Atom-centered Density Matrix Propagation Research Articles

Effect of boron substitution on hydrogen storage capacity of Li and Ti decorated naphthalene

Interaction of molecular hydrogen with Li and Ti doped boron substituted naphthalene viz. C6B4H8Ti2 and C6B4H8Li2 has been studied using density functional theory (DFT) method. The C6B4H8Li2 complex can interact with maximum of four hydrogen molecules, whereas three H2 molecules are adsorbed on C10H8Li2 complex. The C6B4H8Ti2 complex can interact with maximum of eight hydrogen molecules. The gravimetric hydrogen uptake capacity of C6B4H8Ti2 and C6B4H8Li2 complex is found to be 6.85 and 5.55 wt % respectively, which is higher than that of unsubstituted C10H8Ti2 and C10H8Li2 complexes. The boron substitution has significantly affected the hydrogen adsorption energies. The H2 adsorption energy and Gibb's free energy corrected H2 adsorption energy are found to be more prominent after boron substitution. The C6B4H8Ti2 and C6B4H8Li2 complexes are more stable than the respective unsubstituted C10H8Ti2 and C10H8Li2 complexes due to their higher binding energies. According to the atom-centered density matrix propagation (ADMP) molecular dynamics simulations C6B4H8Li2 complex retain not a single adsorbed hydrogen molecule during the simulation at room temperature, whereas five hydrogen molecules at 300 K and eight at 100 K are remain absorbed on C6B4H8Ti2 complex. The C6B4H8Ti2 complex is found to be more promising material for hydrogen storage than C10B4H8Li2.

Transient versus Static Electron Spin Relaxation in Mn(2+) Complexes Relevant as MRI Contrast Agents.

The zero-field splitting (ZFS) parameters of the [Mn(EDTA)(H2O)](2-)·2H2O and [Mn(MeNO2A)(H2O)]·2H2O systems were estimated by using DFT and ab initio CASSCF/NEVPT2 calculations (EDTA = 2,2',2″,2‴-(ethane-1,2-diylbis(azanetriyl))tetraacetate; MeNO2A = 2,2'-(7-methyl-1,4,7-triazonane-1,4-diyl)diacetate). Subsequent molecular dynamics calculations performed within the atom-centered density matrix propagation (ADMP) approach provided access to the transient and static ZFS parameters, as well as to the correlation time of the transient ZFS. The calculated ZFS parameters present a reasonable agreement with the experimental values obtained from the analysis of (1)H relaxation data. The correlation times calculated for the two systems investigated turned out to be very short (τc ∼ 0.02-0.05 ps), which shows that the transient ZFS is modulated by molecular vibrations. On the contrary, the static ZFS is modulated by the rotation of the complexes in solution, which for the small complexes investigated here is characterized by rotational correlation times of τR ∼ 35-60 ps. As a result, electron spin relaxation in small Mn(2+) complexes is dominated by the static ZFS.

Reactivity of molecular oxygen with aluminum clusters: Density functional and Ab Initio molecular dynamics simulation study

Dissociative adsorption of molecular oxygen (O2) on aluminum (Al) clusters has attracted much interest in the field of surface science and catalysis, but theoretical predictions of the reactivity of this reaction in terms of barrier height is still challenging. In this regard, we systematically investigate the reactivity of O2 with Al clusters using density functional theory (DFT) and atom‐centered density matrix propagation (ADMP) simulations. We also calculate potential energy surfaces (PESs) of the reaction between O2 and Al clusters to estimate the barrier energy of this reaction. The M06‐2X functional gives the barrier energy in agreement with the one calculated by coupled cluster singles and doubles with perturbed triples (CCSD(T)) while the TPSSh functional significantly underestimates the barrier height. The ADMP simulation using the M06‐2X functional predicts the reactivity of O2 with the Al cluster in agreement with the experimental findings, that is, singlet O2 readily reacts with Al clusters but triplet O2 is less reactive. We found that the ability of a DFT functional to describe the charge transfer appropriately is critical for calculating the barrier energy and the reactivity of the reaction of O2 with Al clusters. The M06‐2X functional is relevant for investigating chemical reactions involving Al and O2. © 2016 Wiley Periodicals, Inc.

Hydrogen trapping potential of (HF)m (m = 1–8) and (H2O)n (n = 1–10) clusters

An in silico analysis is performed to check the hydrogen storage potential of (HF)m (m=1–8) and (H2O)n (n=1–10) clusters. Each HF unit in (HF)m cluster can bind three H2 molecules whereas each H2O unit in (H2O)n can adsorb one hydrogen molecule (excluding H2O and (H2O)2). It is found that conceptual density functional theory based reactivity descriptors can explain the stability of molecular hydrogen adsorbed (HF)m (m=1–8) and (H2O)n (n=1–10) clusters. The nature of interaction between (HF)m/(H2O)n cluster and the adsorbed H2 molecules is studied using electron density based descriptors. Energy decomposition analysis is carried out to assess the type of interaction between the molecular clusters and adsorbed hydrogen molecules. Ab initio molecular dynamics (AIMD) simulation is also carried out using an atom centered density matrix propagation (ADMP) technique to predict the kinetic stability of hydrogen adsorbed (HF)m and (H2O)n analogues in a one picosecond time scale.

Near-silence of isothiocyanate carbon in (13)C NMR spectra: a case study of allyl isothiocyanate.

(1)H and (13)C NMR spectra of allyl isothiocyanate (AITC) were measured, and the exchange dynamics were studied to explain the near-silence of the ITC carbon in (13)C NMR spectra. The dihedral angles α = ∠(C1-C2-C3-N4) and β = ∠(C2-C3-N4-C5) describe the conformational dynamics (conformation change), and the bond angles γ = ∠(C3-N4-C5) and ε = ∠(N4-C5-S6) dominate the molecular dynamics (conformer flexibility). The conformation space of AITC contains three minima, Cs-M1 and enantiomers M2 and M2'; the exchange between conformers is very fast, and conformational effects on (13)C chemical shifts are small (νM1 - νM2 < 3 ppm). Isotropic chemical shifts, ICS(γ), were determined for sp, sp(x), and sp(2) N-hybridization, and the γ dependencies of δ(N4) and δ(C5) are very large (10-33 ppm). Atom-centered density matrix propagation trajectories show that every conformer can access a large region of the potential energy surface AITC(γ,ε,...) with 120° < γ < 180° and 155° < ε < 180°. Because the extreme broadening of the (13)C NMR signal of the ITC carbon is caused by the structural flexibility of every conformer of AITC, the analysis provides a general explanation for the near-silence of the ITC carbon in (13)C NMR spectra of organic isothiocyanates.

Structure, electronic properties, aromaticity and dynamics of M3N@C80 and M2C2@C82 (M=Sc, Y): A density functional study

The ground state structures, electronic properties and aromaticity of metal nitride and carbide encapsulated endohedral fullerenes, viz., M3N@C80 and M2C2@C82 (M=Sc, Y) is investigated in detail under density functional theory. The effects of nitride and carbide encapsulation inside the fullerene cages are minutely analyzed through density based various quantum mechanical descriptors and nucleus independent chemical shift (NICS) calculations. To gain further insight into such encapsulation, we have also analyzed important frontier molecular orbitals (FMOs) for all the considered systems. Also, an extended Lagrangian molecular dynamics method, viz., atom-centered density matrix propagation (ADMP) is utilized to confirm the bent conformation of Y2C2 due to its encapsulation inside the C82 cage.

Structure and dynamics of H2O vis-á-vis phenylalanine recognition at a DPPC lipid membrane via interfacial H-bond types: insights from polarized FT-IRRAS and ADMP simulations.

Preferential and enantioselective interactions of L-/D-Phenylalanine (L-Phe and D-Phe) and butoxycarbonyl-protected L-/D-Phenylalanine (LPA and DPA) as guest with 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (L-DPPC) as host were tapped by using real time Fourier transform infrared reflection absorption spectroscopy (FT-IRRAS). Polarization-modulated FT-IRRAS of DPPC monolayers above the phenylalanine modified subphases depicted fine structure/conformation differences under considerations of controlled 2D surface pressure. Selective molecular recognition of D-enantiomer over L-enantiomer driven by the DPPC head group via H-bonding and electrostatic interactions was evident spectroscopically. Accordingly, binding constants (K) of 145, 346, 28, and 56 M(-1) for LPA, DPA, L-Phe, and D-Phe, respectively, were estimated. The real time FT-IRRAS water bands were strictly conformation sensitive. The effect of micro-solvation on the structure and stability of the 1:1 diastereomeric L-lipid⋯, LPA/DPA and L-lipid⋯, (L/D)-Phe adducts was investigated with the aid of Atom-centered Density Matrix Propagation (ADMP), a first principle quantum mechanical molecular dynamics approach. The phosphodiester fragment was the primary site of hydration where specific solvent interactions were simulated through single- and triple- "water-phosphate" interactions, as water cluster's "tetrahedral dice" to a "trimeric motif" transformation as a partial de-clusterization was evident. Under all the hydration patterns considered in both static and dynamic descriptions of density functional theory, L-lipid/D-amino acid enantiomer adducts continued to be stable structures while in dynamic systems, water rearranged without getting "squeezed-out" in the process of recognition. In spite of the challenging computational realm of this multiscale problem, the ADMP simulated molecular interactions complying with polarized vibrational spectroscopy unraveled a novel route to chiral recognition and interfacial water structure.

Polarization versus temperature in pyridinium ionic liquids.

Electronic polarization and charge transfer effects play a crucial role in thermodynamic, structural, and transport properties of room-temperature ionic liquids (RTILs). These nonadditive interactions constitute a useful tool for tuning physical chemical behavior of RTILs. Polarization and charge transfer generally decay as temperature increases, although their presence should be expected over an entire condensed state temperature range. For the first time, we use three popular pyridinium-based RTILs to investigate temperature dependence of electronic polarization in RTILs, based on a nonperiodic electronic density description for a cation-anion pair. Atom-centered density matrix propagation molecular dynamics, supplemented by a weak coupling to an external bath, is used to simulate the temperature impact on system properties. We show that, quite surprisingly, nonadditivity in the cation-anion interactions changes negligibly between 300 and 900 K, while the average dipole moment increases due to thermal fluctuations of geometries. Our results contribute to the fundamental understanding of electronic effects in the condensed phase of ionic systems and foster progress in physical chemistry and engineering.

99Tc NMR as a promising technique for structural investigation of biomolecules: theoretical studies on the solvent and thermal effects of phenylbenzothiazole complex

The phenylbenzothiazole compounds show antitumor properties and are highly selective. In this paper, the (99)Tc chemical shifts based on the ((99m)Tc)(CO)3 (NNO) complex conjugated to the antitumor agent 2-(4'-aminophenyl)benzothiazole are reported. Thermal and solvent effects were studied computationally by quantum-chemical methods, using the density functional theory (DFT) (DFT level BPW91/aug-cc-pVTZ for the Tc and BPW91/IGLO-II for the other atoms) to compute the NMR parameters for the complex. We have calculated the (99)Tc NMR chemical shifts of the complex in gas phase and solution using different solvation models (polarizable continuum model and explicit solvation). To evaluate the thermal effect, molecular dynamics simulations were carried, using the atom-centered density matrix propagation method at the DFT level (BP86/LanL2dz). The results highlight that the (99)Tc NMR spectroscopy can be a promising technique for structural investigation of biomolecules, at the molecular level, in different environments.

17O and 1H relaxometric and DFT study of hyperfine coupling constants in [Mn(H2O)6]2+

Nuclear Magnetic Relaxation Dispersion (NMRD) profiles and 17O NMR chemical shifts and transverse relaxation rates of aqueous solutions of [Mn(H2O)6]2+ were recorded to determine the parameters governing the relaxivity in this complex and the 17O and 1H hyperfine coupling constants (HFCCs). The analysis of the NMRD and 17O NMR data provided a water exchange rate of kex298 = 28.2 × 106 s−1, and AO/ħ and AH/ħ hyperfine coupling constants of −34.6 and 5.4 rad s−1, respectively. DFT calculations (TPSSh model) performed on the [Mn(H2O)6]2+ and [Mn(H2O)6]2+·12H2O systems were used to evaluate theoretically the 17O and 1H HFCCs responsible for the 17O NMR chemical shifts and the scalar contributions to 17O and 1H NMR relaxation rates. The use of a mixed cluster–continuum approach with the explicit inclusion of second-sphere water molecules is critical for an accurate calculation of HFCCs of coordinated water molecules. The impact of complex dynamics on the calculated HFCCs was evaluated with the use of molecular dynamics simulations within the atom-centered density matrix propagation (ADMP) approach. These molecular dynamics simulations show that the Aiso values are critically affected by the distance between the oxygen atom of the coordinated water molecule and the MnII ion, as well as by the orientation of the water molecule plane with respect to the Mn–O vector. The substantial scalar contribution to relaxivity observed for [Mn(H2O)6]2+ is related to a combination of a slow water exchange rate and a slow electron spin relaxation.

Time domain simulations of chemical bonding effects in surface-enhanced spectroscopy

The atom-centered density-matrix propagation method is used to illustrate how time-dependent conformational changes affect the electronic structure and derived spectroscopic properties of a prototypical finite metal cluster-bound π-conjugated organic complex, Ag7-benzenethiol. We establish that there is considerable conformational flexibility to the model structure, even at relatively low temperatures, which influences the predicted spectroscopic properties. Namely, the computed electron densities, dipoles, and polarizabilities are all dictated by torsional motion which controls the coupling between the π-framework of the chemisorbed molecular system and the cluster.

Hyperfine Coupling Constants on Inner-Sphere Water Molecules of a Triazacyclononane-based Mn(II) Complex and Related Systems Relevant as MRI Contrast Agents

We report the synthesis of the ligand H2MeNO2A (1,4-bis(carboxymethyl)-7-methyl-1,4,7-triazacyclononane) and a detailed experimental and computational study of the hyperfine coupling constants (HFCCs) on the inner-sphere water molecules of [Mn(MeNO2A)] and related Mn(2+) complexes relevant as potential contrast agents in magnetic resonance imaging (MRI). Nuclear magnetic relaxation dispersion (NMRD) profiles, (17)O NMR chemical shifts, and transverse relaxation rates of aqueous solutions of [Mn(MeNO2A)] were recorded to determine the parameters governing the relaxivity in this complex and the (17)O and (1)H HFCCs. DFT calculations (TPSSh model) performed in aqueous solution (PCM model) on the [Mn(MeNO2A)(H2O)]·xH2O and [Mn(EDTA)(H2O)](2-)·xH2O (x = 0-4) systems were used to determine theoretically the (17)O and (1)H HFCCs responsible for the (17)O NMR chemical shifts and the scalar contributions to (17)O and (1)H NMR relaxation rates. The use of a mixed cluster/continuum approach with the explicit inclusion of a few second-sphere water molecules is critical for an accurate calculation of HFCCs of coordinated water molecules. The impact of complex dynamics on the calculated HFCCs was evaluated with the use of molecular dynamics simulations within the atom-centered density matrix propagation (ADMP) approach. The (17)O and (1)H HFCCs calculated for these complexes and related systems show an excellent agreement with the experimental data. Both the (1)H and (17)O HFCCs (A(iso) values) are dominated by the spin delocalization mechanism. The A(iso) values are significantly affected by the distance between the oxygen atom of the coordinated water molecule and the Mn(2+) ion, as well as by the orientation of the water molecule plane with respect to the Mn-O vector.

Acceleration of Semiempirical Quantum Mechanical Calculations by Extended Lagrangian Molecular Dynamics Approach.

The implementation and performance of the atom-centered density matrix propagation (ADMP) [J. Chem. Phys. 2001, 114, 9758] and the curvy-steps (CURV) methods [J. Chem. Phys. 2004, 121, 1152] are described. These methods solve the electronic Schrödinger equation approximately by propagating the electronic degrees of freedom using the extended Lagrangian molecular dynamics (ELMD) simulation approach. The ADMP and CURV methods are implemented and parallelized to accelerate semiempirical quantum mechanical (QM) methods (such as the MNDO, AM1, PM3, MNDO/d, and AM1/d methods). Test calculations show that both the ADMP and the CURV methods are 2∼4 times faster than the Born-Oppenheimer molecular dynamics (BOMD) method and conserve the total energy well. The accuracy of the ADMP and CURV simulations is comparable to the BOMD simulations. The parallel implementation accelerates the MD simulation by up to 28 fold for the ADMP method and 25 fold for the CURV method, respectively, relative to the speed of the single core BOMD. In addition, a multiple time scale (MTS) approach is introduced to further speed up the semiempirical QM and QM/MM ELMD simulations. Since a larger integration time step is used for the propagation of the nuclear coordinates than that for the electronic degrees of freedom, the MTS approach allows the ELMD simulation to be carried out with a time step that is larger than the time step accessible by the original ADMP and CURV methods. It renders MD simulation to be carried out about 20 times faster than the BOMD simulation, and yields results that are comparable to the single time scale simulation results. The use of the methods introduced in the present work provides an efficient way to extend the length of the QM and QM/MM molecular dynamics simulations beyond the length accessible by BOMD simulation.

Terahertz spectra of biotin based on first principle, molecular mechanical, and hybrid simulations.

Terahertz (THz) absorption of biotin was simulated using the first principle and the density functional theory (DFT) both in the harmonic approximation and with corrections for the anharmonicity. Anharmonicity corrections were calculated using two different approaches. First, the perturbation theory-based first principle calculations were performed to include third- and fourth-order anharmonicity corrections in atomic displacements to harmonic vibrational states. Second, the atom-centered density matrix propagation molecular dynamics model that provides a good energy conservation was used to calculate the atomic trajectories, velocities, and a dipole moment time history of biotin at low and room temperatures. Predicted low-THz lines agree well with the experimental spectra. The influence of the polyethylene (PE) matrix embedment on the THz spectra of biotin at the nanoscale was studied using the developed hybrid DFT/molecular mechanical approach. While PE is almost transparent at THz frequencies, additional low-THz lines are predicted in the biotin/PE system, which reflects a dynamic interaction between biotin and a surrounding PE cavity.

Terahertz Spectra of Biotin Based on First Principle, Molecular Mechanical, and Hybrid Simulations

Terahertz (THz) absorption of biotin was simulated using the first principle and the density functional theory (DFT) both in the harmonic approximation and with corrections for the anharmonicity. Anharmonicity corrections were calculated using two different approaches. First, the perturbation theory-based first principle calculations were performed to include third- and fourth-order anharmonicity corrections in atomic displacements to harmonic vibrational states. Second, the atom-centered density matrix propagation molecular dynamics model that provides a good energy conservation was used to calculate the atomic trajectories, velocities, and a dipole moment time history of biotin at low and room temperatures. Predicted low-THz lines agree well with the experimental spectra. The influence of the polyethylene (PE) matrix embedment on the THz spectra of biotin at the nanoscale was studied using the developed hybrid DFT/molecular mechanical approach. While PE is almost transparent at THz frequencies, additional low-THz lines are predicted in the biotin/PE system, which reflects a dynamic interaction between biotin and a surrounding PE cavity.

A new intermediate in the Prins reaction.

Two Prins reactions were investigated by the use of DFT calculations. A model composed of R–CH=CH2 + H3O+(H2O)13 + (H2C=O)2, R = Me and Ph, was adopted to trace reaction paths. For both alkenes, the concerted path forming 1,3-diols was obtained as the rate determining step (TS1). TS stands for a transition state. From the 1,3-diol, a bimolecular elimination (TS2) leads to the allylic alcohol as the first channel. In the second channel, the 1,3-diol was converted via TS3 into an unprecedented hemiacetal intermediate, HO–CH2–O–CH(R)–CH2–CH2–OH. This intermediate undergoes ring closure (TS4), affording the 1,3-dioxane product. The intermediate is of almost the same stability as the product, and two species were suggested to be in a state of equilibrium. While the geometry of TS1 appears to be forwarded to that of a carbocation intermediate, the cation disappeared through the enlargement of the water cluster. Dynamical calculations of a classical trajectory using the atom-centered density matrix propagation molecular dynamics model on the four TSs were carried out, and results of IRC calculations were confirmed by them.

Multi-functionalized naphthalene complexes for hydrogen storage

A density functional study of hydrogen uptake capacity of multi-functionalized naphthalene with Ti and Li metal atom has been carried out. It is observed that, the naphthalene functionalized with two Ti atoms can interact with total eight hydrogen molecules in which each Ti metal atom interacts with four hydrogen molecules. Naphthalene decorated with two Li atoms can interact with total three H2 molecules only. First (19Li) and second (20Li) Li atom can interact with only one and two hydrogen molecule respectively. It is observed that, hydrogen molecules bind strongly to the C10H8Ti2 complex than C10H8Li2 complex. The gravimetric hydrogen uptake capacity of C10H8Ti2 and C10H8Li2 complex is found to be 6.72 and 3.73 wt% respectively. Moreover, after functionalizing naphthalene with four Li atoms, the uptake capacity is increased to 7.20 wt %. However, the thermochemistry result favors to Ti functionalized naphthalene complex (C10H8Ti2) for hydrogen storage over Li functionalized naphthalene (both C10H8Li2 and C10H8Li4) complexes. Atom-centered density matrix propagation (ADMP) molecular dynamics simulations have been performed which showed that C10H8Li2 and C10H8Li4 complex cannot bind single hydrogen molecule at room temperature whereas C10H8Ti2 can bind five hydrogen molecules.

Gauging the flexibility of the active site in soybean lipoxygenase-1 (SLO-1) through an atom-centered density matrix propagation (ADMP) treatment that facilitates the sampling of rare events.

We present a computational methodology to sample rare events in large biological enzymes that may involve electronically polarizing, reactive processes. The approach includes simultaneous dynamical treatment of electronic and nuclear degrees of freedom, where contributions from the electronic portion are computed using hybrid density functional theory and the computational costs are reduced through a hybrid quantum mechanics/molecular mechanics (QM/MM) treatment. Thus, the paper involves a QM/MM dynamical treatment of rare events. The method is applied to probe the effect of the active site elements on the critical hydrogen transfer step in the soybean lipoxygenase-1 (SLO-1) catalyzed oxidation of linoleic acid. It is found that the dynamical fluctuations and associated flexibility of the active site are critical toward maintaining the electrostatics in the regime where the reactive process can occur smoothly. Physical constraints enforced to limit the active site flexibility are akin to mutations and, in the cases studied, have a detrimental effect on the electrostatic fluctuations, thus adversely affecting the hydrogen transfer process.

Computational simulations of hydrolysis of phosphazene oligomer utilizing atom‐centered density matrix propagation

AbstractDensity functional theory (DFT) calculations, including the ab initio molecular dynamics method, atom‐centered density matrix propagation (ADMP), were used to investigate the hydrolysis reaction of a dichlorophosphazene trimer. The model trimer, intermediate structures and the product of the first step of hydrolysis, were optimized using DFT with the B3LYP density functional, followed by a 600 fs ADMP simulation. Natural bond order analysis (NBO) was used to determine atomic charges and occupancy of the bond orbitals and the lone pair orbitals of the molecule at various points along the simulation pathway. The simulation successfully shows dissociation of the trimer backbone into two distinct product molecules, shown through both increasing separation of the product units and through the more thorough NBO analysis of the bond orbitals. © 2012 Wiley Periodicals, Inc.

“Pump–Probe” Atom-Centered Density Matrix Propagation Studies To Gauge Anharmonicity and Energy Repartitioning in Atmospheric Reactive Adducts: Case Study of the OH + Isoprene and OH + Butadiene Reaction Intermediates

Time-resolved "pump-probe" ab initio molecular dynamics studies are constructed to probe the stability of reaction intermediates, the mechanism of energy transfer, and energy repartitioning, for moieties involved during the interaction of volatile organic compunds with hydroxyl radical. These systems are of prime importance in the atmosphere. Specifically, the stability of reaction intermediates of hydroxyl radical adducts to isoprene and butadiene molecules is used as a case study to develop novel computational techniques involving "pump-probe" ab initio molecular dynamics. Starting with the various possible hydroxyl radical adducts to isoprene and butadiene, select vibrational modes of each of the adducts are populated with excess energy to mimic the initial conditions of an experiment. The flow of energy into the remaining modes is then probed by subjecting the excited adducts to ab initio molecular dynamics simulations. It is found that the stability of the adducts arises directly due to the anhormonically driven coupling of the modes to facilitate repartitioning of the excess vibrational energy. This kind of vibrational repartitioning has a critical influence on the energy density.