Ab Initio 6-31G Research Articles

AB initio study of the structural, electronic, and nonlinear optical properties of pyrrole derivatives

We present ab initio Hartree-Fock 3-21G calculations on the geometric structure, electronic properties, and first-order (α) and second-order (β) polarizabilities of novel donor-acceptor charge-transfer molecules where the conjugated path contains a pyrrole ring with the nitrogen either in the oxidized imine state or in the reduced amine state; the donor is the amino group, and the acceptor is the nitro group. The results of our calculations are compared with those involving more conventional conjugated paths such as polyene linkages or phenyl of the pyrrole-containing conjugated segments.

Measurement and model calculations of the vibrational circular dichroism spectrum of 6,8-dioxabicyclo[3.2.1]octane

Also presented here for the same region are the complete assignment of the vibrational bands, and the calculated absorption and VCD intensities, based on a previously obtained harmonic ab initio 3-21G force field which was scaled and refined to fit 195 observed frequencies of the title compound and five analogues. Relative absorption intensities are predicted successfully by the atomic polar tensor expression (APT), but not with the fixed partial charge model (FPC)

Ab initio oligomer calculations of dynamic properties of polyacetylene

The electronic and dynamic properties of all-trans polyacetylene have been calculated on the basis of oligomer calculations on H–(CH)10–H and H–(CH)22–H at the ab initio 6-31G level. The calculated ir and Raman intensities are in good agreement with the experimental relative intensities.

Quantum-mechanical oligomer approach for the calculation of vibrational spectra of polymers

The force-constant matrix of an oligomer, composed of five or more repeat units with appropriate terminal groups, can be used to construct the force-constant matrix of the corresponding planar or helical polymer. The calculations on some typical polymers (polymeric sulfur, polyacetylene, and polyethylene) show that the oligomer approach is accurate enough to duplicate the vibrational frequencies of frozen-phonon calculations. The oligomer approach has much more predictive power if used in conjunction with some form of empirical scaling (scaled quantum-mechanical oligomer force field for polymers). ir and Raman selection rules for helical polymers are also discussed. Vibrational frequencies and intensities of polymeric sulfur and polyethylene have been calculated at the ab initio STO-3G, 4-31G, 6-31G, and 6-31G* basis-set levels. The agreement of frequencies with experiment is excellent. The quality of calculation is limited by the basis set and theoretical model used rather than the oligomer approach.

A study on the backbone/side-chain interaction in N-formyl-(L)serineamide

The N-formyl-serineamide (For-Ser-NH2), a model diamide for the conformational behaviour of the protein backbone at serine residue, has been gradient optimized for selected conformations at the abinitio 3-21G level. Previous molecular mechanics ECEPP/2 calculations suggested that the optimal side-chain (χ1, χ2) and backbone [Formula: see text] conformations are strongly coupled, due to intramolecular H-bonding formed between the side-chain hydroxyl group and the amide moiety. Four different side-chain geometries (I–IV) were considered at each of the four backbone conformations (α, β, β′, γ) giving a total 16 different critical points on the coupled [Formula: see text] surface. The very fact that upon changing the [Formula: see text] values the global minimum of (χ1, χ2) surface was shifted indicated clearly that the two subspaces are strongly coupled. The present theoretical results were compared to experimental peptide and protein geometries taken from the Cambridge Structure Database and from the Brookhaven Protein Data Bank, respectively. Keywords: conformation of a serinediamide, backbone side-chain interactions, topological analysis of potential energy surfaces, abinitio calculations.

Intramolecular hydrogen bonding of malondialdehyde and its monothio and dithio analogues studied by the PM3 method

The molecular geometries of all the possible conformations of malondialdehyde (MDA), thiomalondialdehyde (TMDA) and dithiomalondialdehyde (DTMDA) were optimized by means of the most recent semiempirical method MNDO-PM3 to test the performance of the new Hamiltonian in evaluating the most probable structures as well as the hydrogen-bond strengths. PM3 results are better than AMI ones in predicting the C-S and CS bond lengths and the energy of theS-H…S bridge, but unreliable geometries for the hydrogen-bonded and open tautomer of DTMDA were obtained. Ab initio 4-31G calculations carried out for these two conformations gave geometrical parameters which agree better with the AMI than with the PM3 ones.

Ab initio SCF investigation of β-alanine

The potential-energy surface of the neutral form of β-alanine was investigated with ab initio 4-31G SCF calculations. Geometries, energies and wavenumbers for all 20 symmetry unique local minima are reported together with the potential barriers of the reactions, which interconnect these minima. Intramolecular interactions involving the groups CO, OH and NH 2 were deduced from these informations.

"Flexible" water molecules in external electrostatic potentials

Effective pairwise potentials for «flexible» water molecules are discussed. It is pointed out that the dependence of the atomic charges on the valence bonds and angle (charge flux) leads to a strong coupling of the inter- and intramolecular coordinates. This coupling significantly modifies the electrostatic forces on the nuclei of the water molecule. It is further pointed out that the contribution of atomic dipoles to the electrostatic forces is comparable to the contribution of the molecular polarizability, Ab initio 6-31G ** Hartree-Fock parameters for charge flux and atomic dipoles that can be used in water potentials are suggested

Reliability of the AM1 wavefunction to compute molecular electrostatic potentials

The reliability of the semiempirical AM1 wavefunction for computing molecular electrostatic potentials (MEP) is examined. The differences between this procedure and the ab initio SCF MEP lie in the freezing of the inner electrons and in the origin of the first-order density matrix. The characteristics of the AM1-derived MEPs are compared with those of MEPs computed from the MNDO and ab initio (STO-3G, 6-31G and 6-31G *) wavefunctions. The statistical analysis of MEP minima points out the goodness of the AM1 wavefunction for reproducing the depth of the ab initio 6-31G * MEP minima originating from well-defined lone pairs.

Acidities of ortho substituted phenols

Theoretical calculations have been made for the relative acidities of ortho substituted phenols at both the ab-initio STO-3G and 3-21G bases. The agreement with experimental results is similar to that found with meta or para substituted phenols, indicating clearly the usefulness of such calculations in ortho substituted benzenes. Interestingly, the results of calculations over a range of ortho substituents are linear against those for the corresponding para substituents, suggesting that steric effects are unimportant in determining the relative acidities of ortho substituted phenols.

Theoretical study of the hydroxyl nucleophilic attack on the 6-aminopyrimidine molecule: functional implications in the reaction mechanism of nucleoside deaminative enzymes

A quantum chemical study of hydroxyl attack on a reduced model of adenosine and cytidine has been performed by using both semiempirical MNDO and ab initio 4-31G methodologies. The biochemical implications of the results obtained on the mechanism of the reaction of both adenosine and cytidine deaminases are extensively discussed in the context of previous theoretical and experimental data. Finally, several possible «microscopic» reaction mechanisms for these enzymes are suggested

Amidines. Part 33. Full ab initio 3-21G optimization of the molecular structures of fluoro derivatives of formamidine and their protonation products. Quantitative structure–basicity relations of amidines

ab initio 3-21G geometry optimizations for eight derivatives of formamidine with up to three fluorine substituents, and all corresponding formamidinium cations protonated at the imino nitrogen, show strong conjugation in the amidine system between the CN double bond and the lone electron pair on the amino nitrogen atom. Substitution with fluorine at each atom of the NC–N group exerts considerable influence on this conjugation, and as a result the geometry of the molecule can be drastically changed. The introduction of the electron-withdrawing fluorine substituent at the amino nitrogen atom of formamidines leads to a tetrahedral bond arrangement at this atom. For amidines unsubstituted at the amino group and for all protonated systems, co-planarity is predicted by calculation, and all substituents lie in the plane of the NC–N group.Calculations of energies of protonations as well as proton transfer between amidines and ammonia show that changes in basicities of amidines caused by substitution at certain sites of the amidine group depend on polar effects of substituents at other sites. This provides an explanation for the observed changes of ρ values caused by substituents at different sites in correlations of experimental pka values of amidines with Hammett σ constants. The influence of substitution at both nitrogen atoms on tautomeric equilibria in amidines is discussed.

Rotational potential energy functions in ethylchlorosilane,(chloromethyl)methylsilane, and (chloromethyl) chlorosilane: MM2, MNDO, and ab initio calculations

The rotational potential energy functions of ethylchlorosilane (ECS), (chloromethyl) methylsilane (CMMS),and (chloromethyl) chlorosilane (CMOS) have been examined by ab initio (GAUSSIAN-82), semi-empirical (MNDO), and molecular mechanics (MM2) techniques, and have been compared with those of carbon analogs, i.e. 1 -chloropropane (CP) and 1,2-dichloroethane (DCE). While ab initio (3-21G( ∗)) calculations give excellent agreement with available experimental data in geometries and relative conformational energies, the MNDO technique shows a definite shortcoming, namely, that relative energies are unacceptably insensitive to conformational changes involving rotation around the central C-C and C-Si bonds, even though the geometries are reproduced reasonably. On the basis of these calculations, we have developed additional MM2 torsional parameters and have applied these in a conformational study of the title compounds. Interpretation of our calculations suggests that: (1) silicon compounds barely show steric congestion, which means that the bonded and non-bonded energy terms are less important factors when compared with corresponding carbon analogs. (2) ECS and CMMS show the “ gauche effect”, which is due to attractive interaction between methyl and chlorine. (3) In CMCS, as two chlorine atoms approach, the repulsive interaction between the two vicinalchlorine atoms rises, apparently as a result of the near parallel alignment between two large vicinal C-Cl and Si-Cl bond dipoles.

A theoretical study of the proton affinities of water, alcohols, and ethers: absolute versus relative basicities

In this work we report the proton affinities (Epa) of water, seven alcohols, and seventeen cyclic and acyclic ethers, as measured by ion cyclotron resonance spectroscopy (ICR) with respect to the same ‘basicity ladder.’ The Epa for selected compounds have been calculated by MNDO, AM1, and ab initio(3-21G and, in some cases, 4-31 G*//4-31 G and 6-31 G*//6-31 G) methods. These results are used for a comparison of the various computational techniques and for the analysis of structural effects on the neutral and protonated species. Methyl and other alkyl affinities of aliphatic alcohols are determined and discussed. The experimental Epa are treated by correlation analysis methods.

Infrared matrix isolation and ab initio studies of 3(2H)-pyridazinone and photoproduced 3-hyroxypyridazine

The infrared spectra of 3(2H)-pyridazinone and its rare tautomeric form, 3-hydroxypyridazine, isolated in an argon matrix are reported and discussed. Only the first tautomer was observed after deposition of the matrix. The second form was photochemically produced after ultraviolet irradiation of the matrix (phototautomeric process). This form has never been observed experimentally before. Ab initio 3-21G normal coordinate calculations were carried out for these two forms and on that basis, an assignment of the experimental spectra of both compounds was performed.

The lone electron pair and crystal packing: observations on pyramidal YEL3ε species, abinitio calculations, and the crystal structures of Me3SOI, Et3SI, (Me3S)2SnCl6, (Me3SO)2SnCl6, and (Et3S)2SnCl6

The results of a detailed analysis of typical situations in crystals containing trigonal-pyramidal YEL3ε species are used to argue that, perse, the lone electron pair (E, LP) on the Y atom determines neither the crystal structure nor the orientation of the YEL3ε units in the crystal. Considered as a space-filling entity, the LP has practically no effective volume of its own. Whatever space-filling or orienting properties may be associated with the presence of the LP, they are not autonomous; they arise from the intrinsic stereochemical involvement of the LP in the geometry of and the charge distribution in the free YEL3ε ion or molecule and hence from the consequences of this geometry for crystal packing. Abinitio (6-31G*) calculations show that the electron density in the region of the LP in an ion is only slightly perturbed by the charge on the counter ion at distances observed in crystals. There is considerable similarity in the electron density distribution in the LP region of Y between free anionic (SO32−) and free cationic (Me3S+) species. The problem of the so-called stereochemical inertness of the LP in the 14-electron octahedral YEX62− ions in crystals is examined in detail. It is concluded that the crystallographic Oh symmetry of the ion in cubic crystals is the result of dynamic averaging of possible orientations of the inherently noncubic YX62− octahedron (cf. the abinitio results for SeCl62−). Such averaging also appears to be responsible for the stereochemical "activation" or "inactivation" of the LP in thermally induced crystallographic transitions in the AYX3 halide perovskites and related crystals. To provide a firmer basis for the discussion of the LP, the crystal structures of the five title compounds have been determined. The crystal chemistry of these and related compounds is discussed. Keywords: abinitio calculations, Me3S+ and SeCl62−; group V trihalides; lone electron pair; trialkylsulfonium salts; VSEPR theory.

The structure of CH 3NH 3+ in aqueous solution: An ab initio study

The structures of CH 3NH 3 + (H 2O) n ( n=0, 1, 2, 3, 4, 5, 6, 9, 10) and (H 2O) 3CH 3NH 3 + (H 2O) m ( m=0, 1, 2, 3, 6) clusters in the gas phase are determined using ab initio MINI-1 and 4-31G (for n=0, 1, 2, 3, 4, 5, 6; m=0, 1, 2, 3) basis sets. Excellent correlations are found between the structural parameters and charge on the H of the outermost H 2O in CH 3NH 3 + (H 2O) m . Based on these structures, the structure of CH 3NH 3 + in aqueous solution is predicted.

ChemInform Abstract: Thermochemistry of Borabenzene and Borepin

Aspects of the thermochemistry of borabenzene and borepin are studied by means of homodesmic reactions and ab initio 6-31G* SCF energies. Model compounds for these analyses include divinylborane, 3-bora-heptatriene, and the pentadienyl and heptatrienyl cations

On the correlation between conformational parameters and deformation energies in syn-1,6 : 8,13-diimino[14]annulenes with connected bridges

Fox six bridged diimino [14] annulenes with the two bridging N atoms connected by aliphatic chains (molecules 1–6), isodesmic alkyl separation enthalpies have been calculated in the MINDO/3 approximation, taking syn-1,6 : 8,13- bis (methylimino) [14] annulene as the reference compound. Calculated geometries for the annulenes are in satisfactory agreement with X-ray diffraction results, already known for molecules, 1, 2 and 3, and presented here for the first time for molecules 4, 5 and 6. Conformational features and their main trends as n (the number of methylene fragments in the aliphatic chain) increases from 1 to 6, are discussed both on the basis of the experimental geometries and in terms of the semiempirical results for the isodesmic reactions. The corresponding Δ H r values show a well-defined correlation both with the dihedral angles at the anthracene skeleton and the degree of pyramidalization of the nitrogen bridging atoms. The greater “softness” of the latter with respect to the “stiffness” of methine groups, which can replace the N atoms in the corresponding isoelectronic annulenes, has been quantitatively evaluated by ab initio 6-31G * calculations on four simple molecules (NH 3, CH 4,NH 2CH 2NH 2, and CH 3CH 2 CH 3).

Thermochemistry of borabenzene and borepin

Aspects of the thermochemistry of borabenzene and borepin are studied by means of homodesmic reactions and ab initio 6-31G* SCF energies. Model compounds for these analyses include divinylborane, 3-bora-heptatriene, and the pentadienyl and heptatrienyl cations