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Machine learning (ML) methods are being used in almost every conceivable area of electronic structure theory and molecular simulation. In particular, ML has become firmly established in the construction of high-dimensional interatomic potentials. Not a day goes by without another proof of principle being published on how ML methods can represent and predict quantum mechanical properties—be they observable, such as molecular polarizabilities, or not, such as atomic charges. As ML is becoming pervasive in electronic structure theory and molecular simulation, we provide an overview of how atomistic computational modeling is being transformed by the incorporation of ML approaches. From the perspective of the practitioner in the field, we assess how common workflows to predict structure, dynamics, and spectroscopy are affected by ML. Finally, we discuss how a tighter and lasting integration of ML methods with computational chemistry and materials science can be achieved and what it will mean for research practice, software development, and postgraduate training. [ABSTRACT FROM AUTHOR]

In the analysis of molecular structure and local order in heterogeneous samples, multiphoton excitation of fluorescence affords chemically specific information and high-resolution imaging. This report presents the results of an investigation that secures a detailed theoretical representation of the fluorescence polarization produced by one-, two-, and three-photon excitations, with orientational averaging procedures being deployed to deliver the fully disordered limits. The equations determining multiphoton fluorescence response prove to be expressible in a relatively simple, generic form, and graphs exhibit the functional form of the multiphoton fluorescence polarization. Amongst other features, the results lead to the identification of a condition under which the fluorescence produced through the concerted absorption of any number of photons becomes completely unpolarized. It is also shown that the angular variation of fluorescence intensities is reliable indicator of orientational disorder. [ABSTRACT FROM AUTHOR]

Recently [Y. S. Djikaev and E. Ruckenstein, J. Phys. Chem. B 111, 886 (2007)], the authors proposed a kinetic model for the nucleation mechanism of protein folding where a protein was modeled as a heteropolymer consisting of hydrophobic and hydrophilic beads and the composition of the growing cluster of protein residues was assumed to be constant and equal to the overall protein composition. Here, they further develop the model by considering a protein as a three-component heteropolymer and by allowing the composition of the growing cluster of protein residues to vary independently of the overall one. All the bonds in the heteropolymer (now consisting of hydrophobic, hydrophilic, and neutral beads) have the same constant length, and all the bond angles are equal and fixed. As a crucial idea of the model, an overall potential around the cluster wherein a residue performs a chaotic motion is considered to be a combination of the average dihedral and average pairwise potentials assigned to the bead. The overall potential as a function of the distance from the cluster center has a double well shape which allows one to determine its emission and absorption rates by using a first passage time analysis. Knowing these rates as functions of three independent variables of a ternary cluster, one can develop a self-consistent kinetic theory for the nucleation mechanism of folding of a protein using a ternary nucleation formalism and evaluate the size and composition of the nucleus and the protein folding time. As an illustration, the model is applied to the folding of bovine pancreatic ribonuclease consisting of 124 amino acids whereof 40 are hydrophobic, 81 hydrophilic, and 3 neutral. With a reasonable choice of diffusion coefficients of the residues in the native state and potential parameters, the model predicts folding times in the range of 1–100 s. [ABSTRACT FROM AUTHOR]

Systematic efforts to synthesize fullerene-containing liquid crystals have produced a variety of successful model compounds. We present a simple molecular theory, based on the interconverting shape approach [Vanakaras and Photinos, J. Mater. Chem. 15, 2002 (2005)], that relates the self-organization observed in these systems to their molecular structure. The interactions are modeled by dividing each molecule into a number of submolecular blocks to which specific interactions are assigned. Three types of blocks are introduced, corresponding to fullerene units, mesogenic units, and nonmesogenic linkage units. The blocks are constrained to move on a cubic three-dimensional lattice and molecular flexibility is allowed by retaining a number of representative conformations within the block representation of the molecule. Calculations are presented for a variety of molecular architectures including twin mesogenic branch monoadducts of C60, twin dendromesogenic branch monoadducts, and conical (badminton shuttlecock) multiadducts of C60. The dependence of the phase diagrams on the interaction parameters is explored. In spite of its many simplifications and the minimal molecular modeling used (three types of chemically distinct submolecular blocks with only repulsive interactions), the theory accounts remarkably well for the phase behavior of these systems. [ABSTRACT FROM AUTHOR]

We present a theoretical analysis of the effects that lead to distortion or symmetry restoration of the nuclear configuration in ions of weakly bound molecular systems and clusters. The vibronic coupling mechanisms involved are reviewed and discussed in terms of simple and general models. Guided by a qualitative characterization of the wave function of a loosely bound system, we study the symmetry determining effects for such ions in terms of first order (Koopmans’), relaxation and correlation distortion energies associated with electron removal from the parent system. Our discussion suggests that the Koopmans’ approximation can reasonably be expected to provide a qualitatively correct dependence of the ion energy on nuclear motion. Exceeding these expectations, it is found in numerical applications to the He+3 and He+4 ions that the relaxation and correlation energy changes accompanying symmetry breaking tend to cancel exactly. This implies, and we show in practice, that while insufficiently accurate correlation energy estimates may easily lead to incorrect geometries, the inexpensive Koopmans’ approximation can often suffice to obtain the correct energy curvature along symmetry breaking coordinates. Further preliminary results for N3 and CO+2 suggest that these findings have a much wider applicability than anticipated. [ABSTRACT FROM AUTHOR]

The Einstein-Brillouin-Keller semiclassical quantization and the topological Maslov index are used to deduce the correct quantum mechanical values for the energy of a one-electron atom (both nonrelativistically and relativistically) and a three-dimensional harmonic oscillator. The development is concise, transparent, and involves only elementary integral calculus and provides a conceptual and intuitive introduction to the quantum nature of the atomic and molecular structure of matter. [ABSTRACT FROM AUTHOR]