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 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 calculations on large molecules using molecular fragments. Generalization of the molecular fragment basis at the minimum basis set level

By determining basis set parameters in molecular environments using other criteria than total energy, it is shown that a generalization of the molecular fragment basis can be obtained in which calculated geometric and electronic structural properties are predicted substantially better than with other basis sets of similar size. As a first step in the development of a series of basis sets having successively greater flexibility and accuracy, several single-zeta basis sets are created, using a two-Gaussian contraction for each basis orbital. The best of these basis sets produced calculated geometric and electronic properties for a series of molecules that model a wide variety of organic molecules that are of better accuracy than the corresponding STO -2G basis, and similar in most cases to STO -3G. In addition, the basis set is shown to be applicable in either a Cartesian Gaussian basis or a floating spherical Gaussian basis.     

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.     

Ab initio molecular orbital calculations

A series of non-empirical calculations on furan, pyrrole and 1,2,5-oxadiazole are reported in which the effect of polarisation functions added to the minimal 7s 3p basis on each atom is studied. The effect on these planar molecules is largely through the rather than the-system. A comparison with the results of work with scaled functions is reported. Both series are shown to lead to much improved agreement with the electron spectroscopy energy levels. The effect on the dipole moments of these changes in basis is more variable but, with the exception of furan, the agreement with experiment is improved in the present method.

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Zusammenfassung Für die Moleküle Furan, Pyrrol und 1,2,5-Oxadiazol wurde eine Reihe von nichtempirischen Rechnungen durchgeführt, in denen der Einfluß von zusätzlichen Polarisationsfunktionen zur minimalen 7s 3p-Basis an jedem Atom untersucht wird. Die Ergebnisse werden mehr durch die Art der Beschreibung des Systems der-Elektronen als durch diejenige der-Elektronen beeinflußt. Ein Vergleich mit den Ergebnissen bei Verwendung skalierter Funktionen wird durchgeführt. Beide Reihen von Ergebnissen zeigen eine verbesserte Übereinstimmung zu den Energiemeßwerten der Elektronenspektroskopie. Die Änderungen des berechneten Dipolmoments bei derartigen Basisvariationen sind größer als bei früheren Methoden. Die Übereinstimmung mit dem Experiment wird, mit Ausnahme von Furan, jedoch verbessert.

     

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 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 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.     

Benzooxirene. Ab initio calculations

Ab initio calculations have been performed on benzooxirene, the corresponding oxo carbene (“ketocarbene”), and the transition state linking the two. At the highest level used, QCISD(T)/6-31G^*//MP2(FULL)/6-1G^* with MP2(FULL)/ 6-31G^* zero point energy corrections, the relative energies of the oxirene, the transition state and the carbene are 0, 24.6, and −17.8 kJ mol⁻¹. Correlation energy effects are very important in this system: at the QCISD(T) level the oxirene lies above the carbene, as at the MP4 and HF levels, but at the MP2 level the ordering is reversed. Benzooxirene is probably slightly nonplanar: the HF/6-31G^* geometry is C_2v but the MP2(Fermi contact)/6-31G^* geometry is C_s with a 6-/3-ring coplanarity deviation of about 6.9 °, although in the MP2(FULL)/6-31G^* geometry this is reduced to about 3.1 °.     

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 molecular dynamics calculations to study catalysis

The modern versions of the density functional theory (DFT), especially those using the generalized gradient approximation (GGA), have reached (almost) chemical accuracy and thus can be applied to study problems of real chemical interest such as catalysis. The important equations for the DFT, the local density approximation (LDA), and GGA are given. The full-potential linearized augmented plane wave method (LAPW) is used to check the accuracy of GGA in solids. The basic concepts of the ab initio molecular dynamics (MD) method by Car and Parrinello and its recent implementation using the projector augmented Wave (PAW) method which use a similar augmentation as LAPW are described. PAW applications to ferrocene and beryllocene are summarized, which illustrate that vibrational or fluxional behavior are well described. Sodalite, an aluminosilicate, is discussed as a generic zeolite in comparison with gmelinite. A study of the dynamics of such a system allows the determination of, e.g., the proton stretch vibrations which can be related to infrared spectra. This is illustrated for the OH stretch vibration of the acid site in silicon-rich sodalite. With this methodology, we are able to study the interaction of methanol trapped inside the cage structure of silicon-rich sodalite and to gain new insight into crucial steps of catalytic reactions, namely, the hydrogen-bonding and the possible protonation in this system, or a proton-exchange reaction. The strategies for parallelizing the PAW code are outlined. © 1997 John Wiley & Sons, Inc.     

Ab initio molecular orbital calculations on large lattice cluster models: Use of translational symmetry

Summary Translational symmetry has been shown to be useful in the calculation of electronic structures of large lattice models. The number of unique integrals has been derived for cases of different dimensionality. For the unique integrals zero screening and approximation methods are described. The method has been applied to arrays of hydrogen atoms and to a zincblende surface model. When the size of the system is increased the translationally unique integrals are shown to become either zero or they can be calculated by simple coulombic approximations.     

Ab initio valence-electron-only calculations on molecules: Test application to NaCl

A new method for performing valence-electron calculations is applied for the first time to a molecular system. The method contains no adjustable parameters and in the limit of a large basis set converges on the all-election frozen-core results.     

Ab initio calculations on urea

Multiconfiguration wave functions constructed from contracted Gaussian-lobe functions have been found for the ground and valence-excited states of urea. ICSCF molecular orbitals of the excited states were used as the parent configurations for the CI calculations except for the ¹A₁(π → π*) state. The ¹A₁(π → π*) state used as its parent configuration an orthogonal linear combination of natural orbitals obtained from the second root of a three-configuration SCF calculation. The lowest excited states are predicted to be the n π → π* and π → π* triplet states. The lowest singlet state is predicted to be the n π → π* state with an energy in good agreement with the one known UV band at 7.2 eV. The π → π* singlet state is predicted to be about 1.9 eV higher, contrary to several previous assignments which assumed the lowest band was a π → π* amide resonance band. The predicted ionization energy of 9.0 eV makes this and higher states autoionizing.     

Ab initio calculations on porphin

Ab initio SCF calculations are reported for the porphin molecule. The positions of the central protons have been optimized, and the equilibrium geometry is found to be a linear NH ? HN arrangement. The NH vibrational frequencies have been computed and are compared to experimentally measured quantities. Several low ionized states have also been studied in separate spin-restricted SCF calculations. The lowest state is found to have B_1u symmetry with an ionization potential of 8.0 eV.