Decomposing total IR spectra of aqueous systems into solute and solvent contributions: a computational approach using maximally localized Wannier orbitals

The theoretical principles underpinning the calculation of infrared spectra for condensed-phase systems in the context of ab initio molecular dynamics have been recently developed in literature. At present, most ab initio molecular dynamics calculations are restricted to relatively small systems and short simulation times. In this paper we devise a method that allows well-converged results for infrared spectra from ab initio molecular dynamics simulations using small systems and short trajectories characteristic of simulations typically performed in practice. We demonstrate the utility of our approach by computing the imaginary part of the dielectric constant epsilon"(omega) for H2O and D2O in solid and liquid phases and show that it compares well with experimental data. We further demonstrate that maximally localized Wannier orbitals can be used to separate the individual contributions of different molecular species to the linear spectrum of complex systems. The new spectral decomposition method is shown to be useful in present-day ab initio molecular dynamics calculations to compute the magnitude of the "continuous absorption" generated by excess protons in aqueous solutions with good accuracy even when other species present in the solutions absorb strongly in the same frequency window.     

Efficient analysis of highly complex nuclear magnetic resonance spectra of flexible solutes in ordered liquids by using molecular dynamics

The NMR spectra of n-pentane as solute in the liquid crystal 5CB are measured at several temperatures in the nematic phase. Atomistic molecular dynamics simulations of this system are carried out to predict the dipolar couplings of the orientationally ordered pentane, and the spectra predicted from these simulations are compared with the NMR experimental ones. The simulation predictions provide an excellent starting point for analysis of the experimental NMR spectra using the covariance matrix adaptation evolutionary strategy. This shows both the power of atomistic simulations for aiding spectral analysis and the success of atomistic molecular dynamics in modeling these anisotropic systems.     

Dynamics and structure of a flexible columnar liquid crystal based on tetrabenzocyclododecatetraene

The dynamical and conformational behaviour of a flexible tetrabenzocyclododecatetraene derivative exhibiting a columnar mesophase has been studied by a combination of deuteron solid state NMR spectroscopy and molecular dynamics (MD) simulations. As shown by two-dimensional (2D) exchange NMR, the mesophase is characterized by slow axial reorientations (∼10^-3s) of single molecular units where the phenylene rings exhibit a well-defined quasi-fourfold potential, while the 2D spectra of the core methylene sites are sensitive to the molecular conformation and reorientation mechanism. Motional narrowing of one-dimensional (1D) spectra reveals additional fast librations due to the internal flexibility of the mesogenic moiety. The various reorientation pathways comprising interconversions and pseudo-rotations between different energetically stable conformations are elucidated on a microscopic level by molecular dynamics simulations. The mesophase dynamics is ascribed to a complex axial motion involving rotational jumps combined with a pseudo-rotation between two symmetry related sofa forms. This is confirmed quantitatively by comparing the experimental 2D NMR spectra of the core methylene sites and the simulations which are based on the molecular geometries obtained by MD simulations. The lineshapes of one- and two-dimensional spectra of magnetically aligned samples specific to the orientation behaviour of the sofa conformer are discussed.     

Elucidating the vibrational spectra of hydrogen-bonded aggregates in solution: electronic structure calculations with implicit solvent and first-principles molecular dynamics simulations with explicit solvent for 1-hexanol in n-hexane

Fourier transform infrared spectroscopy is a popular method for the experimental investigation of hydrogen-bonded aggregates, but linking spectral information to microscopic information on aggregate size distribution and aggregate architecture is an arduous task. Static electronic structure calculations with an implicit solvent model, Car-Parrinello molecular dynamics (CPMD) using the Becke-Lee-Yang-Parr (BLYP) exchange and correlation energy functionals and classical molecular dynamics simulations for the all-atom version of the optimized parameters for liquid simulations (OPLS-AA) force field were carried out for an ensemble of 1-hexanol aggregates solvated in n-hexane. The initial configurations for these calculations were size-selected from a distribution of aggregates obtained from a large-scale Monte Carlo simulation. The vibrational spectra computed from the static electronic structure calculations for monomers and dimers and from the CPMD simulations for aggregates up to pentamers demonstrate the extent of the contribution of dangling or nondonating hydroxyl groups found in linear and branched aggregates to the "monomeric" peak. Furthermore, the computed spectra show that there is no simple relationship between peak shift and aggregate size nor architecture, but the effect of hydrogen-bond cooperativity is shown to differentiate polymer-like (cooperative) and dimer-like (noncooperative) hydrogen bonds in the vibrational spectrum. In contrast to the static electronic structure calculations and the CPMD simulations, the classical molecular dynamics simulations greatly underestimate the vibrational peak shift due to hydrogen bonding.     

Investigating the relationship between infrared spectra of shared protons in different chemical environments: a comparison of protonated diglyme and protonated water dimer

The energetics, dynamics, and infrared spectroscopy of the shared proton in different chemical environments is investigated using molecular dynamics simulations. A three-dimensional potential energy surface (PES) suitable for describing proton transfer between an acceptor and a donor oxygen atom is combined with an all-atom force field to carry out reactive molecular dynamics simulations. The construction of the fully dimensional PES is inspired from the established mixed quantum mechanics/molecular mechanics treatment of larger systems. The "morphing potential" method is used to transform the generic PES for proton transfer along an O...H+...O motif into a three-dimensional PES for proton transfer in protonated diglyme. Using molecular dynamics simulations at finite temperature, the gas phase infrared spectra are calculated for both species from the Fourier transform of the dipole moment autocorrelation function. For protonated diglyme the modes involving the H+ motion are strongly mixed with other degrees of freedom. At low temperature, the O...H+...O asymmetric stretching vibration is found at 870 cm-1, whereas for H5O2+ this band is at 724 cm-1. As expected, the vibrational bands of protonated diglyme show no temperature dependence whereas for H5O2+ at T = 100 K the proton transfer mode is found at 830 cm-1, in good agreement with 861 cm-1 from very recent molecular dynamics simulations.     

Electronic absorption spectra of pyridine and nicotine in aqueous solution with a combined molecular dynamics and polarizable QM/MM approach

The electronic absorption spectra of pyridine and nicotine in aqueous solution have been computed using a multistep approach. The computational protocol consists in studying the solute solvation with accurate molecular dynamics simulations, characterizing the hydrogen bond interactions, and calculating electronic transitions for a series of configurations extracted from the molecular dynamics trajectories with a polarizable QM/MM scheme based on the fluctuating charge model. Molecular dynamics simulations and electronic transition calculations have been performed on both pyridine and nicotine. Furthermore, the contributions of solute vibrational effect on electronic absorption spectra have been taken into account in the so called vertical gradient approximation. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.     

Air-liquid interfaces of aqueous solutions containing ammonium and sulfate: spectroscopic and molecular dynamics studies

Investigations of the air-liquid interface of aqueous salt solutions containing ammonium (NH(4)(+)) and sulfate (SO(4)(2-)) ions were carried out using molecular dynamics simulations and vibrational sum frequency generation spectroscopy. The molecular dynamics simulations show that the predominant effect of SO(4)(2-) ions, which are strongly repelled from the surface, is to increase the thickness of the interfacial region. The vibrational spectra reported are in the O-H stretching region of liquid water. Isotropic Raman and ATR-FTIR (attenuated total reflection Fourier transform infrared) spectroscopies were used to study the effect of ammonium and sulfate ions on the bulk structure of water, whereas surface sum frequency generation spectroscopy was used to study the effect of these ions on the interfacial structure of water. Analysis of the interfacial and bulk vibrational spectra reveal that aqueous solutions containing SO(4)(2-) perturb the interfacial water structure differently than the bulk and, consistent with the molecular dynamics simulations, reveal an increase in the thickness of the interfacial region.     

Hydrated hydride anion clusters

On the basis of density functional theory (DFT) and high level ab initio theory, we report the structures, binding energies, thermodynamic quantities, IR spectra, and electronic properties of the hydride anion hydrated by up to six water molecules. Ground state DFT molecular dynamics simulations (based on the Born-Oppenheimer potential surface) show that as the temperature increases, the surface-bound hydride anion changes to the internally bound structure. Car-Parrinello molecular dynamics simulations are also carried out for the spectral analysis of the monohydrated hydride. Excited-state ab initio molecular dynamics simulations show that the photoinduced charge-transfer-to-solvent phenomena are accompanied by the formation of the excess electron-water clusters and the detachment of the H radical from the clusters. The dynamics of the detachment process of a hydrogen radical upon the excitation is discussed.     

Optical absorption of methoxy and carboethoxy derivatives of 1,3-diphenyl-1H-pyrazolo[3,4-b]quinoline

Paper deals with experimental investigations and quantum chemical calculations of the optical absorption spectra of methoxy and carboethoxy 1,3-diphenyl derivatives of the pyrazoloquinoline ([PQ]): 6-methoxy-1,3-dyphenil-[PQ], 6-methoxy-1,3-(p-methoxyphenyl)-[PQ], 6-methoxy-1-(p-methoxyphenyl)-[PQ] and 6-carboethoxy-1,3-diphenyl-[PQ]. The quantum chemical calculations are performed by means of the semiempirical quantum chemical methods (AM1 or PM3) applied to: (a) the equilibrium molecular conformation in vacuo (T=0 K); (b) the molecular dynamic (MD) trajectory (T=300 K) which includes the dynamics of a certain molecular fragment (moiety) only (fragmental MD simulations); or (c) the MD trajectory obtained for most general case within the total MD simulations at T=300 K. The results of these calculations are compared with the measured spectra of the optical absorption. The quantum chemical simulations show that the dynamics of the methoxy or carboethoxy groups practically does not influence the absorption spectrum whereas the strongest its modification (300相似文献   

Theoretical Study on Co^3＋ in Aqueous Solution in Terms of ABEEM/MM Model

A detailed theoretical investigation on Co^3＋ hydration in aqueous solution has been carded out by means of molecular dynamics （MD） simulations based on the atom-bond electronegativity equalization method fused into molecular mechanics （ABEEM/MM）. The effective Co^3＋ ion-water potential has been constructed by fitting to ab initio structures and binding energies for ionic clusters. And then the ion-water interaction potential was applied in combination with the ABEEM-7P water model to molecular dynamics simulations of single Co^3＋（aq.） solution, managing to reproduce many experimental structural and dynamical properties of the solution. Here, not only the common properties （radial distribution function, angular distribution function and solvation energy） obtained for Co^3＋ in ABEEM-7P water solution were in good agreement with those from the experimental methods and other molecular dynamics simulations but also very interesting properties of charge distributions, geometries of water molecules, hydrogen bond, diffusion coefficients, vibrational spectra are investigated by ABEEM/MM model.     

Molecular dynamics modeling in quantum chemical calculations. Optical absorption spectra of 1,3-Dimethyl-1H-Pyrazolo[3,4-b]quinoline derivatives

Paper presents the quantum chemical modeling of the optical absorption spectra of 6-fluoro, 6-bromo, 7-trifluoromethyl, 6-cyano and 6-carboethoxy derivatives of 1,3-Dimethyl-1H-Pyrazolo[3,4-b]quinoline. The calculations are performed by means of the semiempirical quantum chemical methods (AM1 or PM3) in combination with molecular dynamics (MD) simulations at T=300 K. It is shown that a particular rotational dynamics of the methyl, trifluoromethyl or ethyl groups practically does not influence the optical absorption in the spectral range 200-500 nm whereas broadening of absorption bands may be well reproduced within MD simulations including all types of nuclei vibrations. The results of calculations are compared with the measured spectra of optical absorption. The quantum chemical method AM1 in combination with MD simulations gives for all dyes the best agreement between the calculated and measured spectral positions of the first absorption band (absorption threshold).     

Discontinuous molecular dynamics for rigid bodies: applications

Event-driven molecular dynamics simulations are carried out on two rigid-body systems which differ in the symmetry of their molecular mass distributions. First, simulations of methane in which the molecules interact via discontinuous potentials are compared with simulations in which the molecules interact through standard continuous Lennard-Jones potentials. It is shown that under similar conditions of temperature and pressure, the rigid discontinuous molecular dynamics method reproduces the essential dynamical and structural features found in continuous-potential simulations at both gas and liquid densities. Moreover, the discontinuous molecular dynamics approach is demonstrated to be between 3 and 100 times more efficient than the standard molecular dynamics method depending on the specific conditions of the simulation. The rigid discontinuous molecular dynamics method is also applied to a discontinuous-potential model of a liquid composed of rigid benzene molecules, and equilibrium and dynamical properties are shown to be in qualitative agreement with more detailed continuous-potential models of benzene. The few qualitative differences in the angular dynamics of the two models are related to the relatively crude treatment of variations in the discontinuous repulsive interactions as one benzene molecule rotates by another.     

Terahertz absorption of DNA decamer duplex

This work combines experimental and theoretical approaches to investigate terahertz absorption spectra of the DNA formed by the sequence oligomer 5'-CCGGCGCCGG-3'. The three-dimensional structure of this self-complimentary DNA decamer has been well-studied, permitting us to perform direct identification of the low-frequency phonon modes associated with specific conformation and to conduct comprehensive computer simulations. Two modeling techniques, normal-mode analysis and nanosecond molecular dynamics with explicit solvent molecules, were employed to extract the low-frequency vibrational modes based on which the absorption spectra were calculated. The absorption spectra of the DNA decamer in aqueous solution were measured in the frequency range 10-25 cm(-1) using the terahertz Fourier transform infrared spectroscopy. Multiple well-resolved and reproducible resonance modes were observed. When calculated and experimental spectra were compared, the spectrum based on molecular dynamics simulations showed a better correlation with the experimental spectra than the one based on normal-mode analysis. These results demonstrate that there exist a considerable number of active low-frequency phonon modes in this short DNA duplex.     

Vibrational spectra of methane clathrate hydrates from molecular dynamics simulation

Molecular dynamics simulations were performed on methane clathrate hydrates at ambient conditions. Thermal expansion results over the temperature range 60-300 K show that the unit cell volume increases with temperature in agreement with experiment. Power spectra were obtained at 273 K from velocity autocorrelation functions for selected atoms, and normal modes were assigned. The spectra were further classified according to individual atom types, allowing the assignment of contributions from methane molecules located in small and large cages within the structure I unit cell. The symmetric C-H stretch of methane in the small cages occurs at a higher frequency than for methane located in the large cages, with a peak separation of 14 cm(-1). Additionally, we determined that the symmetric C-H stretch in methane gas occurs at the same frequency as methane in the large cages. Results of molecular dynamics simulations indicate the use of power spectra obtained from the velocity autocorrelation function is a reliable method to investigate the vibrational behavior of guest molecules in clathrate hydrates.     

Effect of molecular vibrations on the MD/QC‐simulated absorption spectra

Effect of molecular vibrations on the absorption spectra simulated via a sequential approach combining molecular dynamics (MD) with quantum‐chemical calculations has been investigated. Simulated spectra have been obtained from the time‐dependent density functional theory results averaged over series of molecular geometries retrieved from Born–Oppenheimer MD trajectories. Distributions of bond lengths have been analyzed and related to the features of calculated spectra. For NVE simulations of small systems, absorption spectra exhibit bimodal bandshape as a result of classical treatment of vibrations. For NVE trajectories of larger systems or simulations in the NVT ensemble calculated absorption bands are symmetric, however, they may not agree with the results of Franck–Condon analysis. These results are practical manifestations of effects predicted theoretically from general principles. Consequences for the modeling of absorption spectra have been discussed. © 2013 Wiley Periodicals, Inc.     

Insights from first principles molecular dynamics studies toward infrared multiple-photon and single-photon action spectroscopy: case study of the proton-bound dimethyl ether dimer

We have used finite temperature ab initio molecular dynamics simulations in conjunction with computation of critical quantum nuclear effects to probe the differences between single-photon argon tagged action spectral results and infrared multiple-photon dissociation experiments for a proton bound molecular ion system. We find that the principal difference between the results in these experimental techniques is essentially that of cluster temperature. The multiple-photon dissociation experiments conducted using room temperature ions reflect a larger degree of conformational freedom compared to the colder single-photon argon tagged action spectral results. Our ab initio molecular dynamics simulation techniques accurately capture the effects of conformational sampling, adequately reproduce both spectra, and can be utilized to assign the dynamically averaged finite temperature spectra.     

Molecular dynamics with restrictions derived from optical spectra

The information about molecular structure coded in the optical spectra must often be deciphered by complicated computational procedures. A combination of spectral modeling with the molecular dynamic simulations makes the process simpler, by implicit accounting for the inhomogeneous band broadening and Boltzmann averaging of many conformations. Ideally, geometries of studied systems can be deduced by a direct confrontation of such modeling with the experiment. In this work, the comparison is enhanced by restrictions to molecular dynamics propagations based on the Raman and Raman optical activity spectra. The methodology is introduced and tested on model systems comprising idealized H(2)O(2), H(2)O(3) molecules, and the alanine zwitterion. An additional gradient term based on the spectral overlap smoothed by Fourier transformation is constructed and added to the molecular energy during the molecular dynamics run. For systems with one prevalent conformation the method did allow to enrich the Boltzmann ensemble by a spectroscopically favored structure. For systems with multiconformational equilibria families preferential conformations can be selected. An alternative algorithm based on the comparison of the averaged spectra with the reference enabling iterative updates of the conformer probabilities provided even more distinct distributions in shorter times. It also accounts for multiconformer equilibria and provided realistic spectra and conformer distribution for the alanine.     

Shielding of ionic interactions by sulfur dioxide in an ionic liquid

The effect of adding SO2 on the structure and dynamics of 1-butyl-3-methylimidazolium bromide (BMIBr) was investigated by low-frequency Raman spectroscopy and molecular dynamics (MD) simulations. The MD simulations indicate that the long-range structure of neat BMIBr is disrupted resulting in a liquid with relatively low viscosity and high conductivity, but strong correlation of ionic motion persists in the BMIBr-SO2 mixture due to ionic pairing. Raman spectra within the 5相似文献   

Excitonic effects in two-dimensional vibrational spectra of liquid formamide

The linear and two-dimensional infrared (2DIR) responses of the amide I vibrational mode in liquid formamide are investigated experimentally and theoretically using molecular dynamics simulations. The recent method based on the numerical integration of the Schr?dinger equation is employed to calculate the 2DIR spectra. Special attention is devoted to the interplay of the structural dynamics and the excitonic nature of the amide I modes in determining the optical response of the studied system. In particular, combining experimental data, simulated spectra and analysis of the simulated atomic trajectory in terms of a transition dipole coupling model, we provide a convincing explanation of the peculiar features of the 2DIR spectra, which show a substantial increase of the antidiagonal bandwidth with increasing frequency. We point out that, at variance with liquid water, the 2DIR spectral profile of formamide is determined more by the excitonic nature of the vibrational states than by the fast structural dynamics responsible for the frequency fluctuations.