Linus Pauling contributions span structural biology, chemistry in its broadest definition, quantum mechanical theory, valence bond theory, and even nuclear physics. A principal tool developed and ...used by Pauling is X‐ray (and electron) diffraction. One possible extension of Pauling's oeuvre could be the “marriage” of crystallography and quantum mechanics. Such an effort dates back to the sixties and has now flourished into an entire subfield termed “Quantum Crystallography”. Quantum Crystallography could be achieved through the application of Clinton equations to yield N‐representable density matrices consistent with experimental data. The implementation of the Clinton equations is qualitatively different for small and for large systems. For a small system, quantum mechanics is extracted from X‐ray data while for a large system, the quantum mechanics is injected into the system. In both cases, N‐representability is imposed by the use of the Clinton equations.
New ternary and quaternary NaYS2(1–x)Te2x alloys (with x = 0, 0.33, 0.67, and 1) are proposed as promising candidates for photon energy conversion in photovoltaic applications. The effects of Te ...doping on crystal, spectral, and optical properties are studied within the framework of periodic density functional theory. Increasing Te content decreases the band gap (E g) considerably (from 3.96 (x = 0) to 1.62 eV (x = 0.67)) and fits a quadratic model (E g(x) = 3.96–6.78x + 4.70x 2, (r 2 = 0.96, n = 4)). The band gap of 1.62 eV makes the NaYS0.67Te1.33 alloy ideal for photovoltaic applications for their ability to absorb in the visible segment of the sunlight spectrum. The calculated exciton binding energies are 9.78 meV for NaYS1.33Te0.67 and 6.06 meV for NaYS0.67Te1.33. These values of the order of the thermal energy at room temperature suggest an easily dissociable hole–electron pair. The family of NaYS2(1–x)Te2x alloys are, therefore, promising candidates for visible photocatalytic devices and worthy of further experimental and theoretical investigations.
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•The physical meaning and information content of electron localization-delocalization matrices (LDMs) are discussed.•New concepts: Multidimensional atomic charges, QTAIM free valence ...indices, molecular digraphs, coarse-grained LDMs, etc.•Matrices from interacting quantum atoms (IQAs) energy decomposition are discussed.•LDMs are contrasted against matrices built from the Bader-Gatti integrated source function.•Dynamic three-dimensional LDMs evolving as three-dimensional matrices over reaction paths are touched upon.
Inspired by chemical graph theory (CGT), a matrix representation of molecules and reaction paths is presented within the framework of Bader’s quantum theory of atoms in molecules (QTAIM). A molecule is viewed as a network of electron delocalization channels or highways (vertices) that connect every pair of atoms in the system and electron localization cul-de-sacs loops connecting any given atom to itself. The representation of a molecule as a fuzzy, complete, non-directed graph, captured mathematically as an electron localization-delocalization matrix (an LDM), is rich with coded physical and chemical information. An LDM contains information on the bond-path molecular graph, bond strengths, molecular geometry, atomic electron populations and atomic charges, newly proposed multidimensional atomic charges, atomic volumes, free valences, NMR proton-proton coupling constants, and molecular branching. LDMs can quantify molecular (di)similarity by matrix difference measures such as the Frobenius distance, possibly after diagonalization and/or size adjustments with ghost atoms, or by the use of principal component analysis (PCA). Because they condense information at an atomic resolution, LDMs can be used to construct predictive quantitative-structure-to-activity/property-relationship (QSAR/QSPR) models with a wide range of applications including, for example, thermochemical properties, stress-corrosion cracking inhibitors’ activity, mosquito repellency, ribotoxicity, pKa's, aromaticity of rings-in-molecules, etc. The LDM philosophy can be extended to other properties that associate to each atom a “self” term and a sum of “interaction” terms with every other atom in the system. Such properties include the Oviedo Group’s “interacting quantum atoms” (IQAs) atomic energy decomposition and the integrated Bader-Gatti source function. The potential uses and connections between these different matrix representations of a molecule are explored. The coarse graining of LDMs to possibly compare macromolecular structures is also briefly discussed.
ATP synthase's intrinsic molecular electrostatic potential (MESP) adds constructively to, and hence reinforces, the chemiosmotic voltage. This ATP synthase voltage represents a new free energy term ...that appears to have been overlooked. This term is at least roughly equal in order of magnitude and opposite in sign to the energy needed to be dissipated as a Maxwell's demon (Landauer principle).
An approach is developed for the fast calculation of the interacting quantum atoms energy decomposition (IQA) from the information contained in the first order reduced density matrix only. The ...proposed methodology utilizes an approximate exchange‐correlation density from Density Matrix Functional Theory without the need to evaluate the correlation‐exchange contribution directly. Instead, weight factors are estimated to decompose the exact Vxc into atomic and pairwise contributions. In this way, the sum of the IQA contributions recovers the energy obtained from the electronic structure calculation. This method can, hence, be applied to obtain atomic contributions in excited states on the same footing as in their ground states using any method that delivers the reduced first‐order density matrix. In this way, one can locate chromophores from first principles quantum chemical calculations. Test calculations on the ground and excited states of a set of small molecules indicate that the scaled atomic contributions reproduce vertical electronic transition energies calculated exactly. This approach may be useful to extend the applicability of the IQA approach in the study of large photochemical systems especially when the calculations of the second order reduced density matrices is prohibitive or not possible.
Taking the Interacting Quantum Atoms (IQA) Method to the next level: The use of scaled atomic and interatomic exchange‐correlation energy components, obtained from approximated electron density functionals, provides a practical extension of the IQA decomposition applicable to any electronic structure method for which the reduced first‐order density is available. As an illustration, this approach is employed for the partitioning of electronic excitation energies of selected molecules into chromophore contributions.
An elastic network model (ENM) represents a molecule as a matrix of pairwise atomic interactions. Rich in coded information, ENMs are hereby proposed as a novel tool for the prediction of the ...activity of series of molecules, with
widely different chemical structures
, but a common biological activity. The new approach is developed and tested using a set of 183 inhibitors of serine/threonine-protein kinase enzyme (Plk3) which is an enzyme implicated in the regulation of cell cycle and tumorigenesis. The elastic network (EN) predictive model is found to exhibit high accuracy and speed compared to descriptor-based machine-trained modeling. EN modeling appears to be a highly promising new tool for the high demands of industrial applications such as drug and material design.
Graphic abstract
Bond paths linking two bonded hydrogen atoms that bear identical or similar charges are found between the ortho‐hydrogen atoms in planar biphenyl, between the hydrogen atoms bonded to the C1–C4 ...carbon atoms in phenanthrene and other angular polybenzenoids, and between the methyl hydrogen atoms in the cyclobutadiene, tetrahedrane and indacene molecules corseted with tertiary‐tetra‐butyl groups. It is shown that each such H–H interaction, rather than denoting the presence of “nonbonded steric repulsions”, makes a stabilizing contribution of up to 10 kcal mol−1 to the energy of the molecule in which it occurs. The quantum theory of atoms in molecules—the physics of an open system—demonstrates that while the approach of two bonded hydrogen atoms to a separation less than the sum of their van der Waals radii does result in an increase in the repulsive contributions to their energies, these changes are dominated by an increase in the magnitude of the attractive interaction of the protons with the electron density distribution, and the net result is a stabilizing change in the energy. The surface virial that determines the contribution to the total energy decrease resulting from the formation of the H–H interatomic surface is shown to account for the resulting stability. It is pointed out that H–H interactions must be ubiquitous, their stabilization energies contributing to the sublimation energies of hydrocarbon molecular crystals, as well as solid hydrogen. H–H bonding is shown to be distinct from “dihydrogen bonding”, a form of hydrogen bonding with a hydridic hydrogen in the role of the base atom.
Bond paths linking two bonded hydrogen atoms that bear identical or similar charges are found between the ortho‐hydrogen atoms in planar biphenyl, between the hydrogen atoms bonded to the C1–C4 carbon atoms in phenanthrene and other angular polybenzenoids, and between the methyl hydrogen atoms in the cyclobutadiene, tetrahedrane, and indacene molecules corseted with tertiary‐tetra‐butyl groups. The picture shows the stabilization of the tetrahedrane cage by the network of H–H bond paths linking tert‐butyl groups.
The mitochondrion is known as the “powerhouse” of eukaryotic cells since it is the main site of adenosine 5′‐triphosphate (ATP) production. Using a temperature‐sensitive fluorescent probe, it has ...recently been suggested that the stray free energy, not captured into ATP, is potentially sufficient to sustain mitochondrial temperatures higher than the cellular environment, possibly reaching up to 50 °C. By 50 °C, some DNA and mitochondrial proteins may reach their melting temperatures; how then do these biomolecules maintain their structure and function? Further, the production of reactive oxygen species (ROS) accelerates with temperature, implying higher oxidative stresses in the mitochondrion than generally appreciated. Herein, it is proposed that mitochondrial heat shock proteins (particularly Hsp70), in addition to their roles in protein transport and folding, protect mitochondrial proteins and DNA from thermal and ROS damage. Other thermoprotectant mechanisms are also discussed.
The mitochondrion may operate at a considerably higher temperature than assumed, possibly exceeding the melting temperatures of some mitochondrial proteins and nucleic acids. It is proposed that heat shock proteins, abundant in the mitochondrion, may have a role in stabilizing its macromolecules against melting and heat‐induced increase in reactive oxygen species. Other heat protection mechanisms are also explored.
Recent DFT calculations have predicted unexpected molecular structures for the ion induced dipole clusters H n – (3 ≤ n-odd ≤ 13). Analysis of these calculations suggests the definition of a new ...bond, called the trihydogen bond (THB). This is placed in context by a review and classification of multihydrogen interactions as usually discussed in the literature. The results of analysis related to the trihydrogen bond are presented. These include a series of linear relations exhibited by the H n – clusters involving the charge carried by the central H– ion, the binding energy of the clusters, and the relative stabilization of the central anion H– with respect to the energy of a free H– atom.
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