Comparison of semiempirical MO methods applied to large molecules

The heats of formation for 19 molecules have been calculated with PM3 and AM1 semiempirical methods. The values obtained have been compared with experimental heats of formation. With PM3 and AM1 the average differences between calculated and experimental heats of formation are 8.45 and 12.34 kcal mol^?1 respectively. There are significant differences when large molecules are considered: this suggests that the parameterization should be done including larger molecules.     

Chain photohalogenation of ethylene at liquid helium temperatures

Photolysis of a halogen in solid 1:1 molecular complexes of ethylene with chlorine (1) and bromine (2) at 18–70 K led to the formation oftrans-1,2-dihaloethanes by a chain mechanism (with quantum yields of 25–30 for 1 and 10–12 for 2 atT45 K) but molecular addition occurred above 90 K to give thegauche isomer. The rate constant for chain growth is independent of temperature atT45 K, but is described by the Arrhenius equation atT50 K (E ₀ 1 kcal/mole). It is proposed that chain growth occurs by a tunneling reaction of the C₂H₄Hal radical with an Hal₂ molecule at a neighboring lattice site.Institute of Chemical Physics, Russian Academy of Sciences, 142432 Chernogolovka. Translated from Izvestiya Akademii Nauk, Seriya Khimicheskaya, No. 10, pp. 2268–2277, October, 1992.     

Transport properties of normal liquid helium: comparison of various methodologies

We revisit the problem of self-diffusion in normal liquid helium above the lambda transition. Several different methods are applied to compute the velocity autocorrelation function. Since it is still impossible to determine the exact result for the velocity autocorrelation function from simulation, we appeal to the computation of short-time moments to determine the accuracy of the different approaches at short times. The main conclusion reached from our study is that both the quantum mode-coupling theory and the numerical analytic continuation approach must be regarded as a viable and competitive methods for the computation of dynamical properties of quantum systems.     

Comparison of methods employing gas chromatography retention data to determine vapour pressures at 298 K

Validity of five models suggested for expressing the relationship between vapour pressures and GC retention times measured on a non-polar capillary column were tested on a common set of compounds [five homologous series of the type H-(CH2)n-Y, where Y denotes Cl, Br, CHO, OCOCH3 and COOCH3, and n varies from 6 to 14]. Standard methods of statistical analysis, as well as vapour pressure values obtained independently from direct vapour pressure measurements were used as validity criteria. For the 40-compound data set examined, the methods provided vapour pressures agreeing within 9.2-24.7% (average absolute percent error) with direct experimental data.     

A study of reorientation effects in CsF—Ar using approximate quantum methods

The EB (exponential Born) and IOS (infinite order sudden) methods are used to calculate a variety of j → j′ and jm → j′m′ integral cross sections and j → j′ differential cross sections for CsF—Ar at E_cm = 87.7 meV. Inelastic rotational cross sections are found to depend primarily on the odd long range parts of the interaction potential. The jm → j′m′ integral cross sections for the quantization axis parallel to the initial relative velocity vector are found to approximately obey the selection rule “Δj + Δm = even” and cross sections for which the orientation of the rotor is left unchanged (i.e. 11 → 11, 11 → 22, and 11 → 33 transitions) are strongly favored over those which are changed for low lying rotational states. Good agreement between the IOS and EB methods is found for most of the scattering quantities calculated.     

Comparison between two INAA methods applied to chemical characterization of ancient ceramics

Two different instrumental neutron activation analysis (INAA) methods were applied to characterize chemically 74 ceramic roof tile samples, found in the town of Pella, Greece and dated back to the Hellenistic Period (3rd century B. C.). The samples were first analyzed for 17 elements with a 4 hour irradiation and two counts and then re-analyzed for 9 elements with a 1 minute irradiation and two counts of short-lived radioisotopes. The results of both methods were very similar, showing the validity of the rapid INAA method (1 min irradiation) in the study of ancient ceramics. All samples were divided into 4 chemical groups, each one representing a different tiling.     

High-performance liquid chromatography with nuclear magnetic resonance detection applied to organosilicon polymers. Part 2. Comparison with other methods

LC-NMR utilizing (1)H and (29)Si NMR spectroscopy is ideally suited for the analysis of silicones. It is shown that reversed phase gradient LC-NMR surpasses standard gel permeation chromatography (GPC) and diffusion ordered spectroscopy (DOSY) in the analysis of model hydride terminated polydimethylsiloxane. (1)H and (29)Si NMR in the stopped-flow arrangement leads to full identification of the components. Concentration gradient introduces a dependence of the (29)Si shifts on solvent composition, this dependence can be substantially reduced by a proposed method of referencing. It is shown that the ADEQUATE version of powerful but insensitive 2D INADEQUATE experiment can be used for complete line assignment.     

Comparison of computational methods applied to oxazole,thiazole, and other heterocyclic compounds

A variety of computational methods, including the semiempirical techniques AM1, PM3, and MNDO, and the thermochemical basis sets of Benson and Stine, was used to calculate and compare heats of formation (ΔH_f°) data for optimized geometries of a variety of aromatic and nonaromatic heterocycles. Detailed analyses, including 6-31G* and MP2/6-31G* ab initio calculations, were performed for the oxazole and thiazole heterocycles. The results indicate a scatter among the methods sensitive to the nature of the heterocycle. This was in particular evident in the oxazole molecule, where AM1 gave a singularly high value of ΔH_f° consistent with longer calculated bond lengths, particularly about the oxygen atom. Aromatic stabilization energy appears to be addressed differently among the employed methods. Implications of this contrast applied to calculation of macromolecular systems containing heterocyclic units are discussed.     

Comparison of two simulation methods to compute solvation free energies and partition coefficients

The thermodynamic integration (TI) and expanded ensemble (EE) methods are used here to calculate the hydration free energy in water, the solvation free energy in 1‐octanol, and the octanol‐water partition coefficient for a six compounds of varying functionality using the optimized potentials for liquid simulations (OPLS) all‐atom (AA) force field parameters and atomic charges. Both methods use the molecular dynamics algorithm as a primary component of the simulation protocol, and both have found wide applications in fields such as the calculation of activity coefficients, phase behavior, and partition coefficients. Both methods result in solvation free energies and 1‐octanol/water partition coefficients with average absolute deviations (AAD) from experimental data to within 4 kJ/mol and 0.5 log units, respectively. Here, we find that in simulations the OPLS‐AA force field parameters (with fixed charges) can reproduce solvation free energies of solutes in 1‐octanol with AAD of about half that for the solute hydration free energies using a extended simple point charge (SPC/E) model of water. The computational efficiency of the two simulation methods are compared based on the time (in nanoseconds) required to obtain similar standard deviations in the solvation free energies and 1‐octanol/water partition coefficients. By this analysis, the EE method is found to be a factor of nine more efficient than the TI algorithm. For both methods, solvation free energy calculations in 1‐octanol consume roughly an order of magnitude more CPU hours than the hydration free energy calculations. © 2012 Wiley Periodicals, Inc.     

Comparison of quantum mechanical methods to compute the biologically relevant reactivities of cyclopenta-polycyclic aromatic hydrocarbons

In computational studies to understand the interaction of polycyclic aromatic hydrocarbons (PAHs) with biomolecular systems, the semiempirical method AM 1 has been used previously to determine the geometry of the PAH and its metabolites and relevant intermediates. A number of studies have shown that AM 1 provides geometries for parent PAHs that are acceptably close to experimentally determined structures. However, many of the properties that determine the manner by which PAHs interact with biological nucleophiles depend on the structure of metabolites and reactive intermediates where less experimental information is available. In a previous study, we used AM 1 to obtain the molecular geometries of reactive intermediates of cyclopenta-PAHs (cPAHs) and then used single-point Hartree-Fock calculations, with the gaussian 3-21g basis set, to obtain molecular energies and charge distributions, in order to predict the direction of epoxide ring opening. Recent advances in the availability of computational hardware and software have provided other, more rigorous, methods for approaching this problem. In this study, we used hartree-fock methods in the gaussian series of programs employing the 3-21_g and 6-31_g basis sets and the local density functional method Dmol to obtain molecular geometries, energies, and charge distributions of the epoxides and the two potential hydroxycarbocations that could result from protonated ring opening, for a series of cPAHs. We have also performed the same calculations with AMSOL /SM 2, a semiempirical method that adds the effect of the aqueous environment to the AM 1 Hamiltonian. The division of the cPAHs into classes is not altered by these more rigorous calculations. The inclusion of water in the Hamiltonian has a greater effect on the results than using the ab initio methods to obtain the structure. © 1994 John Wiley & Sons, Inc.     

Comparison of static first hyperpolarizabilities calculated with various quantum mechanical methods

The prediction of nonlinear electro-optic (EO) behavior of molecules with quantum methods is the first step in the development of organic-based electro-optic devices. Typical EO molecules may require calculations with several hundred electrons, which prevents all but the fastest methods (semiempirical and density functional theory (DFT)) from being used for EO estimation. To test the reliability of these methods, we compare dipole moments, polarizabilities, and first-order hyperpolarizabilities for a wide range of structures of experimental interest with Hartree-Fock (HF), intermediate neglect of differential overlap (INDO), and DFT methods. The relative merits of molecules are consistently predictable with every method.     

Comparison of methods for characterization of reversed-phase liquid chromatographic selectivity

The goal of the present work is to obtain a better understanding of the chemical factors affecting liquid chromatographic retention. One of the most commonly used formats for liquid chromatographic separations is based on a nonpolar stationary phase, typically an octadecyl-derivatized silica material. A wide variety of these reversed-phase columns are commercially available that differ significantly in their chromatographic retention and selectivity. We seek to quantitatively characterize these differences. Retention data for a range of compounds with many diverse characteristics have been measured on several different octadecyl silica columns (J. Chromatogr. A, submitted for publication). Principal components analysis is used to characterize the different properties of these stationary phases and predict retention factors. The key set factor analysis method and the typical solute method are used in conjunction with the principal components analysis to identify small subsets of solutes that can be used to quantitatively describe the retention of a broad range of compounds. In addition, a quantitative comparison to alternative data analysis methods is made, including linear solvation energy relationships and an iterative subtraction method based on linear regression techniques. Although many earlier studies have reported the application of these methods, this study is the first to make a quantitative comparison of these methods using a highly precise and structurally variable set of test compounds.     

Molecular dynamics simulation of the structure and thermodynamic properties of liquid rubidium at pressures of up to 10 GPa and temperatures of up to 3500 K

The models of rubidium at temperatures of up to 3500 K, degrees of compression of up to Y = V/V₀ = 0.3, and pressures of up to 32 GPa were constructed by molecular dynamics (MD) using the interparticle potential ЕАМ. The thermodynamic properties of the MD models agree satisfactorily with experiment in the range of parameters under study at rubidium densities higher than 0.86 g/cm³. The behavior of the models in the range of the van der Waals loop was analyzed; the calculated critical temperature of rubidium T_c is ～2250 ± 25 K, density ～0.41 g/cm³, pressure ～0.019 GPa, and compressibility factor Z = pV/RT ≈ 0.137. The states with the unity factor Z = 1 were observed at pressures of up to 0.30 GPa (at ～3000 K); the temperature dependence of the density of the models with Z = 1 is nearly linear, and the Boyle temperature is T_B ≈ 10160 K. The ratio T_c/T_B = 0.221 is close to this value for cesium (0.23) and mercury (0.276). In the temperature and pressure ranges under study, the inversion of the Joule–Thomson coefficient did not take place, but should be observed at pressures of ?0.3 GPa and elevated temperatures. It was found that the diffusion coefficient D(T) dependences do not straighten in the usually used coordinates within wide temperature ranges. It was concluded that the structure of the liquid smoothly changes when the rubidium models are compressed and this reveals in the change of the degree of asymmetry of the first peak of the radial distribution function.     

Comparison of two adaptive temperature-based replica exchange methods applied to a sharp phase transition of protein unfolding-folding

Temperature-based replica exchange (T-ReX) enhances sampling of molecular dynamics simulations by autonomously heating and cooling simulation clients via a Metropolis exchange criterion. A pathological case for T-ReX can occur when a change in state (e.g., folding to unfolding of a protein) has a large energetic difference over a short temperature interval leading to insufficient exchanges amongst replica clients near the transition temperature. One solution is to allow the temperature set to dynamically adapt in the temperature space, thereby enriching the population of clients near the transition temperature. In this work, we evaluated two approaches for adapting the temperature set: a method that equalizes exchange rates over all neighbor temperature pairs and a method that attempts to induce clients to visit all temperatures (dubbed "current maximization") by positioning many clients at or near the transition temperature. As a test case, we simulated the 57-residue SH3 domain of alpha-spectrin. Exchange rate equalization yielded the same unfolding-folding transition temperature as fixed-temperature ReX with much smoother convergence of this value. Surprisingly, the current maximization method yielded a significantly lower transition temperature, in close agreement with experimental observation, likely due to more extensive sampling of the transition state.     

Surface properties of water ice at 150-191 K studied by elastic helium scattering

A highly surface sensitive technique based on elastic scattering of low-energy helium atoms has been used to probe the conditions in the topmost molecular layer on ice in the temperature range of 150-191 K. The elastically scattered intensity decreased slowly as the temperature was increased to about 180 K, followed by a rapid decrease at higher temperatures. An effective surface Debye temperature of 185+/-10 K was calculated from the data below 180 K. The changes in the ice surface above 180 K are interpreted as the onset of an anomalous enhancement of the mean square vibrational amplitude for the surface molecules and/or the onset of a limited amount of disorder in the ice surface. The interpretation is consistent with earlier experimental studies and molecular dynamics simulations. The observed changes above 180 K can be considered as the first sign of increased mobility of water molecules in the ice surface, which ultimately leads to the formation of a quasiliquid layer at higher temperatures. A small shift and broadening of the specular peak was also observed in the range of 150-180 K and the effect is explained by the inherent corrugation of the crystalline ice surface. The peak shift became more pronounced with increasing temperature, which indicates that surface corrugation increases as the temperature approaches 180 K. The results have implications for the properties and surface chemistry of atmospheric ice particles, and may contribute to the understanding of solvent effects on the internal molecular motion of hydrated proteins and other organic structures such as DNA.     

Structure of liquid 1-chloronaphthalene at 293 K

The structure of 1-chloronaphthalene, C₁₀H₇–Cl, at 293 K was investigated using the X-ray diffraction method. Monochromatic radiation MoK (λ=0.71069 Å) enabled the determination of the scattered radiation intensity between S₀=4πsin ₀/λ=0.430 Å⁻¹ and S_max=14.311 Å⁻¹. The interpretation of the results was carried out using the reduction method of Blum and Narten. Experimental distributions of X-ray scattered intensity were compared with theoretical results predicted for a proposed model of 1-chloronaphthalene molecule. The electron-density radial-distribution function was calculated and some intra- and intermolecular distances in liquid 1-chloronaphthalene were determined. X-ray structural analysis was applied to determine the packing coefficient of 1-chloronaphthalene molecules.     

Speed of sound in liquid tetrachloromethane and benzene at temperatures from 283.15 K to 333.15 K and pressures up to 30 MPa

Speeds of sound in liquid tetrachloromethane and benzene were measured at temperatures from 283.15 K to 333.15 K and pressures up to about 30 MPa. The method used was a sing-around technique employing a fixed path acoustic interferometer operated at a frequency of 2 MHz. The probable uncertainty of the present results is less than ±0.2 percent taking into account the errors of ±20 mK for the temperature, and ±(3 to 5) kPa for the pressure measurements. Measured values are fitted to a polynomial equation as functions of temperature and pressure, and the reliability of the present results is discussed in the light of a comparison with reference data reported in the literature.