Quantum monte carlo study of heats of formation and bond dissociation energies of small hydrocarbons

A quantum Monte Carlo (QMC) benchmark study of heats of formation at 298 K and bond dissociation energies (BDEs) of 22 small hydrocarbons is reported. Diffusion Monte Carlo (DMC) results, obtained using a simple product trial wavefunctions consisting of a single determinant and correlation function, are compared to experiment and to other theory including a version of complete basis set theory (CBS‐Q) and density functional theory (DFT) with the B3LYP functional. For heats of formation, the findings are a mean absolute deviation from experiment of 1.2 kcal/mol for CBS‐Q, 2.0 kcal/mol for B3LYP, and 2.2 kcal/mol for DMC. The mean absolute deviation of 31 BDEs is 2.0 kcal/mol for CBS‐Q, 4.2 kcal/mol for B3LYP, and 2.5 kcal/mol for DMC. These findings are for 17 BDEs of closed‐shell molecules that have mean absolute deviations from experiment of 1.7 kcal/mol (CBS‐Q), 4.0 kcal/mol (B3LYP), and 2.2 kcal/mol (DMC). The corresponding results for the 14 BDEs of open‐shell molecules studied are 2.4 kcal/mol (CBS‐Q), 4.3 kcal/mol (B3LYP), and 2.9 kcal/mol (DMC). The DMC results provide a baseline from which improvement using multideterminant trial functions can be measured. © 2005 Wiley Periodicals, Inc. Int J Chem Kinet 37: 583–592, 2005     

Efficient 3D kinetic monte carlo method for modeling of molecular structure and dynamics

Self‐assembly of molecular systems is an important and general problem that intertwines physics, chemistry, biology, and material sciences. Through understanding of the physical principles of self‐organization, it often becomes feasible to control the process and to obtain complex structures with tailored properties, for example, bacteria colonies of cells or nanodevices with desired properties. Theoretical studies and simulations provide an important tool for unraveling the principles of self‐organization and, therefore, have recently gained an increasing interest. The present article features an extension of a popular code MBN Explorer (MesoBioNano Explorer) aiming to provide a universal approach to study self‐assembly phenomena in biology and nanoscience. In particular, this extension involves a highly parallelized module of MBN Explorer that allows simulating stochastic processes using the kinetic Monte Carlo approach in a three‐dimensional space. We describe the computational side of the developed code, discuss its efficiency, and apply it for studying an exemplary system. © 2014 Wiley Periodicals, Inc.     

RMC_POT: A computer code for reverse monte carlo modeling the structure of disordered systems containing molecules of arbitrary complexity

An approach has been devised and tested for preserving the molecular dynamics molecular geometry taking into account energetic considerations during Reverse Monte Carlo (RMC) modeling. Instead of the commonly used fixed neighbor constraints, where molecules are held together by constraining distance ranges available for the specified atom pairs, here molecules are kept together via bond, angle, and dihedral potential energies. The scaled total potential energy contributes to the measure of the goodness‐of‐fit, thus, the atoms can be prevented from drifting apart. In some of the calculations (Lennard‐Jones and Coulombic) nonbonding potentials were also applied. The algorithm was successfully tested for the X‐ray structure factor‐based structure study of liquid dimethyl trisulfide, for which material now significantly more sensible results have been obtained than during previous attempts via any earlier version of RMC modeling. It is envisaged that structural modeling of a large class of materials, primarily liquids and amorphous solids containing molecules of up to about 100 atoms, will make use of the new code in the near future. © 2012 Wiley Periodicals, Inc.     

A monte carlo study of weak polyampholytes: stiffness and primary structure influences on titration curves and chain conformations

The conformation and titration curves of weak polyampholytes are examined using Monte Carlo simulations with screened Coulomb potentials in the Grand Canonical ensemble. Two different types of monomers are considered. Depending on the solution pH, monomers A are weak acidic sites that can either be negatively charged or uncharged (as carboxylic groups), whereas monomers B are weak basic sites that can either be positively charged or uncharged (as amino groups). The influence of the chain stiffness, primary structure, and ionic concentration on the acid/base properties of the polyampholyte chains are systematically investigated. By adjusting the pH values, titration curves and then the fractions of positively and negatively ionized charged monomers are calculated. Stiffness influence is estimated by comparing two models of chain: a fully flexible and a rod-like polyampholyte. Different primary structures such as statistical (diblock, octablock, and alternating) and random polyampholytes are also considered. We demonstrate that the primary structure plays important roles in the acid/base properties as well as the charge distribution along the polymer backbone of a statistical rod-like polyampholyte. When flexible polyampholytes are considered, polyampholyte conformations promote the attractive electrostatic interactions between positively and negatively charged monomers, hence leading to more or less compact conformations and acid/base properties relatively different in comparison to the rod-like polyampholytes. Various conformations such as extended, globular, and pearl-necklace conformations are found in good agreement with the literature by adjusting the interaction parameter between monomers and monomer stoichiometry.     

Quantum monte carlo study of the energetics of small hydrogenated and fluoride lithium clusters

An investigation of the energetics of small lithium clusters doped either with a hydrogen or with a fluorine atom as a function of the number of lithium atoms using fixed‐node diffusion quantum Monte Carlo (DMC) simulation is reported. It is found that the binding energy (BE) for the doped clusters increases in absolute values leading to a more stable system than for the pure ones in excellent agreement with available experimental measurements. The BE increases for pure, remains almost constant for hydrogenated, and decreases rapidly toward the bulk lithium for the fluoride as a function of the number of lithium atoms in the clusters. The BE, dissociation energy as well as the second difference in energy display a pronounced odd–even oscillation with the number of lithium atoms. The electron correlation inverts the odd–even oscillation pattern for the doped in comparison with the pure clusters and has an impact of 29%–83% to the BE being higher in the pure cluster followed by the hydrogenated and then by the fluoride. The dissociation energy and the second difference in energy indicate that the doped cluster Li₃H is the most stable whereas among the pure ones the more stable are Li₂, Li₄, and Li₆. The electron correlation energy is crucial for the stabilization of Li₃H. © 2016 Wiley Periodicals, Inc.     

Evaluation of the viscosity cross sections for elastic electron-atom collisions in krypton and xenon at low electron energies

The results of viscosity cross sections evaluations for elastic electron-atom scattering from rare gases krypton and xenon, carried out in the energy interval from 0.1 to 54.4 eV are presented and discussed. The evaluations are based on four independent sets of partialwave phaseshifts, one theoretical and three experimental, taken from literature. An analytical estimate for the contribution of all the terms not included in the summation, for truncation at any chosen value of the electron angular momentum, is derived. The validity of assumption of isotropic angular scattering is investigated in the energy range considered. The present results invariably show significant deviations from the values calculated with this assumption.     

Grand canonical monte carlo simulation study of methane adsorption at an open graphite surface and in slit-like carbon pores at 273 K

Grand canonical Monte Carlo (GCMC) simulation was used for the systematic investigation of the supercritical methane adsorption at 273 K on an open graphite surface and in slit-like micropores of different sizes. For both considered adsorption systems the calculated excess adsorption isotherms exhibit a maximum. The effect of the pore size on the maximum surface excess and isosteric enthalpy of adsorption for methane storage at 273 K is discussed. The microscopic detailed picture of methane densification near the homogeneous graphite wall and in slit-like pores at 273 K is presented with selected local density profiles and snapshots. Finally, the reliable pore size distributions, obtained in the range of the microporosity, for two pitch-based microporous activated carbon fibers are calculated from the local excess adsorption isotherms obtained via the GCMC simulation. The current systematic study of supercritical methane adsorption both on an open graphite surface and in slit-like micropores performed by the GCMC summarizes recent investigations performed at slightly different temperatures and usually a lower pressure range by advanced methods based on the statistical thermodynamics.     

Neutron scattering and monte carlo determination of the variation of the critical nucleus size with quench depth

We have used a combination of neutron scattering experiments and Monte Carlo simulations to study the initial stages of first-order phase transitions. We focus on quenches wherein the nascent phase is formed by homogeneous nucleation, and we approach the spinodal, i.e., the quench depth at which the original phase becomes unstable. In this regime, we show how critical nuclei sizes are determined from neutron scattering structure factors. Prevailing thought is that the size of the critical nucleus should increase with increasing quench depth and diverge at the spinodal. To the contrary, our experiments and simulations indicate that the critical nucleus size decreases monotonically as quench depth is increased and is finite at the spinodal.     

A new look at correlations in atomic and molecular systems. I. Application of fermion monte carlo variational method

We are engaged in research directed toward the development of compact and accurate correlation functions for many-electron systems. Our computational tool is the variational method in which the many-electron integrals are calculated by Monte Carlo using the fermion Metropolis sampling algorithm. That is, a many-fermion system is simulated by sampling the square of a correlated antisymmetric wave function. The principal advantage of the method is that interelectronic distance r_ij may be included directly in the wave function without adding significant computational complexity. In addition, other quantities of physical and theoretical interest such as electron correlation functions and representations of Coulomb and Fermi “holes” are very easily obtained. Preliminary results are reported for He, H₂, and Li₂.     

Validity of the classical monte carlo method to model the magnetic properties of a large transition-metal cluster: Mn19

The susceptibility of the large transition-metal cluster [Mn19O12(MOE)14(MOEH)10].MOEH (MOE = OC2H2O-CH3) has been fitted through classical Monte Carlo simulation, and an estimation of the exchange coupling constants has been done. With these results, it has been possible to perform a full-matrix diagonalization of the cluster core, which was used to provide information on the nature of the low-lying levels.     

Calculation of the rates of atomic reactions at low energies

The theory of binary atomic reactions is discussed. The matrix Schrödinger equation in the space of electron channels is used for the wave functions of the relative motion of the nuclei; this gives the corresponding quasiclassical equation by retention of terms linear in . Criterion (10) applies for quasiclassical nuclear motion. The additional restriction (13) causes the quasiclassical matrix equation (9) to go over to the basic equation (15) in the method of the central parameter, which indicates the region of application of that method. An Algol-60 program has been drawn up for calculating the rates of atomic reactions via the central-parameter or quasiclassical methods.     

Methods for the calculation of occupied volumes in glassy polymers: The lattice integration and the monte carlo methods

A new model for characterizing the free volume of a glassy polymer—gas systems is proposed. An improved method for the calculation of occupied volume per monomer unit was developed within the limits of this model. The model assumptions, error estimates and algorithm efficiencies are described. Using the example of polyvinyltrimethylsilane, it is shown that linear dependences of logarithms of the diffusion and the permeability coefficients on specific accessible volume for inert gases exist.     

Calculation of the entropy and free energy from monte carlo simulations of a peptide stretched by an external force

Hypothetical scanning Monte Carlo (HSMC) is a method for calculating the absolute entropy, S, and free energy, F, from a trajectory generated by any simulation technique. HSMC was applied initially to fluids (argon and water) and later to peptides and self-avoiding walks on a lattice. In this paper we make a step further and apply it to a model of decaglycine (at T = 300 K) in vacuum with constant bond lengths where external stretching forces are exerted at the end points; the changes in S and F are calculated as the forces are increased. The molecule is placed initially in a helical structure, which is changed to an extended structure after a short simulation time due to the exerted forces. This study has relevance to problems in polymers (e.g., rubber elasticity) and to the analysis of experiments where individual molecules are stretched by atomic force microscopy (AFM), for example. The results for S and F are accurate and are significantly better than those obtained by the quasi-harmonic approximation and the local states method. However, the molecule is quite stiff due to the strong bond angle potentials and the extensions are small even for relatively large forces. Correspondingly, as the force is increased the decrease in the entropy is relatively small while the potential energy is enhanced significantly. Still, differences, TDeltaS, for different forces are obtained with very good accuracy of approximately 0.2 kcal/mol.     

Thermodynamic characterization of fluids confined in heterogeneous pores by monte carlo simulations in the grand canonical and the isobaric-isothermal ensembles

Materials presenting nanoscale porosity are able to condense gases in their structure. This "capillary condensation" phenomenon has been studied for more than one century. Theoretical models help to understand experimental results but fail in explaining all experimental features. Most of the time, the difficulties in making quantitative or even qualitative predictions are due to the geometric complexity of the porous materials, such as large pore size distribution, chemical heterogeneities, or pore interconnections. Numerical calculations (lattice gas models or molecular simulations) are of considerable interest to calculate the adsorption properties of a fluid confined in a porous model with characteristic sizes up to several tens of nanometers. For instance, the grand canonical Monte Carlo method allows one to compute the average amount of fluid adsorbed in the porous model as a function of the temperature and the chemical potential of the fluid. However, the grand potential, necessary for a complete characterization of the system, is not a direct output of the algorithm. It is shown in this paper that the use of the isobaric-isothermal (NPT) ensemble allows one to circumvent this problem; that is, it is possible to get in one single Monte Carlo run the absolute grand potential for any given thermodynamic state of the fluid. A simplified thermodynamic integration scheme is then used to evaluate the grand potential over the whole isotherm branch passing through this initially given point. Since the usual NPT technique is a priori limited to homogeneous pores, it is proposed, for the first time, to generalize this procedure to a pore presenting a chemical heterogeneity along its axis. The new method gives the same results as the previous for homogeneous pores and allows new predictions for chemically heterogeneous pores. Comparison with the full integration scheme shows that the proposed direct calculation is faster since it avoids multiple Monte Carlo runs and more precise because it avoids the possible cumulative errors of the integration procedure.     

A comparison of electron ionization mass spectra obtained at 70 eV,low electron energies,and with cold EI and their NIST library identification probabilities

Electron ionization (EI) mass spectra of 46 compounds from several different compound classes were measured. Their molecular ion abundances were compared as obtained with 70‐eV EI, with low eV EI (such as 14 eV), and with EI mass spectra of vibrationally cold molecules in supersonic molecular beams (Cold EI). We further compared these mass spectra in their National Institute of Standards and Technology (NIST) library identification probabilities. We found that

1. Low eV EI is not a soft ionization method, and it has little or no influence on the molecular ion relative abundances for large molecules and those with weak or no molecular ions.
2. Low eV EI for compounds with abundant or dominant molecular ions in their 70 eV mass spectra results in the reduction of low mass fragment ions abundances thereby reducing their NIST library identification probabilities thus rarely justifies its use in real‐world applications.
3. Cold EI significantly enhances the relative abundance of the molecular ions particularly for large compounds; yet, it retains the low mass fragment ions; hence, Cold EI mass spectra can be effectively identified by the NIST library.
4. Different standard EI ion sources provide different 70 eV EI mass spectra. Among the Agilent technologies ion sources, the “Extractor” exhibits relatively abundant molecular ions compared with the “Inert” ion source, while the “High efficiency source” (HES) provides mass spectra with depleted molecular ions compared with the “Inert” ion source or NIST library mass spectra.

These conclusions are demonstrated and supported by experimental data in nine figures and two tables.     

Development of polystyrene calorimeter for application at electron energies down to 1.5 MeV

Polystyrene (PS) calorimeters developed at Riso National Laboratory for use below 4 MeV have been modified due to irradiation technology requirements concerning both design principles and dimensions. The temperature–time relationship after irradiation was measured, and two ways of dose measurement were tested: (1) real time temperature measurement during the irradiation and (2) pre- and post-irradiation temperature measurement. The advantages and drawbacks of these methods are discussed.Depth dose measurements have been carried out in the PS calorimeter to define the relationship between the average and the surface dose and to prove the applicability of the new low energy calorimeter for calibration purposes at 1.5 and 2 MeV electron energy. Alanine dosimeters of 2 mm thickness were used to calibrate the calorimeters and their use for nominal dose measurements was demonstrated in a series of intercomparisons. The use as routine dosimeters at electron accelerators operating in the energy range of 1.5–4 MeV was also demonstrated.     

Simulation of organic nonelectrolytes in water and tetrachloromethane by the monte carlo method. New data on the thermodynamics of dissolution

Scientific-Research Institute of Physical and Organic Chemistry, Rostov State University. Translated from Zhurnal Strukturnoi Khimii, Vol. 32, No. 5, pp. 57–68, September–October, 1991.     

Enhancement of ion transmission at low collision energies via modifications to the interface region of a spectrometer

The transmission efficiency of precursor and product ions decreases significantly at lower collision energies in a four-sector tandem mass spectrometer. In an effort to improve the overall ion transmission in this energy regime three modifications were made in the interface region between the two stages of mass analysis. An einzel lens was inserted prior to the deceleration lens of the collision cell block to reduce the precursor ion beam diameter. The collision cel1 block was reduced in thickness while maintaining the collision path length, thus increasing the number of ions which entered and exited the gas chamber, while removing any stray electrical fields. Finally, a second active focusing element was incorporated after the collision cell block to enhance the collection efficiency of the product ions. A tandem mass spectrum of angiotensin I obtained with this interface, at a collision cell block potential of 9200 volts, exhibited classical high energy collision-induced dissociation (CID) fragmentation patterns, a precursor ion transmission of 92% and an overall CID efficiency of approximately 7.5%. These improvements have resulted in a dramatically higher overall ion transmission at high collision cell potentials as well as sufficient sensitivity in acquiring good quality CID spectra in the lower collision energy regime (i.e., 60 eV). (460-469)     

Mutual capture of dipolar molecules at low and very low energies. II. Numerical study

The low-energy rate coefficients of capture of two identical dipolar polarizable rigid rotors in their lowest nonresonant (j(1) = 0 and j(2) = 0) and resonant (j(1) = 0, 1 and j(2) = 1, 0) states are calculated accurately within the close-coupling (CC) approach. The convergence of the quantum rate coefficients to their quantum-classical counterparts is studied. A comparison of the present accurate numerical with approximate analytical results (Nikitin, E. E.; Troe, J. J. Phys. Chem. A 2010, 114, 9762) indicates a good performance of the previous approach which was based on the interpolation between s-wave fly wheel quantal and all-wave classical adiabatic channel limits. The results obtained apply as well to the formation of transient molecular species in the encounter of two atoms at very low collision energy interacting via resonance dipole-dipole interaction.