Journal of Chemical Theory and Computation最新文献

This work provides a comprehensive analysis of the structural, dynamic, and thermodynamic properties of liquid crystals (LCs) along with their evolution through phase transitions and mesophases. A model of purely repulsive semiflexible spherocylinders is used in a molecular dynamics scheme through simulations involving NPT and NVT combinations. The two-phase thermodynamic model was used to obtain the translational, rotational, and vibrational density of states as well as the absolute values of thermodynamic parameters. We show evidence that during the isotropic-nematic-smectic-solid transitions, the translational diffusion coefficient becomes anisotropic, initially increasing by 15% in the nematic mesophase with a 129% rise along the director vector. Subsequent transitions result in a reduction of the diffusion coefficient by 42% in the smectic phase and 90% in the crystalline phase. Rotational diffusion decreases across all transitions (12, 35, and 26% for nematic, smectic, and solid transitions), although a notable increase in rotation around the principal axis is observed during the last transition. Thermodynamic analysis reveals that the primary contribution to the Gibbs free energy arises from the mechanical term (PV). With regard to the components, rotational motion is the dominant contribution to the Helmholtz free energy in the first transition, while translational motion dominates in the last transition. For the intermediate transition, translational, rotational, and vibrational contributions are comparable. A thorough analysis has been conducted into the Cartesian projections and the principal axes of rotation, in addition to the "solid and gas components" from the two-phase thermodynamic model analysis.

Many-body expansions of the electron density and Fock matrix in the fragment molecular orbital method (FMO) are used to reveal the role of polarization and charge transfer on noncovalent interactions (NCI). In addition to the physicochemical insight gained from these analyses, the use of FMO permits a rapid evaluation of electron densities to study NCI. The developed method is applied to a solvated sodium cation and a small polypeptide, validating the accuracy of the approach with respect to full calculations and revealing the role of polarization and charge transfer in NCI. In order to show the full potential of the approach, the FMO/NCI method is applied to a complex of the Trp-cage (PDB: 1L2Y) protein with a ligand, delivering fruitful insights into binding from both density and energy perspectives. NCI is shown to provide a comprehensive visual picture of interactions that might be missed without it, in particular, interactions between functional groups in a fragment.

Theoretical studies on enhancement mechanisms of surface-enhanced Raman scattering (SERS) are usually carried out with full quantum mechanical methods to capture the specific interactions between molecules and substrates. However, due to the computational costs of methods like time-dependent density functional theory (TDDFT), simplified model systems are commonly adopted. In the framework of TDDFT, the damped response theory is usually invoked to give a unified description of both on- and off-resonance Raman spectra based on the calculation of polarizability derivatives. However, the computational costs of full TDDFT allow for modeling SERS spectra only using small metal clusters. In this work, we demonstrate the implementation of an efficient method that simplifies the damped response calculations for the simulation of both on- and off-resonance SERS spectra. This simplified damped response method is named as TBAOResponse. We first compare the absorption spectra of a regular small system calculated with TBAOResponse and full TDDFT to benchmark the new method. Then, we demonstrate the efficiency and accuracy of the new method by comparing the on- and off-resonance SERS spectra calculated with different methods. Compared to full TDDFT, while significant improvement of efficiency is achieved, the simplified damped response maintains good accuracy for SERS calculation. We further showcase the efficiency of TBAOResponse by calculating the SERS spectra for a system that is computationally demanding with full TDDFT. This new method is promising for modeling SERS systems when a full quantum mechanical description of both the substrate and the molecule is necessary.

Understanding the quantum dynamics of strongly coupled molecule-cavity systems remains a significant challenge in molecular polaritonics. This work develops a comprehensive self-consistent model simulating electromagnetic interactions of diatomic molecules with quantum rovibrational degrees of freedom in resonant optical cavities. The approach employs an efficient numerical methodology to solve coupled Schrödinger-Maxwell equations in real spacetime, enabling three-dimensional simulations through a novel molecular mapping technique. The study investigates the relaxation dynamics of an ensemble of molecules following intense resonant pump excitation in Fabry-Perot cavities and at three-dimensional plasmonic metasurfaces. The simulations reveal dramatically modified relaxation pathways inside cavities compared to free space, characterized by persistent molecular alignment arising from cavity-induced rotational pumping. They also indicate the presence of a previously unreported relaxation stabilization mechanism driven by dephasing of the collective molecular-cavity mode. Additionally, the study demonstrates that strong molecular coupling significantly modifies the circular dichroism spectra of chiral metasurfaces, suggesting new opportunities for controlling light-matter interactions in quantum optical systems.

We present here an extension of the monomer transition density approach to spin multiplicity-altering excitation energy transfer (EET) processes. It builds upon complex-valued wave functions of the density functional theory-based multireference spin-orbit coupling configuration interaction method for generating the one-particle transition density matrices of the donor and acceptor molecules, which are then contracted with two-electron Coulomb and exchange integrals of the dimer. Due to the extensive use of symmetry relations between tensor components, the computation of triplet-singlet coupling remains technically feasible. As a proof-of-principle application, we have chosen an EET system, consisting of the phosphorescent platinum complex AG97 as the donor and the fluorescein derivative FITC as the acceptor. Taking experimental conditions into account, we estimate a Förster radius of about 35 Å. For intermolecular donor-acceptor separations close to the Förster radius and beyond, the error introduced by the ideal dipole approximation is rather small.

We present a comprehensive theory for a novel method to discretize the spectral density of a bosonic heat bath, as introduced in [Takahashi, H.; Borrelli, R. J. Chem. Phys. 2024, 161, 151101]. The approach leverages a low-rank decomposition of the Fourier-transform relation connecting the bath correlation function to its spectral density. By capturing the time, frequency, and temperature dependencies encoded in the spectral density-autocorrelation function relation, our method significantly reduces the degrees of freedom required for simulating open quantum system dynamics. We benchmark our approach against existing methods and demonstrate its efficacy through applications to both simple models and a realistic electron transfer process in biological systems. Additionally, we show that this new approach can be effectively combined with the tensor-train formalism to investigate the quantum dynamics of systems interacting with complex non-Markovian environments. Finally, we provide a perspective on the selection and application of various spectral density discretization techniques.

Adhesion of biological cells is essential for various processes, including tissue formation, immune responses, and signaling. It involves multiple length scales, ranging from nanometers to micrometers, which are characteristic of (a) the intercellular receptor-ligand binding that mediates the cell adhesion, (b) the spatial distribution of the receptor and ligand proteins in the membranes of adhering cells, (c) adhesion-induced deformations and thermal undulations of the membranes, (d) the overall size of the interface between adhering cells. Therefore, computer simulations of cell membrane adhesion require multiscale modeling and suitable approximations that capture the essential physics of the system under study. Here, we introduce such a multiscale approach to study membrane adhesion mediated by the CD47-SIRPα binding, which is an immunologically relevant process. The synergetic use of coarse-grained molecular dynamics simulations and mesoscale kinetic Monte Carlo simulations allows us to explore both equilibrium properties and dynamical behavior of adhering membranes on the relevant length scales between 1 nm and 1 μm on time scales ranging from 0.1 ns all the way up to about 20 s. The multiscale simulations not only reproduce available experimental data but also give quantitative predictions on binding-induced conformational changes of SIRPα and membrane-mediated cooperativity of the CD47-SIRPα binding as well as fluctuation-induced interactions between the CD47-SIRPα complexes. Our approach is applicable to various membrane proteins and provides invaluable data for comparison with experimental findings.

We present an implementation of a perturbative triples correction for the coupled cluster ansatz including single and double excitations based on the transcorrelated Hamiltonian. Transcorrelation introduces explicit electron correlation in the electronic Hamiltonian through similarity transformation with a correlation factor. Due to this transformation, the transcorrelated Hamiltonian includes up to three-body couplings and becomes non-Hermitian. Since the conventional coupled cluster equations are solved by projection, it is well suited to harbor non-Hermitian Hamiltonians. The arising three-body operator, however, creates a huge memory bottleneck and increases the runtime scaling of the coupled cluster equations. As it has been shown that the three-body operator can be approximated, by expressing the Hamiltonian in the normal-ordered form, we investigate this approximation for the perturbative triples correction. Results are compared with a code-generation based transcorrelated coupled cluster implementation up to quadruple excitations.

The polarizable continuum model (PCM) is a computationally efficient way to incorporate dielectric boundary conditions into electronic structure calculations, via a boundary-element reformulation of Poisson's equation. This transformation is only rigorously valid for an isotropic dielectric medium. To simulate anisotropic solvation, as encountered at an interface or when parts of a system are solvent-exposed while other parts are in a nonpolar environment, ad hoc modifications to the PCM formalism have been suggested, in which a dielectric constant is assigned separately to each atomic sphere that contributes to the solute cavity. The accuracy of this "heterogeneous" PCM (HetPCM) method is tested here for the first time, by comparison to results from a generalized Poisson equation solver. The latter is a more expensive and cumbersome approach to incorporate arbitrary dielectric boundary conditions, but one that corresponds to a well-defined scalar permittivity function, ε(r). We examine simple model systems for which a function ε(r) can be constructed in a manner that maps reasonably well onto a dielectric constant for each atomic sphere, using a solvent-exposed dielectric constant ε_solv = 78 and a range of smaller values to represent hydrophobic environments. For nonpolar dielectric constants ε_nonp ≤ 2, differences between the HetPCM and Poisson solvation energies are large compared to the effect of anisotropy on the solvation energy. For ε_nonp = 4 and ε_nonp = 10, however, HetPCM and anisotropic Poisson solvation energies agree to within 2 kcal/mol in most cases. As a realistic use case, we apply the HetPCM method to predict solvation energies and pK_a values for blue copper proteins. The HetPCM method affords pK_a values that are more in line with experimental results as compared to either gas-phase calculations or homogeneous (isotropic) PCM results.