Ab Initio SCF Methods Research Articles

Comparative studies for selective deprotection of the N-arylideneamino moiety from heterocyclic amides: kinetic and theoretical studies. Part 2

4-Benzylideneamino-1,2,4-triazine-3,5(2H,4H)-diones (2–5), 6-styryl-1,2,4-triazine-3,5(2H,4H)-dione (6), and 6-styryl-2,3-dihydro-3-thioxo-1,2,4-triazin-5(4H)-one (7) were synthesized and pyrolyzed in the gas phase. The kinetic effect of changing the substituent on the triazine ring from hydrogen to methyl, phenyl, and styryl was measured. Analyses of the pyrolyzates of 2–5 showed the elimination products to be benzonitrile and the triazine fragment, while the pyrolyzates of 6 and 7 reveal the formation of cis- and trans-cinnamonitriles. Theoretical study of the pyrolysis reactions of 2–5 using an ab initio SCF method was investigated.

Free electron model in cluster structure theory. Electronic structures of [Mo6S8(CN)6]6−, [Mo6Se8(CN)6]6−, [Re6S8(CN)6]4−, and Rh6(CO)16 clusters

The results of quantum chemical calculations of the electronic structure and geometry of octahedral clusters [Mo6S8(CN)6]6−, [Mo6Se8(CN)6]6−, [Re6S8(CN)6]4−, and Rh6(CO)16 by the ab initio SCF (RHF) and DFT (B3LYP) methods with various basis sets are presented. The electronic states of the clusters under study in ideal spherically symmetric potential were classified in the orbital quantum number l (1s, 1p, 1d, 1f, 1g, 1h, 1i), l = 0–6. In real crystal field with Oh symmetry these states are split. The calculated new electronic states were matched to the irreducible representations of the point symmetry group Oh. The polarizabilities of the compounds considered are 55–65 A3. A new model for the electronic structure of octahedral clusters containing M6 groups was proposed. The model is based on the idea of free electrons moving in spherically symmetric potential field.

Which base triplet stabilizes triple helix? Ab initio SCF and density functional methods of calculations on some base triplets

Ab initio SCF and density functional methods of calculation have been performed for determining the stability of some experimentally observed base triplets of triple helix. The computed binding energies provide the importance of Hoogsteen hydrogen bonding in forming the stable triplets as observed in C +GC, TAT, GGC and AAT triplets while mismatched triplets GTA, C +AT and TTA show no such bonding. The Hoogsteen hydrogen bonding pattern that emerges in some triplets are contributed from the favorable binding between Watson Crick and single base, whereas the structure of less stable triplets do not show such hydrogen bonding. The substantial differences in the binding energies of triplets obtained from SCF and density functional methods explain the sequence specificity in triplet formation.

Ab initio investigation of electrophilic addition reaction of chlorine to homobenzonorbornadiene

The electronic and geometric structures of homobenzonorbornadiene (HBNB) molecule were investigated by ab initio HF/3-21G*, HF/3-21G**, HF/6-31G* and HF/6-311G* methods. The double bond of molecule is endo pyramidalized. HF/3-21G* calculations have been performed for 1:1 molecular system of chlorine with HBNB and their stable configurations have been determined. The stable configurations of the HBNB–Cl 2 system correspond to HBNB⋯Cl 2(exo) and HBNB⋯Cl 2(endo) molecular complexes which are formed by the exo and endo orientation of Cl 2 molecule to the double bond of HBNB in axial position, respectively. Exo-molecular complex has been found to be relatively more stable than the endo-complex. The cationic intermediates of the reaction have been studied by ab initio SCF method in 3-21G*, 3-21G**, 6-31G* and 6-311G* basis. Exo-chloronium cation is found to be more stable than endo-chloronium cation. Exo-facial selectivity should be observed in the addition reaction to HBNB of chlorine. Nonclassical delocalized (IV) cation is more stable than the classical rearranged (V) cation. For this reason, the conversion of the cation(IV) to ionV is not easy. The nonclassical delocalized chlorocarbonium cation(IV) is the most stable ion among the cationic intermediates, and the ionic addition reactions occurs via this cation. The mechanism of the addition reaction also discussed.

Kinetics and mechanism of thermal gas-phase elimination of α- and β- ( N-arylamino)propanoic acid: experimental and theoretical analysis

2-( N-Phenylamino)propanoic acid 1a and 3-( N-phenylamino)-propanoic acid 2a together with four of their aryl analogues were pyrolysed in the gas-phase. The reactions were homogeneous and free from catalytic and radical pathways. Analysis of the pyrolysate of 1 showed the elimination products to be carbon monoxide, acetaldehyde and aniline, while the pyrolysate of 2 reveals the formation of acrylic acid in addition to aniline. Theoretical study of the pyrolysis of 2 using an ab initio SCF method lend support to a reaction pathway involving a 4-membered cyclic transition state.

Electronic density distorsion of NiO 2 due to intercalation by Li

High resolution measurements of Compton profiles of Li x NiO 2 have been carried out using 60 keV photons at ESRF (Grenoble, France). Theoretical profiles are obtained using the plane wave expansion of wave functions calculated using ab-initio SCF method. Theory and experiment are in good agreement. We have further decomposed the charge density modification into a rigid charge transfer from lithium to e g ∗ states of NiO 2 and the distorsion of NiO 2 charge density mainly due to Ni–O bond changes resulting from lattice parameter change and Jahn-Teller effect.

Ab Initio Structure Investigation of the Enol Forms of β-Diketones RCOCH2COR (R = H, CH3, CF3)

The geometrical parameters, force field parameters, and vibrational frequencies of the enol forms of β-diketones RCOCH2COR (R = H, CH3, CF3) were calculated using the ab initio MO LCAO SCF method involving broad bases of Cartesian Gaussian functions. For acetylacetone (R = CH3), the potential surface of rotation of the two methyl groups was investigated in detail, and the minimal energy route of the transfer of the hydroxyl proton inside the chelate ring was calculated. For hexafluoroacetylacetone (R = CF3) and malonic dialdehyde (R = H), calculations were carried out only for stationary points on the potential energy surface. For all the geometrical configurations under study, the relative energies were refined with inclusion of electron correlation in terms of second-, third-, and fourth-order Moller–Plesset perturbation theory; for molecules with R = H, CH3, the configuration interaction procedure taking account of all single and double excitations was additionally employed. The experimental and theoretical data are compared with those available in the literature. The substituent effect on the geometrical and electronic structure of the chelate ring is studied.

Ab Initio SCF and DFT Studies on Solvent Effects on Intramolecular Rearrangement Reactions

Two intramolecular rearrangement reactions trans-N2H2 → cis-N2H2 and F2S2 → FSSF have been studied in both gas and solution phases using the ab initio SCF method at the Hartree−Fock level as well as using density functional theory with B3LYP exchange-correlation functionals with 6-311G** and 6-311++G** basis sets. Polarizability calculations have been performed using Sadlej's basis set also. Maximum hardness and minimum polarizability principles have been found to be valid in almost all cases. For the former reaction, the maximum molecular valency principle is obeyed. Reactions become more favorable, thermodynamically and kinetically, in the presence of the solvent. Variation of electrophilicity along the internal reaction coordinate is analyzed in terms of the profiles of the global electrophilicity index as well as condensed electrophilic Fukui functions at different atomic sites. It is found that electrophilicity decreases in the solution phase.

Endohedral analogs of ferrocene: ab initio theoretical predictions

The problem of the existence of endohedral analogs of ferrocene is discussed. It is shown that radical CorH 5 , where Cor is corannulene C 20H 10 and five atoms H are added to the α-positions relative to the five-membered cycle ( pent*) of Cor, can form stable polyhedral dimer D 2 h -C 40H 30 (D). The ground state of D is triplet. The energy of dimerization of CorH 5 is equal to 175 kcal mol −1. The geometric and electronic structure of hypothetical endohedral complex D 5 d -2η 5-Fe@D ( 1) and its isomer D 5 d -2η 5-Fe(CorH 5) 2 ( 1b), which is a sandwich complex, are simulated by the ab initio MO LCAO SCF method (HF/3-21G). It is found that the energy of 1 is less than the energy of 1b by 171 kcal mol −1. The energies of the Fe pent* bond in complexes 1 (115 kcal mol −1) and 1b (111 kcal mol −1) are close to those of the FeCp bond in bis(cyclopentadienyl)iron FeCp 2 (110 kcal mol −1). Complex 1 and also complex D 5 d -2η 5-Fe@C 40H 10 ( 2), carbon skeletons of which have an analogous structure to 1 and with ten H added to the α-positions relative to polar pentagons ( pent*), can be considered as endohedral analogs of ferrocene. Atom Fe in these complexes interacts with atoms of both polar pentagons. The binding energy of the atom Fe with the polyhedral fragment C 40H 10 of 2 is a bit less than in 1 (on 6 kcal mol −1).

Validity of the Minimum Polarizability Principle in Molecular Vibrations and Internal Rotations: An ab Initio SCF Study

Molecular vibrations in ammonia (NH3) and hydrogen sulfide (H2S), and internal rotations in hydrogen peroxide (HOOH), hydrogen thioperoxide (HSOH), hydrogen persulfide (HSSH), and ethylene (C2H4) are studied using ab initio SCF methods at the Hartree−Fock level using a standard Pople 6-311G** basis set. Polarizability values are calculated using both Pople's and Sadlej's basis sets. Any nontotally symmetric distortion in bond length or bond angle along the vibrational symmetry coordinates of a molecule around its equilibrium geometry decreases the equilibrium hardness value and increases the equilibrium polarizability value. During rotational isomerization the minimum energy conformation corresponds to the maximum hardness and minimum polarizability values and the maximum energy conformation corresponds to the minimum hardness and maximum polarizability values. Density functional calculations confirm these observed trends. In general we have found that the conditions of maximum hardness and minimum polarizability complement the minimum energy criterion for molecular stability.

Theoretical study of mexiletine and its interaction with cationic and anionic receptor sites

Theoretical methods are applied to study the antiarrhythmic (AA) mexiletine (1-(2,6-dimethylphenoxy)-2-aminopropane). The AM1 method is used to construct a three-centre binding model for this drug. This model consists of an amine nitrogen atom that is protonated to a higher degree at physiological pH, flat hydrophobic regions of aromatic rings and additional functional groups with lone electron pairs of oxygen. Based on these ideas, a model for the binding of mexiletine at the transmembrane protein was constructed. An ab initio SCF method was used to study the two-component mexiletine–receptor binding site composed of acetate (Glu −, Asp −) and protonated methylamine (Lys +, Arg +). The binding of mexiletine to the receptor may be understood by considering a two-step process of recognition and binding of AA to its receptor. Within this model the mexiletine cation is recognised in the first step and bonded to the negatively-charged part of the receptor. In a subsequent step, the interaction between the amide oxygen and cationic amine group of the membrane protein may follow.

The intermolecular interaction between amines and F 2. An ab initio study

Intermolecular interactions between the simple amines NH 3, CH 3NH 2, (CH 3) 2NH, and (CH 3) 3N and the F 2 molecule were investigated by ab initio SCF and MP2 methods, and with a density functional theory approach. In agreement with rotational spectroscopic data, the ammonia–F 2 complex behaves like a weakly bound intermolecular complex with modest intramolecular relaxation of the constituent monomers. Upon successive methyl substitution the interaction energy between the amine and F 2 increases systematically and these complexes should be described as charge transfer complexes with essential contributions originating from intramolecular structure relaxations in the amine and in F 2. The F 2 distance in these complexes is widened by 0.3–0.4 Å relative to the isolated F 2 molecule, and the N⋯F distance shrinks from 2.6 Å in ammonia–F 2 to 1.84 Å in methylamine–F 2 and remains approximately at that value in the other two complexes.

Hydrogen Bonding and Intermolecular Vibrations of 6-Hydroxyquinoline·H2O in the S0 and S1 States

A combined spectroscopic and ab initio theoretical study of the hydrogen-bonded 6-hydroxyquinoline·H2O complex was performed. 6-Hydroxyquinoline (6-HQ) is bifunctional, acting as an H-bond donor at the O−H group and as an acceptor at the N atom in bulk aqueous solution. Excited-state proton transfer (ESPT) from 6-HQ to the solvent occurs adiabatically in the S1 state, involving proton transfer at both functional groups. We have measured the mass- and rotamer-resolved S1 ← S0 vibronic spectra of cis- and trans rotamers of 6-HQ and of both the cis- and trans-6-HQ·H2O complexes in supersonic jets, using two-color resonant two-photon ionization spectroscopy and UV/UV spectral hole-burning techniques. Following the identification of the cis and trans rotamer electronic origins, dispersed fluorescence emission spectra of both rotamers of 6-HQ and 6-HQ·H2O were measured. The results are consistent with H2O bonded exclusively to the hydroxyl group and not to the N atom. Equilibrium structures were calculated by ab initio SCF methods for both rotamers of 6-HQ and both the cis- and trans-6-HQ·H2O complexes and give Cs symmetric structures with trans-linear hydrogen bonds. The calculated torsional transition states for H atom exchange on the H2O subunit are nonplanar with C1 symmetry. The calculated H-bond dissociation energies are ≈ 5.9 kcal/mol for the cis and ≈ 6.0 kcal/mol trans rotamer, slightly stronger than those of 2-naphthol·H2O (5.8 kcal/mol) and phenol·H2O (5.6 kcal/mol). Harmonic normal-mode frequencies allow detailed assignments of the observed inter- and intramolecular vibronic transitions. Agreement between theory and experiment is generally good, with the exception of the β2 wag mode.

Development of a New Force Field for Polynorbornene

A new force field has been customized for the variation of polynorbornene that contains a bicycloheptane group in the backbone structure. The force field was developed from ab initio density functional theory (DFT), and semiempirical electronic structure calculations for both stereochemical dimers of the 2,3 exo−exo isomer of polynorbornene. The bond length and bond angle parameters were determined using the HF/6-311G** ab initio SCF method. The intrinsic torsion potential was determined using the AM1 semiempirical method and the van der Waals parameters are kept same as in the Dreiding 2.21 force field. Both the bonded and torsional energy functions compared well to DFT calculations. The equilibrium geometry and the torsional energetics of the customized force field differ significantly from generic force fields such as Dreiding. Comparisons to experimentally determined geometry and infrared and Raman spectra were used to determine the optimum ab initio and semiempirical method to use for force field par...

The reaction of lithium with carbon dioxide studied by photoelectron spectroscopy

The interaction of CO 2 with clean Li at 120–320 K was studied using photoelectron spectroscopy. To assist in the interpretation of the spectra, the C 1s and O 1s core-level binding energies of various Li cluster compounds were calculated using an ab initio SCF method. To further understand the reaction pathway, we also studied the reaction of CO 2 with an O 2 pre-dosed Li surface, and the adsorption of CO on clean Li. The principal reactions occurring between CO 2 (1–30 L) and Li at 120–320 K are: CO 2⇒[CO 2] ads, 2[CO 2] ads⇒CO 2− 3+CO ads, probably via an oxalate, [C 2O 4] ads, intermediate, and: CO ads⇒C+O 2−, CO 2+O 2−⇒CO 2− 3. The relative rates of these reactions are temperature dependent. At 120 K, the main products are CO 2− 3, CO ads, and [CO 2] ads, whereas at 320 K the main products are O 2− and elemental carbon with a relatively small amount of CO 2− 3. The reactions are similar to those on the other alkali metals, Na, K and Cs, with the important exception being the much stronger interaction with CO, leading to dissociation and carbon formation.

Ab initio calculations of hardness and chemical potential of open shell systems using SCF, MP2 and MP4 methods

The hardness (η) and chemical potential (μ) of a number of open shell systems have been calculated by ab initio SCF, MP2 and MP4 methods. Both vertical and adiabatic values of ionisation potential ( I) and electron affinity (A) have been used to evaluate η and μ. The effect of spin contamination on various calculated quantities has been examined by performing UHF as well as ROHF calculations in appropriate cases. It has been observed that in the case of closely related species the hardness values obtained by almost all the methods of calculation employed here are capable of predicting the empirical hardness sequence of the corresponding anions. However, overall best agreement between theory and experiment is achieved only at the MP4 level. Barring minor exceptions the corresponding calculated values follow the experimental order for both η and μ.

Structure and gas phase stability of complexes L... M, where M = Li+, Na+, Mg2+ and L is formaldehyde, formic acid, formate anion, formamide and their sila derivatives

Ab initio SCF and DFT methods were used to characterize the gas-phase complexes of selected carbonyl and silacarbonyl bases with Li+, Na+ and Mg2+. Geometries were optimized at the Hartree-Fock ab initio and Becke 3LYP DFT levels with the 6-31G* basis set. Frequency computations were performed at the RHF/6-31G* level of theory. Interaction energies of the cation-coordinated systems also were determined with the MP2/6-31G* method. The effect of extension of basis set (to the 6-31+ G* basis) on the computed properties of anion-metal cation complexes was investigated. Calculated energies of formation vary as Mg2+ > Li++ > Na+. The Becke 3LYP DFT binding energies were comparable with those obtained at the correlated MP2 level and are in good agreement with available experimental data.

Conformational and Electrostatic Properties of Naphthazarin, Juglone, and Naphthoquinone: An Ab Initio Theoretical Study

Conformational features of naphthazarin, juglone, and naphthoquinone have been examined via ab initio (Hartree-Fock) SCF calculations at 3-21G level. The results suggest a planar structure for all the three molecules and internally hydrogen-bonded structure for naphthazarin and juglone to be their preferred conformation. The optimized structural features are essentially the same as their crystal geometries. Molecular electrostatic potential (MEP) calculations using ab initio SCF methods ranging from 3-21G to 6-31G levels have been performed to visualize their three-dimensional pharmacophoric patterns and topography. The results indicate that two factors-(1) the depth, extent, and relative location of negative potential around hydroxyl and quinonoid oxygens, and (ii) a gradual loss of negative potential over the molecular plane due to the presence and orientation of the hydroxyl groups in the phenolic part of the molecules-are crucial for recognition interaction of the compounds with their receptors. Aqueous solvation seems to have significant influence on the MEP profiles of the molecules. Although intrinsic nucleophilicity increases for all the compounds, including the different conformers, due to aqueous solvation, the intrinsic electrophilicity shows remarkable decrease for all. It appears that the acidic nature of the hydrogens in these compounds and conformers decreases sharply along with shifts of positions while going from the gas phase to the aqueous phase. These observations may help to explain the mechanism ofaction(s) of the anthracyclin family of cytotoxic antibiotics.

Theoretical study of the structures and racemization barriers of [n]helicenes (n = 3–6, 8)

The minima and saddlepoint structures of [n]helicenes (n = 3–6, 8) have been optimized by semiempirical AM1 and ab initio SCF methods. The racemization barriers have been calculated as the energy difference between the ground state minima possessing C2 symmetry and a twisted transition state having a Cs structure. A qualitatively correct dependence of the barrier heights with n in comparison with experimental data is obtained with both methods showing the reliability of the assumed reaction path. The relative large overestimations in the ab initio SCF barriers (10–14 kcal/mol for n > 5) are attributed to neglect of correlation energy which is larger in the more strained transition state than in the ground state structures. Single-point density-functional calculations yield barrier heights for the racemization of all helicenes accurate to ± 1 kcal/mol.

Interaction of local anaesthetics with an anionic receptor site. An ab initio SCF study on procaine, lidocaine, tocainide and mexiletine and their HCO 2− complexes

The ab initio SCF method was used to study the interaction of the local anaesthetics (LAs) procaine, lidocaine, tocainide and mexiletine with anionic receptor binding sites (Asp −, Glu −) represented by formate. In the case of procaine a two-centre binding site model for the binding of LAs was constructed. This model allows optimum interactions with the cationic amine part and the polar oxygen regions of procaine. The binding of procaine base was also investigated proving that this interaction is much weaker than the interaction of charged LA with its receptor binding sites. Finally, the effect of medium was studied (employing direct reaction field theory). The solvent changes the equilibrium geometry and decreases the energy of the complexes.