We extend the effective fragment molecular orbital method (EFMO) into treating fragments connected by covalent bonds. The accuracy of EFMO is compared to FMO and conventional ab initio electronic structure methods for polypeptides including proteins. Errors in energy for RHF and MP2 are within 2 kcal/mol for neutral polypeptides and 6 kcal/mol for charged polypeptides similar to FMO but obtained two to five times faster. For proteins, the errors are also within a few kcal/mol of the FMO results. We developed both the RHF and MP2 gradient for EFMO. Compared to ab initio, the EFMO optimized structures had an RMSD of 0.40 and 0.44 Å for RHF and MP2, respectively.
We present a non-decomposable approximation for the non-additive non-interacting kinetic energy (NAKE) for covalent bonds based on the exact behavior of the von Weizsäcker (vW) functional in regions dominated by one orbital. This covalent approximation (CA) seamlessly combines the vW and the Thomas-Fermi (TF) functional with a switching function of the fragment densities constructed to satisfy exact constraints. It also makes use of ensembles and fractionally-occupied spin-orbitals to yield highly accurate NAKE for stretched bonds while outperforming other standard NAKE approximations near equ…
We present a collection of covalent radii for the elements H, B, C, N, O, F, Si, P, S, Cl, Ge, As, Se, Br, derived from the recently introduced systematic non-empirical dataset of the covalent bond lengths. As the underlying bond lengths dataset was built basing on 26050 molecular geometries and bond graphs data obtained from quantum-chemical calculations with almost no input of empirical data, the presented covalent radii can be referred to as the first-principle ones. The obtained first-principle covalent radii are in good agreement with their empirical counterparts available in the literatu…
We present an intuitive and general analytical approximation estimating the energy of covalent single and double bonds between participating atoms in terms of their respective nuclear charges with just three parameters, $[{E_\text{AB} \approx a - b Z_\text{A} Z_\text{B} + c (Z_\text{A}^{7/3} + Z_\text{B}^{7/3})}]$. The functional form of our expression models an alchemical atomic energy decomposition between participating atoms A and B. After calibration, reasonably accurate bond energy estimates are obtained for hydrogen-saturated diatomics composed of $p$-block elements coming from the same …
We assess the predictive accuracy of perturbation theory based estimates of changes in covalent bonding due to linear alchemical interpolations among molecules. We have investigated $σ$ bonding to hydrogen, as well as $σ$ and $π$ bonding between main-group elements, occurring in small sets of iso-valence-electronic molecular species with elements drawn from second to fourth rows in the $p$-block of the periodic table. Numerical evidence suggests that first order estimates of covalent bonding potentials can achieve chemical accuracy if (i) the alchemical interpolation is vertical (fixed geometr…
Many atomic liquids can form transient covalent bonds reminiscent of those in the corresponding solid states. These directional interactions dictate many important properties of the liquid state, necessitating a quantitative, atomic-scale understanding of bonding in these complex systems. A prototypical example is liquid silicon, wherein transient covalent bonds give rise to local tetrahedral order and consequent non-trivial effects on liquid state thermodynamics and dynamics. To further understand covalent bonding in liquid silicon, and similar liquids, we present an ab initio simulation-base…
The antiferromagnetic (AF) model is generalized for the quasielectron system composed of identical ionic-covalent dimers. The density-fluctuation and covalent-correlation operators are constructed based on the extended AF density matrices, and the quasielectron system is decomposed into 4-level subsystems for the electron ionization and affinity. By considering the nearest-neighbor hopping near the covalent limit, we can see the importance of the bonding coefficients to the effective mass of the excited carrier in the crystal of the zincblende structure.
The non-additive non-interacting kinetic energy is calculated exactly for fragments of H$_2$, Li$_2$, Be$_2$, C$_2$, N$_2$, F$_2$, and Na$_2$ within partition density-functional theory. The resulting fragments are uniquely determined and their sum reproduces the Kohn-Sham molecular density of the corresponding XC functional. We compare the use of fractional orbital occupation to the usual PDFT ensemble method for treating the fragment energies and densities. We also compare Thomas-Fermi and von Weiz{ä}cker approximate kinetic energy functionals to the numerically exact solution and find signif…
Many new soft but tough rubbery materials have been recently discovered and new applications such as flexible prosthetics, stretchable electrodes or soft robotics continuously emerge. Yet, a credible multi-scale quantitative picture of damage and fracture of these materials has still not emerged, due to our fundamental inability to disentangle the irreversible scission of chemical bonds along the fracture path from dissipation by internal molecular friction. Here, by coupling new fluorogenic mechanochemistry with quantitative confocal microscopy mapping, we uncover how many and where covalent …
We introduce "bond-counting" potentials, which provide an elementary description of covalent bonding. These simplistic potentials are intended for studies of the mechanisms behind a variety of phase transitions in elemental melts, including the liquid-liquid phase transitions (LLPT) in phosphorus and bismuth. As a first study employing such potentials, an analytic solution of a one-dimensional model system is presented, including its thermodynamic properties and its structure factor. In the simplest case, the chemical valency of each atom is $1$, and either single atoms or diatomic molecules a…
A bismuth bond, a type of pnictogen bonding interaction, occurs in chemical systems when there is evidence of a net attractive interaction between the electrophilic region of a covalently or coordinately bonded bismuth atom and the nucleophilic region in another, or the same, molecular entity. In this review, we report on the signatory details of bismuth bonding in several crystalline systems, along with other non-covalent interactions such as hydrogen and halogen bonds, which are important driving forces in the rational design of various types of materials. Illustrative crystal structures wer…
We propose that spatial density matrices, which are singularly important in the study of quantum entanglement, encode the electronic fluctuations and correlations responsible for covalent bonding. From these density matrices, we develop tools that allow us to analyse how many body wave functions can be broken up into real space pieces. We apply these tools to the first row dimers, and in particular, we address the conflicting evidence in the literature about the presence of an inverted fourth bond and anti-ferromagnetic correlations in the $\text{C}_2$ molecule. Our results show that many body…
Unusual chemical bonds are proposed. Each bond is almost covalent but is characterized by the thread of a small radius $\sim 0.6\times 10^{-11}$cm, between two nuclei in a molecule. The main electron density is concentrated outside the thread as in a covalent bond. The thread is formed by the electron wave function which has a tendency to be singular on it. The singularity along the thread is cut off by electron "vibrations" due to the interaction with zero point electromagnetic oscillations. The electron energy has its typical value of (1-10)eV. Due to the small tread radius the uncertainty o…
Non-covalent bonding patterns are commonly harvested as a design principle in the field of catalysis, supramolecular chemistry and functional materials to name a few. Yet, their computational description generally neglects finite temperature and environment effects, which promote competing interactions and alter their static gas-phase properties. Recently, neural network potentials (NNPs) trained on Density Functional Theory (DFT) data have become increasingly popular to simulate molecular phenomena in condensed phase with an accuracy comparable to ab initio methods. To date, most applications…
Nuclear quantum effects (NQE) tend to generate delocalized molecular dynamics due to the inclusion of the zero point energy and its coupling with the anharmonicities in interatomic interactions. Here, we present evidence that NQE often enhance electronic interactions and, in turn, can result in dynamical molecular stabilization at finite temperature. The underlying physical mechanism promoted by NQE depends on the particular interaction under consideration. First, the effective reduction of interatomic distances between functional groups within a molecule can enhance the $n\toπ^*$ interaction …
One-dimensional CL-20 chains have been constructed using CH$_2$ molecular bridges for the covalent bonding between isolated CL-20 fragments. The energy and electronic properties of the nanostructures obtained have been analyzed by means of density functional theory and nonorthogonal tight-binding model considering Landauer-Büttiker formalism. It has been found that such systems become more thermodynamically stable as the efficient length of the chain increases. Thus, the formation of bulk covalent CL-20 solids may be energetically favorable, and such structures may possess high kinetic stabili…
There are views prevalent in the noncovalent chemistry literature that i) the O atom in molecules cannot form a chalcogen bond, and ii) if formed, this bond is very weak. We have shown in this study that these views are not necessarily true since the attractive energy between the oxygen atom of some molecules and several electron rich anionic bases examined in a series of 34 ion-molecule complexes varied from the weak (ca -2.30 kcal/mol) to the ultrastrong (-90.10 kcal/mol). The [MP2/aug-cc-pVTZ] binding energies for several of these complexes were found to be comparable to or significantly la…
