Ab Initio 6-31G Research Articles

Boron and gallium esters derived from 2-(1,3,5-dithiazinan-5-yl)-ethanols

Compounds 2-(1,3,5-dithiazinan-5-yl)ethanol (1), 2-methyl-2-(1,3,5-dithiazinan-5-yl)ethanol (2) and 2-phenyl-2-(1,3,5-dithiazinan-5-yl)ethanol (3) reacted with BF3⋅OEt2 and BCl3⋅DMS, 1 and 2 with (Ph2B)O, and 2 and 3 with GaCl3 giving the corresponding chelates, bearing N→BF2O, N→BCl2O N→BPh2O, and N→GaCl2O groups. The internal coordination N→M (M = B or Ga) afforded spiro-compounds, where nitrogen is the central atom. Compounds were mainly characterized by 11 B, 1 H and 13 C NMR. The N→B or N→Ga coordination bond was detected in the 1 H spectra because coordination stops the ring inversion of the dithiazinane ring differentiating equatorial and axial protons. The presence of a sterogenic center at the ethanol arm (ligands 2 and 3), differentiates C4H2 and C6H2 upon coordination. Minimum energy structures for boron compounds were calculated (ab initio 6-31G(d,p)). VT NMR experiments for diphenyl borinic esters were performed in order to estimate the N→BPh2 coordination energy. X-ray diffraction analyses of the hydrochloride of ligand 1 and of the gallium compound prepared from 2 were obtained.

Gas-Phase Reactions and Rearrangements of Alkyl Esters with H3O+, NO+, and O2•+: A Selected Ion Flow Tube Study

Selected ion flow tube mass spectrometry (SIFT-MS) has been employed to study the ion-molecule reactions of 17 alkyl esters reacting with the common SIFT-MS reagent ions, H3O+, H3O+.nH2O (n = 1, 2, 3), NO+, and O2+. The majority of reactions were observed to proceed at or near collision rate, with the exception of H3O+.3H2O, which was found to be slow for 8 of 17 alkyl esters. Unexpected product ions in the form of the parent carboxylic acid cation were observed to arise from the H3O+ and NO+ reactions of some alkyl esters. The observed reactions have been probed by the ab initio CBS-4M and G2(MP2,SVP) methods. The postulated reaction pathway involves a 1,5 H atom migration from a beta-carbon onto the carbonyl oxygen.

Ab Initio G3-type/Statistical Theory Study of the Formation of Indene in Combustion Flames. I. Pathways Involving Benzene and Phenyl Radical

Ab initio G3(MP2,CC)//B3LYP calculations of the potential energy surface (PES) for the formation of indene involving hydrocarbon species abundant in combustion, including benzene, phenyl, propargyl, and methyl radicals, and acetylene, have been performed to investigate the build-up of an additional cyclopenta moiety over the existing six-member aromatic ring. They were followed by statistical calculations of high-pressure-limit thermal rate constants in the temperature range of 300-3000 K for all reaction steps utilizing conventional Rice-Ramsperger-Kassel-Marcus (RRKM) and transition-state (TST) theories. The hydrogen abstraction acetylene addition (HACA) type mechanism, which involves the formation of benzyl radical followed by addition of acetylene, is shown to have low barriers (12-16 kcal/mol) and to be a viable candidate to account for indene formation in combustion flames, such as the 1,3-butadiene flame, where this mechanism was earlier suggested as the major indene formation route (Granata et al. Combust. Flame 2002, 131, 273). The mechanism of indene formation involving the addition of propargyl radical to benzene and rearrangements on the C9H9 PES is demonstrated to have higher barriers for all reaction steps as compared to an alternative pathway, which starts from the recombination of phenyl and propargyl radicals and then proceeds by activation of the C9H8 adducts by H abstraction or elimination followed by five-member ring closure in C9H7 and H addition to the 2-indenyl radical. The suggested pathways represent potentially important contributors to the formation of indene in combustion flames, and the computed rate constants can be utilized in kinetic simulations of the reaction mechanisms leading to indene and to higher cyclopentafused polycyclic aromatic hydrocarbons (CP-PAH).

Carbon chains and the (5,5) single-walled nanotube: Structure and energetics versus length

Reliable thermochemistry is computed for infinite stretches of pure-carbon materials including acetylenic and cumulenic carbon chains, graphene sheet, and single-walled carbon nanotubes (SWCNTs) by connection to the properties of finite size molecules that grow into the infinitely long systems. Using ab initio G3 theory, the infinite cumulenic chain (:C[double bond]C[double bond]C[double bond]C:) is found to be 1.9+/-0.4 kcal/mol per carbon less stable in free energy at room temperature than the acetylenic chain (.C[triple bond]C-C[triple bond]C.) which is 24.0 kcal/mol less stable than graphite. The difference between carbon-carbon triple, double, and single bond lengths (1.257, 1.279, and 1.333 A, respectively) in infinite chains is evident but much less than with small hydrocarbon molecules. These results are used to evaluate the efficacy of similar calculations with the less rigorous PM3 semiempirical method on the (5,5) SWCNT, which is too large to be studied with high-level ab initio methods. The equilibrium electronic energy change for C(g)-->C[infinite (5,5) SWCNT] is -166.7 kcal/mol, while the corresponding free energy change at room temperature is -153.3 kcal/mol (6.7 kcal/mol less stable than graphite). A threefold alternation (6.866, 6.866, and 6.823 A) in the ring diameter of the equilibrium structure of infinitely long (5,5) SWCNT is apparent, although the stability of this structure over the constant diameter structure is small compared to the zero point energy of the nanotube. In general, different (n,m) SWCNTs have different infinite tube energetics, as well as very different energetic trends that vary significantly with length, diameter, and capping.

Theoretical prediction of relative and absolute p Ka values of aminopyridines

This work presents a study aimed at the theoretical prediction of p K a values of aminopyridines, as a factor responsible for the activity of these compounds as blockers of the voltage-dependent K + channels. To cover a large range of p K a values, a total of seven substituted pyridines is considered as a calibration set: pyridine, 2-aminopyridine, 3-aminopyridine, 4-aminopyridine, 2-chloropyridine, 3-chloropyridine, and 4-methylpirydine. Using ab initio G1, G2 and G3 extrapolation methods, and the CPCM variant of the Polarizable Continuum Model for solvation, we calculate gas phase and solvation free energies. p K a values are obtained from these data using a thermodynamic cycle for describing protonation in aqueous and gas phases. The results show that the relatively inexpensive G1 level of theory is the most accurate at predicting p K a values in aminopyridines. The highest standard deviation with respect to the experimental data is 0.69 p K a units for absolute values calculations. The difference increases slightly to 0.74 p K a units when the p K a is computed relative to the pyridine molecule. Considering only compounds at least as basic as pyridine (the values of interest for bioactive aminopyridines) the error falls to 0.10 and 0.12 p K a units for the absolute and relative computations, respectively. The technique can be used to predict the effect of electronegative substituents in the p K a of 4-AP, the most active aminopyridine considered in this work. Thus, 2-chloro and 3-chloro-4-aminopyridine are taken into account. The results show a decrease of the p K a, suggesting that these compounds are less active than 4-AP at blocking the K + channel.

Theoretical analysis of the initial stages of the thermal decomposition of trinitromethane

The hybrid method B3LYP/6-311G* of density functional theory is used to optimize the geometries of nitroform and some intermediates of its decomposition (CH(NO 2 ) 2 , CH(NO 2 ) 2 ONO, CH(NO 2 ), and HC(O)NO) and to locate the transition states of the dissociation and isomerization reactions involving these species. The heat of formation of nitroform and of the intermediates of its decomposition and the Gibbs energies of activation of the reactions examined are calculated using the modern ab initio multilevel procedures G2M(CC5) and G2. The high-pressure limits of the rate constants of these reactions in the temperature range 300-2000 K are calculated using transition state theory or its variational analogue.

Quantum mechanical study of Burkholderia cepacia lipase enantioselectivity

Quantum mechanical, semiempirical (AM1) and ab initio (6-31G*) study of the Burkholderia cepacia lipase (BCL) catalysed reactions of the secondary alcohol esterification and its ester hydrolysis is presented. We have selected BCL for our study because of numerous experimental results available, but also because of its broad selectivity and stability that makes it interesting for industrial use. Previously we developed models for predicting lipase stereo-selectivity towards primary and secondary alcohols according to their structural parameters. In this work we show that not all of the experimentally determined binding modes are catalytically competent and that additional molecular modelling should be accomplished in order to find good starting points to study chemical reactions. The binding modes from which chemical modification of a substrate is possible are the most relevant for understanding enzyme selectivity and for the rational enzyme engineering. We also investigated the influence of the tetrahedral atom type, C and P, upon the energy barriers in the proton transfer reactions from the catalytic histidine (His286) to either the catalytic serine (Ser87) or the alcohol oxygen of the substrate.

Gas-Phase Structure of Protonated Histidine and Histidine Methyl Ester: Combined Experimental Mass Spectrometry and Theoretical ab Initio Study

Gas-phase H/D exchange experiments with CD3OD and D2O and quantum chemical ab initio G3(MP2) calculations were carried out on protonated histidine and protonated histidine methyl ester in order to elucidate their bonding and structure. The H/D exchange experiments show that both ions have three equivalent fast hydrogens and one appreciably slower exchangeable hydrogen assigned to the protonated amino group participating in a strong intramolecular hydrogen bond (IHB) with the nearest N(sp2) nitrogen of the imidazole fragment and to the distal ring NH-group, respectively. It is taken for granted that the proton exchange in the IHB is much faster than the H/D exchange. Unlike in other protonated amino acids (glycine, proline, phenylalanine, tyrosine, and tryptophan) studied earlier, the exchange rate of the carboxyl group in protonated histidine is slower than that of the amino group. The most stable conformers and the enthalpies of neutral and protonated histidine and its methyl ester are calculated at the G3(MP2) level of theory. It is shown that strong intramolecular hydrogen bonding between the amino group and the imidazole ring nitrogen sites is responsible for the stability and specific properties of the protonated histidine. It is found that the proton fluctuates between the amino and imidazole groups in the protonated form across an almost vanishing barrier. Proton affinity (PA) of histidine calculated by the G3(MP2) method is 233.2 and 232.4 kcal mol(-1) for protonation at the imidazole ring and at the amino group nitrogens, respectively, which is about 3-5 kcal mol(-1) lower than the reported experimental value.

The inhibition of mild steel corrosion in acidic solutions by 2,5-bis(4-pyridyl)-1,3,4-thiadiazole: Structure–activity correlation

The effect of 2,5-bis(4-pyridyl)-1,3,4-thiadiazole (4-PTH) on the corrosion of mild steel in acidic media (1 M HCl, 0.5 M H 2SO 4, 1 M HClO 4) has been investigated using weight loss measurements, electrochemical impedance spectroscopy and potentiodynamic polarisation. These studies have shown that 2,5-bis(4-pyridyl)-1,3,4-thiadiazole is good inhibitor for mild steel in 1 M HCl, 0.5 M H 2SO 4 and 1 M HClO 4 solutions, the better performances are seen in the case of 1 M HCl solutions. But in 1 M HClO 4, the 4-PTH stimulates corrosion at low concentrations. Polarisation curves indicate that the 4-PTH is a mixed-type inhibitor in all acidic media and E (%) is temperature-dependent. Adsorption on the mild steel surface follows the Langmuir isotherm model in all acidic media. The electronic properties obtained using the Hartree–Fock AB initio 3-21G quantum chemical approach, were correlated with the experimental efficiencies.

Extraordinary β-silyl effects on C–H, N–H, and O–H bond dissociation energies

Composite ab initio G3 calculations show that most of the β substituents have very little effects (less than 2 kcal/mol) on the C–H, N–H, and O–H bond dissociation energies (BDEs). However, β-silyl groups are found to be able to dramatically reduce the C–H, N–H, and O–H BDEs by ca. 3, 6, and 10 kcal/mol, respectively. Natural bond orbital analysis suggests that the extraordinary β-silyl effect is caused by the strong hyperconjugation interaction between the σ Si–C bonding orbital and the half-filled p-orbital of the radical center.

Theoretical calculation of self-assembled alkynyl thin films

PM3 calculations of monomer and dimer structures of H–C C–(CH 2) 6–C C–Sn and H–C C– p–C 6H 4–C C–Sn molecules gave geometries and energies comparable to ab initio 3-21G(d,p) and LANL2DZ methods, with more localized molecular orbitals. PM3 optimization of the PGO-S alkyl and phenyl repeat units illustrate the usefulness of the RRSM and PGO-S methods to find potential energy minima. MO analysis of the self-assembled monolayers showed the Sn–O headgroups extend π-conjugation of the monolayer chains to allow infinite thin films to act as semi-conducting materials.

Quantum chemical studies on EGDN and its monovalent ions

An explosive material, ethylene glycol dinitrate (EGDN) and its mono ionic forms have been subjected to semiempirical AM1 (UHF) and ab initio 6-31G (UHF) type quantum chemical analyses. The AM1 treatment reveals that the neutral and anionic forms are exothermic whereas the cation is endothermic. All of the systems are found to be stable (by AM1 and 6-31G methods) but the calculations indicate that plus and minus charge developments in AM1 treatment and minus charge development in 6-31G treatment cause drastic geometrical changes in the molecular structures resulting in bond elongation, possibly bond cleavage in esteric N–O bond.

Energetic and bonding study of hexamethylenetetramine and fourteen related cage molecules: An ab initio G3 (MP2) investigation

The ab initio G3(MP2)method has been applied to hexamethylenetetramine (HMT) and fourteen related cage systems. The agreement between the calculated and experimental molecular dimensions, which are available for five of the 15 cage species, ranges from satisfactory to excellent. In addition, the G3(MP2) heat of formation at 298 K for HMT is in excellent accord with experimental results. Hence, the calculated heats of formation for the other 14 cage systems should be reliable estimates.

Ab initio vs Molecular Mechanics Thermochemistry: Homocubanes.

The standard enthalpies of formation and strain energies for a series of homocubanes have been investigated by high-level ab initio G3(MP2)/B3LYP method. The relative stabilities of isomers are discussed. The comparison is made between the results of ab initio and molecular mechanics methods with the aim of assessing their performances. The usefulness of high-level calculations for generating thermochemical databases of relatively large molecules (e.g. C11H14) was also demonstrated.

Ab initio study of aniline and n-propylamine associates with nitrobenzene and m-cresol

An ab initio (6-31G**) study of binary associates of aniline and n-propylamine with nitrobenzene and m-cresol has been carried out. The structures corresponding to the total energy minimum of the system have been found for the associates, and their geometrical and energy characteristics have been determined. Basic types of intermolecular interactions have been established, and their effects on the reactivity of the amino group have been investigated.

DFT and HF Studies of the Geometry, Electronic Structure, and Vibrational Spectra of 2-Nitrotetraphenylporphyrin and Zinc 2-Nitrotetraphenylporphyrin

The ground-state geometries and electronic structures of 2-nitrotetraphenylporphyrin (H2-2-NO2-TPP) and zinc 2-nitrotetraphenylporphyrin (Zn-2-NO2-TPP) with Cs and C1 symmetry have been determined from density functional theory, using the Becke−Lee−Yang−Parr composite exchange-correlation functional (B3-LYP) and ab initio RHF method and 6-31G(d) basis set. The optimized geometries are then compared with the crystallographic data of related compounds. The energy and electronic structures of different conformers are analyzed and compared with each other. The conformers with C1 symmetry are found to be more stable than that of Cs symmetry. The relative order of the highest occupied a2u and a1u orbitals determined by B3LYP (a2u > a1u) is reversed by RHF (a1u > a2u). The vibrational wavenumber, IR, and Raman intensities are also calculated at B3LYP/6-31G(d) optimized geometries. The calculated wavenumbers are scaled by a uniform scaling factor and compared with the experimental one. Most of the scaled modes are found to be in good agreement with the observed fundamentals. A single β-NO2 substitution slightly changes the geometries, the vibrational wavenumbers, and the frontier orbitals energy level.

Accuracy of free energies of hydration using CM1 and CM3 atomic charges.

Absolute free energies of hydration (DeltaGhyd) have been computed for 25 diverse organic molecules using partial atomic charges derived from AM1 and PM3 wave functions via the CM1 and CM3 procedures of Cramer, Truhlar, and coworkers. Comparisons are made with results using charges fit to the electrostatic potential surface (EPS) from ab initio 6-31G* wave functions and from the OPLS-AA force field. OPLS Lennard-Jones parameters for the organic molecules were used together with the TIP4P water model in Monte Carlo simulations with free energy perturbation theory. Absolute free energies of hydration were computed for OPLS united-atom and all-atom methane by annihilating the solutes in water and in the gas phase, and absolute DeltaGhyd values for all other molecules were computed via transformation to one of these references. Optimal charge scaling factors were determined by minimizing the unsigned average error between experimental and calculated hydration free energies. The PM3-based charge models do not lead to lower average errors than obtained with the EPS charges for the subset of 13 molecules in the original study. However, improvement is obtained by scaling the CM1A partial charges by 1.14 and the CM3A charges by 1.15, which leads to average errors of 1.0 and 1.1 kcal/mol for the full set of 25 molecules. The scaled CM1A charges also yield the best results for the hydration of amides including the E/Z free-energy difference for N-methylacetamide in water.

The conversion of 3- and 4-hydroxybenzonitriles ( m- and p-cyanophenols) into oxyanions, followed by IR spectra, ab initio and density functional calculations

The conversion of 3- and 4-hydroxybenzonitriles ( m- and p-cyanophenols) into oxyanions has been followed by IR spectra, ab initio HF, MP2 6-31G(d) and density functional BLYP, B3LYP 6-31G(d) force field calculations. In a general agreement between theory and experiment, the conversion causes a 34 cm −1 frequency decrease in the cyano stretching band, 3.2-fold increase in its integrated intensity and other essential spectral changes in the para-isomer; for the meta-one the corresponding values are 13 cm −1 and 2.3-fold, respectively. According to the calculations, both molecule and anion of 4-hydroxybenzonitrile are more stable (due to the polar resonance) than the corresponding meta-substituted species. The strongest structural changes, caused by deprotonation, are the 0.105 Å shortenings of the Ph–O bonds, 0.054 Å lengthenings (mean values) of the adjacent CC bonds and essential bond angle changes in the phenylene rings near the oxyanionic centers. In the case of para-isomer these changes are related to the formation of a quasi- para-quinonoidal structure of the phenylene ring in the oxyanion. According to the electronic density analysis, a bit less (Mulliken) or a bit more (natural bond orbital) than halves of the anionic charges remain localized at the oxyanionic centers. Hydrogen bonds have also been discussed.

Experimental and Theoretical Evaluation of Proton Affinities of Furan, the Methylphenols, and the Related Anisoles

The proton affinities of furan, 2-, 3-, and 4-methylphenol, and the related anisoles have been determined with Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry. The proton affinity of furan is redetermined to be 812 kJ mol - 1 on the basis of the experimental equilibrium constant for the proton transfer to acetone. The present value is significantly higher than that recommended in the literature (803 kJ mol - 1 ), but in agreement with ab initio G3(MP2) calculations, which suggest a proton affinity of 814 kJ mol - 1 for the 2-position in furan. The determination of the equilibrium constant for the reaction between a protonated methylphenol or methylanisole and a suitable reference base results in the following proton affinities: 2-methylphenol, 832 kJ mol - 1 ; 3-methylphenol, 841 kJ mol - 1 ; 4-methylphenol, 814 kJ mol - 1 ; 2-methylanisole, 850 kJ mol - 1 ; 3-methylanisole, 860 kJ mol - 1 ; and 4-methylanisole, 841 kJ mol - 1 . Calculations at the G3(MP2) level indicate that the 4-position is the most basic site in the 2- and 3-methyl-substituted phenols, whereas almost the same proton affinity is obtained for the 2- and 4-position in 4-methylphenol. The G3(MP2) proton affinity for the most basic site in a given methylphenol is in agreement with the present experimental values.

Ab Initio vs Molecular Mechanics Thermochemistry: Homocubanes

The standard enthalpies of formation and strain energies for a series of homocubanes have been investigated by high-level ab initio G3(MP2)/B3LYP method. The relative stabilities of isomers are discussed. The comparison is made between the results of ab initio and molecular mechanics methods with the aim of assessing their performances. The usefulness of high-level calculations for generating thermochemical databases of relatively large molecules (e.g. C(11)H(14)) was also demonstrated.