Ab Initio MO Study Research Articles

Ab initio MO study on direct production of H2O, N2O and CO3 from the respective CH2OO “Bee-sting-like” attack at H2, N2 and CO2

ContextWe have computationally elucidated the mechanism for formation of H2O, N2O and CO3 from the reactions of CH2OO with H2, N2 and CO2, respectively, by the direct attack of the terminal O atom of CH2OO. This unique mechanism, which is characteristically “bee-sting-like” in nature, was found to be closely parallel to their reactions with the O(1D) atom. Reactions with H2 and CO2 take place by side-on attack, while the N2 reaction occurs by end-on attack with predicted barriers, 19.4, 13.1 and 25.3 kcal.mol−1, respectively. The CO2 reaction with CH2OO was found to occur by producing the C2v CO3, O = C < (O)O, instead of its D3h conformer, essentially similar to the O(1D) + CO2 reaction. The rate constants for the three reactions have been computed by the transition state theory (TST) based on the predicted potential energy profiles. We have also utilized the isodesmic nature of the dative bond exchange in the N2 reaction, CH2O → O + N2 = CH2O + N2 → O, to estimate the heat of the formation of CH2OO. Based on the heat of reaction computed at the highest level of theory employed, we obtained ΔfHo0 (CH2OO) = 27.5 kcal.mol−1; the value agrees with the recent results within ± 1 kcal.mol−1.MethodsAll calculations were performed using Gaussian 16 software. Geometry, frequency, and IRC analysis calculations were conducted at the M06-2X/aug-cc-pVTZ level of theory. The heats of reaction have been evaluated at the highest level, CCSD(T)/CBS(T,Q,5)//M06-2x/aug-cc-pvTz.

An ab initio MO study of heavy atom effects on the zero-field splitting tensors of high-spin nitrenes: how the spin–orbit contributions are affected

The CASSCF and the hybrid CASSCF-MRMP2 methods are applied to the calculations of spin-spin and spin-orbit contributions to the zero-field splitting tensors (D tensors) of the halogen-substituted spin-septet 2,4,6-trinitrenopyridines, focusing on the heavy atom effects on the spin-orbit term of the D tensors (D(SO) tensors). The calculations reproduced experimentally determined |D| values within an error of 15%. Halogen substitutions at the 3,5-positions are less influential in the spin-spin dipolar (D(SS)) term of 2,4,6-trinitrenopyridines, although the D(SO) terms are strongly affected by the introduction of heavier halogens. The absolute sign of the D(SO) value (D = D(ZZ) - (D(XX) + D(YY))/2) of 3,5-dibromo derivative 3 is predicted to be negative, which contradicts the Pederson-Khanna (PK) DFT result previously reported. The large negative contributions to the D(SO) value of 3 arise from the excited spin-septet states ascribed mainly to the excitations of in-plane lone pair of bromine atoms → SOMO of π nature. The importance of the excited states involving electron transitions from the lone pair orbital of the halogen atom is also confirmed in the D(SO) tensors of halogen-substituted para-phenylnitrenes. A new scheme based on the orbital region partitioning is proposed for the analysis of the D(SO) tensors as calculated by means of the PK-DFT approach.

Conformational behaviors of 1,7-dioxa-spiro[5,5]undecane and its dithia and diselena analogs in relation to the anomeric effect: A hybrid-DFT, ab initio MO study and NBO interpretation

NBO analysis, hybrid density functional theory (B3LYP/6-311+G **//B3LYP/6-311+G **) and ab initio molecular orbital (MP2/6-311+G **//B3LYP/6-311+G **) based methods were used to study the impacts of the anomeric effects ( AE) associated with electron delocalization, total dipole differences and steric repulsion effects on the conformational properties of 1,7-dioxa-spiro[5,5]undecane ( 1), 1,7-dithia-spiro[5,5]undecane ( 2) and 1,7-diselena-spiro[5,5]undecane ( 3). Both methods showed the greater stability of conformations A (in which two heteroatoms having each an electron pair oriented antiperiplanar to the carbon–heteroatom bond) compared to their corresponding conformations B (with only one electron pair oriented antiperiplanar to the carbon–heteroatom bond) and C (without electron pair oriented antiperiplanar to the carbon–heteroatom bond). B3LYP/6-311+G ** method showed that total Gibbs free energy difference ( G C − G A and G B − G A) values (i.e . Δ G C–A and Δ G B–A) between conformations A, B and C decrease from compound 1 to compound 3. The NBO analysis of donor–acceptor (LP→σ *) showed that the AE is in favor of conformations A. The AE C–B, AE B–A and AE C–A values calculated (i.e. AE C– AE B, AE B– AE A, AE C– AE A) decrease from compound 1 to compound 3. The calculated total dipole moment values decrease from conformation A to conformation C. The calculated total dipole moment difference ( μ C − μ B, μ B − μ A, μ C − μ A) values between conformations C, B and A increase from conformations C–B to C–A (i.e. Δ μ C–B < Δ μ B–A < Δ μ C–A). However, the variations of the calculated Δ μ C–B, Δ μ B–A and Δ μ C–A values are not in the same trend observed for the corresponding Δ G values. Therefore, the total dipole moment differences do not seem to be sufficient to account for conformation A preferences in compounds 1–3. Although total steric exchange energy ( TSEE) values in conformations A of compounds 1–3 are smaller than those of their corresponding conformations B and C, the calculated Δ( TSEE) values between conformations A, B and C cannot explain the variations of the total energy differences (e.g ., Δ G C–A and Δ G B–A) from compound 1 to compound 3. These findings led to the proposal that the AE, due to LP ax M 1 → σ C 2 – M 7 ∗ hyperconjugation effect, is a reasonable descriptor of the total energy differences between the various conformations of compounds 1–3 compared to the total dipole moment differences and steric effects.

ChemInform Abstract: Structure and Formation Mechanisms of Methyl- and Dimethylacetylene Dimer Cations: ESR and ab initio MO Studies.

ChemInform Abstract: Structure and Formation Mechanisms of Methyl- and Dimethylacetylene Dimer Cations: ESR and ab initio MO Studies.

ChemInform Abstract: Experimental and ab initio MO Studies on (H2,N,O)+ Ions in the Gas Phase: Characterization of the Isomers H2NO+, HNOH+, and NOH+ 2 and the Mechanism of Unimolecular Dehydrogenation of (H2,N,O)+

ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.

Ionic dissociations of chlorosulfonic acid in microsolvated clusters: A density functional theory and ab initio MO study

Ionic dissociation of chlorosulfonic acid (HSO3Cl) in the molecular clusters HSO3Cl-(H2O)n (n = 1–4) and HSO3Cl-NH3-(H2O)n (n = 0–3) was investigated by density functional theory and ab initio molecular orbital theory. The equilibrium structures, binding energies, and thermodynamic properties, such as relative enthalpy and relative Gibbs free energy, and were calculated using the hybrid density functional (B3LYP) method and the second order Moller-Plesset approximation (MP2) method with the 6-311++G** basis set. Chlorosulfonic acid was found to require a minimum of three water molecules for ionization to occur and at least one water molecule to protonate ammonia. The corresponding clusters with fewer water molecules were found to be strongly hydrogen-bonded. The related properties and acid strength of chlorosulfonic acid were discussed and compared to the acid strengths of perchloric acid and sulfuric acid in the context of clusters with ammonia and water. The relative stabilities of these clusters were also investigated.

Ab initio MO study of potential energy surface of NH2 with CN reaction

AbstractAn extensive quantum chemical study of the potential energy surfaces (PES) for the association reaction of NH2 with CN and the subsequent isomerization and dissociation reactions has been carried out using density functional theory (DFT)/B3LYP/6‐311++G(3df,2p) level of theory on both singlet and triplet states. The reaction mechanism on the triplet surface is more complicated than that on the singlet surface. A total of 19 isomers and 46 transition states have been identified and characterized on the triplet PES. Among them, IM2 (IM2a), IM3 (IM3a, IM3b), and IM10 are the lowest‐lying isomers with thermodynamic stability. Twenty available dissociation channels, depending on the different initial isomers, have been identified. On the singlet surface, only 12 isomers and 16 transition states have been found, and among them IM1(S) and IM2(S) are the lowest‐lying isomers. The higher isomerization and dissociation barriers on the singlet surface indicate that the addition and the subsequent reactions of NH2+CN are most likely to occur on the triplet PES because of the lower barriers. A prediction can be made for the possible mechanism explaining the production of H+HNCN. Besides HNCN, other major products are NH+HCN and NH+HNC, which are produced by direct dissociation reactions from triplet IM2 and IM3, respectively. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006

Pharmacophoric Features of Biguanide Derivatives: An Electronic and Structural Analysis

The structure and electronic structure of drugs determine their mechanism of action. Correct structural representation of drugs helps in the proper identification of pharmacophoric features. Biguanide derivatives are a very important class of drugs, but their electronic structure was not clearly understood. Ab initio MO and density functional studies revealed the structure of the most stable tautomer of biguanide. (i) Electron delocalization, (ii) 1,3-H shift, (iii) 1,5-H shift, (iv) protonation, and (v) deprotonation processes, etc., have been investigated for biguanide. The molecular electrostatic potential (MESP) surfaces of neutral, protonated, and deprotonated biguanide have been shown to be similar in their most stable arrangements. The electrostatic potential of the complementary surface where these systems may bind also could be identified. Finally, the most stable structure of the important biguanide derivatives has been given after performing a conformational search.

Ab Initio MO Study on the Reaction Mechanism of Reduction of Hypophosphorous Acid

The reduction mechanism of hypophosphorous acid has been investigated by ab initio calculations at the MP2/6-311G(d,p) and CBS-QB3 levels. Two mechanisms with three possible pathways have been proposed for the process. The first mechanism that can be viewed as a direct mechanism contains two possible pathways, giving . The other, as an indirect mechanism, is . Theoretical calculations predict four transition states with the highest barrier height of in the indirect mechanism, which is the most likely pathway compared to others.

Ab initio MO and quasi-classical direct ab initio MD studies on the nitrogen inversion of trimethylamine

A coupled motion of the skeletal inversion and methyl torsion in trimethylamine is investigated theoretically at various levels up to MP4(SDQ)/aug-cc-pVTZ. Among possible structures, the pyramidal C 3v is the only minimum energy structure, and the planar C s is the transition state structure of the nitrogen inversion. Our best estimate of the barrier height (without zero-point energy) is 3290 cm −1. The quasi-classical direct ab initio MD using HF/6-31G* starting from the pyramidal C 3v structure indicates that the coupled methyl torsional motion is the primary factor for the nitrogen inversion of trimethylamine.

Origin of the Conformational Preference in alpha-Cyano-alpha-fluorophenylacetic acid Analogues: an ab initio MO study

Origin of the Conformational Preference in alpha-Cyano-alpha-fluorophenylacetic acid Analogues: an ab initio MO study

Ab initio MO study on [3 + 2] annulation using β-phenylthio-acryloylsilanes with alkyl methyl ketone enolates and its through-space/bond interaction analysis

Ab initio through-space/bond interaction analysis was applied to [3 + 2] annulation based on Brook rearrangement using beta-phenylthio-acryloylsilanes with alkyl methyl ketone enolates. An uncertain reaction mechanism, wherein a bulky cyclopentenol with large substituents on the same side of the five-membered ring was obtained as a major product, can be explained by the low activation energy of its reaction pathway. Intramolecular orbital interactions related to the carbanion generated by Brook rearrangement preferentially provide the stabilization of the reaction pathway to the bulky cyclopentenol (major product) compared with that provided to the non-bulky cyclopentenol (minor product). In addition, ab initio molecular orbital calculations suggest the existence of an E/Z conformational inversion after Brook rearrangement. This result accurately explains the loss of the E/Z stereochemical integrity in the starting materials of the experiment.

An ab initio MO study on structures and energetics of CH 2Si 2, CH 2Si 2+, and CH 2Si 2−

The geometric structures and isomeric stabilities of various stationary points in CH 2Si 2 neutral, cation and anion are investigated at the coupled-cluster singles, doubles (triples) (CCSD(T)) level of theory. For the geometrical survey, the basis sets used are of the cc-pVTZ for the neutral and cation. The final energies are calculated by the use of the CCSD(T) level of theory with the aug-cc-pVTZ basis set at their optimized geometries. To the competitive two-anion isomers, the aug-cc-pVTZ basis sets are applied. The global minimum ( N-1) of the CH 2Si 2 neutral has a quite different framework from those of the C 3H 2 (cyclopropenylidene) and Si 3H 2 (trisilacyclopropenylidene) neutrals. No competitive low-lying isomers are found in the CH 2Si 2 neutral. The attractive conformer ( C-1) is predicted for the most stable cation, where its framework is quite different from that of the neutral N-1. Both H atoms are connected to the same C atom, but each C–H bond length is different from each other. Two competitive anion isomers with positive (real) electron affinities are predicted. The framework of the most stable anion A-1 is quite similar to that of the cation C-1, whereas both H atoms are equally connected to the same C atom. The framework of the anion isomer A-2 is the same as that in the neutral N-1. The vertical and adiabatic ionization potentials from the most stable neutral N-1 are 9.02 and 8.71 eV, respectively. The adiabatic electron affinity of the lowest lying isomer N-1 is only 0.43 eV and the vertical electron detachment energy form the global minimum anion ( A-1) is 2.02 eV. The multi-centered Si–H–Si bonds are found in the neutral, cation, and anion.

Electronic state of push-pull alkenes: an experimental dynamic NMR and theoretical ab initio MO study.

The (1)H and (13)C NMR spectra of a number of push-pull alkenes were recorded and the (13)C chemical shifts calculated employing the GIAO perturbation method. Of the various levels of theory tried, MP2 calculations with a triple-zeta-valence basis set were found to be the most effective for providing reliable results. The effect of the solvent was also considered but only by single-point calculations. Generally, the agreement between the experimental and theoretically calculated (13)C chemical shifts was good with only the carbons of the carbonyl, thiocarbonyl, and cyano groups deviating significantly. The substituents on the different sides of the central C=C partial double bond were classified qualitatively with respect to their donor (S,S < S,N < N,N) and acceptor properties (C identical with N < C=O < C=S) and according to the ring size on the donor side (6 < 7 < 5). The geometries of both the ground (GS) and transition states (TS) of the restricted rotation about the central C=C partial double bond were also calculated at the HF and MP2 levels of theory and the free energy differences compared with the barriers to rotation determined experimentally by dynamic NMR spectroscopy. Structural differences between the various push-pull alkenes were reproduced well, but the barriers to rotation were generally overestimated theoretically. Nevertheless, by correlating the barriers to rotation and the length of the central C=C partial double bonds, the push-pull alkenes could be classified with respect to the amount of hydrogen bonding present, the extent of donor-acceptor interactions (the push-pull effect), and the level of steric hindrance within the molecules. Finally, by means of NBO analysis of a set of model push-pull alkenes (acceptors: -C identical with N, -CH=O, and -CH=S; donors: S, O, and NH), the occupation numbers of the bonding pi orbitals of the central C=C partial double bond were shown to quantitatively describe the acceptor powers of the substituents and the corresponding occupation numbers of the antibonding pi orbital the donor powers of the substituents. Thus, for the first time an estimation of both the acceptor and the donor properties of the substituents attached to the push-pull double bond have been separately quantified. Furthermore, both the balance between strong donor/weak acceptor substituents (and vice versa) and the additional influences on the barriers to rotation (hydrogen bonding and steric hindrance in the GSs and TSs) could be differentiated.

Origin of the diastereofacial selectivity in the nucleophilic addition to chiral acyclic ketones. An ab initio MO study

Ab initio MO calculations were carried out, at the MP2/6-311G(d,p)//MP2/6-31G(d) level, to investigate the conformational Gibbs energy of alkyl 1-phenylethyl ketones, C6H5CHCH3COR, 1 (R = CH3, C2H5, i-C3H7, t-C4H9). Rotamers a and a′ whereby R is synclinal to C6H5 and the benzylic methyl group is nearly eclipsed to CO have been shown to be the most stable in every case. Rotamer a is stabilized by a 5-member CH/π hydrogen bond and is more abundant than a′, which is stabilized by a less effective 6-member CH/π bond. The diastereomeric ratio of the product secondary alcohols in the nucleophilic addition to 1 was estimated on the basis of the ground-state rotamer distribution. The Gibbs energy of the diastereomeric transition states was also calculated for a model reaction (C6H5CHCH3COR + LiH) at the same level of approximation. The transition-state geometries leading to the predominant product are similar to those of the ground-state conformation. In geometries leading to the minor product, the relevant torsion angles are twisted to avoid unfavourable steric interactions. The short CH/π and CH/O distances suggest that these weak hydrogen bonds are operating in stabilizing the transition structures. The above two methods gave results consistent with each other. The mechanism of 1,2-asymmetric induction can thus be explained on the basis of the simple premise that the geometry of the transition state resembles the ground-state conformation of the substrate and the nucleophilic reagent approaches from the less hindered side of the carbonyl π-face.

Ab initio MO and DFT study of syn-sesquinorbornatrienyl dication and its isoelectronic boron analogueElectronic supplementary information (ESI) available: bond distances and bond angles of structures 6a, 6c, 7a and 7c calculated at the MP2/6-31+G* and B3LYP/6-31G* levels of theory (Table S1). See http://www.rsc.org/suppdata/nj/b4/b403802a/

The structure of dication 3, derived by replacement of the CH2 bridges in syn-sesquinorbornatriene (5) by the +CH groups and its isoelectronic boron analogue 4 were investigated using ab initio MP2/6-31G* and density functional B3LYP/6-31G* methods. Three energy minima were found in both species, all of them exhibiting strong bis-homoaromatic interaction of the electron deficient bridges with either central or peripheral double bond(s). The calculated 13C and 11B chemical shifts support this conclusion.

Structure and spectra of tetrasulfur S 4 – an ab initio MO study

The structures and relative stabilities of eight S 4 isomers were investigated by G3X(MP2), CCSD(T)/cc-pVTZ and MRCI/CASSCF calculations. The cis-planar (C 2v) structure is confirmed to be the global minimum of S 4, while the rectangular D 2h structure is calculated to be a transition state. The predicted stability order of various singlet S 4 isomers is C 2v>C 2h>C s>D 2d>D 3h. Calculated electronic absorption spectra [CIS/6-311 + G(3df)] and vibrational spectra [B3LYP/6-31G(2df)] allow a convincing assignment of the observed green absorbing species as the cis-planar (C 2v) structure (global minimum) and the red absorbing species as the trans-planar (C 2h) isomer, in distinct contrast to the previous assignments.

Electronegativity, Resonance, and Steric Effects and the Structure of Monosubstituted Benzene Rings: An ab Initio MO Study

The deformation of the carbon skeleton of the benzene ring under substituent impact has been analyzed from the structures of 74 monosubstituted derivatives, as determined by ab initio MO calculations. The geometry of the substituted ring is shown to contain valuable information on the electronegativity, resonance, and steric effects of the substituent, and also on other, more subtle effects, affecting primarily the length of the Cipso−Cortho bonds. The results obtained substantially augment previous knowledge from the analysis of experimental geometries (Domenicano, A.; Murray-Rust, P.; Vaciago, A. Acta Crystallogr., Sect. B 1983, 39, 457). Varying the electronegativity of the substituent causes a concerted change of the ring angles at the ipso, ortho, and para positions, coupled with a change in the Cipso−Cortho bond length. The values of the ipso angle span a remarkably wide range, 113−126°. Enhancing the resonance interaction between a substituent and the ring causes a complex pattern of angular distortions, arising from the superposition of two separate effects. The first originates from the decreased length of the C−X bond, and consists primarily in a concerted change of the ipso and ortho angles. It occurs irrespective of whether the substituent is a π donor or a π acceptor. The second effect is associated with π-charge alternation on the ring carbons. It involves all the internal ring angles, and depends on the substituent being a π donor or a π acceptor. These angular changes are generally accompanied by changes in all C−C bond lengths, as expected from an enhanced contribution of polar canonical forms to the electronic structure of the molecule. By using symmetry coordinates, we have derived two orthogonal linear combinations of the internal ring angles, SE and SR, measuring the electronegativity and resonance effects of a substituent, respectively, as seen from their impact on the ring geometry. SE and SR values are affected in a typical way by steric effects.

Ab Initio MO Studies on Polysilane Oligomer Radical Anions as Model Molecules of Polysilane Radical Anions

Polysilane oligomer radical anions with up to six Si atoms have been theoretically investigated as model molecules of high polymer polysilane radical anions by ab initio MO theory. According to the calculated results, the polysilane oligomer radical anions can exist as bound anions having a σ-type ground state with an unpaired electron occupying a Si−Si antibonding σ* orbital. They are stabilized with an increase in the Si−Si main chain length both in terms of the boundness of an unpaired electron and bonding strength. The π-type states, on the other hand, exist as excited states for these oligomer radical anions. The calculated results strongly suggest that polysilane radical anions with a π-type ground state are hardly generated regardless of their molecular size and geometry. The Si 3d orbital contributions in the ground and excited states of the polysilane radical anions, such as dπ−dπ conjugations, have also been investigated.

Structures and Thermodynamics of the Sulfuranes SF3CN and SF2(CN)2 as well as of the Persulfurane SF4(CN)2 − An ab initio MO Study by the G3(MP2) Method

AbstractAt the G3(MP2) level of theory the trans isomer 1a of the hypothetical molecule SF4(CN)2 is more stable than the cis isomer 1b by 8 kJ·mol−1. The isomerization of 1a to 1b requires an activation enthalpy of 319 kJ·mol−1 at 298 K. The decomposition of trans‐SF4(CN)2 to SF2(CN)2 and F2 is endothermic (ΔHo298 = 395 kJ·mol−1) but the elimination of FCN from trans‐SF4(CN)2 is exothermic by −7 kJ·mol−1. The elimination of (CN)2 from cis‐SF4(CN)2 is exothermic by −137 kJ·mol−1. The activation enthalpies for the latter two reactions were calculated as 251 and 311 kJ·mol−1, respectively. Thus, SF4(CN)2 should be a thermally stable compound. In the sulfuranes SF3CN and SF2(CN)2 the CN ligands prefer the equatorial positions; mutual exchange of an axial F atom by an equatorial CN group requires a reaction enthalpy of 51 kJ·mol−1 [SF3CN] or 58 kJ·mol−1 [SF2(CN)2]. (© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2003)