AM1 Calculations Research Articles

Theoretical study of halogen‐substituted benzene at a Si(111)7×7 surface

AbstractThe adsorption of halobenzene (for halogens F, Cl, Br, and I) on Si(111)7×7 was investigated using AM1 quantum mechanical calculations. First the 1,4‐cyclohexadiene type of chemisorbed structures with two C—Si bonds at C atoms 1 and 4 have been calculated. Generally, the calculated binding energy increases with the size of the halogen atom, in the series F, Cl, Br, and I. The sp2 carbon positions are the most favorable for the halogen atom, and for bromobenzene and iodobenzene there is significant additional stabilization for the geometry that allows interaction of the halogen atom with a nearby Si adatom. This stabilization hinders the transfer of the heavier halogen atoms, Br and I, to the surface. Other chemisorbed structures, involving formally divalent halogen atoms in a C‐X‐Si type of binding, have also been found to correspond to energy minima in the AM1 calculations. Furthermore, it was possible to calculate physisorbed structures for chlorobenzene and bromobenzene once the Si rest atoms were capped with H atoms. Two types of binding structures are suggested for chemisorption in excess of three molecules per half‐unit cell: one is a radical structure binding by a single C‐Si adatom bond, and the second one is binding by a single C‐X‐Si adatom interaction. Both of these singly‐bonded structures have been calculated to correspond to energy minima with binding energies smaller than the 1,4‐cyclohexadiene type of chemisorbed structure.

Influence of Structure on the Unusual Spectral Behavior of 4-Dialkylamino-1,8-naphthalimide

Abstract Spectral behavior of 4-amino-1,8-naphthalimide derivatives differing in their amino functionality has been studied in different solvents with varying polarity. The results reveal that despite the +I effect of the methyl group, the charge-transfer absorption band maximum of N-ethyl-4-dimethylamino-1,8-naphthalimide (3) is blue-shifted with respect to that of the un-substituted and monoethyl-substituted derivatives, 1 and 2, respectively. AM1 calculations indicate a lower ground state dipole moment of 3 compared to 1 or 2. The single crystal structure of 3 suggests that low dipole moment and blue-shift of its CT maximum are due to twisting of the dimethylamino moiety relative to the 1,8-naphthalimide ring.

Convergent Synthesis of Nonsymmetric π-Stacked Protophanes Assembled with Urea Linkers

A convergent approach has been developed for the preparation of nonsymmetric tertiary arylureas possessing two or three urea linkages. This approach has been used for the preparation of ureas possessing 1-naphthylenyl and 4-nitrophenyl end groups separated by either one or two phenylene diamine bridging units. These ureas were constructed as prototypes for donor-bridge-acceptor systems based on tertiary arylurea architecture. AM1 calculations indicate a preference of these arylureas for folded, protophane structures in which the aryl groups are loosely pi-stacked. Analysis of the (1)H NMR chemical shifts supports the assignment of folded structures in solution. The absorption and luminescence spectra of tertiary ureas possessing 1-naphthylenyl and/or 4-nitrophenyl are reported. The absence of fluorescence and appearance of structured phosphorescence at 77 K are attributed to nitrophenyl-localized lowest energy singlet and triplet states. Localization of excitation on the acceptor chromophore precludes investigation of charge transfer in these systems.

Reactivity of electrochemically generated radical cations of alkylnaphthalenes interpreted by AM1 calculations

Electro-oxidations of alkylnaphthalenes lead mainly to polymeric products and show a radical cation mechanism. Mechanisms are proposed and discussed based on energetic arguments. Enthalpies of formation and the energies of the HOMO and SOMO, calculated using the AM1 program, are presented. It is shown that the prevailing polymeric products are obtained by way of the intermediate formation of naphthols.

An Experimental and Theoretical Investigation of the Photophysics of 1-Hydroxy-2-naphthoic Acid

Photophysical and photochemical properties of 1-hydroxy-2-naphthoic acid (1,2-HNA) have been investigated experimentally by steady state and time domain fluorescence measurements and theoretically by Hartree-Fock (HF), configuration interaction at the single excitation (CIS) level, density functional theoretic (DFT), and semiempirical (AM1) methods. 1,2-HNA exhibits normal fluorescence that depends on its concentration, nature of the solvent, pH, temperature, and wavelength of excitation. It seems to form different emitting species in different media, akin to 3-hydroxy-2-naphthoic acid (3,2-HNA). The large Stokes shifted emission observed at pH 13 is attributed to species undergoing excited-state intramolecular proton transfer. Nonradiative transition seems to increase on protonation and decrease on deprotonation. AM1(PECI=8) calculations predict the absorption maximum (lambda(max) = 335.9 nm) in reasonable agreement with experiment (lambda(max) = 352 nm) for the neutral 1,2-HNA. They also predict a red shift in absorption on protonation and a blue shift on deprotonation as observed experimentally. CIS calculations tend to overestimate the energy gap and hence underestimate the absorption maxima between the ground and the excited electronic states of 1,2-HNA and its protonated and deprotonated forms. However, they do predict correctly that the excited state intramolecular proton transfer is likely to occur in the deprotonated form of 1,2-HNA and not in the neutral and the protonated forms. A single minimum is found in the potential energy profile for the ground state as well as the first excited state of 1,2-HNA and its protonated species. In contrast, a double minimum with a nominal barrier in between is predicted for the ground state and also the first three excited states of the deprotonated species. The keto form of the deprotonated species is found to be slightly less stable than the enol form in all the states investigated.

Experimental and quantum-chemical calculations on some 1 H-pyrazole-3-carboxamide and -3-carboxylate derivatives formation

The 1 H-pyrazole-3-carboxylic acid was converted via reactions of its acid chloride 1 with various binucleophiles like 1,2-diaminoethane ( 2a), 1,2-diaminopropane ( 2b) and 2-amino-2-methylpropanol ( 2c) into the corresponding 1 H-pyrazole-3-carboxamides and -3-carboxylate 3a– c, respectively, in good yields (66–95%). The reactions of 1 with aliphatic diamines and amino alcohols ( 2a– c) in benzene for 5–6 h with catalytic amounts of pyridine lead to the products 3a– c formation. The structures of these new synthesized compounds were determined from the 13C NMR, 1H NMR, IR spectroscopic data and elemental analyses. All of them were compared with their previous analogs. The mechanism of reaction between 1 and 2a– c was studied by means of semi-empirical AM1 calculations.

Design, synthesis, antibacterial and QSAR studies of benzimidazole and imidazole chloroaryloxyalkyl derivatives

In view of obtaining some potential antibacterial compounds, we have described synthesis of some chloroaryloxyalkyl imidazole and benzimidazole derivatives. The relevant step in the synthetic sequence was the initial condensation of 4-chloro or 2,4-dichlorophenol with 1, n-dibromoalkanes ( n = 2, 4, 5) to provide compounds 3a– f in sufficient yields. The subsequent condensation of 3a– f with some imidazole derivatives and benzimidazole afforded products 4a– l and 5a– e in good yields. Some of compounds 4a– l as well as 5a– e were tested in vitro against Salmonella typhi O-901 and Staphylococcus aureus A 15091. Compounds 4a and 4c showed considerable bactericidal activities against tested bacteria. Compound 4b showed significant activity against S. aureus A 15091 but was inactive against S. typhi O-901. Other compounds showed intermediate activities against S. aureus A 15091 but most of them were inactive against S. typhi O-901. Semiempirical AM1 calculations showed that negative electrostatic potentials around oxygen of the phenoxy and nitrogen of the imidazole moieties have direct effect on the antibacterial activity towards S. aureus A 15091. In QSAR analysis, different electronic, topologic, functional groups and physicochemical descriptors were calculated for each molecule and a three parametric equation was found between the log MIC and HOMO energy, hydration energy and number of primary carbon atoms of the molecules.

Tetrakis(thiadiazolo)porphyrazines. 3. Acid-base Properties and Stability of Tetrakis-3,4-(1,2,5-thiadiazolo)porphyrazine in Sulfuric Acid Solutions

AM1 calculations gave the proton affinities of different types of donor sites in tetrakis-3,4-(1,2,5-thiadiazolo)porphyrazine, H2{[SN2)4PA}, and protonation of the meso-nitrogen atoms was found to be favored. A spectrometric study showed that the basicity of the meso-nitrogen atoms of the porphyrazine macrocycle is strongly diminished and these atoms in CF3CO2H are involved in an incomplete acid-base interaction (ABI) to give acid solvates, while a complete ABI (protonation) is found only in the presence of sulfuric acid. The basicity constants of the meso-nitrogen atoms were determined spectrophotometrically in CF3CO2H-H2SO4. The kinetics of decomposition of the macrocyclic chromophore in concentrated sulfuric acid was studied and a possible mechanism for this process was proposed.

Controlling the rate of shuttling motions in [2]rotaxanes by electrostatic interactions: a cation as solvent-tunable brake

A series of rotaxanes, with phenolic axle centerpieces and tetralactam macrocycles as the wheels, has been prepared in good yields. The threaded rotaxane structure is confirmed in the gas phase by tandem mass spectrometric experiments through a detailed fragmentation pattern analysis, in solution by NMR spectroscopy, and in the solid state through X-ray crystallography. A close inspection of the 1H,1H NOESY and 1H,1H ROESY NMR data reveals the wheel to travel along the axle between two degenerate diamide "stations" close to the two stoppers. By deprotonation of a phenolic OH group in the axle centerpiece with Schwesinger's P1 base, surprisingly no additional shuttling station is generated at the axle center, although the wheel could form rather strong hydrogen bonds with the phenolate. Instead, the wheel continues to travel between the two diamide stations. Experimental data from 1H,1H NOESY spectra, together with theoretical calculations, show that strong electrostatic interactions between the phenolate moiety and the P1 cation displace the wheel from the "phenolate station". The cation acts as a "brake" for the shuttling movement. Instead of suppressing the shuttling motion completely, as observed in other rotaxanes, our rotaxane is the first system in which electrostatic interactions modulate the speed of the mechanical motion between a fast and a slow motion state as a response to a reversible external stimulus. By tuning these electrostatic interactions through solvent effects, the rate of movement can be influenced significantly, when for example different amounts of DMSO are added to dichloromethane. Besides the shuttling motion, circumrotation of the wheel around the axle is observed and analyzed by variable temperature NMR spectroscopy. Force field and AM1 calculations are in good agreement with the experimental findings.

Weak interactions between resorcinarenes and diquaternary alkyl ammonium cations

The interactions of resorcin[4]arenes 1 with alkyl ammonium cations bearing a 1,4-diazabicyclo[2.2.2]octane (DABCO) scaffold (32+, 42+ and 52+) were analyzed in the solid state by X-ray crystallography, in solution by 1H NMR spectroscopy, and in the gas phase by ESI-TOF mass spectrometry. The results are complemented with AM1 calculations and compared to previous reports on complexation studies of resorcinarenes with quaternary alkyl ammonium cations. The NMR titration results indicate that there are hardly any differences in the binding of the quaternary tetramethyl ammonium cation 2+ and the diquaternary N,N’-dimethyl DABCO dication 42+. The large N,N’-dibenzyl DABCO dication 52+ has two potential sites for inclusion, that is, the aryl groups and the central cationic part, and the complexation and interactions of both sites with 1 were verified in the NMR studies as well as in the solid state structures.

Near-infrared Fourier transform Raman, surface-enhanced Raman scattering and Fourier transform infrared spectra andab initio calculations of the natural product nodakenetin angelate

Near-infrared Fourier transform Raman and Fourier transform infrared spectra of nodakenetin angelate (C19H20O5), extracted from seeds of Heracleum candolleaum, were recorded and analysed. The root extract of this plant is used as an antiarthritic and nerve tonic. Ab initio SCF Hartree–Fock computations were performed employing the 6–31G basis set for geometry optimization for the prediction of IR and Raman spectral activities and wavenumber calculations. Parameters initially optimized using AM1 calculations were used as the input for ab initio computations. The computed results were used for the interpretation of the vibrational spectra. Important thermodynamic parameters were also provided. The strong band at 1712 cm−1 and medium-intensity band at 1731 cm−1 resulting from ester and lactone carbonyl vibrations, respectively, are identified in the Raman spectrum. The CO stretching band in IR is broadened around 1717 cm−1 owing to the overlapping of ester and lactone carbonyl vibrations. The lowering of the carbonyl stretching vibrations is due to conjugation. The computed values indicate a larger degree of conjugation for the ester group. The characteristic vibrations of the furanocoumarin ring which is part of the molecule were identified. The CH stretching and bending vibrations of the CH3 group of the ester part indicate the presence of hyperconjugation. Vibrational analysis indicates the presence of blue-shifting H-bonds resulting from interaction of the methyl group The large enhancement of in-plane ring stretching and ring breathing modes in the surface-enhanced Raman scattering spectrum indicates that the molecule is adsorbed on the silver surface in a ‘vertical’ configuration, with the lactone ring perpendicular to the silver surface and probably on the opposite side of the lactonic CO group. Copyright © 2004 John Wiley & Sons, Ltd.

Synthesis of 3,4-dihydro-2H-pyrans by hetero-Diels–Alder reactions of functionalized α,β-unsaturated carbonyl compounds with N-vinyl-2-oxazolidinone

Cycloadditions of 3-aryl-2-benzoyl-2-propenenitriles and 3-phenylsulfonyl-3-buten-2-one to N-vinyl-2-oxazolidinone proceed regio- and diastereoselectively yielding cis and trans diastereoisomers of 4-aryl-3,4-dihydro-2-(2-oxo-3-oxazolidinyl)-2H-pyrans in 37-65% yield. Cycloadducts cis- were the major products. Reaction of 5-arylidene-1,3-dimethylbarbituric acids with dienophile afforded mixtures of 2H-pyrano[2,3-d]pyrimidine-2,4(3H)-diones trans and products resulted from an elimination of 2-oxazolidinone, in 50-52% yield. To confirm the experimental results, semiempirical AM1 and PM3 calculations of frontier orbital energies have been performed.

ESR and electrochemical studies of 2-acylpyridines and 6,6′-diacyl-2,2′-bipyridines

The ESR spectra of radicals obtained by electrolytic reduction of 2-acylpyridines and 6,6′-diacyl-2,2′-bipyridines were measured in dimethylsulfoxide (DMSO) and analyzed by quantum chemical calculations. The electrochemistry of these compounds was characterized using cyclic voltammetry, in DMSO solvent. The results showed a two step reduction mechanism, first wave was assigned to the generation of the correspondent free radical species, and the second wave was assigned to the dianion derivatives. AM1 and DFT calculations were performed to obtain the optimized geometries, theoretical hyperfine constants, and spin distributions, respectively. The theoretical results are in complete agreement with the experimental ones.

Electron Transfer within 2,7-Dinitronaphthalene Radical Anion

The optical spectrum of 2,7-dinitronaphthalene radical anion generated by Na(Hg) reduction in acetonitrile containing a large excess of cryptand[2.2.2] exhibits a Hush-type intervalence charge-transfer band at 1070 nm, estimated to correspond to an off-diagonal matrix coupling element of 310 cm(-)(1). The interpolated rate constant for intramolecular electron transfer at 293 K measured by ESR between 225 and 320 K for this solution is 3.1(+/-0.2) x 10(9) s(-)(1). Rate constants estimated in two ways from the optical parameters using the Marcus-Hush assumption that the diabatic surfaces should be parabolae are 1.0 and 0.11 x 10(9) s(-1), and those using diabatic surfaces that fit the observed charge-transfer band are 9.6 and 3.4 x 10(9) s(-)(1), when used with an electron-transfer distance on the adiabatic surfaces of 6.42 A. Similar measurements and comparisons were also carried out using dimethylformamide and butyronitrile as solvents. The success of simple, classical two-state Marcus-Hush theory precludes an electron-hopping mechanism. UHF calculations predict a planar unsymmetrical gas-phase structure for 1,3-dinitrobenzene radical anion but give serious spin contamination. Semiempirical AM1 calculations using singles excitation configuration interaction with an active space of 70 orbitals and the COSMO solvent model also give a planar unsymmetrical structure. These calculations make the internal vibrational component of the reorganization energy nearly constant, and much smaller than the solvent reorganizational component, and predict the transition energy to lie between that observed in acetonitrile (9360 cm(-1)) and those observed in dimethylformamide (8100 cm(-1)) and butyronitrile (8040 cm(-1)).

A tandem highly stereoselective FeCl 3-promoted synthesis of a bisindoline: synthetic utility of radical cations in heterocyclic construction

A conceptually distinctive stereoselective construction of the novel dimer, N-[ N′-acetyl-7,7′-bis-(3,4-dimethoxy-phenyl)-7,8,7′,8′-tetrahydro- N′ H-[8,8′]biindolyl- N-yl]-ethanone 25 (bisindoline) is described below. These structures, which include 7-(3,4-dimethoxyphenyl)-indoline 24 (veratryl indoline), were obtained by the tactical combination of palladium-catalysed coupling which produced 10-acetamido-3,4-dimethoxystilbene 9 , followed by FeCl 3 induced oxidative cyclization/dimerization. All new structures were fully characterized by 1- and 2D NMR spectroscopy, (proton, carbon-13, COSY, HMBC, HMQC) and mass spectrometry. Configurational assignments were further supported by semi-empirical AM1 calculations. Mechanistic interpretations, consistent with our results, are discussed.

Conformation of Roxatidine Acetate Hydrochloride by 1H, 13C and 15N NMR and AM1 Calculations and Its Interaction with Model Membranes Studied by 31P NMR

Conformation of Roxatidine Acetate Hydrochloride by 1H, 13C and 15N NMR and AM1 Calculations and Its Interaction with Model Membranes Studied by 31P NMR

Synthesis, crystal structure and molecular conformation of (±)-1-oxoferruginol and (±)-shonanol

Abstract (±)-1-oxoferruginol and (±)-shonanol, two potential intermediates in the synthesis of tricyclic diterpenoid ferruginol, have been prepared and crystal structures of the compounds have been investigated using single-crystal X-ray diffraction data. The methyl groups of the isopropyl moiety in (±)-shonanol are disordered over two positions with occupation factors 0.65(1) and 0.35(1), respectively. Although the chemical structures of two compounds are very similar, a C—C single bond in the terminal six-membered ring of (±)-1-oxoferruginol is replaced by a C=C bond in (±)-shonanol, the quantitative isostructurality index calculations indicate that the structures are not isostructural. Intermolecular O—H…O hydrogen bonds between pairs of molecules in the compounds related by center of inversion lead to characteristic dimers forming R2 2(16) rings. The molecular conformation of (±)-1-oxoferruginol obtained from the semi-empirical quantum mechanical AM1 calculation shows good agreement with the X-ray structures.

Theory and experiment in concert: templated synthesis of amide rotaxanes, catenanes, and knots.

The synthesis of amide rotaxanes, amide catenanes, and trefoil amide knots is based on template effects mediated by hydrogen bonds. While a large body of experimental data is available, in-depth theoretical studies of these template syntheses are virtually unavailable, although they would provide a more profound insight into the exact details of the hydrogen-bonding patterns involved in the formation of these mechanically interlocked species. In this article we present a density functional study of the conformational properties of tetralactam macrocycles and the threading mechanism that produces the immediate precursor for rotaxane and catenane formation. Predictions of the geometries and relative energies made on the basis of semi-empirical AM1 calculations are compared with these results in order to judge the reliability of the simpler approach. Since these calculations yield good agreement with the structural features, they have been used to extend the calculations in order to understand the mechanism of formation of a trefoil dodecaamide knot that has recently been synthesized. The inherent topological chirality of the knot is reflected in the intermediates generated during its formation; these involve helical loops. These loops parallel the rotaxane and catenane wheels with respect to the arrangement of the functional groups that mediate the template effect and may well serve as wheel analogues through which one of the precursor molecules can be threaded. This threading step finally results in the knotted structure. Good agreement between the results of the calculations presented here and experimental findings is achieved.

Physicochemical characteristics of reverse micelles of polyoxyethylene nonyl phenol in different organic solvents.

The association of polyoxyethylene nonyl phenol (Igepal) in four different organic solvents such as chloroform, carbon tetrachloride, cyclohexane, and heptane has been studied. The critical micellar concentration of the reverse micelle (RM) formed in different nonaqueous media has been determined using four different techniques: UV-visible spectroscopy, fluorescence spectroscopy, Stokes shift, and NMR spectroscopic studies. From the correlation of cmc with hydrophile-lipophile balance (HLB), we have found that cmc decreases with decrease in HLB. The obtained cmc values using different methods have been found to be consistent and facilitate the determination of DeltaG values associated with the micellization. The association constant of the dye molecule Safranine T (ST) with the reverse micelle, aggregation number of the surfactant monomer, and location of fluorophore in the RM have been determined. The vertical ionization potential of Igepal, electron affinity of the dye, and the degree of charge transfer have been estimated by the theoretical AM1 calculations. A linear relationship has been obtained between cmc(s) and the ionization potential of the solvents. The polarity of the micelle solubilization sites has been determined from the solvatochromic shift, Kosower Z value, and ET(30) value.

Investigation of catalytic effects of the proton and Lewis acids on oligomerization and chemical polymerization of pyrrole

Protonation and oligomerization mechanisms of pyrrole monomer were elucidated in the presence of acid such as HBF 4 and Lewis acid such as AlCl 3, FeCl 3 in acetonitrile solutions, using experimental methods such as UV–vis and AA spectroscopy and semi-empirical AM1 calculations. It was observed that pyrrole interacts with proton and Lewis acids on similar mechanisms to produce pyrrole oligomers. The theoretical studies predicted that the both types of acids add to the pyrrole ring on C β atom. These studies also showed that FeCl 3, which is used as oxidative agent in the chemical polymerizations, adds to the polypyrrole chain as well.