Applying efficient implicit nongeometric constraints in alchemical free energy simulations

Several strategies have been developed for satisfying bond lengths, angle, and other geometric constraints in molecular dynamics simulations. Advanced variations of alchemical free energy perturbation simulations, however, also require nongeometric constraints. In our recently developed multisite λ-dynamics simulation method, the conventional λ parameters that are associated with the progress variables in alchemical transformations are treated as dynamic variables and are constrained such that: 0 ≤ λ(i) ≤ 1 and Σ(i = 1)(N) λ(i) = 1. Here, we present four functional forms of λ that implicitly satisfy these nongeometric constraints, whose values and forces are facile to compute and that yield stable simulations using a 2 fs integration timestep. Using model systems, we present the sampling characteristics of these functional forms and demonstrate the enhanced sampling profiles and improved convergence rates that are achieved by the functional form: λ(i) = e(c sinθ(i))/Σ(j = 1)(N) e(c sinθ(j)) that oscillates between λ(i) = 0 and λ(i) = 1 and has relatively steep transitions between these endpoints.     

A comparison of attack angle dependence of exchange channel of reaction H + HS (v = 0, 1; j = 0) on 3A″ and 3A′ surfaces

In this theoretical work, we report quasiclassical dynamics predictions for the attack angle‐dependence exchange processes for the H + HS (v = 0, 1; j = 0) reaction by using the new triplet 3A″ and 3A′ potential energy surfaces, respectively. The calculated quasiclassical reaction probabilities of exchange reaction channel of reaction H(D)′ + H(D)S for J = 0, 10, 20, 30, 40 are in good agreement with quantum wave packet results over the collision energy range from 0.1 to 2.0 eV on 3A″ surfaces. The attack angle dependence reaction probability of the title reactions at J = 0 are calculated, respectively, on the two surfaces. The reaction probability was found to be strongly dependent on the attack angle. It may be ascribe to the significant difference of the effective potential barrier height in the two reactions. Besides, the reaction probabilities of exchange reaction channel of reaction H(D)′ + H(D)S for J = 0, 10, 20, 30, 40 are also predicted on 3A′ surfaces. © 2013 Wiley Periodicals, Inc.     

Molecular dynamics of minimal B‐DNA

Stable and accurate molecular dynamics (MD) of B‐DNA duplexes can be obtained in inexpensive computational conditions where only the minor groove is filled with water while the bulk solvent is represented implicitly. This model system presents significant theoretical as well as practical interest because, due to its simplicity and exceptional computational performance, it can be employed in simulations of very long DNA fragments. To better understand its properties and clarify the physical background of the effects produced by the limited water shell, dynamics of several different DNA oligomers was studied. It is found that optimal simulation conditions are reached when the explicit water is confined within the minor groove while the major groove is cleaned periodically. The internal solvent mobility appears high enough to observe in the nanosecond time scale spontaneous formation of sequence‐specific hydration patterns known from experiments. It is shown that the model produces stable MD trajectories close to the B‐DNA form regardless of the base pair sequence and that, on the other hand, the dynamics are strongly sequence dependent. Independent observations suggest that B‐DNA with only minor groove hydrated resembles its natural thermodynamic state at low water concentration; therefore, this model system can be tentatively called “minimal B‐DNA.” © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 457–467, 2001     

Solvation Dynamics of a Single Water Molecule Probed by Infrared Spectra—Theory Meets Experiment

The dynamics and energetics of water at interfaces or in biological systems plays a fundamental role in all solvation and biological phenomena in aqueous solution. In particular, the migration of water molecules is the first step that controls the overall process in the time domain. Experimentally, the dynamics of individual water molecules is nearly impossible to follow in solution, because signals from molecules in heterogeneous environments overlap. Although molecular dynamics simulations do not have this restriction, there is a lack of experimental data to validate the calculated dynamics. Here, we demonstrate a new strategy, in which the calculated dynamics are verified by measured time‐resolved infrared spectra. The coexistence of fast and slow migrations of water molecules around a CONH peptide linkage is revealed for a model system representative of a hydrate peptide.     

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.     

Chemical reaction dynamics of PeCB and TCDD decomposition: A tight‐binding quantum chemical molecular dynamics study with first‐principles parameterization

The decomposition reaction dynamics of 2,3,4,4′,5‐penta‐chlorinated biphenyl (2,3,4,4′,5‐PeCB), 3,3′,4,4′,5‐penta‐chlorinated biphenyl (3,3′,4,4′,5‐PeCB), and 2,3,7,8‐tetra‐chlorinated dibenzo‐p‐dioxin (2,3,7,8‐TCDD) was clarified for the first time at atomic and electronic levels, using our novel tight‐binding quantum chemical molecular dynamics method with first‐principles parameterization. The calculation speed of our new method is over 5000 times faster than that of the conventional first‐principles molecular dynamics method. We confirmed that the structure, energy, and electronic states of the above molecules calculated by our new method are quantitatively consistent with those by first‐principles calculations. After the confirmation of our methodology, we investigated the decomposition reaction dynamics of the above molecules and the calculated dynamic behaviors indicate that the oxidation of the 2,3,4,4′,5‐PeCB, 3,3′,4,4′,5‐PeCB, and 2,3,7,8‐TCDD proceeds through an epoxide intermediate, which is in good agreement with the previous experimental reports and consistent with our static density functional theory calculations. These results proved that our new tight‐binding quantum chemical molecular dynamics method with first‐principles parameterization is an effective tool to clarify the chemical reaction dynamics at reaction temperatures. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Self‐Assembly of Bare/Polymer‐Grafted Nanoparticle Blends in Homopolymer

The self‐assembly of a binary blend of nanoparticles in a homopolymer matrix using molecular dynamics (MD) simulations is studied here. The systems consist of polymer matrix, “bare” ungrafted spherical nanoparticles and polymer‐grafted nanoparticles, where the particle cores are identical and grafted chains are similar to matrix polymer. It is observed that addition of grafted nanoparticles to a blend of polymer and bare particles can result in the formation of anisotropic structures. By carefully selecting the graft density and molecular weight of the grafted chains, the clusters go from spherical to cylindrical to branched cylinders. This study suggests that it is indeed possible to control the morphology of bare nanoparticles in polymer without directly modifying their surface properties. It is believed that this phenomenon might be of high importance, especially in cases such as polymer‐based solar cells, where it is not feasible to graft the nanoparticles with polymer chains to achieve a greater level of control over the morphology.

     

Vibrational dynamics of hydrogen‐bonded HCN complexes with OH and NH acids: Computational DFT systematic study

Vibrational properties (band position, infrared [IR], and Raman intensities) of C?N stretching mode were studied in 65 gas phase hydrogen‐bonded 1:1 complexes of HCN with OH acids and NH acids using density functional theory (DFT) calculations at the B3LYP‐6‐311++G(d,p) level. Furthermore, general characteristics of the hydrogen bonds and vibrational changes in acids OH/NH stretching bands were also considered. Experimentally observed blue shift of the C?N stretching band promoted by hydrogen bonding, which shortens the triple bond length, is very well reproduced and quantitatively depends on the hydrogen bond length. Both IR and Raman ν(C?N) band intensities are enhanced, also in good agreement with the experimental results. IR intensity increase is a direct function of the hydrogen bond energy. However, the predicted Raman intensity raise is a more complex function, depending simultaneously on characteristics of both the hydrogen bond (C?N bond length) and the H‐donating acid (polarizability). With these two parameters, ν (C?N) Raman intensities of the complexes are explained with a mean error of ±2.4%. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

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.     

Reconstruction of atomistic details from coarse‐grained structures

We present an algorithm to reconstruct atomistic structures from their corresponding coarse‐grained (CG) representations and its implementation into the freely available molecular dynamics (MD) program package GROMACS. The central part of the algorithm is a simulated annealing MD simulation in which the CG and atomistic structures are coupled via restraints. A number of examples demonstrate the application of the reconstruction procedure to obtain low‐energy atomistic structural ensembles from their CG counterparts. We reconstructed individual molecules in vacuo (NCQ tripeptide, dipalmitoylphosphatidylcholine, and cholesterol), bulk water, and a WALP transmembrane peptide embedded in a solvated lipid bilayer. The first examples serve to optimize the parameters for the reconstruction procedure, whereas the latter examples illustrate the applicability to condensed‐phase biomolecular systems. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Dynamics in the crystalline polymorphic forms I and II and form III of isotactic poly‐1‐butene

Following an earlier study of the ¹H relaxation and NMR line shapes, we have carried out selective one‐dimensional and two‐dimensional ¹³C solid‐state NMR studies that yield to detailed interpretation of the dynamics in form I, II, and III polymorphs of isotactic poly‐1‐butene. A specific defect diffusion along the side group is proposed to account for the temperature dependence of the ¹³C spectra in form I. The backbone of the helix in forms II and III is shown to undergo large angle motions above the glass‐transition temperature. High‐resolution solid‐state ¹³C two‐dimensional exchange NMR under magic‐angle spinning with cross‐polarization techniques demonstrates the existence of slow rotational jumps of the helices in form III with typical jump rates of about 10 s⁻¹. © 2000 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 38: 2611–2624, 2000     

Nuclear quantum effects induce metallization of dense solid molecular hydrogen

We present an accurate computational study of the electronic structure and lattice dynamics of solid molecular hydrogen at high pressure. The band‐gap energies of the , Pc, and structures at pressures of 250, 300, and 350 GPa are calculated using the diffusion quantum Monte Carlo (DMC) method. The atomic configurations are obtained from ab initio path‐integral molecular dynamics (PIMD) simulations at 300 K and 300 GPa to investigate the impact of zero‐point energy and temperature‐induced motion of the protons including anharmonic effects. We find that finite temperature and nuclear quantum effects reduce the band‐gaps substantially, leading to metallization of the and Pc phases via band overlap; the effect on the band‐gap of the structure is less pronounced. Our combined DMC‐PIMD simulations predict that there are no excitonic or quasiparticle energy gaps for the and Pc phases at 300 GPa and 300 K. Our results also indicate a strong correlation between the band‐gap energy and vibron modes. This strong coupling induces a band‐gap reduction of more than 2.46 eV in high‐pressure solid molecular hydrogen. Comparing our DMC‐PIMD with experimental results available, we conclude that none of the structures proposed is a good candidate for phases III and IV of solid hydrogen. © 2017 Wiley Periodicals, Inc.     

Molecular Motion of the Junction Points in Model Networks Prepared by Acyclic Triene Metathesis

The junction dynamics in a selectively deuterated model polymer network containing junctions on every 21st chain carbon is studied by solid state ²H echo NMR. Polymer networks are prepared via acyclic triene metathesis of deuteron‐labeled symmetric trienes with deuteron probes precisely placed at the alpha carbon relative to the junction point. The effect of decreasing the cross‐link density on the junction dynamics is studied by introduction of polybutadiene chains in‐between junctions. The networks are characterized by swelling, gel content, and solid state ¹H MAS NMR. Line shape analysis of the ²H quadrupolar echo spectra reveals that the degree of motion anisotropy and the distribution of motion correlation times depend on the cross‐link density and structural heterogeneity of the polymer networks. A detailed model of the junction dynamics at different temperatures is proposed and explained in terms of the intermolecular cooperativity in densely‐packed systems.

     

Short‐time elasticity of polymer melts: Tobolsky conjecture and heterogeneous local stiffness

An extended molecular‐dynamics study of the short‐time “glassy” elasticity exhibited by a polymer melt of linear fully‐flexible chains above the glass transition is presented. The focus is on the infinite‐frequency shear modulus G_∞ manifested in the picosecond time scale and the relaxed plateau G_p reached at later times and terminated by the structural relaxation. The local stiffness of the interactions with the first neighbors of each monomer exhibits marked distribution with average value given by G_∞. In particular, the neighborhood of the end monomers of each chain are softer than the one of the inner monomers, so that G_∞ increases with the chain length. G_p is not affected by the chain length and is largely set by the nonbonding interactions, thus confirming for polymer melts the conjecture formulated by Tobolsky for glassy polymers. © 2015 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2015 , 53, 1401–1407     

Conformational Preferences of a β‐Octapeptide as Function of Solvent and Force‐Field Parameters

The ability to design properly folded β‐peptides with specific biological activities requires detailed insight into the relationship between the amino acid sequence and the secondary and/or tertiary structure of the peptide. One of the most frequently used spectroscopic techniques for resolving the structure of a biomolecule is NMR spectroscopy. Because only signal intensities and frequencies are recorded in the experiment, a conformational interpretation of the recorded data is not straightforward, especially for flexible molecules. The occurrence of conformational and/or time averaging, and the limited amount and accuracy of experimental data hamper the precise conformational determination of a biomolecule. In addition, the relation between experimental observables with the underlying conformational ensemble is often only approximately known, thereby aggravating the difficulty of structure determination of biomolecules. The problematic aspects of structure refinement based on NMR nuclear Overhauser effect (NOE) intensities and ³J‐coupling data are illustrated by simulating a β‐octapeptide in explicit MeOH and H₂O as solvents using three different force fields. NMR Data indicated that this peptide would fold into a 3₁₄‐helix in MeOH and into a hairpin in H₂O. Our analysis focused on the conformational space visited by the peptide, on structural properties of the peptide, and on agreement of the MD trajectories with available NMR data. We conclude that 1) although the 3₁₄‐helical structure is present when the peptide is solvated in MeOH, it is not the only relevant conformation, and that 2) the NMR data set available for the peptide, when solvated in H₂O, does not provide sufficient information to derive a single secondary structure, but rather a multitude of folds that fulfill the NOE data set.     

Structural fluctuation and concerted motions in F1‐ATPase: A molecular dynamics study

F₁‐ATPase is an adenosine tri‐phosphate (ATP)‐driven rotary motor enzyme. We investigated the structural fluctuations and concerted motions of subunits in F₁‐ATPase using molecular dynamics (MD) simulations. An MD simulation for the α₃β₃γ complex was carried out for 30 ns. Although large fluctuations of the N‐terminal domain observed in simulations of the isolated β_E subunit were suppressed in the complex simulation, the magnitude of fluctuations in the C‐terminal domain was clearly different among the three β subunits (β_E, β_TP, and β_DP). Despite fairly similar conformations of the β_TP and β_DP subunits, the β_DP subunit exhibits smaller fluctuations in the C‐terminal domain than the β_TP subunit due to their dissimilar interface configurations. Compared with the β_TP subunit, the β_DP subunit stably interacts with both the adjacent α_DP and α_E subunits. This sandwiched configuration in the β_DP subunit leads to strongly correlated motions between the β_DP and adjacent α subunits. The β_DP subunit exhibits an extensive network of highly correlated motions with bound ATP and the γ subunit, as well as with the adjacent α subunits, suggesting that the structural changes occurring in the catalytically active β_DP subunit can effectively induce movements of the γ subunit. © 2010 Wiley Periodicals, Inc. J Comput Chem 2010