Computer Simulation of Long Side‐Chain Substituted Poly(phenylene vinylene) Polymers

A molecular dynamics (MD) simulation was employed to investigate structure features and segment orientation of four poly(phenylene vinylene) (PPV) derivatives with long, flexible side chains at room temperature. In the simulations, the main chains of the polymers were found to be semirigid and exhibit a tendency to coil into ellipsoidal helices or form zigzag conformations of limited regularity. The simulations show that continuous quasi‐coplanar segments along the backbone are in a range of ≈2–4 repeat units. The ordered orientation and coupling distance of interchain aromatic rings can be correlated with optical properties of materials. A simplified quantum‐mechanical method was developed to investigate optical properties based on MD trajectories. The method was tested to simulate the absorption spectra of four PPV derivatives. The absorption maxima of the calculated spectra are in reasonable agreement with experimental data. This work implies that long‐range electron transfer along the backbones of these polymers may not occur, but may be mediated by interchain interactions.     

FMO‐MD Simulations on the Hydration of Formaldehyde in Water Solution with Constraint Dynamics

Full‐quantum mechanical fragment molecular orbital‐based molecular dynamics (FMO‐MD) simulations were applied to the hydration reaction of formaldehyde in water solution under neutral conditions. Two mechanisms, a concerted and a stepwise one, were considered with respect to the nucleophilic addition and the proton transfer. Preliminary molecular orbital calculations by means of polarized continuum model reaction field predicted that the hydration prefers a concerted mechanism. Because the calculated activation barriers were too high for free FMO‐MD simulations to give reactive trajectories spontaneously, a More O’Ferrall–Jencks‐type diagram was constructed from the statistical analysis of the FMO‐MD simulations with constraint dynamics. The diagram showed that the hydration proceeds through a zwitterionic‐like (ZW‐like) structure. The free energy changes along the reaction coordinate calculated by means of the blue moon ensemble for the hydration and the amination of formaldehyde indicated that the hydration proceeds through a concerted process through the ZW‐like structure, whereas the amination goes through a stepwise mechanism with a ZW intermediate. In inspection of the FMO‐MD trajectories, water‐mediated cyclic proton transfers were observed in both reactions on the way from the ZW‐like structure to the product. These proton transfers also have an asynchronous character, in which deprotonation from the nucleophilic oxygen atom (or nitrogen atom for amination) precedes the protonation of the carbonyl oxygen atom. The results showed the strong advantage of the FMO‐MD simulations to obtain detailed information at a molecular level for solution reactions.     

Tyrosine absorption spectroscopy: Backbone protonation effects on the side chain electronic properties

The UV–vis spectrum of Tyrosine and its response to different backbone protonation states have been studied by applying the Perturbed Matrix Method (PMM) in conjunction with molecular dynamics (MD) simulations. Herein, we theoretically reproduce the UV–vis absorption spectrum of aqueous solution of Tyrosine in its zwitterionic, anionic and cationic forms, as well as of aqua‐p‐Cresol (i.e., the moiety that constitutes the side chain portion of Tyrosine). To achieve a better accuracy in the MD sampling, the Tyrosine Force Field (FF) parameters were derived de novo via quantum mechanical calculations. The UV–vis absorption spectra are computed considering the occurring electronic transitions in the vertical approximation for each of the chromophore configurations sampled by the classical MD simulations, thus including the effects of the chromophore semiclassical structural fluctuations. Finally, the explicit treatment of the perturbing effect of the embedding environment permits to fully model the inhomogeneous bandwidth of the electronic spectra. Comparison between our theoretical–computational results and experimental data shows that the used model captures the essential features of the spectroscopic process, thus allowing to perform further analysis on the strict relationship between the quantum properties of the chromophore and the different embedding environments. © 2018 Wiley Periodicals, Inc.     

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).     

Simulations of vibrational spectra from classical trajectories: calibration with ab initio force fields

An algorithm allowing simulating vibrational spectra from classical time-dependent trajectories was applied for infrared absorption, vibrational circular dichroism, Raman, and Raman optical activity of model harmonic systems. The implementation of the theory within the TINKER molecular dynamics (MD) program package was tested with ab initio harmonic force fields in order to determine the feasibility for more extended MD simulations. The results suggest that sufficiently accurate frequencies can be simulated with integration time steps shorter than about 0.5 fs. For a given integration time step, lower vibrational frequencies ( approximately 0-2000 cm(-1)) could be reproduced with a higher accuracy than higher-frequency vibrational modes (e.g., O-H and C-H stretching). In principle, the algorithm also provides correct intensities for ideal systems. In applied simulations, however, the intensity profiles are affected by an unrealistic energy distribution between normal modes and a slow energy relaxation. Additionally, the energy fluctuations may cause weakening of the intensities on average. For ab initio force fields, these obstacles could be overcome by an arbitrary normal mode energy correction. For general MD simulations, averaging of many shorter MD trajectories started with randomly distributed atomic velocities provided the best spectral shapes. alpha-pinene, D-gluconic acid, formaldehyde dimer, and the acetylprolineamide molecule were used in the tests.     

Combination of COSMOmic and molecular dynamics simulations for the calculation of membrane–water partition coefficients

The importance of membrane‐water partition coefficients led to the recent extension of the conductor‐like screening model for realistic solvation (COSMO‐RS) to micelles and biomembranes termed COSMOmic. Compared to COSMO‐RS, this new approach needs structural information to account for the anisotropy of colloidal systems. This information can be obtained from molecular dynamics (MD) simulations. In this work, we show that this combination of molecular methods can efficiently be used to predict partition coefficients with good agreement to experimental data and enables screening studies. However, there is a discrepancy between the amount of data generated by MD simulations and the structural information needed for COSMOmic. Therefore, a new scheme is presented to extract data from MD trajectories for COSMOmic calculations. In particular, we show how to calculate the system structure from MD, the influence of lipid conformers, the relation to the COSMOmic layer size, and the water/lipid ratio impact. For a 1,2‐dimyristoyl‐sn‐glycero‐3‐phosphocholine (DMPC) bilayer, 66 partition coefficients for various solutes were calculated. Further, 52 partition coefficients for a 1‐palmitoyl‐2‐oleoyl‐sn‐glycero‐3‐phosphocholine (POPC) bilayer system were calculated. All these calculations were compared to experimental data. © 2013 Wiley Periodicals, Inc.     

Study of conformational properties of a biologically active peptide of fibronectin by circular dichroism, NMR and molecular dynamics simulation

Circular dichroism (CD), and NMR spectra have been recorded and molecular dynamics (MD) simulations have been performed in water and water-trifluoroethanol (TFE) mixed solvent for a synthetic biologically active 13-amino-acid fragment of human fibronectin and two related peptides. The CD results are interpreted on the basis of statistical analyses of MD trajectories and of ensuing calculations of CD spectra based on Schellman's matrix method. It is observed that the peptide conformation is quite variable in water and loses its mobility with the addition of TFE. (1)H-NOE data were found to be consistent with the most abundant calculated conformation.     

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.     

N2,O2水溶液光谱的分子动力学模拟

用分子动力学模拟方法研究了N2和O2水溶液的光谱性质．给出了能描述分子内部运动的溶质－溶剂相互作用势．对溶质和溶剂原子的速度自相关函数（VACF）作了计算．讨论了所得VACF的性质并计算了其谱密度．溶质分子振动谱出现的红移，与液态N2，O2的Raman实验结果相吻合．模拟得出的转动谱表明了溶剂分子对溶质转动运动的阻滞，模拟结果也表明VACF计算对溶液和液体光谱的研究十分有效．     

Molecular simulation of thermophysical properties of aromatic polymers containing oxetane ring in the main chain

Molecular simulation techniques have been applied to newly synthesized aromatic polymers, containing oxetane rings in the main chain, to characterize the shape of rod‐like macromolecules. Single chains and periodic unit cells of a series of aromatic polymers with degree of polymerization 15 were used in the simulations, in accordance with the experimentally obtained one. The total potential energy was minimized and then NVE and NPT molecular dynamics simulations were performed for 1,000 ps at 11 temperatures between 10 and 1,000 K. The coefficient of asymmetry was calculated from the computer‐generated structures. The predictive capability of the NPT molecular dynamics simulation and Polymer Properties modules of Cerius² were used to estimate the orientational properties (order parameter), glass transition temperature, cohesive energy, and decomposition temperature of the polymers simulated. In general, there is a good‐to‐excellent agreement between simulated results and available experimental data of the above investigated properties. © 1999 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 37: 2334–2352, 1999     

QM/MM calculation of solvent effects on absorption spectra of guanine

Electronic spectra of guanine in the gas phase and in water were studied by quantum mechanical/molecular mechanical (QM/MM) methods. Geometries for the excited‐state calculations were extracted from ground‐state molecular dynamics (MD) simulations using the self‐consistent‐charge density functional tight binding (SCC‐DFTB) method for the QM region and the TIP3P force field for the water environment. Theoretical absorption spectra were generated from excitation energies and oscillator strengths calculated for 50 to 500 MD snapshots of guanine in the gas phase (QM) and in solution (QM/MM). The excited‐state calculations used time‐dependent density functional theory (TDDFT) and the DFT‐based multireference configuration interaction (DFT/MRCI) method of Grimme and Waletzke, in combination with two basis sets. Our investigation covered keto‐N7H and keto‐N9H guanine, with particular focus on solvent effects in the low‐energy spectrum of the keto‐N9H tautomer. When compared with the vertical excitation energies of gas‐phase guanine at the optimized DFT (B3LYP/TZVP) geometry, the maxima in the computed solution spectra are shifted by several tenths of an eV. Three effects contribute: the use of SCC‐DFTB‐based rather than B3LYP‐based geometries in the MD snapshots (red shift of ca. 0.1 eV), explicit inclusion of nuclear motion through the MD snapshots (red shift of ca. 0.1 eV), and intrinsic solvent effects (differences in the absorption maxima in the computed gas‐phase and solution spectra, typically ca. 0.1–0.3 eV). A detailed analysis of the results indicates that the intrinsic solvent effects arise both from solvent‐induced structural changes and from electrostatic solute–solvent interactions, the latter being dominant. © 2009 Wiley Periodicals, Inc. J Comput Chem 2010     

Fluorescence spectra of organic dyes in solution: a time dependent multilevel approach

Classical all-atom molecular dynamics (MD) simulations and quantum mechanical (QM) time-dependent density functional theory (TD-DFT) calculations are employed to study the conformational and photophysical properties of the first emitter excited state of tetramethyl-rhodamine iso-thiocyanate fluorophore in aqueous solution. For this purpose, a specific and accurate force field has been parameterised from QM data to model the fluorophore's first bright excited state. During the MD simulations, the consequences of the π→π* electronic transition on the structure and microsolvation sphere of the dye has been analysed in some detail and compared to the ground state behaviour. Thereafter, fluorescence has been calculated at the TD-DFT level on configurations sampled from the simulated MD trajectories, allowing us to include time dependent solvent effects in the computed emission spectrum. The latter, when compared with the absorption spectrum, reproduces well the experimental Stokes shift, further validating the proposed multilevel computational procedure.     

Dyes in Liquid Crystals: Experimental and Computational Studies of a Guest–Host System Based on a Combined DFT and MD Approach

Practical applications of guest–host liquid crystal systems are critically dependent on the alignment of the guest species within the liquid crystal host. UV/Vis absorption spectroscopy shows that the 1,5‐dihydroxy‐2,6‐bis‐(4‐propylphenyl)‐9,10‐anthraquinone dye aligns within the E7 nematic host, giving an experimental dichroic ratio of 9.40 and dye order parameter of 0.74. This alignment was modelled by using a combination of density functional theory (DFT) and molecular dynamics (MD) computational approaches that do not require the input of experimental data. Time‐dependent DFT calculations show that the electronic transition dipole moment is highly aligned with the long molecular axis of the dye. Fully atomistic MD simulations show that the long axis of the dye is less highly aligned within the E7 host, indicating that this contribution limits the overall dye alignment and, thereby, the potential practical applications of this particular system. Importantly, this study demonstrates an experimental and combined DFT and MD computational approach that may be applied generally to guest–host systems, providing a potential route to their rational design.     

Hybrid particle‐field molecular dynamics simulations: Parallelization and benchmarks

The parallel implementation of a recently developed hybrid scheme for molecular dynamics (MD) simulations (Milano and Kawakatsu, J Chem Phys 2009, 130, 214106) where self‐consistent field theory (SCF) and particle models are combined is described. Because of the peculiar formulation of the hybrid method, considering single particles interacting with density fields, the most computationally expensive part of the hybrid particle‐field MD simulation can be efficiently parallelized using a straightforward particle decomposition algorithm. Benchmarks of simulations, including comparisons of serial MD and MD‐SCF program profiles, serial MD‐SCF and parallel MD‐SCF program profiles, and parallel benchmarks compared with efficient MD program GROMACS 4.5.4 are tested and reported. The results of benchmarks indicate that the proposed parallelization scheme is very efficient and opens the way to molecular simulations of large scale systems with reasonable computational costs. © 2012 Wiley Periodicals, Inc.     

Circular dichroism and conformational dynamics of cephams and their carba and oxa analogues

The biological activity of bicyclic beta-lactam antibiotics depends strongly on the absolute configuration of the bridgehead carbon atom. Frelek and co-workers proposed an empirical helicity rule relating the configuration of the bridgehead carbon atom to the sign of the 220 nm band in the electronic circular dichroism (CD) spectrum of beta-lactams. Here we use synthetic organic chemistry, CD spectroscopy, and time-dependent density functional theory (TDDFT) to investigate the validity of this structure-property relationship for eight model compounds. For conformationally flexible beta-lactams, substantial thermal effects are found which must be included in calculations. To this end, we combine TDDFT calculations of CD with full quantum-mechanical Born-Oppenheimer molecular dynamics (MD) simulations for the first time. The CD spectra are sampled with ground-state density functional trajectories of up to 60 ps. The MD simulations show a surprisingly high sensitivity of the CD to the molecular conformation. On the other hand, the relation between CD and thermally averaged structural parameters is much less complex. While the helicity rule does not seem to hold for individual conformers, it is confirmed by the calculations for seven out of eight systems studied if thermally averaged CD spectra and structures are considered. Since thermal effects on CD can be larger than typical inherent inaccuracies of TDDFT, our results emphasize the need for a systematic treatment of conformational dynamics in CD calculations even for moderately flexible systems. Temperature-dependent CD measurements are very useful for this purpose. Our results also suggest that CD spectroscopy may be used as a sensitive probe of conformational dynamics if combined with electronic structure calculations.     

Influence of Intermolecular Vibrations on the Electronic Coupling in Organic Semiconductors: The Case of Anthracene and Perfluoropentacene

We have performed classical molecular dynamics simulations and quantum‐chemical calculations on molecular crystals of anthracene and perfluoropentacene. Our goal is to characterize the amplitudes of the room‐temperature molecular displacements and the corresponding thermal fluctuations in electronic transfer integrals, which constitute a key parameter for charge transport in organic semiconductors. Our calculations show that the thermal fluctuations lead to Gaussian‐like distributions of the transfer integrals centered around the values obtained for the equilibrium crystal geometry. The calculated distributions have been plugged into Monte‐Carlo simulations of hopping transport, which show that lattice vibrations impact charge transport properties to various degrees depending on the actual crystal structure.     

Overcoming dissipation in the calculation of standard binding free energies by ligand extraction

This article addresses calculations of the standard free energy of binding from molecular simulations in which a bound ligand is extracted from its binding site by steered molecular dynamics (MD) simulations or equilibrium umbrella sampling (US). Host–guest systems are used as test beds to examine the requirements for obtaining the reversible work of ligand extraction. We find that, for both steered MD and US, marked irreversibilities can occur when the guest molecule crosses an energy barrier and suddenly jumps to a new position, causing dissipation of energy stored in the stretched molecule(s). For flexible molecules, this occurs even when a stiff pulling spring is used, and it is difficult to suppress in calculations where the spring is attached to the molecules by single, fixed attachment points. We, therefore, introduce and test a method, fluctuation‐guided pulling, which adaptively adjusts the spring's attachment points based on the guest's atomic fluctuations relative to the host. This adaptive approach is found to substantially improve the reversibility of both steered MD and US calculations for the present systems. The results are then used to estimate standard binding free energies within a comprehensive framework, termed attach‐pull‐release, which recognizes that the standard free energy of binding must include not only the pulling work itself, but also the work of attaching and then releasing the spring, where the release work includes an accounting of the standard concentration to which the ligand is discharged. © 2013 Wiley Periodicals, Inc.