We comment on the recently published Martini forcefield for linear polyethylenimine (Beu et al., J. Comput. Chem., 2020, 41, 349). With supporting evidence, we demonstrate that the new coarse-graining methodology presented in that work is inconsistent with the Martini methodology and lacks important validation steps which is usually required by Martini forcefields.

We report the ground state tunneling splittings (ΔE± ) of a number of axially chiral molecules using the ring-polymer instanton (RPI) method (J. Chem. Phys., 2011, 134, 054109). The list includes isotopomers of hydrogen dichalcogenides H2 X2 (X = O, S, Se, Te, and Po), hydrogen thioperoxide HSOH and dichlorodisulfane S2 Cl2 . Ab initio electronic-structure calculations have been performed on the level of second-order Møller-Plesset perturbation (MP2) theory either with split-valance basis sets or augmented correlation-consistent basis sets on H, O, S, and Cl atoms. Energy-consistent pseudopotential and corresponding triple zeta basis sets of the Stuttgart group are used on Se, Te, and Po atoms. The results are further improved using single point calculations performed at the coupled cluster level with iterative singles and doubles and perturbative triples amplitudes. When available for comparison, our computed values of ΔE± are found to lie within the same order of magnitude as values reported in the literature, although RPI also provides predictions for H2 Po2 and S2 Cl2 , which have not previously been directly calculated. Since RPI is a single-shot method which does not require detailed prior knowledge of the optimal tunneling path, it offers an effective way for estimating the tunneling dynamics of more complex chiral molecules, and especially those with small tunneling splittings.

The plasticity of Ag2 S and Ag2 Se crystals important for applications is associated mainly with AgAg metallophilic bonds, which are related to van der Waals interactions and therefore are not directed. This is demonstrated by the first principles DFT M06 LCAO calculations of Ag2 X (X = S, Se) crystals (periodic model) and hypothetical molecules Xn Ag2n (X = S, Se; n = 1, 2, 4) in gas phase (molecular model). A topological analysis of the calculated electron density, was performed both for periodic and molecular models of Ag2 X (X = S, Se). It was found that Ag-Ag interatomic distances are close in periodic and molecular models. The numerical values of electron density, its Laplacian, kinetic, and potential energy densities are also close in both models and confirm the existence of AgAg metallophilic bonds.

We present an inexpensive and robust theoretical approach based on the fragment molecular orbital methodology and the spin-ratio scaled second-order Møller-Plesset perturbation theory to predict the lattice energy of benzene crystals within 2 kJ⋅mol-1 . Inspired by the Harrison method to estimate the Madelung constant, the proposed approach calculates the lattice energy as a sum of two- and three-body interaction energies between a reference molecule and the surrounding molecules arranged in a sphere. The lattice energy converges rapidly at a radius of 13 Å. Adding the corrections to account for a higher correlated level of theory and basis set superposition for the Hartree Fock (HF) level produced a lattice energy of -57.5 kJ⋅mol-1 for the benzene crystal structure at 138 K. This estimate is within 1.6 kJ⋅mol-1 off the best theoretical prediction of -55.9 kJ⋅mol-1 . We applied this approach to calculate lattice energies of the crystal structures of phase I and phase II-polymorphs of benzene-observed at a higher temperature of 295 K. The stability of these polymorphs was correctly predicted, with phase II being energetically preferred by 3.7 kJ⋅mol-1 over phase I. The proposed approach gives a tremendous potential to predict stability of other molecular crystal polymorphs.

We present a systematic assessment of the density functional tight binding (DFTB) method for calculating heats of formation of fullerenes with isodesmic-type reaction schemes. We show that DFTB3-D/3ob can accurately predict Δf H values of the 1812 structural isomers of C60 , reproduce subtle trends in Δf H values for 24 isolated pentagon rule (IPR) isomers of C84 , and predict Δf H values of giant fullerenes that are in effectively exact agreement with benchmark DSD-PBEP86/def2-QZVPP calculations. For fullerenes up to C320 , DFTB Δf H values are within 1.0 kJ mol-1 of DSD-PBEP86/def2-QZVPP values per carbon atom, and on a per carbon atom basis DFTB3-D/3ob yields exactly the same numerical trend of (Δf H [per carbon] = 722n-0.72  + 5.2 kJ mol-1 ). DFTB3-D/3ob is therefore an accurate replacement for high-level DHDFT and composite thermochemical methods in predicting of thermochemical stabilities of giant fullerenes and analogous nanocarbon architectures.

In this paper, we address high performance extreme-scale molecular dynamics (MD) algorithm in the GENESIS software to perform cellular-scale molecular dynamics (MD) simulations with more than 100,000 CPU cores. It includes (1) the new algorithm of real-space nonbonded interactions maximizing the performance on ARM CPU architecture, (2) reciprocal-space nonbonded interactions minimizing communicational cost, (3) accurate temperature/pressure evaluations that allows a large time step, and (4) effective parallel file inputs/outputs (I/O) for MD simulations of extremely huge systems. The largest system that contains 1.6 billion atoms was simulated using MD with a performance of 8.30 ns/day on Fugaku supercomputer. It extends the available size and time of MD simulations to answer unresolved questions of biomacromolecules in a living cell.

The kinematic geometry of protein backbone structures, constrained by either single or multiple hydrogen bonds (H-bonds), possibly in a periodic array, is discussed. These structures include regular secondary structure elements α-helices and β-sheets but also include other short H-bond stabilized irregular structural elements like β-turns. The work here shows that the variations observed in such structures have simple geometrical correlations consistent with constrained motion kinematics. A new classification of the ideal helices is given, in terms of the parameter α, the angle at a Cα atom to its two neighboring Cα 's along the helix, and shown how it can be generalized to include nonideal helices. Specifically, we derive an analytical expression of the backbone dihedrals, (ϕ, ψ), in terms of the parameter α subject to the constraint that the peptide planes are parallel to the helical axis. Helices constructed in this way exhibit near-vertical alignment of the C = O and N - H units and are the canonical objects of this study. These expressions are easily modifiable to include perturbations of parameters relevant to nonplanar peptide units and noncanonical angles. The addition of a second parameter, ε0 , inclination of successive peptide planes along a helix with respect to the helical axis leads to a generalization of the previous expression and provides an efficient parametrization of such structures in terms of coordinates consistent with H-bond parameters. An analogs parametrization of β-turns, using inverse kinematic methods, is also given. Besides offering a unifying viewpoint, our results may find useful applications to protein and peptide design.

Efficient sampling of the conformational space is essential for quantitative simulations of proteins. The multiscale enhanced sampling (MSES) method accelerates atomistic sampling by coupling it to a coarse-grained (CG) simulation. Bias from coupling to the CG model is removed using Hamiltonian replica exchange, such that one could benefit simultaneously from the high accuracy of atomistic models and fast dynamics of CG ones. Here, we extend MSES to allow independent control of the effective temperatures of atomistic and CG simulations, by directly scaling the atomistic and CG Hamiltonians. The new algorithm, named MSES with independent tempering (MSES-IT), supports more sophisticated Hamiltonian and temperature replica exchange protocols to further improve the sampling efficiency. Using a small but nontrivial β-hairpin, we show that setting the effective temperature of CG model in all conditions to its melting temperature maximizes structural transition rates at the CG level and promotes more efficient replica exchange and diffusion in the condition space. As the result, MSES-IT drive faster reversible transitions at the atomic level and leads to significant improvement in generating converged conformational ensembles compared to the original MSES scheme.

The semiempirical INDO/S Hamiltonian is incorporated into a new release of MOPAC2016. The MOPAC2016 software package has long been at the forefront of semiempirical quantum chemical methods (SEQMs) for small molecules, proteins, and solids and until this release has included only NDDO-type SEQMs. The new code enables the calculation of excited states using the INDO/S Hamiltonian combined with a configuration interaction (CI) approach using single excitations (CIS), single and double excitations (CISD), or multiple reference determinants (MRCI) where reference determinants are generated using a complete active space (CAS) approach. The capacity to perform excited-state calculations beyond the CIS level makes INDO/CI one of the few low-cost computational methods capable of accurately modeling states with substantial double-excitation character. Solvent corrections to the ground-state and excited-state energies can be computed using the COSMO implicit solvent model, incorporating state-specific corrections to the excited states based on the solvent refractive index. This code produces physically reasonable electronic structures, absorption spectra, and solvatochromic shifts at low computational costs for systems up to hundreds of atoms, and for both organic molecules and metal clusters.

The bonding and antibonding character of individual molecular orbitals has been previously shown to be related to their orbital energy derivatives with respect to nuclear coordinates, known as dynamical orbital forces. Albeit usually derived from Koopmans' theorem, in this work we show a more general derivation from conceptual DFT, which justifies application in a broader context. The consistency of the approach is validated numerically for valence orbitals in Kohn-Sham DFT. Then, we illustrate its usefulness by showcasing applications in aromatic and antiaromatic systems and in excited state chemistry. Overall, dynamical orbital forces can be used to interpret the results of routine ab initio calculations, be it wavefunction or density based, in terms of forces and occupations.

For the search for promising singlet fission candidates, the calculation of the effective electronic coupling, which is required to estimate the singlet fission rate between the initially excited state (S0S1) and the multiexcitonic state (1TT, two triplets on neighboring molecules, coupled into a singlet), should be sufficiently reliable and fast enough to explore the configuration space. We propose here to modify the calculation of the effective electronic coupling using a nonorthogonal configuration interaction approach by: (a) using only one set of orbitals, optimized for the triplet state of the molecules, to describe all molecular electronic states, and (b) only taking the leading configurations into consideration. Furthermore, we also studied the basis set convergence of the electronic coupling, and we found, by comparison to the complete basis set limit obtained using the cc-pVnZ series of basis sets, that both the aug-cc-pVDZ and 6-311++G** basis sets are a good compromise between accuracy and computational feasibility. The proposed approach enables future work on larger clusters of molecules than dimers.

In this article, we investigate the effects of the isoleucine (ILE)N amino acid chain growth, N = 1.0.6, the ILE conformational effect as well as the solvent presence on the electrical and magnetic spectroscopic properties when these compounds are in aqueous solution. Computational molecular dynamics simulations were performed to include the solvent medium and generate uncorrelated configurations involving solute-solvent structures. The charge point model for solvent was used to obtain the results for quantum mechanical calculation, in special DFT calculations, for (ILE)N structures. Our results for the magnetic shielding constant obtained via GIAO-DFT-NMR calculations show that there is evidence of a magnetic behavior that characterizes the number of peptide bonds and, therefore, how the N isoleucine polypeptide chain is composed. TD-DFT results also show an absorption band shift to larger wavelengths indicating a dependence on N growth.

Drug binding to a protein target is governed by a complex pattern of noncovalent interactions between the ligand and the residues in the protein's binding pocket. Here we introduce a generally applicable, parameter-free, computational method that allows for the identification, quantification, and analysis of the key ligand-residue interactions responsible for molecular recognition. Our strategy relies on Local Energy Decomposition analysis at the "gold-standard" coupled cluster DLPNO-CCSD(T) level. In the study case shown in this paper, nicotine and imidacloprid binding to the nicotinic acetylcholine receptor, our approach provides new insights into how individual amino acids in the active site determine sensitivity and selectivity of the ligands, extending and refining classical pharmacophore hypotheses. By inference, the method is applicable to any kind of host/guest interactions with potential applications in industrial biocatalysis and protein engineering.

As an effective method to analyze complex catalytic reaction networks, microkinetic modeling is gaining increasing popularity in the catalytic activity evaluation and rational design of heterogeneous catalysts. An automated simulator with stable and reliable performance is especially useful and in great request. Here we introduce the CATKINAS package developed for large-scale microkinetic modeling and analysis. Featuring with a multilevel solver and a multifunctional analyzer, CATKINAS can provide both accurate solutions and various quantitative and automatic analysis for a wide range of catalytic systems. The structure and the basic workflow are overviewed with the multilevel solver particularly illustrated. Also, we take the CO methanation reaction as an example to illustrate the application and efficiency of the CATKINAS package.

The DFTB theory was combined with the isothermal Brownian-type molecular dynamics (MD) and metadynamics molecular dynamics (MMD) algorithms to perform simulation studies for Au clusters. Two representative DFTB parametrizations were investigated. In one parametrization, the DFTB-A, the Slater-Koster parameters in the DFTB energy function were determined focusing on the ionic repulsive energy part, Erep and the other, the DFTB-B, due attention was paid to the electronic band-structure energy part, Eband . Minimized structures of these two parametrizations were separately applied in MD and MMD simulations to generate unbiased and biased trajectories in collective variable (CV) space, respectively. Here, we found the MD simulations monitored at 300 K manifest fluxional characteristics in planar cluster Au9 /DFTB-A, but give no discernible tracts of fluxionality for planar Au8 /DFTB-A and Au8 /DFTB-B, for nonplanar Au10 /DFTB-A and, to some extent, for nonplanar Au9 /DFTB-B; they are plausibly being hindered by higher-than kB T energy barriers. Very recent FIR-MPD spectroscopy measurements, however, were reported to have detected at 300 K both the planar and nonplanar neutral Aun clusters in the size range 5 ≤ n ≤ 13. The failure of MD simulations has prompted us to apply the MMD simulation and construct the free energy landscape (FEL) in CV space. Through scrutinizing the FELs of these clusters and their associated structures, we examine the relative importance of Erep /DFTB-A and Eband /DFTB-B in unraveling the covalent-like behavior of valence electrons in Aun . Most important of all, we shall evaluate the DFTB parametrization in MMD strategy through comparing extensively the simulation data recorded with the gas-phase experimental data.

Global energy minimum structures and optoelectronic properties are presented for isolated Cdx Sey + clusters with x + y ≤ 26. The compositional- and size-dependent variation of optical, electronic and geometric properties is systematically studied within the framework of ground state and time-dependent density functional theory. The applied methods are justified by benchmarks with experimental data. It is shown that the optical gap can be tuned by more than 2 eV by only changing the composition for a fixed number of atoms. The stoichiometric species reveal an unexpected size-dependent behavior in comparison to larger colloidal CdSe quantum dots, that is, a redshift of the optical gap was observed with decreasing cluster size in contrast to predictions by quantum-size effects. This unexpected result is discussed in detail taking the positive charge of the clusters into account.