Search

Biased and accelerated molecular simulations (BAMS) are widely used tools to observe relevant molecular phenomena occurring on time scales inaccessible to standard molecular dynamics, but evaluation of the physical time scales involved in the processes is not directly possible from them. For this reason, the problem of recovering dynamics from such kinds of simulations is the object of very active research due to the relevant theoretical and practical implications of dynamics on the properties of both natural and synthetic molecular systems. In a recent paper [A. Rapallo et al., J. Comput. Chem. 42, 586–599 (2021)], it has been shown how the coupling of BAMS (which destroys the dynamics but allows to calculate average properties) with Extended Diffusion Theory (EDT) (which requires input appropriate equilibrium averages calculated over the BAMS trajectories) allows to effectively use the Smoluchowski equation to calculate the orientational time correlation function of the head–tail unit vector defined over a peptide in water solution. Orientational relaxation of this vector is the result of the coupling of internal molecular motions with overall molecular rotation, and it was very well described by correlation functions expressed in terms of weighted sums of suitable time-exponentially decaying functions, in agreement with a Brownian diffusive regime. However, situations occur where exponentially decaying functions are no longer appropriate to capture the actual dynamical behavior, which exhibits persistent long time correlations, compatible with the so called subdiffusive regimes. In this paper, a generalization of EDT will be given, exploiting a fractional Smoluchowski equation (FEDT) to capture the non-exponential character observed in the relaxation of intramolecular distances and molecular radius of gyration, whose dynamics depend on internal molecular motions only. The calculation methods, proper to EDT, are adapted to implement the generalization of the theory, and the resulting algorithm confirms FEDT as a tool of practical value in recovering dynamics from BAMS, to be used in general situations, involving both regular and anomalous diffusion regimes. [ABSTRACT FROM AUTHOR]

The first paper of this series [J. Chem. Phys. 158, 034103 (2023)] demonstrated that excess entropy scaling holds for both fine-grained and corresponding coarse-grained (CG) systems. Despite its universality, a more exact determination of the scaling relationship was not possible due to the semi-empirical nature. In this second paper, an analytical excess entropy scaling relation is derived for bottom-up CG systems. At the single-site CG resolution, effective hard sphere systems are constructed that yield near-identical dynamical properties as the target CG systems by taking advantage of how hard sphere dynamics and excess entropy can be analytically expressed in terms of the liquid packing fraction. Inspired by classical equilibrium perturbation theories and recent advances in constructing hard sphere models for predicting activated dynamics of supercooled liquids, we propose a new approach for understanding the diffusion of molecular liquids in the normal regime using hard sphere reference fluids. The proposed "fluctuation matching" is designed to have the same amplitude of long wavelength density fluctuations (dimensionless compressibility) as the CG system. Utilizing the Enskog theory to derive an expression for hard sphere diffusion coefficients, a bridge between the CG dynamics and excess entropy is then established. The CG diffusion coefficient can be roughly estimated using various equations of the state, and an accurate prediction of accelerated CG dynamics at different temperatures is also possible in advance of running any CG simulation. By introducing another layer of coarsening, these findings provide a more rigorous method to assess excess entropy scaling and understand the accelerated CG dynamics of molecular fluids. [ABSTRACT FROM AUTHOR]

This paper series aims to establish a complete correspondence between fine-grained (FG) and coarse-grained (CG) dynamics by way of excess entropy scaling (introduced in Paper I). While Paper II successfully captured translational motions in CG systems using a hard sphere mapping, the absence of rotational motions in single-site CG models introduces differences between FG and CG dynamics. In this third paper, our objective is to faithfully recover atomistic diffusion coefficients from CG dynamics by incorporating rotational dynamics. By extracting FG rotational diffusion, we unravel, for the first time reported to our knowledge, a universality in excess entropy scaling between the rotational and translational diffusion. Once the missing rotational dynamics are integrated into the CG translational dynamics, an effective translation-rotation coupling becomes essential. We propose two different approaches for estimating this coupling parameter: the rough hard sphere theory with acentric factor (temperature-independent) or the rough Lennard-Jones model with CG attractions (temperature-dependent). Altogether, we demonstrate that FG diffusion coefficients can be recovered from CG diffusion coefficients by (1) incorporating "entropy-free" rotational diffusion with translation-rotation coupling and (2) recapturing the missing entropy. Our findings shed light on the fundamental relationship between FG and CG dynamics in molecular fluids. [ABSTRACT FROM AUTHOR]

In a recent paper [Aschi et al., ChemPhysChem 6, 53 (2005)], we characterized, by means of theoretical-computational procedures, the electronic excitation of water along the typical liquid state isochore (55.32 mol/l) for a large range of temperature. In that paper we were able to accurately reproduce the experimental absorption maximum at room temperature and to provide a detailed description of the temperature dependence of the excitation spectrum along the isochore. In a recent experimental work by Marin et al. [J. Chem. Phys. 125, 104314 (2006)], water electronic excitation energy was carefully analyzed in a broad range of density and temperature, finding a remarkable agreement of the temperature behavior of the experimental data with our theoretical results. Here, by means of the same theoretical-computational procedures (molecular dynamics simulations and the perturbed matrix method), we investigate water electronic absorption exactly in the same density-temperature range used in the experimental work, hence, now considering also the absorption density dependence. Our results point out that, (1) for all the densities and temperatures investigated, our calculated absorption spectra are in very good agreement with the experimental ones and (2) the gradual maxima redshift observed increasing the temperature or decreasing the density has to be ascribed to a real shift of the lowest X→A electronic transition, supporting the conclusions of Marin et al. [ABSTRACT FROM AUTHOR]

Protein folding in confined media has attracted wide attention over the past 15 years due to its importance to both in vivo and in vitro applications. It is generally believed that protein stability increases by decreasing the size of the confining medium, if the medium’s walls are repulsive, and that the maximum folding temperature in confinement is in a pore whose size D0 is only slightly larger than the smallest dimension of a protein’s folded state. Until recently, the stability of proteins in pores with a size very close to that of the folded state has not received the attention it deserves. In a previous paper [L. Javidpour and M. Sahimi, J. Chem. Phys. 135, 125101 (2011)], we showed that, contrary to the current theoretical predictions, the maximum folding temperature occurs in larger pores for smaller α-helices. Moreover, in very tight pores, the free energy surface becomes rough, giving rise to a new barrier for protein folding close to the unfolded state. In contrast to unbounded domains, in small nanopores proteins with an α-helical native state that contain the β structures are entropically stabilized implying that folding rates decrease notably and that the free energy surface becomes rougher. In view of the potential significance of such results to interpretation of many sets of experimental data that could not be explained by the current theories, particularly the reported anomalously low rates of folding and the importance of entropic effects on proteins’ misfolded states in highly confined environments, we address the following question in the present paper: To what extent the geometry of a confined medium affects the stability and folding rates of proteins? Using millisecond-long molecular dynamics simulations, we study the problem in three types of confining media, namely, cylindrical and slit pores and spherical cavities. Most importantly, we find that the prediction of the previous theories that the dependence of the maximum folding temperature Tf on the size D of a confined medium occurs in larger media for larger proteins is correct only in spherical geometry, whereas the opposite is true in the two other geometries that we study. Also studied is the effect of the strength of the interaction between the confined media’s walls and the proteins. If the walls are only weakly or moderately attractive, a complex behavior emerges that depends on the size of the confining medium. [ABSTRACT FROM AUTHOR]

Stable crystalline structures of confined water can be different from bulk ice. In Paper I [T. Yagasaki et al., J. Chem. Phys. 151, 064702 (2019)] of this study, it was shown, using molecular dynamics (MD) simulations, that a zeolite-like ice structure forms in nanobrushes consisting of (6,6) carbon nanotubes (CNTs) when the CNTs are located in a triangle arrangement. The melting temperature of the zeolite-like ice structure is much higher than the melting temperature of ice Ih when the distance between the surfaces of CNTs is ∼0.94 nm, which is the best spacing for the bilayer structure of water. In this paper, we perform MD simulations of nanobrushes of CNTs that are different from (6,6) CNTs in radius. Several new porous ice structures form spontaneously in the MD simulations. A stable porous ice forms when the radius of its cavities matches the radius of the CNTs well. All cylindrical porous ice structures found in this study can be decomposed into a small number of structural blocks. We provide a new protocol to classify cylindrical porous ice crystals on the basis of this decomposition. [ABSTRACT FROM AUTHOR]

This work follows a companion article, which will be referred to as Paper I [Campeggio et al., J. Chem. Phys. 158, 244104 (2023)] in which a quantum-stochastic Liouville equation for the description of the quantum–classical dynamics of a molecule in a dissipative bath has been formulated in curvilinear internal coordinates. In such an approach, the coordinates of the system are separated into three subsets: the quantum coordinates, the classical relevant nuclear degrees of freedom, and the classical irrelevant (bath) coordinates. The equation has been derived in natural internal coordinates, which are bond lengths, bond angles, and dihedral angles. The resulting equation needs to be parameterized. In particular, one needs to compute the potential energy surfaces, the friction tensor, and the rate constants for the nonradiative jumps among the quantum states. While standard methods exist for the calculation of energy and dissipative properties, an efficient evaluation of the transition rates needs to be developed. In this paper, an approximated treatment is introduced, which leads to a simple explicit formula with a single adjustable parameter. Such an approximated expression is compared with the exact calculation of transition rates obtained via molecular dynamics simulations. To make such a comparison possible, a simple sandbox system has been used, with two quantum states and a single internal coordinate (together with its conjugate momentum). Results show that the adjustable parameter, which is an effective decoherence time, can be parameterized from the effective relaxation times of the autocorrelation functions of the conjugated momenta of the relevant nuclear coordinates. [ABSTRACT FROM AUTHOR]

Ninety years ago, Wigner derived the leading order expansion term in ℏ2 for the tunneling rate through a symmetric barrier. His derivation included two contributions: one came from the parabolic barrier, but a second term involved the fourth-order derivative of the potential at the barrier top. He left us with a challenge, which is answered in this paper, to derive the same but for an asymmetric barrier. A crucial element of the derivation is obtaining the ℏ2 expansion term for the projection operator, which appears in the flux-side expression for the rate. It is also reassuring that an analytical calculation of semiclassical transition state theory (TST) reproduces the anharmonic corrections to the leading order of ℏ2. The efficacy of the resulting expression is demonstrated for an Eckart barrier, leading to the conclusion that especially when considering heavy atom tunneling, one should use the expansion derived in this paper, rather than the parabolic barrier approximation. The rate expression derived here reveals how the classical TST limit is approached as a function of ℏ and, thus, provides critical insights to understand the validity of popular approximate theories, such as the classical Wigner, centroid molecular dynamics, and ring polymer molecular dynamics methods. [ABSTRACT FROM AUTHOR]

Erratum: "Physics-based, neural network force fields for reactive molecular dynamics: Investigation of carbene formation from [EMIM+][OAc-]" [J. Chem. Phys. We have recomputed the PMFs with AIMD, utilizing a consistent collective variable definition of Eq. (1). This was done using the plumed/ASE interface with a CP2K calculator.[[2], [5]] Corrected PMFs that employ the collective variable of Eq. (1) for all calculations are shown in the corrected Fig. [Extracted from the article]

Vibrational spectroscopy is a useful technique for probing chemical environments. The development of models that can reproduce the spectra of nitriles and azides is valuable because these probes are uniquely suited for investigating complex systems. Empirical vibrational spectroscopic maps are commonly employed to obtain the instantaneous vibrational frequencies during molecular dynamics simulations but often fail to adequately describe the behavior of these probes, especially in its transferability to a diverse range of environments. In this paper, we demonstrate several reasons for the difficulty in constructing a general-purpose vibrational map for methyl thiocyanate (MeSCN), a model for cyanylated biological probes. In particular, we found that electrostatics alone are not a sufficient metric to categorize the environments of different solvents, and the dominant features in intermolecular interactions in the energy landscape vary from solvent to solvent. Consequently, common vibrational mapping schemes do not cover all essential interaction terms adequately, especially in the treatment of van der Waals interactions. Quantum vibrational perturbation (QVP) theory, along with a combined quantum mechanical and molecular mechanical potential for solute–solvent interactions, is an alternative and efficient modeling technique, which is compared in this paper, to yield spectroscopic results in good agreement with experimental FTIR. QVP has been used to analyze the computational data, revealing the shortcomings of the vibrational maps for MeSCN in different solvents. The results indicate that insights from QVP analysis can be used to enhance the transferability of vibrational maps in future studies. [ABSTRACT FROM AUTHOR]