Interatomic potentials laid at the heart of molecular physics. They are a bridge between the spectroscopic and structural properties of molecular systems. In this paper, a century-old review from 1920 to 2020, of functional forms used to analytically represent potential energy as a function of interatomic distance for diatomic systems is presented. With such a purpose fifty functions were selected. For all of them, motivation and the main mathematical features are discussed. Our goal is to provide a chronological pathway to the reader, even with little knowledge on the subject, to understand how to calculate each parameter that composes the interatomic potentials, as well as obtain spectroscopic constants from them. Comparative evaluation for the N2, CO, and HeH+ systems in their ground electronic states are also presented.

Multi-reference configuration interaction, MR-CI (including extensivity corrections, named +Q) calculations have been performed on S0 to S3 states of cyclohexa-2,4-diene-1-thione (thione 24) and cyclohexa-2,5-diene-1-thione (thione 25), which are thione isomers of thiophenol. Several types of uncontracted MR-CIS and MR-CISD wavefunctions have been employed, comprising MR-CI expansions as large as ~ 374 x 106 configuration state functions. The nature of the studied excited states has been characterized. Vertical excitation energies (ΔE) and oscillator strengths (f) have been computed. The most intense transitions (S0→S2 for 24 and S0→S3 for 25) do not change with the wavefunction, although a variation as large as ~ 1 eV has been obtained for the S3 state of 24. On the other hand, ΔE changes at most ~ 0.15 eV for 25, as the wavefunction changes. The S1 state of both thiones has nπ* character and is in the visible region. For 24 S2 and S3 are ππ* and nπ* states, respectively, while for 25 the reverse order has been obtained. S2 and S3 are in the range from ~ 3.5 to 5.2 eV, at the highest level (MR-CI+Q). It is the first time that the excited states of the title molecules are studied. The computed results agree with the experimental onsets of photoreactions of thiones 24 and 25 found by Reva et. al. (Phys. Chem. Chem. Phys. 2015, 17, 4888).

A kinetic energy functional Ee was developed within the framework of the density-functional theory (DFT) based on the energy electron density for the purpose of realizing the orbital-free DFT. The functional includes the nonlocal term described with the linear-response function (LRF) of a reference system. As a notable feature of the present approach, the LRF is represented on the energy coordinate ε defined for each system of interest. In addition, an atomic system is taken as a reference system for the construction of the LRF, which shows a clear difference from the conventional approach based on the homogeneous electron gas. The explicit form of the functional Ee was formulated by means of the coupling-parameter integration scheme. The functional Ee was applied to the calculations of the kinetic energies of the pseudo atoms that mimics H, He, Ne, and Ar. Explicitly, the kinetic energy of each atom was computed using the functional Ee with respect to the variation of the valence charge Zv of each atom. In these calculations, the electron density n optimized by the Kohn-Sham DFT was adopted as an argument of the functional. It was found that the results are in excellent agreements with those given by the Kohn-Sham DFT. We also devised a method to perform the self-consistent field calculation utilizing the functional Ee The method was applied to the computation of the radial distribution functions of the electrons in the pseudo Ne and Ar atoms. It was demonstrated that the results reasonably agree with those yielded by the Kohn-Sham DFT.

Due to it is potential application in the field of high energy density materials, how to stabilize cyclopentazolate anion (cyclo-N5-) has attracted many interests theoretically and experimentally. Therefore, a series of ion salts containing [cyclo-N5]- were synthesized and studied. The instability of [cyclo-N5]- is caused by the five lone pairs of electrons localized on five neighbored N atoms. In this work, we expect if the [cyclo-N5]- can be stabilized by the coordination with acidic ligands, by weakening the multi repulsion from the lone pairs to stabilize the [cyclo-N5]-. The two compounds of [N5(BH3)5]-, and [N5(AgCN)5]- have been designed and compared based on the Lewis acid-base theory. [N5(H2O)5]- is designed to evaluate the effect of hydrogen bond in the stabilization. For all the structures, we study the bonding properties and thermal stabilities based on the analysis of electronic structures and Car-Parrinello molecular dynamics (CPMD) simulations. The results indicate it is a effective method to stabilize [cyclo-N5]- by introducing the Lewis acid. Our insights on [cyclo-N5]- compounds with high thermal stability under ambient conditions will provide a new idea for the research and synthesis of new high energetic [cyclo-N5]- series compounds.

A systematic benchmark of phosphorus and fluorine NMR chemical shifts predictions at six different density functional theory (DFT) / the gauge-including atomic orbital (GIAO) methods was conducted. Two databases were compiled: one consists of 35 phosphorus-containing molecules, which cover the most common intra-molecular bonding environments of trivalent and pentavalent phosphorus atoms; the other is composed of 46 fluorine-containing molecules. The characteristics of each DFT/GIAO method with different solvent models were demonstrated in details. The application of linear regression between the calculated isotropic shielding constants and experimental chemical shifts was applicable to improve the prediction accuracy. And, the best methods with the SMD and CPCM implicit solvent models for 31P chemical shifts predictions, are able to yield a root-mean-square deviation (RMSDs) of 5.58 ppm and 5.42 ppm, respectively; for 19F, the corresponding lowest prediction errors with these two applied solvent models are 4.43 ppm and 4.12 ppm. The developed scaling factors fitted from linear regression are applicable to enhance the chance of successful structural elucidations of phosphorus or fluorine-containing compounds, as an efficient complement to 13C, 1H, 11B and 15N chemical shifts predictions.

Non covalent biliproteins are found in a growing number of living organisms and even in viruses, such as SARS-CoV-2. Unlike the well described covalent biliproteins, such as the phytochromes, they present a vast structural and functional diversity, and often with limited experimental information. A very important tool (and sometimes the only one available) to study these systems is the UV-Vis spectrum, which is modulated both by conformational changes of the biliverdin chromophore and specific interactions with the apoprotein. In this work we present a theoretical study of the microscopic determinants of the UV-Vis spectrum of these compounds through the use of hybrid QM(TD-DFT)/MM techniques and molecular dynamics simulations. Comparing our results with existing experimental data, we prove that it is possible to predict spectroscopic properties, such as relative position and intensity ratio of main bands, with affordable methods, and to provide a microscopic explanation of them. This systematic information can be very useful for the study of described biliproteins or for those yet unknown.

Photochemical reactions of small molecules occur upon irradiation by ultraviolet or visible light, and they are a very important and controversial chemical process in the Earth’s atmosphere because they impact our quality of life and health. Small-unsaturated carbonyl compounds play an important role in the chemistry of the polluted troposphere. The fluorinated aldehydes are very reactive under the sunlight driving to species that trigger more atmospheric reactions. This paper is focused on a theoretical study of the photochemistry of difluoro-crotonaldehyde using static and dynamic calculations by combination of Global Reaction Route mapping (GRRM) and Trajectory Surface Hopping (TSH) approach. The static analysis of the electronic and geometrical structures at the critical points allowed to rationalize the possible pathways that interconnect the stationary and crossing points in order to get a map of the unimolecular photochemical reactions which take place. The time evolution of the electronic states and the degrees of freedom enabled the identification of the requirements to follow the most probable deactivation pathways. This article reports the unimolecular deactivation pathways after the electronic excitation of the trans and cis isomers. In both cases, the excitation energies were calculated and compared with the analogous in the crotonaldehyde in order to elucidate the effect of fluorine atoms on the electronic structure and stabilities. After the initial excitations to the ππ* excited states, the main deactivation channels follow non-adiabatic pathways via S1/S0 conical intersections. Ultrafast processes leading to the early activation of the S1 govern the decay of the difluoro-crotonaldehyde. Depending on the nature of the S1 state before the crossing with the S0, the system can follow several reaction pathways. The main photochemical processes observed were the cis-trans isomerization, the Norrish type I reaction (α-cleavage), Norrish type II reaction (γ-hydrogen abstraction) and fluorine photodissociation. The time scale, the molecular deformations and the electronic states implied for the different photochemical processes, as well as how these compete with the photophysical deactivation are discussed.

The effect of a directional electric-field on the bonding of the undoped and sulphur doped diarylethene (DTE) switch molecule is investigated using next generation QTAIM (NG-QTAIM). We introduce chemical bonding concepts in the form of the least and most preferred directions of charge density accumulation relative to the associated bond-path, namely the precessions K and Kʹ that are demonstrated to be much more responsive to the electric-field than the Laplacian ∇2ρ(rb). A concept of bond fatigue is presented in terms of the tendency for a bond-path to rupture that provides directional versions of familiar bonding QTAIM concepts. Examples are included where the applied directional electric-field reduces the tendency towards bond-path rupture and also the converse. A brief discussion is undertaken of applications of the precessions K and Kʹ including switches, ring opening reactions and molecular rotary motors in the presence of fields that cause a redistribution of ρ(r).

In order to quantify the site-dependent correlation strengths in terms of the quasi-particle weights and the occupation numbers of 5f electrons in alpha phase plutonium metal with eight crystallographically nonequivalent atomic sites Pun (n=1~8), we perform a first principles calculation by using a many-body method merging density functional theory (DFT) with dynamical mean-field theory (DMFT) plus the relativistic and correlation effects. The quasi-particle weight, the electronic spectrum function, the hybridization function, as well as the occupation number of Pu 5f electrons all suggest that Pu1 and Pu8 atoms have the most itinerant and the most localized 5f electrons, respectively, while the other atoms Pun (n=2~7) exhibit an intermediate correlation strength. The quasi-particle weights demonstrate that only the jj or intermediate coupling scheme is more appropriate for Pu 5f electrons in comparison with the Russel-Saunders (LS) scheme. The electronic spectrum function and the occupation analysis establish that Pu 5f electrons simultaneously have dual itinerant and localized regimes with average 5f occupation numbers of nf between 4.8994 and 4.9628, which are mainly composed of 5f4, 5f5 and 5f6 configurations, irrespective of different atomic sites. Finally, we also estimate the so-called quasi-particle band structure to directly compare with an experimental angle-resolved photoemission spectrum (ARPES).

We present the derivation of a new response method termed rst order po- larization propagator approximation. The electronic structure is given by a density functional representation. We provide a detailed derivation of the method along with explicit expressions for the relevant integrals and matrix elements.

The O-O coupling process in water oxidation on the gamma FeOOH hydroxide catalyst is simulated by means of density functional theory using model iron cubane cluster Fe4O4(OH)4. A key reactive intermediate is proposed to be the HO-FeIV-O• oxyl unit with terminal oxo radical formed from vertex HO-FeIV-OH moiety by withdrawal of proton-electron pair. The O-O coupling goes via water nucleophilic attack on the oxyl oxygen to form the O-O bond with a remarkably low barrier of 11 kcal/mol. This process is far more effective than alternative scenario based on direct interaction of two ferryl FeIV=O sites (with estimated barrier of 36 kcal/mol) and is comparable with the coupling between terminal oxo center and three-coordinated lattice oxo center (12 kcal/mol barrier). The process of hydroxylation of terminal oxygen inhibits the O-O coupling. Nevertheless, being more effective for ferryl oxygen, the hydroxylation in fact enhances selectivity of the O-O coupling initiated by the oxyl oxygen.

Isomorphic titanium dichalcogenide TiX2 (X=S, Se, Te) compounds exhibit very diverse and anisotropic chemical and physical properties. The temperature dependent electrical resistivity of TiSe2 was found to exhibit anomalous behavior at low temperatures (< 200 K) which was connected to the emergence of a unique charge density wave (CDW), which was explained on the basis of 2a0×c0 superstructure formation, whereas bulk TiS2 and TiTe2 do not exhibit CDW instability. In order to understand their diverse nature, we have systematically investigated the electronic structure of titanium dichalcogenides by using the FPLAPW and PAW methods based on the density functional theory (DFT). The energy bands calculated by implementing the latest generalized gradient approximation (GGA) with PBE and TB-mBJ potentials confirm the semiconducting nature of TiS2 and metallic nature of TiSe2 and TiTe2, however the Wu-Cohen potentials show a semi-metallic nature for all three dichalcogenides. The diverse properties of TiX2 are governed by two bands, S/Se/Te p-band close to the Γ-point and Ti 3d-band around M (L)-points. The presence of electron and hole pockets at the Fermi energy level have been previously confirmed experimentally, although our calculated size and extent of overlap of these pockets was overestimated compared to experiments. Various physical parameters such as electrical conductivity, Seebeck coefficient etc. which depend sensitively on nature of states at the Fermi level also amply illustrate the diversity of the compounds. The electron localization function and Bader charge partitioning illustrate the increasing covalency with varying chalcogenide atom, which is consistent with the spectral features observed in the DOS. The lattice dispersion of the titanium dichalcogenides are calculated by using the PAW method with PBE potentials. The phonon band structure is correlated to the electronic band structure in order to explain the occurrence of CDW. In TiSe2, the presence of a phonon mode with imaginary frequency indicated lattice instability against distortion. The displacements of Ti-Se atoms of this phonon mode allows the mixing of states of the electron and hole pockets, which leads to lattice distortion i.e. a CDW structure which lowers the energy of the system. Although there is a weak imaginary mode, the mixing of states is absent in TiS2 due to absence of electron or hole pockets, whereas TiTe2 is structurally most stable.

The first-principles methods based on the density functional theory were employed to study the structural stability, segregation and work function of Mg doped with fourteen metal elements existing in human body. The calculated results show that there is a simple correlation between solid solution and segregation. Doping Sn, Y, Li, Gd, Nd, Sc and Zn atoms have a negative formation energy as well as a positive segregation energy. This suggests that these elements which are not easier to be dissolved in Mg matrix tend to segregate on the Mg (0001) surface. An opposite trend was observed for Ba, Fe, Mn, W, Sr, Ca and Mo. On the other hand, the electronic work function of Mg (0001) surface was increased significantly for doping Mo, W, Fe, and Mn, and was reduced markedly for Ba, Ca and Sr. For Li, Sn, Sc, Gd, and Y, their doping on Mg surface generate a relatively small change in work function. In addition, the relationships of corrosion behavior to segregation and work function were discussed. This study may provide an avenue for seeking a more appropriate alloying element of Mg alloys with improved corrosion resistance in biomedical applications.

We investigate the presence of helical character and chirality using a vector-based charge density perspective instead of energetic or structural measures. The vector-based perspective of the chemical bonding, constructed using the most preferred direction of charge density accumulation, finds the presence of induced symmetry-breaking for α,ω-disubstituted [4]cumulenes as the end groups are torsioned. The stress tensor trajectories Tσ(s) are used to provide the additional symmetry-breaking required to quantify the degree and nature of the chirality and helical character. We find an absence of chirality for [4]cumulene but a very significant degree of axiality as demonstrated by the purely axial form of the Tσ(s) indicating a lack of helical character. The S-1,5-dimethyl-[4]cumulene contains a very low degree of chiral character but significant axiality(helicity) resulting in a weakly helical morphology of the corresponding Tσ(s). The (-)S(-), (+)S(-) and (+)S(+) conformations of S-1,5-diamino-[4]cumulene contain very significant degrees of both chirality and helical character resulting in helical morphology of the corresponding Tσ(s). The chirality assignments are in agreement with the Cahn–Ingold–Prelog (CIP) classifications for the (-)S(-), (+)S(-) and (+)S(+) conformations of S-1,5-diamino-[4]cumulene. We discuss the consequences for the Tσ(s) in locating chiral character in these molecules in future experiment investigations.

The transformation mechanism and kinetics of 2-chloro-1,1,2-trifluoroethyl-difluoromethyl-ether (CTDE, CHF2OCF2CHFCl) triggered by OH radicals were researched by DFT methods and canonical variational transition state theory. The computational rate constant including small-curvature tunneling correction was in commendable agreement with the experimental data. Two hydrogen abstraction channels to form the alkyl radicals of C·F2OCF2CHFCl and CHF2OCF2C·FCl were observed, and the formation of CHF2OCF2C·FCl was more favorable than C·F2OCF2CHFCl in kinetics and thermodynamics. Subsequent evolution of CHF2OCF2C·FCl in the presence of NO and O2 indicated that the organic nitrate (CHF2OCF2CONO2FCl) was the stable product. The dechlorinate of alkoxy radical (CHF2OCF2C(O·)FCl) was the most favorable degradation channel and the estimated ozone depletion potential for CTDE relative to CFC-11 was 0.0204, which could lead to a consequence of ozone depletion. Computed atmospheric lifetime for CTDE was 3.69 years by considering the combined contributions from OH radicals and Cl atoms. The total radiative forcing and global warming potential of CTDE were respectively 0.547 W m-2 ppbv and 628.58 (100 years) at 298 K, suggesting that the contribution of CTDE to the greenhouse effect is moderate.

In this investigation we have used NG-QTAIM to fully quantity the response to the four IR-active modes of all the bonding in benzene in terms of bond-flexing, bond-torsion and bond-anharmonicity that includes the tendencies towards IR-responsivity and IR-non-responsivity. Bond-anharmonicity is found to be lacking for the C-C bonds comprising the lowest frequency mode (721.57 cm-1) measured as the absence of bond critical point (BCP) sliding. Additionally, bond-flexing was absent for this mode harmonic-like variation of the profile of the variation of the wrapping (torsion) of the {p,p’} path-packet, referred to as the Precession K, along the conventional QTAIM bond-path, the remaining three IR-active mode possessed step-like variations in the K profiles. The presence of non-nuclear attractors was detected for the IR-active mode with frequency 1573.93 cm-1 with C-C K profiles that most closely resemble those of the relaxed benzene. We quantified the C-H bonds in terms of bond-flexing and bond-anharmonicity and IR-responsivity and IR-non-responsivity.

The effect of the presence of a deuterium (D) or tritium (T) isotope bonded to the alpha carbon of glycine is determined without the need to apply external forces e.g. electric fields or using normal mode analysis. Isotopic effects were accounted for using the mass-dependent diagonal Born-Oppenheimer energy correction (DBOC) at the CCSD level of theory. We calculated the stress tensor trajectories of the dominant C-N bond within next generation quantum theory of atoms in molecules (NG-QTAIM). S-character chirality was discovered using the stress tensor trajectories, instead of the Cahn–Ingold–Prelog (CIP) rules, for ordinary glycine. The S-character chirality was preserved after the substitution of the H on the alpha carbon for a D isotope but transformed to R-character chirality after replacement with the T isotope. This reversal of the chirality depending on the presence of a single D or T isotope bound to the alpha carbon adds to the debate on the nature of the extraterrestrial origins of chirality in simple amino acids. We demonstrate that NG-QTAIM is a promising tool for understanding isotopic induced electronic charge density changes, useful in analysis of infrared (IR) or circular dichroism (CD) spectra explaining changes in mode couplings and bands intensities or sign.

It is imperative to study the long term corrosion problems of nickel alloys in acidic medium due to breakdown of their passitive oxide. Focus of this work is to enhance the knowledge of adsorption of organic additives (OPD & PPD) onto the Ni-W alloy surface. Deducing the scenario of competitive adsorption of salen-type symmetrical Schiff bases (OPD, and PPD) as additive molecules on Ni-W alloy surface at molecular level was studied by Density Functional Theory (DFT), Monte Carlo simulation (MC), Molecular Dynamics simulation (MD) and Radial Distribution Function (RDF) analysis. Obtained intrinsic molecular parmaters from DFT shows a strong conformity to the corrosion effeciencies of experimental results. Higher polarization value of 650.707 a.u (PPD) explicates its electron donating ability onto the alloy surface. Higher binding energy (Ebinding=1132.241 kJ/mol) and spatial orientation of PPD molecule portrays the closest contacts between active atoms and alloy surface. Significant findings from DFT global descriptors, MC, MD and RDF analysis ratifies the corrosion effeciencies (PPD>OPD) of experimental outcomes, which correlates positively with the larger isomeric spacer. Overall, the present study, reports offers the corrosion inhibition resistance impact of OPD & PPD additives, revealing the fact of PPD as effective one and OPD as moderate ones for Ni-W alloys.