Fortran 90 implementation of the Hartree-Fock approach within the CNDO/2 and INDO models

Despite the tremendous advances made by the ab initio theory of electronic structure of atoms and molecules, its applications are still not possible for very large systems. Therefore, semi-empirical model Hamiltonians based on the zero-differential overlap (ZDO) approach such as the Pariser-Parr-Pople, CNDO, INDO, etc. provide attractive, and computationally tractable, alternatives to the ab initio treatment of large systems. In this paper we describe a Fortran 90 computer program developed by us, that uses CNDO/2 and INDO methods to solve Hartree-Fock(HF) equation for molecular systems. The INDO method can be used for the molecules containing the first-row atoms, while the CNDO/2 method is applicable to those containing both the first-, and the second-row, atoms. We have paid particular attention to computational efficiency while developing the code, and, therefore, it allows us to perform calculations on large molecules such as C_60 on small computers within a matter of seconds. Besides being able to compute the molecular orbitals and total energies, our code is also able to compute properties such as the electric dipole moment, Mulliken population analysis, and linear optical absorption spectrum of the system. We also demonstrate how the program can be used to compute the total energy per unit cell of a polymer. The applications presented in this paper include small organic and inorganic molecules, fullerene C_60, and model polymeric systems, viz., chains containing alternating boron and nitrogen atoms (BN chain), and carbon atoms (C chain).Comment: 29 pages, 3 figures, to appear in Computer Physics Communication

Theoretical aspects of structure bonding and reactivity of some unsaturated organic systems;

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The oretical and experimental investigations of structure, reactivity and bonding in some organic systems

A theoretical study has been made of some aspects of prototype potential energy surfaces for some simple organic reactions. Addition of prototype electrophiles to simple alkenes has been investigated by means of non-empirical and semi-empirical calculations, within the Hartree-Fock formalism, and the resulting carbonium ions studied. The systems under investigation may be formally considered as being derived from electrophilic addition of H(^+) to ethylene, fluoroethylene and chloroethylene, or of X(^+) (X=F,Cl) to ethylene, and may thus be represented as (C(_2)H(_4)X)(^+), X=H,F and Cl. For the simplest system, C(_2)H(_5)(^+), two basic structures have been considered, the classical ethylcation and the bridge-protonated ethylene. The energies of these species have been minimised with respect to the C-C bond lengths and also, in the case of the latter ion, with respect to the distance of the bridging H from the CC bond centre. Examination of conformational processes in the classical ion has shown a virtual absence of any barrier to rigid rotation about the cc bond. The calculated relative energies of the species has indicated, subject to limitations imposed by the basis set size and partial geometry optimisation, that in the gas phase the classical ion should be ~5.2k cal mole(^-1) more stable than the bridge protonated ethylene. Furthermore calculations along an idealised reaction coordinate representing trans-formation between the two species have indicated the absence of an activation barrier thus suggesting the bridged ion to be the transition state for the scrambling of the hydrogen atoms of the ethyl cation. These results have been compared with mass spectrometric data. The approach of a prototype nucleophile (H(^-)) to ethyl cation has been examined, results suggesting a preferential cis attack. Conformational processes in the 1- and 2- fluoroethyl chlorethyl cations have been examined. The rotational barrier in the 2- fluoroethyl cation has been shown to be very large (10.5k cal mole) and, with the exception of the 2- chloroethyl cation, all the barriers for the substituted ethyl cations have been shown to be dominated by attractive terms. In both the fluoro and chloroethyl systems, predicted ordering of stabilities of cations has been 1- haloethyl > bridge-protonated haloethylene > 2- haloethyl, and idealised reaction coordinates have been constructed relating the ions in the fluoro case, the results predict the total absence of any activation barrier in trans-forming 2- to 1- fluoroethyl cation, whilst, in the analogous chloro case, a small barrier (4.3 k cal mole(^-1)) is predicted. Relative thermochemical stabilities of the ions have been computed, and the stabilising/destabilising effects of halogen substitution in these carbonium ions investigated and compared with experimental data. The halogen bridged 'halonium' ions have been studied, and their total energies minimised with respect to the distance of the halogen atom from the CC bond centre. The calculations have indicated that the fluoronium ion should be of marginally greater stability than the 2- fluoroethyl cation (3.6k cal mole(^-1)) and this has been discussed in the light of published nmr studies of the ionisation of 2-halo-3fluoro 2,3-dimethyl butanes in SO(_2)/SbF(_5). Results for the chloronium ion have indicated that this ion should be considerably more stable (15.8k cal mole(^-1)) than the corresponding 2- chloroethyl cation. Electron Spectroscopy for Chemical Applications (ESCA) has been employed for the measurement of core binding energies in three series of closely related molecules (i) a series of acetyl compounds of general formula CH(_3)COX, X=H, CH(_3), OH, OCH(_3), NH(_2), NHCH(_3), COCH(_3), CO(_2)H, CN and OCOCH(_3). (ii) a series of five membered ring heterocycles. (iii) a series of pyrimidine bases and related compounds. Assignment of core levels has been accomplished in two ways, (i) Direct correlation of measured binding energies with orbital energies derived from SCF calculations, i.e. assuming Koopmans' theorem, (ii) Correlation of shifts in core binding energies with computed electron distributions within the molecule using the charge potential model. In general, assignments based upon the different methods have been found to be in agreement. Furthermore in the case of some members of the pyrimidine series comparison has been possible between charge potential assignments using both ab initio and CNDO/II populations. Agreement between the two sets has been complete

Simulation of Smart Materials

The aim of this thesis is the elucidation of structure-properties relationship of molecular semiconductors for electronic devices. This involves the use of a comprehensive set of simulation techniques, ranging from quantum-mechanical to numerical stochastic methods, and also the development of ad-hoc computational tools. In more detail, the research activity regarded two main topics: the study of electronic properties and structural behaviour of liquid crystalline (LC) materials based on functionalised oligo(p-phenyleneethynylene) (OPE), and the investigation on the electric field effect associated to OFET operation on pentacene thin film stability. In this dissertation, a novel family of substituted OPE liquid crystals with applications in stimuli-responsive materials is presented. In more detail, simulations can not only provide evidence for the characterization of the liquid crystalline phases of different OPEs, but elucidate the role of charge transfer states in donor-acceptor LCs containing an endohedral metallofullerene moiety. Such systems can be regarded as promising candidates for organic photovoltaics. Furthermore, exciton dynamics simulations are performed as a way to obtain additional information about the degree of order in OPE columnar phases. Finally, ab initio and molecular mechanics simulations are used to investigate the influence of an applied electric field on pentacene reactivity and stability. The reaction path of pentacene thermal dimerization in the presence of an external electric field is investigated; the results can be related to the fatigue effect observed in OFETs, that show significant performance degradation even in the absence of external agents. In addition to this, the effect of the gate voltage on a pentacene monolayer are simulated, and the results are then compared to X-ray diffraction measurements performed for the first time on operating OFETs

Multi-scale modelling of proto-zeolitic solutions

A number of aspects of the pre-nucleation zeolite synthesis solution are considered. Various environmental and structural e�ects on the 29Si NMR chemical shift of silicon nuclei are investigated, in order to ascertain the necessary computational model for a systematic study of oligomeric silicate species identi�ed or postulated to be present during this phase of zeolite crystal growth. It is demonstrated that, using a model with the oligomer in a fully protonated state and including an implicit representation of the solvent, a reasonably inexpensive model can provide good agreement with experimental results. The systematic study of 59 oligomers reveals several cases for re-assignment of experimentally observed peaks, as well as providing assistance in cases where full assignment has proved impossible from experiment. The e�ects of structure directing agents (SDAs), commonly used in zeolite synthesis, are investigated. Using ab initio molecular dynamics (AIMD) to simulate the SDA in the presence of water and a speci�cally designed computer code, it is demonstrated how SDAs lead to the formation of various rings of water in their hydration layer. Furthermore, di�erent properties of the SDAs are shown to induce the formation of di�erent distributions of the various sizes of rings. It is found that certain SDAs result in the formation of clusters of water rings in a network which is isomorphic with some of the zeolite frameworks for which they are know to direct. Finally a new inter-atomic potential is developed for modelling silicate clusters, in order to allow longer simulations of larger systems than are accessible using AIMD methods. This potential is then used to simulate two cage-like silicate oligomers surrounded by water. In these simulations layers of ordered water, similar to those found at zeolite crystal surfaces, are found. These �ndings have implications for the understanding of the aggregation of oligomeric species prior to nucleation. This work was generously supported by the Engineering and Physical Science Research Council. The �nal chapter was also made possible by a Junior Research Fellowship from the Thomas Young Centre. The simulation presented in chapter 4 were performed on the HPCx supercomputer and UCL's Legion supercomputer