Force Field Calculations Research Articles

Comparison of Different Types of Carbamate Amine for Stripping Process

Amine absorption process is an approach for mitigation of carbon dioxide (CO2) from flue gas that was produced from the power plant. Modelling and simulation of amine absorption process for CO2 removal at macro-scale is well established. This study aims to investigate different carbamate molecules for the regerenation process using molecular dynamic (MD) simulation. MD simulation was installed in the HP240 workstation using the software of Material Studio (version 7.0). The MD simulation was carried out at mole, volume, energy (NVE) (200 ps) and mole, volume, temperature (NVT) (1 ns) ensemble. Condensed-phase Optimized Molecular Potentials for Atomistic Simulation Studies (COMPASS) and Ewald models were used for the force field and summation method calculation within the simulation box. The simulation results show that, the carbamate ions of monoethanolamine (MEA) were difficult to break compared to 2-amino-2-methyl-1- propanol (AMP) and piperazine (PZ) for inter- and intra-molecular interactions on the stripping process. The high tendency for inter- and intra-molecular interactions happened on AMP and PZ, making them good choices to be blended with other amine solvent to overcome the limitation of other less reactive amines. The simulation results obtained from this study gave the fundamental explanation on the experimental and simulations results reported in the literature. The application of MD simulation in amine absorption process is capable to improve the understanding and give insight about this process at molecular level.

Comprehensive rotational spectroscopy of the newly identified atmospheric ozone depleter CF3CH2Cl

The pure rotational spectrum of CF3CH2Cl (1-choro-2,2,2-trifluoroethane, HCFC-133a) was investigated at 8–18GHz in supersonic expansion with chirped pulse and cavity rotational spectroscopy, and at 94–309GHz with broadband millimetre wave spectroscopy. Spectroscopic constants for the two principal isotopic species have been considerably updated from global fits over extensive data sets, numbering close to 3000 lines for the ground state of CF3CH235Cl and 1800 lines for CF3CH237Cl. Four different 13C containing isotopologues have been assigned, as well as several new low lying vibrational states. The new measurements have been augmented with anharmonic force field calculations in an evaluation of the semi-experimental equilibrium geometry for CF3CH2Cl.

Unanticipated Stickiness of α-Pinene.

The adsorption of α-pinene to solid surfaces is an important primary step during the chemical conversion of this common terpene over mesoporous materials, as well as during the formation of atmospheric aerosols. We provide evidence of tight and loose physisorbed states of α-pinene bound on amorphous SiO2 as determined by their adsorption entropy, enthalpy, and binding free energies characterized by computational modeling and vibrational sum frequency generation (SFG) spectroscopy. We find that adsorption is partially (40-60%) irreversible over days at 294-342 K and 1 ATM total pressure of helium, which is supported by molecular dynamics (MD) simulations. The distribution of α-pinene orientation remains invariant with temperature and partial pressure of α-pinene. Using the Redlich-Peterson adsorption model in conjunction with a van't Hoff analysis of adsorption isotherms recorded for up to 2.6 Torr α-pinene in 1 ATM total pressure of helium, we obtain ΔS°ads, ΔH°ads, and ΔG°ads values of -57 (±7) J mol-1 K-1, -39 (±2) kJ mol-1, and -22 (±5) kJ mol-1, respectively, associated with the reversibly bound population of α-pinene. These values are in good agreement with density functional theory (DFT)-corrected force field calculations based on configurational sampling from MD simulations. Our findings are expected to have direct implications on the conversion of terpenes by silica-based catalysts and for the synthesis of secondary organic aerosol (SOA) in atmospheric chambers and flow tubes.

The spectroscopic investigation, NLO, NBO, NMR, HOMO–LUMO and molecular docking analysis on Clonazepam

The geometry and the vibrational frequency of Clonazepam (CPM) were elucidated with the help of structure optimisation and normal coordinate force field computations based on DFT method. Fourier Transform Infra red spectrum has been recorded in the range 4000–400 cm−1 and analysed. The non-linear optical parameters like electric dipole moment, first-order hyperpolarisability and polarisability for CPM were computed. The DFT-based NMR calculation procedure has been used for assigning the 1H and 13C NMR chemical shift of CPM. The Mulliken atomic charges were computed and interpreted. HOMO and LUMO energies have been calculated. Natural bond orbital analyses have been used for interpreting intramolecular interaction. To investigate the biotic behaviour of the compound, molecular docking (ligand and protein) stimulations have been studied and the results were discussed in detail.

Green Synthesis of Zr-CAU-28: Structure and Properties of the First Zr-MOF Based on 2,5-Furandicarboxylic Acid.

A new Zr-based metal-organic framework denoted as Zr-CAU-28 with framework composition [Zr6O4(OH)4(FDC)4(OH)4(H2O)4] (H2FDC = 2,5-furandicarboxylic acid, CAU = Christian-Albrechts-University) was obtained under green synthesis conditions from a mixture of H2O and acetic acid and employing microwave-assisted heating. Zr-CAU-28 is the first Zr-MOF based on H2FDC, which is often considered a promising renewable alternative to terephthalic acid. The crystal structure was determined from powder X-ray diffraction data using a combination of direct methods, force field calculations, and Rietveld refinement. The compound crystallizes in the hexagonal crystal system (space group P63/mmc) with the cell parameters a = 24.9919(9) and c = 24.7688(9) Å. The framework structure adopts a kagome-like topology and hence contains large hexagonal channels with a pore diameter of approximately 16 Å and small trigonal channels with a size of 3 Å. Nitrogen sorption measurements were carried out at -196 °C and gave a specific surface area of SBET = 1006 m2/g and a micropore volume of 0.42 cm3/g. Thermogravimetric analyses showed a stability up to 270 °C although temperature dependent PXRD measurements revealed a decrease in long-range order already above 150 °C. Furthermore, the Ce4+ based analogue Ce-CAU-28 could be obtained employing dimethylformamide/water mixtures as solvent. The structure and framework composition of this MOF are very similar to the ones of the Zr-based compound, but its thermal stability is clearly inferior. Thus, Ce-CAU-28 cannot be fully desolvated and exhibits a specific surface area of only SBET = 360 m2/g and a micropore volume of 0.15 cm3/g.

The complete molecular geometry and electric dipole moment of salicyl aldehyde from rotational spectroscopy

The pure rotational spectrum of salicyl aldehyde, C7H6O2, a classic molecule with an OH⋯O intramolecular hydrogen bond, was investigated in detail with several different spectrometers. Supersonic expansion measurements at 8–18GHz were used to determine rotational constants for 26 different isotopologues, either in natural abundance or prepared synthetically, and including single substitution of each of the 15 atoms in the molecule. Further measurements of the room temperature rotational spectrum at 8–230GHz allowed assignment of the five lowest excited vibrational states. Their rotational constants were used to calibrate anharmonic force field calculations, which were then used to determine the semi-experimental equilibrium reSE geometry. This is compared with several other structural determinations and with quantum chemistry calculations. In addition, Stark measurements in supersonic expansion were used to determine the electric dipole moment of salicyl aldehyde.

Single Conformation Spectroscopy of Suberoylanilide Hydroxamic Acid: A Molecule Bites Its Tail.

Suberoylanilide hydroxamic acid (SAHA) is a histone deacetylase inhibitor that causes growth arrest and differentiation of many tumor types and is an approved drug for the treatment of cancer. The chemical structure of SAHA consists of formanilide "head" and a hydroxamic acid "tail" separated by an n-hexyl chain, C6H5NH(C═O)-(CH2)6-(C═O)NHOH. The alkyl chain's preference for extended structures is in competition with tail-to-head (T-H) or head-to-tail (H-T) hydrogen bonds between the amide and hydroxamic acid groups. Laser desorption was used to bring SAHA into the gas phase and cool it in a supersonic expansion before interrogation with mass-resolved resonant two-photon ionization spectroscopy. Single conformation UV spectra in the S0-S1 region and infrared spectra in the hydride stretch and mid-IR regions were recorded using IR-UV hole-burning and resonant ion-dip infrared spectroscopy, respectively. Three conformers of SAHA were distinguished and spectroscopically characterized. Comparison of the experimental IR spectra with the predictions of density functional theory calculations (DFT, B3LYP D3BJ/6-31+G(d)) leads to assignments for the three conformers, all of which possess tightly folded alkyl chains that enable formation of a T-H (conformer A) or H-T (conformers B and C) hydrogen bonds. A modified version of the generalized Amber force field was developed to more accurately describe the hydroxamic acid OH internal rotor potential, leading to predictions for the relative energies in reasonable agreement with experiment. This force field was used to generate a disconnectivity graph for the low-energy portion of the potential energy landscape of SAHA. This disconnectivity graph contains more than one hundred minima and maps out the lowest-energy pathways between them, which could then be characterized via DFT calculations. This combination of force field and DFT calculations provides insight into the potential energy landscape and how population was funneled into the three observed conformers.

Molecular Dynamic Simulation of Amine-CO2 Absorption Process

Objectives: Modelling and simulation of amine absorption process for CO2 removal at macro-scale is well established. This study used to investigate the amine-CO2 absorption process at molecular level using Molecular Dynamic (MD) simulation. Methods/Statistical Analysis: Analysis on different types of amine and blended amines for absorption process was conducted in this study. COMPASS and Ewald models used for force field and summation method calculation, respectively. Findings: The results shows MEA solvent was the highest tendency (39.70%) to interact with CO2 compared to DEA and MDEA because can directly react with CO2 and easily form carbamate ions. Due to the lack of –HN bond in MDEA, it was determined to be less reactive and suggested to be blended with other reactive amines. Blended MDEA/AMP (33.50%) and MDEA/PZ (23.80%) improved the efficiency of MDEA in CO2 absorption process. The addition of AMP and PZ assisted MDEA to have intermolecular interaction with CO2. Application/Improvements: Research on molecular modelling of amine absorption process for CO2 capture was proposed in this study to give insight about this process at molecular level and to analyse the intermolecular interaction between CO2 and amine solution.

Microsecond Simulation of Electron Transfer in DNA: Bottom-Up Parametrization of an Efficient Electron Transfer Model Based on Atomistic Details.

The transfer of electrons over long distances in complex molecular systems is a phenomenon of significance in both biochemistry and technology. In recent years, we have been developing efficient models to study ET in complex systems, including DNA as a prominent example. Ab initio and model approaches have been combined in an "on-the-fly" calculation of ET parameters, which can be used to propagate nuclear and electronic degrees of freedom simultaneously. These previous efforts have aimed at deriving an efficient nonadiabatic quantum mechanical-molecular mechanical (QM/MM) simulation scheme for ET, making nanosecond simulations of ET in realistic systems possible. This, however, is still insufficient for the treatment of large donor-bridge-acceptor systems, like the ET in DNA, overcoming long adenine bridges. Therefore, we have constructed a theoretical model in a bottom-up manner. All quantum-chemical as well as force-field calculations are substituted by theoretical models of the involved phenomena on a molecular level, including polarization and relaxation of the molecular environment, which are often omitted in other recently developed theoretical models of ET. A nonadiabatic simulation scheme is employed, and no assumptions regarding the ET mechanism are needed. Thus, the predictive power of the simulations is preserved, while pushing the limits of the accessible time scales beyond microseconds. This model-based simulation scheme is applied to ET in various DNA species. Good agreement with the "full" atomistic nonadiabatic QM/MM scheme is observed for the archetypal DNA ET systems, the polyA sequence, as well as the sequences GTnGGG, containing adenines as bridge sites. Furthermore, ET in larger, more complex DNA sequences is simulated, and the results are discussed.

Metal Complexes of a Novel Schiff Base Based on Penicillin: Characterization, Molecular Modeling, and Antibacterial Activity Study.

A novel Schiff base ligand of type HL was prepared by the condensation of amoxicillin trihydrate and nicotinaldehyde. The metal complexes of Co+2, Ni+2, Cu+2, and Zn+2 were characterized and investigated by physical and spectral techniques, namely, elemental analysis, melting point, conductivity, 1H NMR, IR, UV-Vis spectra, ESR, SEM, and mass spectrometry measurements. They were further analyzed by thermal technique (TGA/DTA) to gain better insight about the thermal stability and kinetic properties of the complexes. Thermal data revealed high thermal stability and nonspontaneous nature of the decomposition steps. The Coats-Redfern method was applied to extract thermodynamic parameters to explain the kinetic behavior. The molar conductance values were relatively low, showing their nonelectrolytic nature. The powder XRD pattern revealed amorphous nature except copper complex (1c) that crystallized in the triclinic crystal system. The EPR study strongly recommends the tetrahedral geometry of 1c. The structure optimization by MM force field calculation through ArgusLab 4.0.1 software program supports the concerned geometry of the complexes. The in vitro antibacterial activity of all the compounds, at their two different concentrations, was screened against four bacterial pathogens, namely, E. coli, P. vulgaris, K. pneumoniae, and S. aureus, and showed better activity compared to parent drug and control drug.

Evaluation of the velocity-field-smoothing required for calculation of body force field in plasma actuator

Evaluation of the velocity-field-smoothing required for calculation of body force field in plasma actuator

Asymmetric induction in cyclohexadienones carrying α-d-glucopyranosyl moiety

Cyclohexadienone derivatives possessing α-d-glucopyranosyl moiety were designed and synthesized using chemical oxidation or electrochemical oxidation with boron-doped diamond electrode in the final stage. In the chiral induction studies, catalytic hydrogenation provided high diastereoselectivity (dr ratio: > 9:1). Conformational analyses of the C-glucoside structures were performed by NOE experiments and force field calculations, and supported the observed regio-selectivity.

Predicting Multicomponent Adsorption Isotherms in Open-Metal Site Materials Using Force Field Calculations Based on Energy Decomposed Density Functional Theory.

For the design of adsorptive-separation units, knowledge is required of the multicomponent adsorption behavior. Ideal adsorbed solution theory (IAST) breaks down for olefin adsorption in open-metal site (OMS) materials due to non-ideal donor-acceptor interactions. Using a density-function-theory-based energy decomposition scheme, we develop a physically justifiable classical force field that incorporates the missing orbital interactions using an appropriate functional form. Our first-principles derived force field shows greatly improved quantitative agreement with the inflection points, initial uptake, saturation capacity, and enthalpies of adsorption obtained from our in-house adsorption experiments. While IAST fails to make accurate predictions, our improved force field model is able to correctly predict the multicomponent behavior. Our approach is also transferable to other OMS structures, allowing the accurate study of their separation performances for olefins/paraffins and further mixtures involving complex donor-acceptor interactions.

Vibrational, electronic absorption, thermal and mechanical analyses of organic nonlinear optical material guanidinium phthalate

The FTIR and UV spectroscopic analysis have been carried out on guanidinium phthalate (GUP) crystal, an organic nonlinear optical material. The spectra are interpreted with the aid of normal coordinate analysis following structure optimizations and force field calculations based on density functional theory (DFT). The thermogravimetric (TG) and differential thermal analysis (DTA) ensures the thermal stability of the compound. Vickers microhardness values reveals the mechanical strength of the crystal.

A new force field for the adsorption of H2, O2, N2, CO, H2O, and H2S gases on alkali doped carbon nanotubes

ABSTRACTThe main goal of this work is the generation of a new force field data set to the interaction of several gases such as H2, O2, N2, CO, H2O, and H2S with alkali cation-doped carbon nanotubes (CNTs) using ab initio calculations at the MP2(full)/6-311++G(d,p) level of theory. Different alkali cations including Li+, Na+, K+ and Cs+ were used to dope in the CNT. The calculated potential energy curve for the interaction of each gas molecule with each alkali cation-doped CNTs was fitted to an analytical potential function to obtain the parameters of the potential function. A modified Morse potential function was selected for the fitting in which the electrostatic interactions has been accounted by adding the β/r term to the Morse potential. The accuracy of the calculated force field was checked via Grand Canonical Monte Carlo (GCMC) simulation of the H2 adsorption on Li-doped graphite and Li-doped CNT. The results of these simulations were compared with the experimental measurements and the closeness of the simulation results with the experimental data indicated the accuracy of the proposed force field. The main merit of this work is the derivation of a specific force field for interaction of each of six gases with four alkali cation-doped CNT, which can be used in molecular simulation of these 24 of systems. The simulation results showed the increase of the H2 adsorption capacity of nanotube and graphite up to 50% and 10%, respectively, due to the insertion of Li ions.

Evaluation of the structural, electronic, topological and vibrational properties of N-(3,4-dimethoxybenzyl)-hexadecanamide isolated from Maca (Lepidium meyenii) using different spectroscopic techniques

N-(3,4-dimethoxybenzyl)-hexadecanamide (DMH) was characterized by using Fourier Transform infrared (FT-IR) and Raman (FT-Raman), Ultraviolet- Visible (UV-Visible) and Hydrogen and Carbon Nuclear Magnetic Resonance (1H and 13C NMR) spectroscopies. The structural, electronic, topological and vibrational properties were evaluated in gas phase and in n-hexane employing ONIOM and self-consistent force field (SCRF) calculations. The atomic charges, molecular electrostatic potentials, stabilization energies and topological properties of DMH were analyzed and compared with those calculated for N-(3,4-dimethoxybenzyl)-acetamide (DMA) in order to evaluate the effect of the side chain on the properties of DMH. The reactivity and behavior of this alkamide were predicted by using the gap energies and some descriptors. Force fields and the corresponding force constants were reported for DMA only in gas phase and n-hexane due to the high number of vibration normal modes showed by DMH, while the complete vibrational assignments are presented for DMA and both forms of DMH. The comparisons between the experimental FTIR, FT-Raman, UV-Visible and 1H and 13C NMR spectra with the corresponding theoretical ones showed a reasonable concordance.

Designing IrO2 Nanoparticles for Oxygen Evolution

IrO2 is one of the most efficient electrocatalyst for the oxygen evolution reaction (OER) and water splitting process for the efficient solar energy into fuel (H2) generation. In solar fuels, IrO2 is used in the form of supported nanoparticles and its catalytic activity strongly depends on the size and shape of nanoparticles. Atomistic modeling of IrO2 nanoparticles with different sizes and shapes can enable fundamental understanding of catalytic processes govern at nanoparticle surfaces. Here, we used density functional theory (DFT) and variable charge force field calculations to study catalytic activity changes at the surfaces, edges and corners on the nanoparticle. We used O adsorption energy as a descriptor for the catalytic activity for water splitting reaction and determined the activity changes with respect to atomic coordination and charge transfer at different active sites on the nanoparticle. Calculations with the developed variable charge force field enable investigation of thermodynamic stability of relatively large (up to 2 nm) IrO2 nanoparticles with different shapes. We construct a metric to describe the overall catalytic activity of a nanoparticle and describe the effects of nanoparticle shape and size on the catalytic activity in terms of surface coordination changes, charge transfer and structural stability. Our results will shed light on the design and development of stable nanoscale IrO2 nanoparticle electrocatalytsts that efficiently utilize solar energy for water splitting reaction. ACKNOWLEDGEMENT: Use of the Center for Nanoscale Materials was supported by the U. S. Department of Energy, Office of Science, Office of Basic Energy Sciences, under Contract No. DE-AC02-06CH11357. The submitted abstract has been created by UChicago Argonne, LLC, Operator of Argonne National Laboratory (“Argonne”). Argonne, a U.S. Department of Energy Office of Science laboratory, is operated under Contract No. DE-AC02-06CH11357. The U.S. Government retains for itself, and others acting on its behalf, a paid-up nonexclusive, irrevocable worldwide license in said article to reproduce, prepare derivative works, distribute copies to the public, and perform publicly and display publicly, by or on behalf of the Government.

Nc-AFM Imaging and Manipulation of a Triphenylene Derivative on KBr(001)

The adsorption of single hexamethoxyltriphenylene molecules on KBr(001) at low temperature (T < 10 K) was studied by low-temperature (T = 5 K) noncontact atomic force microscopy in ultrahigh vacuum. Images of the frequency shift, measured at constant height, show intramolecular features that are interpreted on the basis of molecular force-field calculations. The main conclusion is that the experimental contrast originates from the electrostatic interaction between a negatively terminated ionic tip and the atomic charges of the molecule. The main trends of the experimental observations of lateral manipulations could also be reproduced by the same method, giving some insight into the manipulation mechanisms. In particular, it is shown that the strong interaction of the oxygen atoms of the molecule with positive ions of the tip plays a major role by facilitating the partial lifting of the molecule from the substrate during the intermediate stages of these manipulation processes.

Comparison of three empirical force fields for phonon calculations in CdSe quantum dots.

Three empirical interatomic force fields are parametrized using structural, elastic, and phonon dispersion data for bulk CdSe and their predictions are then compared for the structures and phonons of CdSe quantum dots having average diameters of ˜2.8 and ˜5.2 nm (˜410 and ˜2630 atoms, respectively). The three force fields include one that contains only two-body interactions (Lennard-Jones plus Coulomb), a Tersoff-type force field that contains both two-body and three-body interactions but no Coulombic terms, and a Stillinger-Weber type force field that contains Coulombic interactions plus two-body and three-body terms. While all three force fields predict nearly identical peak frequencies for the strongly Raman-active "longitudinal optical" phonon in the quantum dots, the predictions for the width of the Raman peak, the peak frequency and width of the infrared absorption peak, and the degree of disorder in the structure are very different. The three force fields also give very different predictions for the variation in phonon frequency with radial position (core versus surface). The Stillinger-Weber plus Coulomb type force field gives the best overall agreement with available experimental data.

Beyond the Margules equation: a universal thermodynamic equation for solid solutions including coupled substitution, long- and short-range order

Equilibrium calculations in complex chemical systems involving solids require thermodynamic models for solid solutions. This article presents a formalism for solid solutions that assigns an energy contribution for a configuration consisting of a central atom and its neighbors, multiplying it with its probability based on site occupancies and sums the products up to give the total energy of the solid solution. The formulation is a closed-form expression allowing differentiation with respect to composition and hence the direct calculation of the chemical potentials. The formalism is applicable to multicomponent systems as well as to trace elements, handles long- and short-range order and can be applied to coupled substitutions. The necessary parameters can be obtained from force-field , DFT or other calculation methods capable of determining 0 K excess enthalpies and volumes of solid solutions. Because the excess enthalpies are also a function of temperature, methods to calculate excess heat capacities as a function of temperature might be necessary ( e.g . approximation by phonon density of states). For interactions with one neighbor the presented formalism reduces to the regular solution and for two neighbors to the Margules -equation. For a two-site solid solution with interaction to only the neighboring site and the possibility of interchanging atoms between the sites, this formalism reduces to the Bragg-Williams model. As an example, the formalism is applied to the system calcite–dolomite–magnesite and the necessary parameters are derived by computations using force-field methods. Due to the pure computational approach and the limitations of the force-field methods, the phase diagram and the state of order for the respective phases are only reproduced qualitatively.