Elucidating ultrafast nonradiative decay of photoexcited uracil in aqueous solution by ab initio molecular dynamics

Nonradiative decay of the photoexcited RNA base uracil has been studied in fully explicit aqueous solution using nonadiabatic ab initio molecular dynamics. Detailed comparison of the time-dependent nonadiabatic transition probability with specific molecular vibrational motions provides insight into the mechanism of the ultrafast internal conversion. From a monoexponential fit to the excited state ensemble population, the lifetime of the first electronically excited ππ^* singlet state has been determined to be 359 fs. Additional, reference, nonadiabatic simulations have been carried out in the gas phase, pinpointing the effects of the solvent on the photophysics of uracil. The gas phase excited state lifetime is calculated to be 608 fs, somewhat longer than in solution. In terms of excitation energies and geometrical parameters, the differences between gas phase and aqueous solution are found to be generally small. A notable exception is the excited state out-of-plane torsional motion about the CC double bond, which appears severely damped by the solvent. Moreover, hydrogen bond interactions between the uracil oxygens and the solvent hydrogens are seen to enhance internal conversion.     

IMiCMO: a new integrated ab initio multicenter molecular orbitals method for molecular dynamics calculations in solvent cluster systems

A new computational scheme integrating ab initio multicenter molecular orbitals for determining forces of individual atoms in large cluster systems is presented. This method can be used to treat systems of many molecules, such as solvents by quantum mechanics. The geometry parameters obtained for three models of water clusters by the present method are compared with those obtained by the full ab initio MO method. The results agree very well. The scheme proposed in this article also intended for use in modeling cluster systems using parallel algorithms. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1107–1112, 2001     

Density functional theory for efficient ab initio molecular dynamics simulations in solution

We present a density functional for first-principles molecular dynamics simulations that includes the electrostatic effects of a continuous dielectric medium. It allows for numerical simulations of molecules in solution in a model polar solvent. We propose a smooth dielectric model function to model solvation into water and demonstrate its good numerical properties for total energy calculations and constant energy molecular dynamics.     

Thermal decomposition mechanisms of the energetic benzotrifuroxan:1,3,3-trinitroazetidine cocrystal using ab initio molecular dynamics simulations

Ab initio molecular dynamics simulations were performed to investigate the thermal decomposition mechanisms of the energetic benzotrifuroxan (BTF):1,3,3-trinitroazetidine (TNAZ) cocrystal at high temperature. It is found that there are four initial reaction mechanisms involved in the decomposition of the cocrystal. Subsequent decomposition channels can be divided into three types: BTF-chain isomerization, C─NO₂ bond homolysis, and ring opening. After that, one main path is that long chains decomposed into small radicals gradually after the ring opening. The other is that a new ring was formed after the ring opening and then it will break by degrees. Releasing of the H radicals and oxygen-containing groups plays an important role in the whole decomposition process. We also studied the release mechanisms of nitrogen gas and carbon dioxide in the later decomposition stage. Our study may provide new insights into the initiation mechanisms and subsequent decomposition of cocrystal explosives at high temperature.     

Lithium hydroxide phase transition under high pressure: an ab initio molecular dynamics study.

The high-pressure phase transition in the deuterated lithium hydroxide crystalline state has been studied by Car-Parrinello molecular dynamics simulations, in the constant-pressure, constant-temperature ensemble. The recently developed metadynamics approach has been applied to encourage the system to transform into different phases in an affordable simulation time. A previously not completely characterized high-pressure phase has been obtained. The structural and spectroscopic properties have been studied and compared with the neutron scattering, infrared and Raman measurements. It has been found that the calculated structure differs slightly from the experimental hypothesis, and that the presence of strong hydrogen bonds is the source of the red shift and of the characteristic features of the OD-stretching bands in both IR and Raman spectra.     

The Jahn-Teller effect of the TiIII ion in aqueous solution: extended ab initio QM/MM molecular dynamics simulations.

Combined ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulations, including only the first and the first and second hydration shells in the QM region, were performed for TiIII in aqueous solution. The hydration structure of TiIII is discussed in terms of radial distribution functions, coordination-number distributions and several angle distributions. Dynamical properties, such as librational and vibrational motions and TiIII-O vibrations, were evaluated. A fast dynamical Jahn-Teller effect of TiIII(aq) was observed in the QM/MM simulations, in particular when the second hydration shell was included into the QM region. The results justify the computational effort required for the inclusion of the second hydration shell into the QM region and show the importance of this effort for obtaining accurate hydration-shell geometries, dynamical properties, and details of the Jahn-Teller effect.     

Exploring the hydration of Pb2+: ab initio studies and first-principles molecular dynamics

Even though lead is a well-known toxicant widely scattered throughout the world since antiquity, its chemistry is poorly documented at the molecular level. Here we investigate the hydration of the Pb(2+) ion by means of first-principles molecular dynamics (Car-Parrinello molecular dynamics, CPMD). We found that the hydrated cation is heptacoordinated in a dynamically holodirected arrangement roughly corresponding to a fluxional distorted pentagonal bipyramid. The time-averaged Pb-O bond length is especially large and amounts to 2.70 A with an associated root-mean-square deviation of 0.26 A. This results from a dynamic exchange between short (<2.6 A), intermediate (2.6-3.0 A) and long (>3.0 A) Pb-O bonds. The latter very long Pb-O distance implies that the determination of the coordination number n(c) from experimental work may not necessarily yield values directly comparable to the theoretical value of n(c)=7, since not all experimental techniques would recognize such a long distance as a bond to the metal cation. Pronounced disorders are evidenced in the second shell, characteristic of a chaotropic cation, and exchanges between the first and second shells cannot be excluded on a timescale of a few tens of picoseconds.     

Interconversion behavior of the C-H bond in the CH4+ radical cation: ab initio molecular dynamics study

Thermal motion of CH4+ is investigated by performing an ab initio molecular dynamics method with the second-order M?ller-Plesset (MP2)/6-311G** force field. In the trajectories obtained at 400 K, we have observed rapid interconversion behavior of the geometrical parameters of CH4+ with the frequency of 0.6/ps, where the C-H pair forming the small angle around 55 degrees is switched to another pair on subpicosecond time scale. The switching patterns are found to be classified into the following two types. Type 1: one C-H of the small angled C-H pair is switched to one C-H of the other C-H pair. Type 2: the small angled C-H pair is switched to the other C-H pair, which has been newly observed in the present ab initio MD calculation. The four C-H bonds of CH4+ are characterized by the long and short C-H bonds in a time region of the trajectories, and also for the time-evolution of C-H bonds such interconversion behavior is observed. The switching patterns of the geometrical parameters are compared with those in the interconversion scheme between six equivalent C2v symmetry structures of CH4+ [Paddon-Row, M. N. et al., J Am Chem Soc 1985, 107, 7696]. We have also investigated the electronic energy fluctuation due to thermal motion of CH4+. The standard deviation of total electronic energy at 400 K is evaluated to be 1.2 kcal/mol.     

Anharmonic force field and spectroscopic constants of silene: an ab initio study

High-level ab initio calculations with large basis sets are reported for silene, H₂C=SiH₂. Correlated harmonic force fields are obtained from coupled cluster CCSD(T) calculations with the cc-pVQZ basis (cc-pVTZ for H) while the anharmonic force fields are computed at the MP2/TZ2Pf level. There is excellent agreement with the available experimental data, in particular the equilibrium geometry and the fundamental vibrational frequencies. Many other spectroscopic constants are predicted for the C _{2 v} isotopomers of silene. Received: 27 May 1998 / Accepted: 23 July 1998 / Published online: 9 October 1998     

Wavelet transform analysis of ab initio molecular dynamics simulation: application to core-excitation dynamics of BF3

We propose a novel analysis method of ab initio molecular dynamics (AIMD) simulation using a continuous wavelet transform (c-WT) technique. The c-WT technique, one of the time-frequency signal analysis methods, provides a clear view of the dynamical information in time developments. Combined with the auto-correlation function of velocity by AIMD simulation, c-WT analysis enables us to well understand dynamical distribution, such as the vibrational properties following a change of electronic structure in a molecular system. As a practical application, AIMD simulation of core-excited BF(3) (B1s --> 2a(2) (')) is illustrated. AIMD simulation leads to the change of vibrational motion as well as structural deformation by core-excitation. The c-WT analysis clarifies the relationship between structural deformation and the related significant vibrational modes in core-excitation within 50 fs.     

Ab initio molecular dynamics study of the keto-enol tautomerism of acetone in solution.

We have studied the keto-enol interconversion of acetone to understand the mechanism of tautomerism relevant to numerous organic and biochemical processes. Applying the ab initio metadynamics method, we simulated the keto-enol isomerism both in the gas phase and in the presence of water. For the gas-phase intramolecular mechanism we show that no other hydrogen-transfer reactions can compete with the simple keto-enol tautomerism. We obtain an intermolecular mechanism and remarkable participation of water when acetone is solvated by neutral water. The simulations reveal that C deprotonation is the kinetic bottleneck of the keto-enol transformation, in agreement with experimental observations. The most interesting finding is the formation of short H-bonded chains of water molecules that provide the route for proton transfer from the carbon to the oxygen atom of acetone. The mechanistic picture that emerged from the present study involves proton migration and emphasizes the importance of active solvent participation in tautomeric interconversion.     

Nuclear quantum effects at aqueous metal interfaces captured by molecular dynamics simulations

In this review, we summarize the recent development in modeling nuclear quantum effects at aqueous metal interfaces. First, we review the nuclear quantum effects on the water-metal interface at ultrahigh vacuum. Then, we illustrate the nuclear quantum effects at the potential of zero charge conditions. At last, we give some outlook for the perspective work in modeling the nuclear quantum effects at electrochemical interfaces and some practical simulation strategies.     

Structure and dynamics of phosphate ion in aqueous solution: an ab initio QMCF MD study

A simulation of phosphate in aqueous solution was carried out employing the new QMCF MD approach which offers the possibility to investigate composite systems with the accuracy of a QMMM method but without the time consuming creation of solute-solvent potential functions. The data of the simulations give a clear picture of the hydration shells of the phosphate anion. The first shell consists of 13 water molecules and each oxygen of the phosphate forms in average three hydrogens bonds to different solvent molecules. Several structural parameters such as radial distribution functions and coordination number distributions allow to fully characterize the embedding of the highly charged phosphate ion in the solvent water. The dynamics of the hydration structure of phosphate are described by mean residence times of the solvent molecules in the first hydration shell and the water exchange rate.     

All electron ab initio investigations of the electronic states of the MoN molecule

The low lying electronic states of the molecule MoN were investigated by performing all electron ab initio multi-configuration self-consistent-field (CASSCF) calculations. The relativistic corrections for the one electron Darwin contact term and the relativistic mass-velocity correction were determined in perturbation calculations. The electronic ground state is confirmed as being ⁴∑⁻. The chemical bond of MoN has a triple bond character because of the approximately fully occupied delocalized bonding π and σ orbitals. The spectroscopic constants for the ground state and ten excited states were derived. The excited doublet states ²∑⁻, ²Γ, ²Δ, and ²∑⁺ are found to be lower lying than the ⁴Π state that was investigated experimentally. Elaborate multi-configuration configuration-interaction (MRCI) calculations were carried out for the states ⁴∑⁻ and ⁴∏ using various basis sets. The spectroscopic constants for the ⁴∑⁻ ground state were determined as r_e=1.636 Å and ω_e=1109 cm⁻¹, and for the ⁴∏ state as r_e=1.662 Å and ω_e=941 cm⁻¹. The values for the ground state are in excellent agreement with available experimental data. The MoN molecule is polar with a charge transfer from Mo to N. The dipole moment was determined as 2.11 D in the ⁴∑⁻ state and as 4.60 D in the ⁴∏ state. These values agree well with the revised experimental values determined from molecular Stark spectroscopic measurements. The dissociation energy, D_e, is determined as 5.17 eV, and D₀ as 5.10 eV.     

In cation interactions with some organics: ab initio molecular orbital and density functional theory

Ab initio molecular orbital and density functional theory studies were undertaken to investigate the structural and energetic characteristics of complexes of In⁺ with several different organic molecules for the first time. HF, MP2, QCISD, and CCD levels of theory in ab initio MO as well as B3LYP, B3PW91 hybrid functionals in density functional theory were used. A valence TZ+P basis set with relativistic effective core potentials was used for the In atom while the 6-311++G(3d, 2p) basis set was utilized for all other atoms. Both closed-shell (H₂O, CH₄, CH₃OH, and C₆H₆) and open-shell (CH₃ and C₂H₃) molecules were considered for complexation with In⁺. In⁺ affinities of 21.5, 24.8, 28.6, 18.4, and 23.0 kcal/mol were obtained with the B3PW91 hybrid functional for H₂O, CH₃OH, C₆H₆, CH₃, and C₂H₃, respectively. The large values for the calculated affinities indicate the validity of our recent experimental detection of In⁺ ion attachment to some organic molecules.     

Comparative analysis of molecular interactions in quaternary fluid system performed by classical and ab initio molecular dynamics

Molecular interactions in the quaternary fluid system acetic acid–n-propanol–n-propyl acetate–water were analyzed by classical and ab initio molecular dynamics methods. It was shown that ab initio molecular dynamics simulation can reproduce the molecular mobility tendency and structural features of a multicomponent system without empirical parameters.     

Ab initio molecular dynamics of protonated water clusters by integrated multicenter molecular-orbital method

To analyze large-scale cluster systems theoretically, we recently developed an "integrated multicenter molecular-orbital" (IMiC-MO) method. This method calculates the force of an entire system by dividing the system into small regions. We used the method to analyze the effect of cluster size and the process of hydrogen bond network (HBN) growth to form H(+)(H(2)O)(n) (n = 9, 17, and 33) clusters. Our simulations reveal that H(3)O(+) and water molecules in the first solvation shell function take an important role to grow the HBN. In addition, the number of hydrogen donors in each water molecule is strongly related to the shape of the HBN.     

Car-Parrinello molecular dynamics simulations and EPR property calculations on aqueous ubisemiquinone radical anion

Car-Parrinello molecular dynamics (CPMD) simulations have been performed on ubisemiquinone radical anion in aqueous solution. The different types of hydrogen bonding formed between the semiquinone and the solvent were studied in terms of frequency and directionality, in comparison with the parent benzosemiquinone radical anion. The EPR parameters (g-tensors and hyperfine coupling constants) were obtained from quantum chemical property calculations performed on snapshots along the MD trajectory, and the contributions of different solvation effects to the EPR parameters have been evaluated. The influence of the anion’s conformational behaviour was examined, including the orientation-dependent effects of hyperconjugation on side-chain hyperfine coupling.