Quantum Molecular Dynamics Approach Research Articles

Asphaltene aggregation under the influence of structural features and interaction energies: Combination of quantum mechanical and molecular dynamics approaches

The importance of the model to predict the aggregation behavior of asphaltene molecules at the molecular level was well established in different studies. Elucidation of the relationship between the interaction energy and the structural characteristics of asphaltene molecules to their aggregation behavior still needs further investigation. For this purpose, we combined the quantum mechanics and molecular dynamics approaches and analyzed the interaction energy of asphaltene to find out the effect of structural features on the aggregation behavior. The interaction energy of asphaltene is used in this study to evaluate the potential of aggregation. We found that asphaltene molecules with smaller aromatic cores and shorter side chains form longer but more unstable stacks in the aggregation phase. If these structures do not have polar groups in the side chains, they will not show significant aggregation behavior in the clustering phase. Also, the length of stacks formed in the accumulation phase can be interpreted and predicted based on the terms such as attractive dispersion energy and steric repulsion in the interaction energy of asphaltene dimers. The aggregation process is explained by analyzing the nature of the interaction energy. As a result, by examining the effect of structural features on interaction energy, a relatively acceptable picture of the aggregation behavior of the asphaltene molecules can be obtained.

Quasi-Isentropic Compression of a Nonideal Helium Plasma at a Constant Final Temperature of 21 000 K and Pressures up to 600 GPa

The quasi-isentropic compressibility of a strongly nonideal helium plasma in the pressure range 250–600 GPa is experimentally studied in devices with cylindrical geometry. The temperature at the front of a cylindrical shock wave in helium (T ≈ 10 000 K) and the flight speed of the inner cascade (W ≈ 3.5 km/s), in the cavity of which the maximum compressed plasma density is achieved, are measured. Data on the compression of a nonideal helium plasma to a density ρ ≈ 3 g/cm3 at an approximately constant final temperature of 21000 K are obtained. The trajectories of the metallic shells compressing the plasma are detected using high-power pulsed X-ray sources with a boundary electron energy of up to 60 MeV. The helium plasma density is determined using the radii of the shells measured at the time of their “stop.” The compressed plasma pressure is obtained using gasdynamic calculations. Comparative theoretical calculations of the quasi-isentropic compression parameters have been carried out using the following two theoretical models: the traditional chemical plasma model (SAHA code) and an ab initio quantum molecular dynamics (QMD) approach. No anomaly of the experimental data in the pressure range of the plasma phase transition theoretically assumed in helium is detected.

Catalytic Descriptors to Investigate Catalytic Power in the Reaction of Haloalkane Dehalogenase Enzyme with 1,2-Dichloroethane.

Enzymes play a fundamental role in many biological processes. We present a theoretical approach to investigate the catalytic power of the haloalkane dehalogenase reaction with 1,2-dichloroethane. By removing the three main active-site residues one by one from haloalkane dehalogenase, we found two reactive descriptors: one descriptor is the distance difference between the breaking bond and the forming bond, and the other is the charge difference between the transition state and the reactant complex. Both descriptors scale linearly with the reactive barriers, with the three-residue case having the smallest barrier and the zero-residue case having the largest. The results demonstrate that, as the number of residues increases, the catalytic power increases. The predicted free energy barriers using the two descriptors of this reaction in water are 23.1 and 24.2 kcal/mol, both larger than the ones with any residues, indicating that the water solvent hinders the reactivity. Both predicted barrier heights agree well with the calculated one at 25.2 kcal/mol using a quantum mechanics and molecular dynamics approach, and also agree well with the experimental result at 26.0 kcal/mol. This study shows that reactive descriptors can also be used to describe and predict the catalytic performance for enzyme catalysis.

Thermodynamics of monoclinic and tetragonal hafnium dioxide (HfO2) at ambient pressure

Accurate and precise thermodynamic models of oxide compounds and their phases are important for calculating the phase stability of oxide materials. We develop and use a coupled quantum mechanical and molecular dynamics approach to create thermodynamic models of hafnia (HfO2) polymorphs from 0 K to 3000 K at ambient pressure. The approach is based on the quasi-harmonic approximation below the Debye temperature and on ab-initio molecular dynamics calculations above the Debye temperature to predict constant pressure heat capacities (Cp). A Bayesian model provides interpolated values between these regimes. As a case study, we develop thermodynamic models of monoclinic and tetragonal HfO2 polymorphs. The predicted heat capacities are in excellent agreement with experiment, and the predicted temperature of the monoclinic to tetragonal phase transition (2173 K) is in good agreement with the experimental value (2078K). These results provide a comprehensive and accurate thermodynamic model of the monoclinic and tetragonal phases of hafnia on a broad range of temperatures and can serve as input to CALPHAD assessment of multi-component hafnia-based phase diagrams.

Momentum-dependent potential and collective flows within the relativistic quantum molecular dynamics approach based on relativistic mean-field theory

Relativistic quantum molecular dynamics based on the relativistic mean field theory (RQMD.RMF) is extended by including momentum-dependent potential. The equation of state (EoS) dependence of the directed and the elliptic flow of protons in the beam energy range of $2.3 < \sqrt{s_{NN}}< 20$ GeV is examined. It is found that the directed flow depends strongly on the optical potential at high energies,$\sqrt{s_{NN}} > 3 $ GeV, where no information is available experimentally. The correlation between effective mass at saturation density and the optical potential is found: smaller values of effective mass require smaller strengths of the optical potential to describe the directed flow data.This correlation can also be seen in the beam energy dependence of the elliptic flow at $\sqrt{s_{NN}}>3$ GeV, although its effect is rather weak. On the other hand, stiff EoS is required to describe the elliptic flow at lower energies.Experimental constraints on the optical potential from $pA$ collisions will provide important information on the EoS at high energies.The proton directed and the elliptic flow are well described in the RQMD.RMF model from $\sqrt{s_{NN}}=2.3$ to 8.8 GeV. In contrast,to reproduce the collapse of the directed flow above 10 GeV, pressure has to be reduced, which indicates a softening of the EoS around $\sqrt{s_{NN}} =10 $ GeV.

Electron-ion coupling factor for temperature relaxation in dense plasmas.

We compare two formulas obtained from first principles to calculate the electron-ion coupling factor for temperature relaxation in dense plasmas. The quantum average-atom model is used to calculate this electron-ion coupling factor. It is shown that if the two formulas agree at sufficiently high temperature so that the potential energy is of limited importance, i.e., when the plasma is said to be kinetic, and are consistent with the Landau-Spitzer formula, then they strongly differ in the warm-dense-matter regime. Only one of the two is shown to be consistent with quantum molecular dynamics approach. We use this point to determine which formula is valid to describe temperature relaxation between electrons and ions in warm and hot dense plasmas.

Observation of the Low‐Frequency Spectrum of the Water Dimer as a Sensitive Test of the Water Dimer Potential and Dipole Moment Surfaces

AbstractUsing the helium nanodroplet isolation setup at the ultrabright free‐electron laser source FELIX in Nijmegen (BoHeNDI@FELIX), the intermolecular modes of water dimer in the frequency region from 70 to 550 cm−1 were recorded. Observed bands were assigned to donor torsion, acceptor wag, acceptor twist, intermolecular stretch, donor torsion overtone, and in‐plane and out‐of‐plane librational modes. This experimental data set provides a sensitive test for state‐of‐the‐art water potentials and dipole moment surfaces. Theoretical calculations of the IR spectrum are presented using high‐level quantum and approximate quasiclassical molecular dynamics approaches. These calculations use the full‐dimensional ab initio WHHB potential and dipole moment surfaces. Based on the experimental data, a considerable increase of the acceptor switch and a bifurcation tunneling splitting in the librational mode is deduced, which is a consequence of the effective decrease in the tunneling barrier.

Observation of the Low-Frequency Spectrum of the Water Dimer as a Sensitive Test of the Water Dimer Potential and Dipole Moment Surfaces.

Using the helium nanodroplet isolation setup at the ultrabright free‐electron laser source FELIX in Nijmegen (BoHeNDI@FELIX), the intermolecular modes of water dimer in the frequency region from 70 to 550 cm−1 were recorded. Observed bands were assigned to donor torsion, acceptor wag, acceptor twist, intermolecular stretch, donor torsion overtone, and in‐plane and out‐of‐plane librational modes. This experimental data set provides a sensitive test for state‐of‐the‐art water potentials and dipole moment surfaces. Theoretical calculations of the IR spectrum are presented using high‐level quantum and approximate quasiclassical molecular dynamics approaches. These calculations use the full‐dimensional ab initio WHHB potential and dipole moment surfaces. Based on the experimental data, a considerable increase of the acceptor switch and a bifurcation tunneling splitting in the librational mode is deduced, which is a consequence of the effective decrease in the tunneling barrier.

HCES1 and hCES2 mediated activation of epalrestat-antioxidant mutual prodrugs: Unwinding the hydrolytic mechanism using in silico approaches

Herein, we report four series of mutual prodrugs of epalrestat by combining it with different antioxidants using glycine, beta-alanine, and phenylalanine as a linker and by directly linking them through an ester linkage. The designed prodrugs were subjected to pharmacophore and docking-based virtual screening to determine the susceptibility of these prodrugs to be hydrolyzed by human carboxylesterases (hCES1 and hCES2). Five best prodrugs from each series were further submitted to detailed mechanistic study of hCES1 and hCES2 based hydrolytic activation using quantum mechanics and molecular dynamics approach. Additionally, Verloop'ssterimol parameters (B1-B5, L) were calculated in order to investigate the steric constraint of prodrugs to the catalytic sites of hCES1 and hCES2 enzymes. Our results indicated that, among these prodrugs, EP-D4, EP-E13, EP-F5, and EP-F14 are best substrates for hCES1 while EP-G3 and EP-G15 are potential substrates for hCES2. On the other hand, EP-D19 serves as good substrates for both enzymes.

Molecular orbitals of delocalized electron clouds in neuronal domains

We have further developed the two-brains hypothesis as a form of complementarity (or complementary relationship) of endogenously induced weak magnetic fields in the electromagnetic brain. The locally induced magnetic field between electron magnetic dipole moments of delocalized electron clouds in neuronal domains is complementary to the exogenous electromagnetic waves created by the oscillating molecular dipoles in the electro-ionic brain. In this paper, we mathematically model the operation of the electromagnetic grid, especially in regard to the functional role of atomic orbitals of dipole-bound delocalized electrons. A quantum molecular dynamic approach under quantum equilibrium conditions is taken to illustrate phase differences between quasi-free electrons tethered to an oscillating molecular core. We use a simplified version of the many-body problem to analytically solve the macro-quantum wave equation (equivalent to the Kohn-Sham equation). The resultant solution for the mechanical angular momentum can be used to approximate the molecular orbital of the dipole-bound delocalized electrons. In addition to non-adiabatic motion of the molecular core, ‘guidance waves’ may contribute to the delocalized macro-quantum wave functions in generating nonlocal phase correlations. The intrinsic magnetic properties of the origins of the endogenous electromagnetic field are considered to be a nested hierarchy of electromagnetic fields that may also include electromagnetic patterns in three-dimensional space. The coupling between the two-brains may involve an ‘anticipatory affect’ based on the conceptualization of anticipation as potentiality, arising either from the macro-quantum potential energy or from the electrostatic effects of residual charges in the quantum and classical subsystems of the two-brains that occurs through partitioning of the potential energy of the combined quantum molecular dynamic system.

Quantum molecular dynamic approach to modeling the vibrational spectra of propynenitrile and its 1:1 complexes with water

We present here a quantum molecular dynamic approach from DFT molecular dynamics (DFT/MD) trajectories around 150 K, 300 K, 450 K and 600 K to compute the IR spectra of the propynenitrile (or cyanoacetylene) molecule HC3N, the simplest linear cyanopolyyne detected in interstellar clouds and circumstellar envelopes of stars. The DFT/MD results in fair agreement with the experimental data for the isolated molecule are close to those obtained, for all the valence modes, from an effective second order treatment (VPT2) at the CCSD(T) level of theory. This DFT/MD simulation is used to predict the IR spectra of the1:1 complexes with water and analyse the shifts expected for the micro-hydrated molecule.

Making and breaking of small water clusters: A combined quantum chemical and molecular dynamics approach.

We present a combined quantum chemical and molecular dynamics study of cyclic and noncyclic water n-mers ([(H2 O]n , n = 2-6) at four different temperatures and showcase that the dynamics of small water clusters can reproduce the known properties of bulk water reasonably well. We investigate the making and breaking of the water clusters by computing the hydrogen bond strengths, average lifetimes, and relative stabilities, which are important to understand the complex solution dynamics. We compare the behavior of water clusters in the gas phase and in the solution phase as well as the variation in the properties as a function of cluster size and highlight the notably more interesting cluster dynamics of the water trimer when compared to the other water clusters. © 2019 Wiley Periodicals, Inc.

Accurate quantum molecular dynamics for multidimensional systems by the basis expansion leaping multi-configuration Gaussian (BEL MCG) method.

Quantum phenomena are quite often of critical importance in chemical reactions. Thus the development of quantum molecular dynamics approaches is required to study the role of quantum effects such as tunnelling in chemical processes. The basis expansion leaping multi-configuration Gaussian (BEL MCG) method has been developed to obtain time-propagated wave packets describing reactive molecular systems. Here we examine the applicability of BEL MCG to double well problems in several dimensions. We pay particular attention to what is required to yield highly accurate dynamics with respect to several key features of the BEL MCG propagation. The importance of using basis functions of a width appropriate to the nature of the potential energy surface in the region of configuration space where each basis function is located is highlighted, which has implications for virtually all quantum molecular dynamics methods utilising Gaussian basis functions.

Exploring the relevance of thiophene rings as bridge unit in acceptor-bridge-donor dyes on self-aggregation and performance in DSSCs.

The possibility of dye charge recombination in DSSCs remains a challenge for the field. This consists of: (a) back-transfer from the TiO2 to the oxidized dye and (b) intermolecular electron transfer between dyes. The latter is attributed to dye aggregation due to dimeric conformations. This leads to poor electron injection which decreases the photocurrent conversion efficiency. Most organic sensitizers are characterized by an Acceptor-Bridge-Donor (A-Bridge-D) arrangement that is commonly employed to provide charge separation and, therefore, lowering the unwanted back-transfer. Here, we address the intermolecular electron transfer by studying the dimerization and photovoltaic performance of a group of A-Bridge-D structured dyes. Specifically, eight famous sulfur containing π-bridges were analyzed (A and D remained fixed). Through quantum mechanical and molecular dynamics approaches, it was found that the formation of weakly stabilized dimers is allowed. The dyes with covalently bonded and fused thiophene rings as Bridges, 6d and 7d as well as 8d with a fluorene, would present high aggregation and, therefore, high probability of recombination processes. Conversely, using TiO2 cluster and surface models, delineated the shortest bridges to improve the adsorption energy and the stability of the system. Finally, the elongation of the bridge up to 2 and 3 units and their photovoltaic parameters were studied. These results showed that all the sensitizers are able to provide similar photocurrent outcomes, regardless of whether the bridge is elongated. © 2017 Wiley Periodicals, Inc.

Pharmacophore-Based 3D-QSAR Analysis of Thienyl Chalcones as a New Class of Human MAO-B Inhibitors: Investigation of Combined Quantum Chemical and Molecular Dynamics Approach.

Selective monoamine oxidase-B (MAO-B) inhibitors are imperative in the treatment of various neurodegenerative disorders. Herein, we describe the pharmacophore generation and atom-based three-dimensional quantitative structure-activity relationship (3D-QSAR) analyses of previously reported thiophene-based hMAO-B inhibitors by our research group. The aim of this study was to identify the principal structural features that could potentially be responsible for the inhibitory activity of hMAO-B inhibitors. The best pharmacophore model generated was the four-point assay of AHRR.8. The pharmacophore model exhibited good correlation with its predictability of the statistically valid 3D-QSAR analyses. Density functional theory calculations were further employed on the lead molecule (2E)-1-(5-bromothiophen-2-yl)-3-[4-(dimethylamino) phenyl] prop-2-en-1-one (Tb5) to investigate the electrostatic potential surface and analyze the natural bond orbital toward the binding characteristics. Molecular dynamics simulations were performed to characterize the molecular level interactions and relative energies of the hMAO isoforms: hMAO-A and hMAO-B with three potent and selective hMAO-B inhibitors (Tb5, Tb6, and Tb9). The results of both continuous and accelerated molecular dynamics simulations demonstrate a distinct preference of the three ligands to bind to hMAO-B rather than hMAO-A.

Particle production and chemical freezeout from the hybrid UrQMD approach at NICA energies

The energy dependence of various particle ratios is calculated within the Ultra-Relativistic Quantum Molecular Dynamics approach and compared with the hadron resonance gas (HRG) model and measurements from various experiments, including RHIC-BES, SPS and AGS. It is found that the UrQMD particle ratios agree well with the experimental results at the RHIC-BES energies. Thus, we have utilized UrQMD in simulating particle ratios at other beam energies down to 3 GeV, which will be accessed at NICA and FAIR future facilities. We observe that the particle ratios for crossover and first-order phase transition, implemented in the hybrid UrQMD v3.4, are nearly indistinguishable, especially at low energies (at large baryon chemical potentials or high density).

Structural Modeling and Conformational Analysis of Aromatic Polypeptoid Models Confined to Different Environmental Conditions

Conformations of achiral and chiral aromatic homopolypeptoids of Nphe, Nspe and Nrpe were studied by quantum mechanics and molecular dynamics approaches. The amide bond geometry in model peptoids Ac-X-NMe2 could be both cis and trans and the Nphe peptoids adopted degenerate conformations of opposite handedness with Φ, Ψ values of ~ ± 120o, ± 150o with trans amide bond geometry. This degeneracy was lifted with increase in chain length; in favor of the structure with Φ = -120o, Ψ = -150o. Polypeptoids of Nspe and Nrpe with and without protecting groups populated states with Φ, Ψ values of ~ 110o, 155o & -110o, -165o respectively with trans amide bond geometry. Simulation studies in water revealed that with protecting groups peptoid Ac-(Nspe/Nrpe)5-NMe2 populated with cis amide bond geometry in PP type I and inverse PP type I helices respectively due to interactions between the solvent molecules and carbonyl oxygens of the backbone. Without protecting groups these polypeptoids populated poly-Lproline type II conformations. In DMSO these peptoids were shown to populate in PP type-I and inverse PP type-I helices and without protecting groups they could be realized in PP type-I as well as inverse PP type-I conformation whereas the peptoid -Nrpe6-NH2 could be realized in inverse PP type-I conformation. Analysis of simulation results as a function of time ruled out amide bond inter-conversions between cis and trans geometry. Hence, like polyproline peptoids can also be exploited as molecular spacers.

Nonadiabatic quantum molecular dynamics with hopping. I. General formalism and case study

An extension of the nonadiabatic quantum molecular dynamics approach is presented to account for electron-nuclear correlations in the dynamics of atomic many-body systems. The method combines electron dynamics described within time-dependent density-functional or Hartree-Fock theory with trajectory-surface-hopping dynamics for the nuclei, allowing us to take into account explicitly a possible external laser field. As a case study, a model system of ${\mathrm{H}}^{+}+\mathrm{H}$ collisions is considered where full quantum-mechanical calculations are available for comparison. For this benchmark system the extended surface-hopping scheme exactly reproduces the full quantum results. Future applications are briefly outlined.

Dilepton Production in Transport Calculations and Coarse-Grained Dynamics

We present transport calculations with the Ultra-relativistic Quantum Molecular Dynamics approach (UrQMD) for dilepton spectra at SIS energies and simulations for NA60 within a coarse-graining approach. While the transport model obtains a good agreement with experiment for elementary reactions, in heavy-ion collisions an excess in the invariant mass spectra is observed which cannot be described by the model. As the pure transport calculations do not include explicit in-medium effects and are limited to hadronic degrees of freedom, we present an alternative approach that uses coarse-grained output from transport calculations to determine thermal dilepton emission rates. For this we apply the medium-modified ρ spectral function by Eletsky et al. In a first exemplary comparison to data from the NA60 experiment we find that the coarse-graining approach gives reasonable results.

A Unique Conformational Behaviour of Glutamine Peptides

Trinucleotide repeat expansions (CAG) lead to increase in glutamine residues and hence increase in glutamine stretch. This leads to number of neurodegenerative diseases. Therefore, the conformation of poly Q of varying chain lengths has been investigated by quantum mechanical and molecular dynamics approaches. Glutamine contains amide linkage in the side chain. It is the interaction between side chain amide linkage and the peptide bond of the backbone which dictates the conformational behaviour. Some of the glutamine residues adopt phi psi values corresponding to poly-L-proline type II structure. Not more than three glutamine residues are found to have the same set of values and hence polyglutamine is adopting random coil structure. Carbonyl-carbonyl, CH-O interactions and hydrogen bond formation involving backbone and side chain amide chain linkages are found to contribute to the stability of the adopted structure. In simulation studies due to interaction of water molecules with the amide linkages the values undergo change and this leads to weakening of carbonyl-carbonyl interactions and hydrogen bonds. The conformational behaviour of polyglutamine peptides is shown to be chain length dependent and this may provide some insight regarding the aggregation behaviour of proteins containing poly Q stretch. Possibly this is the first systematic study of the conformational behaviour of polyglutamine peptides.