Semiempirical Results Research Articles

Ab initio molecular orbital study of adsorption of atomic hydrogen on graphite:: Insight into hydrogen storage in carbon nanotubes

Ab initio molecular orbital (MO) calculations are performed to study the adsorption of H atoms on three faces of graphite: (0001) basal plane, (1010) zigzag edge and (1121) armchair edge. The relative energies of adsorption (or C–H bond energies) follow the order: zigzag edge>armchair edge>basal-plane edge, in agreement with previous semi-empirical MO results. However, it is found that adsorption on the basal plane sites is exothermic and stable, in contrast to previous semi-empirical results. On the edge sites, the C–H bond energy decreases by nearly 30 kcal/mol when two H atoms are adsorbed on the same site. On the basal plane, the C–H bond energy decreases from 46 kcal/mol when two H are adsorbed on alternating sites to 27 kcal/mol when they are adsorbed on two adjacent sites. Literature MO results of H adsorption on the exterior wall of SWNT are in fair agreement with that on the basal plane of graphite. The value 27 kcal/mol agrees well with experiment (23 kcal/mol) of TPD of hydrogen from MWNT. Three common features exist in the reported experiments on hydrogen storage in carbon nanotubes: slow uptake, irreversibly adsorbed species, and the presence of reduced transition metals (Fe, Co or Ni). Combined with the MO results, a mechanism that involves H 2 dissociation (on metal catalyst) followed by H spillover and adsorption (on nanotubes) is proposed for hydrogen storage in carbon nanotubes.

Tribochemical Reactions of Cutting-Edge Material During Secondary Wood-Product Cutting

In this paper, evidence of tribochemical reactions of a cutting-edge material during cutting of secondary wood products (SWP) is reported. The heat of frictional contact of the cutting edge with material of the SWP is a source of rapidly increasing temperature in the cutting zone. Once the cutting edge reaches a certain level of wear, the temperatures generated are high enough to initiate thermal decomposition of the basic components of the material being cut. Applying Quantum Chemical (QC) methods, with semiempirical results verified using Density Functional Theory (DFT), it was determined that some products of thermal degradation of the principal components of SWP stabilize cobalt, from the cobalt binder in cemented carbide tool material, in an oxidized state via octahedral hydroxy organometallic complexes.

Electronic branching ratios of spontaneous emission for transitions between states of the 3d and 2p singlet complexes of terms of H2

The ratios of probabilities (the electronic branching ratios) for the rovibronic spontaneous transitions are for the first time measured for transitions from the rotational levels with J′≤6 of the I 1Π g − , v′=0–2 and J 1Δ g − , v′=0 states to the vibrational-rotational levels of different low-lying electronic states B 1Σ u + , v″, J′ and C 1Π u − , v‴, J′−1 of the H2 molecule (for the vibrational quantum numbers v″≤4 and v‴≤2). Values of these quantities provide a new channel of information on the internal structure of the hydrogen molecule thus far unused and should be particularly sensitive to the adiabatic values of the electronic transition dipole moments. In studying the entire set of rovibronic radiative transitions, they may significantly add to the experimental data on rovibronic terms, radiative lifetimes, and vibrational and rotational branching ratios used before. The experimental data obtained are compared to the corresponding values derived from the results of an earlier semiempirical determination and ab initio calculation of the absolute transition probabilities. Our experimental data are in remarkable agreement with the semiempirical results and significantly differ from the ab initio results. This fact directly suggests the necessity of performing more accurate ab initio calculations of the rovibronic transition probabilities for the given systems of bands.

Solvent Effects on Solute Electronic Structure and Properties: Theoretical Study of a Betaine Dye Molecule in Polar Solvents

The electronic structure of the betaine dye molecule, pyridinium- N-phenoxide [4-(1-pyridinio)phenolate] including the effects of geometry and polar solvents, has been studied at an ab initio level using the reference interaction site model self-consistent-field (RISM-SCF) method. Acetonitrile (CH3CN) and water (H2O) were selected as polar solvents. We obtain both the optimized solute geometry in solution and the total free energy profile with respect to variation in the torsion angle between the pyridinium and phenoxide rings and analyze the various electronic and solvation contributions. The betaine molecule in the gas phase has a twisted geometry, which is slightly more twisted in solution. In acetonitrile, the calculated structure shows good agreement with earlier semiempirical results for the minimum free energy structure. It is shown that the solute dipole moment is strongly enhanced in polar solution, also in accord with earlier semiempirical calculations. However, in solution, there is relatively little change in dipole moment with changes in the torsion angle, in contrast to the marked variation in the gas phase. Correspondingly, the solvation free energy is only weakly more negative with increasing twist. Electron correlation in the solute molecule is shown to play an important role in the torsional free energy, destabilizing the twisted form. This destabilization decreases by a factor of 4 from the gas phase to water, with increasing charge localization induced by the solvent. The implications of these results for interaction site models of charge-separated conjugated molecules in solution are discussed.

Conformational analysis of 2,3-substituted propenoates

Three X-ray structure analyses and theoretical conformational analyses combining molecular mechanics (SYBYL), semiempirical (AM1) and ab initio (HF/6-31G∗) calculations of nine 2,3-substituted propenoates are presented. The results of the quantochemical and crystallographic calculations and a survey of structural related molecules using the Cambridge Structural Database System are in concordance and show that steric hindering among substituents and possible inter and intramolecular hydrogen bonding are major factors that influence the geometrical configuration of substituents. The physical and chemical sense of these factors and the reasonable agreement between the semiempirical and ab initio results as well as between theoretical and experimental results have confirmed that the method which was applied for the theoretical conformational analysis is good and useful for related organic molecules.

Energetics of hole transfer in DNA

Using the semi-empirical scheme NDDO-G, we estimated energies for hole transfer in DNA duplexes on the basis of calculated ionization potentials (IP) of nucleobases in triplets of regular structure. All possible triad 5′-XBY-3′ duplexes (X,B,Y=A,G,C,T) were considered. We find that the stabilization of B + is considerably influenced by the subsequent base Y while the effect of the preceding base X is rather small. We test the application of triplet models by comparison with a decamer duplex. The present semi-empirical results have also been compared with data from ab initio calculations and experiment.

Structure Effect on Photochromic Mechanism of Spirooxazines

Structure effect on photochromic mechanism of 1,3,3-trimethylspiro[indoline-2,3′-[3H]naphtho[2,1,-b][1,4]oxazine] (SP1), 1,3-Dimethyl-3,2′-(1,3 -propylene)spiro[indoline-2,3′-[3H] naphtho[2,1-b][1,4]oxazine] (SP2) and 1,2′-(1,3-propylene),3,3-dimethylspiro[indo- line-2,3′ [3H]naphtho[2,1-b][1,4]oxazine](SP3) have been studied by nanosecond laser photolysis. Because of different connective positions of 1,3-propylene group in SP2 and SP3, the photochromic behaviours of them are quite different. One photoproduct of SP2 was only detected, and its lifetime is about 0.15μs. However, two colored forms of SP3 were detected after UV irradiation. The lifetimes of them are much longer than that of C-SP2. The semiempirical computational results by AM1 method were coincided with the experimental results.

The subtle role of heteroaromatics in the second-order susceptibility in a series of amphiphilic styryl dye Langmuir–Blodgett films

A series of amphiphilic styryl dyes: 2-(4-dihexadecylaminostyryl) benzothiazole methiodide (BTM), 2-(4-dihexadecylaminostyryl) benzoxazole methiodide (BOM), and 2-(4-dihexadecylaminostyryl) benzimidazole methiodide (BIM), were synthesized; their monolayers were successfully deposited on quartz slides by the Langmuir–Blodgett technique and formed H aggregates. Second-order susceptibilities χzzz(2) of the monolayers were determined with a polarized laser beam (Nd:YAG, λ=1.064 μm). The values of χzzz(2) are 215, 132, and 67 pm V−1 for BTM, BOM and BIM, respectively. Charge distributions over the entire molecules for the dye models were calculated using the MINDO/3 method in the MOPAC 7.0 program. Experimental data and semiempirical quantum chemical calculation results show that electron deficiencies of the heteroaromatic rings play an important role in determining the second harmonic generation of organic dye LB films.

Time-dependent density functional study on the electronic excitation energies of polycyclic aromatic hydrocarbon radical cations of naphthalene, anthracene, pyrene, and perylene

Time-dependent density functional theory (TDDFT) and its modification, the Tamm–Dancoff approximation to TDDFT, are employed to calculate the electronic excitation energies and oscillator strengths for a series of polycyclic aromatic hydrocarbon radical cations. For the radical cations of naphthalene and anthracene, TDDFT using the Becke–Lee–Yang–Parr functional and the 6-31G** basis set provides the excitation energies that are roughly within 0.3 eV of the experimental data. The assignments of the electron transitions proposed by TDDFT accord with the previous assignments made by accurate ab initio calculations, except that TDDFT indicates the existence of a few additional transitions of π*←σ character among the several low-lying transitions. The calculated energies for these π*←σ transitions are found to be consistent with the onset of a σ electron ionization manifold in the photoelectron spectra. For the pyrene radical cation, TDDFT supports the previous assignments made by semiempirical calculations, whereas for the perylene radical cation, TDDFT suggests the energy ordering of the three lowest-lying excited states be changed from those of the semiempirical results.

A semi-empirical and ab initio study of diazoazole cycloaddition reactions with ethyne, ynamine, and cyanoethyne

Semi-empirical AM1, MNDO and PM3 calculations of the mechanisms of diazoazole cycloaddition reactions with ethyne, ynamine, and cyanoethyne explain why cyanoethyne does not react. Ethyne reacts by either a [7+2] cycloaddition, directly forming the azolotriazine products, or by a [3+2] cycloaddition which forms spirobicyclic intermediates. The lowest energy reaction path for ynamine was neither the [7+2] nor the [3+2] concerted cycloaddition, but a two-step mechanism involving an azo-coupled intermediate. The proposed mechanism for ynamine/diazoazole cycloaddition predicts both the experimentally observed regioselectivity, and the increased reactivity of ynamine relative to ethyne. The relative reactivities of ynamine, enamine and 1,2-diaminoethene with diazoazoles were also compared. No transition states were found for cyanoethyne/diazoazole cycloadditions, which is why these reactions have not been observed. Ab initio (RHF/6-31G**) methods were used in certain instances to test the semi-empirical results.

Computational methods for conformational analysis of unsymmetrical 1,3-diamines: 3-aminotropanes

A comparative study has been performed to evaluate the ability of a range of computational theories to predict the relative basicity and the conformations of diamine systems. Specifically, molecular mechanics (MM3), semiempirical (AM1), and ab initio (Hartree–Fock) methods have been used in the conformational analyses of unprotonated, monoprotonated, and diprotonated 3-aminotropanes, a pair of isomeric 1,3-diamines. Use of the molecular mechanics force field, with the recently determined parameter set for protonated amines, affords results that are in agreement with experimental data, when corrected for water solvent (by setting the dielectric constant to 80). Ab initio and semiempirical calculations, in contrast, give inconsistent and incorrect results. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 1371–1378, 1999

Is There a Covalent Intermediate in the Viral Neuraminidase Reaction? A Hybrid Potential Free-Energy Study

The neuraminidase from the influenza virus is essential for maintaining viral infectivity as it aids in the transmission of the virus between cells. Although there are large variations in the amino acid sequences of neuraminidases from different influenza strains, there are several amino acids in the active site region of the protein that are strictly conserved. This has raised hopes that a single neuraminidase inhibitor and, hence a drug, can be found that is effective against all influenza strains. In this paper, we examine with theoretical simulation techniques one aspect of the reaction catalyzed by the viral neuraminidase that could be important for inhibitor design studiesnamely, whether a covalently bound complex can be formed between the enzyme and the sialosyl cation intermediate that occurs during the reaction. We used a hybrid semiempirical quantum mechanical/molecular mechanical (QM/MM) potential in conjunction with potential of mean force calculations to determine the free-energy profiles for formation of the covalent intermediate and its hydrolysis to sialic acid and for the direct hydroxylation of the sialosyl cation to sialic acid. Ab initio QM calculations were used to check the validity of the semiempirical results. We find that direct hydroxylation of the sialosyl cation is the energetically preferred pathway but not by so much that the possibility of being able to design covalently bound inhibitors need be completely abandoned.

Conformational Studies of an N-Acylated Hindered Amine Light Stabilizer

The low-energy conformations of a commercial, N-acylated, hindered amine light stabilizer, Tinuvin 440, are examined both theoretically and experimentally. Candidate structures are determined from an empirical force-field search algorithm and re-optimized using a variety of semiempirical and first-principles quantum chemical methods. The global minimum is robustly predicted to have a twist-boat configuration with the substituted N in its six-membered heterocycle not one of the “flagpole” substituents. First-principles Hartree−Fock, post-Hartree−Fock, and density functional theory calculations agree well on the relative stabilities of different conformers, while force-field and semiempirical methods prove unreliable. The present study disagrees with earlier semiempirical results and contradicts their implication that the oxidation and photostabilization behavior of Tinuvin 440 are strongly influenced by a trans-annular, intramolecular hydrogen bond. An alternative boat conformation containing such a bond i...

Femtosecond photoelectron spectroscopy of the I2− anion: Characterization of the Ã′ 2Πg,1/2 excited state

A potential energy curve for the Ã′ 2Πg,1/2 state of I2− is constructed based on femtosecond photoelectron spectroscopy of the I2− Ã′ 2Πg,1/2←X̃ 2Σu+ transition at 780 nm. The experiment is sensitive to the slope of the repulsive potential wall, the well depth, equilibrium bond length, and the long-range attractive portion of the upper state potential. The Ã′ 2Πg,1/2 potential is fit to a piecewise potential which is flexible in each of these regions. Simulations of the spectrum using a previously determined Morse potential for the X̃ 2Σu+ state of I2− [J. Chem. Phys. 107, 7613 (1997)] yields a well depth (De) of 0.017±0.010 eV for the Ã′ 2Πg,1/2 state with an equilibrium bond length (Re) of 6.2±0.6 Å. These values differ significantly from previous semiempirical results.

The effect of the geometry and the load level on the dynamic failure of rotating disks

The simplified and the higher order curved beam theory published previously ( International Journal of Solids and Structures 30 (1) , 137–149 (1993) and International Journal of Solids and Structures 31 (14) , 1949–1965 (1994) ) are applied to rotating disks with rectangular cross section subject to an instantaneous radial failure. The dependence of the angular size of the debris on the inner to outer radius ratio and on the load level is examined and compared with semi-empirical and experimental results in the literature. Finite element calculations confirm the results obtained with the higher order beam theory for moderate to high inner to outer radius ratios. It is shown that agreement with the experimental results can be further improved by a proper choice of the boundary conditions.

“Edge” or “Vertex” Inversion at Phosphorus in thecis-transIsomerization of Diazadiphosphetidines? Model MNDO and abinitioMolecular Orbital Calculations

Ab initio (3-21G(*), MP2/3-21G(*)), molecular orbital calculations show that the cis-trans interconversion of diazadiphosphetidines proceeds rather via an “edge” inversion than the classical “vertex” inversion at phosphorus. The semiempirical MNDO results are largely of the same quality as those obtained with the 3-21G(*) basis.

Electronic structure and optical spectra of MDF-2 oligoetheracrylate

The molecular spatial structure and electronic energy levels of MDF-2 oligoetheracrylate have been theoretically investigated using a Hyperchem 4.5 computer package. We have optimized the MDF-2 geometry, obtaining a non-linear structure with one benzene ring situated near one of the molecule ends. The electron charge density of the MDF-2 photopolymer is distributed non-uniformly, showing the highest absolute values in the vicinity of the benzene ring. C=O double chemical bonds are perpendicular with regard to the central chain. We have calculated a relatively large value of the HOMO-LUMO energy gap on one hand and, on the other hand, we have estimated a substantially smaller experimental energy gap based on our spectroscopic measurements. An essential influence of the benzene rings on the non-linear optical properties has also been suggested. To check the above semi-empirical results, ab initio calculations have been performed for the molecule fragments as well as for the full MDF-2 structure. An enlarged structure (a tetramer) has also been investigated using the UHF method with a PM3 parametrization.

A Theoretical Study of the Interaction of Anhydrotetracycline with Al(III)

In this article the complexation of anhydrotetracycline (AHTC), the major toxic decomposition product of the antibiotic tetracycline, with Al(III) has been investigated using the AM1 semiempirical and ab initio Hartree–Fock levels of theory. Different modes of complexation have been considered with the structure of tetra- and pentacoordinated complexes being fully optimized. In the gas phase, processes ii and iii, which lead to the complexes with stoichiometry MHL2+, are favored. Structure II ([AlLH2(OH)(H2O)]2+) has the metal coordinated to the O11 and O12 groups and the O3 group protonated and is the global minimum on the potential energy surface for the interaction. In water solution, the Al(III) is predicted to form predominantly a tetracoordinated complex at the Oam and O3 site (Ѵ) of the AHTC with the stoichiometry MH2L3+ (process i). The experimental proposal is the complexed form with the metal ion coordinated to the O11–O12 moiety (site II). The intramolecular proton transfer, which leads to the most stable Al(III)–AHTC MHL2+ complex, has not been considered by the experimentalists. The experimental structure was found to be unfavorable in our calculations in both gas phase and water solution. All the semiempirical results are in perfect agreement with the ab initio calculations. So, we suggest that the experimental assignments should be revised, taking into account the results obtained in the present study.

Semi-empirical atomic charges and dipole moments in hypervalent sulfonamide molecules: descriptors in QSAR studies

The Mulliken and ESP-based atomic charges and dipole moments have been calculated for a group of substituted methanesulfonamides by several ab initio and semi-empirical methods, in order to find the most reliable semi-empirical method of calculating these quantities in hypervalent molecules. It was found that the ab initio Mulliken charges on the sulfonamide H were meaningless, and that the ab initio ESP-based atomic charges calculated using any non-minimal basis set well reproduced the dipole moments. The semi-empirical results were less satisfactory, but in general, the ESP-based charges were more promising than the Mulliken charges, and CNDO-based dipole moments agreed better with ab initio dipole moments than with those calculated by AM1 or PM3. All charges for hypervalent molecules such as sulfonamides, calculated with semi-empirical methods, should be treated with caution.

Critical test of PM3-calculated proton transfer activation energies: a comparison with ab initio and AM1 calculations

Intra- and intermolecular proton transfer activation energies are calculated by means of the semiempirical PM3 method and compared with ab initio results obtained at MP2/6–31G ∗ or MP2/6–31G ∗∗ level. It is shown that corrections for zero-point vibrational energy (ZPVE) and thermal contributions do not affect the correlation between semiempirical and ab initio results. The linear relationship obtained suggests that PM3, in spite of some weaknesses, can be employed with a certain confidence to predict proton transfer activation barriers of large molecules or to obtain semi-quantitative trends for large numbers of interrelated systems. It is also shown that PM3 and AM1 results are of comparable quality for intramolecular proton transfers, whereas PM3 is to be preferred for intermolecular reactions, in particular when water molecules are involved.