Ab initio calculations on large molecules using molecular fragments. Characterization of the zwitterion of glycine

The ab initio molecular fragment approach is applied to a characterization study of the ground state of the zwitterion of glycine. Included among the properties studied are the — conformational energy surface, the electronic structure, and the magnitude and direction of the dipole moment. The results of the present study are compared to the results of other theoretical and experimental studies.This work was supported in part by the National Science Foundation, the University of Kansas, and the Upjohn Company, Kalamazoo, Michigan 49001.NSF Trainee (1969-1972).Alfred P. Sloan Research Fellow (1971–1973).     

Ab initio calculations on large molecules using molecular fragments. Initial studies on open shell systems

An ab initio procedure, designed for investigation of large molecules and based upon studies of molecular fragments, is extended to open shell systems using the unrestricted Hartree-Fock method. Investigated initially are the ethyl and vinyl radicals, and the ethylene triplet state.     

Ab initio calculations on large molecules using molecular fragments First order electronic properties for hydrocarbons

A number of first order electronic properties for the hydrocarbons C₂H₆, C₃H₈, C₂H₄, C₆H₆, and C₁₀H₈ are investigated. The wavefunctions employed here result from SCF calculations, using basis orbitals that have been optimized in molecular fragment studies. Comparisons are made with experimental values as well as with other calculated values, and the suitability of various molecular fragment bases is discussed.     

Ab initio calculations on large molecules using molecular fragments. Preliminary investigation of ethyl chlorophyllide a and related molecules

Ab initio SCF calculations using the molecular fragment method are reported for four molecules related to chlorophyll a, i.e., free-base porphine, magnesium porphine, magnesium chlorin, and ethyl chlorophyllide a. Molecular orbital structure, the “four-orbital model”, reactivity sites, and Mg···N interactions are discussed.     

Ab initio molecular fragment calculations with pseudopotentials. Some fragments containing nitrogen and oxygen

Parameters for the OH (sp²) and NH₃ (planar, sp²) pseudopotential–FSGO molecular fragments have been established in this paper. Calculations for the molecules of formic acid, formaldehyde, and formamide show good agreement with experiment.     

Ab initio CI calculations on benzene with an extended basis set

An extended basis set of triple zeta plus polarization quality is employed to carry out configuration interaction (CI ) calculations of the three lowest singlet and triplet excited states of benzene. The CI calculation is carried out by taking into account single and double excitations of π and σ electrons. In the CI , composite natural orbitals (CNO s), which are constructed from the natural orbitals of the ground state of ethylene, are used as virtual orbitals. The aim of using CNOs is to reduce the number of virtual orbitals to be used in constructing configuration-state functions, thus cutting down CI dimensions without losing reasonable accuracy. The excitation energies resulting from the CI are in fairly good agreement with experiment. The root mean square of the deviation is 0.22 eV for the six calculated energies and the largest disagreement is 0.37 eV for the third singlet excited state. To obtain better excitation energies by an ab initio calculation, it seems likely that we need to take into account more electron correlation than in the present calculation. © 1994 John Wiley & Sons, Inc.     

Ab initio molecular dynamics with dual basis set methods

On-the-fly, ab initio classical molecular dynamics are demonstrated with an underlying dual basis set potential energy surface. Dual-basis self-consistent field (Hartree-Fock and density functional theory) and resolution-of-the-identity second-order M?ller-Plesset perturbation theory (RI-MP2) dynamics are tested for small systems, including the water dimer. The resulting dynamics are shown to be faithful representations of their single-basis analogues for individual trajectories, as well as vibrational spectra. Computational cost savings of 58% are demonstrated for SCF methods, even relative to Fock-extrapolated dynamics, and savings are further increased to 71% with RI-MP2. Notably, these timings outperform an idealized estimate of extended-Lagrangian molecular dynamics. The method is subsequently demonstrated on the vibrational absorption spectrum of two NO(+)(H?O)? isomers and is shown to recover the significant width of the shared-proton bands observed experimentally.     

Ab initio calculations on large molecules: The multiplicative integral approximation

In the multiplicative integral approximation (MIA), two-electron integrals are evaluated using an expansion of a product of two Gaussians in terms of auxiliary functions. An estimator of the error introduced by the approximation is incorporated in the self-consistent field (SCF) calculations and the integrals for which the error estimate is larger than a preset value are systematically corrected. In this way the results of a MIA-assisted calculation have the same accuracy as a conventional calculation. The full exploitation of the expansion technique while constructing the Fock-matrix allows important time savings. Results are presented for a number of test cases.     

Optimum Gaussian basis set for the Bromine atom. Ab initio calculations on the HBr molecule

An optimum (15 ^s 12 ^p 2 ^d ) Gaussian basis set was obtained for the Bromine atom by minimizing the open shell energy functional. In the minimization procedure the method of conjugate gradients was applied. The optimum (15 ^s 12 ^p 2 ^d ) basis set was contracted to an [8 ^s 6 ^p 2 ^d ] “double zeta” quality basis set and this contracted set was tested on the HBr molecule.     

Ab initio molecular fragment calculations with pseudopotentials: Model peptide studies

The energetics of rotation about the N? C′(ω); N? C^α(φ), and C^α? C′(?) bonds of the peptide unit have been investigated in the pseudo-FSGO fragment scheme on model compounds formamide and N-methylacetamide. The results indicated that the position of the minimum in ω is in the near vicinity of 0°, i.e., the planar arrangement of the peptide unit. The minimum in φ (C′? N? C^α? H) has been found to be 180° and in ψ(H? C^α? C′? N) to be 60°, in good agreement with PCILO and Gaussian-70 results.     

Ab initio Hartree—Fock calculations of model polyacetylene chains using a Christoffersen basis set

Ab initio crystal orbital calculations using a Christoffersen basis set have been performed on the relative stabilities of model polyacetylene chains. Results indicate the all-trans isomer as the most stable. Among the cis structures, the cis-transoid backbone is very slightly preferred to the trans-cisoid backbone.     

Small gaussian basis sets for AB initio calculations on large molecules

Gaussian basis sets of (5s, 2p) for carbon, nitrogen, and oxygen, and (7s, 4p) for phosphorous and sulfur have been developed for ab initio calculations of biological molecules. Double zeta contracted bases are given for all five atoms. Minimum bases are given for carbon, nitrogen and oxygen, and a method is developed for replicating primitives in order to minimize the energy loss when contracting small bases. The contracted bases are applied to formamide and the results are compared with those obtained from other small basis sets.     

Ab initio calculations on the molecular structure of fluorocyanopolyynes

The molecular structure of the first three members of the fluorocyanopolyynes was studied by ab initio Hartree-Fock calculations with a polarized double zeta basis set and at MP2 level with the same basis set. Alternating triple and single bonds were found; a theoretical estimate of rotational constants and dipole moments was performed and a comparison with the available experimental data was made. An analysis of the theoretical vibrational frequencies of the title compounds was carried out.     

Ab initio crystal orbital calculations on three-dimensional crystals of large bioorganic molecules and polymers

Ab initio crystal orbital calculations on three-dimensional crystals of tetrathiafulvalene-tetracyanoquinodimethane (TTF-TCNQ), diprotonated deoxycytidine-5′-monophosphate monohydrate (5′-dCMP*2H*1Water), disodium deoxyguanosine-5′-monophosphate tetrahydrate (5′-dGMP*2Na*4Water), disodium uridine-3′-monophosphate tetrahydrate (3′-UMP*2Na*4Water), monosodium monoprotonated deoxyadenosine-5′-monophosphate hexahydrate (5′-dAMP*1H*1Na*6Water), disodium deoxycytidine-5′-monophosphate heptahydrate (5′-dCMP*2Na*7Water), cis-polyacetylene (cis-PA), and polythiophene (PTP) were carried out using the CRYSTAL92 routine package. A suitable basis set has been found that enables one to carry out the above calculations at the STO -3G level of accuracy using SILICON GRAPHICS workstations. However, to obtain reasonable results for three-dimensional crystals of polymers, one has to use much more extended basis sets. © 1996 John Wiley & Sons, Inc.     

Ab initio calculations,using a small Gaussian basis set,of the electronic structure of the sulphate ion

Ab initio molecular orbital calculations of the electronic structure of the sulphate ion have been performed in which three Gaussian-type functions are used to simulate each member of a minimal basis of Slater-type orbitals. Comparative calculations on H₂S show that such a basis excellently reproduces the properties of the valence electrons given by calculations in a Slater basis. The expansion of the basis by the addition of sulphur 3d orbitals results in a large decrease in the molecular energy (1 a.u.) and has a pronounced effect on the ordering and energy of the molecular orbitals. The results of a number of semiempirical schemes are discussed in the light of these results.     

Ab initio molecular orbital calculation of fe-porphine with a double zeta basis set

An ab initio LCAO SCF MO calculation was performed on planar Fe-porphine with a double zeta basis set consisting of 300 CGTO 's. SCF wave functions of several states of Fe-porphine and its cation were obtained. The net charge of Fe is in the range of 1.39 to 1.53. The highest occupied orbital is ascertained to be a pure porphine π-MO , 1a_1u. The calculated ionization potentials of the two highest occupied orbitals, 1a_1u and 5a_2u are 5.98 and 6.43 eV, respectively. They are in good agreement with experiments. The role of the porphine macrocycle on the oxidation of Fe is discussed in terms of gross atomic populations and with contour maps of the density difference.