Simulation of slow reaction with quantum character: Neutral hydrolysis of carboxylic ester

By computer simulation, using both quantum and classical dynamics, we determined the rate constant and the kinetic isotope effect of the rate-determining step in the neutral hydrolysis of p-methoxyphenyl dichloroacetate in aqueous solution. This step involves a proton transfer concerted with the formation of a C O bond. A method of biased sampling was used; the Gibbs free energy of the biased configuration from which proton transfer is likely to occur was determined by a combination of semiempirical quantum calculations and thermodynamic integration. The proton dynamics was modeled with the quantum-dynamical density matrix evolution method that includes nonadiabatic pathways. The proton dynamics is driven by a fluctuating proton potential that was derived from a classical molecular dynamics simulation of the system including solvent. The calculated rate constant of 3×10⁻² s⁻¹ agrees within the error of the calculation with the experimentally observed value of 2.78×10⁻³. The calculated pseudo-first-order kinetic isotope effect of 3.9 is in good agreement with the experimentally observed value of 3.2. The results show the feasibility of computational approaches to slow reactions in complex environments, where proton transfer with an essential quantum-dynamical nature is the rate-limiting step. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 886–895, 1999     

Reactive chemical dynamics through conical intersections

Reaction dynamics of prototypical, D + H₂ and Cl (²P) + H₂, chemical reactions occurring through the conical intersections of the respective coupled multi-sheeted potential energy surfaces is examined here. In addition to the electronic coupling, nonadiabatic effects due to relativistic spin-orbit coupling are also considered for the latter reaction. A time-dependent wave packet propagation approach is undertaken and the quantum dynamical observables viz., energy resolved reaction probabilities, integral reaction cross-sections and thermal rate constants are reported.     

Nonadiabatic molecular dynamics with solvent effects: A LR-TDDFT QM/MM study of ruthenium (II) tris (bipyridine) in water

The previously derived trajectory-based nonadiabatic molecular dynamics scheme [E. Tapavicza, I. Tavernelli, U. Rothlisberger, Phys. Rev. Lett. 98 (2007) 023001] is extended to include the coupling of the quantum system with a classically described environment. The dynamics is performed using LR-TDDFT energies and forces computed on-the-fly together with the nonadiabatic coupling vectors needed for the propagation of the nuclear coefficients according to Tully’s fewest-switches surface hopping algorithm. The resulting LR-TDDFT-QM/MM approach is applied to the study of the ultrafast relaxation of the photoexcited singlet metal-to-ligand-charge-transfer state (¹MLCT) of [Ru(bpy)₃]²⁺ (bpy = 2,2′-bipyridine) in water. The observed intersystem crossing dynamics with the triplet MLCT is in good agreement with available experimental results.     

Nonadiabatic photodissociation dynamics

The photodissociation dynamics of the triatomic (or pseudo‐triatomic) system in the nonadiabatic multiple electronic states is investigated by employing a time‐dependent quantum wave packet method, while the time propagation of the wave packet is carried out using the split‐operator scheme. As a numerical example, the photodissociation dynamics of CH₃I in three electronic states ¹Q₁(A′), ¹Q₁(A″), and ³Q₀₊ is studied and CH₃I is treated as a pseudotriatomic model. The absorption spectra and product vibrational state distributions are calculated and compared with previous theoretical work. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

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 ([(H₂O]_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.     

Theoretical Study on the Gas‐Phase SN2 Reaction of Microhydrated Fluoride with Methyl Fluoride

The rate constants for the gas‐phase S_N2 reaction of F^?(H₂O) with CH₃F have been calculated using the dual‐level variational transition state theory including multidimensional tunneling from 50 to 500 K. Tunneling was found to dominate the reaction below 200 K. The deuterium, ¹³C, and ¹⁴C kinetic isotope effects (KIEs) and solvent (D₂O) isotope effects (SKIEs) were also calculated in the same temperature range. The results indicated that the deuterium and heavy water substitutions resulted in inverse KIEs (0.6～0.8 ) while the ¹³C and ¹⁴C substitutions resulted in normal KIEs (1.0～1.2) at room temperature. The calculated carbon KIEs increased significantly below 80 K due to the differences in the magnitude of the tunneling effects for different isotopic substitutions.     

On-the-Fly Ring-Polymer Molecular Dynamics Calculations of the Dissociative Photodetachment Process of the Oxalate Anion

The dissociative photodetachment dynamics of the oxalate anion, C₂O₄H⁻ + hν → CO₂ + HOCO + e⁻, were theoretically studied using the on-the-fly path-integral and ring-polymer molecular dynamics methods, which can account for nuclear quantum effects at the density-functional theory level in order to compare with the recent experimental study using photoelectron–photofragment coincidence spectroscopy. To reduce computational time, the force acting on each bead of ring-polymer was approximately calculated from the first and second derivatives of the potential energy at the centroid position of the nuclei beads. We find that the calculated photoelectron spectrum qualitatively reproduces the experimental spectrum and that nuclear quantum effects are playing a role in determining spectral widths. The calculated coincidence spectrum is found to reasonably reproduce the experimental spectrum, indicating that a relatively large energy is partitioned into the relative kinetic energy between the CO₂ and HOCO fragments. This is because photodetachment of the parent anion leads to Franck–Condon transition to the repulsive region of the neutral potential energy surface. We also find that the dissociation dynamics are slightly different between the two isomers of the C₂O₄H⁻ anion with closed- and open-form structures.     

Mechanism of the O2(1Δg) generation from the Cl2/H2O2 basic aqueous solution explored by the combined ab initio calculation and nonadiabatic dynamics simulation

In the present work, mechanism of the O₂(¹Δ_g) generation from the reaction of the dissolved Cl₂ with H₂O₂ in basic aqueous solution has been explored by the combined ab initio calculation and nonadiabatic dynamics simulation, together with different solvent models. Three possible pathways have been determined for the O₂(¹Δ_g) generation, but two of them are sequentially downhill processes until formation of the OOCl⁻ complex with water, which are of high exothermic character. Once the complex is formed, singlet molecular oxygen is easily generated by its decomposition along the singlet-state pathway. However, triplet molecular oxygen of O₂() can be produced with considerable probability through nonadiabatic intersystem crossing in the ¹Δ_g/ intersection region. It has been found that the coupled solvent, heavy-atom, and nonadiabatic effects have an important influence on the quantum yield of the O₂(¹Δ_g) generation. © 2018 Wiley Periodicals, Inc.     

Deuterium MAS NMR Studies of Dynamics on Multiple Timescales: Histidine and Oxalic Acid

Deuterium (²H) magic‐angle spinning (MAS) nuclear magnetic resonance is applied to monitor the dynamics of the exchanging labile deuterons of polycrystalline L ‐histidine hydrochloride monohydrate‐d₇ and α‐oxalic acid dihydrate‐d₆. Direct experimental evidence of fast dynamics is obtained from T_1Z and T_1Q measurements. Further motional information is extracted from two‐dimensional single‐quantum (SQ) and double‐quantum (DQ) MAS spectra. Differences between the SQ and DQ linewidths clearly indicate the presence of motions on intermediate timescales for the carboxylic moiety and the D₂O in α‐oxalic acid dihydrate, and for the amine group and the D₂O in L ‐histidine hydrochloride monohydrate. Comparison of the relaxation rate constants of Zeeman and quadrupolar order with the relaxation rate constants of the DQ coherences suggests the co‐existence of fast and slow motional processes.     

Molecular dynamics simulation of the interaction between methyl benzotriazole and Cu2O crystal

In circulating water system , methyl benzotriazole (TTA) is one of the common corrosion inhibitors for copper. But the inhibition mechanisms have not been clearly understood so far. In different number of water molecules, the interaction between TTA and Cu₂O (copper surface) was investigated with molecular dynamics (MD) method. The results showed that the MD simulation result with water was more consistent with the experiment results. In different number of water molecules, the sequence of the interaction energies between TTA and Cu₂O (001) was ? E ₁ (150H₂O) > ? E ₁(200H₂O) > ? E ₁(100H₂O) > ? E ₁(50H₂O) > ? E ₁(0H₂O). The number of water molecules had an important influence on the interaction between corrosion inhibitors and Cu₂O crystal. From non‐bond energy and pair correlation functions, the interaction energies of the model system were mainly contributed by the non‐bond interaction. Strong adsorption could be raised by the Coulomb interaction between the negatively charged functional groups in TTA and the positive copper ions in the Cu₂O (001) face, and further interaction between aggressive media and copper could be restricted. So, copper corrosion could be avoided. Chemical bonds and non‐bond interactions were formed between TTA and Cu₂O (001) in different number of water molecules. Water molecules could not be ignored during the MD simulation, too. The results obtained here may provide theoretical supports for developing new corrosion inhibitors.     

Micelle and Solvent Relaxation in Aqueous Sodium Dodecylsulfate Solutions

Dielectric spectra have been measured for aqueous sodium dodecylsulfate (SDS) solutions up to 0.1 mol L^?1 at 25 °C over the frequency range 0.005≤ν GHz^?1≤89. The spectra exhibit two relaxation processes at approximately 0.03 GHz and 0.2 GHz associated with the presence of micelles in addition to the dominant solvent relaxation process at approximately 18 GHz and a small contribution at approximately 1.8 GHz due to H₂O molecules hydrating the micelles. Detailed analysis reveals that the micelles bind 20 water molecules per SDS unit, but not as strongly as trimethylalkylammonium halide surfactants do. The relaxation times and amplitudes of both micelle relaxation processes can be simultaneously analysed with the theory of Grosse, yielding the effective volume of a SDS unit in the micelle and the lateral diffusion coefficient of the bound counterions. The findings of this investigation fully corroborate recent molecular dynamics simulations on structure and dynamics of SDS micelles.     

Molecular Reorientational Dynamics of the Neat Ionic Liquid 1‐Butyl‐3‐methylimidazolium Hexafluorophosphate by Measurement of 13C Nuclear Magnetic Relaxation Data

The reorientational dynamics of the ionic liquid 1butyl‐3‐methylimidazolium hexafluorophosphate ([BMIM]PF₆) were studied over a wide range of temperatures by measurement of ¹³C spin–lattice relaxation rates and NOE factors. The reorientational dynamics were evaluated by performing fits to the experimental relaxation data. Thus, the overall reorientational motion was described by a Cole–Davidson spectral density with a Vogel–Fulcher–Tammann temperature dependence of the correlation times. The reorientational motion of the butyl chain was modelled by a combination of the latter model for the overall motion with a Bloembergen–Purcell–Pound spectral density and an Arrhenius temperature dependence for the internal motion. Except for C2 in the aromatic ring, an additional reduction of the spectral density by the Lipari–Szabo model had to be employed. This reduction is a consequence of fast molecular motions before the rotational diffusion process becomes effective. The C2 atom did not exhibit this reduction, because the librational motion of the corresponding C2? H vector is severely hindered due to hydrogen bonding with the hexafluorophosphate anion. The observed dynamic features of the [BMIM]⁺ cation confirm quantum‐chemical structures obtained in a former study.     

Molecular dynamics in nanostructured polyimide–silica hybrid materials and their thermal stability

Molecular motion and thermal stability in two series of nanophase‐separated polyimide–silica (PI–SiO₂) hybrid materials with chemically bound components were studied. The hybrids were synthesized from p‐aminophenyltrimethoxysilane‐terminated poly(amic acid)s as PI precursors and tetramethoxysilane as a silica precursor via a sol–gel process. The hybrids differed in their PI chemical structure and chain length (number‐average molecular weight = 5.000, 7.500, or 10.000) and in their SiO₂ content, which ranged from 0 to 50 wt %. Differential scanning calorimetry, laser‐interferometric creep rate spectroscopy, and thermally stimulated depolarization current techniques were used for studying the dynamics from 100 to 650 K and from 10^?3 to 10^?2 Hz. Comparative thermogravimetric measurements were also carried out from 300 to 900 K. Silica nano‐ or submicrodomains that formed affected PI dynamics in two opposite directions. Because of the loosening of the molecular packing of PI chains confined to nanometer‐scale spaces between silica constraints, an enhancement of small‐scale motion, mostly at temperatures below the β‐relaxation region, occurred. However, a partial or total suppression of segmental motion could be observed above the β‐relaxation temperature, drastically so for the shortest PI chains at elevated silica contents and within or close to the glass‐transition range, because of the covalent anchoring of chain ends to silica domains. Large changes in thermal stability, including a 2.5‐fold increase in the apparent activation energy of degradation, were observed in the hybrids studied. A greater than 100 °C rise in long‐term thermal stability could be predicted for some hybrids with respect to pure PI. © 2002 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 40: 1056–1069, 2002     

Structure and dynamics of room temperature ionic liquids with bromide anion: results from 81Br NMR spectroscopy

We report the results of a comprehensive ⁸¹Br NMR spectroscopic study of the structure and dynamics of two room temperature ionic liquids (RTILs), 1‐butyl‐3‐methylimidazolium bromide ([C₄mim]Br) and 1‐butyl‐2,3‐dimethylimidazolium bromide ([C₄C₁mim]Br), in both liquid and crystalline states. NMR parameters in the gas phase are also simulated for stable ion pairs using quantum chemical calculations. The combination of ⁸¹Br spin‐lattice and spin‐spin relaxation measurements in the motionally narrowed region of the stable liquid state provides information on the correlation time of the translational motion of the cation. ⁸¹Br quadrupolar coupling constants (C_Q) of the two RTILs were estimated to be 6.22 and 6.52 MHz in the crystalline state which were reduced by nearly 50% in the liquid state, although in the gas phase, the values are higher and span the range of 7–53 MHz depending on ion pair structure. The C_Q can be correlated with the distance between the cation–anion pairs in all the three states. The ⁸¹Br C_Q values of the bromide anion in the liquid state indicate the presence of some structural order in these RTILs, the degree of which decreases with increasing temperature. On the other hand, the ionicity of these RTILs is estimated from the combined knowledge of the isotropic chemical shift and the appropriate mean energy of the excited state. [C₄C₁mim]Br has higher ionicity than [C₄mim]Br in the gas phase, while the situation is reverse for the liquid and the crystalline states. Copyright © 2015 John Wiley & Sons, Ltd.     

Semiclassical Trajectory Studies of Reactive and Nonreactive Scattering of OH(A 2Σ+) by H2 Based on an Improved Full-Dimensional Ab Initio Diabatic Potential Energy Matrix

We present a new full-dimensional diabatic potential energy matrix (DPEM) for electronically nonadiabatic collisions of OH(A ²Σ⁺) with H₂, and we calculate the probabilities of electronically adiabatic inelastic collisions, nonreactive quenching, and reactive quenching to form H₂O+H. The DPEM was fitted using a many-body expansion with permutationally invariant polynomials in bond-order functions to represent the many-body part. The dynamics calculations were carried out with the fewest-switches with time uncertainty and stochastic decoherence (FSTU/SD) semiclassical trajectory method. We present results both for head-on collisions (impact parameter b equal to zero) and for a full range of impact parameters. The results are compared to experiment and to earlier FSTU/SD and quantum dynamics calculations with a previously published DPEM. The various theoretical results all agree that nonreactive quenching dominates reactive quenching, but there are quantitative differences between the two DPEMs and between the b=0 results and the all-b results, especially for the probability of reactive quenching.     

Ab initio quantum chemistry and molecular dynamics simulations studies of LiPF6/poly(ethylene oxide) interactions

Ab initio and molecular mechanics studies of LiPF₆ and the interaction of the salt with the poly(ethylene oxide) (PEO) oligomer dimethylether have been performed. Optimized geometries and energies of Li⁺/PF₆^? complexes obtained from quantum chemistry revealed a preference for C_3V symmetry structures for Li⁺–P separations under 2.8 Å, C_2V symmetry for Li⁺–P in the range of 2.8–3.3 Å and C_4V symmetry for Li⁺–P separations larger than 3.3 Å. Electron correlation effects were found to make an insignificant contribution to binding in the Li⁺/PF₆^? complex. By contrast, analogous studies of PF₆^?/PF₆^? and PF₆^?/dimethyl ether complexes revealed important contributions of electron correlation to the complex interaction energy. A molecular mechanics force field for simulations of PEO/LiPF₆ melts was parameterized to reproduce the geometries and energies of Li⁺/PF₆^?, PF₆^?/PF₆^?, PF₆^?/dimethylether complexes. Molecular dynamics simulations of PEO/LiPF₆ melts were performed to validate this quantum chemistry‐based force field. Accurate reproduction of the increase in solution density with addition of salt was found while the electrical conductivity of PEO/LiPF₆ solutions was found to be within an order of magnitude of the experimental values. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 641–654, 2001     

Photoisomerization of Arylazopyrazole Photoswitches: Stereospecific Excited‐State Relaxation

Electronic structure calculations and nonadiabatic dynamics simulations (more than 2000 trajectories) are used to explore the Z–E photoisomerization mechanism and excited‐state decay dynamics of two arylazopyrazole photoswitches. Two chiral S₁/S₀ conical intersections with associated enantiomeric S₁ relaxation paths that are barrierless and efficient (timescale of ca. 50 fs) were found. For the parent arylazopyrazole (Z8) both paths contribute evenly to the S₁ excited‐state decay, whereas for the dimethyl derivative (Z11) each of the two chiral cis minima decays almost exclusively through one specific enantiomeric S₁ relaxation path. To our knowledge, the Z11 arylazopyrazole is thus the first example for nearly stereospecific unidirectional excited‐state relaxation.     

Magnesium sulfate against oxidative damage of membrane lipids: A theoretical model

The role of magnesium sulfate as an inhibitor of lipid peroxidation has been poorly understood, although this salt has been intensively used in a wide range of diseases related to lipid peroxidation, for example, preeclampsia. Classical molecular dynamics (MD) simulations of a lipid bilayer in the presence of ^?OH radicals and MgSO₄ were performed to study their effects on membrane properties. Additionally, quantum chemistry (QC) calculations for MgSO₄, ^?OH, MgSO₄^?OH, [MgSO₄(H₂O)₄], and [MgSO₄(H₂O)₄^?OH] were performed to analyze the interactions between ^?OH^…Mg. The MD results showed that the Mg salt is hydrated, forming a contact ion pair (CIP) that is adsorbed on the membrane surface close to phosphate groups. Comparisons of MD calculations for Mg? O distances indicate good agreement with theoretical QC and experimental studies. MD results also reveal that MgSO₄ increases the thickness and the compressibility modulus of the membrane, indicating that it is less compressible. In contrast, DFT calculations show important ^?OH^…Mg? SO₄ interactions in hydrated systems that inhibit the radical action by resonance in the group (smearing the spin density). These results, together with the reported experimental findings of ^?OH high mobility in water and fast water exchange in Mg⁺², may explain the MgSO₄ protective effect against lipid peroxidation on cellular membranes.     

Surface Charges at the CaF2/Water Interface Allow Very Fast Intermolecular Vibrational‐Energy Transfer

We investigate the dynamics of water in contact with solid calcium fluoride, where at low pH, localized charges can develop upon fluorite dissolution. We use 2D surface‐specific vibrational spectroscopy to quantify the heterogeneity of the interfacial water (D₂O) molecules and provide information about the sub‐picosecond vibrational‐energy‐relaxation dynamics at the buried solid/liquid interface. We find that strongly H‐bonded OD groups, with a vibrational frequency below 2500 cm^?1, display very rapid spectral diffusion and vibrational relaxation; for weakly H‐bonded OD groups, above 2500 cm^?1, the dynamics slows down substantially. Atomistic simulations based on electronic‐structure theory reveal the molecular origin of energy transport through the local H‐bond network. We conclude that strongly oriented H‐bonded water molecules in the adsorbed layer, whose orientation is pinned by the localized charge defects, can exchange vibrational energy very rapidly due to the strong collective dipole, compensating for a partially missing solvation shell.     

Nuclear quantum and H/D isotope effects on three-centered bonding diborane: Path integral molecular dynamics simulations

Nuclear quantum and H/D isotope effects of bridging and terminal hydrogen atoms of diborane (B₂H₆) molecules were systematically studied by classical ab initio molecular dynamics (CLMD) and ab initio path integral molecular dynamics (PIMD) simulations with BHandHLYP/6-31++G** level of theory at room temperature (298.15 K). Calculated results clearly show that H/D isotope effect appears in the distribution of hydrogen (deuterium) of B₂H₆ (B₂D₆). Geometry of B₂H₆ also plays a significant role in the nuclear quantum effect proved by PIMD simulations, but slightly deviated from its equilibrium structure when simulated via CLMD simulation. The bond lengths between boron atoms R (B1 … B2) and the bridging hydrogen atoms R_HH (H_B1 … H_B2) of the B₂H₆ molecule obtained from PIMD simulations are slightly longer than those of the deuterated form of the diborane (B₂D₆) molecule. The principal component analysis (PCA) was also employed to distinguish the important modes of bridging hydrogen as related to the nuclear quantum and H/D isotope effects. The highest level of contribution obtained from PCA of PIMD simulations is bending, while various mixed vibrations with less contribution were also found. Therefore, the nuclear quantum and H/D isotope effects need to be taken into account for a better understanding of diborane geometry.