Quantum Chemical Semiempirical PM3 Method Research Articles

PM3 QUANTUM CHEMICAL CALCULATIONS OF THE BIOACTIVE ALA-TYR DIPEPTIDE

Ala-Tyr (Alanine-Tyrosine) dipeptide is a compound with hypertensive and high antioxidant effect. Here, the structural features of this molecule were studied using the PM3 semi-empirical quantum-chemical method. In order to investigate the research, the initial coordinates of the molecule were obtained by the molecular mechanics method. Geometric and electronic parameters, HOMO and LUMO energies, energy gap, dipole moment and partial charges of atoms were calculated for the stable conformations, belonging to both folded and extended shapes of the dipeptide backbone. The obtained results can be used in the research of the structure-function relationships of the investigated bioactive dipeptide and in the design of new peptidomimetics.

Monolayers of amino acid-type amphiphiles

The monolayer characteristics of selected N-alkanoyl substituted α-amino acid are studied with the objective to demonstrate the specific effect of the chemical structure of the polar head group which is highlighted with the D- and L-enantiomers of the following selected examples: R-alanine, R-serine, R-threonine, R-allo-threonine, and R-aspartic acid (R = C16, C18). The thermodynamic effect of the head group variation is studied. Experimental π-A isotherms of the N-tetradecyl-L-alanine monolayers show similar behavior as those of usual amphiphiles. The -CH3-group in R-alanine with the simplest head group structure is substituted by a -CH2-OH group in R-serine and serine methylester and by a -CH- CH3-OH group in R-threonine (or allo-threonine) and threonine methylester. The introduction of the methyl group in 3-position of serine (serine to 3-methyl-serine = threonine) shifts the characteristic temperatures by >20 K to lower values determined for N-C16-Dl-serine. The formation of the corresponding methylester decreases these temperatures by 15 K for serine with the shorter (C16) alkyl chain and only by ∼5 K for threonine with the longer chain (C18). The π–A curves of the enantiomeric and racemic allo-forms show similar features to those of N-stearoyl-threonine. The absolute T0-values (disappearance of the LE/LC-transition) are 4–5 K larger compared with the corresponding N-stearoyl-threonines, but the ΔT0 between the enantiomeric (D) and the racemic (DL) forms is only slightly larger than that of N-stearoyl-threonine.Monolayers of different N-alkanoyl substituted α-amino acid amphiphiles have been mesoscopically characterized. Substantial topological differences are observable at the condensed phase domains of several amino acid amphiphiles, such as, N-palmitoyl aspartic acid, N-palmitoyl- or N-stearoyl serine methyl ester, N-stearoyltyrosine, N-palmitoyl or N-myristoyl alanine. Many fascinating domain shapes are found, but always the curvatures of the two enantiomeric forms are directed in an opposite sense. The domain shape of the 1:1 racemic mixtures is usually different, but very often oppositely curved texture elements are observable.GIXD is used to study the characteristic features of the lattice structure of condensed monolayer phases on the Angstrom scale. Specific for all structures is the large tilt angle with respect to the surface normal, which decreases only marginally by compression. The large size of the head groups and strong interactions between them dominate the monolayer structure. As presented for NC16 and N-C18-threonine, N-C16-DL -serine, N-C16-L -serine, NC16 DL -serine-ME, NC16 L -serine-ME, NC18 DL -threonine-ME, and NC18 L -threonine-ME the enantiomers form an oblique lattice structure (3 diffraction peaks), whereas two peaks are observed for the racemates forming NNN tilted orthorhombic structures. A complete phase diagram of mixed monolayers of the D- and L-enantiomers of N-stearoyl-threonine with two eutectic points at xD ≈ 0.25 and xD ≈ 0.75 is proposed.The quantum chemical semiempirical PM3 method is applied to calculate the thermodynamic and structural parameters of clusterization in finite and infinite clusters for N-alkanoyl-substituted alanine with n = 8–17 carbon atoms in the chain at the air/water interface with the aim to obtain a new theoretical verification of the experimental results.

Relationship between the Bulk and Surface Basicity of Aliphatic Amines: A Quantum Chemical Approach.

To assess the surface basicity constant (pKb) of aliphatic amine films, the use of a theoretical approach recently developed to evaluate the pKa of carboxylic acid monolayers on the water surface is tested. The present paper gives a new full picture of the change of acid–base properties of surfactants during their aggregation at the air/water interface. The exploited approach is simple because it does not involve the construction of thermodynamic cycles but uses the Gibbs energies of the formation and dimerization of surfactant monomers in neutral and ionized forms in the aqueous and gaseous phases. The quantum chemical semiempirical PM3 method is applied to perform calculations using a conductor-like screening model, which takes into account the aqueous phase. The calculation shows that aliphatic amines, as well as carboxylic acids, are characterized by a change of the value of the basicity/acidity constant during the film formation. The film formation of surfactants leads to a decrease in their acid–base properties, i.e., the surface pKa values of carboxylic acids and pKb values of amines increase. However, unlike carboxylic acids, there is practically no dependence of the surface pKb value on the alkyl chain length of the aliphatic amine, which is caused by almost identical contributions of one CH2 fragment to the solvation Gibbs energy of neutral and ionized monomers within the calculation error. The obtained results agree with existing experimental data.

Theoretical Description of Mixed Film Formation at the Air/Water Interface: Carboxylic Acids–Fatty Amines

Clusterization thermodynamic parameters of mixed monolayers of aliphatic amines CnH2n+1NH2 and carboxylic acids CnH2n+1СОOH (n=6-16) are calculated using the quantum chemical semi-empirical PM3 method. Four types of mixed dimers and tetramers amine-acid are considered. The total contribution of interactions between the hydrophilic parts of amine and acid into clusterization Gibbs’ energy is slightly lower than the corresponding interactions for individual surfactants. It suggests synergetic interaction between the regarded amphiphilic compounds proved by experimental data in literature. Two types of competitive film formation are possible: mixed 2D film 1, where the molecules of the minor component are single distributed among the molecules of the prevailing second component (mixture of components on molecular level) and 2D film 2 of domain structure comprised of separate regions of the same components bound together. The dependence of the clusterization Gibbs’ energy per monomer of 2D film 1 on the compo...

Pyroelectric properties of ferroelectric composites based on polyvinylidene fluoride (PVDF) with graphene and graphene oxide

Novel composites based on polymer ferroelectrics with graphene (G) and graphene oxide (GO) have many advantages over pristine materials. In this work, the results of the computational molecular modeling of the composite nanostructures are presented and analyzed. The calculations were focused on pyroelectric properties of the composites based on polyvinylidene fluoride (PVDF) films with G/GO layers. The pyroelectric effect was modeled and pyroelectric coefficients were calculated for several models using molecular dynamics simulation with quantum-chemical semi-empirical PM3 method from HyperChem tool. The obtained results present a new prospective for further studies of the ferroelectric polymer-graphene multifunctional nanomaterials and their applications.

Theoretical Description of Mixed Film Formation at the Air/Water Interface: Carboxylic Acids-Alcohols.

The thermodynamic parameters of formation and clusterization of aliphatic alcohols CnH2n+1OH and carboxylic acids CnH2n+1COOH (n = 6–16) are calculated using the quantum-chemical semiempirical PM3 method. Four types of dimers are constructed in two directions of the spread monolayer comprising the most energetically advantageous monomer structures. The hydrophobic chains of alcohol and carboxylic acid molecules in the regarded dimers are found to be tilted within 12° to the normal of the spread monolayer. The structures of the mixed and pure surfactant dimers are the basis for the mixed alcohol–carboxylic acid monolayers of the following types: two dimensional (2D) film 1 with single distribution of the individual component in the other one, when the molecules of the first component do not interact with each other but are completely surrounded by the molecules of the second component; 2D film 2 with domain structure, when the film consists of “islands” of the individual components. The dependences of the clusterization Gibbs’ energy per one monolayer molecule on the molar fraction of the components for the mixed 2D films 1 formed by surfactants with equal alkyl chain length are found to be limited from top to bottom by the corresponding dependences for pure components. This indicates the absence of synergetic interaction between the hydrophilic head groups of carboxylic acids and alcohols and conforms to the available experimental data. The formation of the described types of mixed films is competitive. The preferential formation of 2D films 1 with single distribution of the first component among the molecules of the second one is possible when the length of the carboxylic acid hydrocarbon chain is longer by Δn = 1–2 methylene units than that of the corresponding alcohol alkyl chain. According to the fractionally linear law, the highest possible content of the carboxylic acids in such 2D films 1 depends on the Δn value and does not exceed 33.3%.

Ferroelectric PVDF films and graphene-based composites

Advantages in the studies of new composite nanomaterials based on polymer ferroelectrics and graphene are presented. We analyzed the main results of the computational molecular modeling of nanostructures and the pyroelectric properties of the composites from polyvinylidene fluoride (PVDF) films and graphene layers. The pyroelectric effect was modelled and pyroelectric coefficients were calculated for several models using molecular dynamics simulation with quantum-chemical semi-empirical PM3 method from HyperChem tool. The results obtained provide important insights into our understanding of the mechanisms of pyroelectricity in the new nanocomposites, give us new prospective for further studies of the ferroelectric polymer–graphene multifunctional nanomaterials.

Quantum-chemical analysis of condensed monolayer phases of N-alkanoyl-substituted alanine at the air/water interface

The thermodynamic and structural parameters of monolayers of N-alkanoyl-substituted alanine with 8–17 methylene fragments in the alkyl chain are calculated on the basis of the quantum chemical semiempirical PM3 method. Four optimized structures of monomers are obtained. The energetically most preferred conformer is used for construction of dimers with “sequential” and “parallel” orientation of the hydrophilic parts of the monomers and tetramers with square structure. The hydrophobic chains of N-alkanoyl-substituted alanine are found to be inclined in the dimers to the normal of the spread monolayer: δ = 10° and φ = 43°.Comparison of clusterization Gibbs’ energy for small clusters suggests that 2D film formation takes place by formation of linear associates comprised of dimers with “parallel” orientation of the hydrophilic groups. The temperature increase causes growth of linear 1D clusters leading to the dendritic structure of the monolayer. The parameters of the unit cell of 2D film are calculated: a = 4.65 Ǻ, b = 6.20 Ǻ, the angle between the sides of the cell θ = 105˚. The tilt angle of amphiphilic molecules to the normal of the air/water interface is t = 47°. The calculated parameters of the unit cell are in good agreement with the existing experimental data. The spontaneous clusterization threshold for N-alkanoyl-substituted alanine at the air/water interface is calculated to be 15 carbon atoms in the chain at 288 K. This is only 2 carbon atoms more than the experimental value and within the margin of error of the model used for the calculation.

Synthesis and thermal conversions of unsaturated nickel(II) dicarboxylates as precursors of metallopolymer nanocomposites

The synthesis and IR spectroscopic and thermoanalytical study of cobalt(II) hydrogen salts with unsaturated dicarboxylic acids, such as maleic, itaconic, acetylenedicarboxylic, allylmalonic, glutaconic, and cis-,cis-muconic acids, were performed. Co3O4 polymer based nanocomposites were prepared through the thermal decomposition of the carboxylates synthesized. The size distribution of nanoparticles and their average diameter (d avg) were determined. The formation enthalpies of cobalt hydrogen carboxylates (ΔH p o ) were calculated using the PM3 semi-empirical quantum-chemical method. A correlation between d avg and ΔH p o was established. The magnetic characteristics of the synthesized composites, namely the maximum residual magnetization and coercive force, were determined. The critical diameter of nanoparticles for their transition from multidomain to one-domain particles was found to be 3.8 nm.

Quantum chemical approach to the description of the amphiphile clusterization at the air/liquid and liquid/liquid interfaces with phase nature accounting. II. 1-( n -Alkyl)-imidazoles at the air/water interface

Abstract In the framework of the model for surfactant clusterization description at the air/liquid and liquid/liquid interfaces proposed earlier (Vysotsky et al. J. Phys. Chem. B, 2015, 119 (7), 3281–3296) and based on the quantum chemical semi-empirical PM3 method the structural and thermodynamic parameters of the formation of 1-( N -alkyl)-imidazole monolayers with alkyl chain lengths of 6–16 carbon atoms at the air/water interface are calculated. The model allows the calculation of the thermodynamic parameters (enthalpy, entropy and the Gibbs’ energy) of monomers, clusters and monolayers at the interface between two liquids or between the air and liquid phases. To obtain such results one needs to calculate the corresponding thermodynamic parameters for both adjacent phases within the semi-empirical PM3 method (in the frameworks of the COSMО procedure), then to calculate the increments from the different types of the pairwise interactions and, with the help of the additive scheme, to calculate the required parameters. It has been shown that 1-( n -alkyl)-imidazole forms monolayers with hexagonal and oblique unit cells normal conditions. The parameters of the unit cell are calculated for each of these monolayers: 4.6 Ǻ and 7.2 Ǻ (the angle γ between the sides of the unit cell is equal to 62°) for the hexagonal unit cells and 4.6 Ǻ and 4.6 Ǻ ( γ = 80°) for the oblique unit cells. Enthalpy, entropy and Gibbs’ energy for small clusters (dimers–hexamers), representing the structural elements of the investigated monolayers, are calculated. The probable way of the clusterization process is proposed on the basis of these parameters. In the framework of the model the thermodynamic functions of the monolayer formation are calculated. These results indicate that for both types of the monolayers (with oblique and hexagonal unit cells) spontaneous clusterization is possible when the alkyl chain length is ≥14–15 carbon atoms.

Theoretical description of 2D-cluster formation of nonionic surfactants at the air/water interface

Recent progress in modeling of the surfactant behavior from atomistic to continuous at the air/water interface across different space-time scales is reviewed. Advantages and disadvantages of modern quantum mechanical, molecular dynamical, and mesoscale methods are discussed for description of interactions between amphiphilic molecules leading to formation of 2D films. The use of nonempirical and semiempirical methods for assessment of the thermodynamic and structural parameters of large van der Waals complexes is of particular interest. An approach for calculation of the thermodynamic and structural parameters of clusterization for nonionic surfactants at the air/water interface is proposed on the basis of the quantum chemical semiempirical PM3 method. This approach implicitly takes into account the influence of the interface on the surfactant molecules via stretching and orienting effect. The calculations are carried out in the supermolecule approximation for a limited number of small amphiphilic aggregates with different alkyl chain. The correlation analysis of the calculated data array provides the increments contributing by the intermolecular CH · · · HC interactions and interactions between hydrophilic parts into the thermodynamic parameters of formation and clusterization. Obtained increments are further used for constructing the dependencies of the thermodynamic clusterization parameters per one monomer on the alkyl chain length for large clusters up to 2D films. In the framework of the proposed theoretical approach, the next parameters are calculated as follows: enthalpy, entropy, and Gibbs’ energy of clusterization for 11 homologous series of nonionic surfactants, threshold chain length enabling the process of monolayer formation at standard conditions, the “temperature effect” of clusterization, and the structural parameters of the monolayer unit cell (particularly the tilt angle) depending on the size of the hydrophilic headgroup of the amphiphilic compound.

Quantum chemical approach in the description of the amphiphile clusterization at the air/liquid and liquid/liquid interfaces with phase nature accounting. I. Aliphatic normal alcohols at the air/water interface.

A new model based on the quantum chemical approach is proposed to describe structural and thermodynamic parameters of clusterization for substituted alkanes at the air/liquid and liquid/liquid interfaces. The new model by the authors, unlike the previous one, proposes an explicit account of the liquid phase (phases) influence on the parameters of monomers, clusters and monolayers of substituted alkanes at the regarded interface. The calculations were carried out in the frameworks of the quantum chemical semiempirical PM3 method (Mopac 2012), using the COSMO procedure. The new model was tested in the calculations of the clusterization parameters of fatty alcohols under the standard conditions at the air/water interface. The enthalpy, Gibbs' energy and absolute entropy of formation for alcohol monomers alongside with clusterization parameters for the cluster series including the monolayer at air/water interface were calculated. In our calculations the sinkage of monomers, molecules in clusters and monolayers was varied from 1 up to 5 methylene groups. Thermodynamic parameters calculated using the proposed model for the alcohol monolayers are in a good agreement with the corresponding experimental data. However, the proposed model cannot define the most energetically preferable immersion of the monolayer molecules in the water phase.

Quantum-chemical analysis of hexagonal crystalline monolayers of ethoxylated nonionic surfactants at the air/water interface.

In the framework of the quantum chemical semiempirical PM3 method the monolayers of the monoethoxylated normal alcohols CnH2n+1OCH2CH2OH with n = 6-16 (CnE1) at the air/water interface are described. The optimized structures of small clusters (dimers, trimers, tetramers, pentamers, hexamers and heptamers) comprising the hexagonal monolayer are obtained. For these aggregates thermodynamic parameters of formation and clusterization are calculated. The correlation dependencies of the clusterization enthalpy, entropy and Gibbs energy on the number of CHHC interactions and interactions between the functional groups realized in the cluster are obtained on the basis of calculated data. The calculated parameters of the hexagonal monolayer unit cell are: a = 4.02 Å; b = 7.94 Å, t = 4°, close to those for an aliphatic alcohol monolayer according to GIXD experiments: a = 5.0 Å; b = 7.5 Å, t = 0-9°. Spontaneous clusterization of monoethoxylated alcohols at the air/water interface under standard conditions is shown to be possible for molecules possessing more than 14 carbon atoms in the alkyl chain, in good agreement with the characteristics of the surface pressure-molecular area (π-A) isotherms. It is found that addition of the -O-CH2-CH2- unit to the hydrophilic part of aliphatic alcohols results in a shift of their spontaneous clusterization threshold to that of the compounds with hydrocarbon chains 3 methylene units longer. The temperature effect of CnE1 is assessed. It corresponds to the spontaneous clusterization temperature decrease of 10-20 K per two methylene units taken from the alkyl chain in agreement with experimental data. The comparison of clusterization Gibbs energy dependencies for small aggregates of CnE1 confirms the experimental fact that the crystalline monolayers are formed by preferential aggregation of trimers.

Quantum chemical analysis of the thermodynamics of 2D cluster formation of 2-hydroxycarboxylic acids at the air/water interface

In the framework of the quantum chemical semiempirical PM3 method, the thermodynamic and structural parameters of formation and clusterization were calculated for 2-hydroxycarboxylic acids with the general formula CnH2n+1CHOHCOOH (n = 5–15). Dimers and tetramers were formed on the basis of optimized monomer structures. It was shown that the alkyl chains in the considered associates orientate themselves with the following values of the tilt angles with respect to the p- and q-directions of the interface: δ = 7.2–21.2° and φ = 9.8–21.1° depending on the monomer structure of the cluster. Comparing the Gibbs energy values of clusterization for small aggregates, a possible scheme of 2D clusterization is proposed based on the formation of linear aggregates constructed by dimers with ‘parallel’ orientation of the functional groups for 2-hydroxycarboxylic acid monomers with n ≤ 16 carbon atoms in the alkyl chain. The following parameters of the unit cell for the most energetically preferred structure of 2D film 3 were found: a = 4.85 Å, b = 5.41 Å, and the angle between them θ = 95°. The molecular tilt angle of 2-hydroxycarboxylic acids with respect to the air/water interface was calculated to be t = 21.7°. The spontaneous clusterization threshold is 14 carbon atoms in the 2-hydroxycarboxylic acid chain at the air/water interface for a monolayer built on the basis of monomer 3 in good agreement with the existing experimental data.

On the inclusion of alkanes into the monolayer of aliphatic alcohols at the water/alkane vapor interface: a quantum chemical approach

In the framework of the quantum chemical semiempirical PM3 method thermodynamic and structural parameters of the formation and clusterization of aliphatic alcohols C(n)H(2n+1)OH (n(OH) = 8-16) at 298 K at the water/alkane vapor C(n)H(2n+2), (n(CH(3)) = 6-16) interface were calculated. The dependencies of enthalpy, entropy and Gibbs' energy of clusterization per one monomer molecule of 2D films on the alkyl chain length of corresponding alcohols and alkanes, the molar fraction of alkanes in the monolayers and the immersion degree of alcohol molecules into the water phase were shown to be linear or stepwise. The threshold of spontaneous clusterization of aliphatic alcohols at the water/alkane vapor interface was 10-11 carbon atoms at 298 K which is in line with experimental data at the air/water interface. It is shown that the presence of alkane vapor does not influence the process of alcohol monolayer formation. The structure of these monolayers is analogous to those obtained at the air/water interface in agreement with experimental data. The inclusion of alkane molecules into the amphiphilic monolayer at the water/alkane vapor interface is possible for amphiphiles with the spontaneous clusterization threshold at the air/water interface (n(s)(0)) of at least 16 methylene units in the alkyl chain, and it does not depend on the molar fraction of alkanes in the corresponding monolayer. The inclusion of alkanes from the vapor phase into the amphiphilic monolayer also requires that the difference between the alkyl chain lengths of alcohols and alkanes is not larger than n(s)(0) - 15 and n(s)(0) - 14 for the 2D film 1 and 2D film 2, respectively.

Temperature Effect on the Monolayer Formation of Substituted Alkanes at the Air/Water Interface: A Quantum Chemical Approach

An approach to calculation of the threshold temperature for spontaneous clusterization of substituted alkanes (amines, nitriles, alcohols, thioalcohols, saturated and unsaturated carboxylic acids, α-amino acids, carboxylic acid amides, and melamine derivatives) at the air/water interface with dependence on the alkyl chain length was developed. In the framework of this approach, four schemes for the description of the temperature dependencies of the thermodynamic parameters of clusterization of the concerned amphiphilic compounds were proposed. They use the data obtained previously in the framework of quantum chemical semiempirical PM3 method and differ from each other by the degree of their theoretical accuracy. It was shown that the threshold temperature for spontaneous clusterization of the regarded classes of substituted alkanes can be described using a fractionally linear function in dependence on the alkyl chain length. It was found that, in agreement with the presented experimental data, the effect of the alkyl chain elongation of the substituted alkanes by two methylene units correlates with the decrease of the subphase temperature (ΔT) by 10-20 K. The general shape of the obtained dependencies indicates that the difference in the ΔT values for the amphiphilic molecules decreases with increasing alkyl chain length. This implies that the contribution of the intermolecular CH···HC interactions between the alkyl chains of monolayer molecules should be a decisive factor.

A simple method for estimation of the 2D cluster formation temperature of substituted alkanes at the air/water interface

A simple method for estimation of the 2D spontaneous clusterization temperature of substituted alkanes at the air/water interface versus alkyl chain length is proposed using the quantum chemical semiempirical PM3 method. The method is approved by long-chain amines, alcohols, thioalcohols, saturated and unsaturated carboxylic acids, α-amino acids and amides of carboxylic acids.The method is based on the experimental fact that short chain amphiphilic molecules cannot form condensed 2D monolayers whereas above a specific alkyl chain length condensed monolayer phases can be observed under the same conditions. That is, elongation of the alkyl chain of amphiphilic molecules causes the increase of intermolecular interaction energy between them what stimulates their close packing and structuring. This leads to linear or stepwise dependencies of enthalpy and entropy of cluster formation on the alkyl chain length. It is possible to obtain an equation for the estimation of the temperature of the spontaneous clusterization threshold of the considered substituted alkane types by setting Gibbs’ energy equal to zero and by knowing the regression expressions for determination of enthalpy and entropy of cluster formation calculated under the condition of 298K using coefficients which determine the contribution of the hydrophilic head group interactions of molecules and CH⋯HC-interactions between the alkyl chains.It is shown that the temperature dependence of the spontaneous clusterization threshold on the alkyl chain length of the amphiphile is fractionally linear with a relative error of 3–8%. The effect of the alkyl chain elongation of substituted alkanes by two methylene units corresponds to subphase temperature reduction (ΔТ) by 10–20K in good agreement with the available experimental data. The difference between ΔТ values for considered types of amphiphilic compounds becomes less significant with the lengthening of the alkyl chain. This indicates the basic contribution of intermolecular CH⋯HC-interactions between the alkyl chains to the process of the 2D clusterization.

Thermodynamics of the Clusterization Process of trans-Isomers of Unsaturated Fatty Acids at the Air/Water Interface

In the frameworks of the quantum-chemical semiempirical PM3 method, the thermodynamic parameters of trans-isomers of unsaturated carboxylic acids at the air/water interface were studied. Systems with 18-26 carbon atoms in the alkyl chain and different positions of the double bond are considered. Using quantum-chemical semiempirical PM3 method enthalpy, Gibbs' energy of monomers' formation from the elementary compounds and absolute entropy of trans-unsaturated carboxylic acids are calculated. It has been shown that thermodynamic parameters mentioned above for isomers with the same number of carbon atoms in the hydrocarbon chain but different position of double bond are practically the same within the margin of error. For dimers, trimers, and tetramers of the four trans-unsaturated carboxylic acids, the thermodynamic parameters of clusterization were calculated. It is shown that the position of double bond does not significantly affect the values of thermodynamic parameters of formation and clusterization of carboxylic acids with equal alkyl chain lengths. The only exception is the case that the double bond is in the ω-position (extremely distanced from the carboxylic group). In this case, the number of intermolecular interactions between alkyl chains is changed. Spontaneous clusterization of trans- in the standard conditions is possible for molecules that possess more than 16-17 carbon atoms in the alkyl chain. These threshold values exceed the corresponding values that were calculated previously using the quantum-chemical PM3 method for saturated carboxylic acids (12-13 carbon atoms in the alkyl chain) and are a little bit smaller than the corresponding parameters for cis-unsaturated carboxylic acids (18-19 carbon atoms). These values agree with experimental parameters. Also, the calculated structural parameters of trans-unsaturated carboxylic acids' monolayer for the unit cell with a = 6.98 Å, b = 8.30 Å, and for the molecular tilt angle with 64.95° agree with the experimental parameters.

Armchair [3,3] Carbon Nanotube Junctions with Tetrahedral Symmetry

We investigate the structure and stability of armchair [3,3] carbon nanotube junctions. The structures are constructed by opening a fullerene at the core hexagon in the sumanene unit. Series of objects are built up by increasing the tube length. The changes appearing in stability with the tube length is discussed. The geometry optimizations and single point computations (i.e., heat of formation, total energy, and molecular orbital energy levels) are performed by using the PM3 semiempirical quantum-chemical method.

Simulation of Silica Cluster Overcharging

The interaction of an e-beam with silica glass has been simulated using the 27SiO2 cluster, charged from 0 to −18 by a PM3 semiempirical quantum chemical method. The structures of the charged 27SiO2 silica clusters and their physicochemical characteristics, namely the heat of formation, relative volume, electron density of states distribution, gap between HOMO and LUMO and charge distribution, have been derived and analyzed in order to study the processes occurring on the atomic level at an e-beam-irradiated surface. The overcharging of the silica cluster led to its expansion by 30% in volume and evaporation of the charged species, followed by cluster densification. The silica cluster expansion should lead to structural changes in the neighbouring silica glass areas.