Computation of (3)J(HH) coupling constants with a combination of density functional theory and semiempirical calculations. Application to complex molecules

This work evaluates the efficiency of economic levels of theory for the prediction of (3)J(HH) spin-spin coupling constants, to be used when robust electronic structure methods are prohibitive. To that purpose, DFT methods like mPW1PW91. B3LYP and PBEPBE were used to obtain coupling constants for a test set whose coupling constants are well known. Satisfactory results were obtained in most of cases, with the mPW1PW91/6-31G(d,p)//B3LYP/6-31G(d,p) leading the set. In a second step. B3LYP was replaced by the semiempirical methods PM6 and RM1 in the geometry optimizations. Coupling constants calculated with these latter structures were at least as good as the ones obtained by pure DFT methods. This is a promising result, because some of the main objectives of computational chemistry - low computational cost and time, allied to high performance and precision - were attained together. (C) 2012 Elsevier B.V. All rights reserved.

Chemical bond analysis of nonlinearity of urea crystal

A novel and quantitative study on structure-property relationships has been carried out in urea crystal, based on the dielectric theory of complex crystals and the modified Levine bond charge model, mainly from the chemical bond viewpoint. For the first time, it was treated like this, and the bond parameters and linear and nonlinear characteristics of constituent chemical bonds were presented quantitatively. The theoretical result agrees satisfactorily with the experimental datum and can reasonably explain the nonlinear origin of urea crystal, that is, the C-N bond in the conjugated system of bonds O double left arrow C<--N-H. At the same time, the novel method should be a useful tool toward the future development of the search for new nonlinear optical (NLO) materials in the organic crystal field.

Electron-impact ionization of diatomic molecules using a configuration-average distorted-wave method

Electron-impact ionization cross sections for diatomic molecules are calculated in a configuration-average distorted-wave method. Core bound orbitals for the molecular ion are calculated using a single-configuration self-consistent-field method based on a linear combination of Slater-type orbitals. The core bound orbitals are then transformed onto a two-dimensional (r,θ) numerical lattice from which a Hartree potential with local exchange is constructed. The single-particle Schrödinger equation is then solved for the valence bound orbital and continuum distorted-wave orbitals with S-matrix boundary conditions. Total cross section results for H2 and N2 are compared with those from semiempirical calculations and experimental measurements.

Nonlinear Optical Properties of Organic and Polymer Systems

Present thesis has discussed the design and synthesis of polymers suitable for nonlinear optics. Most of the molecules that were studied have shown good nonlinear optical activity. The second order nonlinear optical activity of the polymers was measured experimentally by Kurtz and Perry powder technique. The thesis comprises of eight chapters.The theory of NLO phenomenon and a review about the various nonlinear optical polymers has been discussed in chapter 1. The review has provided a survey of NLO active polymeric materials with a general introduction, which included the principles and the origin of nonlinear optics, and has given emphasis to polymeric materials for nonlinear optics, including guest-host systems, side chain polymers, main chain polymers, crosslinked polymers, chiral polymers etc.Chapter 2 has discussed the stability of the metal incorporated tetrapyrrole molecules, porphyrin, chlorin and bacteriochlorin.Chapter 3 has provided the NLO properties of certain organic molecules by computational tools. The chapter is divided into four parts. The first part has described the nonlinear optical properties of chromophore (D-n-A) and bichromophore (D-n-A-A-n-D) systems, which were separated by methylene spacer, by making use of DPT and semiempirical calculations.Chapter 4: A series of polyurethanes was prepared from cardanol, a renewable resource and a waste of the cashew industry by previously designed bifunctional and multifunctional polymers using quantum theoretical approach.Chapter 5: A series of chiral polyurethanes with main chain bis azo diol groups in the polymer backbone was designed and NLO activity was predicted by ZlNDO/ CV methods.In Chapter 7, polyurethanes were first designed by computational methods and the NLO properties were predicted by correction vector method. The designed bifunctional and multifunctional polyurethanes were synthesized by varying the chiral-achiral diol compositions

”Nonlinear optical properties of polymers containing azomesogens and chiral molecules: theoretical and experimental evaluations."

The present work emphasizes the use of chirality as an efficient tool to synthesize new types of second order nonlinear materials. Second harmonic generation efficiency (SHG) is used as a measure of second order nonlinear response. Nonlinear optical properties of polymers have been studied theoretically and experimentally. Polymers were designed theoretically by ab initio and semiempirical calculations. All the polymeric systems have been synthesized by condensation polymerization. Second harmonic generation efficiency of the synthesized systems has been measured experimentally by Kurtz and Perry powder method

Polymethine cyanine dyes in beta-cyclodextrin solution: multiple equilibria and chemical oxidation

Absorption and fluorescence spectroscopy, electrochemical techniques, and semiempirical calculations were employed to characterize the multiple complexation equilibria between two polymethine cyanine dyes (IR-786 and Indocyanine green-ICG, 5) and beta-cyclodextrin (beta-CD, L), as well as the chemical reactivity of the complexed and uncomplexed species against the oxidizing agents hypochlorite (HC) and hydrogen peroxide (HP). IR-786 dimerization is favored with the increase in beta-CD concentration in the form of (SL)(2) complexes. In the case of ICG, free dimers (D) and SL complexes are favored. Both IR-786 and ICG react and discolor in the presence of HC and HP. For IR-786, the reaction with HP and HC proceeds with observed rate constants of 10(-3) and 0.28 s(-1) and second-order rate constants (k(2)) of similar to 10(-3) and 10(4) M(-1) s(-1), respectively. The intermediate species observed in the bleaching reactions of IR-786 and ICG were shown, by cyclic voltammetry and VIS absorption, to result from one electron oxidation. IR-786 complexed with beta-CD is protected against bleaching in the presence of HP and HC by factors of 20 and 4, respectively. This protection was not observed in ICG complexes. Superdelocalizability profile of both dyes and frontier orbital analysis indicates that beta-CD does not protect ICG from oxidation by HP or HC, whereas the 2:2 IR-786/beta-Cd complex is able to avoid the oxidation of IR-786. We concluded that the decrease in the chemical reactivity of the dyes against oxidant agents in the presence of beta-CD is due to the formation of (SL)(2) complexes. Copyright (C) 2010 John Wiley & Sons, Ltd.

Modeling of alkynes: synthesis and theoretical properties

ABSTRACT: In this paper we present the synthesis and simulation of alkynes derivatives. Semiempirical calculations were carried out for the ground and first excited states, including the spectroscopic properties of the absorption and emission (fluorescence and phosphorescence) spectra by INDO/S-CI and DNdM-INDO/S-CI methods with geometries fully optimized by PM3/CI. The fact that the theoretical spectra are in accord with the experimental absorption spectra gives us a new possible approach on how structure modifications could affect the non-linear optical properties of alkynes.

Squaraine mit ausgedehnter Konjugation

Squaraine mit ausgedehnter Konjugation: Die vorliegende Arbeit ist in zwei Teilbereiche gegliedert, wobei der erste Teil die Synthese und Eigenschaftsuntersuchung symmetrischer und unsymmetrischer, stilbenoider Squaraine mit ausgedehnter Konjugation (DAD-Systeme) betrifft. Im zweiten Teil der Arbeit werden als Modellverbindungen für diese Squaraine Oligo(phenylenvinylen)e (OPVs) mit terminaler Donor-Acceptor-Substitution hergestellt.Es wurden drei unterschiedliche Klassen von konjugationsverlängerten Squarainen synthetisiert: unsymmetrische und symmetrische Monosquaraine sowie Oligosquaraine mit zwei, drei oder vier quarylium-Einheiten. Um eine bessere Löslichkeit zu gewährleisten, tragen die meisten Verbindungen voluminöse, flexible Bis(2-hexyloctyl)amino-Reste. Teilweise konnte die Löslichkeit auch durch zusätzliche Hexylseitenketten noch weiter verbessert werden. Der Aufbau der stilbenoiden Resorcine, die zur Synthese der entsprechenden Squaraine benötigt werden, erfolgte fast ausschließlich über die Wittig-Horner-Reaktion. Die 3,5-Dihydroxysubstitution erhöht die Nucleophilie in der 4-Position, so daß sich die stilbenoiden Resorcine in guten Ausbeuten mit Quadratsäure oder mit einer Semiquadratsäure zu den gewünschten Squarainen kondensieren ließen. Die Herstellung der Donor-Acceptor-substituierten OPVs erfolgte nach einer konvergenten Synthesestrategie, bei der auf eine repetitive Wittig-Horner-Reaktion und eine einfache Schutzgruppentechnik zurückgegriffen wurde. Als Acceptorgruppen dienten Formyl-, Cyano- und Nitrosubstituenten, als Donorgruppe wurden Bis(2-Hexyloctyl)amino-Reste eingesetzt. Die igenschaftsuntersuchungen an den konjugierten Oligomeren konnten zur Aufklärung des ungewöhnlichen spektroskopischen Verhaltens der Squaraine beitragen. Es wurde ein athematischer Ansatz entwickelt, der das Absorptionsverhalten D-A-substituierter Oligo(phenylenvinylen)e exakt beschreiben kann. Semiempirische Rechnungen und elektrooptische bsorptionsmessungen an diesen Verbindungen bestätigten die experimentell gefundenen Trends.

Further Quantum Mechanical Evidence that Difluorotoluene does not Hydrogen Bond

Calculations were run on the methylated DNA base pairs adenine:thymine and adenine:difluorotoluene to further investigate the hydrogen-bonding properties of difluorotoluene (F). Geometries were optimized using hybrid density functional theory. Single-point calculations at the MP2(full) level were performed to obtain more rigorous energies. The functional counterpoise method was used to correct for the basis set superposition error (BSSE), and the interaction energies were also corrected for fragment relaxation. These corrections brought the B3LYP and MP2 interaction energies into excellent agreement. In the gas phase, the Gibbs free energies calculated at the B3LYP and MP2 levels of theory predict that A and T will spontaneously form an A:T pair while A:F spontaneously dissociates into A and F. Solvation effects on the pairing of the bases were explored using implicit solvent models for water and chloroform. In aqueous solution, both A:T and A:F are predicted to dissociate into their component monomers. Semiempirical calculations were performed on small sections of B-form DNA containing the two pairs, and the results provide support for the concept that base stacking is more important than hydrogen bonding for the stability of the A:F pair within a DNA helix.

Quantum Mechnical Investion of Cyclic 3',5'- Adenosine Monophosphate, the Second Hormonal Messenger

Full geometry optimizations using the PM3, AM1, 3-21G∗/HF and 6-31G∗/HF levels of theory were conducted on the syn and anti conformations of cyclic3′,5′-adenosine monophosphate (cAMP). Comparison of the anti crystal structures with the semiempirical and ab initio results revealed that the ab initio results agree well with the experimental results. The results of semiempirical calculations are in qualitative agreement with experimental and ab initio values, with the exception of the glycosyl torsion angle for the anti conformer. Sugar puckering, which is not handled properly by semiempirical methods for unconstrained sugars, nucleosides, nucleotides and nucleotide base pairs, is modeled reasonably well by the semiempirical methods for cAMP. This improvement results from the constraints introduced by the cyclization of AMP to form the phosphodiester.

The quest for planarizing distortions in hydrocarbons: two stereoisomeric 4.5.5.5 fenestranes

According to semiempirical calculations the planarizing distortions in the central C(C)4 substructure of fenestranes, represented as 1, can be enhanced by a variety of structural modifications. Based on these results we selected the 7-hydroxy-c,c,c,c- and c,t,c,c[4.5.5.5]fenestranones 13 and 16 as precursors for the introduction of a bridgehead double bond. The efficient synthesis of these precursors and their chemical transformations are reported. Attempts to activate the hydroxyl group in 16 for introduction of a bridgehead double bond led to the rearrangement of the [4.5.5.5]fenestrane to a triquinacane skeleton. (C) 2011 Elsevier Ltd. All rights reserved.

Intermolecular and Intramolecular Charge Transfer in Functional Molecular Materials

This thesis is devoted to the investigation of inter and intramolecular charge transfer (CT) in molecular functional materials and specifically organic dyes and CT crystals. An integrated approach encompassing quantum-chemical calculations, semiempirical tools, theoretical models and spectroscopic measurements is applied to understand structure-property relationships governing the low-energy physics of these materials. Four main topics were addressed: 1) Spectral properties of organic dyes. Charge-transfer dyes are constituted by electron donor (D) and electron acceptor (A) units linked through bridge(s) to form molecules with different symmetry and dimensionality. Their low-energy physics is governed by the charge resonance between D and A groups and is effectively described by a family of parametric Hamiltonians known as essential-state models. These models account for few electronic states, corresponding to the main resonance structures of the relevant dye, leading to a simple picture that is completed introducing the coupling of the electronic system to molecular vibrations, treated in a non-adiabatic way, and an effective classical coordinate, describing polar solvation. In this work a specific essential-state model was proposed and parametrized for the dye Brilliant Green. The central issue in this work has been the definition of the diabatic states, a not trivial task for a multi-branched chromophore. In a second effort, we have used essential-state models for the description of the early-stage dynamics of excited states after ultrafast excitation. Crucial to this work is the fully non-adiabatic treatment of the coupled electronic and vibrational motion, allowing for a reliable description of the dynamics of systems showing a multistable, broken-symmetry excited state. 2) Mixed-stack CT salts. Mixed-stack (MS) CT crystals are an interesting class of multifunctional molecular materials, where D and A molecules arrange themselves to form stacks, leading to delocalized electrons in one dimension. The interplay between the intermolecular CT, electrostatic interactions, lattice phonons and molecular vibrations leads to intriguing physical properties that include (photoinduced) phase transitions, multistability, antiferromagnetism, ferroelectricity and potential multiferroicity. The standard microscopic model to describe this family of materials is the Modified Hubbard model accounting for electron-phonon coupling (Peierls coupling), electron-molecular vibrations coupling (Holstein coupling) and electrostatic interactions. We adopt and validate a method, based on DFT calculations on dimeric DA structures, to extract relevant model parameters. The approach offers a powerful tool to shed light on the complex physics of MS-CT salts. 3) Charge transfer in organic radical dipolar dyes. In collaboration with the group of Prof. Jaume Veciana (ICMAB- Barcellona), we have studied spectral properties of a special class of CT dyes with D-bridge-A structure where the acceptor group is a stable radical (of the perchlorotriphenylmethyl, PTM, family), leading to an open-shell CT dyes. These materials are of interest since they associate the electronic and optical properties of CT dyes with magnetic properties from the unpaired electron. The first effort was devoted to the parametrization of the relevant essential-state model. Two strategies were adopted, one based on the calculation of the low-energy spectral properties, the other based on the variation of ground state properties with an applied electric field. 4) The spectral properties of organic nanoparticles based on radical species are investigated in collaboration with Dr. I. Ratera (ICMAB- Barcellona). Intriguing spectroscopic behavior was observed pointing to the presence of excimer states. In an attempt to rationalize these findings, extensive calculations (TD-DFT and ZINDO) were performed. The results for the isolated dyes are validated against experimental spectra in solution. To address intermolecular interactions we studied dimeric structures in the gas phase, but the preliminary results obtained do not support excimer formation.

Cycloadditions of isobenzofuran to a constrained template bearing neighboring dienophiles

A high yielding synthesis of the pentacyclic diene-dione 1 has enabled investigation of its reactivity as a double dienophile in Diels-Alder [4+2] cycloadditions with isobenzofuran, leading to novel and highly symmetrical three-sided cavitands 3 and 4.

CALCULATIONS FOR THE VIBRATION FREQUENCIES OF THE O-H...O BOND IN KH2PO4 BY A SEMIEMPIRICAL METHOD

The frequencies of the stretching vibration and the bending vibration of the 0-H ... 0 bond in potassium dihydrogen phosphate have been calculated by means of two semiempirical formulae with three parameters. The calculated results can give satisfactory explanation for the experimental spectra of the potassium dihydrogen phosphate crystal. The parameters used in the calculations may be related to the chemical bonding and the charge distribution about the two oxygen atoms of the 0-H ... 0 bond system.

Hydrolysis of genotoxic methyl-substituted oxiranes : Experimental kinetic and semiempirical studies

The kinetics of acid-catalyzed hydrolysis of seven methylated aliphatic epoxides - R1R2C(O)CR3R4 (A: R1=R2=R3=R4=H; B: R1=R2=R3=H, R4=Me; C: R1=R2=H, R3=R4=Me; D: R1=R3=H, R2=R4=Me(trans); E: R1=R3=H, R2=R4=Me(cis); F: R1=R3=R4=Me, R2=H; G: R1=R2=R3=R4=Me) - has been studied at 36 ± 1.5°C. Compounds with two methyl groups at the same carbon atom of the oxirane ring exhibit highest rate constants (k(eff) in reciprocal molar concentration per second: 11.0 ± 1.3 for C, 10.7 ± 2.1 for F, and 8.7 ± 0.7 for G as opposed to 0.124 ± 0.003 for B, 0.305 ± 0.003 for D, and 0.635 ± 0.036 for E). Ethylene oxide (A) displays the lowest rate of hydrolysis (0.027 M-1 s-1). The results are consistent with literature data available for compounds A, B, and C. To model the reactivities we have employed quantum chemical calculations (MNDO, AM1, PM3, and MINDO/3) of the main reaction species. There is a correlation of the logarithm k(eff) with the total energy of epoxide ring opening. The best correlation coefficients (r) were obtained using the AM1 and MNDO methods (0.966 and 0.957, respectively). However, unlike MNDO, AM1 predicts approximately zero energy barriers for the oxirane ring opening of compounds B, C, E and G, which is not consistent with published kinetic data. Thus, the MNDO method provides a preferential means of modeling the acidic hydrolysis of the series of methylated oxiranes. The general ranking of mutagenicity in vitro, A > B > C, is in line with the concept that this sequence also gradually leaves the expoxide reactivity optimal for genotoxicity toward reactivities leading to higher biological detoxifications.