Atom-centered Density Matrix Propagation Research Articles

Second-Order Mass-Weighting Scheme for Atom-Centered Density Matrix Propagation Molecular Dynamics.

The atom-centered density matrix propagation (ADMP) method is an extended Lagrangian approach to ab initio molecular dynamics, which includes the density matrix in an orthonormalized atom-centered Gaussian basis as additional, fictitious, electronic degrees of freedom, classically propagated along with the nuclear ones. A high adiabaticity between the nuclear and electronic subsystems is mandatory in order to keep the trajectory close to the Born-Oppenheimer (BO) surface. In this regard, the fictitious electronic mass μ, being a symmetric, nondiagonal matrix in its most general form, represents a free parameter, exploitable to optimize the propagation of the electronic density. Although mass-weighting schemes in ADMP exist, a systematic procedure to define an optimal value of the fictitious masses is not available yet. In this work, in order to rationally evaluate the electronic mass, fictitious electronic normal modes are defined through the diagonalization of the Hessian of the electronic density matrix. If the same frequency is imposed on all such modes (compatible with the chosen integration time step), then the corresponding μ matrix can be calculated and then employed for the following propagation. Analysis of several ADMP test simulations reveals that such Hessian-based mass-weighting approach is able to ensure, together with a 0.1/0.2 fs time steps, a high separation between the (real) nuclear and the (fictitious) electronic frequencies, which determines a high adiabaticity. This high, unprecedented, accuracy in the propagation leads, in turn, to low errors in the estimated nuclear vibrational frequencies, making the ADMP method totally comparable to a fully converged BO molecular dynamics simulation but more computationally efficient. This work, therefore, contributes to a further development of the ADMP ab initio molecular dynamics method, aimed at improving its accuracy through a more rational evaluation of the fictitious electronic mass parameter.

Elucidating the hydrogen adsorption mechanism in bare and TMs (Ni, Pd and Cd) decorated Al12P12, B12P12 and C24 nanocages for hydrogen storage via DFT study

This density functional theory investigation aims to assess the hydrogen adsorption potential of bare and metal catalysts (Ni, Pd, and Cd) decorated Al12P12, B12P12, and C24 nanocages for hydrogen storage applications. To find stability of the cages, cohesive energy and Atom-centered Density Matrix Propagation (ADMP) simulation is obtained. The computed adsorption energy (Ead) reveals the physisorption of H2 molecule in all bare cages. Thus, to improve hydrogen adsorption, Ni, Pd and Cd atoms are decorated in bare cages as a catalyst. After H and H2 adsorption in metal decorated cages, the highest Ead obtained is −3.49 and −0.91 eV in Ni decorated Al12P12 cages. The obtained gravimetric densities of ∼6 wt% for all Ni and Pd decorated Al12P12, B12P12, and C24 nanocages meet the Department of Energy (DOE) target. Hence, Ni and Pd catalysts decorated Al12P12, B12P12, and C24 nanocages are proposed as viable materials for hydrogen storage applications.

Atomistic Details of Methyl Linoleate Pyrolysis: Direct Molecular Dynamics Simulation of Converting Biodiesel to Petroleum Products

Dependence on petroleum and petrochemical products is unsustainable; it is both a finite resource and an environmental hazard. Biodiesel has many attractive qualities, including a sustainable feedstock; however, it has its complications. The pyrolysis (a process already in common use in the petroleum industry) of biodiesel has demonstrated the formation of smaller hydrocarbons comprising many petrochemical products but experiments suffer from difficulty quantifying the myriad reaction pathways followed and products formed. A computational simulation of pyrolysis using “ab initio molecular dynamics” offers atomic-level detail of the reaction pathways and products formed. Herein, the most prevalent fatty-acid ester (methyl linoleate) from the most prevalent feedstock for biodiesel in the United States (soybean oil) is studied. Temperature acceleration within the atom-centered density matrix propagation formalism (Car–Parrinello) utilizing the D3-M06-2X/6-31+G(d,p) model chemistry is used to compose an ensemble of trajectories. The results are grounded in comparison to experimental studies through agreement in the following: (1) the extent of reactivity (40% in the experimental and 36.1% in this work), (2) the homology of hydrocarbon products formed (wt % of C6–C10 products), and (3) the CO/CO2 product ratio. Deoxygenation pathways are critically analyzed (as the presence of oxygen in biodiesel represents a disadvantage in its current use). Within this ensemble, deoxygenation was found to proceed through two subclasses: (1) spontaneous deoxygenation, following one of four possible pathways; or (2) induced deoxygenation, following one of three possible pathways.

Deciphering the irradiation induced fragmentation-rearrangement mechanisms in valence ionized CF3CH2F.

The increasing presence of 1,1,1,2-tetrafluoroethane (CF3CH2F) in the atmosphere has prompted detailed studies into its complex photodissociation behavior. Experiments focusing on CF3CH2F irradiation have unveiled an array of ions, with the persistent observation of the rearrangement product CHF2+ not yet fully understood. In this work, we combine density functional theory, coupled-cluster calculations with a complete basis set formalism, and atom-centered density matrix propagation molecular dynamics to investigate the energetics and dynamics of different potential pathways leading to CHF2+. We found that the two-body dissociation pathway involving an HF rearrangement, which was previously considered complex for CHF2+ formation, is actually straightforward but not likely due to the facile loss of HF. In contrast, our calculations reveal that the H elimination pathway, once thought of as a potential route to CHF2+, is not only comparably disadvantageous from both thermodynamic and kinetic points of view but also does not align with experimental data, particularly the lack of a rebound peak at m/z 101-102. We establish that the formation of CHF2+ is predominantly via the HF elimination channel, a conclusion experimentally corroborated by studies involving the trifluoroethylene cation CF2CHF+, a key intermediate in this process.

Pyridine-M2+ [M = Mg, Ca]: A promising organometallic system for potential hydrogen storage: In silico study

Pyridine-M2+ [M = Mg, Ca] hosts have been identified as potent H2 storage material, and this has been explored by a variety of functionals within the density functional theory (DFT) context. Around the linearly connected metal centre, the pyridine-Mg2+ and pyridine-Ca2+ building blocks can adsorb 6 and 7H2 molecules, respectively. The stability of Pyridine-M2+ [M = Mg, Ca] hosts has been proven by chemical hardness, aromaticity, and molecular dynamic simulations. After H2 adsorption, the aromaticity still remains. Adsorption of H2 molecules at a quasi-molecular type is supported by the fact that their average adsorption energy/H2 (Eads/H2) is between 0.22 and 0.72 eV. Pyridine-Mg2+@6H2 and pyridine-Ca2+@7H2 both have very impressive gravimetric wt % values (10.43 and 10.53 respectively). Average delocalization correction energy (ΔECTav) supports the charge transfer type interaction between metal ions and adsorbed H2 molecules. The topological analysis reflects that bonding between metals (Mg & Ca) and trapped H2 molecules are mostly non-covalent types. Gibbs free energy changes (ΔG) [eV] indicate that the molecular hydrogen adsorption process will be spontaneous at 298 K for pyridine-Mg2+@nH2 systems and at or below 205 K for pyridine-Ca2+@nH2 systems and atom centered density matrix propagation (ADMP) study suggests the higher temperature for desorption.

Thermodynamics, Kinetics, and Optical Properties of Rotaxane: A First-Principles Molecular Dynamics Study.

Through molecular mechanics using the force field along with the quantum dynamical aspect of mechanically interlocked compounds, rotaxanes (defined as macromolecular rings that are threaded on a dumbbell-shaped axle molecule) are investigated with advanced quantum mechanical methods, including the atom-centered density matrix propagation simulation technique, at different temperatures like 300, 500, 700, 900, 2000, and 2500 K for 1.2 ps. Ab initio molecular dynamics simulation is carried out. In addition to, we investigate the noncovalent interaction present in the rotaxane compound 2R-D-2PF6 with the help of reduced density gradient, average reduced density gradient, density overlap region indicator, and interaction region indicator as well as Hirshfeld surface analyses. Furthermore, the stability of 2R-D-2PF6 at room temperature and higher temperatures is elucidated by analyzing the thermal fluctuation index through a dynamic process. In order to check the optical behavior of our selected rotaxane compound, an evaluation of the electronic dipole moment, static and frequency-dependent average polarizability, and first- and second-order hyperpolarizability is carried out. The rotaxane compound shows very promising linear and nonlinear optical responses, which indicates its utility as a very good optical material. The calculation of the time-dependent density-functional theory highlights the broad absorption band of rotaxane spanning the UV-visible domain. Therefore, we also unravel that this can tap into solar radiation or harnessing of solar energy.

Comprehensive Study of the Ammonium Sulfamate–Urea Binary System

The physicochemical properties of binary systems are of great importance for the application of the latter. We report on the investigation of an ammonium sulfamate-urea binary system with different component ratios using a combination of experimental (FTIR, XRD, TGA/DSC, and melting point) and theoretical (DFT, QTAIM, ELF, RDG, ADMP, etc.) techniques. It is shown that, at a temperature of 100 °C, the system under study remains thermally and chemically stable for up to 30 min. It was established using X-ray diffraction analysis that the heating time barely affects the X-ray characteristics of the system. Data on the aggregate states in specified temperature ranges were obtained with thermal analysis and determination of the melting point. The structures of the ammonium sulfamate-urea system with different component ratios were optimized within the density functional theory. The atom-centered density matrix propagation calculation of the ammonium sulfamate-urea system with different component ratios was performed at temperatures of 100, 300, and 500 K. Regardless of the component ratio, a regular increase in the potential energy variation (curve amplitude) with an increase in temperature from 100 to 500 K was found.

Non-ergodic fragmentation upon collision-induced activation of cysteine-water cluster cations.

Cysteine-water cluster cations Cys(H2O)3,6+ and Cys(H2O)3,6H+ are assembled in He droplets and probed by tandem mass spectrometry with collision-induced activation. Benchmark experimental data for this biologically important system are complemented with theory to elucidate the details of the collision-induced activation process. Experimental energy thresholds for successive release of water are compared to water dissociation energies from DFT calculations showing that clusters do not only fragment exclusively by sequential emission of single water molecules but also by the release of small water clusters. Release of clustered water is observed also in the ADMP (atom centered density matrix propagation) molecular dynamics model of small Cys(H2O)3+ and Cys(H2O)3H+ clusters. For large clusters Cys(H2O)6+ and Cys(H2O)6H+ the less computationally demanding statistical Microcanonical Metropolis Monte-Carlo method (M3C) is used to model the experimental fragmentation patterns. We are able to detail the energy redistribution in clusters upon collision activation. In the present case, about two thirds of the collision energy redistribute via an ergodic process, while the remaining one third is transferred into a non-ergodic channel leading to ejection of a single water molecule from the cluster. In contrast to molecular fragmentation, which can be well described by statistical models, modelling of collision-induced activation of weakly bound clusters requires inclusion of non-ergodic processes.

Behavior of HF and (HF)2 inside a fullerene cage: An in silico study using different density functionals

AbstractAn in silico study on the properties of HF and its dimer inside C60 using density functional theory (DFT) based approaches is presented. For this purpose, 10 different DFT functionals following Jacob's Ladder have been chosen. The geometrical parameters such as bond length and bond angle, of the molecules and their dipole moment have been computed. Two types of orientations, namely, L‐shaped and anti‐parallel of (HF)2 inside C60 are considered, the latter with an extremely short hydrogen bond. HF bond lengths are elongated upon encapsulation in comparison to its free state analogue. The calculated value of stabilization energy of HF@C60 is found to be functional dependent, whereas, (HF)2@C60 is thermodynamically unstable for all the functionals. The kinetic stability of (HF)2@C60 is assessed using the atom‐centered density matrix propagation (ADMP) simulation at 300 K temperature. The red shift in HF stretching frequencies is noticed in all cases. Non‐covalent index (NCI) analysis revealed non‐covalent interactions between HF dimer and the C60 cage. Energy decomposition analysis (EDA) showed a high value for the repulsive ΔEpauli which makes the (HF)2@C60 system unstable except for the functional BP86‐D3 of GGA family. Furthermore, the quantum theory of atoms in molecules (QTAIM) analysis is performed and it confirmed the presence of (3, −1) bond critical point along the hydrogen bond region of the L‐shaped (HF)2@C60.

Metal doped tetrahedral silsesquioxane cages for hydrogen storage

The hydrogen adsorption properties of Tetrahedral Silsesquioxane Si4O6H4 (TS) cages doped with Be, Li, Sc and Ti atoms are studied in different spin state using density functional theory with M062X functional. Initially-one of the four hydrogen atoms in TS cage was substituted by metal atoms. Doublet and singlet are the lowest energy state for TS-Be and TS-Li respectively with respective H2 uptake capacity of 1.79 and 3.56 wt%. Triplet and quartet are the lowest energy state for TS-Sc and TS-Ti respectively. TS-Sc (singlet) and TS-Ti (doublet) cage interacts with seven and six hydrogen molecules respectively with respective gravimetric H2 capacity of 5.25 and 4.51 wt%. TS-Sc in triplet state could adsorb six H2 molecules whereas TS-Ti in quartet state could adsorb five H2 molecules with respective H2 uptake capacity of 4.5 wt% and 3.7 wt%. Then all the four hydrogen atoms in a TS cage are substituted by four Be, Li or Sc atoms (lowest energy state is Singlet for all the three) with respective hydrogen uptake capacity of 6.19, 12.69 and 12.01 wt%. When all the four hydrogens in TS cage are substituted by four Ti atoms, clustering of Ti atoms occurs and the cage structure gets distorted and therefore not considered for H2 adsorption. H2 adsorption on one Be(doublet), Sc(triplet) and Ti(quartet) atom doped TS cage is thermodynamically favourable below 210, 160 and 320 K respectively at 1 atm. pressure. At room temperature, it is thermodynamically favourable at higher pressure also. Four Sc and Be atom doped TS cages are found to be thermodynamically suitable for hydrogen storage below 210 K at 1 atm pressure. It is also suitable at room temperature but at higher pressure. One as well as four Li atom doped TS cages are not suitable for hydrogen storage for the entire temperature and pressure range considered. Molecular dynamics simulations performed using atom centered density matrix propagation (ADMP) show that the loosely bonded H2 molecules fly away during the simulations.

The hydrogen storage capacities of 4d transition metals in various boron systems

The hydrogen adsorption and storage properties of BxM2 (M = Y-Mo, RuAg, x = 5–8) have been researched in detail. In B5M2 systems, most of compounds can adsorb multiple H2 with high gravimetric density, and their maximum adsorption are energetically favorable under room temperature. The atom-centered density matrix propagation (ADMP) molecular dynamics simulations show that B5Y2, B5Zr2, B5Nb2, and B5Ru2 can adsorb 6–10 H2 within 1000 fs at 300 K, and their gravimetric density are still close to or even higher the target of US Department of Energy (DOE). However, in more than half of the B5M2 systems, some H2 tend to dissociate and bond atomically on transition atoms in the process of adsorption. With the increase of boron atoms, the dissociation of adsorbed H2 will decrease. In B7M2 and B8M2, all of the H2 are adsorbed in the molecular form. Due to reversible average adsorption energy, satisfactory gravimetric density, ambient operating condition, the B5Pd2, B6Pd2, B7Y2, B7Zr2, B7Pd2, and B8Y2 complexes are the most promising hydrogen storage materials.

DFT and molecular docking study of the effect of a green solvent (water and DMSO) on the structure, MEP, and FMOs of the 1-ethylpiperazine-1,4-diium bis(hydrogenoxalate) compound

We report in this study the influence of green solvents (water and DMSO) effect in structural parameters, frontier molecular orbital's (FMO's) and molecular electrostatic potential surface analysis (MEPS) of 1-ethylpiperazine-1,4-diium bis(hydrogenoxalate) (1EPBH) compound by means of DFT method. The compound has been examined by signal-crystal X-ray diffraction (XRD), infrared (IR) and nuclear magnetic resonance (NMR) spectroscopy. The theoretical calculations were carried out by density functional theory (DFT) method by using B3LYP/6-311++G(d,p) as the basis set. The Atom Centered Density Matrix propagation (ADMP) dynamic approach has been used. Based on the density functional theory calculation, a series of studies have been carried out to determine the noncovalent interactions in the 1EPBH compound. The types and strengths of interactions between hydrogen bonds have been established using the atoms in molecule method (AIM), electron localization function (ELF) and localization orbital locator (LOL). The average local ionization energy (ALIE) study has been carried out. The Hirsfeld surface analysis has been employed to examine the nature of intermolecular contacts in the crystal structure. The strong and weak attractive, repulsive, and van der Waals interactions in the 1EPBH molecule have been determined by the reduced density gradient method (RDG). The natural bonding orbital (NBO) and the Mulliken charges have been computed for the investigated molecule with the density functional theory. The 13C and 1H nuclear magnetic resonance has been applied to confirm the molecular structure. Fourier-transform (IR) and ultraviolet–visible spectra (UV–visible) of the 1EPBH compound has been recorded in the ranges of 4000–500 cm−1 and 250–400 nm, respectively. Finally, the biological activities of 1-Ethylpiperazine-1,4-diium bis(hydrogenoxalate) have been examined. It is shown that the investigated compound (chosen as a ligand) can serve as an important epilepsy and cancer inhibitor.

Microsolvation of lithium cation in xenon clusters: An octahedral growth pattern

The structural and energetic proprieties for the Li + Xen (n = 1–18) clusters are investigated using both Basin-Hopping combined with Potential Model description (BH-PM) and DFT methods. A structural transition from tetrahedral (4 coordination) form to octahedral (6 coordination) one is observed for n = 6. Above this size, all structures have an octahedral core. The cubic-face-centered arrangement for xenon atoms is detected for Li + Xe14. To the best of our knowledge, the Li + Xen (n = 1–18) clusters are studied in the present work for the first time using the DFT theoretical approach. The M062X functional combined with aug-cc-pVDZ (for Li) and def2-TZVP (for Xe) basis sets reproduces accurately the CCSD(T) potential energy curve of Li + Xe system. Atom-Centered Density Matrix Propagation (ADMP) molecular dynamic calculations have been carried. Moreover, we investigate the larger sizes n = 31–35, 44, and 55 for the first time using the BH-PM theoretical approach. The closing of the first and second octahedron shells are proved for the n = 6 and 34 sizes, respectively. The relative stabilities of the Li + Xen molecules are also studied by computing the total energy, the binding energy per atoms for each size n. Then, the second energy difference between the size n and its two near neighbors allows identifying the magic number series. Our present data are analyzed, discussed and compared with the available theoretical and experimental data.

Non‐statistical dynamics for the allene oxide to cyclopropanone conversion

Whether one is interested in mode selective chemistry or non-statistical reaction dynamics, understanding which vibrational modes contribute to a reaction is important. We investigated the ring-opening of 2-methylideneoxirane (a.k.a., allene oxide) to the oxyallyl diradical and subsequent ring-closure to cyclopropanone using hybrid density functional theory (DFT) and atom centered density matrix propagation (ADMP) molecular dynamics in Gaussian. DFT calculations for this ring-opening and subsequent ring-closure show that the energetics allow for the possibility of non-statistical events, as suggested by the similarities between the imaginary vibrational modes and a twisting motion. ADMP simulations starting near the ring-opening transition state lead to faster ring-closure than for simulations starting from the intermediate diradical with the same energy. Analysis of the simulation data identified the presence of a vibrational state near 200 cm−1, corresponding to a disrotatory twisting motion. Selectively exciting this mode leads to a fast reaction time of 50 fs. This work predicts non-statistical dynamics in the conversion of allene oxide to cyclopropanone.

Interactions of CO2 Anion Radicals with Electrolyte Environments from First-Principles Simulations.

Successful transformation of carbon dioxide (CO2) into value-added products is of great interest, as it contributes in part to the circular carbon economy. Understanding chemical interactions that stabilize crucial reaction intermediates of CO2 is important, and in this contribution, we employ atom centered density matrix propagation (ADMP) molecular dynamics simulations to investigate interactions between CO2– anion radicals with surrounding solvent molecules and electrolyte cations in both aqueous and nonaqueous environments. We show how different cations and solvents affect the stability of the CO2– anion radical by examining its angle and distance to a coordinating cation in molecular dynamics simulations. We identify that the strength of CO2– interactions can be tailored through choosing an appropriate cation and solvent combination. We anticipate that this fundamental understanding of cation/solvent interactions can facilitate the optimization of a chemical pathway that results from selective stabilization of a crucial reaction intermediate.

Direct Observation of the Dynamics of Ylide Solvation by Hydrogen-bond Donors Using Time-Resolved Infrared Spectroscopy.

The photoexcitation of α-diazocarbonyl compounds produces singlet carbene intermediates that react with nucleophilic solvent molecules to form ylides. The zwitterionic nature of these newly formed ylides induces rapid changes in their interactions with the surrounding solvent. Here, ultrafast time-resolved infrared absorption spectroscopy is used to study the ylide-forming reactions of singlet carbene intermediates from the 270 nm photoexcitation of ethyl diazoacetate in various solvents and the changes in the subsequent ylide–solvent interactions. The results provide direct spectroscopic observation of the competition between ylide formation and C–H insertion in reactions of the singlet carbene with nucleophilic solvent molecules. We further report the specific solvation dynamics of the tetrahydrofuran (THF)-derived ylide (with a characteristic IR absorption band at 1636 cm–1) by various hydrogen-bond donors and the coordination by lithium cations. Hydrogen-bonded ylide bands shift to a lower wavenumber by −19 cm–1 for interactions with ethanol, −14 cm–1 for chloroform, −10 cm–1 for dichloromethane, −9 cm–1 for acetonitrile or cyclohexane, and −16 cm–1 for Li+ coordination, allowing the time evolution of the ylide–solvent interactions to be tracked. The hydrogen-bonded ylide bands grow with rate coefficients that are close to the diffusional limit. We further characterize the specific interactions of ethanol with the THF-derived ylide using quantum chemical (MP2) calculations and DFT-based atom-centered density matrix propagation trajectories, which show preferential coordination to the α-carbonyl group. This coordination alters the hybridization character of the ylidic carbon atom, with the greatest change toward sp2 character found for lithium-ion coordination.

XNgNSi (X = HCC, F; Ng = Kr, Xe, Rn): A New Class of Metastable Insertion Compounds Containing Ng-C/F and Ng-N Bonds and Possible Isomerization therein.

Recently, astronomically important silaisocyanoacetylene (HCCNSi) possessing a large dipole moment has been detected for the first time with the help of crossed molecular beam experiments. Quantum chemical computations at higher levels of theory have also been performed to characterize the transient species. In this study, we have analyzed the equilibrium geometry, stability, reactivity, and energetics as well as the nature of bonding in the noble gas (Ng) inserted HCCNSi compound. We have also considered its F analogue to understand the influence of the most electronegative atom in the compound. Metastable behavior of the XNgNSi compounds (X = HCC, F; Ng = Kr-Rn) is examined by calculating thermochemical parameters like free energy change (ΔG) and zero-point-energy-corrected dissociation energy (D0) at 298 K for all possible two-body (2B) and three-body (3B) (both neutral as well as ionic) dissociation channels using coupled-cluster theory [CCSD(T)] in addition to density functional theory (DFT) as well as second order Møller-Plesset perturbation theory (MP2). The set of predicted compounds is found to be endergonic in nature, having high positive free energy change suggesting the thermochemical stability of the compounds except for the 2B Ng-release paths. Though thermodynamically feasible, they are kinetically protected with very high activation free energy barriers. Interestingly, the release of Ng from the parent moiety XNgNSi produces the XSiN isomer, by 180° flipping of the NSi moiety. This can also be seen in the dynamical simulation carried out with the help of atom-centered density matrix propagation (ADMP) technique at 2000K for 1 ps. The bonding in Ng-C, Ng-F, and Ng-N bonds of the studied compounds is analyzed and described with the aid of natural bond orbital (NBO), topological parameters computed using atoms-in-molecules theory (AIM), energy decomposition analysis (EDA), and adaptive natural density partitioning (AdNDP) methods. The natural charge distribution on the constituent atoms suggests that the compounds can be partitioned into both ways of representations, viz., neutral radical as well as ionic fragments. Lastly, the reactivity of the compounds is scrutinized using certain reactivity descriptors calculated within the domain of conceptual density functional theory (CDFT).

Determination of stable structure of a cluster using convolutional neural network and particle swarm optimization

Minimization of the energy of a molecule is an important research problem in quantum chemistry. The use of appropriate global optimization algorithms for determining the most stable configuration is a matter of active interest, and various efforts have been made toward achieving the same. Instead of using single method-based techniques, a recent method has been developed for constructing new models where particle swarm optimization can be made use of. In the present study, we propose a convolutional neural network (CNN) model for learning and predicting the energy of a system by training geometries of cluster units containing both metal and non-metal atoms, viz. C5, N42−, N64−, Aun (n = 2 − 8) and AunAgm (2 ≤ n + m ≤ 8) clusters as prototype examples. Initially, several random clusters are generated within a given range in the three-dimensional space and their energies determined using the atom-centered density matrix propagation molecular dynamics simulation (ADMP). A CNN model is constructed from this initial set of clusters, which is later used for generating a huge number of systems required while searching for the stable structure, instead of using time-consuming quantum mechanical calculations in an iterative process. While several global optimization algorithms could have been used, we choose to employ particle swarm optimization (PSO) due to its ease of implementation and efficient rate of convergence.

Theoretical insights into the dissociation process for dissociative electron attachment to adenine and its tautomer

AbstractThe ab initio molecular dynamics (MD) simulations using an atom-centered density matrix propagation method are carried out in the first time to investigate the dissociative electron attachment (DEA) processes of adenine and its tautomer in the gas phase. Since the incoming electron are captured on the lowest π∗ anti-bond orbital, which is led to the different N–H bond, the C–H bond and the C–N bond are broken. The dominant anion observed in DEA dissociation process is the closed-shell dehydrogenated anion (Ade − H)−. The additional anions (Ade − NH2)− and (Ade − 2H)− are also obtained in ADMP simulation. The results are well consistent with the previous DEA experimental results. Thus, the ADMP method is used to gain a more intuitive and better understanding of the necessary dissociation process in the DEA experiment.

Finite-Temperature Single Molecule Vibrational Dynamics from Combined Density Functional Tight Binding Extended Lagrangian Dynamics Simulations and Time Series Analysis

Abstract Combining a computationally efficient and affordable molecular dynamics approach, based on atom-centered density matrix propagation scheme, with the density functional tight binding semiempirical quantum mechanics, we study the vibrational dynamics of a single molecule at series of finite temperatures, spanning quite wide range. Data generated by molecular dynamics simulations are further analyzed and processed using time series analytic methods, based on correlation functions formalism, leading to both vibrational density of states spectra and infrared absorption spectra at finite temperatures. The temperature-induced dynamics in structural intramolecular parameters is correlated to the observed changes in the spectral regions relevant to molecular detection. In particular, we consider a case when an intramolecular X-H stretching vibrational states are notably dependent on the intramolecular torsional degree of freedom, the dynamics of which is, on the other hand, strongly temperature-dependent.