Complete Geometry Optimization Research Articles

AM1 calculations on inclusion complexes of cyclomaltoheptaose (β-cyclodextrin) with 1,7-dioxaspiro[5.5]undecane and nonanal, and comparison with experimental results

Semiempirical calculations on cyclomaltoheptaose (βCD), 1,7-dioxaspiro[5.5]undecane ( 1), nonanal ( 2), and the inclusion complexes of βCD with 1 and 2 were carried out using the AM1 method. The structure of βCD after complete geometry optimization was in very good agreement with crystallographic structures. Moreover, the calculated dipole moment of βCD was found to depend strongly upon the orientation of the primary hydroxyl groups. Different possible positions of the guest molecules in the βCD cavity were examined, a few of them resulting in a gain of energy. These corresponded to partial inclusion of 1 from the secondary side but total inclusion of 2. Conclusions regarding the geometries of the complexes were in satisfactory agreement with the dominant structures in aqueous solutions as derived from NMR experiments. Thermodynamic data ( ΔH 0, ΔS 0) in aqueous solutions were obtained from van't Hoff plots using 1H NMR, and were compared with the computed heats of formation. The forces responsible for host-guest association are discussed in the light of the above results.

EXACT MANY-BODY APPROACH TO MAGNETISM AND CLUSTER STRUCTURE

The magnetic and structural properties of small clusters having N≤8 atoms were determined rigorously in the framework of the Hubbard model by performing the exact many-body electronic calculations together with a complete geometry optimization. We discuss the resulting interplay between electron correlations, magnetism, and cluster structure at T=0, as well as the stability of cluster ferromagnetism against temperature-induced electronic excitation and structural changes.

Calculation of Proton Affinities Using Density Functional Procedures: A Critical Study

Density functional theory has been used with different combinations of exchange and correlation functionals to study the proton affinities of six organic molecules, namely H2CO, CH3CHO, CH3OH, C2H5OH, HCOOH, and CH3COOH. Complete geometry optimizations have been carried out for both the neutral and protonated species with all combinations of functionals. The proton affinity values are then compared with the corresponding experimental values. It has been observed that combination of Perdew's and Becke's exchanges with Proynov's correlation functional is the most effective in reproducing the proton affinity.

Ab initio calculations of the rotational barrier in dimethyl diselenide

The heights of the rotational barriers of the diselenide bridge in dimethyl diselenide have been calculated at the Hartree-Fock level with the 3-21G basis set. The minimum in the rotational potential energy function occurs at a torsional angle of 85.64°. The barriers were determined by complete geometry optimization at each point along the potential surface. The results are compared with other calculations and with the available experimental results. © 1996 John Wiley & Sons, Inc.

Structure and conformation of some saturated four-membered rings, [formula omitted

Complete geometry optimizations of the ground state of three four-membered molecules with structures known from experiment (oxetane. silacyclobutane and thietane) have been carried out by ab initio SCF calculations at the 6-31G level. Additionally, calculations were made for two similar compounds CH 2 CH 2 CH 2 X ⎵ H (X = B, Al) not yet studied experimentally. Although comparison with available experimental data confirms that this level of theory somewhat underestimates both the dihedral angles in these molecules and the barriers to ring planarity, this study fills the gaps previously existing in structural investigations of four-membered ring molecules at a consistent level of theory, making possible the development of a uniform picture of seven monosubstituted heterocyclic compounds together with the parent molecule cyclobutane. Seven structural relationships common to all four-membered rings are systematized and discussed giving emphasis to the changes of C-C bond lengths and angular deformations around tetrahedral carbon and silicon atoms.

Infrared spectra and the structure of 1-methyladenine in an argon matrix and solutions

The spectral characteristics of the so-called “rare” imine form of methylated nucleotide purine base adenine is investigated. A study is made of 1-methyladenine (1-mAde) having generally the three tautomeric forms: amine, imino-N9H, and imino-N7H. IR spectra of 1-mAde isolated in Ar matrix at 12 K are obtained in the range 4000-400 cm−1. The normal-coordinate analysis is employed to interpret the experimental spectra. It is shown that isolated 1-mAde molecules can only exist as imine. The set of fundamental vibrational frequencies and force constants of the imine tautomer is found. The relative energies of the 1-mAde tautomers are calculated by the SCF MO LCAO method in the AM1 approximation with complete geometry optimization. This method predicts the stability of the tautomers in decreasing order: imine-N9H, imine-N7H, amine. An IR spectroscopic study of solutions of 1-mAde, and also adenine, 9-methyladenine, 1-methyladenosine, 2-aminopyrimidine, 2- and 4-oxopyrimidine in polar solvents in the range 1750-1500 cm− is carried out. The results show the presence of a considerable amount of the “rare” imine tautomer in water, as well in nonaqueous solutions.

Solvent effect on the conformational behavior of substituted spiro[4.5]decanes and spiro[5.5]undecanes

We studied the relatively complex polar systems 6-substituted-1,4-dioxospiro[4.5]decanes and 7-substituted-1,5-dioxospiro[5.5]undecanes with substituents X = CH3, F, Cl, CN, OH, OCH3, and NO2. Solvent effects on the equilibrium have been analysed by means of a Self-Consistent-Reaction-Field model and the PM3 method. Complete geometry optimizations have been carried out for all the structures in the gas phase and in solution. For some substituents, a set of rotamers have been separately optimized. The discussion of the results is focussed on the effects arising from structural aspects and from steric and electrostatic interactions on the axial/equatorial relative stability. The role played by multipole moment is considered. In general, good agreement with available experimental data and with previous theoretical studies has been obtained. Though the use of semiempirical methods and simple solvent models prevents us from reaching definitive conclusions, this approach seems to be very useful in predicting the main role of solute–solvent interactions in conformational equilibria of complex systems for which ab initio calculations cannot be performed. Keywords: conformational equilibria, spiro decanes and undecanes, cavity model, SCRF, solvent effect, PM3 calculations.

Interaction between Li + and C 60 molecules

MNDO calculations with complete geometry optimization were used to calculate the interaction between Li + and C 60, C − 60 and C 2− 60 molecules. In order to determine the more stable configuration, Li + was approximated to the C 60 molecule or to their reduced forms from 10 Å up to the geometric center of the molecule. From the simulations we determine that Li + remains close to the surface at 5 Å from the geometric center of the C 60 molecules.

Ab Initio and Semiempirical Conformation Potentials for Phospholipid Head Groups

The conformational potential of the dimethyl phosphate (DMP) anion and the 2-ammonioethanol (AME) cation, which are substructures of the phosphoethanolamine head group of phospholipids, has been investigated at the Hartree-Fock (HF) level using the 3-21G, 3-21G(*), 6-31G*, and 6-31+G* basis set. For this purpose, both the DMP anion and the AME cation were considered as geminal double rotors with the two rotor groups OCH3 in the case of DMP and OH and CH2NH3+ in the case of AME. Extensive scans (17 points including eight stationary points for DMP and 30 points including seven stationary points for AME) of the conformational energy surface were carried out by complete geometry optimizations at the HF/3-21G and HF/3-21G(*) levels, respectively, and subsequent single point calculations with larger basis sets. The most stable DMP form has the two OCH3 groups in syn-clinal (+sc) positions (both dihedral angles a2 and a3 = 75.3') while the AME cation prefers an anti-periplanar (ap) (Q = 173.3'), syn-clinal (+sc) (a5 = 48.5') conformation with regard to the OH and CH2NH3+ groups. The DMP anion is a rather flexible rotor that can undergo various flip-flop rotations (barriers 1 and 6 kcal/mol) that indicate strong coupling between the rotor groups. The AME cation, on the other hand, is conformationally not flexible, which has to do with the fact that the two rotor groups OH and CH2NH3+ are electronically very different. The preferred rotational processes of the AME cation involve inwardly or outwardly directed rotations at the CC bond (barriers of 5.1 and 9.3 kcaymol) with the OH group kept essentially in an ap position. Calculations reveal that semiempirical methods such as PM3 are not able to describe the conformational tendencies of either DMP anion or AME cation correctly.

Metallated ketenimines: Deprotonation of N-isopropyl-diphenylketenimine and subsequent trapping reactions with electrophiles A theoretical and experimental study

Deprotonation of N-isopropyl-diphenylketenimim 1 maybe achieved by surplus strong organic base (2,2,6,6-tetramethylpiperidine, n-butyllithium, potassium tert.butylate in tert.butyhnethyl ether). The resulting organometallic suspension is investigalled by means of fWpingreactions using various eleetrophiles. From the structures of the trapping products obtained the intermediacy of a substituted 1-methyleno-2-azaallyl anion 9 and of a 3-azapentadienyl anion 10 is deduced. Thus, proton sources yield a mixture of the 2-azabutadiene 2 together with two dimenc products, the 3-azahexatriew 3 and the heterocyclus 4. Methyl iodide leads to the formation of a cross-conjugated dimeric product 5. The 2-azabutadiene derivatives 6 and 7 are the trapping products using trimethylacetyl chloride or dimethyl disulfide, resp., as electrophiles, exiibiting multiple addition to intermediate substituted 3-azapentadienyl anion systems. Quantum chemical calculations (MNDO, PM3, ab initio-methods) are used for the prediction of the gas phase acidities of N-isopropyfformimine and N-isopropylketenimine as model systems; the structures obtained by complete geometry optimizations of the postulated monomeric anions and lithium compounds are discussed.

Ab initio study of tetrahydro-imidazo[4,5,1- jk][1,4]-benzodiazepin-2(1H)-one and -thione (TIBO) derivatives R79882 and R82913

The gas phase structures of two TIBO compounds (R79882 and R82913), potent inhibitors of the reverse transcriptase of HIV 1, were studied with ab initio Hartree-Fock methods. For compound R82913 the geometries of a dimer and of the respective monomers were fully optimized and compared with experiment. For compound R79882 a complete geometry optimization of 15 different conformers was performed.

Further studies on Norrish type II reactions including a reaction in the first excited singlet state and cyclization of 1:4 biradicals

The Norrish type II processes of methyl-2,2-dimethyl- cyclopropyl ketone, α-alkoxy acetones and alkyl pyruvates have been examined using the AM1 semi-empirical molecular orbital method with complete geometry optimization at the partial configuration interaction level in the restricted Hartree-Fock (RHF) frame. The results reveal that the methyl-substituted cyclopropyl ketone has a constrained geometry favourable for hydrogen abstraction from the γ-position relative to the carbonyl group in the excited singlet state. The presence of the ether oxygen atom in the β-position relative to the carbonyl group in alkoxy acetones and alkyl pyruvates leads to increased reactivity relative to alkyl monoketones and diketones respectively. The cyclization of 1:4 biradicals has been studied in the unrestricted Hartree-Fock (UHF) frame, and the results reveal that the 1:4 biradical derived from alkoxy acetones readily cyclizes to form oxetanols. On the other hand, in the 1:4 biradicals derived from methyl-substituted cyclopropyl ketone, the three-membered ring breaks readily to form an enol intermediate. Delocalization of an odd electron in 1:4 biradicals derived from alkyl pyruvates is thought to make cyclization difficult.

Synthesis and conformational study of acridine derivatives related to 1,4‐dihydropyridines

AbstractNovel acridine derivatives have been synthesized from dimedone and different aromatic aldehydes by following the classical Hantzsch's procedure. The particular substitution pattern of these compounds is responsible for the observed strong push‐pull effect. Quantum chemical calculations were carried out on these molecules by using the AM1 method with complete geometry optimization. The calculated heats of formation reveal two equally favoured conformations. The parameter of planarity and the charge density calculations are in agreement with the 13C nmr spectroscopic data.

Role of tunneling of hydrogen in photoenolization of a ketone

AbstractPhotoenolization of a ketone in its lowest triplet state was examined using the AM1 semiempirical molecular orbital method with complete geometry optimization at the configuration interaction level in the restricted Hartree–Fock frame. The theoretical barrier fits with a polynomial given by Eq. (1) and the probability of tunneling of hydrogen was calculated by the WKB method. The density of states above the zero‐point level was estimated by the Whitten–Rabinovitch approximation. Rate constants for the hydrogen and deuterium‐abstraction processes via tunneling were then computed at different temperatures. © 1994 John Wiley & Sons, Inc.

The conformational flexibility of aromatic retinoids

AM1 and PM3 complete geometry optimizations were performed on 19 arotinoids congeneric with (E)-4-[2-(5,6,7,8-tetrahydro-5,5,8,8-tetramethyl-2-naphthalenyl)-1-propenyl] benzoic acid (TTNPB), a very potent agent in carcinoprevention and carcinotherapy. Sixteen TTNPB conformations with close energy were obtained and characterized; four representative conformations were then studied for 14 derivative compounds, for which we found a substantial non-planarity of the two aromatic moieties. Large rotational flexibility of the arotinoid ring fragments was predicted by both methods. Very low barriers (0.4–3.9 kcal/mol) were found for the tetralenyl ring rotation. The two methods also agreed in predicting benzoic acid moiety rotation in a wide range of torsion angle values except those close to 0 or 180 degrees for which the PM3 rotational barriers were found to be considerably lower than the AM1 ones. This high conformational flexibility of arotinoid molecules may facilitate their favorable orientation in the process of fitting to the receptor sites.

A kinetic study on the formation of some carbon-centered and silicon-centered free radicals

The specific rate constants for formation of methyl, aminomethyl, hydroxymethyl and cyanomethyl free radicals were calculated using the transition state theory. The activation energies were calculated using the UHF in the MNDO level with complete geometry optimization. Force field calculations were performed on the reactants as well as on the activated complex. The position and geometry of the active complex were determined through a total energy as well as vibration frequency calculation. Similar calculations were performed on the corresponding silicon-centered radicals and the results were rationalized.

The inversion barrier in NF+⋅3

Ab initio molecular orbital theory has been used to investigate the barrier to inversion in NF+̇3. Complete geometry optimizations have been carried out with a variety of basis sets and electron correlation methods. It is shown that for this problem the use of single-point energy calculations needs to be treated with caution. Discrepancies amongst previous theoretical values are shown to be due to the use of inappropriate geometries and inadequate inclusion of electron correlation. With a variety of quantum chemical methods, the barrier to inversion is predicted to be in the range 11.3–13.3 kcal/mol. We have also predicted the vibrational splittings for the NF+̇3 potential energy surface and attempted to reconcile the differences with experiment.

On the dimerization process of nitroso compounds

Many organic C-nitroso compounds R-NO form stable dimers with a covalent NN bond. To gain insight into the dimerization reaction 2 R-NO ↓ (R-NO)2 a theoretical study of the dimerization to atrans-form was performed using HNO as a model compound. Complete geometry optimizations were carried out at the HF, MP2 and QCISD levels using a 6–31G* basis. In the stationary points energies were calculated at the MP4(SDTQ) and QCISD(T) levels. For the equilibrium structure of the monomer and dimers stable RHF solutions were found, whereas for the TS UHF and UMPn calculations were applied. Extensive spin contamination was found in the UHF wavefunction, and projections up tos+4 were invoked. Relative energies were corrected for differences in ZPE. Calculations were made (a) for the least-motion path (C 2h symmetry) and (b) for a path with complete relaxation of all internal coordinates. Along the latter path a TS having virtuallyC i symmetry was found. Along path (a) an activation energy of around 150 kcal/mol was predicted, in conformity with a symmetry forbidden reaction. On the relaxed path (b) the barrier to dimerization was estimated to be 10.7 kcal/mol at the MP4(SDTQ)//MP2 level, and 10.9 kcal/mol at the QCISD(T)//QCISD level. Unscaled ZPE corrections, calculated at the SCF level, changed these values to 12.7 and 12.9 kcal/mol, respectively. The reaction energy for the dimerization process is predicted to be − 17.2 kcal/mol at the MP4(SDTQ)//MP2 level corrected for ZPE. Calculations at the G1 level gave a corresponding value of − 16.4 kcal/mol. The equilibrium constant for the association to thetrans dimer is estimated to beK p =259 atm, indicating that the dimer should be an observable species in the gas phase.

The structure and conformation of 4-hydroxyphenyl terephthalate: a model compound for a liquid crystalline polyester

A theoretical analysis using ab initio calculations of the possible conformations of 4-hydroxyphenyl terephthalate which represents the repeat unit for poly( p-phenylene terephthalate) is reported. The study includes complete geometry optimizations and calculation of vibrational frequencies at the SCF/STO-3G level of ten distinct stationary points on the molecular potential surface. The calculations show that both the terephthalic and the hydroquinone fragments of the system prefer planar conformations. For the entire molecule, the low energy form is a twisted conformation where the hydroquinone portion is twisted by about 65° relative to the terephthalic portion of the molecule. The barrier to internal rotation around the ester bond is about 2 kcal mol -1.

Conformational equilibria of 5-substituted 1,3-dioxanes. study of solvent effects

Conformational equilibria of 5-substituted, 1,3-dioxanes have been studied by means of the PM3 method. The role of the solvent is analyzed by using a self-consistent reaction field model. Complete geometry optimizations have been carried out for the isolated and solvated species. A noticeable solvent effect on the equilibrium geometry has been found for the methoxy derivative. The modification of the axial-equatorial equilibrium under the solvent effect is discussed and the theoretical energy variations are compared to available experimental data. Specific solute-solvent interactions seem to be implied in some particular cases in which the observed Solvent effect goes in the opposite direction to that expected on the basis of pure electrostatic interactions. This point is analyzed by comparing the results obtained in cavity and supermolecule model computations.