Determining molecule-carbon surface adsorption energies using molecular mechanics and graphene nanostructures

Five model surfaces were developed using molecular mechanics with MM2 parameters. A smooth, flat model surface was constructed of three parallel graphene layers where each graphene layer contained 127 interconnected benzene rings. Four rough surfaces were constructed by varying the separation between a pair of graphene nanostructures placed on the topmost layer of graphene. Each nanostructure contained 17 benzene rings arranged in a linear strip. The parallel nanostructures were moved closer together to increase the surface roughness and to enhance the molecule-surface interaction. Experimental adsorption energy values from the temperature variation of second gas-solid virial coefficients values were available for 16 different alkanes, haloalkanes, and ether molecules adsorbed on Carbopack B (Supelco, 100 m(2)/g). For each of the five different surface models, sets of 16 calculated adsorption energies, E(cal)( *), were determined and compared to the available experimental adsorption energies, E( *). The best linear regression correlation between E( *) and E(cal)( *) was found for a 1.20 nm internuclei separation of the surface nanostructures, and for this surface model the calculated gas-solid interaction energies closely matched the experimental values (E( *)=1.018E(cal)( *), r(2)=0.964).     

Binding energies for alkane molecules on a carbon surface from gas-solid chromatography and molecular mechanics

Gas-solid chromatography was used to determine B(2s) (gas-solid virial coefficient) values for 12 alkanes (10 branched and 2 cyclic) interacting with a carbon powder (Carbopack B, Supelco). B(2s) values were determined by multiple size variant injections within the temperature range of 393 to 623 K with each alkane measured at 5 or 6 different temperatures. The temperature variations of the gas-solid virial coefficients were used to find the experimental adsorption energy or binding energy values (E( *)) for each alkane. A molecular mechanics based, rough-surface model was used to calculate the molecule-surface binding energy (E(cal)( *)) using augmented MM2 parameters. The surface model consisted of three parallel graphene layers with each layer containing 127 interconnected benzene rings and two separated nanostructures each containing 17 benzene rings arranged in a linear strip. As the parallel nanostructures are moved closer together, the surface roughness increases and molecule-surface interactions are enhanced. A comparison of the experimental and calculated binding energies showed excellent agreement with an average difference of 3.8%. Linear regressions of E( *) versus E(cal)( *) for the current data set and a combined current and prior alkane data set both gave excellent correlations. For the combined data set with 18 linear, branched and cyclic alkanes; a linear regression of E( *)=0.9848E(cal)( *) and r(2)=0.976 was obtained. The results indicate that alkane-surface binding energies may be calculated from MM2 parameters for some gas-solid systems.     

Adsorption energies for a nanoporous carbon from gas-solid chromatography and molecular mechanics

Gas-solid chromatography was used to obtain second gas-solid virial coefficients, B2s, in the temperature range 342-613 K for methane, ethane, propane, butane, 2-methylpropane, chloromethane, chlorodifluoromethane, dichloromethane, and dichlorodifluoromethane. The adsorbent used was Carbosieve S-III (Supelco), a carbon powder with fairly uniform, predominately 0.55 nm slit width pores and a N2 BET surface area of 995 m2/g. The temperature dependence of B2s was used to determine experimental values of the gas-solid interaction energy, E*, for each of these molecular adsorbates. MM2 and MM3 molecular mechanics calculations were used to determine the gas-solid interaction energy, E*(cal), for each of the molecules on various flat and nanoporous model surfaces. The flat model consisted of three parallel graphene layers with each graphene layer containing 127 interconnected benzene rings. The nanoporous model consisted of two sets of three parallel graphene layers adjacent to one another but separated to represent the pore diameter. A variety of calculated adsorption energies, E*(cal), were compared and correlated to the experimental E* values. It was determined that simple molecular mechanics could be used to calculate an attraction energy parameter between an adsorbed molecule and the carbon surface. The best correlation between the E*(cal) and E* values was provided by a 0.50 nm nanoporous model using MM2 parameters.     

Substituent effects in the benzene dimer are due to direct interactions of the substituents with the unsubstituted benzene

The prevailing views of substituent effects in the sandwich configuration of the benzene dimer are flawed. For example, in the polar/pi model of Cozzi and co-workers (J. Am. Chem. Soc. 1992, 114, 5729), electron-withdrawing substituents enhance binding in the benzene dimer by withdrawing electron density from the pi-cloud of the substituted ring, reducing the repulsive electrostatic interaction with the nonsubstituted benzene. Conversely, electron-donating substituents donate excess electrons into the pi-system and diminish the pi-stacking interaction. We present computed interaction energies for the sandwich configuration of the benzene dimer and 24 substituted dimers, as well as sandwich complexes of substituted benzenes with perfluorobenzene. While the computed interaction energies correlate well with sigmam values for the substituents, interaction energies for related model systems demonstrate that this trend is independent of the substituted ring. Instead, the observed trends are consistent with direct electrostatic and dispersive interactions of the substituents with the unsubstituted ring.     

Molecular similarity based on atomic electrostatic potential

We propose a new similarity measure operating in the space spanned by the potential values, evaluated at atoms constituting the benzene ring and the COOH group in para-substituted benzoic acids and at benzene ring atoms in monosubstituted benzenes. The similarity measures are equivalent to the Euclidean distance between points in that space. Only the distances between the potentials at corresponding atoms in different molecules are included. The distances for benzene rings were very similar, regardless of whether they were calculated in para-substituted acids or in monosubstituted benzenes. As reference reactions, dissociation of benzoic acids and nitration of monosubstituted benzenes have been used. The effects of reduction of dimensionality of the potential space on the comparison of similarity measures with the free energies of the reference reactions have been investigated. It became obvious that the potentials at individual atoms in molecules of the acids and monosubstituted benzenes are mutually correlated to a high degree.     

Thermodynamic ionization energies and charge transfer reactions in benzene and substituted benzenes

Ionization energies of 11 substituted benzenes of CS₂ related to the ionization energy of benzene were obtained by measurements of the charge exchange equilibrium constants for C₆H₅X⁺ + C₆H₅Y ? C₆H₅Y⁺ + C₆H₅X at 450 and K. Thermodynamic ionization energies of substituted benzenes, related to that of benzene, are found to be higher by 0.5–2.0 kcal/mole than the corresponding photoionization (0—0) values. Exothermic charge transfer reactions between substituted benzenes are found to proceed with rate constants of (1.3–1.6) × 10^?9 cm³/mol s, which agree well with calculated collision rates.     

Dispersion-corrected density functional theory calculations of the molecular binding of n-alkanes on Pd(111) and PdO(101)

We investigated the molecular binding of n-alkanes on Pd(111) and PdO(101) using conventional density functional theory (DFT) and the dispersion-corrected DFT-D3 method. In agreement with experimental findings, DFT-D3 predicts that the n-alkane desorption energies scale linearly with the molecule chain length on both surfaces, and that n-alkanes bind more strongly on PdO(101) than on Pd(111). The desorption energies computed using DFT-D3 are slightly higher than the measured values for n-alkanes on Pd(111), though the agreement between computation and experiment is a significant improvement over conventional DFT. The measured desorption energies of n-alkanes on PdO(101) and the energies computed using DFT-D3 agree to within better than 2.5 kJ/mol (< 5%) for chain lengths up to n-butane. The DFT-D3 calculations predict that the molecule-surface dispersion energy for a given n-alkane is similar in magnitude on Pd(111) and PdO(101), and that dative bonding between the alkanes and coordinatively unsaturated Pd atoms is primarily responsible for the enhanced binding of n-alkanes on PdO(101). From analysis of the DFT-D3 results, we estimate that the strength of an alkane η(2)(H, H) interaction on PdO(101) is ~16 kJ/mol, while a single η(1) H-Pd dative bond is worth about 10 kJ/mol.     

Face-to-face arene-arene binding energies: dominated by dispersion but predicted by electrostatic and dispersion/polarizability substituent constants

Parallel face-to-face arene-arene complexes between benzene and substituted benzenes have been investigated at the MP2(full)/6-311G** and M05-2X/6-311G** levels of theory. A reasonably good correlation was found between the binding energies and the ∑|σ(m)| values of the substituted aromatics. It is proposed that a substituent |σ(m)| value informs on both the aromatic substituent dispersion/polarizability and the effect the substituent has on the aromatic electrostatics. Supporting this hypothesis, a combination of electrostatic (∑σ(m)) and dispersion/polarizability (∑M(r)) substituent constant terms gives an excellent, and statistically significant, correlation with the benzene-substituted benzene binding energy. Symmetry adapted perturbation theory energy decomposition calculations show the dominant attractive force is dispersion; however, the sum of all nonelectrostatic forces is essentially a constant, while the electrostatic component varies significantly. This explains the importance of including an electrostatic term when predicting benzene-substituted benzene binding energies.     

Substituent effects on benzdiyne: a density functional theory study

Density functional theory (DFT) studies were performed to investigate the effect of substituents on the properties of benzdiyne derivatives. Twelve substituted benzdiynes-C(6)X(2), where X = F, Cl, Br, Me, CF(3), CN, OH, NO(2), NH(2), OMe, NMe(2), and Ph-were considered along with the unsubstituted 1,4-benzdiyne. The structures, vibrational frequencies, and IR intensities of these benzdiynes were studied with a popular three-parameter hybrid density functional (B3LYP) combined with the split-valence 6-31G(d) basis set and Dunning's correlation-consistent polarized triple-zeta (cc-pVTZ) basis set. The relative stabilities of the substituted benzdiynes were studied with the help of reaction energies of isodesmic reactions, which showed that the electron-withdrawing groups destabilized the benzdiynes more than they did the corresponding benzenes, whereas the electron-donating groups stabilized the benzdiynes more than they did their benzene counterparts. Correlation analyses revealed that field/inductive effects played a more important role than did resonance effects. The changes in atomic charges and spin populations due to the substituents were also studied. The asymmetric nu(Ctbd1;C) stretching modes obtained were close to the 1500-cm(-)(1) mark. Reinvestigation of the experimental results supported these results; a weak IR band at 1486 cm(-)(1) was assigned to this asymmetric stretching mode in C(6)(CF(3))(2) F. Some other benzdiynes also had large IR intensity values for their asymmetric nu(Ctbd1;C) vibrational modes due to the coupling with other vibrational modes. Heats of formation for the substituted benzdiynes were obtained from the reaction energies calculated at the B3LYP/cc-pVTZ level of theory.     

Monte Carlo simulations of the hydration of substituted benzenes with OPLS potential functions

Intermolecular potential functions have been developed for use in computer simulations of substituted benzenes. Previously reported optimized potentials for liquid simulations (OPLS) for benzene and organic functional groups were merged and tested by computing free energies of hydration for toluene, p-xylene, phenol, anisole, benzonitrile, p-cresol, hydroquinone, and p-dicyanobenzene. The calculations featured Monte Carlo simulations at 25°C and 1 atm with statistical perturbation theory. The average difference between the computed results and experimental data for the absolute free energies of hydration is 0.5 kcal/mol. The AM1-SM2 method is also found to perform well in predicting the free energies of hydration for the substituted benzenes. In addition, the Monte Carlo simulations provided details on the hydration of the substituted benzenes, in particular for the solute–water hydrogen bonding. © 1993 John Wiley & Sons, Inc.     

The influence of substituent groups on the resonance stabilization of benzene. An ab initio computational study

Accurate G3(MP2) calculations of the enthalpies of formation (Delta(f)H298) of organic molecules permit replication and extension of calculations that were formerly dependent on experimental thermochemical results. A case in point is Kistiakowski's classical calculation of the total stabilization enthalpy of benzene relative to that of cyclohexene, called for many years the "resonance energy". This paper investigates extension of the classical calculation to substituted benzenes. Slight modification of the usual procedure for Delta(f)H298 determination permits exclusion of all empirical information, leaving a purely ab initio result. Stabilization enthalpies relative to the corresponding 4-substituted cyclohexenes are presented for benzene, toluene, aniline, phenol, phenylacetylene, styrene, ethylbenzene, and phenylhydrazine. In the process of calculating these stabilization enthalpies, we have also obtained 42 values of Delta(f)H298 for monosubstituted benzenes, cyclohexenes, and cyclohexanes, 24 of which are not in the standard reference literature. For the remaining 18 G3(MP2) results, the unsigned mean difference between calculated Delta(f)H298 values and experimental results is +/-0.91 kcal x mol(-1).     

Ab Initio Study of the Adsorption of CO2 on Functionalized Benzenes

The interaction of carbon dioxide with a series of functionalized aromatic molecules was studied by using quantum mechanical methods (MP2), to examine the effect of the substituent on the adsorption of CO₂. Several different initial configurations of CO₂ were taken into account for each functionalized benzene to locate the energetically most favorable configuration. To get a better estimation of the binding energies, we applied an extrapolation scheme to approach the complete basis set. CH₂N₃‐, COOH‐, and SO₃H‐functionalized benzenes were found to have the strongest interaction with CO₂, and the corresponding binding energies were calculated to be ?3.62, ?3.65, and ?4.3 kcal mol^?1, respectively. Electrostatic potential maps of the functionalized benzenes and electron redistribution density plots of the complexes were also created to get a better insight into the nature of the interaction of CO₂ with the functionalized benzenes. The functional groups that were examined can be potentially incorporated in organic bridging molecules that connect the inorganic corners in MOF.     

Molecular thin films on solid surfaces: mechanisms of melting

We use molecular dynamics simulations to study the melting of pentane and hexane monolayers adsorbed on the basal plane of graphite. For both of these systems, the temperature-dependent structures and the melting temperatures agree well with experiment. A detailed analysis reveals that a mechanism involving the promotion of molecules to the second layer underlies melting in these systems. In the second-layer promotion mechanism, a small fraction of molecules transition into the second layer around the melting temperature, leaving vacant space in the first layer to facilitate disordering. The second-layer promotion mechanism arises because of the weaker molecule-surface interaction in our study than that in previous studies. The weaker molecule-surface interaction is consistent with experimental temperature-programmed desorption studies.     

Spectroscopic, and thermal studies of some new binuclear transition metal(II) complexes with hydrazone ligands containing acetoacetanilide and isoxazole

A new chelating ligand, 2-(2-(5-tert-butylisoxazol-3-yl)hydrazono)-N-(2,4-dimethylphenyl)-3-oxobutanamide (HL), and its four binuclear transition metal complexes, M(2)(L)(2) (micro-OCH(3))(2) [M=Ni(II), Co(II), Cu(II), Zn(II)], were synthesized using the procedure of diazotization, coupling and metallization. Their structures were postulated based on elemental analysis, (1)H NMR, MALDI-MS, FT-IR spectra and UV-vis electronic absorption spectra. Smooth films of these complexes on K9 glass substrates were prepared using the spin-coating method and their absorption properties were evaluated. The thermal properties of the metal(II) complexes were investigated by thermogravimetry (TG) and differential scanning calorimetry (DSC). Different thermodynamic and kinetic parameters namely activation energy (E*), enthalpy of activation (DeltaH*), entropy of activation (DeltaS*) and free energy change of activation (DeltaG*) are calculated using Coats-Redfern (CR) equation.     

最小二乘法计算苯、噻吩和正辛烷在NaY上程序升温脱附活化能

采用程序升温脱附(TPD)技术测定了苯、噻吩和正辛烷在NaY上以不同升温速率升温时的TPD谱图. 利用TPD谱图的峰形和其微分曲线判断了程序升温脱附过程中的脱附级数. 提出了一种利用最小二乘法计算吸附剂/催化剂的脱附活化能及其动力学参数的方法. 以这些TPD谱图为基础, 分别采用传统TPD计算模型、最小二乘法以及一阶微分曲线法计算了苯、噻吩和正辛烷在NaY上的脱附活化能和动力学参数. 结果表明, 最小二乘法对在不同线性升温速率时的程序升温脱附活化能的计算结果是一致的.     

Empty level structure in phenyl and benzyl isocyanates

The energies of the lowest-lying anion states of phenyl (C6H5N=C=O) and benzyl (C6H5CH2N=C=O) isocyanates have been determined experimentally in the gas phase for the first time using electron transmission spectroscopy (ETS), and their localization properties have been evaluated using HF/6-31G, MP2/6-31G*, and B3LYP/6-31G* calculations. The lowest-lying anion state of phenyl isocyanate, mainly of benzene ring character but with some contribution also from the N=C=O pi-system, lies at significantly higher energy than that of other benzenes substituted by pi-functionals, such as benzaldehyde or styrene. The scaling with the use of suitable empirical equations of the virtual orbital energies (VOEs) for orbitals with predominantly pi*(ring) character calculated for the neutral-state molecules leads to vertical attachment energies (VAEs) which closely correspond to those determined experimentally, whereas those calculated for the predominantly pi*(CO) and pi*(NC) orbitals (3rd and 4th LUMO, respectively) are significantly different from the corresponding measured values notwithstanding the fact that the calculations reproduce the shortening of the N=C and C=O double bonds.     

有效主量子数拓扑指数与分子总键能和晶格能的关系

作者定义ＡｊＢｋ分子的有效主量子数拓扑指数（Ｐ）为：Ｐ＝∑（ｎＡ·ｎＢ）－０．５。它与化合物的总键能（ΔＥ）、晶格能（Ｕ）呈现高度相关性,其直线回归方程为：ΔＥ＝－２８．４５１８＋１１１７．８９８Ｐ,Ｒ＝０．９３５４Ｕ＝１９６．６７０３＋１６６５．６２６６Ｐ,Ｒ＝０．９８８２用它预测ΔＥ、Ｕ,估算值与实验值基本吻合     

Metal complexes of antibiotic drugs. Studies on dicluxacillin complexes of FeII, FeIII, CoII NiII and CuII

The synthesis and characterization of dicluxacillin (DC) complexes with di- and tri-valent metal ions are described. The nature of bonding of the chelated DC and its metal complexes structures have been elucidated on the basis of their spectroscopic (infrared, solid reflectance, magnetic spectra, mass and thermal analysis) properties. In all the complexes studied, the DC acts as a chelate monoanionic ligand with coordination involving the carboxylate O atom and the endocyclic N of the thiazole ring. The DC ligand forms mono-ligand complexes of the general formula [M(DC)(H2O)x(A)]. yH2O where DC is the uninegatively charged bidentate ligand and A = OAc in case of CuII and Cl in case of FeIII, FeII, CoII and NiII ions. IR, solid reflectance spectra and magnetic moment measurement are used to infer the structure and to illustrate the coordinating capacity of the ligand. From the thermal decomposition curves, the water molecules of crystallization are removed in a single stage while the decomposition of the ligand and coordinated water molecules occur in the second and subsequent stages. Different thermodynamic kinetic parameters namely activation energy (E*), enthalpy of activation (AH*), entropy of activation (AS*) and free energy change of activation (AG*) are calculated using Coats and Redfern equation.     

Substituent effects on the acidity of weak acids. 2. Calculated gas-phase acidities of substituted benzoic acids

To investigate the origin of substituent effects on the acidity of benzoic acids, the structures of a series of substituted benzoic acids and benzoates have been calculated at the B3LYP/6-311+G* and MP2/6-311+G* theoretical levels. The vibrational frequencies were calculated using B3LYP/6-311+G* and allowed corrections for the change in zero-point energies on ionization, and the change in energy on going from 0 K (corresponding to the calculations) to 298 K. A more satisfactory agreement with the experimental values was obtained by energy calculations at the MP2/ 6-311++G* level using the above structures. The resulting Delta H(acid) values agree very well with the experimental gas-phase acidities. The energies of compounds with pi-electron-accepting or -releasing substituents, rotated to give the transition state geometries, provided rotational barriers that could be compared with those found for the corresponding substituted benzenes. Isodesmic reactions allowed the separate examination of the substituent effects on the energies of the acids and on the anions. Electron-withdrawing groups stabilize the benzoate anions more than they destabilize the benzoic acids. Electron-donating groups stabilize the acids and destabilize the anions by approximately equal amounts. The gas-phase acidities of meta- and para-substituted benzoic acids are linearly related. This is also found for the acidities of substituted phenylacetic acids and benzoic acids. Since direct pi-electron interactions are not possible with the phenylacetic acids, this indicates that the acidities are mainly controlled by a field effect interaction between the charge distribution in the substituted benzene ring and the negative charge of the carboxylate group. The Hammett sigma(M) and sigma(P) values are also linearly related for many small substituents from NO(2) through the halogens and to OH and NH(2). Most of the other substituents fall on a line with a different slope     

On the resonance energy in new all-metal aromatic molecules

We have recently advanced the aromaticity concept into all-metal molecules containing Al(4)(2-), XAl(3)(-), Ga(4)(2-), In(4)(2-), Hg(4)(6-), Al(3)(-), and Ga(3)(-) aromatic units. All these systems are electron deficient species compared to the corresponding aromatic hydrocarbons. The electron deficiency results in an interesting new feature in all-metal aromatic systems, which should be considered as having both pi- and sigma-aromaticity, and that should result in their additional stability. In this work, we obtain crude evaluations of the resonance energies for Na(2)Al(4) and Na(2)Ga(4) all-metal aromatic molecules. The resonance energies were found to be unusually high: 30 kcal/mol (B3LYP/6-311+G*) and 48 kcal/mol (CCSD(T)/6-311+G(2df)) for Na(2)Al(4) and 21 kcal/mol (B3LYP/6-311+G*) for Na(2)Ga(4) compared to 20 kcal/mol in benzene. We believe that the high resonance energies in Na(2)Al(4) and in Na(2)Ga(4) are due to the presence of three completely delocalized bonds, one pi-bond and two sigma-bonds, thus confirming the presence of pi- and sigma-aromaticity.