MOPAC Program Research Articles

An improved parameterization procedure for NDDO-descendant semi-empirical methods

ConceptMNDO-based semi-empirical methods in quantum chemistry have found widespread application in the modelling of large and complex systems. A method for the analytic evaluation of first and second derivatives of molecular properties against semi-empirical parameters in MNDO-based NDDO-descendant models is presented, and the resultant parameter Hessian is compared against the approximant currently used in parameterization for the PMx models.MethodsAs a proof of concept, the exact parameter Hessian is employed in a limited reparameterization of MNDO for the elements C, H, N, O and F using 1206 molecules for reference data (heats of formation, ionization energies, dipole moments and reference geometries). The correctness of our MNDO implementation was verified by comparing the calculated molecular properties with the MOPAC program.

Supercomputer Search for the New Inhibitors of the Coagulation Factor XIIa

A virtual structure-oriented screening of candidates for inhibitors of blood coagulation factor XIIa was carried out. This coagulation factor is one of the most promising therapeutic targets for the development of anticoagulants without disturbing normal hemostasis. The screening was carried out in the database of organic compounds of the Voronezh State University, consisting of more than 19 thousand molecules. At the first stage of virtual screening, ligands were positioned in the active center of factor XIIa using the SOL docking program. At the second stage, for the best ligands, the protein-ligand binding enthalpy was calculated using the MOPAC program and the PM7 quantum-chemical method, taking into account the solvent in the COSMO continuum model. All calculations were carried out using the supercomputing resources at Lomonosov Moscow State University. In total, more than 30 thousand ligand conformers are docked, and for more than 400 of the best of them, the protein-ligand binding enthalpy was calculated. 16 compounds are selected as the most promising candidates for subsequent in vitro testing of their ability to inhibit factor XIIa.

Quantum-Chemical Quasi-Docking for Molecular Dynamics Calculations.

The quantum quasi-docking procedure is used to compare the docking accuracies of two quantum-chemical semiempirical methods, namely, PM6-D3H4X and PM7. Quantum quasi-docking is an approximation to quantum docking. In quantum docking, it is necessary to search directly for the global minimum of the energy of the protein-ligand complex calculated by the quantum-chemical method. In quantum quasi-docking, firstly, we look for a wide spectrum of low-energy minima, calculated using the MMFF94 force field, and secondly, we recalculate the energies of all these minima using the quantum-chemical method, and among these recalculated energies we determine the lowest energy and the corresponding ligand position. Both PM6-D3H4X and PM7 are novel methods that describe well-dispersion interactions, hydrogen and halogen bonds. The PM6-D3H4X and PM7 methods are used with the COSMO implicit solvent model as it is implemented in the MOPAC program. The comparison is made for 25 high quality protein-ligand complexes. Firstly, the docking positioning accuracies have been compared, and we demonstrated that PM7+COSMO provides better positioning accuracy than PM6-D3H4X. Secondly, we found that PM7+COSMO demonstrates a much higher correlation between the calculated and measured protein–ligand binding enthalpies than PM6-D3H4X. For future quantum docking PM7+COSMO is preferable, but the COSMO model must be improved.

Supercomputing, Docking and Quantum Mechanics in Quest for Inhibitors of Papain-like Protease of SARS-CoV-2

Lomonosov-2 supercomputer is used to search for new organic compounds that can suppress the replication of the SARS-CoV-2 coronavirus. The latter is responsible for the COVID-19 pandemic. Docking and a quantum-chemical semiempirical atomistic modeling method are used to find inhibitors of the SARS-CoV-2 papain-like protease, which is one of the key coronavirus enzymes responsible for its replication. The atomistic model of the papain-like protease of this coronavirus is based on the high-resolution structure deposited in the Protein Data Bank. The SOL docking program has been used for virtual screening of more than 40000 low molecular weight molecules (ligands). Ligands with the highest protein-ligand binding energy, selected using the docking results, were subjected to quantum-chemical calculations. The latters are performed by the PM7 semiempirical method with the COSMO implicit solvent model using the MOPAC program. The enthalpy of protein-ligand binding is calculated for the best position of the ligand in the protein. 19 ligands were selected for experimental in vitro testing as candidates for papain-like protease inhibitors base on docking and quantum-chemical results. In case of experimental confirmation, these compounds may become the basis for direct-acting antiviral drugs for the SARS-CoV-2 coronavirus.

RegioSQM20: improved prediction of the regioselectivity of electrophilic aromatic substitutions

We present RegioSQM20, a new version of RegioSQM (Chem Sci 9:660, 2018), which predicts the regioselectivities of electrophilic aromatic substitution (EAS) reactions from the calculation of proton affinities. The following improvements have been made: The open source semiempirical tight binding program xtb is used instead of the closed source MOPAC program. Any low energy tautomeric forms of the input molecule are identified and regioselectivity predictions are made for each form. Finally, RegioSQM20 offers a qualitative prediction of the reactivity of each tautomer (low, medium, or high) based on the reaction center with the highest proton affinity. The inclusion of tautomers increases the success rate from 90.7 to 92.7%. RegioSQM20 is compared to two machine learning based models: one developed by Struble et al. (React Chem Eng 5:896, 2020) specifically for regioselectivity predictions of EAS reactions (WLN) and a more generally applicable reactivity predictor (IBM RXN) developed by Schwaller et al. (ACS Cent Sci 5:1572, 2019). RegioSQM20 and WLN offers roughly the same success rates for the entire data sets (without considering tautomers), while WLN is many orders of magnitude faster. The accuracy of the more general IBM RXN approach is somewhat lower: 76.3–85.0%, depending on the data set. The code is freely available under the MIT open source license and will be made available as a webservice (regiosqm.org) in the near future.

Quantitative Explanation of Basic Compound Retention Mechanisms in Reversed-Phase Mode Liquid Chromatography

The quantitative analysis of the chromatographic behavior of basic compounds measured with pentyl-, hexenyl-, and octyl-bonded silica gels were analyzed in silico employing model phases. The main retention force was the van der Waals (VW) interaction, and the main desorption force was an electrostatic (ES) interaction. The contribution of hydrogen bonding (HB) was weak compared to that for acidic compounds. The quantitative explanation was achieved utilizing the calculated VW, HB, and ES energy values obtained from a molecular mechanics program. The electron localization was observed at the molecular interaction-site calculated MOPAC program. This fundamental approach was like that of explaining chemical reactions. The difference was electron localization in chromatography or electron transfer in a chemical reaction.

A dynamic look on molecular symmetry

J.H. van’t Hoff’s seminal paper variously titled as either: Chemistry in Space, The Placement of Atoms in Space or other with similar wording, depending on the language it was published in, suggested that the structure of a molecule would be independent of its physical state: solid, liquid, vapor, gaseous, or in solution. However, this is definitely not true so much so that during the last decades many examples have accumulated showing that the structure of a molecule in a crystalline solid can differ substantially from its structure in solution. This would have important consequences not only on how molecules are structurally described and the way they react, but also that molecular symmetry may not be a static property and has to be considered from a dynamic point of view. To add additional evidence to this conception, we took advantage of a family of trans-1,4-di- and tetra-substituted cyclohexane derivatives that appear to have a centre of symmetry but show a substantial dipole moment in solution. In the present work, we used the trans-1,4-dicarboxymethylcyclohexane and its 1,4-dibrominated derivative and were able, through dipole moment determinations IR, Raman, NMR studies, and computational calculations with the SpinWorks, MOPAC, and MOLDEN programs, to confirm our assumption that the molecular symmetry and the molecular structure are dependent on the environment.

GAFit: A general-purpose, user-friendly program for fitting potential energy surfaces

We have developed a software package based on a genetic algorithm that fits an analytic function to a given set of data points. The code, called GAFit, was also interfaced with the CHARMM and MOPAC programs in order to facilitate force field parameterizations and fittings of specific reaction parameters (SRP) for semiempirical Hamiltonians. The present tool may be applied to a wide range of fitting problems, though it has been especially designed to significantly reduce the hard work involved in the development of potential energy surfaces for complex systems. For this purpose, it has been equipped with several programs to help the user in the preparation of the input files. We showcase the application of the computational tool to several chemical-relevant problems: force-field parameterization, with emphasis on nonbonded energy terms or intermolecular potentials, derivation of SRP for semiempirical Hamiltonians, and fittings of generic analytical functions. Program summaryProgram title : GAFitProgram Files doi : http://dx.doi.org/10.17632/9gy6bjcwk5.1Licensing provisions : GNU General Public License 3 (GPL)Programming language : Fortran 90, C, Perl and JavaNature of problem : Potential energy surfaces (PESs) have a key role in reaction dynamics and molecular dynamics. Chemical dynamics simulations can be performed by using analytical PESs or by direct dynamics, that is, by computing energies and forces “on-the-fly” by molecular structure calculations. The development of analytical PESs is, quite often, a very complex and tedious task. There are several programs in the literature that may help to develop PESs but, as far as we know, none of them show, at the same time, great generality and flexibility.Solution method : GAFit was designed to help users develop analytical potential energy functions. We made special efforts to write a code that exhibits the three features mentioned above. For this reason, we have also interfaced GAFit with the CHARMM and MOPAC programs. The former is one of the popular packages for molecular dynamics and the latter is a semiempirical quantum chemistry program that may be conveniently used for direct dynamics simulations. Because, in general, the fitting of PESs involves a simultaneous optimization of many nonlinear parameters, we have selected a genetic algorithm as the driver for the parameterizations. As shown in the paper, GAFit may be applied to other fitting problems.

Introduction of In Silico Chromatography

Molecular interaction (MI) is fundamental phenomena in nature. Chromatography is a tool to quantitatively measure the degree of molecular interactions. The qualitative explanation has been performed using solubility factors [1]. The quantitative explanation is achieved using computational chemical calculation (In silico). The molecular interaction forces are combination of solubility factors, and can be obtained as van der Waals, hydrogen bonding and electrostatic energy values after molecular mechanics (MM2) calculations. Simple study can be done using small molecules. The model analyses should help to quantitatively understand the chromatographic retention mechanisms. When one small molecule is replaced to a macro molecule, (chromatography model phase), we can quantitatively analyze chromatography retention time with the retention times of standard compounds. Furthermore, when the macro molecule is a protein, we can study affinity level of proteins. In addition, the apc calculated using MOPAC program indicates the enzyme reactivity. Prediction of boiling point, dissociation constant, and albumin-drug binding affinity were demonstrated as practical applications of in silico chromatography [2].

IN SILICO PREDICTION OF MELTING POINTS OF IONIC LIQUIDS BY USING MULTILAYER PERCEPTRON NEURAL NETWORKS

Quantitative structure–property relationship (QSPR) was used to predict melting points of 62 ionic liquids (ILs), which include ammonium, pyrrolidiniu, imidazolium, pyridiniu, piperidiniu, phosphonium ionic liquid salts. The structures of ionic liquids were optimized by Hyperchem software and MOPAC program, and stepwise multiple linear regression method was applied to select the relevant structural descriptors. The predicting models correlating selected descriptors and melting points were set up using multiple linear regressions (MLR) and multilayer perceptron neural network (MLP NN), separately. The obtained linear and nonlinear QSPR models were validated by internal and external test sets. According to the obtained results, the correlation coefficients between predicted and experimental melting points for training, test and validation sets were; 0.91, 0.86 and 0.79 for MLR model. These values for MLP NN model were; 0.97, 0.96 and 0.85, respectively. The results of this study revealed the high applicability of QSPR approach to melting point prediction of ILs.

CHANGE IN SURFACE CHARGE PROPERTIES OF NANO-BALL ALLOPHANE AS INFLUENCED BY SULFATE ADSORPTION

Change in surface charge of nano-ball allophane after sulfate adsorption was studied. Cation exchange capacity (CEC) was found to increase with increasing pH as well as after sulfate adsorption, with KnP (allophane sample with high Si/Al ratio) having higher CEC value as compared to KyP (low Si/Al ratio). The increase in CEC after adsorption for both samples was attributed to the charge carried by the anion. However, plotting the increase in CEC vs. the amount of sulfate adsorbed showed a slope of much less than 1, which showed that most of the sulfate adsorption occurred as bidentate reaction. This can be attributed to the adsorption mechanism with sulfate being adsorbed through ligand exchange aside from anion exchange reaction. Further, the adsorption of sulfate on allophane enhanced the deprotonation of the near silanol group, thus providing a new negative charge, thus an increase in the CEC. Molecular orbital calculation using MOPAC program affirmed these experimental results. The amount of positive charge or AEC on the other hand was found to decrease after sulfate adsorption for both KyP and KnP samples. The decrease in AEC was much lower than the sulfate adsorption, although more sulfate than AEC was adsorbed. This implies that some AEC site remains after much sulfate adsorption, providing nutrients such as Cl - and NO 3 - for plants.

Experimental and Semiempirical Investigation of Interaction Between Fast Sm Membrane Sensor and 1, 3-Di(Thiophene Imino) Benzoic Acid

This work describes, for the first time, the theoretical modeling of structure and interaction between Sm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3+</sup> ion and 1, 3-di(thiophene imino)benzoic acid (DTBA) as a chelating reagent in the membrane and solution which were performed using the PM6/SPARKLE semiempirical method in the MOPAC program. Computational modeling results can be predicted behavior of Sm-DTBA interactions which was used as an ionophore for construction of samarium-selective potentiometric membrane sensor. The best performance was obtained with a membrane composition of 31% (w/w) PVC, 62% tributylphosphate (TBP), 4.8% DTBA and 3.2% sodium tetraphenyl borate (NaTBP). This sensor has a Nernstian slope of 19.6 mV decade for Sm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3+</sup> ions in the range of 1.0 × 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-1</sup> - 5.0 × 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">6</sup> M and the detection limit was 3.1 × 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-6</sup> M. The response time of the sensor is very fast (≤ 5 s) and the potentiometric response is independent of the pH of the solution in the pH range of 4.5-8.5. This sensor shows good selectivity for Sm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3+</sup> ion with respect to alkali, alkaline earth and heavy metal cations. The proposed sensor has been used for indirect determination of some drugs such as homatropine hydrobromide and hyoscine N-butylbromide in their pharmaceutical formulations and fluoride ions in mouthwash samples.

XAFS study of the complex of an acetylacetonate-based ligand and copper ion

An X-ray absorption fine structure (XAFS) study has been conducted to reveal the local structure and chemical state of the copper in the complex of an acetylacetonate-based ligand (L1) and copper ion in acetonitrile solution. The copper ion in the complex was found to be divalent from the Cu K-edge X-ray absorption near-edge structure (XANES) spectrum. The FEFF (ab initio multiple scattering calculations of XAFS) were performed with the model compounds, whose structures were optimized by using MOPAC program with AM1 Hamiltonian. The comparative study of the experimental XAFS spectra and theoretical calculations from FEFF gave the perspectives for clarifying the coordination structure of the complex of L1 and copper ion.

Modeling Free-Radical Reactions, Produced by Hydrocarbon Cracking, with Asphaltenes

Radical adsorptions and reactions produced in oil hydrocarbon cracking with an asphaltene model molecule were carried out with CATIVIC and MOPAC programs. Density functional theory (DFT) calculations were also performed for comparison. Eley—Rideal (ER) and Langmuir-Hinshelwood (LH) reaction mechanisms, of H•, CH 3 •, and CH 3 CH 2 • radicals with adsorbed H•, were studied on asphaltene unsaturated fragments. Qualitative results indicated that it is possible that radical adsorptions on the asphaltene surface lead to bond activations (surface deformation). The following adsorption energy trend was found for the three different programs: H• > CH 3 • > CH 3 CH 2 •. Approximate reaction energy barriers were evaluated. The ER mechanism has smaller reaction barriers and higher exothermic reactions than the LH mechanism, which means that ER is energetically more feasible than LH. These results indicate that, at low temperatures and high pressure, the asphaltene surface may play an important role in the recombination of free radicals.

QSAR correlation of the melting points for imidazolium bromides and imidazolium chlorides ionic liquids

The melting points of ionic liquids (ILs) of imidazolium bromides and imidazolium chlorides have been investigated by means of quantitative structure–activity relationship (QSAR) approach in order to develop prediction models for predicting the melting points of ionic liquid salts. The cationic structures of these ILs were optimized by means of Hyperchem software and MOPAC program. QSAR module of Materials Studio software and Genetic Algorithm (GA) programs were employed to calculate and select the structure descriptors of ILs, then prediction models correlating the selected structure descriptors and melting points of ionic liquids were set up by using the multiple linear regressions (MLR) method and the back-propagation artificial neural network (BP ANN) method, separately. Finally, the obtained QSAR models, including MLR model and BP ANN model, were validated by external test sets. In this work, three data sets, which were 30 imidazolium bromides, 20 imidazolium chlorides and the merging of above two data sets, respectively, were used to investigate the QSAR correlation of the melting points of ILs. The results demonstrated that the prediction mean absolute errors (MAEs) of MLR models for test sets of those three data sets were in the order of 20.52 K, 13.59 K and 21.95 K, and the prediction MAEs of BP ANN models were 8.77 K, 4.98 K and 9.31 K, respectively. It indicated that the predictions of two models for all melting points of ILs were reliable, and the prediction precision of BP ANN model was higher than that of MLR model.

Adsorption of lambda-cyhalothrin and cypermethrin on two typical Chinese soils as affected by copper

Pesticides and heavy metals pollution in soil environment has become a serious problem in many countries including China. Repeated applications of bordeaux mixture (a blend of copper sulfate and calcium hydroxide) and pyrethroid (Pys) insecticides have led to elevated copper (Cu) and Pys concentrations in vineyard surface soils. However, few studies focused on the interaction of Pys and heavy metals in the soil environment. Our previous studies had indicated the combined effect of cypermethrin (CPM) and Cu on soil catalase activity. Also, we had suggested that the addition of Cu could catalyze photo-degradation of CPM and lambda-cyhalothrin (lambda-CHT) in aqueous solution and restrain their degradation in soil. To better understand the potential influence of Cu on the fate of Pys in the soil environment, the aim of the present work was to examine the effect of Cu on the adsorption of lambda-CHT and CPM on two typical Chinese soils with different soil characteristics, which was one of the key processes controlling the fate of Pys, and to provide more information about the potential ecological risk of chemicals on the soil ecosystem. Fourier transform infrared and point charges analysis using the MOPAC program of the Gaussian system were also used to reveal the probable adsorption mechanism of lambda-CHT and CPM on soils. Two vineyard soils with different properties were chosen as experimental samples. They were sampled from 0 to 10 cm, dried, and sieved to 2 mm. Each soil was spiked with copper sulfate solution to obtain the following total soil Cu concentrations: 100, 200, 400, 800, and 1,600 mg.kg(-1). The treated soils were incubated for 2 weeks and then dried at 20 degrees C. For each soil sample and at each soil Cu concentration, the adsorption of lambda-CHT and CPM was measured using a batch equilibrium method. The concentration of lambda-CHT was determined by HPLC, and the amount of lambda-CHT and CPM adsorbed by the soil sample at equilibrium was determined by the difference between the initial and equilibrium concentrations in solution corrected by the blank adsorption measurement. Without the addition of Cu, the adsorption of lambda-CHT and CPM on Black soil is greater than that on Red soil, while the adsorption of lambda-CHT on both soils is significantly stronger than that of CPM. As the soil Cu concentration increased from 19 (or 18; background) to 1,600 mg.kg(-1), the adsorption coefficient (K (d)) of lambda-CHT decreased from 12.2 to 5.9 L.kg(-1) for Red soil, and from 26.1 to 16.8 L.kg(-1) for Black soil, whereas the CPM adsorption coefficient in both soils decreased nearly by 100% (K (d) decreased from 9.4 to 0.2 L.kg(-1) for Red soil and from 16.2 to 0.5 L.kg(-1) for Black soil). Pys adsorption is a surface phenomenon which depends on the surface area and the organic matter content. Thus, the Black soil, having higher organic matter and greater surface area than that of the Red soil, show greater adsorption affinity to lambda-CHT and CPM. In our study, the different adsorption affinity of the two Pys was obtained, which was probably attributed to differences with respect to their physical-chemical properties. Further comparison upon the two Pys was conducted. The point charges of halogen atoms in the lambda-CHT and CPM were calculated, the differences of which probably lead to the fact that lambda-CHT has a stronger binding capacity to soils than CPM. Also, FTIR spectra show that competitive adsorption occurs between CPM and Cu for the same adsorption sites, which is responsible for the obtained suppression of CPM adsorption affected by Cu. Lambda-cyhalothrin shows a significantly stronger adsorption than cypermethrin on both soils. This phenomenon may be due to several reasons: (1) lambda-CHT has lower solubility and a higher octanol-water partition coefficient value than CPM; (2) lambda-CHT consists of specific isomers, whereas CPM is mixtures of eight different isomers; (3) the chlorine and fluorine atoms in the lambda-CHT have a negative point charge, whereas the chlorine atoms in the CPM have a positive point charge. As the soil Cu concentrations increased from 19 (or 18) mg.kg(-1) to 1,600 mg.kg(-1), the adsorption coefficient of lambda-CHT and CPM decreased on both soils. This is mainly due to a competition between Cu and Pys for occupying the adsorption sites on soils. The information from this study have important implications for vineyard and orchard soils, which often contain elevated levels of Cu and Pys. These results are also useful in assessing the environmental fate and health effect of lambda-CHT and CPM. It is important for environmental scientists and engineers to get a better understanding of soil-metal-organic contaminant interactions. However, pesticide adsorption involves complex processes, and shortcomings in understanding them still restrict the ability to predict the fate and behavior of pesticide. Therefore, considerable research should be carried out to understand the mechanism of interaction between Pys and heavy metal on soils clearly.

Semi-empirical topological method for prediction of the gas chromatographic relative retention times of Polybrominated Diphenyl Ethers (PBDEs)

Quantitative structure-retention relationship (QSRR) studies have proved to be a valuable approach in the prediction of the gas chromatographic relative retention time (GC-RRT) of organic chemicals. Polybrominated diphenyl ether (PBDE) congeners are now ubiquitous environmental pollutants. Of the 209 possible PBDE congeners, 126 have been synthesized and their retention-time data on seven different stationary phases has been determined [Korytár et al.:J Chromatography A 1065:239-249, (2005)]. To estimate and predict the GC-RRT values of all 209 PBDEs on different stationary phases, 17 molecular descriptors from the semi-experience algorithm in MOPAC program and the topological structures of PBDE molecules were calculated. By means of the VSMP (variable selection and modeling based on prediction) program [Liu et al.:J Chem Inf Comput Sci 43:964-969, (2003)], six optimal descriptors were selected to develop a QSRR model for the prediction of GC-RRT of PBDE. The descriptors contain some energy information (such as the energy of the lowest unoccupied molecular orbital and highest occupied molecular orbital) and topological information (the number of ortho-, meta-, and para- substituted bromine atoms) as well as the molecular weight (lnM (W)). All the models developed were cross-validated using leave-one-out (LOO). For seven GC stationary phases, the estimated correlation coefficients (r(2)) are all more than 0.985 but for the column CP-Sil 19 (r(2) = 0.9392) and LOO-validated correlation coefficients (q(2)) all more than 0.985 but for the column CP-Sil 19 (q(2) = 0.9345).

ZnS deposition on oxadiazole–terpyridine copolymer

AbstractThe combination of inorganic salts and macromolecules leads to supramolecular structures with new interesting physical and chemical properties. The deposition of ZnS (Wurtzite) on oxadiazole–terpyridine copolymer P‐90/10 synthesized by free radical copolymerization were investigated. The apparent order of the crystallization process was found to be 2 that indicated a surface diffusion‐controlled mechanism. Critical nucleus formation proceeds via complexation of the ZnS molecules to the N atoms as concluded from computational chemistry calculations. The number of ions forming the critical nucleus was found experimentally to be (n*exp = 1.71 ± 0.24) in accordance with the computational chemistry calculations by the PM3 method of the MOPAC program package. The surface energy of the growing ZnS phase was found to be 121 mJ/m2 typical for sparingly soluble salts. © 2006 Wiley Periodicals, Inc. J Appl Polym Sci 101: 1913–1918, 2006

Self-Assembled Monolayers of Alkanethiol and Fluoroalkanethiol Investigated by Noncontact Atomic Force Microscopy

We investigated single-component fluoroalkanethiol self-assembled monolayers (SAMs) and phase-separated SAMs composed of alkanethiol and fluoroalkanethiol by noncontact atomic force microscopy (NC-AFM). We obtained molecularly resolved images of the single-component fluoroalkanethiol SAMs. Their molecular film structures were compared with those of alkanethiol SAMs. In addition, energy dissipation and surface potential (SP) images were obtained for the phase-separated SAMs. These images clearly showed the feature of phase separation. The contrast in energy dissipation images was discussed in terms of their structural rigidity. The molecular dipole moments were calculated using a MOPAC program and the theoretical SP difference was compared with the experimental results.

Calcite crystallization on oxadiazole-terpyridine copolymer

The nucleation and further crystallization of calcite on oxadiazole-terpyridine copolymer were investigated by the constant composition method. The apparent order of the crystallization process was found to be 2.3±0.2 indicative of a surface diffusion-controlled spiral growth mechanism. The number of ions forming the critical nucleus was found experimentally to be ( n * = ) 3 in accordance with the simulation by the PM3 method included in the MOPAC program package. The surface energy of the growing phase was found to be 29.5 mJ m −2.