturated hydrocarbon molecules, including all the linear C₁-C₂₀ molecules and branched C₄-C₁₀ molecules with methyl substituents; also the heats of vaporization are calculated for 72 molecules including all linear C₁-C₂₀ molecules and branched C₄-C₉ molecules with methyl substituents. The accuracy of all the estimates is high. When the linear contribution is taken into account more accurately, with correction for nonlinear variation of properties of linear molecules, it becomes possible to highly accurately in estimate various properties of both linear and branched molecules, using the molecular connectivity indices.     

Comparison of knowledge-based and distance geometry approaches for generation of molecular conformations.

A knowledge-based approach for generating conformations of molecules has been developed. The method described here provides a good sampling of the molecule's conformational space by restricting the generated conformations to those consistent with the reference database. The present approach, internally named et for enumerate torsions, differs from previous database-mining approaches by employing a library of much larger substructures while treating open chains, rings, and combinations of chains and rings in the same manner. In addition to knowledge in the form of observed torsion angles, some knowledge from the medicinal chemist is captured in the form of which substructures are identified. The knowledge-based approach is compared to Blaney et al.'s distance geometry (DG) algorithm for sampling the conformational space of molecules. The structures of 113 protein-bound molecules, determined by X-ray crystallography, were used to compare the methods. The present knowledge-based approach (i) generates conformations closer to the experimentally determined conformation, (ii) generates them sooner, and (iii) is significantly faster than the DG method.     

An effective, orthogonal deprotection strategy for differentially functionalized, linear and Y-shaped oligo phenylene ethynylenes

Several methodologies for the selective deprotection acetylenes have been reported previously. However, as is shown here, they are often not reliable or convenient. Here, an approach is reported that is efficient and general. Use of this approach to synthesize several two- and three-armed oligo(phenylene ethynylene) molecules with differentiated end groups is reported. In addition, preliminary characterization of the fluorescent properties of some of these molecules and their ability to form self-assembled monolayers (SAMs) is reported.     

Automated structure elucidation of organic molecules from (13)c NMR spectra using genetic algorithms and neural networks.

The automated structure elucidation of organic molecules from experimentally obtained properties is extended by an entirely new approach. A genetic algorithm is implemented that uses molecular constitution structures as individuals. With this approach, the structure of organic molecules can be optimized to meet experimental criteria, if in addition a fast and accurate method for the prediction of the used physical or chemical features is available. This is demonstrated using (13)C NMR spectrum as readily obtainable information. (13)C NMR chemical shift, intensity, and multiplicity information is available from (13)C NMR DEPT spectra. By means of artificial neural networks a fast and accurate method for calculating the (13)C NMR spectrum of the generated structures exists. The approach is limited by the size of the constitutional space that has to be searched and by the accuracy of the shift prediction for the unknown substance. The method is implemented and tested successfully for organic molecules with up to 20 non-hydrogen atoms.     

Charge decomposition analysis of the electron localizability indicator: a bridge between the orbital and direct space representation of the chemical bond

The novel functional electron localizability indicator is a useful tool for investigating chemical bonding in molecules and solids. In contrast to the traditional electron localization function (ELF), the electron localizability indicator is shown to be exactly decomposable into partial orbital contributions even though it displays at the single-determinantal level of theory the same topology as the ELF. This approach is generally valid for molecules and crystals at either the single-determinantal or the explicitly correlated level of theory. The advantages of the new approach are illustrated for the argon atom, homonuclear dimers N2 and F2, unsaturated hydrocarbons C2H4 and C6H6, and the transition-metal-containing molecules Sc(2)2+ and TiF4.     

Microgels for the encapsulation and stimulus-responsive release of molecules with distinct polarities

A microfluidic strategy for the encapsulation and stimulus-responsive release of molecules with distinct polarities from the interior of microgels is reported. The approach relies on (i) the generation of a primary O/W emulsion by the ultrasonication method, (ii) MF emulsification of the primary emulsion, and (iii) photopolymerization of the monomer present in the aqueous phase of the droplets, thereby transforming them into microgels. Non-polar molecules are dissolved in oil droplets embedded in the microgels. Polar molecules are physically associated with the hydrogel network. Upon heating, the microgels contract and release polar and non-polar cargo molecules. The approach paves the way for stimuli-responsive vehicles for multiple drug delivery.     

Photo‐Cross‐Linked Small‐Molecule Microarrays as Chemical Genomic Tools for Dissecting Protein–Ligand Interactions

We have developed a unique photo‐cross‐linking approach for immobilizing a variety of small molecules in a functional‐group‐independent manner. Our approach depends on the reactivity of the carbene species generated from trifluoromethylaryldiazirine upon UV irradiation. It was demonstrated in model experiments that the photogenerated carbenes were able to react with every small molecule tested, and they produced multiple conjugates in most cases. It was also found in on‐array immobilization experiments that various small molecules were immobilized, and the immobilized small molecules retained their ability to interact with their binding proteins. With this approach, photo‐cross‐linked microarrays of about 2000 natural products and drugs were constructed. This photo‐cross‐linked microarray format was found to be useful not merely for ligand screening but also to study the structure–activity relationship, that is, the relationship between the structural motif (or pharmacophore) found in small molecules and its binding affinity toward a protein, by taking advantage of the nonselective nature of the photo‐cross‐linking process.     

Generalized energy-based fragmentation approach for computing the ground-state energies and properties of large molecules

We present a generalized energy-based fragmentation (GEBF) approach for approximately predicting the ground-state energies and molecular properties of large molecules, especially those charged and polar molecules. In this approach, the total energy (or properties) of a large molecule can be approximately obtained from energy (or properties) calculations on various small subsystems, each of which is constructed to contain a certain fragment and its local surroundings within a given distance. In the quantum chemistry calculation of a given subsystem, those distant atoms (outside this subsystem) are modeled as background point charges at the corresponding nuclear centers. This treatment allows long-range electrostatic interaction and polarization effects between distant fragments to be taken into account approximately, which are very important for polar and charged molecules. We also propose a new fragmentation scheme for constructing subsystems. Our test calculations at the Hartree-Fock and second-order M?ller-Plesser perturbation theory levels demonstrate that the approach could yield satisfactory ground-state energies, the dipole moments, and static polarizabilities for polar and charged molecules such as water clusters and proteins.     

Modeling chromatographic parameters by a novel graph theoretical sub-structural approach.

A novel approach to the study of quantitative relationships between chromatographic parameters and the chemical structure is introduced. It is based on the computation of the spectral moments of the topological bond matrix by using different weights as diagonal entries of this matrix. The main advantage of the present approach is that the quantitative contributions of the structural fragments of molecules to the chromatographic parameters studied can be obtained explicitly. By using this approach we study two data sets: one composed of 156 alkanes and the other of 81 oxygen-containing organic molecules. In both cases excellent quantitative structure-chromatographic retention relationships were obtained. The contributions of the different fragments to the chromatographic retention were generated obtaining tables of additive contributions to the properties studied. The physicochemical interpretation of the results on the basis of the retention mechanisms is also analyzed in light of this new approach.